Coral reefs

@article{doi1023071943285,
    author = "Odum, Howard T. and Odum, Eugene P.",
    title = "Trophic Structure and Productivity of a Windward Coral Reef Community on Eniwetok Atoll",
    year = "1955",
    journal = "Ecological Monographs",
    url = "https://doi.org/10.2307/1943285",
    doi = "10.2307/1943285",
    openalex = "W2089591395"
}

1. A method is described for the accurate measurement of calcification rates in reef-building corals under various controlled conditions, using calcium-45 as tracer.2. At the temperatures of the experiments, there was a slow but appreciable isotopic exchange between the coral skeleton and sea water. There are indications that this is considerably less in living coral where the tissue forms a barrier against such exchange.3. In many of the reef-building corals tested so far, the calcification rate was significantly lowered by the exclusion of light.4. The calcification rate of reef corals grown in darkness for prolonged periods of time to remove the zooxanthellae is considerably reduced and seems independent of the light intensity.5. Variations in the growth rates of different parts of coral colonies were measured. The existence of growth gradients was demonstrated in a number of species.6. Calcium uptake was greatly reduced on the addition of Diamox, a specific carbonic anhydrase inhibitor. In those species tested, the effect of carbonic anhydrase inhibition and exclusion of light was in the same direction. In the presence of complete inhibition of carbonic anhydrase there was still an uptake, even in darkness.7. It was concluded that the effect of light on reef coral growth is in part mediated through the zooxanthellae. The decreased calcification rates of reef corals in darkness, in the absence of zooxanthellae or in the presence of a carbonic anhydrase inhibitor suggest that the rapid calcification of these corals may be dependent on efficient removal of H2CO3.

@article{doi1023071539156,
    author = "Goreau, Thomas F.",
    title = "THE PHYSIOLOGY OF SKELETON FORMATION IN CORALS. I. A METHOD FOR MEASURING THE RATE OF CALCIUM DEPOSITION BY CORALS UNDER DIFFERENT CONDITIONS",
    year = "1959",
    journal = "Biological Bulletin",
    abstract = "1. A method is described for the accurate measurement of calcification rates in reef-building corals under various controlled conditions, using calcium-45 as tracer.2. At the temperatures of the experiments, there was a slow but appreciable isotopic exchange between the coral skeleton and sea water. There are indications that this is considerably less in living coral where the tissue forms a barrier against such exchange.3. In many of the reef-building corals tested so far, the calcification rate was significantly lowered by the exclusion of light.4. The calcification rate of reef corals grown in darkness for prolonged periods of time to remove the zooxanthellae is considerably reduced and seems independent of the light intensity.5. Variations in the growth rates of different parts of coral colonies were measured. The existence of growth gradients was demonstrated in a number of species.6. Calcium uptake was greatly reduced on the addition of Diamox, a specific carbonic anhydrase inhibitor. In those species tested, the effect of carbonic anhydrase inhibition and exclusion of light was in the same direction. In the presence of complete inhibition of carbonic anhydrase there was still an uptake, even in darkness.7. It was concluded that the effect of light on reef coral growth is in part mediated through the zooxanthellae. The decreased calcification rates of reef corals in darkness, in the absence of zooxanthellae or in the presence of a carbonic anhydrase inhibitor suggest that the rapid calcification of these corals may be dependent on efficient removal of H2CO3.",
    url = "https://doi.org/10.2307/1539156",
    doi = "10.2307/1539156",
    openalex = "W2471464552"
}

Several parameters of water samples collected from Grand Bahama Bank in June 1962 and in June 1963 were measured. They include the partial pressure of CO2, the total dissolved inorganic CO2, the C14/C12 ratio in the inorganic CO2, and the CaCO3 saturation (by the Weyl saturometer). From these results absolute residence times of water on the bank up to 250 days have been computed. An average CaCO3 precipitation rate of 50 mg/cm2 yr is estimated. The rate of CaCO3 deposition is proportional to the degree of supersaturation. By elimination of 0.6 mole of CO2 for each mole of CaCO3 precipitated, the bank water maintains a nearly constant CO2 partial pressure. Combining measurements made with the Weyl saturometer with estimates of the observed activity product made it possible to estimate an activity product for aragonite of 0.80×10−8. This agrees satisfactorily with the value calculated from the free energies of the CO32− ion, Ca2+ ion, and aragonite solid. The waters come onto the bank with an activity product of 1.68×10−8. The value falls to about 0.9×10−8 for those samples residing longest on the bank. C14 measurements on material centrifuged from ‘whitings’ indicate that their turbidity results from resuspension of sediment rather than in situ precipitation. The methods used here should have broad application to problems involving shallow-water CaCO3 deposition.

@article{doi101029jz071i006p01575,
    author = "Broecker, Wallace S. and Takahashi, Taro",
    title = "Calcium carbonate precipitation on the Bahama Banks",
    year = "1966",
    journal = "Journal of Geophysical Research Atmospheres",
    abstract = "Several parameters of water samples collected from Grand Bahama Bank in June 1962 and in June 1963 were measured. They include the partial pressure of CO2, the total dissolved inorganic CO2, the C14/C12 ratio in the inorganic CO2, and the CaCO3 saturation (by the Weyl saturometer). From these results absolute residence times of water on the bank up to 250 days have been computed. An average CaCO3 precipitation rate of 50 mg/cm2 yr is estimated. The rate of CaCO3 deposition is proportional to the degree of supersaturation. By elimination of 0.6 mole of CO2 for each mole of CaCO3 precipitated, the bank water maintains a nearly constant CO2 partial pressure. Combining measurements made with the Weyl saturometer with estimates of the observed activity product made it possible to estimate an activity product for aragonite of 0.80×10−8. This agrees satisfactorily with the value calculated from the free energies of the CO32− ion, Ca2+ ion, and aragonite solid. The waters come onto the bank with an activity product of 1.68×10−8. The value falls to about 0.9×10−8 for those samples residing longest on the bank. C14 measurements on material centrifuged from ‘whitings’ indicate that their turbidity results from resuspension of sediment rather than in situ precipitation. The methods used here should have broad application to problems involving shallow-water CaCO3 deposition.",
    url = "https://doi.org/10.1029/jz071i006p01575",
    doi = "10.1029/jz071i006p01575",
    openalex = "W2090959934"
}

Oxygen exchange is reported for 14 species of Florida reef corals in the dark and at different light intensities. Oxygen tension was monitored with a recording polarographic electrode. Results are given as grams of carbon fixed per square meter of coral surface per day, and compensation light intensities were given for each species. Maximum ratios of photosynthesis to respiration varied from 1.9 to 5.8. Boring, filamentous green algae living in the skeleton of Dichocoenia stokesii were not observed to change their rate of oxygen consumption from dark conditions up to 5000 footcandles of light. It is concluded that reef corals are among the most productive organisms known and that, in Florida corals, the boring green algae contribute very little indeed to this productivity. Some data are given on the light impinging on Florida reefs and the light penetrating coral skeleton. Reasons for believing boring green algae are of minor importance are given in the discussion.

@article{doi1023071539833,
    author = "Kanwisher, John and Wainwright, Stephen A.",
    title = "OXYGEN BALANCE IN SOME REEF CORALS",
    year = "1967",
    journal = "Biological Bulletin",
    abstract = "Oxygen exchange is reported for 14 species of Florida reef corals in the dark and at different light intensities. Oxygen tension was monitored with a recording polarographic electrode. Results are given as grams of carbon fixed per square meter of coral surface per day, and compensation light intensities were given for each species. Maximum ratios of photosynthesis to respiration varied from 1.9 to 5.8. Boring, filamentous green algae living in the skeleton of Dichocoenia stokesii were not observed to change their rate of oxygen consumption from dark conditions up to 5000 footcandles of light. It is concluded that reef corals are among the most productive organisms known and that, in Florida corals, the boring green algae contribute very little indeed to this productivity. Some data are given on the light impinging on Florida reefs and the light penetrating coral skeleton. Reasons for believing boring green algae are of minor importance are given in the discussion.",
    url = "https://doi.org/10.2307/1539833",
    doi = "10.2307/1539833",
    openalex = "W2343544780"
}

@article{doi1010160016703770900414,
    author = "Edmond, John M. and Gieskes, J.M.",
    title = "On the calculation of the degree of saturation of sea water with respect to calcium carbonate under in situ conditions",
    year = "1970",
    journal = "Geochimica et Cosmochimica Acta",
    url = "https://doi.org/10.1016/0016-7037(70)90041-4",
    doi = "10.1016/0016-7037(70)90041-4",
    openalex = "W1997582396"
}

Primary productivity of reef—building algae was studied by putting samples from the reef in a closed system and measuring oxygen exchange in the light and in the dark. Gross productivity determined for 32 samples in full sunlight had a mean value of 0.048 mg O 2 cm — 2 hr — 1. Photosynthesis was found to increase with the logarithm of light intensity up to 1,000 ft—c and was constant between 1,000 and 8,000 ft—c. Rates of gas exchange in flowing water showed no correlation with water velocity but were greater than rates in still water. Daily patterns of photosynthesis were calculated for populations of calcareous algae living on the submarine faces of the windward sides of atolls. During most of the daylight hours light is probably not a limiting factor for photosynthesis in these populations. Calculated productivity of various calcareous algal zones indicates that these do not contribute significantly to overall reef production on atolls of the northern Marshall Islands. Island reefs are less productive than previously studied inter—island reefs.

@article{doi1023071933661,
    author = "Marsh, James A.",
    title = "Primary Productivity of Reef‐Building Calcareous Red Algae",
    year = "1970",
    journal = "Ecology",
    abstract = "Primary productivity of reef—building algae was studied by putting samples from the reef in a closed system and measuring oxygen exchange in the light and in the dark. Gross productivity determined for 32 samples in full sunlight had a mean value of 0.048 mg O 2 cm — 2 hr — 1. Photosynthesis was found to increase with the logarithm of light intensity up to 1,000 ft—c and was constant between 1,000 and 8,000 ft—c. Rates of gas exchange in flowing water showed no correlation with water velocity but were greater than rates in still water. Daily patterns of photosynthesis were calculated for populations of calcareous algae living on the submarine faces of the windward sides of atolls. During most of the daylight hours light is probably not a limiting factor for photosynthesis in these populations. Calculated productivity of various calcareous algal zones indicates that these do not contribute significantly to overall reef production on atolls of the northern Marshall Islands. Island reefs are less productive than previously studied inter—island reefs.",
    url = "https://doi.org/10.2307/1933661",
    doi = "10.2307/1933661",
    openalex = "W2054147099",
    references = "doi101017s0025315400029829, doi101029tr029i006p00855, doi101029tr030i002p00245, doi10113000167606194859861robmi20co2, doi1023071539833, doi1023071943285, doi104319lo1956120072, doi104319lo1956120102, doi104319lo1959420210, openalexw2029721882"
}

1. In branches of the coral Acropora cervicornis, the abundance of symbiotic algae (zooxanthellae) increases from tip to base, while active calcification decreases. Light enhancement of calcification rates is, paradoxically, greatest in the algae-poor tips of branches. 2. Calcium-45 experiments on intact and isolated tips of the coral branches suggest that light enhancement of calcification in the algae-poor tip results from photosynthesis by zooxanthellae farther down in the branch. 3. Carbon-14 experiments indicate that organic products of algal photosynthesis are translocated to the coral tip. The main carbon-14 labeled products in the tip are lipids, glycerol and glucose. 4. Our data are consistent with the hypothesis that translocated algal products enhance coral calcification rates.

@article{doi1023071540123,
    author = "Pearse, Vicki B. and Muscatine, L.",
    title = "ROLE OF SYMBIOTIC ALGAE (ZOOXANTHELLAE) IN CORAL CALCIFICATION",
    year = "1971",
    journal = "Biological Bulletin",
    abstract = "1. In branches of the coral Acropora cervicornis, the abundance of symbiotic algae (zooxanthellae) increases from tip to base, while active calcification decreases. Light enhancement of calcification rates is, paradoxically, greatest in the algae-poor tips of branches. 2. Calcium-45 experiments on intact and isolated tips of the coral branches suggest that light enhancement of calcification in the algae-poor tip results from photosynthesis by zooxanthellae farther down in the branch. 3. Carbon-14 experiments indicate that organic products of algal photosynthesis are translocated to the coral tip. The main carbon-14 labeled products in the tip are lipids, glycerol and glucose. 4. Our data are consistent with the hypothesis that translocated algal products enhance coral calcification rates.",
    url = "https://doi.org/10.2307/1540123",
    doi = "10.2307/1540123",
    openalex = "W2339084534"
}

@misc{chave1972calcium1,
    author = "Chave, K. E. and Smith, S. V. and Roy, K. J",
    title = "Calcium carbonate production by coral reefs",
    year = "1972",
    howpublished = "Marine Geology, v. 12, no. 2, p. 123-140",
    note = "talkorigins\_source = {true}; raw\_reference = {Chave, K. E., Smith, S. V., and Roy, K. J., 1972, Calcium carbonate production by coral reefs: Marine Geology, v. 12, no. 2, p. 123-140.}"
}

@article{chave1972carbonate,
    author = "Chave, Keith E. and Smith, Stephen V. and Roy, Kenneth J.",
    title = "Carbonate production by coral reefs",
    year = "1972",
    journal = "Marine Geology",
    url = "https://doi.org/10.1016/0025-3227(72)90024-2",
    doi = "10.1016/0025-3227(72)90024-2",
    number = "2",
    openalex = "W1978422970",
    pages = "123-140",
    volume = "12",
    references = "doi101007bf00379161, doi101016001282526790311x, doi101029tr030i002p00245, doi101111j1469185x1969tb00609x, doi101126science16238581121, doi101130mem67v2, doi10130674d7173a2b2111d78648000102c1865d, doi1023071943285, openalexw2404703234, openalexw3216129607"
}

Although calcareous organisms are abundant on hard‐bottom portions of the southern California mainland shelf, negligible amounts of CaCO 3 are accumulating there. Data collected at three localities and 22 stations along the southern California coastline give subtidal rates of CaCO 3 production by calcareous organisms, from turnover rates calculated from growth rate data, from mortality calculations based on size distribution and growth data, and from miscellaneous information, near 400 g CaCO 3 m ‒2 yr ‒1. Although this temperate climate production rate is lower than rates of coral reef production, it is similar to tropical nonreef production rates and much higher than pelagic production rates of CaCO 3. The CaCO 3 produced is lost from the mainland shelf, probably by transportation to adjacent basins, and then is apparently in large part dissolved. About 4 × 10 10 g CaCO 3 yr ‒1 are produced across 10 3 km 2 of the shallow hard‐bottom shelf areas of southern California and subsequently removed from those areas.

@article{doi104319lo19721710028,
    author = "Smith, Stephen V.",
    title = "PRODUCTION OF CALCIUM CARBONATE ON THE MAINLAND SHELF OF SOUTHERN CALIFORNIA1",
    year = "1972",
    journal = "Limnology and Oceanography",
    abstract = "Although calcareous organisms are abundant on hard‐bottom portions of the southern California mainland shelf, negligible amounts of CaCO 3 are accumulating there. Data collected at three localities and 22 stations along the southern California coastline give subtidal rates of CaCO 3 production by calcareous organisms, from turnover rates calculated from growth rate data, from mortality calculations based on size distribution and growth data, and from miscellaneous information, near 400 g CaCO 3 m ‒2 yr ‒1. Although this temperate climate production rate is lower than rates of coral reef production, it is similar to tropical nonreef production rates and much higher than pelagic production rates of CaCO 3. The CaCO 3 produced is lost from the mainland shelf, probably by transportation to adjacent basins, and then is apparently in large part dissolved. About 4 × 10 10 g CaCO 3 yr ‒1 are produced across 10 3 km 2 of the shallow hard‐bottom shelf areas of southern California and subsequently removed from those areas.",
    url = "https://doi.org/10.4319/lo.1972.17.1.0028",
    doi = "10.4319/lo.1972.17.1.0028",
    openalex = "W2144760189"
}

@article{doi105479si007756301531,
    author = "Risk, Michael J.",
    title = "Fish Diversity on a Coral Reef in the Virgin Islands",
    year = "1972",
    journal = "Atoll research bulletin",
    url = "https://doi.org/10.5479/si.00775630.153.1",
    doi = "10.5479/si.00775630.153.1",
    openalex = "W1965577217"
}

@incollection{doi101016b9780123955265500158,
    author = "Connell, Joseph H.",
    title = "POPULATION ECOLOGY OF REEF-BUILDING CORALS",
    year = "1973",
    booktitle = "Elsevier eBooks",
    url = "https://doi.org/10.1016/b978-0-12-395526-5.50015-8",
    doi = "10.1016/b978-0-12-395526-5.50015-8",
    openalex = "W2501142627",
    references = "knightjones1953laboratory"
}

Organic carbon production, respiration, and calcification alter the CO content of water crossing the Eniwetok windward reef flat. Changes in pH and total alkalinity can be used to partition the CO 2 changes into those due to production‐respiration and those due to calcification. Gas transfer across the air‐sea interface is minor. Both a transect visually dominated by a mixture of corals and algae and a transect dominated by an algal turf calcified at an average rate of 4,000 g CaCO 3 m −2 yr −1, with no apparent day‐to‐night difference. Although nighttime respiration on both transects was 0.12 g C m −2 hr −1, the algal transect exhibited a much higher daytime net production rate than did the coral‐algal transect (0.72 vs. 0.25 g C m −2 hr −1). Although little particulate CaCO 3 was removed from the reef flat during these studies, there has been virtually no net CaCO 3 accumulation there over the last several thousand years.

@article{doi104319lo19731810106,
    author = "Smith, Stephen V.",
    title = "CARBON DIOXIDE DYNAMICS: A RECORD OF ORGANIC CARBON PRODUCTION, RESPIRATION, AND CALCIFICATION IN THE ENIWETOK REEF FLAT COMMUNITY1",
    year = "1973",
    journal = "Limnology and Oceanography",
    abstract = "Organic carbon production, respiration, and calcification alter the CO content of water crossing the Eniwetok windward reef flat. Changes in pH and total alkalinity can be used to partition the CO 2 changes into those due to production‐respiration and those due to calcification. Gas transfer across the air‐sea interface is minor. Both a transect visually dominated by a mixture of corals and algae and a transect dominated by an algal turf calcified at an average rate of 4,000 g CaCO 3 m −2 yr −1, with no apparent day‐to‐night difference. Although nighttime respiration on both transects was 0.12 g C m −2 hr −1, the algal transect exhibited a much higher daytime net production rate than did the coral‐algal transect (0.72 vs. 0.25 g C m −2 hr −1). Although little particulate CaCO 3 was removed from the reef flat during these studies, there has been virtually no net CaCO 3 accumulation there over the last several thousand years.",
    url = "https://doi.org/10.4319/lo.1973.18.1.0106",
    doi = "10.4319/lo.1973.18.1.0106",
    openalex = "W1969180616"
}

@article{doi1010160022098174900240,
    author = "Buddemeier, R.W. and Maragos, James E. and Knutson, D W",
    title = "Radiographic studies of reef coral exoskeletons: Rates and patterns of coral growth",
    year = "1974",
    journal = "Journal of Experimental Marine Biology and Ecology",
    url = "https://doi.org/10.1016/0022-0981(74)90024-0",
    doi = "10.1016/0022-0981(74)90024-0",
    openalex = "W1991009275",
    references = "chave1972carbonate"
}

It has been generally assumed that the deep borings on Pacific atolls have confirmed Darwin's theory of coral reef development which holds that continued subsidence results in the successive appearance of fringing reefs, barrier reefs and atolls. It is certainly true that the considerable thicknesses of shallow water carbonates encountered in these core holes necessitates subsidence; however it does not necessarily follow that this subsidence has resulted in the genetic succession of reef types advocated by Darwin. It is the purpose of the present paper to enlarge on an alternate theory first presented by MacNeil, and in so doing to demonstrate that many, if not most, of the shape attributes of modern reefs are fundamentally karst-induced rather than growth- induced.

@incollection{doi102110pec74180009,
    author = "Purdy, Edward G.",
    title = "REEF CONFIGURATIONS: CAUSE AND EFFECT",
    year = "1974",
    booktitle = "SEPM (Society for Sedimentary Geology) eBooks",
    abstract = "It has been generally assumed that the deep borings on Pacific atolls have confirmed Darwin's theory of coral reef development which holds that continued subsidence results in the successive appearance of fringing reefs, barrier reefs and atolls. It is certainly true that the considerable thicknesses of shallow water carbonates encountered in these core holes necessitates subsidence; however it does not necessarily follow that this subsidence has resulted in the genetic succession of reef types advocated by Darwin. It is the purpose of the present paper to enlarge on an alternate theory first presented by MacNeil, and in so doing to demonstrate that many, if not most, of the shape attributes of modern reefs are fundamentally karst-induced rather than growth- induced.",
    url = "https://doi.org/10.2110/pec.74.18.0009",
    doi = "10.2110/pec.74.18.0009",
    openalex = "W1748273630"
}

@article{doi101007bf00390714,
    author = "Dustan, P.",
    title = "Growth and form in the reef-building coral Montastrea annularis",
    year = "1975",
    journal = "Marine Biology",
    url = "https://doi.org/10.1007/bf00390714",
    doi = "10.1007/bf00390714",
    openalex = "W2140294536"
}

Species of ectoprocts and solitary encrusting animals were subjected in aquaria to homogenates of 11 sympatric species of sponges and colonial ascidians. Five of the nine sponge species and one of the two ascidian species exhibited species-specific allelochemical effects. Evidence suggests that alleochemical provide a wide-spread, specific, and complex mechanism for interference competition for space among natural populations of coral reef organisms. The existence of such species-specific mechanisms may provide a basis for maintenance of diversity in space-limited systems in the absence of high levels of predation and physical disturbance.

@article{doi101073pnas72125160,
    author = "Jackson, Jeremy B. C. and Buss, Leo W.",
    title = "Alleopathy and spatial competition among coral reef invertebrates",
    year = "1975",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Species of ectoprocts and solitary encrusting animals were subjected in aquaria to homogenates of 11 sympatric species of sponges and colonial ascidians. Five of the nine sponge species and one of the two ascidian species exhibited species-specific allelochemical effects. Evidence suggests that alleochemical provide a wide-spread, specific, and complex mechanism for interference competition for space among natural populations of coral reef organisms. The existence of such species-specific mechanisms may provide a basis for maintenance of diversity in space-limited systems in the absence of high levels of predation and physical disturbance.",
    url = "https://doi.org/10.1073/pnas.72.12.5160",
    doi = "10.1073/pnas.72.12.5160",
    openalex = "W2042055120"
}

@article{doi105479si007756301871,
    author = "Adey, Walter H.",
    title = "The algal ridges and coral reefs of St. Croix: their structure and Holocene development",
    year = "1975",
    journal = "Atoll research bulletin",
    url = "https://doi.org/10.5479/si.00775630.187.1",
    doi = "10.5479/si.00775630.187.1",
    openalex = "W1983537003"
}

@article{doi101007bf02407510,
    author = "Shinn, Eugene A.",
    title = "Coral reef recovery in Florida and the Persian Gulf",
    year = "1976",
    journal = "Environmental Geology",
    url = "https://doi.org/10.1007/bf02407510",
    doi = "10.1007/bf02407510",
    openalex = "W1977280542"
}

Shallow, seaward portions of modern coral reefs produce about 4 kilograms of calcium carbonate per square meter per year, and protected areas produce about 0.8 kilogram per square meter per year. The difference is probably largely a function of water motion. The more rapid rate, equivalent to a maximum vertical accretion of 3 to 5 millimeters per year, places an upper limit on the potential of modern coral reef communities to create a significant vertical structure on a rising sea.

@article{doi101126science1944268937,
    author = "Smith, Stephen V. and Kinsey, D.W.",
    title = "Calcium Carbonate Production, Coral Reef Growth, and Sea Level Change",
    year = "1976",
    journal = "Science",
    abstract = "Shallow, seaward portions of modern coral reefs produce about 4 kilograms of calcium carbonate per square meter per year, and protected areas produce about 0.8 kilogram per square meter per year. The difference is probably largely a function of water motion. The more rapid rate, equivalent to a maximum vertical accretion of 3 to 5 millimeters per year, places an upper limit on the potential of modern coral reef communities to create a significant vertical structure on a rising sea.",
    url = "https://doi.org/10.1126/science.194.4268.937",
    doi = "10.1126/science.194.4268.937",
    openalex = "W2134744478",
    references = "chave1972carbonate, doi101007bf00390714, doi1010160022098173900506, doi1010160022098174900240, doi1010160025322772900114, doi101029jz071i006p01575, doi102216i00318884142551, doi104319lo19721710028, doi104319lo19731810106, doi105479si007756301871"
}

@book{doi101016b9780123955289x50015,
    title = "Biology and Geology of Coral Reefs",
    year = "1977",
    booktitle = "Elsevier eBooks",
    url = "https://doi.org/10.1016/b978-0-12-395528-9.x5001-5",
    doi = "10.1016/b978-0-12-395528-9.x5001-5",
    openalex = "W3186772751"
}

Journal Article Reef Corals: Mutualistic Symbioses Adapted to Nutrient-Poor Environments Get access L. Muscatine, L. Muscatine Search for other works by this author on: Oxford Academic Google Scholar James W. Porter James W. Porter Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 27, Issue 7, July 1977, Pages 454–460, https://doi.org/10.2307/1297526 Published: 01 July 1977 Article history Accepted: 21 December 1976 Published: 01 July 1977

@article{doi1023071297526,
    author = "Muscatine, L. and Porter, James W.",
    title = "Reef Corals: Mutualistic Symbioses Adapted to Nutrient-Poor Environments",
    year = "1977",
    journal = "BioScience",
    abstract = "Journal Article Reef Corals: Mutualistic Symbioses Adapted to Nutrient-Poor Environments Get access L. Muscatine, L. Muscatine Search for other works by this author on: Oxford Academic Google Scholar James W. Porter James W. Porter Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 27, Issue 7, July 1977, Pages 454–460, https://doi.org/10.2307/1297526 Published: 01 July 1977 Article history Accepted: 21 December 1976 Published: 01 July 1977",
    url = "https://doi.org/10.2307/1297526",
    doi = "10.2307/1297526",
    openalex = "W2110117799",
    references = "doi101021j150446a008, doi101111j1469185x1969tb00609x"
}

@article{doi101038273225a0,
    author = "Smith, Stephen V.",
    title = "Coral-reef area and the contributions of reefs to processes and resources of the world's oceans",
    year = "1978",
    journal = "Nature",
    url = "https://doi.org/10.1038/273225a0",
    doi = "10.1038/273225a0",
    openalex = "W1988641212",
    references = "doi101126science1944268937"
}

The commonly observed high diversity of trees in tropical rain forests and corals on tropical reefs is a nonequilibrium state which, if not disturbed further, will progress toward a low-diversity equilibrium community. This may not happen if gradual changes in climate favor different species. If equilibrium is reached, a lesser degree of diversity may be sustained by niche diversification or by a compensatory mortality that favors inferior competitors. However, tropical forests and reefs are subject to severe disturbances often enough that equilibrium may never be attained.

@article{doi101126science19943351302,
    author = "Connell, Joseph H.",
    title = "Diversity in Tropical Rain Forests and Coral Reefs",
    year = "1978",
    journal = "Science",
    abstract = "The commonly observed high diversity of trees in tropical rain forests and corals on tropical reefs is a nonequilibrium state which, if not disturbed further, will progress toward a low-diversity equilibrium community. This may not happen if gradual changes in climate favor different species. If equilibrium is reached, a lesser degree of diversity may be sustained by niche diversification or by a compensatory mortality that favors inferior competitors. However, tropical forests and reefs are subject to severe disturbances often enough that equilibrium may never be attained.",
    url = "https://doi.org/10.1126/science.199.4335.1302",
    doi = "10.1126/science.199.4335.1302",
    openalex = "W2166722801",
    references = "doi101086282171, doi101086282687, doi101086283164, doi101086283241, doi101086283366, doi101111j1469185x1969tb00609x, doi101126science1653889131, doi101126science185414527, doi1023071218190, doi1023071942565, doi1023072256497, doi1023072260296, doi1023072989823"
}

Nonhierarchial sequences of interference competitive abilities, competitive networks, have been observed in Jamaican cryptic coral reef environments and also appear to exist in Jamaican open reef surface environments. These competitive networks are both numerous and complex; they appear more likely to be formed by interactions between than within major taxonomic groups. The exact spatial position an organism occupies and the rate at which organisms overgrow one another will be important determinants of patterns of species distribution on substrata supporting competitive networks. This will not be the case if a competitive hierarchy exists. The existence of a competitive network on a particular substratum will serve to increase the length of time required for single species resource monopolization relative to the time which would be required if a competitive hierarchy exists, assuming equivalent rates of overgrowth in both cases. The competitive networks situation provides a mechanism for the development of specific types of coevolutionary relationships.

@article{doi101086283381,
    author = "Buss, Leo W. and Jackson, Jeremy B. C.",
    title = "Competitive Networks: Nontransitive Competitive Relationships in Cryptic Coral Reef Environments",
    year = "1979",
    journal = "The American Naturalist",
    abstract = "Nonhierarchial sequences of interference competitive abilities, competitive networks, have been observed in Jamaican cryptic coral reef environments and also appear to exist in Jamaican open reef surface environments. These competitive networks are both numerous and complex; they appear more likely to be formed by interactions between than within major taxonomic groups. The exact spatial position an organism occupies and the rate at which organisms overgrow one another will be important determinants of patterns of species distribution on substrata supporting competitive networks. This will not be the case if a competitive hierarchy exists. The existence of a competitive network on a particular substratum will serve to increase the length of time required for single species resource monopolization relative to the time which would be required if a competitive hierarchy exists, assuming equivalent rates of overgrowth in both cases. The competitive networks situation provides a mechanism for the development of specific types of coevolutionary relationships.",
    url = "https://doi.org/10.1086/283381",
    doi = "10.1086/283381",
    openalex = "W2012413510",
    references = "connell1961effects, dayton1971competition, doi101016s0065250408603190, doi101073pnas72125160, doi101086282400, doi101086282973, doi101086283203, doi101126science1733997623, openalexw2092424122, openalexw2962874606"
}

The regular echinoid Eucidaris thouarsii is a conspicuous omnivore on coral bottoms in the Galápagos. Unlike Eucidaris in Panama and mainland Ecuador, Galápagos Eucidaris are large and abundant and graze heavily in the open on live corals day and night. These differences are probably due in large part to more intense predation by fishes on mainland compared with island urchin populations. An assessment of coral growth versus coral attrition from grazing shows that Eucidaris interferes with the establishment of pocilloporid reef frame and therefore reduces reef growth in the Galápagos.

@article{doi101126science203437547,
    author = "Glynn, Peter W. and Wellington, Gerard M. and Birkeland, Charles",
    title = "Coral Reef Growth in the Galápagos: Limitation by Sea Urchins",
    year = "1979",
    journal = "Science",
    abstract = "The regular echinoid Eucidaris thouarsii is a conspicuous omnivore on coral bottoms in the Galápagos. Unlike Eucidaris in Panama and mainland Ecuador, Galápagos Eucidaris are large and abundant and graze heavily in the open on live corals day and night. These differences are probably due in large part to more intense predation by fishes on mainland compared with island urchin populations. An assessment of coral growth versus coral attrition from grazing shows that Eucidaris interferes with the establishment of pocilloporid reef frame and therefore reduces reef growth in the Galápagos.",
    url = "https://doi.org/10.1126/science.203.4375.47",
    doi = "10.1126/science.203.4375.47",
    openalex = "W2007671401"
}

Population dynamics of corals and other colonial animals are complicated by their modular construction and growth. Partial colony mortality, colony fission, and colony fusion distort any simple relationship between size and age among reef corals.

@article{doi101126science2094457713,
    author = "Hughes, Terry P. and Jackson, Jeremy B. C.",
    title = "Do Corals Lie About Their Age? Some Demographic Consequences of Partial Mortality, Fission, and Fusion",
    year = "1980",
    journal = "Science",
    abstract = "Population dynamics of corals and other colonial animals are complicated by their modular construction and growth. Partial colony mortality, colony fission, and colony fusion distort any simple relationship between size and age among reef corals.",
    url = "https://doi.org/10.1126/science.209.4457.713",
    doi = "10.1126/science.209.4457.713",
    openalex = "W2021183063"
}

@article{doi101007bf00301691,
    author = "Done, T. J.",
    title = "Patterns in the distribution of coral communities across the central Great Barrier Reef",
    year = "1982",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/bf00301691",
    doi = "10.1007/bf00301691",
    openalex = "W2039919289"
}

Production of new colonies by fragmentation of established colonies is shown to be an extremely important mode of reproduction and local distribution anlong major reef-bu~lding corals. This type of reproduction avoids the high mortality rates of larvae and juveniles and spreads the risk of mortality for the genotype Fragmentation by corals wlth high growth rates results In their domination of certain reef zones, rapid growth of reefs on which these corals are abundant, and rapid recovery from disturbances. I conclude that a number of the most successful corals are adapted to fragment, 1.e have incorporated fragmentation into their life histories

@article{doi103354meps007207,
    author = "Highsmith, R. Tod",
    title = "Reproduction by Fragmentation in Corals",
    year = "1982",
    journal = "Marine Ecology Progress Series",
    abstract = "Production of new colonies by fragmentation of established colonies is shown to be an extremely important mode of reproduction and local distribution anlong major reef-bu\textasciitilde lding corals. This type of reproduction avoids the high mortality rates of larvae and juveniles and spreads the risk of mortality for the genotype Fragmentation by corals wlth high growth rates results In their domination of certain reef zones, rapid growth of reefs on which these corals are abundant, and rapid recovery from disturbances. I conclude that a number of the most successful corals are adapted to fragment, 1.e have incorporated fragmentation into their life histories",
    url = "https://doi.org/10.3354/meps007207",
    doi = "10.3354/meps007207",
    openalex = "W2007323570",
    references = "doi101007bf02407510, doi101016b9780123955265500158, doi101016b9780123955289x50015, doi101086283186, doi101086627283, doi101126science19943351302, doi101126science203437547, doi101126science2094457713, doi102110pec74180009, doi1023071540123"
}

The population dynamics of five species of foliaceous corals (Agaricia agaricites forma purpurea, A. lamarcki, Leptoseris cucullata, Montastrea annularis, and Porites astreoides) was followed on Jamaican reefs using annual photographic censuses. Overall, population cover, size frequencies, and number of colonies were stable over the monitored period from 1977 to 1980. However, individual colonies were in turmoil: of the original 883 colonies, 315 were killed outright and 499 suffered partial colony mortality (injury) at least once during the 3 yr. Partial mortality generated an additional 189 colonies by fission, while larval recruitment added another 201, and fusion subtracted 40 colonies. The net result was a decrease of <10% in number of colonies. There was considerable variation among years and sites in measured life history parameters, as well as striking differences between species. The most stable populations were M. annularis and A. lamarcki, followed by P. astreoides, A. agaricites, and L. cucullata. Rates of partial— and whole—colony mortality were strongly dependent on colony size for all species. Typically, small colonies either were unharmed, or were killed outright, while most large colonies survived but were injured each year, often by extensive amounts. The amount of tissue lost from a population through injuries was usually much greater than through the death of whole colonies, even in a year which included a major winter storm. Frequently, large corals were split asunder by partial mortality to produce several daughter colonies, which presumably were of identical genotype. Therefore counts of physically separate colonies exceeded the number of genetically distinct individuals (genets), by at least 20%. Individual genets, measured as the lateral extent of known daughter colonies, were frequently up to 5 m across, and for M. annularis and A. lamarcki were certainly several centuries old. Colony extension rates measured in situ were very weakly dependent on depth from —10 to —55 m, and were independent of colony size. Small colonies showed much faster relative changes in area, although even the largest corals continued to grow if they avoided major injuries. Within a size—class, the fates of colonies were diverse because of differential rates of growth and shrinkage, so that size was a very poor indicator of age. Differences in the life history and "mobility" between species are reflected in the taxonomic and morphological composition of coral communities over the reef. Shallow—water assemblages of foliaceous corals are composed of more dynamic, delicately built species, while many deeper water communities are dominated by slower growing, robust species. Ironically, disturbance on coral reefs often seems to favor the organisms most vulnerable to damage.

@article{doi1023071942555,
    author = "Hughes, Terry P. and Jackson, Jeremy B. C.",
    title = "Population Dynamics and Life Histories of Foliaceous Corals",
    year = "1985",
    journal = "Ecological Monographs",
    abstract = {The population dynamics of five species of foliaceous corals (Agaricia agaricites forma purpurea, A. lamarcki, Leptoseris cucullata, Montastrea annularis, and Porites astreoides) was followed on Jamaican reefs using annual photographic censuses. Overall, population cover, size frequencies, and number of colonies were stable over the monitored period from 1977 to 1980. However, individual colonies were in turmoil: of the original 883 colonies, 315 were killed outright and 499 suffered partial colony mortality (injury) at least once during the 3 yr. Partial mortality generated an additional 189 colonies by fission, while larval recruitment added another 201, and fusion subtracted 40 colonies. The net result was a decrease of <10\% in number of colonies. There was considerable variation among years and sites in measured life history parameters, as well as striking differences between species. The most stable populations were M. annularis and A. lamarcki, followed by P. astreoides, A. agaricites, and L. cucullata. Rates of partial— and whole—colony mortality were strongly dependent on colony size for all species. Typically, small colonies either were unharmed, or were killed outright, while most large colonies survived but were injured each year, often by extensive amounts. The amount of tissue lost from a population through injuries was usually much greater than through the death of whole colonies, even in a year which included a major winter storm. Frequently, large corals were split asunder by partial mortality to produce several daughter colonies, which presumably were of identical genotype. Therefore counts of physically separate colonies exceeded the number of genetically distinct individuals (genets), by at least 20\%. Individual genets, measured as the lateral extent of known daughter colonies, were frequently up to 5 m across, and for M. annularis and A. lamarcki were certainly several centuries old. Colony extension rates measured in situ were very weakly dependent on depth from —10 to —55 m, and were independent of colony size. Small colonies showed much faster relative changes in area, although even the largest corals continued to grow if they avoided major injuries. Within a size—class, the fates of colonies were diverse because of differential rates of growth and shrinkage, so that size was a very poor indicator of age. Differences in the life history and "mobility" between species are reflected in the taxonomic and morphological composition of coral communities over the reef. Shallow—water assemblages of foliaceous corals are composed of more dynamic, delicately built species, while many deeper water communities are dominated by slower growing, robust species. Ironically, disturbance on coral reefs often seems to favor the organisms most vulnerable to damage.},
    url = "https://doi.org/10.2307/1942555",
    doi = "10.2307/1942555",
    openalex = "W2098101447",
    references = "doi1023073225209, doi103354meps007207"
}

@article{doi1010160022098189901093,
    author = "Hoegh‐Guldberg, Ove and Smith, G. Jason",
    title = "The effect of sudden changes in temperature, light and salinity on the population density and export of zooxanthellae from the reef corals Stylophora pistillata Esper and Seriatopora hystrix Dana",
    year = "1989",
    journal = "Journal of Experimental Marine Biology and Ecology",
    url = "https://doi.org/10.1016/0022-0981(89)90109-3",
    doi = "10.1016/0022-0981(89)90109-3",
    openalex = "W2000754412",
    references = "doi1023071933661"
}

@article{doi101007bf00265014,
    author = "Szmant, Alina M. and Gassman, Nancy J.",
    title = "The effects of prolonged?bleaching? on the tissue biomass and reproduction of the reef coral Montastrea annularis",
    year = "1990",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/bf00265014",
    doi = "10.1007/bf00265014",
    openalex = "W2107011582",
    references = "doi1023071933661"
}

Detailed reproductive data are now available for 210 of the ca 600 identified scleractinian reef coral species. The majonty (131 species) are hermaphroditic broadcast spawners, although hermaphroditic brooders (1 1 species), gonochoristic broadcasters (37 species), and gonochoristic brooders (7 species) have also been reported. Characteristics of sexuality and mode of reproduction are generally conservative within species, genera, and even families, although some exceptions occur. Variation in timing or mode of reproduction in allopatric populations may represent adaptations to local environmental conditions or indicate problems in the taxonomy of some groups. Synchronous spawning of numerous species occurs on the Great Barrier Reef, while asynchrony among and withln species has been observed in the Red Sea, Caribbean, Central Pacific, Hawall, and southern Japan. Sexual reproduct~on is the primary means for successful recruitment for some coral populations, while asexual processes may be the dominant or sole means of recruitment for these same species at the limits of their ranges. Recruitment success of different reproductive strategies may vary within and between localities, and is mediated by both biotic (predation, competition) and abiotic (environmental variability, disturbance) factors. Data on reproductive patterns and recruitment success may be applied to coral reef management practices.

@article{doi103354meps060185,
    author = "Richmond, RH and Hunter, Cynthia",
    title = "Reproduction and recruitment of corals: comparisons among the Caribbean, the Tropical Pacific, and the Red Sea",
    year = "1990",
    journal = "Marine Ecology Progress Series",
    abstract = "Detailed reproductive data are now available for 210 of the ca 600 identified scleractinian reef coral species. The majonty (131 species) are hermaphroditic broadcast spawners, although hermaphroditic brooders (1 1 species), gonochoristic broadcasters (37 species), and gonochoristic brooders (7 species) have also been reported. Characteristics of sexuality and mode of reproduction are generally conservative within species, genera, and even families, although some exceptions occur. Variation in timing or mode of reproduction in allopatric populations may represent adaptations to local environmental conditions or indicate problems in the taxonomy of some groups. Synchronous spawning of numerous species occurs on the Great Barrier Reef, while asynchrony among and withln species has been observed in the Red Sea, Caribbean, Central Pacific, Hawall, and southern Japan. Sexual reproduct\textasciitilde on is the primary means for successful recruitment for some coral populations, while asexual processes may be the dominant or sole means of recruitment for these same species at the limits of their ranges. Recruitment success of different reproductive strategies may vary within and between localities, and is mediated by both biotic (predation, competition) and abiotic (environmental variability, disturbance) factors. Data on reproductive patterns and recruitment success may be applied to coral reef management practices.",
    url = "https://doi.org/10.3354/meps060185",
    doi = "10.3354/meps060185",
    openalex = "W1986959501",
    references = "doi103354meps007207"
}

Unprecedented development along tropical shorelines is causing severe degradation of coral reefs primarily from increases in sedimentation. Sediment particles smother reef organisms and reduce light available for photosynthesis. Excessive sedmentation can adversely affect the structure and function of the coral reef ecosystem by altering both physical and biological processes. Mean sediment rates and suspended sediment concentrations for reefs not subject to stresses from human activities are < 1 to ca 10 mg cm-* d-' and < 10 mg I-', respectively. Chronic rates and concentrations above these values are 'hlgh'. Heavy sedmentation is associated with fewer coral species, less live coral, lower coral growth rates, greater abundance of branching forms, reduced coral recruitment, decreased calcification, decreased net productivity of corals, and slower rates of reef accretion. Coral species have different capabilities of clearing themselves of sediment particles or surviving lower light levels. Sedlment rejection is a function of morphology, orientation, growth habit, and behavior; and of the amount and type of s e l m e n t. Coral growth rates are not simple indicators of sediment levels. Decline of tropical fisheries is partially attributable to deterioration of coral reefs, seagrass beds, and mangroves from sedimentation. Sedimentation can alter the complex interactions between fish and their reef habitat. For example, sedimentation can lull major reef-building corals, leading to eventual collapse of the reef framework. A decline in the amount of shelter the reef provides leads to reductions in both number of individuals and number of species of fish. Currently, we are unable to rigorously predict the responses of coral reefs and reef organisms to excessive sedimentation from coastal development and other sources. Given information on the amount of sediment which will be introduced into the reef environment, the coral community composition, the depth of the reef, the percent coral cover, and the current patterns, we should be able to predict the consequences of a particular activity. Models of physical processes (e.g. sediment transport) must be complemented with better understanding of organism and ecosystem responses to sediment stress. Specifically, we need data on the threshold levels for reef orgarusms and for the reef ecosystem as a whole -the levels above which sedimentation has lethal effects for particular species and above which normal functioning of the reef ceases. Additional field studies on the responses of reef organisms to both temgenous and calcium carbonate sediments are necessary. To effectively assess trends on coral reefs, e.g. changes in abundance and spatial arrangement of dominant benthic organisms, scientists must start using standardized monitoring methods. Long-term data sets are critical for tracking these complex ecosystems.

@article{doi103354meps062185,
    author = "Rogers, CS",
    title = "Responses of coral reefs and reef organisms to sedimentation",
    year = "1990",
    journal = "Marine Ecology Progress Series",
    abstract = "Unprecedented development along tropical shorelines is causing severe degradation of coral reefs primarily from increases in sedimentation. Sediment particles smother reef organisms and reduce light available for photosynthesis. Excessive sedmentation can adversely affect the structure and function of the coral reef ecosystem by altering both physical and biological processes. Mean sediment rates and suspended sediment concentrations for reefs not subject to stresses from human activities are < 1 to ca 10 mg cm-* d-' and < 10 mg I-', respectively. Chronic rates and concentrations above these values are 'hlgh'. Heavy sedmentation is associated with fewer coral species, less live coral, lower coral growth rates, greater abundance of branching forms, reduced coral recruitment, decreased calcification, decreased net productivity of corals, and slower rates of reef accretion. Coral species have different capabilities of clearing themselves of sediment particles or surviving lower light levels. Sedlment rejection is a function of morphology, orientation, growth habit, and behavior; and of the amount and type of s e l m e n t. Coral growth rates are not simple indicators of sediment levels. Decline of tropical fisheries is partially attributable to deterioration of coral reefs, seagrass beds, and mangroves from sedimentation. Sedimentation can alter the complex interactions between fish and their reef habitat. For example, sedimentation can lull major reef-building corals, leading to eventual collapse of the reef framework. A decline in the amount of shelter the reef provides leads to reductions in both number of individuals and number of species of fish. Currently, we are unable to rigorously predict the responses of coral reefs and reef organisms to excessive sedimentation from coastal development and other sources. Given information on the amount of sediment which will be introduced into the reef environment, the coral community composition, the depth of the reef, the percent coral cover, and the current patterns, we should be able to predict the consequences of a particular activity. Models of physical processes (e.g. sediment transport) must be complemented with better understanding of organism and ecosystem responses to sediment stress. Specifically, we need data on the threshold levels for reef orgarusms and for the reef ecosystem as a whole -the levels above which sedimentation has lethal effects for particular species and above which normal functioning of the reef ceases. Additional field studies on the responses of reef organisms to both temgenous and calcium carbonate sediments are necessary. To effectively assess trends on coral reefs, e.g. changes in abundance and spatial arrangement of dominant benthic organisms, scientists must start using standardized monitoring methods. Long-term data sets are critical for tracking these complex ecosystems.",
    url = "https://doi.org/10.3354/meps062185",
    doi = "10.3354/meps062185",
    openalex = "W2077170976"
}

@article{doi101016s0022098105800061,
    author = "Stimson, John and Kinzie, Robert A.",
    title = "The temporal pattern and rate of release of zooxanthellae from the reef coral Pocillopora damicornis (Linnaeus) under nitrogen-enrichment and control conditions",
    year = "1991",
    journal = "Journal of Experimental Marine Biology and Ecology",
    url = "https://doi.org/10.1016/s0022-0981(05)80006-1",
    doi = "10.1016/s0022-0981(05)80006-1",
    openalex = "W1966872871"
}

@article{doi101007bf00255465,
    author = "Ware, John R. and Smith, Stephen V. and Reaka-Kudla, Marjorie L.",
    title = "Coral reefs: sources or sinks of atmospheric CO2?",
    year = "1992",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/bf00255465",
    doi = "10.1007/bf00255465",
    openalex = "W2062791578",
    references = "doi101126science1944268937"
}

@article{doi101007bf00303779,
    author = "Glynn, Peter W.",
    title = "Coral reef bleaching: ecological perspectives",
    year = "1993",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/bf00303779",
    doi = "10.1007/bf00303779",
    openalex = "W2004619429",
    references = "doi101111j1469185x1969tb00609x, doi101126science2434891638, doi102110pec77250019, doi1023071942565, doi103354meps007207"
}

Present‐day production of CaCO 3 in tne world ocean is calculated to be about 5 billion tons (bt) per year, of which about 3 bt accumulate in sediments; the other 40% is dissolved. Nearly half of the carbonate sediment accumulates on reefs, banks, and tropical shelves, and consists largely of metastable aragonite and magnesian calcite. Deep‐sea carbonates, predominantly calcitic coccoliths and planktonic foraminifera, have orders of magnitude lower productivity and accumulation rates than shallow‐water carbonates, but they cover orders of magnitude larger basin area. Twice as much calcium is removed from the oceans by present‐day carbonate accumulation as is estimated to be brought in by rivers and hydrothermal activity (1.6 bt), suggesting that outputs have been overestimated or inputs underestimated, that one or more other inputs have not been identified, and/or that the oceans are not presently in steady state. One “missing” calcium source might be groundwater, although its present‐day input is probably much smaller than that of rivers. If, as seems likely, CaCO 3 accumulation presently exceeds terrestial and hydrothermal input, this imbalance presumably is offset by decreased accumulation and increased input during lowered sea level: shallow‐water accumulation decreases by an order of magnitude with a 100 m drop in sea level, while groundwater influx increases because of heightened piezometric head and the diagenesis of metastable aragonite and magnesian calcite from subaerially exposed shallow‐water carbonates.

@article{doi10102993gb02524,
    author = "Milliman, John D.",
    title = "Production and accumulation of calcium carbonate in the ocean: Budget of a nonsteady state",
    year = "1993",
    journal = "Global Biogeochemical Cycles",
    abstract = "Present‐day production of CaCO 3 in tne world ocean is calculated to be about 5 billion tons (bt) per year, of which about 3 bt accumulate in sediments; the other 40\% is dissolved. Nearly half of the carbonate sediment accumulates on reefs, banks, and tropical shelves, and consists largely of metastable aragonite and magnesian calcite. Deep‐sea carbonates, predominantly calcitic coccoliths and planktonic foraminifera, have orders of magnitude lower productivity and accumulation rates than shallow‐water carbonates, but they cover orders of magnitude larger basin area. Twice as much calcium is removed from the oceans by present‐day carbonate accumulation as is estimated to be brought in by rivers and hydrothermal activity (1.6 bt), suggesting that outputs have been overestimated or inputs underestimated, that one or more other inputs have not been identified, and/or that the oceans are not presently in steady state. One “missing” calcium source might be groundwater, although its present‐day input is probably much smaller than that of rivers. If, as seems likely, CaCO 3 accumulation presently exceeds terrestial and hydrothermal input, this imbalance presumably is offset by decreased accumulation and increased input during lowered sea level: shallow‐water accumulation decreases by an order of magnitude with a 100 m drop in sea level, while groundwater influx increases because of heightened piezometric head and the diagenesis of metastable aragonite and magnesian calcite from subaerially exposed shallow‐water carbonates.",
    url = "https://doi.org/10.1029/93gb02524",
    doi = "10.1029/93gb02524",
    openalex = "W2058721748",
    references = "doi10102993gb01731, doi101126science1944268937, doi101126science2264677965, doi101126science2434891638, doi1011300091761319920200733rotcrh23co2, openalexw1490382454"
}

Many coral reefs have been degraded over the past two to three decades through a combination of human and natural disturbances. In Jamaica, the effects of overfishing, hurricane damage, and disease have combined to destroy most corals, whose abundance has declined from more than 50 percent in the late 1970s to less than 5 percent today. A dramatic phase shift has occurred, producing a system dominated by fleshy macroalgae (more than 90 percent cover). Immediate implementation of management procedures is necessary to avoid further catastrophic damage.

@article{doi101126science26551781547,
    author = "Hughes, Terry P.",
    title = "Catastrophes, Phase Shifts, and Large-Scale Degradation of a Caribbean Coral Reef",
    year = "1994",
    journal = "Science",
    abstract = "Many coral reefs have been degraded over the past two to three decades through a combination of human and natural disturbances. In Jamaica, the effects of overfishing, hurricane damage, and disease have combined to destroy most corals, whose abundance has declined from more than 50 percent in the late 1970s to less than 5 percent today. A dramatic phase shift has occurred, producing a system dominated by fleshy macroalgae (more than 90 percent cover). Immediate implementation of management procedures is necessary to avoid further catastrophic damage.",
    url = "https://doi.org/10.1126/science.265.5178.1547",
    doi = "10.1126/science.265.5178.1547",
    openalex = "W2102998760",
    references = "doi101126science19943351302"
}

ABSTRACT Bleaching of reef corals is a phenomenon linked to temperature stress which involves loss of the symbiotic algae of the coral, which are known as zooxanthellae, and/or loss of algal pigments. The photosynthetic efficiency of zooxanthellae within the corals Montastrea annularis, Agaricia lamarki, Agaricia agaricites and Siderastrea radians was examined by pulse‐amplitude modulation fluorometry (PAM) during exposure to elevated temperatures (30–36°C). Zooxanthellae within M. annularis and A. lamarki were found to be more sensitive to elevated temperature, virtually complete disruption of photosynthesis being noted during exposure to temperatures of 32 and 34°C. The photosynthetic efficiency of zooxanthellae within S. radians and A. agaricites decreased to a lesser extent. Differences in the loss of algal cells on an aerial basis and in the cellular chlorophyll concentration were also found between these species. By combining the non‐invasive PAM technique with whole‐cell fluorescence of freshly isolated zooxanthellae, we have identified fundamental differences in the physiology of the symbionts within different species of coral. Zooxanthellae within M. annularis appear to be more susceptible to heat‐induced damage at or near the reaction centre of Photosystem II, while zooxanthellae living in S. radians remain capable of dissipating excess excitation energy through non‐photochemical pathways, thereby protecting the photosystem from damage during heat exposure.

@article{doi101111j136530401996tb00251x,
    author = "Warner, Mark E. and Fitt, William K. and Schmidt, Gregory W.",
    title = "The effects of elevated temperature on the photosynthetic efficiency of zooxanthellae in hospite from four different species of reef coral: a novel approach",
    year = "1996",
    journal = "Plant Cell \& Environment",
    abstract = "ABSTRACT Bleaching of reef corals is a phenomenon linked to temperature stress which involves loss of the symbiotic algae of the coral, which are known as zooxanthellae, and/or loss of algal pigments. The photosynthetic efficiency of zooxanthellae within the corals Montastrea annularis, Agaricia lamarki, Agaricia agaricites and Siderastrea radians was examined by pulse‐amplitude modulation fluorometry (PAM) during exposure to elevated temperatures (30–36°C). Zooxanthellae within M. annularis and A. lamarki were found to be more sensitive to elevated temperature, virtually complete disruption of photosynthesis being noted during exposure to temperatures of 32 and 34°C. The photosynthetic efficiency of zooxanthellae within S. radians and A. agaricites decreased to a lesser extent. Differences in the loss of algal cells on an aerial basis and in the cellular chlorophyll concentration were also found between these species. By combining the non‐invasive PAM technique with whole‐cell fluorescence of freshly isolated zooxanthellae, we have identified fundamental differences in the physiology of the symbionts within different species of coral. Zooxanthellae within M. annularis appear to be more susceptible to heat‐induced damage at or near the reaction centre of Photosystem II, while zooxanthellae living in S. radians remain capable of dissipating excess excitation energy through non‐photochemical pathways, thereby protecting the photosystem from damage during heat exposure.",
    url = "https://doi.org/10.1111/j.1365-3040.1996.tb00251.x",
    doi = "10.1111/j.1365-3040.1996.tb00251.x",
    openalex = "W2120307232",
    references = "doi1023071933661"
}

@article{doi101016s0921818198000356,
    author = "Gattuso, Jean‐Pierre",
    title = "Effect of calcium carbonate saturation of seawater on coral calcification",
    year = "1998",
    journal = "Global and Planetary Change",
    url = "https://doi.org/10.1016/s0921-8181(98)00035-6",
    doi = "10.1016/s0921-8181(98)00035-6",
    openalex = "W1999570930"
}

@article{doi101046j152988171998340393x,
    author = "Adey, Walter H.",
    title = "REVIEW—CORAL REEFS: ALGAL STRUCTURED AND MEDIATED ECOSYSTEMS IN SHALLOW, TURBULENT, ALKALINE WATERS",
    year = "1998",
    journal = "Journal of Phycology",
    url = "https://doi.org/10.1046/j.1529-8817.1998.340393.x",
    doi = "10.1046/j.1529-8817.1998.340393.x",
    openalex = "W2059567047",
    references = "doi101126science1944268937"
}

▪ Abstract The coastal zone is where land, ocean, and atmosphere interact. It exhibits a wide diversity of geomorphological types and ecosystems, each one displaying great variability in terms of physical and biogeochemical forcings. Despite its relatively modest surface area, the coastal zone plays a considerable role in the biogeochemical cycles because it receives massive inputs of terrestrial organic matter and nutrients, is among the most geochemically and biologically active areas of the biosphere, and exchanges large amounts of matter and energy with the open ocean. Coastal ecosystems have therefore attracted much attention recently and are the focus of several current national and international research programs (e.g. LOICZ, ELOISE). The primary production, respiration, calcification, carbon burial and exchange with adjacent systems, including the atmosphere, are reviewed for the major coastal ecosystems (estuaries, macrophyte communities, mangroves, coral reefs, and the remaining continental shelf). All ecosystems examined, except estuaries, are net autotrophic. The contribution of the coastal zone to the global carbon cycle both during pristine times and at present is difficult to assess due to the limited metabolic data available as well as because of major uncertainties concerning the magnitude of processes such as respiration, exchanges at the open ocean boundary, and air-sea fluxes of biogases.

@article{doi101146annurevecolsys291405,
    author = "Gattuso, Jean‐Pierre and Frankignoulle, Michel and Wollast, Roland",
    title = "CARBON AND CARBONATE METABOLISM IN COASTAL AQUATIC ECOSYSTEMS",
    year = "1998",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "▪ Abstract The coastal zone is where land, ocean, and atmosphere interact. It exhibits a wide diversity of geomorphological types and ecosystems, each one displaying great variability in terms of physical and biogeochemical forcings. Despite its relatively modest surface area, the coastal zone plays a considerable role in the biogeochemical cycles because it receives massive inputs of terrestrial organic matter and nutrients, is among the most geochemically and biologically active areas of the biosphere, and exchanges large amounts of matter and energy with the open ocean. Coastal ecosystems have therefore attracted much attention recently and are the focus of several current national and international research programs (e.g. LOICZ, ELOISE). The primary production, respiration, calcification, carbon burial and exchange with adjacent systems, including the atmosphere, are reviewed for the major coastal ecosystems (estuaries, macrophyte communities, mangroves, coral reefs, and the remaining continental shelf). All ecosystems examined, except estuaries, are net autotrophic. The contribution of the coastal zone to the global carbon cycle both during pristine times and at present is difficult to assess due to the limited metabolic data available as well as because of major uncertainties concerning the magnitude of processes such as respiration, exchanges at the open ocean boundary, and air-sea fluxes of biogases.",
    url = "https://doi.org/10.1146/annurev.ecolsys.29.1.405",
    doi = "10.1146/annurev.ecolsys.29.1.405",
    openalex = "W2138329568",
    references = "doi1011300091761319920200733rotcrh23co2, doi101146annureves05110174000351"
}

@article{doi101016s0921800999000099,
    author = "Moberg, Fredrik and Folke, Carl",
    title = "Ecological goods and services of coral reef ecosystems",
    year = "1999",
    journal = "Ecological Economics",
    url = "https://doi.org/10.1016/s0921-8009(99)00009-9",
    doi = "10.1016/s0921-8009(99)00009-9",
    openalex = "W2161890892",
    references = "doi101016017626809290034e, doi101038387253a0, doi101086282400, doi101093icb326674, doi101126science19943351302, doi101126science260510417, doi101126science26551781547, doi101146annureves04110173000245, doi1023072269460, doi1023073146384, doi1023073244191"
}

Sea temperatures in many tropical regions have increased by almost 1°C over the past 100 years, and are currently increasing at ~1–2°C per century. Coral bleaching occurs when the thermal tolerance of corals and their photosynthetic symbionts (zooxanthellae) is exceeded. Mass coral bleaching has occurred in association with episodes of elevated sea temperatures over the past 20 years and involves the loss of the zooxanthellae following chronic photoinhibition. Mass bleaching has resulted in significant losses of live coral in many parts of the world. This paper considers the biochemical, physiological and ecological perspectives of coral bleaching. It also uses the outputs of four runs from three models of global climate change which simulate changes in sea temperature and hence how the frequency and intensity of bleaching events will change over the next 100 years. The results suggest that the thermal tolerances of reef-building corals are likely to be exceeded every year within the next few decades. Events as severe as the 1998 event, the worst on record, are likely to become commonplace within 20 years. Most information suggests that the capacity for acclimation by corals has already been exceeded, and that adaptation will be too slow to avert a decline in the quality of the world’s reefs. The rapidity of the changes that are predicted indicates a major problem for tropical marine ecosystems and suggests that unrestrained warming cannot occur without the loss and degradation of coral reefs on a global scale.

@article{doi101071mf99078,
    author = "Hoegh‐Guldberg, Ove",
    title = "Climate change, coral bleaching and the future of the world's coral reefs",
    year = "1999",
    journal = "Marine and Freshwater Research",
    abstract = "Sea temperatures in many tropical regions have increased by almost 1°C over the past 100 years, and are currently increasing at \textasciitilde 1–2°C per century. Coral bleaching occurs when the thermal tolerance of corals and their photosynthetic symbionts (zooxanthellae) is exceeded. Mass coral bleaching has occurred in association with episodes of elevated sea temperatures over the past 20 years and involves the loss of the zooxanthellae following chronic photoinhibition. Mass bleaching has resulted in significant losses of live coral in many parts of the world. This paper considers the biochemical, physiological and ecological perspectives of coral bleaching. It also uses the outputs of four runs from three models of global climate change which simulate changes in sea temperature and hence how the frequency and intensity of bleaching events will change over the next 100 years. The results suggest that the thermal tolerances of reef-building corals are likely to be exceeded every year within the next few decades. Events as severe as the 1998 event, the worst on record, are likely to become commonplace within 20 years. Most information suggests that the capacity for acclimation by corals has already been exceeded, and that adaptation will be too slow to avert a decline in the quality of the world’s reefs. The rapidity of the changes that are predicted indicates a major problem for tropical marine ecosystems and suggests that unrestrained warming cannot occur without the loss and degradation of coral reefs on a global scale.",
    url = "https://doi.org/10.1071/mf99078",
    doi = "10.1071/mf99078",
    openalex = "W1991462310",
    references = "doi101007bf00303779, doi101007s003380050249, doi101016000527289090088l, doi10103819505, doi101073pnas892110302, doi101093icb391146, doi101126science26551781547, doi101126science2845411118, doi1023071297526, openalexw1759145845, openalexw2341328186"
}

SYNOPSIS. Understanding how reefs vary over the present ranges of environmental conditions is key to understanding how coral reefs will adapt to a changing environment. Global environmental data of temperature, salinity, light, carbonate saturation state, and nutrients were recently compiled for nearly 1,000 reef locations. These data were statistically analyzed to (1) re-define environmental limits over which reefs exist today, (2) identify “marginal” reefs; i.e., those that exist near or beyond “normal” environmental limits of reef distribution, and (3) broadly classify reefs based on these major environmental variables. Temperature and salinity limits to coral reefs, as determined by this analysis, are very near those determined by previous researchers; but precise nutrient levels that could be considered limiting to coral reefs were not obvious at the scale of this analysis. However, in contrast to many previous studies that invoke low temperature as the reef-limiting factor at higher latitudes, this study indicates that reduced aragonite saturation and light penetration, both of which covary with temperature, may also be limiting. Identification of “marginal” reef environments, and a new classification of reefs based on suites of environmental conditions, provide an improved global perspective toward predicting how reefs will respond to changing environmental conditions.

@article{doi101093icb391146,
    author = "Kleypas, Joan A. and McManus, John and Menez, L.A.B.",
    title = "Environmental Limits to Coral Reef Development: Where Do We Draw the Line?",
    year = "1999",
    journal = "American Zoologist",
    abstract = "SYNOPSIS. Understanding how reefs vary over the present ranges of environmental conditions is key to understanding how coral reefs will adapt to a changing environment. Global environmental data of temperature, salinity, light, carbonate saturation state, and nutrients were recently compiled for nearly 1,000 reef locations. These data were statistically analyzed to (1) re-define environmental limits over which reefs exist today, (2) identify “marginal” reefs; i.e., those that exist near or beyond “normal” environmental limits of reef distribution, and (3) broadly classify reefs based on these major environmental variables. Temperature and salinity limits to coral reefs, as determined by this analysis, are very near those determined by previous researchers; but precise nutrient levels that could be considered limiting to coral reefs were not obvious at the scale of this analysis. However, in contrast to many previous studies that invoke low temperature as the reef-limiting factor at higher latitudes, this study indicates that reduced aragonite saturation and light penetration, both of which covary with temperature, may also be limiting. Identification of “marginal” reef environments, and a new classification of reefs based on suites of environmental conditions, provide an improved global perspective toward predicting how reefs will respond to changing environmental conditions.",
    url = "https://doi.org/10.1093/icb/39.1.146",
    doi = "10.1093/icb/39.1.146",
    openalex = "W2152904629",
    references = "doi1010160031018288901009, doi1010160037073888901285, doi101016s0921818198000356, doi1010291999gb001195, doi101029eo064i049p0096202, doi101038371123a0, doi1011751520044219930060114airtgs20co2, doi1023073514476, doi102475ajs2837780, openalexw1587057093"
}

peer reviewed

@article{doi101093icb391160,
    author = "Gattuso, Jean‐Pierre and Allemand, Denis and Frankignoulle, Michel",
    title = "Photosynthesis and Calcification at Cellular, Organismal and Community Levels in Coral Reefs: A Review on Interactions and Control by Carbonate Chemistry",
    year = "1999",
    journal = "American Zoologist",
    abstract = "peer reviewed",
    url = "https://doi.org/10.1093/icb/39.1.160",
    doi = "10.1093/icb/39.1.160",
    openalex = "W2103819980",
    references = "doi101093icb391146, doi1011300091761319920200733rotcrh23co2"
}

A coral reef represents the net accumulation of calcium carbonate (CaCO3) produced by corals and other calcifying organisms. If calcification declines, then reef-building capacity also declines. Coral reef calcification depends on the saturation state of the carbonate mineral aragonite of surface waters. By the middle of the next century, an increased concentration of carbon dioxide will decrease the aragonite saturation state in the tropics by 30 percent and biogenic aragonite precipitation by 14 to 30 percent. Coral reefs are particularly threatened, because reef-building organisms secrete metastable forms of CaCO3, but the biogeochemical consequences on other calcifying marine ecosystems may be equally severe.

@article{doi101126science2845411118,
    author = "Kleypas, Joan A. and Buddemeier, Robert W. and Archer, David and Gattuso, Jean‐Pierre and Langdon, Chris and Opdyke, Bradley N.",
    title = "Geochemical Consequences of Increased Atmospheric Carbon Dioxide on Coral Reefs",
    year = "1999",
    journal = "Science",
    abstract = "A coral reef represents the net accumulation of calcium carbonate (CaCO3) produced by corals and other calcifying organisms. If calcification declines, then reef-building capacity also declines. Coral reef calcification depends on the saturation state of the carbonate mineral aragonite of surface waters. By the middle of the next century, an increased concentration of carbon dioxide will decrease the aragonite saturation state in the tropics by 30 percent and biogenic aragonite precipitation by 14 to 30 percent. Coral reefs are particularly threatened, because reef-building organisms secrete metastable forms of CaCO3, but the biogeochemical consequences on other calcifying marine ecosystems may be equally severe.",
    url = "https://doi.org/10.1126/science.284.5411.118",
    doi = "10.1126/science.284.5411.118",
    openalex = "W1976061944",
    references = "doi101007bf01054491, doi101016001670379400354o, doi1010160198014987900215, doi1010160304420374900152, doi101029gm032, doi10103837333, doi101093icb391146, doi101093icb391160, doi102475ajs2837780, openalexw1587057093"
}

@article{doi101007s003380000086,
    author = "Marshall, Paul and Baird, Andrew H.",
    title = "Bleaching of corals on the Great Barrier Reef: differential susceptibilities among taxa",
    year = "2000",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/s003380000086",
    doi = "10.1007/s003380000086",
    openalex = "W2011181238"
}

@article{doi101007s003380050220,
    author = "Glynn, Peter W. and Ault, Jerald S.",
    title = "A biogeographic analysis and review of the far eastern Pacific coral reef region",
    year = "2000",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/s003380050220",
    doi = "10.1007/s003380050220",
    openalex = "W2163066808",
    references = "chave1972carbonate, doi1010160012821x87901543, doi101038342637a0, doi101093aibsbulletin3217e, doi101146annureves24110193001201, doi1023072531616, doi1023073514476, doi105962bhltitle46292, doi105962bhltitle59991, openalexw1524247963, openalexw2341328186"
}

@article{doi101016s0025326x99002374,
    author = "Edinger, Evan and Limmon, Gino V. and Jompa, Jamaluddin and Widjatmoko, Wisnu and Heikoop, Jeffrey M. and Risk, Michael J.",
    title = "Normal Coral Growth Rates on Dying Reefs: Are Coral Growth Rates Good Indicators of Reef Health?",
    year = "2000",
    journal = "Marine Pollution Bulletin",
    url = "https://doi.org/10.1016/s0025-326x(99)00237-4",
    doi = "10.1016/s0025-326x(99)00237-4",
    openalex = "W2090898773",
    references = "doi101007bf00391957, doi1010160025326x89905006, doi101016s0025326x98000472, doi10108000785236199510422044, doi10113000167606198192197tpodra20co2, doi1018901051076119970070737haotgn20co2, doi1023073514476, doi103354meps062185, doi104319lo1997425part21119, openalexw2100271629"
}

The concentration of CO 2 in the atmosphere is projected to reach twice the preindustrial level by the middle of the 21st century. This increase will reduce the concentration of CO 3 2− of the surface ocean by 30% relative to the preindustrial level and will reduce the calcium carbonate saturation state of the surface ocean by an equal percentage. Using the large 2650 m 3 coral reef mesocosm at the BIOSPHERE‐2 facility near Tucson, Arizona, we investigated the effect of the projected changes in seawater carbonate chemistry on the calcification of coral reef organisms at the community scale. Our experimental design was to obtain a long (3.8 years) time series of the net calcification of the complete system and all relevant physical and chemical variables (temperature, salinity, light, nutrients, Ca 2+, p CO 2, T CO 2, and total alkalinity). Periodic additions of NaHCO 3, Na 2 CO 3, and/or CaCl 2 were made to change the calcium carbonate saturation state of the water. We found that there were consistent and reproducible changes in the rate of calcification in response to our manipulations of the saturation state. We show that the net community calcification rate responds to manipulations in the concentrations of both Ca 2+ and CO 3 2− and that the rate is well described as a linear function of the ion concentration product, [Ca 2+] 0.69 [CO 3 2−]. This suggests that saturation state or a closely related quantity is a primary environmental factor that influences calcification on coral reefs at the ecosystem level. We compare the sensitivity of calcification to short‐term (days) and long‐term (months to years) changes in saturation state and found that the response was not significantly different. This indicates that coral reef organisms do not seem to be able to acclimate to changing saturation state. The predicted decrease in coral reef calcification between the years 1880 and 2065 A.D. based on our long‐term results is 40%. Previous small‐scale, short‐term organismal studies predicted a calcification reduction of 14‐30%. This much longer, community‐scale study suggests that the impact on coral reefs may be greater than previously suspected. In the next century coral reefs will be less able to cope with rising sea level and other anthropogenic stresses.

@article{doi1010291999gb001195,
    author = "Langdon, Chris and Takahashi, Taro and Sweeney, Colm and Chipman, Dave and Goddard, J. and Marubini, Francesca and Aceves, Heather L. and Barnett, H. and Atkinson, Marlin J.",
    title = "Effect of calcium carbonate saturation state on the calcification rate of an experimental coral reef",
    year = "2000",
    journal = "Global Biogeochemical Cycles",
    abstract = "The concentration of CO 2 in the atmosphere is projected to reach twice the preindustrial level by the middle of the 21st century. This increase will reduce the concentration of CO 3 2− of the surface ocean by 30\% relative to the preindustrial level and will reduce the calcium carbonate saturation state of the surface ocean by an equal percentage. Using the large 2650 m 3 coral reef mesocosm at the BIOSPHERE‐2 facility near Tucson, Arizona, we investigated the effect of the projected changes in seawater carbonate chemistry on the calcification of coral reef organisms at the community scale. Our experimental design was to obtain a long (3.8 years) time series of the net calcification of the complete system and all relevant physical and chemical variables (temperature, salinity, light, nutrients, Ca 2+, p CO 2, T CO 2, and total alkalinity). Periodic additions of NaHCO 3, Na 2 CO 3, and/or CaCl 2 were made to change the calcium carbonate saturation state of the water. We found that there were consistent and reproducible changes in the rate of calcification in response to our manipulations of the saturation state. We show that the net community calcification rate responds to manipulations in the concentrations of both Ca 2+ and CO 3 2− and that the rate is well described as a linear function of the ion concentration product, [Ca 2+] 0.69 [CO 3 2−]. This suggests that saturation state or a closely related quantity is a primary environmental factor that influences calcification on coral reefs at the ecosystem level. We compare the sensitivity of calcification to short‐term (days) and long‐term (months to years) changes in saturation state and found that the response was not significantly different. This indicates that coral reef organisms do not seem to be able to acclimate to changing saturation state. The predicted decrease in coral reef calcification between the years 1880 and 2065 A.D. based on our long‐term results is 40\%. Previous small‐scale, short‐term organismal studies predicted a calcification reduction of 14‐30\%. This much longer, community‐scale study suggests that the impact on coral reefs may be greater than previously suspected. In the next century coral reefs will be less able to cope with rising sea level and other anthropogenic stresses.",
    url = "https://doi.org/10.1029/1999gb001195",
    doi = "10.1029/1999gb001195",
    openalex = "W2059732463"
}

Population decline, local extinction, and recovery are profoundly influenced by variation in demography and life-history traits. In open populations, changes in patterns of recruitment may also have a major influence on the size of local populations, particularly for short-lived organisms. We examine here the demographic processes underlying a slow decline of corals on Jamaican reefs, where coral cover has decreased by fourfold over a 16-yr period. We divided the study into three approximately equal intervals (1977–1982, 1982–1987, and 1987–1993) and constructed size-based transition matrices for each of three abundant species of corals (Montastrea annularis, Agaricia agaricites, and Leptoseris cucullata) that differ substantially in life history: Montastrea is slower-growing, longer-lived, and has lower rates of recruitment than the other two species. Rates of survival, population growth (λ), and recruitment declined substantially over time for all species and the stable size structures became increasingly dominated by small colonies. Elasticity and life table response analysis showed that changes in the persistence of large colonies had the biggest impact on population growth in all species. Simulations indicated that the levels of larval recruitment required to maintain populations at 1977 levels increased sharply over time, even as the actual recruitment rate declined. Recruitment failure was much more important to A. agaricites and L. cucullata than to M. annularis, which could survive long periods with minimal larval input. Recovery of these populations will require an increase in both survival and recruitment. The likelihood of the latter will depend on the scale of larval dispersal, and on the impact of large-scale mortality of adults on stock-recruitment relationships. Differences in connectivity and life histories of corals will determine future patterns of recovery or further decline.

@article{doi1018900012965820000812250rflhal20co2,
    author = "Hughes, Terry P. and Tanner, Jason E.",
    title = "RECRUITMENT FAILURE, LIFE HISTORIES, AND LONG-TERM DECLINE OF CARIBBEAN CORALS",
    year = "2000",
    journal = "Ecology",
    abstract = "Population decline, local extinction, and recovery are profoundly influenced by variation in demography and life-history traits. In open populations, changes in patterns of recruitment may also have a major influence on the size of local populations, particularly for short-lived organisms. We examine here the demographic processes underlying a slow decline of corals on Jamaican reefs, where coral cover has decreased by fourfold over a 16-yr period. We divided the study into three approximately equal intervals (1977–1982, 1982–1987, and 1987–1993) and constructed size-based transition matrices for each of three abundant species of corals (Montastrea annularis, Agaricia agaricites, and Leptoseris cucullata) that differ substantially in life history: Montastrea is slower-growing, longer-lived, and has lower rates of recruitment than the other two species. Rates of survival, population growth (λ), and recruitment declined substantially over time for all species and the stable size structures became increasingly dominated by small colonies. Elasticity and life table response analysis showed that changes in the persistence of large colonies had the biggest impact on population growth in all species. Simulations indicated that the levels of larval recruitment required to maintain populations at 1977 levels increased sharply over time, even as the actual recruitment rate declined. Recruitment failure was much more important to A. agaricites and L. cucullata than to M. annularis, which could survive long periods with minimal larval input. Recovery of these populations will require an increase in both survival and recruitment. The likelihood of the latter will depend on the scale of larval dispersal, and on the impact of large-scale mortality of adults on stock-recruitment relationships. Differences in connectivity and life histories of corals will determine future patterns of recovery or further decline.",
    url = "https://doi.org/10.1890/0012-9658(2000)081[2250:rflhal]2.0.co;2",
    doi = "10.1890/0012-9658(2000)081[2250:rflhal]2.0.co;2",
    openalex = "W1992601320",
    references = "doi103354meps007207"
}

@incollection{doi10100797894017328402,
    author = "Aronson, Richard B. and Precht, William F.",
    title = "White-band disease and the changing face of Caribbean coral reefs",
    year = "2001",
    url = "https://doi.org/10.1007/978-94-017-3284-0\_2",
    doi = "10.1007/978-94-017-3284-0\_2",
    openalex = "W1561144917",
    references = "doi101007s003380050213, doi101016s0169534797897911, doi101038342637a0, doi101126science19943351302, doi101126science26551781547, doi101126science2845411118, doi101126science28554331505, doi103354meps007207, doi103354meps062185, openalexw2341328186"
}

Sea surface temperatures were warmer throughout 1998 at Sesoko Island, Japan, than in the 10 preceding years. Temperatures peaked at 2.8 °C above average, resulting in extensive coral bleaching and subsequent coral mortality. Using random quadrat surveys, we quantitatively documented the coral community structure one year before and one year after the bleaching event. The 1998 bleaching event reduced coral species richness by 61% and reduced coral cover by 85%. Colony morphology affected bleaching vulnerability and subsequent coral mortality. Finely branched corals were most susceptible, while massive and encrusting colonies survived. Most heavily impacted were the branched Acropora and pocilloporid corals, some of which showed local extinction. We suggest two hypotheses whose synergistic effect may partially explain observed mortality patterns (i.e. preferential survival of thick‐tissued species, and shape‐dependent differences in colony mass‐transfer efficiency). A community‐structural shift occurred on Okinawan reefs, resulting in an increase in the relative abundance of massive and encrusting coral species.

@article{doi101046j14610248200100203x,
    author = "Loya, Yossi and Sakai, Kazuhiko and Yamazato, K. and Nakano, Y. and Sambali, Hariyani and van Woesik, Robert",
    title = "Coral bleaching: the winners and the losers",
    year = "2001",
    journal = "Ecology Letters",
    abstract = "Sea surface temperatures were warmer throughout 1998 at Sesoko Island, Japan, than in the 10 preceding years. Temperatures peaked at 2.8 °C above average, resulting in extensive coral bleaching and subsequent coral mortality. Using random quadrat surveys, we quantitatively documented the coral community structure one year before and one year after the bleaching event. The 1998 bleaching event reduced coral species richness by 61\% and reduced coral cover by 85\%. Colony morphology affected bleaching vulnerability and subsequent coral mortality. Finely branched corals were most susceptible, while massive and encrusting colonies survived. Most heavily impacted were the branched Acropora and pocilloporid corals, some of which showed local extinction. We suggest two hypotheses whose synergistic effect may partially explain observed mortality patterns (i.e. preferential survival of thick‐tissued species, and shape‐dependent differences in colony mass‐transfer efficiency). A community‐structural shift occurred on Okinawan reefs, resulting in an increase in the relative abundance of massive and encrusting coral species.",
    url = "https://doi.org/10.1046/j.1461-0248.2001.00203.x",
    doi = "10.1046/j.1461-0248.2001.00203.x",
    openalex = "W2155454753"
}

Coral reefs, with their millions of species, have changed profoundly because of the effects of people, and will continue to do so for the foreseeable future. Reefs are subject to many of the same processes that affect other human-dominated ecosystems, but some special features merit emphasis: (i) Many dominant reef builders spawn eggs and sperm into the water column, where fertilization occurs. They are thus particularly vulnerable to Allee effects, including potential extinction associated with chronic reproductive failure. (ii) The corals likely to be most resistant to the effects of habitat degradation are small, short-lived "weedy" corals that have limited dispersal capabilities at the larval stage. Habitat degradation, together with habitat fragmentation, will therefore lead to the establishment of genetically isolated clusters of inbreeding corals. (iii) Increases in average sea temperatures by as little as 1 degrees C, a likely result of global climate change, can cause coral "bleaching" (the breakdown of coral-algal symbiosis), changes in symbiont communities, and coral death. (iv) The activities of people near reefs increase both fishing pressure and nutrient inputs. In general, these processes favor more rapidly growing competitors, often fleshy seaweeds, and may also result in explosions of predator populations. (v) Combinations of stress appear to be associated with threshold responses and ecological surprises, including devastating pathogen outbreaks. (vi) The fossil record suggests that corals as a group are more likely to suffer extinctions than some of the groups that associate with them, whose habitat requirements may be less stringent.

@article{doi101073pnas091092998,
    author = "Knowlton­, Nancy­",
    title = "The future of coral reefs",
    year = "2001",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {Coral reefs, with their millions of species, have changed profoundly because of the effects of people, and will continue to do so for the foreseeable future. Reefs are subject to many of the same processes that affect other human-dominated ecosystems, but some special features merit emphasis: (i) Many dominant reef builders spawn eggs and sperm into the water column, where fertilization occurs. They are thus particularly vulnerable to Allee effects, including potential extinction associated with chronic reproductive failure. (ii) The corals likely to be most resistant to the effects of habitat degradation are small, short-lived "weedy" corals that have limited dispersal capabilities at the larval stage. Habitat degradation, together with habitat fragmentation, will therefore lead to the establishment of genetically isolated clusters of inbreeding corals. (iii) Increases in average sea temperatures by as little as 1 degrees C, a likely result of global climate change, can cause coral "bleaching" (the breakdown of coral-algal symbiosis), changes in symbiont communities, and coral death. (iv) The activities of people near reefs increase both fishing pressure and nutrient inputs. In general, these processes favor more rapidly growing competitors, often fleshy seaweeds, and may also result in explosions of predator populations. (v) Combinations of stress appear to be associated with threshold responses and ecological surprises, including devastating pathogen outbreaks. (vi) The fossil record suggests that corals as a group are more likely to suffer extinctions than some of the groups that associate with them, whose habitat requirements may be less stringent.},
    url = "https://doi.org/10.1073/pnas.091092998",
    doi = "10.1073/pnas.091092998",
    openalex = "W2166377141",
    references = "doi101073pnas101092598, doi101126science2785338692"
}

@article{doi101007bf02804903,
    author = "Szmant, Alina M.",
    title = "Nutrient enrichment on coral reefs: Is it a major cause of coral reef decline?",
    year = "2002",
    journal = "Estuaries",
    url = "https://doi.org/10.1007/bf02804903",
    doi = "10.1007/bf02804903",
    openalex = "W1998393588",
    references = "doi101038141548c0, doi103354meps007207"
}

Despite extensive research into the coral bleaching phenomena there are very few data which examine the population biology of affected species. These data are required in order to predict the capacity of corals to respond to environmental change. We monitored individual colonies of 4 common coral species for 8 mo following historically high sea-surface temperatures on the Great Barrier Reef in 1998 to compare their response to, and recovery from, thermal stress and to examine the effect of bleaching on growth and reproduction in 2 Acropora species. Platygyra daedalea and P. lobata colonies took longer to bleach, longer to recover and longer to die. In contrast, Acropora hyacinthus and A. millepora colonies bleached quickly and most had either recovered, or died, within 14 wk of the initial reports of bleaching. Whole colony mortality was high in A. hyacinthus (88%) and A. millepora (32%) and partial mortality rare. In contrast, most colonies of P. daedalea and P. lobata lost some tissue and few whole colonies died. The mean proportion of tissue lost per colony was 43 6.6 % and 11 1.1 % respectively. Consequently, observed hierarchies of species susceptibility will depend critically on the time since the onset of stress and must consider both whole and partial colony mortality. Colony mortality was highly dependent on visual estimates of the severity of bleaching but independent of size. Growth rates of Acropora colonies were highly variable and largely independent of the severity of bleaching. A. hyacinthus was more susceptible to bleaching than A. millepora with 45% of surviving colonies gravid compared to 88%. High whole-colony mortality combined with a reduction in the reproductive output of surviving Acropora suggests that recovery to former levels of abundance is likely to be slow.

@article{doi103354meps237133,
    author = "Baird, AH and Marshall, PA",
    title = "Mortality, growth and reproduction in scleractinian corals following bleaching on the Great Barrier Reef",
    year = "2002",
    journal = "Marine Ecology Progress Series",
    abstract = "Despite extensive research into the coral bleaching phenomena there are very few data which examine the population biology of affected species. These data are required in order to predict the capacity of corals to respond to environmental change. We monitored individual colonies of 4 common coral species for 8 mo following historically high sea-surface temperatures on the Great Barrier Reef in 1998 to compare their response to, and recovery from, thermal stress and to examine the effect of bleaching on growth and reproduction in 2 Acropora species. Platygyra daedalea and P. lobata colonies took longer to bleach, longer to recover and longer to die. In contrast, Acropora hyacinthus and A. millepora colonies bleached quickly and most had either recovered, or died, within 14 wk of the initial reports of bleaching. Whole colony mortality was high in A. hyacinthus (88\%) and A. millepora (32\%) and partial mortality rare. In contrast, most colonies of P. daedalea and P. lobata lost some tissue and few whole colonies died. The mean proportion of tissue lost per colony was 43 6.6 \% and 11 1.1 \% respectively. Consequently, observed hierarchies of species susceptibility will depend critically on the time since the onset of stress and must consider both whole and partial colony mortality. Colony mortality was highly dependent on visual estimates of the severity of bleaching but independent of size. Growth rates of Acropora colonies were highly variable and largely independent of the severity of bleaching. A. hyacinthus was more susceptible to bleaching than A. millepora with 45\% of surviving colonies gravid compared to 88\%. High whole-colony mortality combined with a reduction in the reproductive output of surviving Acropora suggests that recovery to former levels of abundance is likely to be slow.",
    url = "https://doi.org/10.3354/meps237133",
    doi = "10.3354/meps237133",
    openalex = "W2148447618",
    references = "doi103354meps007207"
}

@article{doi101002aqc558,
    author = "Epstein, N. and Bak, R. P. M. and Rinkevich, Baruch",
    title = "Applying forest restoration principles to coral reef rehabilitation",
    year = "2003",
    journal = "Aquatic Conservation Marine and Freshwater Ecosystems",
    url = "https://doi.org/10.1002/aqc.558",
    doi = "10.1002/aqc.558",
    openalex = "W2165115241"
}

The diversity, frequency, and scale of human impacts on coral reefs are increasing to the extent that reefs are threatened globally. Projected increases in carbon dioxide and temperature over the next 50 years exceed the conditions under which coral reefs have flourished over the past half-million years. However, reefs will change rather than disappear entirely, with some species already showing far greater tolerance to climate change and coral bleaching than others. International integration of management strategies that support reef resilience need to be vigorously implemented, and complemented by strong policy decisions to reduce the rate of global warming.

@article{doi101126science1085046,
    author = "Hughes, Terry P. and Baird, Andrew H. and Bellwood, David R. and Card, M. A. and Connolly, Sean R. and Folke, Carl and Grosberg, Richard K. and Hoegh‐Guldberg, Ove and Jackson, Jeremy B. C. and Kleypas, Joan A. and Lough, Janice and Marshall, Paul and Nyström, Magnus and Palumbi, Stephen R. and Pandolfi, John M. and Rosen, Brian and Roughgarden, Joan",
    title = "Climate Change, Human Impacts, and the Resilience of Coral Reefs",
    year = "2003",
    journal = "Science",
    abstract = "The diversity, frequency, and scale of human impacts on coral reefs are increasing to the extent that reefs are threatened globally. Projected increases in carbon dioxide and temperature over the next 50 years exceed the conditions under which coral reefs have flourished over the past half-million years. However, reefs will change rather than disappear entirely, with some species already showing far greater tolerance to climate change and coral bleaching than others. International integration of management strategies that support reef resilience need to be vigorously implemented, and complemented by strong policy decisions to reduce the rate of global warming.",
    url = "https://doi.org/10.1126/science.1085046",
    doi = "10.1126/science.1085046",
    openalex = "W2142598180",
    references = "doi101016s0921800999000099, doi101071mf99078, doi101126science1059199, doi101126science1085706, doi101126science2845411118"
}

Degradation of coral reef ecosystems began centuries ago, but there is no global summary of the magnitude of change. We compiled records, extending back thousands of years, of the status and trends of seven major guilds of carnivores, herbivores, and architectural species from 14 regions. Large animals declined before small animals and architectural species, and Atlantic reefs declined before reefs in the Red Sea and Australia, but the trajectories of decline were markedly similar worldwide. All reefs were substantially degraded long before outbreaks of coral disease and bleaching. Regardless of these new threats, reefs will not survive without immediate protection from human exploitation over large spatial scales.

@article{doi101126science1085706,
    author = "Pandolfi, John M. and Bradbury, Roger and Sala, Enric and Hughes, Terry P. and Bjorndal, Karen A. and Cooke, Richard G. and McArdle, Deborah and McClenachan, Loren and Newman, Marah J. H. and Paredes, Gustavo and Warner, Robert R. and Jackson, Jeremy B. C.",
    title = "Global Trajectories of the Long-Term Decline of Coral Reef Ecosystems",
    year = "2003",
    journal = "Science",
    abstract = "Degradation of coral reef ecosystems began centuries ago, but there is no global summary of the magnitude of change. We compiled records, extending back thousands of years, of the status and trends of seven major guilds of carnivores, herbivores, and architectural species from 14 regions. Large animals declined before small animals and architectural species, and Atlantic reefs declined before reefs in the Red Sea and Australia, but the trajectories of decline were markedly similar worldwide. All reefs were substantially degraded long before outbreaks of coral disease and bleaching. Regardless of these new threats, reefs will not survive without immediate protection from human exploitation over large spatial scales.",
    url = "https://doi.org/10.1126/science.1085706",
    doi = "10.1126/science.1085706",
    openalex = "W2100216289",
    references = "doi10100797894017328402, doi101016014362289090024j, doi101016016953479090113r, doi101071mf99078, doi101126science1059199, doi101126science1085046, doi101126science26551781547, doi101126science28554331505, doi1018900012961519970670461aysoca20co2, doi103354meps062185, openalexw570265017"
}

We report a massive region-wide decline of corals across the entire Caribbean basin, with the average hard coral cover on reefs being reduced by 80%, from about 50% to 10% cover, in three decades. Our meta-analysis shows that patterns of change in coral cover are variable across time periods but largely consistent across subregions, suggesting that local causes have operated with some degree of synchrony on a region-wide scale. Although the rate of coral loss has slowed in the past decade compared to the 1980s, significant declines are persisting. The ability of Caribbean coral reefs to cope with future local and global environmental change may be irretrievably compromised.

@article{doi101126science1086050,
    author = "Gardner, Toby and Côté, Isabelle M. and Gill, Jennifer A. and Grant, Alastair and Watkinson, Andrew R.",
    title = "Long-Term Region-Wide Declines in Caribbean Corals",
    year = "2003",
    journal = "Science",
    abstract = "We report a massive region-wide decline of corals across the entire Caribbean basin, with the average hard coral cover on reefs being reduced by 80\%, from about 50\% to 10\% cover, in three decades. Our meta-analysis shows that patterns of change in coral cover are variable across time periods but largely consistent across subregions, suggesting that local causes have operated with some degree of synchrony on a region-wide scale. Although the rate of coral loss has slowed in the past decade compared to the 1980s, significant declines are persisting. The ability of Caribbean coral reefs to cope with future local and global environmental change may be irretrievably compromised.",
    url = "https://doi.org/10.1126/science.1086050",
    doi = "10.1126/science.1086050",
    openalex = "W2024763652"
}

@article{doi101016jmarpolbul200411028,
    author = "Fabricius, Katharina",
    title = "Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis",
    year = "2004",
    journal = "Marine Pollution Bulletin",
    url = "https://doi.org/10.1016/j.marpolbul.2004.11.028",
    doi = "10.1016/j.marpolbul.2004.11.028",
    openalex = "W2164337693",
    references = "doi101016s0025326x99002374, doi101038nature02691, doi101126science2775325504"
}

@article{doi101038nature02691,
    author = "Bellwood, David R. and Hughes, Terry P. and Folke, Carl and Nyström, Magnus",
    title = "Confronting the coral reef crisis",
    year = "2004",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature02691",
    doi = "10.1038/nature02691",
    openalex = "W1989974377",
    references = "doi101007s003380050220, doi101016jtree200309002, doi101016s0921800999000099, doi10103835002501, doi10103835098000, doi101038nature01017, doi101093icb326674, doi101126science1059199, doi101126science1063699, doi101126science1085046, doi101126science1085706, doi101126science1091015, doi101126science26551781547, doi101146annurevecolsys35021103105711"
}

The worldwide decline in coral cover has serious implications for the health of coral reefs. But what is the future of reef fish assemblages? Marine reserves can protect fish from exploitation, but do they protect fish biodiversity in degrading environments? The answer appears to be no, as indicated by our 8-year study in Papua New Guinea. A devastating decline in coral cover caused a parallel decline in fish biodiversity, both in marine reserves and in areas open to fishing. Over 75% of reef fish species declined in abundance, and 50% declined to less than half of their original numbers. The greater the dependence species have on living coral as juvenile recruitment sites, the greater the observed decline in abundance. Several rare coral-specialists became locally extinct. We suggest that fish biodiversity is threatened wherever permanent reef degradation occurs and warn that marine reserves will not always be sufficient to ensure their survival.

@article{doi101073pnas0401277101,
    author = "Jones, Geoffrey P. and McCormick, Mark I. and Srinivasan, Maya and Eagle, Janelle V.",
    title = "Coral decline threatens fish biodiversity in marine reserves",
    year = "2004",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "The worldwide decline in coral cover has serious implications for the health of coral reefs. But what is the future of reef fish assemblages? Marine reserves can protect fish from exploitation, but do they protect fish biodiversity in degrading environments? The answer appears to be no, as indicated by our 8-year study in Papua New Guinea. A devastating decline in coral cover caused a parallel decline in fish biodiversity, both in marine reserves and in areas open to fishing. Over 75\% of reef fish species declined in abundance, and 50\% declined to less than half of their original numbers. The greater the dependence species have on living coral as juvenile recruitment sites, the greater the observed decline in abundance. Several rare coral-specialists became locally extinct. We suggest that fish biodiversity is threatened wherever permanent reef degradation occurs and warn that marine reserves will not always be sufficient to ensure their survival.",
    url = "https://doi.org/10.1073/pnas.0401277101",
    doi = "10.1073/pnas.0401277101",
    openalex = "W2132675942"
}

The skeletons of adult echinoderms comprise large single crystals of calcite with smooth convoluted fenestrated morphologies, raising many questions about how they form. By using water etching, infrared spectroscopy, electron diffraction, and environmental scanning electron microscopy, we show that sea urchin spine regeneration proceeds via the initial deposition of amorphous calcium carbonate. Because most echinoderms produce the same type of skeletal material, they probably all use this same mechanism. Deposition of transient amorphous phases as a strategy for producing single crystals with complex morphology may have interesting implications for the development of sophisticated materials.

@article{doi101126science1102289,
    author = "Politi, Yael and Arad, Talmon and Klein, Eugenia and Weiner, Steve and Addadi, Lia",
    title = "Sea Urchin Spine Calcite Forms via a Transient Amorphous Calcium Carbonate Phase",
    year = "2004",
    journal = "Science",
    abstract = "The skeletons of adult echinoderms comprise large single crystals of calcite with smooth convoluted fenestrated morphologies, raising many questions about how they form. By using water etching, infrared spectroscopy, electron diffraction, and environmental scanning electron microscopy, we show that sea urchin spine regeneration proceeds via the initial deposition of amorphous calcium carbonate. Because most echinoderms produce the same type of skeletal material, they probably all use this same mechanism. Deposition of transient amorphous phases as a strategy for producing single crystals with complex morphology may have interesting implications for the development of sophisticated materials.",
    url = "https://doi.org/10.1126/science.1102289",
    doi = "10.1126/science.1102289",
    openalex = "W1974595472"
}

Habitat recognition and selective settlement by dispersive propagules greatly increases the post-settlement survival chances of sessile organisms. To better understand the key role some species can play in the structure of highly complex coral reef ecosystems, we compare the role of two independent, but sequential, processes: settlement choice and post-settlement survival. This study describes the chemical and physical recognition and ranking of specific settlement substrata by coral larvae. Several species of crustose coralline algae (CCA) are known to induce coral settlement; however they also employ physical and biological anti-settlement defense strategies that vary greatly in effectiveness. We examine the interactions between settling larvae of two common reef building coral species (Acropora tenuis and A. millepora) and five species of CCA (Neogoniolithon fosliei, Porolithon onkodes, Hydrolithon reinboldii, Titanoderma prototypum, and Lithoporella melobesioides) that co-occur on reef crests and slopes of the Great Barrier Reef, Australia. Distinct settlement patterns were observed when coral larvae were provided with a choice of settlement substrata. Settlement on the most preferred substratum, the CCA species T. prototypum, was 15 times higher than on N. fosliei, the least preferred substratum. The rates of post-settlement survival of the corals also varied between CCA species in response to their anti-settlement strategies (shedding of surface cell layers, overgrowth, and potential chemical deterrents). Rates of larval settlement, post-settlement survival, and the sensitivity of larvae to chemical extracts of CCA were all positively correlated across the five species of CCA. Nonliving settlement substrata on coral reefs is sparse; consequently the fact that only a few CCA species (notably T. prototypum) facilitate coral recruitment, has important implications for structuring the reef ecosystem.

@article{doi101890040298,
    author = "Harrington, Lindsay and Fabricius, Katharina and De’ath, Glenn and Negri, Andrew P.",
    title = "RECOGNITION AND SELECTION OF SETTLEMENT SUBSTRATA DETERMINE POST-SETTLEMENT SURVIVAL IN CORALS",
    year = "2004",
    journal = "Ecology",
    abstract = "Habitat recognition and selective settlement by dispersive propagules greatly increases the post-settlement survival chances of sessile organisms. To better understand the key role some species can play in the structure of highly complex coral reef ecosystems, we compare the role of two independent, but sequential, processes: settlement choice and post-settlement survival. This study describes the chemical and physical recognition and ranking of specific settlement substrata by coral larvae. Several species of crustose coralline algae (CCA) are known to induce coral settlement; however they also employ physical and biological anti-settlement defense strategies that vary greatly in effectiveness. We examine the interactions between settling larvae of two common reef building coral species (Acropora tenuis and A. millepora) and five species of CCA (Neogoniolithon fosliei, Porolithon onkodes, Hydrolithon reinboldii, Titanoderma prototypum, and Lithoporella melobesioides) that co-occur on reef crests and slopes of the Great Barrier Reef, Australia. Distinct settlement patterns were observed when coral larvae were provided with a choice of settlement substrata. Settlement on the most preferred substratum, the CCA species T. prototypum, was 15 times higher than on N. fosliei, the least preferred substratum. The rates of post-settlement survival of the corals also varied between CCA species in response to their anti-settlement strategies (shedding of surface cell layers, overgrowth, and potential chemical deterrents). Rates of larval settlement, post-settlement survival, and the sensitivity of larvae to chemical extracts of CCA were all positively correlated across the five species of CCA. Nonliving settlement substrata on coral reefs is sparse; consequently the fact that only a few CCA species (notably T. prototypum) facilitate coral recruitment, has important implications for structuring the reef ecosystem.",
    url = "https://doi.org/10.1890/04-0298",
    doi = "10.1890/04-0298",
    openalex = "W2150835767",
    references = "doi1010160022098188900275, doi1023071933661"
}

The scientific discipline of active restoration of denuded coral reef areas has drawn much attention in the past decade as it became evident that this ecosystem does not often recover naturally from anthropogenic stress without manipulation. Essentially, the choices are eitherthe continuous degradation of the reefs or active restoration to encourage reef development. As a result, worldwide restoration operations during the past decade have been recognized as being a major tool for reef rehabilitation. This situation has also stirred discussions and debates on the various restoration measures suggested as management options, supplementary to the traditional conservation acts. The present essay reviews past decade's (1994-2004) approaches and advances in coral reef restoration. While direct coral transplantation is still the primer vehicle of operations used, the concept of in situ and ex situ coral nurseries (the gardening concept), where coral materials (nubbins, branches, spats) are maricultured to a size suitable for transplantation, has been gaining recognition. The use of nubbins (down to the size of a single or few polyps) has been suggested and employed as a unique technique for mass production of coral colonies. Restoration of ship grounding sites and the use of artificial reefs have become common tools for specific restoration needs. Substrate stabilization, 3-D structural consideration of developing colonies, and the use of molecular/biochemical tools are part of novel technology approaches developed in the past decade. Economic considerations for reef restoration have become an important avenue for evaluating success of restoration activities. It has been suggested that landscape restoration and restoration genetics are important issues to be studied. In the future, as coral reef restoration may become the dominant conservation act, there would be the need not only to develop improved protocols but also to define the conceptual bases.

@article{doi101021es0482583,
    author = "Rinkevich, Baruch",
    title = "Conservation of Coral Reefs through Active Restoration Measures: Recent Approaches and Last Decade Progress",
    year = "2005",
    journal = "Environmental Science \& Technology",
    abstract = "The scientific discipline of active restoration of denuded coral reef areas has drawn much attention in the past decade as it became evident that this ecosystem does not often recover naturally from anthropogenic stress without manipulation. Essentially, the choices are eitherthe continuous degradation of the reefs or active restoration to encourage reef development. As a result, worldwide restoration operations during the past decade have been recognized as being a major tool for reef rehabilitation. This situation has also stirred discussions and debates on the various restoration measures suggested as management options, supplementary to the traditional conservation acts. The present essay reviews past decade's (1994-2004) approaches and advances in coral reef restoration. While direct coral transplantation is still the primer vehicle of operations used, the concept of in situ and ex situ coral nurseries (the gardening concept), where coral materials (nubbins, branches, spats) are maricultured to a size suitable for transplantation, has been gaining recognition. The use of nubbins (down to the size of a single or few polyps) has been suggested and employed as a unique technique for mass production of coral colonies. Restoration of ship grounding sites and the use of artificial reefs have become common tools for specific restoration needs. Substrate stabilization, 3-D structural consideration of developing colonies, and the use of molecular/biochemical tools are part of novel technology approaches developed in the past decade. Economic considerations for reef restoration have become an important avenue for evaluating success of restoration activities. It has been suggested that landscape restoration and restoration genetics are important issues to be studied. In the future, as coral reef restoration may become the dominant conservation act, there would be the need not only to develop improved protocols but also to define the conceptual bases.",
    url = "https://doi.org/10.1021/es0482583",
    doi = "10.1021/es0482583",
    openalex = "W2074261860",
    references = "doi101016s0169534701022820"
}

The ability of coral reefs to survive the projected increases in temperature due to global warming will depend largely on the ability of corals to adapt or acclimatize to increased temperature extremes over the next few decades. Many coral species are highly sensitive to temperature stress and the number of stress (bleaching) episodes has increased in recent decades. We investigated the acclimatization potential of Acropora millepora, a common and widespread Indo-Pacific hard coral species, through transplantation and experimental manipulation. We show that adult corals, at least in some circumstances, are capable of acquiring increased thermal tolerance and that the increased tolerance is a direct result of a change in the symbiont type dominating their tissues from Symbiodinium type C to D. Our data suggest that the change in symbiont type in our experiment was due to a shuffling of existing types already present in coral tissues, not through exogenous uptake from the environment. The level of increased tolerance gained by the corals changing their dominant symbiont type to D (the most thermally resistant type known) is around 1-1.5 degrees C. This is the first study to show that thermal acclimatization is causally related to symbiont type and provides new insight into the ecological advantage of corals harbouring mixed algal populations. While this increase is of huge ecological significance for many coral species, in the absence of other mechanisms of thermal acclimatization/adaptation, it may not be sufficient to survive climate change under predicted sea surface temperature scenarios over the next 100 years. However, it may be enough to 'buy time' while greenhouse reduction measures are put in place.

@article{doi101098rspb20063567,
    author = "Berkelmans, Ray and van Oppen, Madeleine J. H.",
    title = "The role of zooxanthellae in the thermal tolerance of corals: a ‘nugget of hope’ for coral reefs in an era of climate change",
    year = "2006",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "The ability of coral reefs to survive the projected increases in temperature due to global warming will depend largely on the ability of corals to adapt or acclimatize to increased temperature extremes over the next few decades. Many coral species are highly sensitive to temperature stress and the number of stress (bleaching) episodes has increased in recent decades. We investigated the acclimatization potential of Acropora millepora, a common and widespread Indo-Pacific hard coral species, through transplantation and experimental manipulation. We show that adult corals, at least in some circumstances, are capable of acquiring increased thermal tolerance and that the increased tolerance is a direct result of a change in the symbiont type dominating their tissues from Symbiodinium type C to D. Our data suggest that the change in symbiont type in our experiment was due to a shuffling of existing types already present in coral tissues, not through exogenous uptake from the environment. The level of increased tolerance gained by the corals changing their dominant symbiont type to D (the most thermally resistant type known) is around 1-1.5 degrees C. This is the first study to show that thermal acclimatization is causally related to symbiont type and provides new insight into the ecological advantage of corals harbouring mixed algal populations. While this increase is of huge ecological significance for many coral species, in the absence of other mechanisms of thermal acclimatization/adaptation, it may not be sufficient to survive climate change under predicted sea surface temperature scenarios over the next 100 years. However, it may be enough to 'buy time' while greenhouse reduction measures are put in place.",
    url = "https://doi.org/10.1098/rspb.2006.3567",
    doi = "10.1098/rspb.2006.3567",
    openalex = "W2144114664",
    references = "doi101007s0022700414272, doi101146annurevecolsys34011802132417"
}

@article{doi101016jcub200612049,
    author = "Hughes, Terry P. and da Silva Rodrigues, Maria Júlia and Bellwood, David R. and Ceccarelli, Daniela M. and Hoegh‐Guldberg, Ove and McCook, Laurence J. and Moltschaniwskyj, Natalie A. and Pratchett, Morgan S. and Steneck, Robert S. and Willis, Bette L.",
    title = "Phase Shifts, Herbivory, and the Resilience of Coral Reefs to Climate Change",
    year = "2007",
    journal = "Current Biology",
    url = "https://doi.org/10.1016/j.cub.2006.12.049",
    doi = "10.1016/j.cub.2006.12.049",
    openalex = "W2171552191",
    references = "doi101016s0921800999000099, doi101126science1085706"
}

Atmospheric carbon dioxide concentration is expected to exceed 500 parts per million and global temperatures to rise by at least 2 degrees C by 2050 to 2100, values that significantly exceed those of at least the past 420,000 years during which most extant marine organisms evolved. Under conditions expected in the 21st century, global warming and ocean acidification will compromise carbonate accretion, with corals becoming increasingly rare on reef systems. The result will be less diverse reef communities and carbonate reef structures that fail to be maintained. Climate change also exacerbates local stresses from declining water quality and overexploitation of key species, driving reefs increasingly toward the tipping point for functional collapse. This review presents future scenarios for coral reefs that predict increasingly serious consequences for reef-associated fisheries, tourism, coastal protection, and people. As the International Year of the Reef 2008 begins, scaled-up management intervention and decisive action on global emissions are required if the loss of coral-dominated ecosystems is to be avoided.

@article{doi101126science1152509,
    author = "Hoegh‐Guldberg, Ove and Mumby, Peter J. and Hooten, Anthony J. and Steneck, Robert S. and Greenfield, Paul and Gomez, E. D. and Harvell, C. Drew and Sale, Peter F. and Edwards, Alasdair J. and Caldeira, K. and Knowlton­, Nancy­ and Eakin, C. Mark and Iglesias‐Prieto, Roberto and Muthiga, Nyawira A. and Bradbury, Roger and Dubi, Alfonse and Hatziolos, Marea Eleni",
    title = "Coral Reefs Under Rapid Climate Change and Ocean Acidification",
    year = "2007",
    journal = "Science",
    abstract = "Atmospheric carbon dioxide concentration is expected to exceed 500 parts per million and global temperatures to rise by at least 2 degrees C by 2050 to 2100, values that significantly exceed those of at least the past 420,000 years during which most extant marine organisms evolved. Under conditions expected in the 21st century, global warming and ocean acidification will compromise carbonate accretion, with corals becoming increasingly rare on reef systems. The result will be less diverse reef communities and carbonate reef structures that fail to be maintained. Climate change also exacerbates local stresses from declining water quality and overexploitation of key species, driving reefs increasingly toward the tipping point for functional collapse. This review presents future scenarios for coral reefs that predict increasingly serious consequences for reef-associated fisheries, tourism, coastal protection, and people. As the International Year of the Reef 2008 begins, scaled-up management intervention and decisive action on global emissions are required if the loss of coral-dominated ecosystems is to be avoided.",
    url = "https://doi.org/10.1126/science.1152509",
    doi = "10.1126/science.1152509",
    openalex = "W2123920115",
    references = "doi101016s0012825202001046, doi101016s0921800999000099, doi10103820859, doi101071mf99078, doi101073pnas0702737104, doi101093icb326674, doi101093icb391146, doi101126science1063699, doi101126science1085046, doi101126science1116448, doi101146annurevecolsys271477, doi101371journalpone0000711, doi102475ajs294156, doi102475ajs3012182, openalexw1621450917, openalexw2907110490, openalexw2939474406, openalexw2986345846, openalexw617039848"
}

BACKGROUND: A number of factors have recently caused mass coral mortality events in all of the world's tropical oceans. However, little is known about the timing, rate or spatial variability of the loss of reef-building corals, especially in the Indo-Pacific, which contains 75% of the world's coral reefs. METHODOLOGY/PRINCIPLE FINDINGS: We compiled and analyzed a coral cover database of 6001 quantitative surveys of 2667 Indo-Pacific coral reefs performed between 1968 and 2004. Surveys conducted during 2003 indicated that coral cover averaged only 22.1% (95% CI: 20.7, 23.4) and just 7 of 390 reefs surveyed that year had coral cover >60%. Estimated yearly coral cover loss based on annually pooled survey data was approximately 1% over the last twenty years and 2% between 1997 and 2003 (or 3,168 km(2) per year). The annual loss based on repeated measures regression analysis of a subset of reefs that were monitored for multiple years from 1997 to 2004 was 0.72 % (n = 476 reefs, 95% CI: 0.36, 1.08). CONCLUSIONS/SIGNIFICANCE: The rate and extent of coral loss in the Indo-Pacific are greater than expected. Coral cover was also surprisingly uniform among subregions and declined decades earlier than previously assumed, even on some of the Pacific's most intensely managed reefs. These results have significant implications for policy makers and resource managers as they search for successful models to reverse coral loss.

@article{doi101371journalpone0000711,
    author = "Bruno, John F. and Selig, Elizabeth R.",
    title = "Regional Decline of Coral Cover in the Indo-Pacific: Timing, Extent, and Subregional Comparisons",
    year = "2007",
    journal = "PLoS ONE",
    abstract = "BACKGROUND: A number of factors have recently caused mass coral mortality events in all of the world's tropical oceans. However, little is known about the timing, rate or spatial variability of the loss of reef-building corals, especially in the Indo-Pacific, which contains 75\% of the world's coral reefs. METHODOLOGY/PRINCIPLE FINDINGS: We compiled and analyzed a coral cover database of 6001 quantitative surveys of 2667 Indo-Pacific coral reefs performed between 1968 and 2004. Surveys conducted during 2003 indicated that coral cover averaged only 22.1\% (95\% CI: 20.7, 23.4) and just 7 of 390 reefs surveyed that year had coral cover >60\%. Estimated yearly coral cover loss based on annually pooled survey data was approximately 1\% over the last twenty years and 2\% between 1997 and 2003 (or 3,168 km(2) per year). The annual loss based on repeated measures regression analysis of a subset of reefs that were monitored for multiple years from 1997 to 2004 was 0.72 \% (n = 476 reefs, 95\% CI: 0.36, 1.08). CONCLUSIONS/SIGNIFICANCE: The rate and extent of coral loss in the Indo-Pacific are greater than expected. Coral cover was also surprisingly uniform among subregions and declined decades earlier than previously assumed, even on some of the Pacific's most intensely managed reefs. These results have significant implications for policy makers and resource managers as they search for successful models to reverse coral loss.",
    url = "https://doi.org/10.1371/journal.pone.0000711",
    doi = "10.1371/journal.pone.0000711",
    openalex = "W2068226428",
    references = "doi10100797894017328402, doi101038nature01610, doi101038nature02691, doi101071mf99078, doi101126science1070656, doi101126science1085046, doi101126science1085706, doi101126science1086050, doi101126science1128035, doi101126science26551781547, doi10164100063568200656987agcfse20co2"
}

@article{doi101016jecss200809003,
    author = "Baker, Andrew C. and Glynn, Peter W. and Riegl, Bernhard",
    title = "Climate change and coral reef bleaching: An ecological assessment of long-term impacts, recovery trends and future outlook",
    year = "2008",
    journal = "Estuarine Coastal and Shelf Science",
    url = "https://doi.org/10.1016/j.ecss.2008.09.003",
    doi = "10.1016/j.ecss.2008.09.003",
    openalex = "W2086993800",
    references = "doi101007s100219900037, doi101038425365a, doi101038nature01286, doi101038nature03906, doi101071mf99078, doi101073pnas892110302, doi101126science1059199, doi101126science1085046, doi101126science1085706, doi101126science1152509, doi101126science26551781547, doi101126science2845411118, doi101146annurevecolsys34011802132417, doi101371journalpone0000711, openalexw2939474406, openalexw617039848"
}

@article{doi101016jjembe200801024,
    author = "Shaish, Lee and Levy, Gideon and Gomez, Edgardo D. and Rinkevich, Baruch",
    title = "Fixed and suspended coral nurseries in the Philippines: Establishing the first step in the “gardening concept” of reef restoration",
    year = "2008",
    journal = "Journal of Experimental Marine Biology and Ecology",
    url = "https://doi.org/10.1016/j.jembe.2008.01.024",
    doi = "10.1016/j.jembe.2008.01.024",
    openalex = "W2164557179"
}

Ocean acidification represents a key threat to coral reefs by reducing the calcification rate of framework builders. In addition, acidification is likely to affect the relationship between corals and their symbiotic dinoflagellates and the productivity of this association. However, little is known about how acidification impacts on the physiology of reef builders and how acidification interacts with warming. Here, we report on an 8-week study that compared bleaching, productivity, and calcification responses of crustose coralline algae (CCA) and branching (Acropora) and massive (Porites) coral species in response to acidification and warming. Using a 30-tank experimental system, we manipulated CO(2) levels to simulate doubling and three- to fourfold increases [Intergovernmental Panel on Climate Change (IPCC) projection categories IV and VI] relative to present-day levels under cool and warm scenarios. Results indicated that high CO(2) is a bleaching agent for corals and CCA under high irradiance, acting synergistically with warming to lower thermal bleaching thresholds. We propose that CO(2) induces bleaching via its impact on photoprotective mechanisms of the photosystems. Overall, acidification impacted more strongly on bleaching and productivity than on calcification. Interestingly, the intermediate, warm CO(2) scenario led to a 30% increase in productivity in Acropora, whereas high CO(2) lead to zero productivity in both corals. CCA were most sensitive to acidification, with high CO(2) leading to negative productivity and high rates of net dissolution. Our findings suggest that sensitive reef-building species such as CCA may be pushed beyond their thresholds for growth and survival within the next few decades whereas corals will show delayed and mixed responses.

@article{doi101073pnas0804478105,
    author = "Anthony, Kenneth R. N. and Kline, David I. and Díaz-Pulido, Guillermo and Dove, Sophie and Hoegh‐Guldberg, Ove",
    title = "Ocean acidification causes bleaching and productivity loss in coral reef builders",
    year = "2008",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Ocean acidification represents a key threat to coral reefs by reducing the calcification rate of framework builders. In addition, acidification is likely to affect the relationship between corals and their symbiotic dinoflagellates and the productivity of this association. However, little is known about how acidification impacts on the physiology of reef builders and how acidification interacts with warming. Here, we report on an 8-week study that compared bleaching, productivity, and calcification responses of crustose coralline algae (CCA) and branching (Acropora) and massive (Porites) coral species in response to acidification and warming. Using a 30-tank experimental system, we manipulated CO(2) levels to simulate doubling and three- to fourfold increases [Intergovernmental Panel on Climate Change (IPCC) projection categories IV and VI] relative to present-day levels under cool and warm scenarios. Results indicated that high CO(2) is a bleaching agent for corals and CCA under high irradiance, acting synergistically with warming to lower thermal bleaching thresholds. We propose that CO(2) induces bleaching via its impact on photoprotective mechanisms of the photosystems. Overall, acidification impacted more strongly on bleaching and productivity than on calcification. Interestingly, the intermediate, warm CO(2) scenario led to a 30\% increase in productivity in Acropora, whereas high CO(2) lead to zero productivity in both corals. CCA were most sensitive to acidification, with high CO(2) leading to negative productivity and high rates of net dissolution. Our findings suggest that sensitive reef-building species such as CCA may be pushed beyond their thresholds for growth and survival within the next few decades whereas corals will show delayed and mixed responses.",
    url = "https://doi.org/10.1073/pnas.0804478105",
    doi = "10.1073/pnas.0804478105",
    openalex = "W2145406894",
    references = "doi102134jeq199800472425002700010038x"
}

Effective conservation requires rigorous baselines of pristine conditions to assess the impacts of human activities and to evaluate the efficacy of management. Most coral reefs are moderately to severely degraded by local human activities such as fishing and pollution as well as global change, hence it is difficult to separate local from global effects. To this end, we surveyed coral reefs on uninhabited atolls in the northern Line Islands to provide a baseline of reef community structure, and on increasingly populated atolls to document changes associated with human activities. We found that top predators and reef-building organisms dominated unpopulated Kingman and Palmyra, while small planktivorous fishes and fleshy algae dominated the populated atolls of Tabuaeran and Kiritimati. Sharks and other top predators overwhelmed the fish assemblages on Kingman and Palmyra so that the biomass pyramid was inverted (top-heavy). In contrast, the biomass pyramid at Tabuaeran and Kiritimati exhibited the typical bottom-heavy pattern. Reefs without people exhibited less coral disease and greater coral recruitment relative to more inhabited reefs. Thus, protection from overfishing and pollution appears to increase the resilience of reef ecosystems to the effects of global warming.

@article{doi101371journalpone0001548,
    author = "Sandin, Stuart A. and Smith, Jennifer E. and DeMartini, Edward E. and Dinsdale, Elizabeth A. and Donner, Simon D. and Friedlander, Alan M. and Konotchick, Talina and Malay, Maria Celia D. and Maragos, James E. and Obura, David and Pantos, Olga and Paulay, Gustav and Richie, Morgan and Rohwer, Forest and Schroeder, Robert E. and Walsh, Sheila and Jackson, Jeremy B. C. and Knowlton­, Nancy­ and Sala, Enric",
    title = "Baselines and Degradation of Coral Reefs in the Northern Line Islands",
    year = "2008",
    journal = "PLoS ONE",
    abstract = "Effective conservation requires rigorous baselines of pristine conditions to assess the impacts of human activities and to evaluate the efficacy of management. Most coral reefs are moderately to severely degraded by local human activities such as fishing and pollution as well as global change, hence it is difficult to separate local from global effects. To this end, we surveyed coral reefs on uninhabited atolls in the northern Line Islands to provide a baseline of reef community structure, and on increasingly populated atolls to document changes associated with human activities. We found that top predators and reef-building organisms dominated unpopulated Kingman and Palmyra, while small planktivorous fishes and fleshy algae dominated the populated atolls of Tabuaeran and Kiritimati. Sharks and other top predators overwhelmed the fish assemblages on Kingman and Palmyra so that the biomass pyramid was inverted (top-heavy). In contrast, the biomass pyramid at Tabuaeran and Kiritimati exhibited the typical bottom-heavy pattern. Reefs without people exhibited less coral disease and greater coral recruitment relative to more inhabited reefs. Thus, protection from overfishing and pollution appears to increase the resilience of reef ecosystems to the effects of global warming.",
    url = "https://doi.org/10.1371/journal.pone.0001548",
    doi = "10.1371/journal.pone.0001548",
    openalex = "W2113903666",
    references = "doi101046j14429993200101070x, doi101371journalpone0000711, openalexw2726333806"
}

Degradation of coral reefs is often associated with changes in community structure where macroalgae become the dominant benthic life form. These phase shifts can be difficult to reverse. The debate on coral reef phase shifts has not focused on reports of coral reefs becoming dominated by other life forms following disturbance. A review of the primary and grey literature indicates that reefs dominated by corallimorpharia, soft corals, sponges and sea urchins can enter an alternative state as a result of a phase shift. Shifts can be triggered by pulse disturbances that cause largescale coral mortality, and may become stable as a result of positive feedback mechanisms. However, they may differ from the archetypical coral-macroalgae shift, depending on the factors driving the shift; whereas coral-macroalgae and coral-urchin shifts seem to be driven by loss of top-down control through overfishing, shifts to corallimorpharian, soft coral and sponge dominance seem more associated with changes in bottom-up dynamics. Understanding the differences and similarities in mechanisms that cause and maintain this variety of alternative states will aid management aimed at preventing and reversing phase shifts of coral reefs.

@article{doi103354meps07815,
    author = "Norström, Albert V. and Nyström, Magnus and Lokrantz, Jerker and Folke, Carl",
    title = "Alternative states on coral reefs: beyond coral–macroalgal phase shifts",
    year = "2008",
    journal = "Marine Ecology Progress Series",
    abstract = "Degradation of coral reefs is often associated with changes in community structure where macroalgae become the dominant benthic life form. These phase shifts can be difficult to reverse. The debate on coral reef phase shifts has not focused on reports of coral reefs becoming dominated by other life forms following disturbance. A review of the primary and grey literature indicates that reefs dominated by corallimorpharia, soft corals, sponges and sea urchins can enter an alternative state as a result of a phase shift. Shifts can be triggered by pulse disturbances that cause largescale coral mortality, and may become stable as a result of positive feedback mechanisms. However, they may differ from the archetypical coral-macroalgae shift, depending on the factors driving the shift; whereas coral-macroalgae and coral-urchin shifts seem to be driven by loss of top-down control through overfishing, shifts to corallimorpharian, soft coral and sponge dominance seem more associated with changes in bottom-up dynamics. Understanding the differences and similarities in mechanisms that cause and maintain this variety of alternative states will aid management aimed at preventing and reversing phase shifts of coral reefs.",
    url = "https://doi.org/10.3354/meps07815",
    doi = "10.3354/meps07815",
    openalex = "W2100437705",
    references = "doi10100797894017328402"
}

Coral reefs are rich in biodiversity, in large part because their highly complex architecture provides shelter and resources for a wide range of organisms. Recent rapid declines in hard coral cover have occurred across the Caribbean region, but the concomitant consequences for reef architecture have not been quantified on a large scale to date. We provide, to our knowledge, the first region-wide analysis of changes in reef architectural complexity, using nearly 500 surveys across 200 reefs, between 1969 and 2008. The architectural complexity of Caribbean reefs has declined nonlinearly with the near disappearance of the most complex reefs over the last 40 years. The flattening of Caribbean reefs was apparent by the early 1980s, followed by a period of stasis between 1985 and 1998 and then a resumption of the decline in complexity to the present. Rates of loss are similar on shallow (20 m) reefs and are consistent across all five subregions. The temporal pattern of declining architecture coincides with key events in recent Caribbean ecological history: the loss of structurally complex Acropora corals, the mass mortality of the grazing urchin Diadema antillarum and the 1998 El Nino Southern Oscillation-induced worldwide coral bleaching event. The consistently low estimates of current architectural complexity suggest regional-scale degradation and homogenization of reef structure. The widespread loss of architectural complexity is likely to have serious consequences for reef biodiversity, ecosystem functioning and associated environmental services.

@article{doi101098rspb20090339,
    author = "Álvarez‐Filip, Lorenzo and Dulvy, Nicholas K. and Gill, Jennifer A. and Côté, Isabelle M. and Watkinson, Andrew R.",
    title = "Flattening of Caribbean coral reefs: region-wide declines in architectural complexity",
    year = "2009",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Coral reefs are rich in biodiversity, in large part because their highly complex architecture provides shelter and resources for a wide range of organisms. Recent rapid declines in hard coral cover have occurred across the Caribbean region, but the concomitant consequences for reef architecture have not been quantified on a large scale to date. We provide, to our knowledge, the first region-wide analysis of changes in reef architectural complexity, using nearly 500 surveys across 200 reefs, between 1969 and 2008. The architectural complexity of Caribbean reefs has declined nonlinearly with the near disappearance of the most complex reefs over the last 40 years. The flattening of Caribbean reefs was apparent by the early 1980s, followed by a period of stasis between 1985 and 1998 and then a resumption of the decline in complexity to the present. Rates of loss are similar on shallow (20 m) reefs and are consistent across all five subregions. The temporal pattern of declining architecture coincides with key events in recent Caribbean ecological history: the loss of structurally complex Acropora corals, the mass mortality of the grazing urchin Diadema antillarum and the 1998 El Nino Southern Oscillation-induced worldwide coral bleaching event. The consistently low estimates of current architectural complexity suggest regional-scale degradation and homogenization of reef structure. The widespread loss of architectural complexity is likely to have serious consequences for reef biodiversity, ecosystem functioning and associated environmental services.",
    url = "https://doi.org/10.1098/rspb.2009.0339",
    doi = "10.1098/rspb.2009.0339",
    openalex = "W2150724621",
    references = "doi101002sim1545, doi1010079780387217062, doi10100797894017328402, doi101126science1085046, doi101126science1086050, doi101126science1152509, doi101371journalpone0000711, doi1023071932254, doi1023073802723, openalexw1608366422"
}

Reef-building corals are under increasing physiological stress from a changing climate and ocean absorption of increasing atmospheric carbon dioxide. We investigated 328 colonies of massive Porites corals from 69 reefs of the Great Barrier Reef (GBR) in Australia. Their skeletal records show that throughout the GBR, calcification has declined by 14.2% since 1990, predominantly because extension (linear growth) has declined by 13.3%. The data suggest that such a severe and sudden decline in calcification is unprecedented in at least the past 400 years. Calcification increases linearly with increasing large-scale sea surface temperature but responds nonlinearly to annual temperature anomalies. The causes of the decline remain unknown; however, this study suggests that increasing temperature stress and a declining saturation state of seawater aragonite may be diminishing the ability of GBR corals to deposit calcium carbonate.

@article{doi101126science1165283,
    author = "De’ath, Glenn and Lough, Janice and Fabricius, Katharina",
    title = "Declining Coral Calcification on the Great Barrier Reef",
    year = "2009",
    journal = "Science",
    abstract = "Reef-building corals are under increasing physiological stress from a changing climate and ocean absorption of increasing atmospheric carbon dioxide. We investigated 328 colonies of massive Porites corals from 69 reefs of the Great Barrier Reef (GBR) in Australia. Their skeletal records show that throughout the GBR, calcification has declined by 14.2\% since 1990, predominantly because extension (linear growth) has declined by 13.3\%. The data suggest that such a severe and sudden decline in calcification is unprecedented in at least the past 400 years. Calcification increases linearly with increasing large-scale sea surface temperature but responds nonlinearly to annual temperature anomalies. The causes of the decline remain unknown; however, this study suggests that increasing temperature stress and a declining saturation state of seawater aragonite may be diminishing the ability of GBR corals to deposit calcium carbonate.",
    url = "https://doi.org/10.1126/science.1165283",
    doi = "10.1126/science.1165283",
    openalex = "W2036387847"
}

Coral reefs were one of the first ecosystems to be recognized as vulnerable to ocean acidification. To date, most scientific investigations into the effects of ocean acidification on coral reefs have been related to the reefs’ unique ability to produce voluminous amounts of calcium carbonate. It has been estimated that the main reef-building organisms, corals and calcifying macroalgae, will calcify 10–50% less relative to pre-industrial rates by the middle of this century. This decreased calcification is likely to affect their ability to function within the ecosystem and will almost certainly affect the workings of the ecosystem itself. However, ocean acidification affects not only the organisms, but also the reefs they build. The decline in calcium carbonate production, coupled with an increase in calcium carbonate dissolution, will also diminish reef building and the benefits that reefs provide, such as high structural complexity that supports biodiversity on reefs, and breakwater effects that protect shorelines and create quiet habitats for other ecosystems, such as mangroves and seagrass beds. The focus on calcification in reefs is warranted, but the responses of many other organisms, such as fish, noncalcifying algae, and seagrasses, to name a few, deserve a close look as well.

@article{doi105670oceanog2009101,
    author = "Kleypas, Joan A. and Yates, Kimberly K.",
    title = "Coral Reefs and Ocean Acidification",
    year = "2009",
    journal = "Oceanography",
    abstract = "Coral reefs were one of the first ecosystems to be recognized as vulnerable to ocean acidification. To date, most scientific investigations into the effects of ocean acidification on coral reefs have been related to the reefs’ unique ability to produce voluminous amounts of calcium carbonate. It has been estimated that the main reef-building organisms, corals and calcifying macroalgae, will calcify 10–50\% less relative to pre-industrial rates by the middle of this century. This decreased calcification is likely to affect their ability to function within the ecosystem and will almost certainly affect the workings of the ecosystem itself. However, ocean acidification affects not only the organisms, but also the reefs they build. The decline in calcium carbonate production, coupled with an increase in calcium carbonate dissolution, will also diminish reef building and the benefits that reefs provide, such as high structural complexity that supports biodiversity on reefs, and breakwater effects that protect shorelines and create quiet habitats for other ecosystems, such as mangroves and seagrass beds. The focus on calcification in reefs is warranted, but the responses of many other organisms, such as fish, noncalcifying algae, and seagrasses, to name a few, deserve a close look as well.",
    url = "https://doi.org/10.5670/oceanog.2009.101",
    doi = "10.5670/oceanog.2009.101",
    openalex = "W2076025165",
    references = "doi101038nature02691, doi101038nature07051, doi101073pnas0401277101, doi101073pnas0804478105, doi101093icb391146, doi101098rspb20090339, doi101126science1102289, doi101126science1109004, doi101126science26551781547, doi105670oceanog200995"
}

@article{doi101007s1011301001892,
    author = "Hoegh‐Guldberg, Ove",
    title = "Coral reef ecosystems and anthropogenic climate change",
    year = "2010",
    journal = "Regional Environmental Change",
    url = "https://doi.org/10.1007/s10113-010-0189-2",
    doi = "10.1007/s10113-010-0189-2",
    openalex = "W1963622158",
    references = "doi101126science1944268937, doi101126science2434891638"
}

@article{doi101016jtree201007011,
    author = "Hughes, Terry P. and Graham, Nicholas A. J. and Jackson, Jeremy B. C. and Mumby, Peter J. and Steneck, Robert S.",
    title = "Rising to the challenge of sustaining coral reef resilience",
    year = "2010",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/j.tree.2010.07.011",
    doi = "10.1016/j.tree.2010.07.011",
    openalex = "W2094165220",
    references = "doi101016jecss200809003, doi101098rspb20090339, doi101371journalpone0000711, doi105751es01606110119"
}

BACKGROUND: The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS: Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE: Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.

@article{doi101371journalpone0013969,
    author = "Eakin, C. Mark and Morgan, JA and Heron, Scott F. and Smith, Tyler B. and Liu, Gang and Álvarez‐Filip, Lorenzo and Baca, Bart J. and Bartels, Erich and Bastidas, Carolina and Bouchon, Claude and Brandt, Marilyn E. and Bruckner, Andrew W. and Bunkley-Williams, Lucy and Cameron, A D and Causey, Billy and Chiappone, Mark and Christensen, Tyler and Crabbe, M. James C. and Day, Owen and de la Guardia, Elena and Díaz-Pulido, Guillermo and DiResta, Daniel and Gil-Agudelo, Diego L. and Gilliam, David S. and Ginsburg, Robert N. and Gore, Shannon and Guzmán, Héctor M. and Hendee, James C. and Hernández‐Delgado, Edwin A. and Husain, Ellen and Jeffrey, Christopher F.G. and Jones, Ross and Jordán-Dahlgren, Eric and Kaufman, Les and Kline, David I. and Kramer, Philip and Lang, Judith C. and Lirman, Diego and Mallela, Jennie and Manfrino, Carrie and Maréchal, Jean‐Philippe and Marks, Ken and Mihaly, Jennifer and Miller, William J. and Mueller, Erich and Muller, Erinn M. and Orozco-Toro, Carlos A. and Oxenford, Hazel A. and Ponce-Taylor, Daniel and Quinn, Norman J. and Ritchie, Kim B. and Rodríguez, Sebastián and Rodriguez‐Ramirez, Alberto and Romano, Sandra and Samhouri, Jameal F. and Sánchez, Juan A. and Schmahl, George P. and Shank, Burton and Skirving, William and Steiner, Sascha C. C. and Villamizar, Estrella and Walsh, Sheila and Walter, Cory and Weil, Ernesto and Williams, Ernest H. and Roberson, K.W. and Yusuf, Yusri",
    title = "Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005",
    year = "2010",
    journal = "PLoS ONE",
    abstract = "BACKGROUND: The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS: Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80\% of corals bleached and over 40\% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE: Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.",
    url = "https://doi.org/10.1371/journal.pone.0013969",
    doi = "10.1371/journal.pone.0013969",
    openalex = "W2156568771",
    references = "doi101016jecss200809003"
}

Events occurring early in life history can have profound effects on the structure of populations and communities. In particular, susceptibility to predation is often highest early in life, and can greatly influence community structure. To better understand these events in reef-forming coral communities, we investigated how spatial variation in recruitment and early post-settlement predation influenced the spatial structure of a coral assemblage. Over a 5 yr period, we compared recruitment of corals and abundance of juveniles and adults at a combination of 3 locations and 3 depths in French Polynesia. We then measured mortality of recruits (< 3 mo old) and juveniles (about 1 to 4 yr old), and abundance of potential predators. Results demonstrate the crucial role of events occurring in the first weeks of the benthic stage. The abundance of scraping herbivorous parrotfishes explained substantial spatial variation in the mortality of recruits, but not juveniles, revealing a likely effect of incidental removal by grazing. Conversely, abundance of coral-feeding butterflyfishes explained substantial spatial variation in the mortality of juveniles. These findings underscore the importance of incidental mortality from grazing and specialized corallivory on coral populations. Moreover, these processes can play a key role in determining spatial patterns in coral assemblage structure.

@article{doi103354meps08554,
    author = "Penin, Lucie and Michonneau, François and Baird, AH and Connolly, Sean R. and Pratchett, Morgan S. and Kayal, Mohsen and Adjeroud, Mehdi",
    title = "Early post-settlement mortality and the structure of coral assemblages",
    year = "2010",
    journal = "Marine Ecology Progress Series",
    abstract = "Events occurring early in life history can have profound effects on the structure of populations and communities. In particular, susceptibility to predation is often highest early in life, and can greatly influence community structure. To better understand these events in reef-forming coral communities, we investigated how spatial variation in recruitment and early post-settlement predation influenced the spatial structure of a coral assemblage. Over a 5 yr period, we compared recruitment of corals and abundance of juveniles and adults at a combination of 3 locations and 3 depths in French Polynesia. We then measured mortality of recruits (< 3 mo old) and juveniles (about 1 to 4 yr old), and abundance of potential predators. Results demonstrate the crucial role of events occurring in the first weeks of the benthic stage. The abundance of scraping herbivorous parrotfishes explained substantial spatial variation in the mortality of recruits, but not juveniles, revealing a likely effect of incidental removal by grazing. Conversely, abundance of coral-feeding butterflyfishes explained substantial spatial variation in the mortality of juveniles. These findings underscore the importance of incidental mortality from grazing and specialized corallivory on coral populations. Moreover, these processes can play a key role in determining spatial patterns in coral assemblage structure.",
    url = "https://doi.org/10.3354/meps08554",
    doi = "10.3354/meps08554",
    openalex = "W2080646149"
}

Mortality of corals is increasing due to bleaching, disease and algal overgrowth. In the Caribbean, low rates of coral recruitment contribute to the slow or undetectable rates of recovery in reef ecosystems. Although algae have long been suspected to interfere with coral recruitment, the mechanisms of that interaction remain unclear. We experimentally tested the effects of turf algal abundance on 3 sequential factors important to recruitment of corals: the biophysical delivery of planktonic coral larvae, their propensity to settle, and the availability of microhabitats where they survive. We deployed coral settlement plates inside and outside damselfish Stegastes spp. gardens and cages. Damselfish aggression reduced herbivory from fishes, and cages became fouled with turf algae, both locally increasing algal biomass surrounding the plates. This reduced flushing rates in nursery microhabitats on the plate underside, limiting larvae available for settlement. Coral spat settled preferentially on an early successional crustose coralline alga Titanoderma prototypum but also on or near other coralline algae, biofilms, and calcareous polychaete worm tubes. Post-settlement survival was highest in the fully grazed, lowest algal biomass treatment, and after 27 mo 'spat' densities were 73% higher in this treatment. The 'gauntlet' refers to the sequence of ecological processes through which corals must survive to recruit. The highest proportion of coral spat successfully running the gauntlet did so under conditions of low algal biomass resulting from increased herbivory. If coral recruitment is heavily controlled at very local scales by this gauntlet, then coral reef managers could improve a reef's recruitment potential by managing for reduced algal biomass.

@article{doi103354meps08724,
    author = "Arnold, SN and Steneck, RS and Mumby, Peter J.",
    title = "Running the gauntlet: inhibitory effects of algal turfs on the processes of coral recruitment",
    year = "2010",
    journal = "Marine Ecology Progress Series",
    abstract = "Mortality of corals is increasing due to bleaching, disease and algal overgrowth. In the Caribbean, low rates of coral recruitment contribute to the slow or undetectable rates of recovery in reef ecosystems. Although algae have long been suspected to interfere with coral recruitment, the mechanisms of that interaction remain unclear. We experimentally tested the effects of turf algal abundance on 3 sequential factors important to recruitment of corals: the biophysical delivery of planktonic coral larvae, their propensity to settle, and the availability of microhabitats where they survive. We deployed coral settlement plates inside and outside damselfish Stegastes spp. gardens and cages. Damselfish aggression reduced herbivory from fishes, and cages became fouled with turf algae, both locally increasing algal biomass surrounding the plates. This reduced flushing rates in nursery microhabitats on the plate underside, limiting larvae available for settlement. Coral spat settled preferentially on an early successional crustose coralline alga Titanoderma prototypum but also on or near other coralline algae, biofilms, and calcareous polychaete worm tubes. Post-settlement survival was highest in the fully grazed, lowest algal biomass treatment, and after 27 mo 'spat' densities were 73\% higher in this treatment. The 'gauntlet' refers to the sequence of ecological processes through which corals must survive to recruit. The highest proportion of coral spat successfully running the gauntlet did so under conditions of low algal biomass resulting from increased herbivory. If coral recruitment is heavily controlled at very local scales by this gauntlet, then coral reef managers could improve a reef's recruitment potential by managing for reduced algal biomass.",
    url = "https://doi.org/10.3354/meps08724",
    doi = "10.3354/meps08724",
    openalex = "W2049298673",
    references = "doi101146annureves17110186001421"
}

[1] Rising temperatures caused by climatic warming may cause poleward range shifts and/or expansions in species distribution. Tropical reef corals (hereafter corals) are some of the world's most important species, being not only primary producers, but also habitat-forming species, and thus fundamental ecosystem modification is expected according to changes in their distribution. Although most studies of climate change effects on corals have focused on temperature-induced coral bleaching in tropical areas, poleward range shifts and/or expansions may also occur in temperate areas. We show the first large-scale evidence of the poleward range expansion of modern corals, based on 80 years of national records from the temperate areas of Japan, where century-long measurements of in situ sea-surface temperatures have shown statistically significant rises. Four major coral species categories, including two key species for reef formation in tropical areas, showed poleward range expansions since the 1930s, whereas no species demonstrated southward range shrinkage or local extinction. The speed of these expansions reached up to 14 km/year, which is far greater than that for other species. Our results, in combination with recent findings suggesting range expansions of tropical coral-reef associated organisms, strongly suggest that rapid, fundamental modifications of temperate coastal ecosystems could be in progress.

@article{doi1010292010gl046474,
    author = "Yamano, Hiroya and Sugihara, Kaoru and Nomura, Keiichi",
    title = "Rapid poleward range expansion of tropical reef corals in response to rising sea surface temperatures",
    year = "2011",
    journal = "Geophysical Research Letters",
    abstract = "[1] Rising temperatures caused by climatic warming may cause poleward range shifts and/or expansions in species distribution. Tropical reef corals (hereafter corals) are some of the world's most important species, being not only primary producers, but also habitat-forming species, and thus fundamental ecosystem modification is expected according to changes in their distribution. Although most studies of climate change effects on corals have focused on temperature-induced coral bleaching in tropical areas, poleward range shifts and/or expansions may also occur in temperate areas. We show the first large-scale evidence of the poleward range expansion of modern corals, based on 80 years of national records from the temperate areas of Japan, where century-long measurements of in situ sea-surface temperatures have shown statistically significant rises. Four major coral species categories, including two key species for reef formation in tropical areas, showed poleward range expansions since the 1930s, whereas no species demonstrated southward range shrinkage or local extinction. The speed of these expansions reached up to 14 km/year, which is far greater than that for other species. Our results, in combination with recent findings suggesting range expansions of tropical coral-reef associated organisms, strongly suggest that rapid, fundamental modifications of temperate coastal ecosystems could be in progress.",
    url = "https://doi.org/10.1029/2010gl046474",
    doi = "10.1029/2010gl046474",
    openalex = "W1638036560"
}

@article{doi101038nclimate1122,
    author = "Fabricius, Katharina and Langdon, Chris and Uthicke, Sven and Humphrey, Craig and Noonan, Sam H. C. and De’ath, Glenn and Okazaki, Remy R. and Muehllehner, Nancy and Glas, Martin S. and Lough, Janice",
    title = "Losers and winners in coral reefs acclimatized to elevated carbon dioxide concentrations",
    year = "2011",
    journal = "Nature Climate Change",
    url = "https://doi.org/10.1038/nclimate1122",
    doi = "10.1038/nclimate1122",
    openalex = "W2169558027",
    references = "doi101111j14610248201001518x, doi1025607obp1342"
}

Many physiological responses in present-day coral reefs to climate change are interpreted as consistent with the imminent disappearance of modern reefs globally because of annual mass bleaching events, carbonate dissolution, and insufficient time for substantial evolutionary responses. Emerging evidence for variability in the coral calcification response to acidification, geographical variation in bleaching susceptibility and recovery, responses to past climate change, and potential rates of adaptation to rapid warming supports an alternative scenario in which reef degradation occurs with greater temporal and spatial heterogeneity than current projections suggest. Reducing uncertainty in projecting coral reef futures requires improved understanding of past responses to rapid climate change; physiological responses to interacting factors, such as temperature, acidification, and nutrients; and the costs and constraints imposed by acclimation and adaptation.

@article{doi101126science1204794,
    author = "Pandolfi, John M. and Connolly, Sean R. and Marshall, Dustin J. and Cohen, Anne L.",
    title = "Projecting Coral Reef Futures Under Global Warming and Ocean Acidification",
    year = "2011",
    journal = "Science",
    abstract = "Many physiological responses in present-day coral reefs to climate change are interpreted as consistent with the imminent disappearance of modern reefs globally because of annual mass bleaching events, carbonate dissolution, and insufficient time for substantial evolutionary responses. Emerging evidence for variability in the coral calcification response to acidification, geographical variation in bleaching susceptibility and recovery, responses to past climate change, and potential rates of adaptation to rapid warming supports an alternative scenario in which reef degradation occurs with greater temporal and spatial heterogeneity than current projections suggest. Reducing uncertainty in projecting coral reef futures requires improved understanding of past responses to rapid climate change; physiological responses to interacting factors, such as temperature, acidification, and nutrients; and the costs and constraints imposed by acclimation and adaptation.",
    url = "https://doi.org/10.1126/science.1204794",
    doi = "10.1126/science.1204794",
    openalex = "W2075421824",
    references = "doi101016jecss200809003, doi101016jgca200511032, doi101016s0169534702000447, doi101071mf99078, doi101093icb391146, doi101093icesjmsfsn048, doi101093oso97801985052350010001, doi101098rspb20063567, doi101126science1081056, doi101126science1085046, doi101126science1085706, doi101126science1152509, doi101130g30210a1, doi105670oceanog2009101"
}

Tropical reefs shelter one quarter to one third of all marine species but one third of the coral species that construct reefs are now at risk of extinction. Because traditional methods for assessing reef diversity are extremely time consuming, taxonomic expertise for many groups is lacking, and marine organisms are thought to be less vulnerable to extinction, most discussions of reef conservation focus on maintenance of ecosystem services rather than biodiversity loss. In this study involving the three major oceans with reef growth, we provide new biodiversity estimates based on quantitative sampling and DNA barcoding. We focus on crustaceans, which are the second most diverse group of marine metazoans. We show exceptionally high numbers of crustacean species associated with coral reefs relative to sampling effort (525 species from a combined, globally distributed sample area of 6.3 m(2)). The high prevalence of rare species (38% encountered only once), the low level of spatial overlap (81% found in only one locality) and the biogeographic patterns of diversity detected (Indo-West Pacific>Central Pacific>Caribbean) are consistent with results from traditional survey methods, making this approach a reliable and efficient method for assessing and monitoring biodiversity. The finding of such large numbers of species in a small total area suggests that coral reef diversity is seriously under-detected using traditional survey methods, and by implication, underestimated.

@article{doi101371journalpone0025026,
    author = "Plaisance, Laetitia and Caley, M. Julian and Brainard, Russell E. and Knowlton­, Nancy­",
    title = "The Diversity of Coral Reefs: What Are We Missing?",
    year = "2011",
    journal = "PLoS ONE",
    abstract = "Tropical reefs shelter one quarter to one third of all marine species but one third of the coral species that construct reefs are now at risk of extinction. Because traditional methods for assessing reef diversity are extremely time consuming, taxonomic expertise for many groups is lacking, and marine organisms are thought to be less vulnerable to extinction, most discussions of reef conservation focus on maintenance of ecosystem services rather than biodiversity loss. In this study involving the three major oceans with reef growth, we provide new biodiversity estimates based on quantitative sampling and DNA barcoding. We focus on crustaceans, which are the second most diverse group of marine metazoans. We show exceptionally high numbers of crustacean species associated with coral reefs relative to sampling effort (525 species from a combined, globally distributed sample area of 6.3 m(2)). The high prevalence of rare species (38\% encountered only once), the low level of spatial overlap (81\% found in only one locality) and the biogeographic patterns of diversity detected (Indo-West Pacific>Central Pacific>Caribbean) are consistent with results from traditional survey methods, making this approach a reliable and efficient method for assessing and monitoring biodiversity. The finding of such large numbers of species in a small total area suggests that coral reef diversity is seriously under-detected using traditional survey methods, and by implication, underestimated.",
    url = "https://doi.org/10.1371/journal.pone.0025026",
    doi = "10.1371/journal.pone.0025026",
    openalex = "W2129529838"
}

@article{doi101007s003380120984y,
    author = "Graham, Nicholas A. J. and Nash, Kirsty L.",
    title = "The importance of structural complexity in coral reef ecosystems",
    year = "2012",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/s00338-012-0984-y",
    doi = "10.1007/s00338-012-0984-y",
    openalex = "W2022851871",
    references = "doi101098rspb20090339, doi101126science1204794, doi1023072937124"
}

A review of published literature on the sensitivity of corals to turbidity and sedimentation is presented, with an emphasis on the effects of dredging. The risks and severity of impact from dredging (and other sediment disturbances) on corals are primarily related to the intensity, duration and frequency of exposure to increased turbidity and sedimentation. The sensitivity of a coral reef to dredging impacts and its ability to recover depend on the antecedent ecological conditions of the reef, its resilience and the ambient conditions normally experienced. Effects of sediment stress have so far been investigated in 89 coral species (~10% of all known reef-building corals). Results of these investigations have provided a generic understanding of tolerance levels, response mechanisms, adaptations and threshold levels of corals to the effects of natural and anthropogenic sediment disturbances. Coral polyps undergo stress from high suspended-sediment concentrations and the subsequent effects on light attenuation which affect their algal symbionts. Minimum light requirements of corals range from 100 mg L(-1) in marginal nearshore reefs. Some individual coral species can tolerate short-term exposure (days) to suspended-sediment concentrations as high as 1000 mg L(-1) while others show mortality after exposure (weeks) to concentrations as low as 30 mg L(-1). The duration that corals can survive high turbidities ranges from several days (sensitive species) to at least 5-6 weeks (tolerant species). Increased sedimentation can cause smothering and burial of coral polyps, shading, tissue necrosis and population explosions of bacteria in coral mucus. Fine sediments tend to have greater effects on corals than coarse sediments. Turbidity and sedimentation also reduce the recruitment, survival and settlement of coral larvae. Maximum sedimentation rates that can be tolerated by different corals range from 400 mg cm(-2) d(-1). The durations that corals can survive high sedimentation rates range from 4 weeks of high sedimentation or >14 days complete burial) for very tolerant species. Hypotheses to explain substantial differences in sensitivity between different coral species include the growth form of coral colonies and the size of the coral polyp or calyx. The validity of these hypotheses was tested on the basis of 77 published studies on the effects of turbidity and sedimentation on 89 coral species. The results of this analysis reveal a significant relationship of coral sensitivity to turbidity and sedimentation with growth form, but not with calyx size. Some of the variation in sensitivities reported in the literature may have been caused by differences in the type and particle size of sediments applied in experiments. The ability of many corals (in varying degrees) to actively reject sediment through polyp inflation, mucus production, ciliary and tentacular action (at considerable energetic cost), as well as intraspecific morphological variation and the mobility of free-living mushroom corals, further contribute to the observed differences. Given the wide range of sensitivity levels among coral species and in baseline water quality conditions among reefs, meaningful criteria to limit the extent and turbidity of dredging plumes and their effects on corals will always require site-specific evaluations, taking into account the species assemblage present at the site and the natural variability of local background turbidity and sedimentation.

@article{doi101016jmarpolbul201205008,
    author = "Erftemeijer, P.L.A. and Riegl, Bernhard and Hoeksema, Bert W. and Todd, Peter A.",
    title = "Environmental impacts of dredging and other sediment disturbances on corals: A review",
    year = "2012",
    journal = "Marine Pollution Bulletin",
    abstract = "A review of published literature on the sensitivity of corals to turbidity and sedimentation is presented, with an emphasis on the effects of dredging. The risks and severity of impact from dredging (and other sediment disturbances) on corals are primarily related to the intensity, duration and frequency of exposure to increased turbidity and sedimentation. The sensitivity of a coral reef to dredging impacts and its ability to recover depend on the antecedent ecological conditions of the reef, its resilience and the ambient conditions normally experienced. Effects of sediment stress have so far been investigated in 89 coral species (\textasciitilde 10\% of all known reef-building corals). Results of these investigations have provided a generic understanding of tolerance levels, response mechanisms, adaptations and threshold levels of corals to the effects of natural and anthropogenic sediment disturbances. Coral polyps undergo stress from high suspended-sediment concentrations and the subsequent effects on light attenuation which affect their algal symbionts. Minimum light requirements of corals range from 100 mg L(-1) in marginal nearshore reefs. Some individual coral species can tolerate short-term exposure (days) to suspended-sediment concentrations as high as 1000 mg L(-1) while others show mortality after exposure (weeks) to concentrations as low as 30 mg L(-1). The duration that corals can survive high turbidities ranges from several days (sensitive species) to at least 5-6 weeks (tolerant species). Increased sedimentation can cause smothering and burial of coral polyps, shading, tissue necrosis and population explosions of bacteria in coral mucus. Fine sediments tend to have greater effects on corals than coarse sediments. Turbidity and sedimentation also reduce the recruitment, survival and settlement of coral larvae. Maximum sedimentation rates that can be tolerated by different corals range from 400 mg cm(-2) d(-1). The durations that corals can survive high sedimentation rates range from 4 weeks of high sedimentation or >14 days complete burial) for very tolerant species. Hypotheses to explain substantial differences in sensitivity between different coral species include the growth form of coral colonies and the size of the coral polyp or calyx. The validity of these hypotheses was tested on the basis of 77 published studies on the effects of turbidity and sedimentation on 89 coral species. The results of this analysis reveal a significant relationship of coral sensitivity to turbidity and sedimentation with growth form, but not with calyx size. Some of the variation in sensitivities reported in the literature may have been caused by differences in the type and particle size of sediments applied in experiments. The ability of many corals (in varying degrees) to actively reject sediment through polyp inflation, mucus production, ciliary and tentacular action (at considerable energetic cost), as well as intraspecific morphological variation and the mobility of free-living mushroom corals, further contribute to the observed differences. Given the wide range of sensitivity levels among coral species and in baseline water quality conditions among reefs, meaningful criteria to limit the extent and turbidity of dredging plumes and their effects on corals will always require site-specific evaluations, taking into account the species assemblage present at the site and the natural variability of local background turbidity and sedimentation.",
    url = "https://doi.org/10.1016/j.marpolbul.2012.05.008",
    doi = "10.1016/j.marpolbul.2012.05.008",
    openalex = "W2051907680",
    references = "doi101093icb391146"
}

In an effort to deliver better outcomes for people and the ecosystems they depend on, many governments and civil society groups are engaging natural resource users in collaborative management arrangements (frequently called comanagement). However, there are few empirical studies demonstrating the social and institutional conditions conducive to successful comanagement outcomes, especially in small-scale fisheries. Here, we evaluate 42 comanagement arrangements across five countries and show that: (i) comanagement is largely successful at meeting social and ecological goals; (ii) comanagement tends to benefit wealthier resource users; (iii) resource overexploitation is most strongly influenced by market access and users' dependence on resources; and (iv) institutional characteristics strongly influence livelihood and compliance outcomes, yet have little effect on ecological conditions.

@article{doi101073pnas1121215109,
    author = "Cinner, Joshua E. and McClanahan, Tim R. and MacNeil, M. Aaron and Graham, Nicholas A. J. and Daw, Tim M. and Mukminin, Ahmad and Feary, David A. and Rabearisoa, Ando and Wamukota, Andrew and Jiddawi, Narriman and Campbell, Stuart and Baird, Andrew H. and Januchowski‐Hartley, Fraser A. and Hamed, Salum S. and Lahari, Rachael and Morove, Tau and Kuange, John",
    title = "Comanagement of coral reef social-ecological systems",
    year = "2012",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "In an effort to deliver better outcomes for people and the ecosystems they depend on, many governments and civil society groups are engaging natural resource users in collaborative management arrangements (frequently called comanagement). However, there are few empirical studies demonstrating the social and institutional conditions conducive to successful comanagement outcomes, especially in small-scale fisheries. Here, we evaluate 42 comanagement arrangements across five countries and show that: (i) comanagement is largely successful at meeting social and ecological goals; (ii) comanagement tends to benefit wealthier resource users; (iii) resource overexploitation is most strongly influenced by market access and users' dependence on resources; and (iv) institutional characteristics strongly influence livelihood and compliance outcomes, yet have little effect on ecological conditions.",
    url = "https://doi.org/10.1073/pnas.1121215109",
    doi = "10.1073/pnas.1121215109",
    openalex = "W2137332005"
}

The world's coral reefs are being degraded, and the need to reduce local pressures to offset the effects of increasing global pressures is now widely recognized. This study investigates the spatial and temporal dynamics of coral cover, identifies the main drivers of coral mortality, and quantifies the rates of potential recovery of the Great Barrier Reef. Based on the world's most extensive time series data on reef condition (2,258 surveys of 214 reefs over 1985-2012), we show a major decline in coral cover from 28.0% to 13.8% (0.53% y(-1)), a loss of 50.7% of initial coral cover. Tropical cyclones, coral predation by crown-of-thorns starfish (COTS), and coral bleaching accounted for 48%, 42%, and 10% of the respective estimated losses, amounting to 3.38% y(-1) mortality rate. Importantly, the relatively pristine northern region showed no overall decline. The estimated rate of increase in coral cover in the absence of cyclones, COTS, and bleaching was 2.85% y(-1), demonstrating substantial capacity for recovery of reefs. In the absence of COTS, coral cover would increase at 0.89% y(-1), despite ongoing losses due to cyclones and bleaching. Thus, reducing COTS populations, by improving water quality and developing alternative control measures, could prevent further coral decline and improve the outlook for the Great Barrier Reef. Such strategies can, however, only be successful if climatic conditions are stabilized, as losses due to bleaching and cyclones will otherwise increase.

@article{doi101073pnas1208909109,
    author = "De’ath, Glenn and Fabricius, Katharina and Sweatman, Hugh and Puotinen, Marji",
    title = "The 27–year decline of coral cover on the Great Barrier Reef and its causes",
    year = "2012",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "The world's coral reefs are being degraded, and the need to reduce local pressures to offset the effects of increasing global pressures is now widely recognized. This study investigates the spatial and temporal dynamics of coral cover, identifies the main drivers of coral mortality, and quantifies the rates of potential recovery of the Great Barrier Reef. Based on the world's most extensive time series data on reef condition (2,258 surveys of 214 reefs over 1985-2012), we show a major decline in coral cover from 28.0\% to 13.8\% (0.53\% y(-1)), a loss of 50.7\% of initial coral cover. Tropical cyclones, coral predation by crown-of-thorns starfish (COTS), and coral bleaching accounted for 48\%, 42\%, and 10\% of the respective estimated losses, amounting to 3.38\% y(-1) mortality rate. Importantly, the relatively pristine northern region showed no overall decline. The estimated rate of increase in coral cover in the absence of cyclones, COTS, and bleaching was 2.85\% y(-1), demonstrating substantial capacity for recovery of reefs. In the absence of COTS, coral cover would increase at 0.89\% y(-1), despite ongoing losses due to cyclones and bleaching. Thus, reducing COTS populations, by improving water quality and developing alternative control measures, could prevent further coral decline and improve the outlook for the Great Barrier Reef. Such strategies can, however, only be successful if climatic conditions are stabilized, as losses due to bleaching and cyclones will otherwise increase.",
    url = "https://doi.org/10.1073/pnas.1208909109",
    doi = "10.1073/pnas.1208909109",
    openalex = "W2069864946",
    references = "doi10100797894017328402, doi101371journalpone0000711"
}

Classifying the biological traits of organisms can test conceptual frameworks of life-history strategies and allow for predictions of how different species may respond to environmental disturbances. We apply a trait-based classification approach to a complex and threatened group of species, scleractinian corals. Using hierarchical clustering and random forests analyses, we identify up to four life-history strategies that appear globally consistent across 143 species of reef corals: competitive, weedy, stress-tolerant and generalist taxa, which are primarily separated by colony morphology, growth rate and reproductive mode. Documented shifts towards stress-tolerant, generalist and weedy species in coral reef communities are consistent with the expected responses of these life-history strategies. Our quantitative trait-based approach to classifying life-history strategies is objective, applicable to any taxa and a powerful tool that can be used to evaluate theories of community ecology and predict the impact of environmental and anthropogenic stressors on species assemblages.

@article{doi101111j14610248201201861x,
    author = "Darling, Emily S. and Álvarez‐Filip, Lorenzo and Oliver, Thomas A. and McClanahan, Tim R. and Côté, Isabelle M.",
    title = "Evaluating life‐history strategies of reef corals from species traits",
    year = "2012",
    journal = "Ecology Letters",
    abstract = "Classifying the biological traits of organisms can test conceptual frameworks of life-history strategies and allow for predictions of how different species may respond to environmental disturbances. We apply a trait-based classification approach to a complex and threatened group of species, scleractinian corals. Using hierarchical clustering and random forests analyses, we identify up to four life-history strategies that appear globally consistent across 143 species of reef corals: competitive, weedy, stress-tolerant and generalist taxa, which are primarily separated by colony morphology, growth rate and reproductive mode. Documented shifts towards stress-tolerant, generalist and weedy species in coral reef communities are consistent with the expected responses of these life-history strategies. Our quantitative trait-based approach to classifying life-history strategies is objective, applicable to any taxa and a powerful tool that can be used to evaluate theories of community ecology and predict the impact of environmental and anthropogenic stressors on species assemblages.",
    url = "https://doi.org/10.1111/j.1461-0248.2012.01861.x",
    doi = "10.1111/j.1461-0248.2012.01861.x",
    openalex = "W2091692960",
    references = "doi101098rspb20090339, doi101111j13652664201102048x"
}

The persistence of carbonate structures on coral reefs is essential in providing habitats for a large number of species and maintaining the extraordinary biodiversity associated with these ecosystems. As a consequence of ocean acidification (OA), the ability of marine calcifiers to produce calcium carbonate (CaCO(3)) and their rate of CaCO(3) production could decrease while rates of bioerosion and CaCO(3) dissolution could increase, resulting in a transition from a condition of net accretion to one of net erosion. This would have negative consequences for the role and function of coral reefs and the eco-services they provide to dependent human communities. In this article, we review estimates of bioerosion, CaCO(3) dissolution, and net ecosystem calcification (NEC) and how these processes will change in response to OA. Furthermore, we critically evaluate the observed relationships between NEC and seawater aragonite saturation state (Ω(a)). Finally, we propose that standardized NEC rates combined with observed changes in the ratios of dissolved inorganic carbon to total alkalinity owing to net reef metabolism may provide a biogeochemical tool to monitor the effects of OA in coral reef environments.

@article{doi101146annurevmarine121211172241,
    author = "Andersson, Andreas J. and Gledhill, D. K.",
    title = "Ocean Acidification and Coral Reefs: Effects on Breakdown, Dissolution, and Net Ecosystem Calcification",
    year = "2012",
    journal = "Annual Review of Marine Science",
    abstract = "The persistence of carbonate structures on coral reefs is essential in providing habitats for a large number of species and maintaining the extraordinary biodiversity associated with these ecosystems. As a consequence of ocean acidification (OA), the ability of marine calcifiers to produce calcium carbonate (CaCO(3)) and their rate of CaCO(3) production could decrease while rates of bioerosion and CaCO(3) dissolution could increase, resulting in a transition from a condition of net accretion to one of net erosion. This would have negative consequences for the role and function of coral reefs and the eco-services they provide to dependent human communities. In this article, we review estimates of bioerosion, CaCO(3) dissolution, and net ecosystem calcification (NEC) and how these processes will change in response to OA. Furthermore, we critically evaluate the observed relationships between NEC and seawater aragonite saturation state (Ω(a)). Finally, we propose that standardized NEC rates combined with observed changes in the ratios of dissolved inorganic carbon to total alkalinity owing to net reef metabolism may provide a biogeochemical tool to monitor the effects of OA in coral reef environments.",
    url = "https://doi.org/10.1146/annurev-marine-121211-172241",
    doi = "10.1146/annurev-marine-121211-172241",
    openalex = "W2131106625",
    references = "chave1972carbonate, doi101016s0012825201000836, doi101126science1944268937"
}

Coral reef restoration has gained recent popularity in response to the steady decline of corals and the recognition that coral reefs may not be able to recover naturally without human intervention. To synthesize collective knowledge about reef restoration focused particularly on the threatened genus Acropora in the Caribbean and western Atlantic, we conducted a literature review combined with personal communications with restoration practitioners and an online questionnaire to identify the most effective reef restoration methods and the major obstacles hindering restoration success. Most participants (90%) strongly believe that Acropora populations are severely degraded, continue to decline, and may not recover without human intervention. Low-cost methods such as coral gardening and fragment stabilization were ranked as the most effective restoration activities for this genus. High financial costs, the small footprint of restoration activities, and the potential damage to wild populations were identified as major concerns, while increased public awareness and education were ranked as the highest benefits of coral reef restoration. This study highlights the advantages and outlines the concerns associated with coral reef restoration and creates a unique synthesis of coral restoration activities as a complementary management tool to help guide best-practices for future restoration efforts throughout the region.

@article{doi105343bms20111143,
    author = "Young, C. and Schopmeyer, Stephanie and Lirman, Diego",
    title = "A Review of Reef Restoration and Coral Propagation Using the Threatened Genus Acropora in the Caribbean and Western Atlantic",
    year = "2012",
    journal = "Bulletin of Marine Science",
    abstract = "Coral reef restoration has gained recent popularity in response to the steady decline of corals and the recognition that coral reefs may not be able to recover naturally without human intervention. To synthesize collective knowledge about reef restoration focused particularly on the threatened genus Acropora in the Caribbean and western Atlantic, we conducted a literature review combined with personal communications with restoration practitioners and an online questionnaire to identify the most effective reef restoration methods and the major obstacles hindering restoration success. Most participants (90\%) strongly believe that Acropora populations are severely degraded, continue to decline, and may not recover without human intervention. Low-cost methods such as coral gardening and fragment stabilization were ranked as the most effective restoration activities for this genus. High financial costs, the small footprint of restoration activities, and the potential damage to wild populations were identified as major concerns, while increased public awareness and education were ranked as the highest benefits of coral reef restoration. This study highlights the advantages and outlines the concerns associated with coral reef restoration and creates a unique synthesis of coral restoration activities as a complementary management tool to help guide best-practices for future restoration efforts throughout the region.",
    url = "https://doi.org/10.5343/bms.2011.1143",
    doi = "10.5343/bms.2011.1143",
    openalex = "W2057524613"
}

[Extract from the Preface] The 12th International Coral Reef Symposium (ICRS 2012), held in Cairns, Queensland, Australia from July 9-13th, 2012, was attended by nearly 2000 delegates. The program included over 1500 talks and posters. We are pleased to present the Proceedings, which contains almost 200 contributions from scientists around the world arising from the Symposium. The Proceedings encompass a broad spectrum of coral reef science, and demonstrates a growing expansion from the biological and earth sciences to non-traditional disciplines, including the social sciences and economics. The trend in earlier ICRS Symposia, towards a larger contribution from the fields of conservation planning and management, continued in Cairns in 2012. The Symposium also included an increased focus on climate change and ocean acidification, as well as reef management and governance issues including the Coral Triangle Initiative. For the first time in the history of ICRS Symposia, the organizers of the meeting invited submission of manuscripts for peer review prior to the Symposium so that delegates could receive the Proceedings when they arrive at the Symposium. We hope the benefits of rapid publication will allow prompt dissemination of the latest breakthroughs in coral reef science, and stimulate further advances in the knowledge necessary for sustaining the world's coral reefs. An additional advantage of rapid publication is the benefit of immediately placing the Proceedings online on the ICRS 2012 website (http://www.icrs2012.com/), where it is freely accessible to a global audience. The Symposium website will also archive many other outcomes of ICRS 2012, including video recordings of the Plenary Talks. We thank the WorldFish Center in Penang, Malaysia, for agreeing to upload the ICRS 2012 Proceedings to ReefBase (http://www.reefbase.org) along with earlier ICRS Symposia.

@book{openalexw171744082,
    author = "Yellowlees, David and Hughes, Terry P.",
    title = "Proceedings of the 12th International Coral Reef Symposium",
    year = "2012",
    booktitle = "ResearchOnline at James Cook University (James Cook University)",
    abstract = "[Extract from the Preface] The 12th International Coral Reef Symposium (ICRS 2012), held in Cairns, Queensland, Australia from July 9-13th, 2012, was attended by nearly 2000 delegates. The program included over 1500 talks and posters. We are pleased to present the Proceedings, which contains almost 200 contributions from scientists around the world arising from the Symposium. The Proceedings encompass a broad spectrum of coral reef science, and demonstrates a growing expansion from the biological and earth sciences to non-traditional disciplines, including the social sciences and economics. The trend in earlier ICRS Symposia, towards a larger contribution from the fields of conservation planning and management, continued in Cairns in 2012. The Symposium also included an increased focus on climate change and ocean acidification, as well as reef management and governance issues including the Coral Triangle Initiative. For the first time in the history of ICRS Symposia, the organizers of the meeting invited submission of manuscripts for peer review prior to the Symposium so that delegates could receive the Proceedings when they arrive at the Symposium. We hope the benefits of rapid publication will allow prompt dissemination of the latest breakthroughs in coral reef science, and stimulate further advances in the knowledge necessary for sustaining the world's coral reefs. An additional advantage of rapid publication is the benefit of immediately placing the Proceedings online on the ICRS 2012 website (http://www.icrs2012.com/), where it is freely accessible to a global audience. The Symposium website will also archive many other outcomes of ICRS 2012, including video recordings of the Plenary Talks. We thank the WorldFish Center in Penang, Malaysia, for agreeing to upload the ICRS 2012 Proceedings to ReefBase (http://www.reefbase.org) along with earlier ICRS Symposia.",
    openalex = "W171744082"
}

Coral reefs are complex, dynamic ecosystems occurring over a range of spatial and temporal scales. They provide a range of goods and services to mankind, including shoreline protection and support a large portion of marine life. The value of coral reefs exemplifies the need to empirically evaluate the complex interactions operating on them to efficiently manage these systems in light of anthropogenic induced climate change. This study was on Lizard Island’s coral reef system, situated within the northern lagoon of the Great Barrier Reef, Australia. Carbonate production is an important process, which underpins reef development and island security. Wave energy is one of the most important physical processes influencing coral reef carbonate production by flushing nutrients around the system, and removing metabolic waste. Other important functions include mechanically breaking down and transporting calcium carbonate. The empirical relationship between carbonate production and wave energy has not been addressed in the current literature and warrants a comprehensive investigation. The aim of this thesis was to employ a unique geospatial approach to combine in situ field observations, remote sensing and modelling techniques to develop a spatially continuous distribution model of coral reef calcium carbonate production and to empirically evaluate its relationship against a spatially continuous model of wave energy. Census-based methods and video samples were used to quantify carbonate production using published carbonate production rates of various benthic organisms. Individual benthic models of carbonate producing components included live coral, carbonate sand, green calcareous macroalgae and encrusting calcified algae. Regression analysis used surrogates derived from a digital elevation model of the seafloor and satellite imagery from Worldview-2 to predict the distribution of each component. The spatially continuous carbonate production model was the combined result of each benthic component layer, using their respective carbonate production rates as a weight. Comparing carbonate production and wave energy datasets was performed using global techniques and a series of transects, traversing across the entire reef platform. Results suggest that carbonate production increases with wave energy. However, transect comparisons suggest that a threshold of carbonate production occurs when wave energy exceeds 300 J/m2. These empirical results further the scientific understanding of coral reef ecosystems and can be incorporated into environmental models to predict the impacts of increased wave energy on reef and island development due to rapid climate change.

@article{openalexw2165625223,
    author = "Pescud, Alexander",
    title = "An empirical evaluation of the relationship between coral reef calcium carbonate production and wave energy using geospatial techniques at Lizard Island, Great Barrier Reef, Australia",
    year = "2012",
    journal = "Research Online (University of Wollongong)",
    abstract = "Coral reefs are complex, dynamic ecosystems occurring over a range of spatial and temporal scales. They provide a range of goods and services to mankind, including shoreline protection and support a large portion of marine life. The value of coral reefs exemplifies the need to empirically evaluate the complex interactions operating on them to efficiently manage these systems in light of anthropogenic induced climate change. This study was on Lizard Island’s coral reef system, situated within the northern lagoon of the Great Barrier Reef, Australia. Carbonate production is an important process, which underpins reef development and island security. Wave energy is one of the most important physical processes influencing coral reef carbonate production by flushing nutrients around the system, and removing metabolic waste. Other important functions include mechanically breaking down and transporting calcium carbonate. The empirical relationship between carbonate production and wave energy has not been addressed in the current literature and warrants a comprehensive investigation. The aim of this thesis was to employ a unique geospatial approach to combine in situ field observations, remote sensing and modelling techniques to develop a spatially continuous distribution model of coral reef calcium carbonate production and to empirically evaluate its relationship against a spatially continuous model of wave energy. Census-based methods and video samples were used to quantify carbonate production using published carbonate production rates of various benthic organisms. Individual benthic models of carbonate producing components included live coral, carbonate sand, green calcareous macroalgae and encrusting calcified algae. Regression analysis used surrogates derived from a digital elevation model of the seafloor and satellite imagery from Worldview-2 to predict the distribution of each component. The spatially continuous carbonate production model was the combined result of each benthic component layer, using their respective carbonate production rates as a weight. Comparing carbonate production and wave energy datasets was performed using global techniques and a series of transects, traversing across the entire reef platform. Results suggest that carbonate production increases with wave energy. However, transect comparisons suggest that a threshold of carbonate production occurs when wave energy exceeds 300 J/m2. These empirical results further the scientific understanding of coral reef ecosystems and can be incorporated into environmental models to predict the impacts of increased wave energy on reef and island development due to rapid climate change.",
    url = "https://openalex.org/W2165625223",
    openalex = "W2165625223",
    references = "doi101016s0304380000003549, doi101073pnas1208909109, doi10108001621459197610480949, doi101126science1152509, doi101126science2845411118, doi102307143141, doi1023072333282, openalexw1606936601, openalexw2764433274, openalexw2939474406"
}

Global-scale deteriorations in coral reef health have caused major shifts in species composition. One projected consequence is a lowering of reef carbonate production rates, potentially impairing reef growth, compromising ecosystem functionality and ultimately leading to net reef erosion. Here, using measures of gross and net carbonate production and erosion from 19 Caribbean reefs, we show that contemporary carbonate production rates are now substantially below historical (mid- to late-Holocene) values. On average, current production rates are reduced by at least 50%, and 37% of surveyed sites were net erosional. Calculated accretion rates (mm year(-1)) for shallow fore-reef habitats are also close to an order of magnitude lower than Holocene averages. A live coral cover threshold of ~10% appears critical to maintaining positive production states. Below this ecological threshold carbonate budgets typically become net negative and threaten reef accretion. Collectively, these data suggest that recent ecological declines are now suppressing Caribbean reef growth potential.

@article{doi101038ncomms2409,
    author = "Perry, Chris T. and Murphy, Gary N. and Kench, Paul S. and Smithers, S and Edinger, Evan and Steneck, Robert S. and Mumby, Peter J.",
    title = "Caribbean-wide decline in carbonate production threatens coral reef growth",
    year = "2013",
    journal = "Nature Communications",
    abstract = "Global-scale deteriorations in coral reef health have caused major shifts in species composition. One projected consequence is a lowering of reef carbonate production rates, potentially impairing reef growth, compromising ecosystem functionality and ultimately leading to net reef erosion. Here, using measures of gross and net carbonate production and erosion from 19 Caribbean reefs, we show that contemporary carbonate production rates are now substantially below historical (mid- to late-Holocene) values. On average, current production rates are reduced by at least 50\%, and 37\% of surveyed sites were net erosional. Calculated accretion rates (mm year(-1)) for shallow fore-reef habitats are also close to an order of magnitude lower than Holocene averages. A live coral cover threshold of \textasciitilde 10\% appears critical to maintaining positive production states. Below this ecological threshold carbonate budgets typically become net negative and threaten reef accretion. Collectively, these data suggest that recent ecological declines are now suppressing Caribbean reef growth potential.",
    url = "https://doi.org/10.1038/ncomms2409",
    doi = "10.1038/ncomms2409",
    openalex = "W2047295906",
    references = "doi1010079780387874586, doi1010079781441903181, doi101016jecss200809003, doi101038nature02691, doi101038ngeo202, doi101098rspb20090339, doi101126science1086050, doi101126science1152509, doi101198tech2001s574, doi101371journalpone0000711"
}

Recent advances in DNA-sequencing technologies now allow for in-depth characterization of the genomic stress responses of many organisms beyond model taxa. They are especially appropriate for organisms such as reef-building corals, for which dramatic declines in abundance are expected to worsen as anthropogenic climate change intensifies. Different corals differ substantially in physiological resilience to environmental stress, but the molecular mechanisms behind enhanced coral resilience remain unclear. Here, we compare transcriptome-wide gene expression (via RNA-Seq using Illumina sequencing) among conspecific thermally sensitive and thermally resilient corals to identify the molecular pathways contributing to coral resilience. Under simulated bleaching stress, sensitive and resilient corals change expression of hundreds of genes, but the resilient corals had higher expression under control conditions across 60 of these genes. These "frontloaded" transcripts were less up-regulated in resilient corals during heat stress and included thermal tolerance genes such as heat shock proteins and antioxidant enzymes, as well as a broad array of genes involved in apoptosis regulation, tumor suppression, innate immune response, and cell adhesion. We propose that constitutive frontloading enables an individual to maintain physiological resilience during frequently encountered environmental stress, an idea that has strong parallels in model systems such as yeast. Our study provides broad insight into the fundamental cellular processes responsible for enhanced stress tolerances that may enable some organisms to better persist into the future in an era of global climate change.

@article{doi101073pnas1210224110,
    author = "Barshis, Daniel J. and Ladner, Jason T. and Oliver, Thomas A. and Seneca, François and Traylor‐Knowles, Nikki and Palumbi, Stephen R.",
    title = "Genomic basis for coral resilience to climate change",
    year = "2013",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {Recent advances in DNA-sequencing technologies now allow for in-depth characterization of the genomic stress responses of many organisms beyond model taxa. They are especially appropriate for organisms such as reef-building corals, for which dramatic declines in abundance are expected to worsen as anthropogenic climate change intensifies. Different corals differ substantially in physiological resilience to environmental stress, but the molecular mechanisms behind enhanced coral resilience remain unclear. Here, we compare transcriptome-wide gene expression (via RNA-Seq using Illumina sequencing) among conspecific thermally sensitive and thermally resilient corals to identify the molecular pathways contributing to coral resilience. Under simulated bleaching stress, sensitive and resilient corals change expression of hundreds of genes, but the resilient corals had higher expression under control conditions across 60 of these genes. These "frontloaded" transcripts were less up-regulated in resilient corals during heat stress and included thermal tolerance genes such as heat shock proteins and antioxidant enzymes, as well as a broad array of genes involved in apoptosis regulation, tumor suppression, innate immune response, and cell adhesion. We propose that constitutive frontloading enables an individual to maintain physiological resilience during frequently encountered environmental stress, an idea that has strong parallels in model systems such as yeast. Our study provides broad insight into the fundamental cellular processes responsible for enhanced stress tolerances that may enable some organisms to better persist into the future in an era of global climate change.},
    url = "https://doi.org/10.1073/pnas.1210224110",
    doi = "10.1073/pnas.1210224110",
    openalex = "W2145335031",
    references = "doi101126science1204794"
}

Coral reef recovery from major disturbance is hypothesized to depend on the arrival of propagules from nearby undisturbed reefs. Therefore, reefs isolated by distance or current patterns are thought to be highly vulnerable to catastrophic disturbance. We found that on an isolated reef system in north Western Australia, coral cover increased from 9% to 44% within 12 years of a coral bleaching event, despite a 94% reduction in larval supply for 6 years after the bleaching. The initial increase in coral cover was the result of high rates of growth and survival of remnant colonies, followed by a rapid increase in juvenile recruitment as colonies matured. We show that isolated reefs can recover from major disturbance, and that the benefits of their isolation from chronic anthropogenic pressures can outweigh the costs of limited connectivity.

@article{doi101126science1232310,
    author = "Gilmour, James and Smith, Luke and Heyward, Andrew and Baird, Andrew H. and Pratchett, Morgan S.",
    title = "Recovery of an Isolated Coral Reef System Following Severe Disturbance",
    year = "2013",
    journal = "Science",
    abstract = "Coral reef recovery from major disturbance is hypothesized to depend on the arrival of propagules from nearby undisturbed reefs. Therefore, reefs isolated by distance or current patterns are thought to be highly vulnerable to catastrophic disturbance. We found that on an isolated reef system in north Western Australia, coral cover increased from 9\% to 44\% within 12 years of a coral bleaching event, despite a 94\% reduction in larval supply for 6 years after the bleaching. The initial increase in coral cover was the result of high rates of growth and survival of remnant colonies, followed by a rapid increase in juvenile recruitment as colonies matured. We show that isolated reefs can recover from major disturbance, and that the benefits of their isolation from chronic anthropogenic pressures can outweigh the costs of limited connectivity.",
    url = "https://doi.org/10.1126/science.1232310",
    doi = "10.1126/science.1232310",
    openalex = "W2049337196"
}

The world's coastal zones are experiencing rapid development and an increase in storms and flooding. These hazards put coastal communities at heightened risk, which may increase with habitat loss. Here we analyse globally the role and cost effectiveness of coral reefs in risk reduction. Meta-analyses reveal that coral reefs provide substantial protection against natural hazards by reducing wave energy by an average of 97%. Reef crests alone dissipate most of this energy (86%). There are 100 million or more people who may receive risk reduction benefits from reefs or bear hazard mitigation and adaptation costs if reefs are degraded. We show that coral reefs can provide comparable wave attenuation benefits to artificial defences such as breakwaters, and reef defences can be enhanced cost effectively. Reefs face growing threats yet there is opportunity to guide adaptation and hazard mitigation investments towards reef restoration to strengthen this first line of coastal defence.

@article{doi101038ncomms4794,
    author = "Ferrario, Filippo and Beck, Michael W. and Storlazzi, Curt D. and Micheli, Fiorenza and Shepard, Christine C. and Airoldi, Laura",
    title = "The effectiveness of coral reefs for coastal hazard risk reduction and adaptation",
    year = "2014",
    journal = "Nature Communications",
    abstract = "The world's coastal zones are experiencing rapid development and an increase in storms and flooding. These hazards put coastal communities at heightened risk, which may increase with habitat loss. Here we analyse globally the role and cost effectiveness of coral reefs in risk reduction. Meta-analyses reveal that coral reefs provide substantial protection against natural hazards by reducing wave energy by an average of 97\%. Reef crests alone dissipate most of this energy (86\%). There are 100 million or more people who may receive risk reduction benefits from reefs or bear hazard mitigation and adaptation costs if reefs are degraded. We show that coral reefs can provide comparable wave attenuation benefits to artificial defences such as breakwaters, and reef defences can be enhanced cost effectively. Reefs face growing threats yet there is opportunity to guide adaptation and hazard mitigation investments towards reef restoration to strengthen this first line of coastal defence.",
    url = "https://doi.org/10.1038/ncomms4794",
    doi = "10.1038/ncomms4794",
    openalex = "W2107960291",
    references = "doi101098rspb20090339, doi101126science1204794"
}

Abstract Global carbon emissions continue to acidify the oceans, motivating growing concern for the ability of coral reefs to maintain net positive calcification rates. Efforts to develop robust relationships between coral reef calcification and carbonate parameters such as aragonite saturation state (Ω arag) aim to facilitate meaningful predictions of how reef calcification will change in the face of ocean acidification. Here we investigate natural trends in carbonate chemistry of a coral reef flat over diel cycles and relate these trends to benthic carbon fluxes by quantifying net community calcification and net community production. We find that, despite an apparent dependence of calcification on Ω arag seen in a simple pairwise relationship, if the dependence of net calcification on net photosynthesis is accounted for, knowing Ω arag does not add substantial explanatory value. This suggests that, over short time scales, the control of Ω arag on net calcification is weak relative to factors governing net photosynthesis.

@article{doi1010022015gl063488,
    author = "Albright, Rebecca and Benthuysen, Jessica A. and Cantin, Neal E. and Caldeira, Ken and Anthony, Kenneth R. N.",
    title = "Coral reef metabolism and carbon chemistry dynamics of a coral reef flat",
    year = "2015",
    journal = "Geophysical Research Letters",
    abstract = "Abstract Global carbon emissions continue to acidify the oceans, motivating growing concern for the ability of coral reefs to maintain net positive calcification rates. Efforts to develop robust relationships between coral reef calcification and carbonate parameters such as aragonite saturation state (Ω arag) aim to facilitate meaningful predictions of how reef calcification will change in the face of ocean acidification. Here we investigate natural trends in carbonate chemistry of a coral reef flat over diel cycles and relate these trends to benthic carbon fluxes by quantifying net community calcification and net community production. We find that, despite an apparent dependence of calcification on Ω arag seen in a simple pairwise relationship, if the dependence of net calcification on net photosynthesis is accounted for, knowing Ω arag does not add substantial explanatory value. This suggests that, over short time scales, the control of Ω arag on net calcification is weak relative to factors governing net photosynthesis.",
    url = "https://doi.org/10.1002/2015gl063488",
    doi = "10.1002/2015gl063488",
    openalex = "W2158006323",
    references = "archer2009atmospheric, doi101002lno10048, doi1010079781475729177, doi101017cbo9781107415324, doi1010292004jc002671, doi101038nature04095, doi101038srep00412, doi101073pnas0702737104, doi101073pnas0804478105, doi101371journalpone0028983"
}

Abstract There are few in situ studies showing how net community calcification (G net) of coral reefs is related to carbonate chemistry, and the studies to date have demonstrated different predicted rates of change. In this study, we measured net community production (P net), G net, and carbonate chemistry of a reef flat at One Tree Island, Great Barrier Reef. Diurnal p CO 2 variability of 289–724 μatm was driven primarily by photosynthesis and respiration. The reef flat was found to be net autotrophic, with daily production of ∼ 35 mmol C m −2 d −1 and net calcification of ∼ 33 mmol C m −2 d −1. G net was strongly related to P net, which drove a hysteresis pattern in the relationship between G net and aragonite saturation state (Ω ar). Although P net was the main driver of G net, Ω ar was still an important factor, where 95% of the variance in G net could be described by P net and Ω ar. Based on the observed in situ relationship, G net would be expected to reach zero when Ω ar is ∼ 2.5. It is unknown what proportion of a decline in G net would be through reduced calcification and what would occur through increased dissolution, but the results here support predictions that overall calcium carbonate production will decline in coral reefs as a result of ocean acidification.

@article{doi101002lno10048,
    author = "Shaw, Emily C. and Phinn, Stuart and Tilbrook, Bronte and Steven, Andy",
    title = "Natural in situ relationships suggest coral reef calcium carbonate production will decline with ocean acidification",
    year = "2015",
    journal = "Limnology and Oceanography",
    abstract = "Abstract There are few in situ studies showing how net community calcification (G net) of coral reefs is related to carbonate chemistry, and the studies to date have demonstrated different predicted rates of change. In this study, we measured net community production (P net), G net, and carbonate chemistry of a reef flat at One Tree Island, Great Barrier Reef. Diurnal p CO 2 variability of 289–724 μatm was driven primarily by photosynthesis and respiration. The reef flat was found to be net autotrophic, with daily production of ∼ 35 mmol C m −2 d −1 and net calcification of ∼ 33 mmol C m −2 d −1. G net was strongly related to P net, which drove a hysteresis pattern in the relationship between G net and aragonite saturation state (Ω ar). Although P net was the main driver of G net, Ω ar was still an important factor, where 95\% of the variance in G net could be described by P net and Ω ar. Based on the observed in situ relationship, G net would be expected to reach zero when Ω ar is ∼ 2.5. It is unknown what proportion of a decline in G net would be through reduced calcification and what would occur through increased dissolution, but the results here support predictions that overall calcium carbonate production will decline in coral reefs as a result of ocean acidification.",
    url = "https://doi.org/10.1002/lno.10048",
    doi = "10.1002/lno.10048",
    openalex = "W1941146301",
    references = "doi101016002196149090074z, doi1010160198014987900215, doi101016s0921800999000099, doi10102992jc00188, doi101111j14610248201001518x, doi101126science1152509, doi104319lo19731860897, doi104835025539, openalexw1007704209, openalexw2907110490"
}

The genetic enhancement of wild animals and plants for characteristics that benefit human populations has been practiced for thousands of years, resulting in impressive improvements in commercially valuable species. Despite these benefits, genetic manipulations are rarely considered for noncommercial purposes, such as conservation and restoration initiatives. Over the last century, humans have driven global climate change through industrialization and the release of increasing amounts of CO2, resulting in shifts in ocean temperature, ocean chemistry, and sea level, as well as increasing frequency of storms, all of which can profoundly impact marine ecosystems. Coral reefs are highly diverse ecosystems that have suffered massive declines in health and abundance as a result of these and other direct anthropogenic disturbances. There is great concern that the high rates, magnitudes, and complexity of environmental change are overwhelming the intrinsic capacity of corals to adapt and survive. Although it is important to address the root causes of changing climate, it is also prudent to explore the potential to augment the capacity of reef organisms to tolerate stress and to facilitate recovery after disturbances. Here, we review the risks and benefits of the improvement of natural and commercial stocks in noncoral reef systems and advocate a series of experiments to determine the feasibility of developing coral stocks with enhanced stress tolerance through the acceleration of naturally occurring processes, an approach known as (human)-assisted evolution, while at the same time initiating a public dialogue on the risks and benefits of this approach.

@article{doi101073pnas1422301112,
    author = "van Oppen, Madeleine J. H. and Oliver, James K. and Putnam, Hollie M. and Gates, Ruth D.",
    title = "Building coral reef resilience through assisted evolution",
    year = "2015",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "The genetic enhancement of wild animals and plants for characteristics that benefit human populations has been practiced for thousands of years, resulting in impressive improvements in commercially valuable species. Despite these benefits, genetic manipulations are rarely considered for noncommercial purposes, such as conservation and restoration initiatives. Over the last century, humans have driven global climate change through industrialization and the release of increasing amounts of CO2, resulting in shifts in ocean temperature, ocean chemistry, and sea level, as well as increasing frequency of storms, all of which can profoundly impact marine ecosystems. Coral reefs are highly diverse ecosystems that have suffered massive declines in health and abundance as a result of these and other direct anthropogenic disturbances. There is great concern that the high rates, magnitudes, and complexity of environmental change are overwhelming the intrinsic capacity of corals to adapt and survive. Although it is important to address the root causes of changing climate, it is also prudent to explore the potential to augment the capacity of reef organisms to tolerate stress and to facilitate recovery after disturbances. Here, we review the risks and benefits of the improvement of natural and commercial stocks in noncoral reef systems and advocate a series of experiments to determine the feasibility of developing coral stocks with enhanced stress tolerance through the acceleration of naturally occurring processes, an approach known as (human)-assisted evolution, while at the same time initiating a public dialogue on the risks and benefits of this approach.",
    url = "https://doi.org/10.1073/pnas.1422301112",
    doi = "10.1073/pnas.1422301112",
    openalex = "W2096973757",
    references = "doi101016jcell201402045, doi101016jtree201202003, doi101038ismej2007106, doi101073pnas1208909109, doi101073pnas1218525110, doi101098rspb20063567, doi1011111574697612025, doi101111gcb12179, doi101111j17524571201100192x, doi101146annurevecolsys34011802132417, doi101146annurevgenet110410132549, doi101371journalpone0000711, doi1018900617151"
}

Abstract Coral reefs are threatened worldwide, and there is a need to develop new approaches to monitor reef health under natural conditions. Because simultaneous measurements of net community production (NCP) and net community calcification (NCC) are used as important indicators of reef health, tools are needed to assess them in situ. Here we present the Benthic Ecosystem and Acidification Measurement System (BEAMS) to provide the first fully autonomous approach capable of sustained, simultaneous measurements of reef NCP and NCC under undisturbed, natural conditions on time scales ranging from tens of minutes to weeks. BEAMS combines the chemical and velocity gradient in the benthic boundary layer to quantify flux from the benthos for a variety of parameters to measure NCP and NCC. Here BEAMS was used to measure these rates from two different sites with different benthic communities on the western reef terrace at Palmyra Atoll for 2 weeks in September 2014. Measurements were made every ∼15 min. The trends in metabolic rates were consistent with the benthic communities between the two sites with one dominated by fleshy organisms and the other dominated by calcifiers (degraded and healthy reefs, respectively). This demonstrates the potential utility of BEAMS as a reef health monitoring tool. NCP and NCC were tightly coupled on time scales of minutes to days, and light was the primary driver for the variability of daily integrated metabolic rates. No correlation between CO 2 levels and daily integrated NCC was observed, indicating that NCC at these sites were not significantly affected by CO 2.

@article{doi1010022016jc011886,
    author = "Takeshita, Yuichiro and McGillis, Wade R. and Briggs, Ellen M. and Carter, Amanda L. and Donham, Emily M. and Martz, Todd R. and Price, Nichole N. and Smith, Jennifer E.",
    title = "Assessment of net community production and calcification of a coral reef using a boundary layer approach",
    year = "2016",
    journal = "Journal of Geophysical Research Oceans",
    abstract = "Abstract Coral reefs are threatened worldwide, and there is a need to develop new approaches to monitor reef health under natural conditions. Because simultaneous measurements of net community production (NCP) and net community calcification (NCC) are used as important indicators of reef health, tools are needed to assess them in situ. Here we present the Benthic Ecosystem and Acidification Measurement System (BEAMS) to provide the first fully autonomous approach capable of sustained, simultaneous measurements of reef NCP and NCC under undisturbed, natural conditions on time scales ranging from tens of minutes to weeks. BEAMS combines the chemical and velocity gradient in the benthic boundary layer to quantify flux from the benthos for a variety of parameters to measure NCP and NCC. Here BEAMS was used to measure these rates from two different sites with different benthic communities on the western reef terrace at Palmyra Atoll for 2 weeks in September 2014. Measurements were made every ∼15 min. The trends in metabolic rates were consistent with the benthic communities between the two sites with one dominated by fleshy organisms and the other dominated by calcifiers (degraded and healthy reefs, respectively). This demonstrates the potential utility of BEAMS as a reef health monitoring tool. NCP and NCC were tightly coupled on time scales of minutes to days, and light was the primary driver for the variability of daily integrated metabolic rates. No correlation between CO 2 levels and daily integrated NCC was observed, indicating that NCC at these sites were not significantly affected by CO 2.",
    url = "https://doi.org/10.1002/2016jc011886",
    doi = "10.1002/2016jc011886",
    openalex = "W2472142622",
    references = "doi1010022015gl063488"
}

@incollection{doi10100797894017749945,
    author = "Glynn, Peter W. and Alvarado, Juan José and Banks, Stuart and Cortés, Jorge and Feingold, Joshua S. and Jiménez, Carlos and Maragos, James E. and Martínez, Priscilla and Maté, Juan L. and Moanga, Diana and Navarrete, Sérgio A. and Reyes‐Bonilla, Héctor and Riegl, Bernhard and Rivera, Fernando and Vargas-Ángel, Bernardo and Wieters, Evie A. and Zapata, Fernando A.",
    title = "Eastern Pacific Coral Reef Provinces, Coral Community Structure and Composition: An Overview",
    year = "2016",
    booktitle = "Coral reefs of the world",
    url = "https://doi.org/10.1007/978-94-017-7499-4\_5",
    doi = "10.1007/978-94-017-7499-4\_5",
    openalex = "W2512962919",
    references = "doi101111zoj12092"
}

@article{doi101038nature17155,
    author = "Albright, Rebecca and Caldeira, Lilian and Hosfelt, J. D. and Kwiatkowski, Lester and Maclaren, Jana K. and Mason, Benjamin and Nebuchina, Yana and Ninokawa, Aaron T. and Pongratz, Julia and Ricke, Katharine and Rivlin, Tanya and Schneider, K.J. and Sesboüé, Marine and Shamberger, Kathryn E. F. and Silverman, Jacob and Wolfe, Kennedy and Zhu, Kai and Caldeira, Ken",
    title = "Reversal of ocean acidification enhances net coral reef calcification",
    year = "2016",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature17155",
    doi = "10.1038/nature17155",
    openalex = "W2291098356",
    references = "doi1010022015gl063488, doi1010029783527613984, doi101002lno10048, doi1010160198014987900215, doi101016019801499090004f, doi101093icesjmsfsn048, doi101093icesjmsfsv075, doi101111j14610248201001518x, doi101139f99128, doi101146annurevmarine010908163834, doi10277766906, doi104319lo19731860897, doi105670oceanog200995"
}

@article{doi101038nature18607,
    author = "Cinner, Joshua E. and Huchery, Cindy and MacNeil, M. Aaron and Graham, Nicholas A. J. and McClanahan, Tim R. and Maina, Joseph and Maire, Eva and Kittinger, John N. and Hicks, Christina C. and Mora, Camilo and Allison, Edward H. and D’Agata, Stéphanie and Hoey, Andrew S. and Feary, David A. and Crowder, Larry B. and Williams, Ivor D. and Kulbicki, Michel and Vigliola, Laurent and Wantiez, Laurent and Edgar, Graham J. and Stuart‐Smith, Rick D. and Sandin, Stuart A. and Green, Alison L. and Hardt, Marah J. and Beger, Maria and Friedlander, Alan M. and Campbell, Stuart and Holmes, Katherine E. and Wilson, Shaun K. and Brokovich, Eran and Brooks, Andrew J. and Cruz‐Motta, Juan J. and Booth, David J. and Chabanet, Pascale and Gough, Charlie and Tupper, Mark and Ferse, Sebastian C. A. and Sumaila, U. Rashid and Mouillot, David",
    title = "Bright spots among the world’s coral reefs",
    year = "2016",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature18607",
    doi = "10.1038/nature18607",
    openalex = "W2443667990",
    references = "doi101007bf01386390, doi101016s0959378001000073, doi101017cbo9780511807763, doi101038nature02691, doi101126science1085706, doi1012019780429258411, doi101214ss1177011136, doi1023072979181, doi1023073146384, openalexw1531609150"
}

of reef area. Emissions scenario RCP4.5 represents lower emissions mid-century than will eventuate if pledges made following the 2015 Paris Climate Change Conference (COP21) become reality. These pledges do little to provide reefs with more time to adapt and acclimate prior to severe bleaching conditions occurring annually. RCP4.5 adds 11 years to the global average ASB timing when compared to RCP8.5; however, >75% of reefs still experience ASB before 2070 under RCP4.5. Coral reef futures clearly vary greatly among and within countries, indicating the projections warrant consideration in most reef areas during conservation and management planning.

@article{doi101038srep39666,
    author = "van Hooidonk, Ruben and Maynard, Jeffrey and Tamelander, Jerker and Gove, Jamison M. and Ahmadia, Gabby N. and Raymundo, Laurie J. and Williams, Gareth J. and Heron, Scott F. and Planes, Serge",
    title = "Local-scale projections of coral reef futures and implications of the Paris Agreement",
    year = "2016",
    journal = "Scientific Reports",
    abstract = "of reef area. Emissions scenario RCP4.5 represents lower emissions mid-century than will eventuate if pledges made following the 2015 Paris Climate Change Conference (COP21) become reality. These pledges do little to provide reefs with more time to adapt and acclimate prior to severe bleaching conditions occurring annually. RCP4.5 adds 11 years to the global average ASB timing when compared to RCP8.5; however, >75\% of reefs still experience ASB before 2070 under RCP4.5. Coral reef futures clearly vary greatly among and within countries, indicating the projections warrant consideration in most reef areas during conservation and management planning.",
    url = "https://doi.org/10.1038/srep39666",
    doi = "10.1038/srep39666",
    openalex = "W2566943586"
}

Large rivers create major gaps in reef distribution along tropical shelves. The Amazon River represents 20% of the global riverine discharge to the ocean, generating up to a 1.3 × 10(6)-km(2) plume, and extensive muddy bottoms in the equatorial margin of South America. As a result, a wide area of the tropical North Atlantic is heavily affected in terms of salinity, pH, light penetration, and sedimentation. Such unfavorable conditions were thought to imprint a major gap in Western Atlantic reefs. We present an extensive carbonate system off the Amazon mouth, underneath the river plume. Significant carbonate sedimentation occurred during lowstand sea level, and still occurs in the outer shelf, resulting in complex hard-bottom topography. A permanent near-bottom wedge of ocean water, together with the seasonal nature of the plume's eastward retroflection, conditions the existence of this extensive (~9500 km(2)) hard-bottom mosaic. The Amazon reefs transition from accretive to erosional structures and encompass extensive rhodolith beds. Carbonate structures function as a connectivity corridor for wide depth-ranging reef-associated species, being heavily colonized by large sponges and other structure-forming filter feeders that dwell under low light and high levels of particulates. The oxycline between the plume and subplume is associated with chemoautotrophic and anaerobic microbial metabolisms. The system described here provides several insights about the responses of tropical reefs to suboptimal and marginal reef-building conditions, which are accelerating worldwide due to global changes.

@article{doi101126sciadv1501252,
    author = "Moura, Rodrigo L. and Amado‐Filho, Gilberto M. and de Moraes, Fernando Coreixas and Brasileiro, Poliana S. and Salomon, Paulo S. and de Mahiques, Michel Michaelovitch and Bastos, Alex Cardoso and de Almeida, Marcelo Gomes and Silva, Jomar M. and Araújo, Beatriz Ferreira and Brito, Frederico P. and Rangel, Thiago Pessanha and de Oliveira, Bráulio Cherene Vaz and Bahia, Ricardo G. and Paranhos, Rodolfo and Dias, Rodolfo Jasão Soares and Siegle, Eduardo and Figueiredo, Alberto G. and Pereira, Renato Crespo and Leal, Camille V. and Hajdu, Eduardo and Asp, Nils E. and Gregoracci, Gustavo Bueno and Neumann‐Leitão, Sigrid and Yager, Patricia L. and Francini‐Filho, Ronaldo B. and Fróes, Adriana M. and Campeão, Mariana E. and da Silva, Bruno Santana and Moreira, Ana Paula B. and de Oliveira, Louisi and Soares, Ana Carolina and Araújo, Laís Moreira Borges and Oliveira, Nara L. and Teixeira, João Batista and Valle, R.A.B. and Thompson, Cristiane C. and de Rezende, Carlos Eduardo and Thompson, Fabiano L.",
    title = "An extensive reef system at the Amazon River mouth",
    year = "2016",
    journal = "Science Advances",
    abstract = "Large rivers create major gaps in reef distribution along tropical shelves. The Amazon River represents 20\% of the global riverine discharge to the ocean, generating up to a 1.3 × 10(6)-km(2) plume, and extensive muddy bottoms in the equatorial margin of South America. As a result, a wide area of the tropical North Atlantic is heavily affected in terms of salinity, pH, light penetration, and sedimentation. Such unfavorable conditions were thought to imprint a major gap in Western Atlantic reefs. We present an extensive carbonate system off the Amazon mouth, underneath the river plume. Significant carbonate sedimentation occurred during lowstand sea level, and still occurs in the outer shelf, resulting in complex hard-bottom topography. A permanent near-bottom wedge of ocean water, together with the seasonal nature of the plume's eastward retroflection, conditions the existence of this extensive (\textasciitilde 9500 km(2)) hard-bottom mosaic. The Amazon reefs transition from accretive to erosional structures and encompass extensive rhodolith beds. Carbonate structures function as a connectivity corridor for wide depth-ranging reef-associated species, being heavily colonized by large sponges and other structure-forming filter feeders that dwell under low light and high levels of particulates. The oxycline between the plume and subplume is associated with chemoautotrophic and anaerobic microbial metabolisms. The system described here provides several insights about the responses of tropical reefs to suboptimal and marginal reef-building conditions, which are accelerating worldwide due to global changes.",
    url = "https://doi.org/10.1126/sciadv.1501252",
    doi = "10.1126/sciadv.1501252",
    openalex = "W2341905429",
    references = "doi10100797814615074751, doi101016s0012825201000897, doi101093nargkf436, doi101111j13652699200701790x, doi101126science1152509, doi101126science1196889, doi101126science1204794, doi101126science1241981, doi101146annurevpp40060189002443, doi103354meps07815, openalexw253507229"
}

Coral recruitment and calcium carbonate (CaCO₃) accretion are fundamental processes that help maintain coral reefs. Many reefs worldwide have experienced degradation, including a decrease in coral cover and biodiversity. Successful coral recruitment helps degraded reefs to recover, while CaCO₃ accretion by early successional benthic organisms maintains the topographic complexity of a coral reef system. It is therefore important to understand the processes that affect coral recruitment and CaCO₃ accretion rates in order to understand how coral reefs recover from disturbances. The aim of this thesis was to determine how biophysical forcing factors affect coral recruitment, calcification and bioerosion on a pristine coral reef. I used artificial settlement tiles to measure coral recruitment and CaCO₃ accretion at ten sites (four on the fore reef, four on the Western Reef Terrace and two at the Entrance Channel) at Palmyra Atoll. Fungia skeletons and pieces of dead coral rock were used to measure bioerosion rates, which were combined with the CaCO₃ accretion rates to obtain a net CaCO₃ budget of the reef substratum. Interactions between coral recruits and other benthic organisms on the settlement tiles were recorded to determine the settlement preferences and competitive strength of coral recruits. The settlement preference of Pocillopora damicornis for divots shaped like steephead and bumphead parrotfish bites marks was determined by adding P. damicornis larvae to a container with a settlement tile with the aforementioned divots. I found that coral recruitment and CaCO₃ accretion are influenced by biophysical forcing factors. Most pocilloporids likely recruit close to their parents while the origin of poritid larvae is much more distant. Pocilloporid recruitment rates were also significantly correlated with the successional stage of the benthic community on the settlement tiles, especially the cover of biofilm and bryozoa. Biofilm and crustose coralline algae (CCA) were preferred as settlement substrata by coral larvae, however both pocilloporids and poritids settled on a large number of different benthic substrata. P. damicornis larvae showed a significant settlement preference for divots shaped like parrotfish bite marks over a flat settlement surface. Coral recruits were good competitors against encrusting algae but were often outcompeted by filamentous and upright algae. Settlement tiles were almost entirely colonised by benthic organisms within three to twelve months of deployment. The mass of CaCO₃ deposited onto the settlement tiles negatively correlated with herbivore grazing pressure on the benthic community. Bioerosion rates within pieces of coral (internal bioerosion) increased over time but overall bioerosion rates (internal and external) rarely exceeded CaCO₃ deposition by CCA. My results show how variability in biophysical forcing factors leads to natural variation in coral recruitment and CaCO₃ accretion. This thesis highlights the importance of measuring herbivore grazing, CCA and turf algae cover to gain a better understanding of reef resilience. I conclude that models constructed for Caribbean reefs may not be suited to predict resilience in Pacific reefs and that within the Pacific, two different kinds of resilience models need to be constructed, one for human-inhabited coral reefs and one for uninhabited coral reefs.

@phdthesis{doi1026686wgtn17057996,
    author = "Elmer, Franziska",
    title = "Factors Affecting Coral Recruitment and Calcium Carbonate Accretion Rates on a Central Pacific Coral Reef",
    year = "2016",
    abstract = "Coral recruitment and calcium carbonate (CaCO₃) accretion are fundamental processes that help maintain coral reefs. Many reefs worldwide have experienced degradation, including a decrease in coral cover and biodiversity. Successful coral recruitment helps degraded reefs to recover, while CaCO₃ accretion by early successional benthic organisms maintains the topographic complexity of a coral reef system. It is therefore important to understand the processes that affect coral recruitment and CaCO₃ accretion rates in order to understand how coral reefs recover from disturbances. The aim of this thesis was to determine how biophysical forcing factors affect coral recruitment, calcification and bioerosion on a pristine coral reef. I used artificial settlement tiles to measure coral recruitment and CaCO₃ accretion at ten sites (four on the fore reef, four on the Western Reef Terrace and two at the Entrance Channel) at Palmyra Atoll. Fungia skeletons and pieces of dead coral rock were used to measure bioerosion rates, which were combined with the CaCO₃ accretion rates to obtain a net CaCO₃ budget of the reef substratum. Interactions between coral recruits and other benthic organisms on the settlement tiles were recorded to determine the settlement preferences and competitive strength of coral recruits. The settlement preference of Pocillopora damicornis for divots shaped like steephead and bumphead parrotfish bites marks was determined by adding P. damicornis larvae to a container with a settlement tile with the aforementioned divots. I found that coral recruitment and CaCO₃ accretion are influenced by biophysical forcing factors. Most pocilloporids likely recruit close to their parents while the origin of poritid larvae is much more distant. Pocilloporid recruitment rates were also significantly correlated with the successional stage of the benthic community on the settlement tiles, especially the cover of biofilm and bryozoa. Biofilm and crustose coralline algae (CCA) were preferred as settlement substrata by coral larvae, however both pocilloporids and poritids settled on a large number of different benthic substrata. P. damicornis larvae showed a significant settlement preference for divots shaped like parrotfish bite marks over a flat settlement surface. Coral recruits were good competitors against encrusting algae but were often outcompeted by filamentous and upright algae. Settlement tiles were almost entirely colonised by benthic organisms within three to twelve months of deployment. The mass of CaCO₃ deposited onto the settlement tiles negatively correlated with herbivore grazing pressure on the benthic community. Bioerosion rates within pieces of coral (internal bioerosion) increased over time but overall bioerosion rates (internal and external) rarely exceeded CaCO₃ deposition by CCA. My results show how variability in biophysical forcing factors leads to natural variation in coral recruitment and CaCO₃ accretion. This thesis highlights the importance of measuring herbivore grazing, CCA and turf algae cover to gain a better understanding of reef resilience. I conclude that models constructed for Caribbean reefs may not be suited to predict resilience in Pacific reefs and that within the Pacific, two different kinds of resilience models need to be constructed, one for human-inhabited coral reefs and one for uninhabited coral reefs.",
    url = "https://doi.org/10.26686/wgtn.17057996",
    doi = "10.26686/wgtn.17057996",
    openalex = "W2602296912",
    references = "openalexw2165625223"
}

Coral recruitment and calcium carbonate (CaCO₃) accretion are fundamental processes that help maintain coral reefs. Many reefs worldwide have experienced degradation, including a decrease in coral cover and biodiversity. Successful coral recruitment helps degraded reefs to recover, while CaCO₃ accretion by early successional benthic organisms maintains the topographic complexity of a coral reef system. It is therefore important to understand the processes that affect coral recruitment and CaCO₃ accretion rates in order to understand how coral reefs recover from disturbances. The aim of this thesis was to determine how biophysical forcing factors affect coral recruitment, calcification and bioerosion on a pristine coral reef. I used artificial settlement tiles to measure coral recruitment and CaCO₃ accretion at ten sites (four on the fore reef, four on the Western Reef Terrace and two at the Entrance Channel) at Palmyra Atoll. Fungia skeletons and pieces of dead coral rock were used to measure bioerosion rates, which were combined with the CaCO₃ accretion rates to obtain a net CaCO₃ budget of the reef substratum. Interactions between coral recruits and other benthic organisms on the settlement tiles were recorded to determine the settlement preferences and competitive strength of coral recruits. The settlement preference of Pocillopora damicornis for divots shaped like steephead and bumphead parrotfish bites marks was determined by adding P. damicornis larvae to a container with a settlement tile with the aforementioned divots. I found that coral recruitment and CaCO₃ accretion are influenced by biophysical forcing factors. Most pocilloporids likely recruit close to their parents while the origin of poritid larvae is much more distant. Pocilloporid recruitment rates were also significantly correlated with the successional stage of the benthic community on the settlement tiles, especially the cover of biofilm and bryozoa. Biofilm and crustose coralline algae (CCA) were preferred as settlement substrata by coral larvae, however both pocilloporids and poritids settled on a large number of different benthic substrata. P. damicornis larvae showed a significant settlement preference for divots shaped like parrotfish bite marks over a flat settlement surface. Coral recruits were good competitors against encrusting algae but were often outcompeted by filamentous and upright algae. Settlement tiles were almost entirely colonised by benthic organisms within three to twelve months of deployment. The mass of CaCO₃ deposited onto the settlement tiles negatively correlated with herbivore grazing pressure on the benthic community. Bioerosion rates within pieces of coral (internal bioerosion) increased over time but overall bioerosion rates (internal and external) rarely exceeded CaCO₃ deposition by CCA. My results show how variability in biophysical forcing factors leads to natural variation in coral recruitment and CaCO₃ accretion. This thesis highlights the importance of measuring herbivore grazing, CCA and turf algae cover to gain a better understanding of reef resilience. I conclude that models constructed for Caribbean reefs may not be suited to predict resilience in Pacific reefs and that within the Pacific, two different kinds of resilience models need to be constructed, one for human-inhabited coral reefs and one for uninhabited coral reefs.

@phdthesis{doi1026686wgtn17057996v1,
    author = "Elmer, Franziska",
    title = "Factors Affecting Coral Recruitment and Calcium Carbonate Accretion Rates on a Central Pacific Coral Reef",
    year = "2016",
    abstract = "Coral recruitment and calcium carbonate (CaCO₃) accretion are fundamental processes that help maintain coral reefs. Many reefs worldwide have experienced degradation, including a decrease in coral cover and biodiversity. Successful coral recruitment helps degraded reefs to recover, while CaCO₃ accretion by early successional benthic organisms maintains the topographic complexity of a coral reef system. It is therefore important to understand the processes that affect coral recruitment and CaCO₃ accretion rates in order to understand how coral reefs recover from disturbances. The aim of this thesis was to determine how biophysical forcing factors affect coral recruitment, calcification and bioerosion on a pristine coral reef. I used artificial settlement tiles to measure coral recruitment and CaCO₃ accretion at ten sites (four on the fore reef, four on the Western Reef Terrace and two at the Entrance Channel) at Palmyra Atoll. Fungia skeletons and pieces of dead coral rock were used to measure bioerosion rates, which were combined with the CaCO₃ accretion rates to obtain a net CaCO₃ budget of the reef substratum. Interactions between coral recruits and other benthic organisms on the settlement tiles were recorded to determine the settlement preferences and competitive strength of coral recruits. The settlement preference of Pocillopora damicornis for divots shaped like steephead and bumphead parrotfish bites marks was determined by adding P. damicornis larvae to a container with a settlement tile with the aforementioned divots. I found that coral recruitment and CaCO₃ accretion are influenced by biophysical forcing factors. Most pocilloporids likely recruit close to their parents while the origin of poritid larvae is much more distant. Pocilloporid recruitment rates were also significantly correlated with the successional stage of the benthic community on the settlement tiles, especially the cover of biofilm and bryozoa. Biofilm and crustose coralline algae (CCA) were preferred as settlement substrata by coral larvae, however both pocilloporids and poritids settled on a large number of different benthic substrata. P. damicornis larvae showed a significant settlement preference for divots shaped like parrotfish bite marks over a flat settlement surface. Coral recruits were good competitors against encrusting algae but were often outcompeted by filamentous and upright algae. Settlement tiles were almost entirely colonised by benthic organisms within three to twelve months of deployment. The mass of CaCO₃ deposited onto the settlement tiles negatively correlated with herbivore grazing pressure on the benthic community. Bioerosion rates within pieces of coral (internal bioerosion) increased over time but overall bioerosion rates (internal and external) rarely exceeded CaCO₃ deposition by CCA. My results show how variability in biophysical forcing factors leads to natural variation in coral recruitment and CaCO₃ accretion. This thesis highlights the importance of measuring herbivore grazing, CCA and turf algae cover to gain a better understanding of reef resilience. I conclude that models constructed for Caribbean reefs may not be suited to predict resilience in Pacific reefs and that within the Pacific, two different kinds of resilience models need to be constructed, one for human-inhabited coral reefs and one for uninhabited coral reefs.",
    url = "https://doi.org/10.26686/wgtn.17057996.v1",
    doi = "10.26686/wgtn.17057996.v1",
    openalex = "W4372132062",
    references = "openalexw2165625223"
}

Coral reef net ecosystem calcification (NEC) has decreased for many Caribbean reefs over recent decades primarily due to a combination of declining coral cover and changing benthic community composition. Chemistry-based approaches to calculate NEC utilize the drawdown of seawater total alkalinity (TA) combined with residence time to calculate an instantaneous measurement of NEC. Census-based approaches combine annual growth rates with benthic cover and reef structural complexity to estimate NEC occurring over annual timescales. Here, NEC was calculated for Hog Reef in Bermuda using both chemistry and census-based NEC techniques to compare the mass-balance generated by the two methods and identify the dominant biocalcifiers at Hog Reef. Our findings indicate close agreement between the annual 2011 census-based NEC 2.35±1.01 kg CaCO3•m-2•y-1 and the chemistry-based NEC 2.23±1.02 kg CaCO3•m-2•y-1 at Hog Reef. An additional record of Hog Reef TA data calculated from an autonomous CO2 mooring measuring pCO2 and modeled pHtotal every 3-hours highlights the dynamic temporal variability in coral reef NEC. This ability for chemistry-based NEC techniques to capture higher frequency variability in coral reef NEC allows the mechanisms driving NEC variability to be explored and tested. Just four coral species, Diploria labyrinthiformis, Pseudodiploria strigosa, Millepora alcicornis, and Orbicella franksi, were identified by the census-based NEC as contributing to 94±19% of the total calcium carbonate production at Hog Reef suggesting these species should be highlighted for conservation to preserve current calcium carbonate production rates at Hog Reef. As coral cover continues to decline globally, the agreement between these NEC estimates suggest that either method, but ideally both methods, may serve as a useful tool for coral reef managers and conservation scientists to monitor the maintenance of coral reef structure and ecosystem services.

@article{doi103389fmars201600181,
    author = "Courtney, Travis A. and Andersson, Andreas J. and Bates, Nicholas R. and Collins, Andrew and Cyronak, Tyler and de Putron, Samantha J. and Eyre, Bradley D. and Garley, Rebecca and Hochberg, Eric J. and Johnson, Rodney J. and Musielewicz, Sylvia and Noyes, Tim J. and Sabine, Christopher L. and Sutton, Adrienne J. and Toncin, Jessy and Tribollet, Aline",
    title = "Comparing Chemistry and Census-Based Estimates of Net Ecosystem Calcification on a Rim Reef in Bermuda",
    year = "2016",
    journal = "Frontiers in Marine Science",
    abstract = "Coral reef net ecosystem calcification (NEC) has decreased for many Caribbean reefs over recent decades primarily due to a combination of declining coral cover and changing benthic community composition. Chemistry-based approaches to calculate NEC utilize the drawdown of seawater total alkalinity (TA) combined with residence time to calculate an instantaneous measurement of NEC. Census-based approaches combine annual growth rates with benthic cover and reef structural complexity to estimate NEC occurring over annual timescales. Here, NEC was calculated for Hog Reef in Bermuda using both chemistry and census-based NEC techniques to compare the mass-balance generated by the two methods and identify the dominant biocalcifiers at Hog Reef. Our findings indicate close agreement between the annual 2011 census-based NEC 2.35±1.01 kg CaCO3•m-2•y-1 and the chemistry-based NEC 2.23±1.02 kg CaCO3•m-2•y-1 at Hog Reef. An additional record of Hog Reef TA data calculated from an autonomous CO2 mooring measuring pCO2 and modeled pHtotal every 3-hours highlights the dynamic temporal variability in coral reef NEC. This ability for chemistry-based NEC techniques to capture higher frequency variability in coral reef NEC allows the mechanisms driving NEC variability to be explored and tested. Just four coral species, Diploria labyrinthiformis, Pseudodiploria strigosa, Millepora alcicornis, and Orbicella franksi, were identified by the census-based NEC as contributing to 94±19\% of the total calcium carbonate production at Hog Reef suggesting these species should be highlighted for conservation to preserve current calcium carbonate production rates at Hog Reef. As coral cover continues to decline globally, the agreement between these NEC estimates suggest that either method, but ideally both methods, may serve as a useful tool for coral reef managers and conservation scientists to monitor the maintenance of coral reef structure and ecosystem services.",
    url = "https://doi.org/10.3389/fmars.2016.00181",
    doi = "10.3389/fmars.2016.00181",
    openalex = "W2522267892",
    references = "doi1010022015gl063488, doi101002lno10048, doi101016002196149090074z, doi1010160198014987900215, doi101016jecoser201207005, doi101016s0921800999000099, doi101038nmeth2089, doi101093icb391146, doi101126science1086050, doi1023071941447, doi104319lo19731860897, openalexw171744082"
}

Abstract Coral reefs are built of calcium carbonate (CaCO 3) produced biogenically by a diversity of calcifying plants, animals, and microbes. As the ocean warms and acidifies, there is mounting concern that declining calcification rates could shift coral reef CaCO 3 budgets from net accretion to net dissolution. We quantified net ecosystem calcification (NEC) and production (NEP) on Dongsha Atoll, northern South China Sea, over a 2 week period that included a transient bleaching event. Peak daytime pH on the wide, shallow reef flat during the nonbleaching period was ∼8.5, significantly elevated above that of the surrounding open ocean (∼8.0–8.1) as a consequence of daytime NEP (up to 112 mmol C m −2 h −1). Diurnal‐averaged NEC was 390 ± 90 mmol CaCO 3 m −2 d −1, higher than any other coral reef studied to date despite comparable calcifier cover (25%) and relatively high fleshy algal cover (19%). Coral bleaching linked to elevated temperatures significantly reduced daytime NEP by 29 mmol C m −2 h −1. pH on the reef flat declined by 0.2 units, causing a 40% reduction in NEC in the absence of pH changes in the surrounding open ocean. Our findings highlight the interactive relationship between carbonate chemistry of coral reef ecosystems and ecosystem production and calcification rates, which are in turn impacted by ocean warming. As open‐ocean waters bathing coral reefs warm and acidify over the 21st century, the health and composition of reef benthic communities will play a major role in determining on‐reef conditions that will in turn dictate the ecosystem response to climate change.

@article{doi1010022016jc012326,
    author = "DeCarlo, Thomas M. and Cohen, Anne L. and Wong, George T.F. and Shiah, Fuh‐Kwo and Lentz, Steven J. and Davis, Kristen A. and Shamberger, Kathryn E. F. and Lohmann, Pat",
    title = "Community production modulates coral reef pH and the sensitivity of ecosystem calcification to ocean acidification",
    year = "2017",
    journal = "Journal of Geophysical Research Oceans",
    abstract = "Abstract Coral reefs are built of calcium carbonate (CaCO 3) produced biogenically by a diversity of calcifying plants, animals, and microbes. As the ocean warms and acidifies, there is mounting concern that declining calcification rates could shift coral reef CaCO 3 budgets from net accretion to net dissolution. We quantified net ecosystem calcification (NEC) and production (NEP) on Dongsha Atoll, northern South China Sea, over a 2 week period that included a transient bleaching event. Peak daytime pH on the wide, shallow reef flat during the nonbleaching period was ∼8.5, significantly elevated above that of the surrounding open ocean (∼8.0–8.1) as a consequence of daytime NEP (up to 112 mmol C m −2 h −1). Diurnal‐averaged NEC was 390 ± 90 mmol CaCO 3 m −2 d −1, higher than any other coral reef studied to date despite comparable calcifier cover (25\%) and relatively high fleshy algal cover (19\%). Coral bleaching linked to elevated temperatures significantly reduced daytime NEP by 29 mmol C m −2 h −1. pH on the reef flat declined by 0.2 units, causing a 40\% reduction in NEC in the absence of pH changes in the surrounding open ocean. Our findings highlight the interactive relationship between carbonate chemistry of coral reef ecosystems and ecosystem production and calcification rates, which are in turn impacted by ocean warming. As open‐ocean waters bathing coral reefs warm and acidify over the 21st century, the health and composition of reef benthic communities will play a major role in determining on‐reef conditions that will in turn dictate the ecosystem response to climate change.",
    url = "https://doi.org/10.1002/2016jc012326",
    doi = "10.1002/2016jc012326",
    openalex = "W2568883838",
    references = "doi1010022015gl063488, doi101002lno10048, doi1010160198014987900215, doi1010160304420374900152, doi101016jcageo200511009, doi101016jgloenvcha201404002, doi1010292004gb002247, doi10102992jc00188, doi101126science1152509, doi101146annurevmarine010908163834, doi1015159781400849079, doi103389fmars201600181, doi104319lo19731860897"
}

@article{doi101038nature22901,
    author = "Hughes, Terry P. and Barnes, Michele L. and Bellwood, David R. and Cinner, Joshua E. and Cumming, Graeme S. and Jackson, Jeremy B. C. and Kleypas, Joanie and van de Leemput, Ingrid A. and Lough, Janice and Morrison, Tiffany H. and Palumbi, Stephen R. and van Nes, Egbert H. and Scheffer, Marten",
    title = "Coral reefs in the Anthropocene",
    year = "2017",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature22901",
    doi = "10.1038/nature22901",
    openalex = "W2619701599",
    references = "doi101016jtree201508009, doi101038nature04095, doi101038nature18607, doi101038nature21707, doi101073pnas1422301112, doi101126science1085706, doi101126science1152509, doi101126science1204794, doi105751es03180140232"
}

A 2 °C increase in global temperature above pre-industrial levels is considered a reasonable target for avoiding the most devastating impacts of anthropogenic climate change. In June 2015, sea surface temperature (SST) of the South China Sea (SCS) increased by 2 °C in response to the developing Pacific El Niño. On its own, this moderate, short-lived warming was unlikely to cause widespread damage to coral reefs in the region, and the coral reef "Bleaching Alert" alarm was not raised. However, on Dongsha Atoll, in the northern SCS, unusually weak winds created low-flow conditions that amplified the 2 °C basin-scale anomaly. Water temperatures on the reef flat, normally indistinguishable from open-ocean SST, exceeded 6 °C above normal summertime levels. Mass coral bleaching quickly ensued, killing 40% of the resident coral community in an event unprecedented in at least the past 40 years. Our findings highlight the risks of 2 °C ocean warming to coral reef ecosystems when global and local processes align to drive intense heating, with devastating consequences.

@article{doi101038srep44586,
    author = "DeCarlo, Thomas M. and Cohen, Anne L. and Wong, George T.F. and Davis, Kristen A. and Lohmann, Pat and Soong, Keryea",
    title = "Mass coral mortality under local amplification of 2 °C ocean warming",
    year = "2017",
    journal = "Scientific Reports",
    abstract = {A 2 °C increase in global temperature above pre-industrial levels is considered a reasonable target for avoiding the most devastating impacts of anthropogenic climate change. In June 2015, sea surface temperature (SST) of the South China Sea (SCS) increased by 2 °C in response to the developing Pacific El Niño. On its own, this moderate, short-lived warming was unlikely to cause widespread damage to coral reefs in the region, and the coral reef "Bleaching Alert" alarm was not raised. However, on Dongsha Atoll, in the northern SCS, unusually weak winds created low-flow conditions that amplified the 2 °C basin-scale anomaly. Water temperatures on the reef flat, normally indistinguishable from open-ocean SST, exceeded 6 °C above normal summertime levels. Mass coral bleaching quickly ensued, killing 40\% of the resident coral community in an event unprecedented in at least the past 40 years. Our findings highlight the risks of 2 °C ocean warming to coral reef ecosystems when global and local processes align to drive intense heating, with devastating consequences.},
    url = "https://doi.org/10.1038/srep44586",
    doi = "10.1038/srep44586",
    openalex = "W2600378448",
    references = "doi1010022016jc012326"
}

Coral reefs are found in a wide range of environments, where they provide food and habitat to a large range of organisms as well as other ecological goods and services. Warm-water coral reefs, for example, occupy shallow sunlit, warm and alkaline waters in order to grow and calcify at the high rates necessary to build and maintain their calcium carbonate structures. At deeper locations (40 – 150 m), “mesophotic” (low light) coral reefs accumulate calcium carbonate at much lower rates (if at all in some cases) yet remain important as habitat for a wide range of organisms, including those important for fisheries. Finally, even deeper, down to 2000 m or more, the so-called ‘cold-water’ coral reefs are found in the dark depths. Despite their importance, coral reefs are facing significant challenges from human activities including pollution, over-harvesting, physical destruction, and climate change. In the latter case, even lower greenhouse gas emission scenarios (such as Representative Concentration Pathway RCP 4.5) are likely drive the elimination of most warm-water coral reefs by 2040-2050. Cold-water corals are also threatened by warming temperatures and ocean acidification although evidence of the direct effect of climate change is less clear. Evidence that coral reefs can adapt at rates which are sufficient for them to keep up with rapid ocean warming and acidification is minimal, especially given that corals are long-lived and hence have slow rates of evolution. Conclusions that coral reefs will migrate to higher latitudes as they warm are equally unfounded, with the observations of tropical species appearing at high latitudes ‘necessary but not sufficient’ evidence that entire coral reef ecosystems are shifting. On the contrary, coral reefs are likely to degrade rapidly over the next 20 years, presenting fundamental challenges for the 500 million people who derive food, income, coastal protection, and a range of other services from coral reefs. Unless rapid advances to the goals of the Paris Climate Change Agreement occur over the next decade, hundreds of millions of people are likely to face increasing amounts of poverty and social disruption, and, in some cases, regional insecurity.

@article{doi103389fmars201700158,
    author = "Hoegh‐Guldberg, Ove and Poloczanska, Elvira S. and Skirving, William and Dove, Sophie",
    title = "Coral Reef Ecosystems under Climate Change and Ocean Acidification",
    year = "2017",
    journal = "Frontiers in Marine Science",
    abstract = "Coral reefs are found in a wide range of environments, where they provide food and habitat to a large range of organisms as well as other ecological goods and services. Warm-water coral reefs, for example, occupy shallow sunlit, warm and alkaline waters in order to grow and calcify at the high rates necessary to build and maintain their calcium carbonate structures. At deeper locations (40 – 150 m), “mesophotic” (low light) coral reefs accumulate calcium carbonate at much lower rates (if at all in some cases) yet remain important as habitat for a wide range of organisms, including those important for fisheries. Finally, even deeper, down to 2000 m or more, the so-called ‘cold-water’ coral reefs are found in the dark depths. Despite their importance, coral reefs are facing significant challenges from human activities including pollution, over-harvesting, physical destruction, and climate change. In the latter case, even lower greenhouse gas emission scenarios (such as Representative Concentration Pathway RCP 4.5) are likely drive the elimination of most warm-water coral reefs by 2040-2050. Cold-water corals are also threatened by warming temperatures and ocean acidification although evidence of the direct effect of climate change is less clear. Evidence that coral reefs can adapt at rates which are sufficient for them to keep up with rapid ocean warming and acidification is minimal, especially given that corals are long-lived and hence have slow rates of evolution. Conclusions that coral reefs will migrate to higher latitudes as they warm are equally unfounded, with the observations of tropical species appearing at high latitudes ‘necessary but not sufficient’ evidence that entire coral reef ecosystems are shifting. On the contrary, coral reefs are likely to degrade rapidly over the next 20 years, presenting fundamental challenges for the 500 million people who derive food, income, coastal protection, and a range of other services from coral reefs. Unless rapid advances to the goals of the Paris Climate Change Agreement occur over the next decade, hundreds of millions of people are likely to face increasing amounts of poverty and social disruption, and, in some cases, regional insecurity.",
    url = "https://doi.org/10.3389/fmars.2017.00158",
    doi = "10.3389/fmars.2017.00158",
    openalex = "W2613802059",
    references = "doi1010022016jc012326, doi101016jecss200809003, doi101016jgloenvcha201404002, doi101017cbo9781107415386, doi1010292002jd002670, doi10103820859, doi101038nature04095, doi101093icb391146, doi101126science1059199, doi101126science1152509, doi101146annurevmarine010908163834, doi101371journalpone0030580, doi105194bg616712009, openalexw2530597942, openalexw2924055038"
}

Slow growing, massive stony corals have often been overlooked in reef-restoration activities, despite their resilience to climate change and contribution to reef framework. Techniques to effectively propagate and outplant these species have proven challenging. However, advancement in methodology may increase rates of success. In 2013, Orbicella faveolata and Montastrea cavernosa fragments were outplanted on reefs in the Florida Keys at a nearshore and offshore location, to determine whether “microfragmenting” corals, the process of creating ∼1 cm2 fragments, increased outplant survival and growth compared with larger fragments (16–64 cm2). Arrays of eight microfragments were planted near one larger fragment of similar size at each location. Six replicate pairs were haphazardly placed within each ∼700 m2 study site. Fragments at both sites were monitored for growth and survival over 31 months, spanning two bleaching events. Initial predation occurred on microfragments, but was absent in the larger fragments. Survival and growth differed between sites, but did not differ between the larger fragments and microfragment arrays. However, excluding plots with >40% predation at the nearshore site showed that O. faveolata microfragment arrays produced 10 times more tissue than traditionally used larger fragments. Results from this study suggest that if predation events are reduced, massive corals can be successfully grown and outplanted for restoration purposes.

@article{doi101016jecoleng201808017,
    author = "Page, Christopher and Muller, Erinn M. and Vaughan, David",
    title = "Microfragmenting for the successful restoration of slow growing massive corals",
    year = "2018",
    journal = "Ecological Engineering",
    abstract = "Slow growing, massive stony corals have often been overlooked in reef-restoration activities, despite their resilience to climate change and contribution to reef framework. Techniques to effectively propagate and outplant these species have proven challenging. However, advancement in methodology may increase rates of success. In 2013, Orbicella faveolata and Montastrea cavernosa fragments were outplanted on reefs in the Florida Keys at a nearshore and offshore location, to determine whether “microfragmenting” corals, the process of creating ∼1 cm2 fragments, increased outplant survival and growth compared with larger fragments (16–64 cm2). Arrays of eight microfragments were planted near one larger fragment of similar size at each location. Six replicate pairs were haphazardly placed within each ∼700 m2 study site. Fragments at both sites were monitored for growth and survival over 31 months, spanning two bleaching events. Initial predation occurred on microfragments, but was absent in the larger fragments. Survival and growth differed between sites, but did not differ between the larger fragments and microfragment arrays. However, excluding plots with >40\% predation at the nearshore site showed that O. faveolata microfragment arrays produced 10 times more tissue than traditionally used larger fragments. Results from this study suggest that if predation events are reduced, massive corals can be successfully grown and outplanted for restoration purposes.",
    url = "https://doi.org/10.1016/j.ecoleng.2018.08.017",
    doi = "10.1016/j.ecoleng.2018.08.017",
    openalex = "W2890773647"
}

Coral reefs can provide significant coastal protection benefits to people and property. Here we show that the annual expected damages from flooding would double, and costs from frequent storms would triple without reefs. For 100-year storm events, flood damages would increase by 91% to $US 272 billion without reefs. The countries with the most to gain from reef management are Indonesia, Philippines, Malaysia, Mexico, and Cuba; annual expected flood savings exceed $400 M for each of these nations. Sea-level rise will increase flood risk, but substantial impacts could happen from reef loss alone without better near-term management. We provide a global, process-based valuation of an ecosystem service across an entire marine biome at (sub)national levels. These spatially explicit benefits inform critical risk and environmental management decisions, and the expected benefits can be directly considered by governments (e.g., national accounts, recovery plans) and businesses (e.g., insurance).

@article{doi101038s4146701804568z,
    author = "Beck, Michael W. and Losada, Íñigo J. and Menéndez, Pelayo and Reguero, Borja G. and Díaz-Simal, Pedro and Fernández, Felipe",
    title = "The global flood protection savings provided by coral reefs",
    year = "2018",
    journal = "Nature Communications",
    abstract = "Coral reefs can provide significant coastal protection benefits to people and property. Here we show that the annual expected damages from flooding would double, and costs from frequent storms would triple without reefs. For 100-year storm events, flood damages would increase by 91\% to $US 272 billion without reefs. The countries with the most to gain from reef management are Indonesia, Philippines, Malaysia, Mexico, and Cuba; annual expected flood savings exceed $400 M for each of these nations. Sea-level rise will increase flood risk, but substantial impacts could happen from reef loss alone without better near-term management. We provide a global, process-based valuation of an ecosystem service across an entire marine biome at (sub)national levels. These spatially explicit benefits inform critical risk and environmental management decisions, and the expected benefits can be directly considered by governments (e.g., national accounts, recovery plans) and businesses (e.g., insurance).",
    url = "https://doi.org/10.1038/s41467-018-04568-z",
    doi = "10.1038/s41467-018-04568-z",
    openalex = "W2805548573",
    references = "doi101038nature18607, doi101098rspb20090339, doi101126science1204794, doi1011751520042620020190183eimobo20co2"
}

@article{doi101038s4158601800412,
    author = "Hughes, Terry P. and Kerry, James T. and Baird, Andrew H. and Connolly, Sean R. and Dietzel, Andreas and Eakin, C. Mark and Heron, Scott F. and Hoey, Andrew S. and Hoogenboom, Mia O. and Liu, Gang and McWilliam, Mike and Pears, Rachel and Pratchett, Morgan S. and Skirving, William and Stella, Jessica and Torda, Gergely",
    title = "Global warming transforms coral reef assemblages",
    year = "2018",
    journal = "Nature",
    url = "https://doi.org/10.1038/s41586-018-0041-2",
    doi = "10.1038/s41586-018-0041-2",
    openalex = "W2796944804",
    references = "doi101016jecss200809003, doi101038nature21707, doi101126scienceaan8048"
}

@article{doi101038s415860180194z,
    author = "Perry, Chris T. and Álvarez‐Filip, Lorenzo and Graham, Nicholas A. J. and Mumby, Peter J. and Wilson, Shaun K. and Kench, Paul S. and Manzello, Derek P. and Morgan, Kyle M. and Slangen, Aimée B. A. and Thomson, Damian P. and Januchowski‐Hartley, Fraser A. and Smithers, S and Steneck, Robert S. and Carlton, R. and Edinger, Evan and Enochs, Ian C. and Estrada‐Saldívar, Nuria and Haywood, Michael D. E. and Kolodziej, Graham and Murphy, Gary N. and Pérez‐Cervantes, Esmeralda and Suchley, Adam and Valentino, Lauren and Boenish, Robert and Wilson, Margaret W. and MacDonald, Chancey",
    title = "Loss of coral reef growth capacity to track future increases in sea level",
    year = "2018",
    journal = "Nature",
    url = "https://doi.org/10.1038/s41586-018-0194-z",
    doi = "10.1038/s41586-018-0194-z",
    openalex = "W2808355995",
    references = "doi101038ncomms2409, doi101126science1944268937"
}

addition on reef calcification is likely both a direct physiological response to nutrients and also an indirect response to a shifting pH environment from altered NCP rates. Here, we show that nutrient pollution could make reefs more vulnerable to global changes associated with ocean acidification and accelerate the predicted shift from net accretion to net erosion.

@article{doi101098rspb20172718,
    author = "Silbiger, Nyssa J. and Nelson, Craig E. and Remple, Kristina and Sevilla, Jessica K. and Quinlan, Zachary A. and Putnam, Hollie M. and Fox, Michael D. and Donahue, Megan J.",
    title = "Nutrient pollution disrupts key ecosystem functions on coral reefs",
    year = "2018",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "addition on reef calcification is likely both a direct physiological response to nutrients and also an indirect response to a shifting pH environment from altered NCP rates. Here, we show that nutrient pollution could make reefs more vulnerable to global changes associated with ocean acidification and accelerate the predicted shift from net accretion to net erosion.",
    url = "https://doi.org/10.1098/rspb.2017.2718",
    doi = "10.1098/rspb.2017.2718",
    openalex = "W2807516628",
    references = "doi1010022015gl063488, doi1010022016jc012326"
}

Abstract The ecology of many coral reefs has changed markedly over recent decades in response to various combinations of local and global stressors. These ecological changes have important implications for the abundance of taxa that regulate the production and erosion of skeletal carbonates, and thus for many of the geo‐ecological functions that coral reefs provide, including reef framework production and sediment generation, the maintenance of reef habitat complexity and reef growth potential. These functional attributes underpin many of the ecosystem goods and services that reefs provide to society. Rapidly changing conditions of reefs in the Anthropocene are likely to significantly impact the capacity of reefs to sustain these geo‐ecological functions. Although the Anthropocene footprint of disturbance will be expressed differently across ecoregions and habitats, the end point for many reefs may be broadly similar: (a) progressively shifting towards net neutral or negative carbonate budget states; (b) becoming structurally flatter; and (c) having lower vertical growth rates. It is also likely that a progressive depth‐homogenisation will occur in terms of these processes. The Anthropocene is likely to be defined by an increasing disconnect between the ecological processes that drive carbonate production on the reef surface, and the net geological outcome of that production, that is, the accumulation of the underlying reef structure. Reef structures are thus likely to become increasingly relict or senescent features, which will reduce reef habitat complexity and sediment generation rates, and limit reef potential to accrete vertically at rates that can track rising sea levels. In the absence of pervasive stressors, recovery of degraded coral communities has been observed, resulting in high net‐positive budgets being regained. However, the frequency and intensity of climate‐driven bleaching events are predicted to increase over the next decades. This would increase the spatial footprint of disturbances and exacerbate the magnitude of the changes described here, limiting the capacity of many reefs to maintain their geo‐ecological functions. The enforcement of effective marine protection or the benefits of geographic isolation or of favourable environmental conditions (“refugia” sites) may offer the hope of more optimistic futures in some locations. A >plain language summary is available for this article.

@article{doi1011111365243513247,
    author = "Perry, Chris T. and Álvarez‐Filip, Lorenzo",
    title = "Changing geo‐ecological functions of coral reefs in the Anthropocene",
    year = "2018",
    journal = "Functional Ecology",
    abstract = "Abstract The ecology of many coral reefs has changed markedly over recent decades in response to various combinations of local and global stressors. These ecological changes have important implications for the abundance of taxa that regulate the production and erosion of skeletal carbonates, and thus for many of the geo‐ecological functions that coral reefs provide, including reef framework production and sediment generation, the maintenance of reef habitat complexity and reef growth potential. These functional attributes underpin many of the ecosystem goods and services that reefs provide to society. Rapidly changing conditions of reefs in the Anthropocene are likely to significantly impact the capacity of reefs to sustain these geo‐ecological functions. Although the Anthropocene footprint of disturbance will be expressed differently across ecoregions and habitats, the end point for many reefs may be broadly similar: (a) progressively shifting towards net neutral or negative carbonate budget states; (b) becoming structurally flatter; and (c) having lower vertical growth rates. It is also likely that a progressive depth‐homogenisation will occur in terms of these processes. The Anthropocene is likely to be defined by an increasing disconnect between the ecological processes that drive carbonate production on the reef surface, and the net geological outcome of that production, that is, the accumulation of the underlying reef structure. Reef structures are thus likely to become increasingly relict or senescent features, which will reduce reef habitat complexity and sediment generation rates, and limit reef potential to accrete vertically at rates that can track rising sea levels. In the absence of pervasive stressors, recovery of degraded coral communities has been observed, resulting in high net‐positive budgets being regained. However, the frequency and intensity of climate‐driven bleaching events are predicted to increase over the next decades. This would increase the spatial footprint of disturbances and exacerbate the magnitude of the changes described here, limiting the capacity of many reefs to maintain their geo‐ecological functions. The enforcement of effective marine protection or the benefits of geographic isolation or of favourable environmental conditions (“refugia” sites) may offer the hope of more optimistic futures in some locations. A >plain language summary is available for this article.",
    url = "https://doi.org/10.1111/1365-2435.13247",
    doi = "10.1111/1365-2435.13247",
    openalex = "W2901925152",
    references = "doi103389fmars201600181"
}

Spatially adjacent habitats on coral reefs can represent highly distinct environments, often harbouring different coral communities. Yet, certain coral species thrive across divergent environments. It is unknown whether the forces of selection are sufficiently strong to overcome the counteracting effects of the typically high gene flow over short distances, and for local adaptation to occur. We screened the coral genome (using restriction site-associated sequencing) and characterized both the dinoflagellate photosymbiont- and tissue-associated prokaryote microbiomes (using metabarcoding) of a reef flat and slope population of the reef-building coral, Pocillopora damicornis, at two locations on Heron Island in the southern Great Barrier Reef. Reef flat and slope populations were separated by <100 m horizontally and ~5 m vertically, and the two study locations were separated by ~1 km. For the coral host, genetic divergence between habitats was much greater than between locations, suggesting limited gene flow between the flat and slope populations. Consistent with environmental selection, outlier loci primarily belonged to the conserved, minimal cellular stress response, likely reflecting adaptation to the different temperature and irradiance regimes on the reef flat and slope. The prokaryote community differed across both habitat and, to a lesser extent, location, whereas the dinoflagellate photosymbionts differed by habitat but not location. The observed intraspecific diversity associated with divergent habitats supports that environmental adaptation involves multiple members of the coral holobiont. Adaptive alleles or microbial associations present in coral populations from the environmentally variable reef flat may provide a source of adaptive variation for assisted evolution approaches, through assisted gene flow, artificial cross-breeding or probiotic inoculations, with the aim to increase climate resilience in the slope populations.

@article{doi101111mec14763,
    author = "van Oppen, Madeleine J. H. and Bongaerts, Pim and Frade, Pedro R. and Peplow, Lesa M. and Boyd, Sarah E. and Nim, Hieu T. and Bay, Line K.",
    title = "Adaptation to reef habitats through selection on the coral animal and its associated microbiome",
    year = "2018",
    journal = "Molecular Ecology",
    abstract = "Spatially adjacent habitats on coral reefs can represent highly distinct environments, often harbouring different coral communities. Yet, certain coral species thrive across divergent environments. It is unknown whether the forces of selection are sufficiently strong to overcome the counteracting effects of the typically high gene flow over short distances, and for local adaptation to occur. We screened the coral genome (using restriction site-associated sequencing) and characterized both the dinoflagellate photosymbiont- and tissue-associated prokaryote microbiomes (using metabarcoding) of a reef flat and slope population of the reef-building coral, Pocillopora damicornis, at two locations on Heron Island in the southern Great Barrier Reef. Reef flat and slope populations were separated by <100 m horizontally and \textasciitilde 5 m vertically, and the two study locations were separated by \textasciitilde 1 km. For the coral host, genetic divergence between habitats was much greater than between locations, suggesting limited gene flow between the flat and slope populations. Consistent with environmental selection, outlier loci primarily belonged to the conserved, minimal cellular stress response, likely reflecting adaptation to the different temperature and irradiance regimes on the reef flat and slope. The prokaryote community differed across both habitat and, to a lesser extent, location, whereas the dinoflagellate photosymbionts differed by habitat but not location. The observed intraspecific diversity associated with divergent habitats supports that environmental adaptation involves multiple members of the coral holobiont. Adaptive alleles or microbial associations present in coral populations from the environmentally variable reef flat may provide a source of adaptive variation for assisted evolution approaches, through assisted gene flow, artificial cross-breeding or probiotic inoculations, with the aim to increase climate resilience in the slope populations.",
    url = "https://doi.org/10.1111/mec.14763",
    doi = "10.1111/mec.14763",
    openalex = "W2807822404",
    references = "doi1010022015gl063488"
}

Tropical reef systems are transitioning to a new era in which the interval between recurrent bouts of coral bleaching is too short for a full recovery of mature assemblages. We analyzed bleaching records at 100 globally distributed reef locations from 1980 to 2016. The median return time between pairs of severe bleaching events has diminished steadily since 1980 and is now only 6 years. As global warming has progressed, tropical sea surface temperatures are warmer now during current La Niña conditions than they were during El Niño events three decades ago. Consequently, as we transition to the Anthropocene, coral bleaching is occurring more frequently in all El Niño-Southern Oscillation phases, increasing the likelihood of annual bleaching in the coming decades.

@article{doi101126scienceaan8048,
    author = "Hughes, Terry P. and Anderson, Kristen D. and Connolly, Sean R. and Heron, Scott F. and Kerry, James T. and Lough, Janice and Baird, Andrew H. and Baum, Julia K. and Berumen, Michael L. and Bridge, Tom C. L. and Claar, Danielle C. and Eakin, C. Mark and Gilmour, James and Graham, Nicholas A. J. and Harrison, Hugo B. and Hobbs, J. and Hoey, Andrew S. and Hoogenboom, Mia O. and Lowe, Ryan and McCulloch, Malcolm T. and Pandolfi, John M. and Pratchett, Morgan S. and Schoepf, Verena and Torda, Gergely and Wilson, Shaun K.",
    title = "Spatial and temporal patterns of mass bleaching of corals in the Anthropocene",
    year = "2018",
    journal = "Science",
    abstract = "Tropical reef systems are transitioning to a new era in which the interval between recurrent bouts of coral bleaching is too short for a full recovery of mature assemblages. We analyzed bleaching records at 100 globally distributed reef locations from 1980 to 2016. The median return time between pairs of severe bleaching events has diminished steadily since 1980 and is now only 6 years. As global warming has progressed, tropical sea surface temperatures are warmer now during current La Niña conditions than they were during El Niño events three decades ago. Consequently, as we transition to the Anthropocene, coral bleaching is occurring more frequently in all El Niño-Southern Oscillation phases, increasing the likelihood of annual bleaching in the coming decades.",
    url = "https://doi.org/10.1126/science.aan8048",
    doi = "10.1126/science.aan8048",
    openalex = "W2782456798",
    references = "doi1010079780387217062, doi101007bf00303779, doi101016jecss200809003, doi1010292002jd002670, doi101038461472a, doi101038nature21707, doi101038nature22901, doi101126science1085046, doi1018637jssv067i01, doi103354meps237133"
}

reaches 2.92 ± 0.16 (expected circa 2050 CE). Notably, some reefs are already experiencing net sediment dissolution.

@article{doi101126scienceaao1118,
    author = "Eyre, Bradley D. and Cyronak, Tyler and Drupp, P. S. and Carlo, Eric H. De and Sachs, Julian P. and Andersson, Andreas J.",
    title = "Coral reefs will transition to net dissolving before end of century",
    year = "2018",
    journal = "Science",
    abstract = "reaches 2.92 ± 0.16 (expected circa 2050 CE). Notably, some reefs are already experiencing net sediment dissolution.",
    url = "https://doi.org/10.1126/science.aao1118",
    doi = "10.1126/science.aao1118",
    openalex = "W2788474355",
    references = "doi101002lno10048, doi1010160198014987900215, doi1010291999gb001195, doi10102993gb02524, doi101038nature21707, doi101038ngeo100, doi101071mf99078, doi101126science1152509, doi101126science1204794, doi101146annurevecolsys291405, doi104319lo19731860897"
}

Worldwide, coral reef ecosystems are experiencing increasing pressure from a variety of anthropogenic perturbations including ocean warming and acidification, increased sedimentation, eutrophication, and overfishing, which could shift reefs to a condition of net calcium carbonate (CaCO3) dissolution and erosion. Herein, we determine the net calcification potential and the relative balance of net organic carbon metabolism (net community production; NCP) and net inorganic carbon metabolism (net community calcification; NCC) within 23 coral reef locations across the globe. In light of these results, we consider the suitability of using these two metrics developed from total alkalinity (TA) and dissolved inorganic carbon (DIC) measurements collected on different spatiotemporal scales to monitor coral reef biogeochemistry under anthropogenic change. All reefs in this study were net calcifying for the majority of observations as inferred from alkalinity depletion relative to offshore, although occasional observations of net dissolution occurred at most locations. However, reefs with lower net calcification potential (i.e., lower TA depletion) could shift towards net dissolution sooner than reefs with a higher potential. The percent influence of organic carbon fluxes on total changes in dissolved inorganic carbon (DIC) (i.e., NCP compared to the sum of NCP and NCC) ranged from 32% to 88% and reflected inherent biogeochemical differences between reefs. Reefs with the largest relative percentage of NCP experienced the largest variability in seawater pH for a given change in DIC, which is directly related to the reefs ability to elevate or suppress local pH relative to the open ocean. This work highlights the value of measuring coral reef carbonate chemistry when evaluating their susceptibility to ongoing global environmental change and offers a baseline from which to guide future conservation efforts aimed at preserving these valuable ecosystems.

@article{doi101371journalpone0190872,
    author = "Cyronak, Tyler and Andersson, Andreas J. and Langdon, Chris and Albright, Rebecca and Bates, Nicholas R. and Caldeira, Ken and Carlton, R. and Corredor, Jorge E. and Dunbar, Robert B. and Enochs, Ian C. and Erez, Jonathan and Eyre, Bradley D. and Gattuso, Jean‐Pierre and Gledhill, D. K. and Kayanne, Hajime and Kline, David I. and Koweek, David A. and Lantz, Coulson A. and Lazar, Boáz and Manzello, Derek P. and McMahon, Ashly and Meléndez, Melissa and Page, Heather N. and Santos, Isaac R. and Schulz, Kai G. and Shaw, Emily C. and Silverman, Jacob and Suzuki, Atsushi and Teneva, Lida and Watanabe, Atsushi and Yamamoto, Shoji",
    title = "Taking the metabolic pulse of the world’s coral reefs",
    year = "2018",
    journal = "PLoS ONE",
    abstract = "Worldwide, coral reef ecosystems are experiencing increasing pressure from a variety of anthropogenic perturbations including ocean warming and acidification, increased sedimentation, eutrophication, and overfishing, which could shift reefs to a condition of net calcium carbonate (CaCO3) dissolution and erosion. Herein, we determine the net calcification potential and the relative balance of net organic carbon metabolism (net community production; NCP) and net inorganic carbon metabolism (net community calcification; NCC) within 23 coral reef locations across the globe. In light of these results, we consider the suitability of using these two metrics developed from total alkalinity (TA) and dissolved inorganic carbon (DIC) measurements collected on different spatiotemporal scales to monitor coral reef biogeochemistry under anthropogenic change. All reefs in this study were net calcifying for the majority of observations as inferred from alkalinity depletion relative to offshore, although occasional observations of net dissolution occurred at most locations. However, reefs with lower net calcification potential (i.e., lower TA depletion) could shift towards net dissolution sooner than reefs with a higher potential. The percent influence of organic carbon fluxes on total changes in dissolved inorganic carbon (DIC) (i.e., NCP compared to the sum of NCP and NCC) ranged from 32\% to 88\% and reflected inherent biogeochemical differences between reefs. Reefs with the largest relative percentage of NCP experienced the largest variability in seawater pH for a given change in DIC, which is directly related to the reefs ability to elevate or suppress local pH relative to the open ocean. This work highlights the value of measuring coral reef carbonate chemistry when evaluating their susceptibility to ongoing global environmental change and offers a baseline from which to guide future conservation efforts aimed at preserving these valuable ecosystems.",
    url = "https://doi.org/10.1371/journal.pone.0190872",
    doi = "10.1371/journal.pone.0190872",
    openalex = "W2783159541",
    references = "doi1010022015gl063488, doi101002lno10048, doi101016001670379400354o, doi101016s0921800999000099, doi101016s0924796302001793, doi1010292004gb002247, doi101038nature02691, doi101126science1059199, doi101126science1085046, doi101126science1085706, doi101126science1152509, doi101126science1204794"
}

Global climate change and localised anthropogenic stressors are driving rapid declines in coral reef health. In vitro experiments have been fundamental in providing insight into how reef organisms will potentially respond to future climates. However, such experiments are inevitably limited in their ability to reproduce the complex interactions that govern reef systems. Studies examining coral communities that already persist under naturally-occurring extreme and marginal physicochemical conditions have therefore become increasingly popular to advance ecosystem scale predictions of future reef form and function, although no single site provides a perfect analogue to future reefs. Here we review the current state of knowledge that exists on the distribution of corals in marginal and extreme environments, and geographic sites at the latitudinal extremes of reef growth, as well as a variety of shallow reef systems and reef-neighbouring environments (including upwelling and CO2 vent sites). We also conduct a synthesis of the abiotic data that have been collected at these systems, to provide the first collective assessment on the range of extreme conditions under which corals currently persist. We use the review and data synthesis to increase our understanding of the biological and ecological mechanisms that facilitate survival and success under sub-optimal physicochemical conditions. This comprehensive assessment can begin to: (i) highlight the extent of extreme abiotic scenarios under which corals can persist, (ii) explore whether there are commonalities in coral taxa able to persist in such extremes, (iii) provide evidence for key mechanisms required to support survival and/or persistence under sub-optimal environmental conditions, and iv) evaluate the potential of current sub-optimal coral environments to act as potential refugia under changing environmental conditions. Such a collective approach is critical to better understand the future survival of corals in our changing environment. We finally outline priority areas for future research on extreme and marginal coral environments, and discuss the additional management options they may provide for corals through refuge or by providing genetic stocks of stress tolerant corals to support proactive management strategies.

@article{doi103389fmars201800004,
    author = "Camp, Emma F. and Schoepf, Verena and Mumby, Peter J. and Hardtke, Leonardo A. and Rodolfo‐Metalpa, Riccardo and Smith, David J. and Suggett, David J.",
    title = "The Future of Coral Reefs Subject to Rapid Climate Change: Lessons from Natural Extreme Environments",
    year = "2018",
    journal = "Frontiers in Marine Science",
    abstract = "Global climate change and localised anthropogenic stressors are driving rapid declines in coral reef health. In vitro experiments have been fundamental in providing insight into how reef organisms will potentially respond to future climates. However, such experiments are inevitably limited in their ability to reproduce the complex interactions that govern reef systems. Studies examining coral communities that already persist under naturally-occurring extreme and marginal physicochemical conditions have therefore become increasingly popular to advance ecosystem scale predictions of future reef form and function, although no single site provides a perfect analogue to future reefs. Here we review the current state of knowledge that exists on the distribution of corals in marginal and extreme environments, and geographic sites at the latitudinal extremes of reef growth, as well as a variety of shallow reef systems and reef-neighbouring environments (including upwelling and CO2 vent sites). We also conduct a synthesis of the abiotic data that have been collected at these systems, to provide the first collective assessment on the range of extreme conditions under which corals currently persist. We use the review and data synthesis to increase our understanding of the biological and ecological mechanisms that facilitate survival and success under sub-optimal physicochemical conditions. This comprehensive assessment can begin to: (i) highlight the extent of extreme abiotic scenarios under which corals can persist, (ii) explore whether there are commonalities in coral taxa able to persist in such extremes, (iii) provide evidence for key mechanisms required to support survival and/or persistence under sub-optimal environmental conditions, and iv) evaluate the potential of current sub-optimal coral environments to act as potential refugia under changing environmental conditions. Such a collective approach is critical to better understand the future survival of corals in our changing environment. We finally outline priority areas for future research on extreme and marginal coral environments, and discuss the additional management options they may provide for corals through refuge or by providing genetic stocks of stress tolerant corals to support proactive management strategies.",
    url = "https://doi.org/10.3389/fmars.2018.00004",
    doi = "10.3389/fmars.2018.00004",
    openalex = "W2787517606",
    references = "doi101002lno10048, doi101016jmarpolbul200411028, doi101038nature21707, doi101038s4158601803839, doi101046j14610248200100203x, doi101086282070, doi101111gcb12179, doi101126science1097329, doi101126science1155676, doi101126scienceaac4722, doi101146annurevmarine041911111611"
}

There is a growing recognition for the need to understand how seawater carbonate chemistry over coral reef environments will change in a high-CO2 world to better assess the impacts of ocean acidification on these valuable ecosystems. Coral reefs modify overlying water column chemistry through biogeochemical processes reflected in thesuch as net community organic carbon production (NCP) and calcification (NCC). However, the relative importance and influence of these processes on seawater carbonate chemistry vary across multiple functional scales (defined here as space, time, and benthic community composition), and have not been fully constrained. Here, we use Bermuda as a case study to assess 1) spatiotemporal variability in physical and chemical parameters along a depth gradient at a rim reef location, 2) the spatial variability of total alkalinity (TA) and dissolved inorganic carbon (DIC) over distinct benthic habitats to infer NCC:NCP ratios (< several km2; rim reef vs seagrass and calcium carbonate (CaCO3) sediments) on diel timescales, and 3) compare how TA-DIC relationships and NCC:NCP vary as we expand functional scales from local habitats to the entire reef platform (10’s of km2) on seasonal to interannual timescales. Our results demonstrate that TA-DIC relationships were strongly driven by local benthic metabolism and community composition over diel cycles. However, as the spatial scale expanded to the reef platform, the TA-DIC relationship reflected processes that were integrated over larger spatiotemporal scales, with effects of NCC becoming increasingly more important over NCP. This study demonstrates the importance of considering drivers across multiple functional scales to constrain carbonate chemistry variability over coral reefs.

@article{doi103389fmars201800175,
    author = "Takeshita, Yuichiro and Cyronak, Tyler and Martz, Todd R. and Kindeberg, Theodor and Andersson, Andreas J.",
    title = "Coral Reef Carbonate Chemistry Variability at Different Functional Scales",
    year = "2018",
    journal = "Frontiers in Marine Science",
    abstract = "There is a growing recognition for the need to understand how seawater carbonate chemistry over coral reef environments will change in a high-CO2 world to better assess the impacts of ocean acidification on these valuable ecosystems. Coral reefs modify overlying water column chemistry through biogeochemical processes reflected in thesuch as net community organic carbon production (NCP) and calcification (NCC). However, the relative importance and influence of these processes on seawater carbonate chemistry vary across multiple functional scales (defined here as space, time, and benthic community composition), and have not been fully constrained. Here, we use Bermuda as a case study to assess 1) spatiotemporal variability in physical and chemical parameters along a depth gradient at a rim reef location, 2) the spatial variability of total alkalinity (TA) and dissolved inorganic carbon (DIC) over distinct benthic habitats to infer NCC:NCP ratios (< several km2; rim reef vs seagrass and calcium carbonate (CaCO3) sediments) on diel timescales, and 3) compare how TA-DIC relationships and NCC:NCP vary as we expand functional scales from local habitats to the entire reef platform (10’s of km2) on seasonal to interannual timescales. Our results demonstrate that TA-DIC relationships were strongly driven by local benthic metabolism and community composition over diel cycles. However, as the spatial scale expanded to the reef platform, the TA-DIC relationship reflected processes that were integrated over larger spatiotemporal scales, with effects of NCC becoming increasingly more important over NCP. This study demonstrates the importance of considering drivers across multiple functional scales to constrain carbonate chemistry variability over coral reefs.",
    url = "https://doi.org/10.3389/fmars.2018.00175",
    doi = "10.3389/fmars.2018.00175",
    openalex = "W2802113425",
    references = "doi1010022015gl063488, doi101371journalpone0190872"
}

Abstract Internal waves can influence water properties in coastal ecosystems through the shoreward transport and mixing of subthermocline water into the nearshore region. In June 2014, a field experiment was conducted at Dongsha Atoll in the northern South China Sea to study the impact of internal waves on a coral reef. Instrumentation included a distributed temperature sensing system, which resolved spatially and temporally continuous temperature measurements over a 4‐km cross‐reef section from the lagoon to 50‐m depth on the fore reef. Our observations show that during summer, internal waves shoaling on the shallow atoll regularly transport cold, nutrient‐rich water shoreward, altering near‐surface water properties on the fore reef. This water is transported shoreward of the reef crest by tides, breaking surface waves and wind‐driven flow, where it significantly alters the water temperature and nutrient concentrations on the reef flat. We find that without internal wave forcing on the fore reef, temperatures on the reef flat could be up to 2.0°C ± 0.2°C warmer. Additionally, we estimate a change in degree heating weeks of 0.7°C‐weeks warmer without internal waves, which significantly increases the probability of a more severe bleaching event occurring at Dongsha Atoll. Furthermore, using nutrient samples collected on the fore reef during the study, we estimated that instantaneous onshore nitrate flux is about four‐fold higher with internal waves than without internal waves. This work highlights the importance of internal waves as a physical mechanism shaping the nearshore environment, and likely supporting resilience of the reef.

@article{doi101002lno11162,
    author = "Reid, Emma and DeCarlo, Thomas M. and Cohen, Anne L. and Wong, George T.F. and Lentz, Steven J. and Safaie, Aryan and Hall, Austin and Davis, Kristen A.",
    title = "Internal waves influence the thermal and nutrient environment on a shallow coral reef",
    year = "2019",
    journal = "Limnology and Oceanography",
    abstract = "Abstract Internal waves can influence water properties in coastal ecosystems through the shoreward transport and mixing of subthermocline water into the nearshore region. In June 2014, a field experiment was conducted at Dongsha Atoll in the northern South China Sea to study the impact of internal waves on a coral reef. Instrumentation included a distributed temperature sensing system, which resolved spatially and temporally continuous temperature measurements over a 4‐km cross‐reef section from the lagoon to 50‐m depth on the fore reef. Our observations show that during summer, internal waves shoaling on the shallow atoll regularly transport cold, nutrient‐rich water shoreward, altering near‐surface water properties on the fore reef. This water is transported shoreward of the reef crest by tides, breaking surface waves and wind‐driven flow, where it significantly alters the water temperature and nutrient concentrations on the reef flat. We find that without internal wave forcing on the fore reef, temperatures on the reef flat could be up to 2.0°C ± 0.2°C warmer. Additionally, we estimate a change in degree heating weeks of 0.7°C‐weeks warmer without internal waves, which significantly increases the probability of a more severe bleaching event occurring at Dongsha Atoll. Furthermore, using nutrient samples collected on the fore reef during the study, we estimated that instantaneous onshore nitrate flux is about four‐fold higher with internal waves than without internal waves. This work highlights the importance of internal waves as a physical mechanism shaping the nearshore environment, and likely supporting resilience of the reef.",
    url = "https://doi.org/10.1002/lno.11162",
    doi = "10.1002/lno.11162",
    openalex = "W2922870589",
    references = "doi1010022016jc012326"
}

Abstract Coral reefs are facing intensifying stressors, largely due to global increases in seawater temperature and decreases in pH. However, there is extensive environmental variability within coral reef ecosystems, which can impact how organisms respond to global trends. We deployed spatial arrays of autonomous sensors across distinct shallow coral reef habitats to determine patterns of spatiotemporal variability in seawater physicochemical parameters. Temperature and pH were positively correlated over the course of a day due to solar heating and light‐driven metabolism. The mean temporal and spatial ranges of temperature and pH were positively correlated across all sites, with different regimes of variability observed in different reef types. Ultimately, depth was a reliable predictor of the average diel ranges in both seawater temperature and pH. These results demonstrate that there is widespread environmental variability on diel timescales within coral reefs related to water column depth, which needs to be included in assessments of how global change will locally affect reef ecosystems.

@article{doi101002lol210129,
    author = "Cyronak, Tyler and Takeshita, Yuichiro and Courtney, Travis A. and DeCarlo, Eric H. and Eyre, Bradley D. and Kline, David I. and Martz, Todd R. and Page, Heather N. and Price, Nichole N. and Smith, Jennifer E. and Stoltenberg, Laura and Tresguerres, Martín and Andersson, Andreas J.",
    title = "Diel temperature and pH variability scale with depth across diverse coral reef habitats",
    year = "2019",
    journal = "Limnology and Oceanography Letters",
    abstract = "Abstract Coral reefs are facing intensifying stressors, largely due to global increases in seawater temperature and decreases in pH. However, there is extensive environmental variability within coral reef ecosystems, which can impact how organisms respond to global trends. We deployed spatial arrays of autonomous sensors across distinct shallow coral reef habitats to determine patterns of spatiotemporal variability in seawater physicochemical parameters. Temperature and pH were positively correlated over the course of a day due to solar heating and light‐driven metabolism. The mean temporal and spatial ranges of temperature and pH were positively correlated across all sites, with different regimes of variability observed in different reef types. Ultimately, depth was a reliable predictor of the average diel ranges in both seawater temperature and pH. These results demonstrate that there is widespread environmental variability on diel timescales within coral reefs related to water column depth, which needs to be included in assessments of how global change will locally affect reef ecosystems.",
    url = "https://doi.org/10.1002/lol2.10129",
    doi = "10.1002/lol2.10129",
    openalex = "W2995843607",
    references = "doi1010022016jc012326, doi101371journalpone0190872"
}

@article{doi101016jecoleng201901002,
    author = "Tortolero‐Langarica, J. J. Adolfo and Rodríguez‐Troncoso, Alma Paola and Cupul‐Magaña, Amilcar Leví and Alarcón-Ortega, Lucy Coral and Santiago-Valentín, Jeimy Denisse",
    title = "Accelerated recovery of calcium carbonate production in coral reefs using low-tech ecological restoration",
    year = "2019",
    journal = "Ecological Engineering",
    url = "https://doi.org/10.1016/j.ecoleng.2019.01.002",
    doi = "10.1016/j.ecoleng.2019.01.002",
    openalex = "W2908714274",
    references = "doi101016jecss200809003, doi101016jpocean200603009, doi101071mf99078, doi101098rspb20090339, doi101126science1152509, doi101126science1204794, doi101126science2845411118, doi101126scienceaan8048, doi101371journalpone0000711, doi103354meps007207"
}

@article{doi101016jecolind2019105857,
    author = "Lange, Ines D. and Perry, Chris T. and Álvarez‐Filip, Lorenzo",
    title = "Carbonate budgets as indicators of functional reef “health”: A critical review of data underpinning census-based methods and current knowledge gaps",
    year = "2019",
    journal = "Ecological Indicators",
    url = "https://doi.org/10.1016/j.ecolind.2019.105857",
    doi = "10.1016/j.ecolind.2019.105857",
    openalex = "W2981500367",
    references = "doi101126scienceaao1118"
}

Thermal-stress events associated with climate change cause coral bleaching and mortality that threatens coral reefs globally. Yet coral bleaching patterns vary spatially and temporally. Here we synthesize field observations of coral bleaching at 3351 sites in 81 countries from 1998 to 2017 and use a suite of environmental covariates and temperature metrics to analyze bleaching patterns. Coral bleaching was most common in localities experiencing high intensity and high frequency thermal-stress anomalies. However, coral bleaching was significantly less common in localities with a high variance in sea-surface temperature (SST) anomalies. Geographically, the highest probability of coral bleaching occurred at tropical mid-latitude sites (15-20 degrees north and south of the Equator), despite similar thermal stress levels at equatorial sites. In the last decade, the onset of coral bleaching has occurred at significantly higher SSTs (∼0.5 °C) than in the previous decade, suggesting that thermally susceptible genotypes may have declined and/or adapted such that the remaining coral populations now have a higher thermal threshold for bleaching.

@article{doi101038s41467019092382,
    author = "Sully, Shannon and Burkepile, Deron E. and Donovan, Mary K. and Hodgson, Gregor and van Woesik, Robert",
    title = "A global analysis of coral bleaching over the past two decades",
    year = "2019",
    journal = "Nature Communications",
    abstract = "Thermal-stress events associated with climate change cause coral bleaching and mortality that threatens coral reefs globally. Yet coral bleaching patterns vary spatially and temporally. Here we synthesize field observations of coral bleaching at 3351 sites in 81 countries from 1998 to 2017 and use a suite of environmental covariates and temperature metrics to analyze bleaching patterns. Coral bleaching was most common in localities experiencing high intensity and high frequency thermal-stress anomalies. However, coral bleaching was significantly less common in localities with a high variance in sea-surface temperature (SST) anomalies. Geographically, the highest probability of coral bleaching occurred at tropical mid-latitude sites (15-20 degrees north and south of the Equator), despite similar thermal stress levels at equatorial sites. In the last decade, the onset of coral bleaching has occurred at significantly higher SSTs (∼0.5 °C) than in the previous decade, suggesting that thermally susceptible genotypes may have declined and/or adapted such that the remaining coral populations now have a higher thermal threshold for bleaching.",
    url = "https://doi.org/10.1038/s41467-019-09238-2",
    doi = "10.1038/s41467-019-09238-2",
    openalex = "W2924041486",
    references = "doi101126science1204794, doi101126scienceaan8048"
}

‘Multiple drivers’ (also termed ‘multiple stressors’) is the term used to describe the cumulative effects of multiple environmental factors on organisms or ecosystems. Here, we consider ocean acidification as a multiple driver because many inorganic carbon parameters are changing simultaneously, including total dissolved inorganic carbon, CO2, HCO3–, CO32–, H+ and CaCO3 saturation state. With the rapid expansion of ocean acidification research has come a greater understanding of the complexity and intricacies of how these simultaneous changes to the seawater carbonate system are affecting marine life. We start by clarifying key terms used by chemists and biologists to describe the changing seawater inorganic carbon system. Then, using key groups of non-calcifying (fish, seaweeds, diatoms) and calcifying (coralline algae, coccolithophores, corals, molluscs) organisms, we consider how various physiological processes are affected by different components of the carbonate system.

@article{doi101071mf19267,
    author = "Hurd, Catriona L. and Beardall, John and Comeau, Steeve and Cornwall, Christopher E. and Havenhand, Jonathan N. and Munday, Philip L. and Parker, Laura M. and Raven, John A. and McGraw, Christina M.",
    title = "Ocean acidification as a multiple driver: how interactions between changing seawater carbonate parameters affect marine life",
    year = "2019",
    journal = "Marine and Freshwater Research",
    abstract = "‘Multiple drivers’ (also termed ‘multiple stressors’) is the term used to describe the cumulative effects of multiple environmental factors on organisms or ecosystems. Here, we consider ocean acidification as a multiple driver because many inorganic carbon parameters are changing simultaneously, including total dissolved inorganic carbon, CO2, HCO3–, CO32–, H+ and CaCO3 saturation state. With the rapid expansion of ocean acidification research has come a greater understanding of the complexity and intricacies of how these simultaneous changes to the seawater carbonate system are affecting marine life. We start by clarifying key terms used by chemists and biologists to describe the changing seawater inorganic carbon system. Then, using key groups of non-calcifying (fish, seaweeds, diatoms) and calcifying (coralline algae, coccolithophores, corals, molluscs) organisms, we consider how various physiological processes are affected by different components of the carbonate system.",
    url = "https://doi.org/10.1071/mf19267",
    doi = "10.1071/mf19267",
    openalex = "W2991558845",
    references = "doi101093icesjmsfsv075"
}

Abstract Coral reefs underpin a range of ecosystem goods and services that contribute to the well‐being of millions of people. However, tropical coral reefs in the Anthropocene are likely to be functionally different from reefs in the past. In this perspective piece, we ask, what does the Anthropocene mean for the provision of ecosystem services from coral reefs? First, we provide examples of the provisioning, regulating, cultural and supporting services underpinned by coral reef ecosystems. We conclude that coral reef ecosystem service research has lagged behind multidisciplinary advances in broader ecosystem services science, such as an explicit recognition that interactions between social and ecological systems underpin ecosystem services. Second, drawing on tools from functional ecology, we outline how these social–ecological relationships can be incorporated into a mechanistic understanding of service provision and how this might be used to anticipate future changes in coral reef ecosystem services. Finally, we explore the emergence of novel reef ecosystem services, for example from tropicalized coastlines, or through changing technological connections to coral reefs. Indeed, when services are conceived as coming from social–ecological system dynamics, novelty in services can emerge from elements of the interactions between people and the ecosystem. This synthesis of the coral reef ecosystem services literature suggests the field is poorly prepared to understand the changing service provision anticipated in the Anthropocene. A new research agenda is needed that better connects reef functional ecology to ecosystem service provision. This research agenda should embrace more holistic approaches to ecosystem service research, recognizing them as co‐produced by ecosystems and society. Importantly, the likelihood of novel ecosystem service configurations requires further conceptualization and empirical assessment. As with current ecosystem services, the loss or gain of services will not affect all people equally and must be understood in the context in which they occur. With the uncertainty surrounding the future of coral reefs in the Anthropocene, research exploring how the benefits to people change will be of great importance. A plain language summary is available for this article.

@article{doi1011111365243513331,
    author = "Woodhead, Anna J. and Hicks, Christina C. and Norström, Albert V. and Williams, Gareth J. and Graham, Nicholas A. J.",
    title = "Coral reef ecosystem services in the Anthropocene",
    year = "2019",
    journal = "Functional Ecology",
    abstract = "Abstract Coral reefs underpin a range of ecosystem goods and services that contribute to the well‐being of millions of people. However, tropical coral reefs in the Anthropocene are likely to be functionally different from reefs in the past. In this perspective piece, we ask, what does the Anthropocene mean for the provision of ecosystem services from coral reefs? First, we provide examples of the provisioning, regulating, cultural and supporting services underpinned by coral reef ecosystems. We conclude that coral reef ecosystem service research has lagged behind multidisciplinary advances in broader ecosystem services science, such as an explicit recognition that interactions between social and ecological systems underpin ecosystem services. Second, drawing on tools from functional ecology, we outline how these social–ecological relationships can be incorporated into a mechanistic understanding of service provision and how this might be used to anticipate future changes in coral reef ecosystem services. Finally, we explore the emergence of novel reef ecosystem services, for example from tropicalized coastlines, or through changing technological connections to coral reefs. Indeed, when services are conceived as coming from social–ecological system dynamics, novelty in services can emerge from elements of the interactions between people and the ecosystem. This synthesis of the coral reef ecosystem services literature suggests the field is poorly prepared to understand the changing service provision anticipated in the Anthropocene. A new research agenda is needed that better connects reef functional ecology to ecosystem service provision. This research agenda should embrace more holistic approaches to ecosystem service research, recognizing them as co‐produced by ecosystems and society. Importantly, the likelihood of novel ecosystem service configurations requires further conceptualization and empirical assessment. As with current ecosystem services, the loss or gain of services will not affect all people equally and must be understood in the context in which they occur. With the uncertainty surrounding the future of coral reefs in the Anthropocene, research exploring how the benefits to people change will be of great importance. A plain language summary is available for this article.",
    url = "https://doi.org/10.1111/1365-2435.13331",
    doi = "10.1111/1365-2435.13331",
    openalex = "W2925018832"
}

Continued declines in coral reef health over the past three decades have been punctuated by severe mass coral bleaching-induced mortality events that have grown in intensity and frequency under climate change. Intensive global research efforts have therefore persistently focused on bleaching phenomena to understand where corals bleach, when and why-resulting in a large-yet still somewhat patchy-knowledge base. Particularly catastrophic bleaching-induced coral mortality events in the past 5 years have catalyzed calls for a more diverse set of reef management tools, extending far beyond climate mitigation and reef protection, to also include more aggressive interventions. However, the effectiveness of these various tools now rests on rapidly assimilating our knowledge base of coral bleaching into more integrated frameworks. Here, we consider how the past three decades of intensive coral bleaching research has established the basis for complex biological and environmental networks, which together regulate outcomes of bleaching severity. We discuss how we now have enough scaffold for conceptual biological and environmental frameworks underpinning bleaching susceptibility, but that new tools are urgently required to translate this to an operational system informing-and testing-bleaching outcomes. Specifically, adopting network models that can fully describe and predict metabolic functioning of coral holobionts, and how this functioning is regulated by complex doses and interactions among environmental factors. Identifying knowledge gaps limiting operation of such models is the logical step to immediately guide and prioritize future experiments and observations. We are at a time-critical point where we can implement new capacity to resolve how coral bleaching patterns emerge from complex biological-environmental networks, and so more effectively inform rapidly evolving ecological management and social adaptation frameworks aimed at securing the future of coral reefs.

@article{doi101111gcb14871,
    author = "Suggett, David J. and Smith, David J.",
    title = "Coral bleaching patterns are the outcome of complex biological and environmental networking",
    year = "2019",
    journal = "Global Change Biology",
    abstract = "Continued declines in coral reef health over the past three decades have been punctuated by severe mass coral bleaching-induced mortality events that have grown in intensity and frequency under climate change. Intensive global research efforts have therefore persistently focused on bleaching phenomena to understand where corals bleach, when and why-resulting in a large-yet still somewhat patchy-knowledge base. Particularly catastrophic bleaching-induced coral mortality events in the past 5 years have catalyzed calls for a more diverse set of reef management tools, extending far beyond climate mitigation and reef protection, to also include more aggressive interventions. However, the effectiveness of these various tools now rests on rapidly assimilating our knowledge base of coral bleaching into more integrated frameworks. Here, we consider how the past three decades of intensive coral bleaching research has established the basis for complex biological and environmental networks, which together regulate outcomes of bleaching severity. We discuss how we now have enough scaffold for conceptual biological and environmental frameworks underpinning bleaching susceptibility, but that new tools are urgently required to translate this to an operational system informing-and testing-bleaching outcomes. Specifically, adopting network models that can fully describe and predict metabolic functioning of coral holobionts, and how this functioning is regulated by complex doses and interactions among environmental factors. Identifying knowledge gaps limiting operation of such models is the logical step to immediately guide and prioritize future experiments and observations. We are at a time-critical point where we can implement new capacity to resolve how coral bleaching patterns emerge from complex biological-environmental networks, and so more effectively inform rapidly evolving ecological management and social adaptation frameworks aimed at securing the future of coral reefs.",
    url = "https://doi.org/10.1111/gcb.14871",
    doi = "10.1111/gcb.14871",
    openalex = "W2980750327",
    references = "doi101038s41467019109695, doi103389fmars201800004"
}

The CO 2 concentration of air has increased over the last two centuries and recently surpassed 400 ppm. Carbon cycle models project CO 2 concentrations of 720 to 1000 ppm for the IPCC intermediate scenario (RCP 6.0), resulting in an increase in global mean temperature of ~2.6 C and a decrease in seawater pH of ~0.3. Together, global warming and ocean acidification are often referred to as the "evil twins" of climate change, potentially inducing severe threats in the near future. In this paper, our discussion is focused on the response of two major calcifiers, foraminifera and corals, which contribute much to the global carbonate burial rate. Photosymbiosis is regarded as an adaptive ecology for living in warm and oligotrophic oceans, especially for reef-building corals and larger reefdwelling benthic foraminifera. As a consequence of global warming, bleaching may be a global threat to algal symbiont-bearing marine calcifying organisms under conditions of high temperature and light intensity. If CO 2 is dissolved in seawater, the partial pressure of CO 2 in seawater (pCO 2) and dissolved inorganic carbon (DIC) increases while pH and the saturation state of carbonate minerals decreases without any change in total alkalinity. Generally, marine calcifying organisms show decreases in calcification rates in response to acidified seawater. However, the response often differs depending on situations, species, and life-cycle stage. Some benthic foraminifera showed a positive response to low pH conditions. The Acropora digitifera coral calcification of adult branches was not reduced markedly at higher pCO 2 conditions, although calcification tended to decrease versus pCO 2 in both aposymbiotic and symbiotic polyps. New analytical technologies help identify important constraints on calcification processes. Based upon Ca isotopes, the transport path of Ca 2+ and the degree of its activity would predominantly control the carbonate precipitation rate. Visualization of the extracellular pH distribution shows that proton pumping produces the high internal pH and large internal-external pH gap in association with foraminiferal calcification. From the perspective of a long-term change in the Earth's surface environment, foraminifera seem to be more adaptive and robust than corals in coping with ocean warming and acidification but it is necessary to further understand the mechanisms underlying variations in sensitivity to heat stress and acidified seawater for future prediction. Since CO 2 is more soluble in lower temperature seawater, ocean acidification is more critical in the polar and high-latitude

@article{doi101186s4064501802399,
    author = "Kawahata, Hodaka and Fujita, Kazuhiko and Iguchi, Akira and Inoue, Mayuri and Iwasaki, Shinya and Kuroyanagi, Azumi and Maeda, Ayumi and Manaka, Takuya and Moriya, Kazuyoshi and Takagi, Haruka and Toyofuku, Takashi and Yoshimura, Toshihiro and Suzuki, Atsushi",
    title = "Perspective on the response of marine calcifiers to global warming and ocean acidification—Behavior of corals and foraminifera in a high CO2 world “hot house”",
    year = "2019",
    journal = "Progress in Earth and Planetary Science",
    abstract = {The CO 2 concentration of air has increased over the last two centuries and recently surpassed 400 ppm. Carbon cycle models project CO 2 concentrations of 720 to 1000 ppm for the IPCC intermediate scenario (RCP 6.0), resulting in an increase in global mean temperature of \textasciitilde 2.6 C and a decrease in seawater pH of \textasciitilde 0.3. Together, global warming and ocean acidification are often referred to as the "evil twins" of climate change, potentially inducing severe threats in the near future. In this paper, our discussion is focused on the response of two major calcifiers, foraminifera and corals, which contribute much to the global carbonate burial rate. Photosymbiosis is regarded as an adaptive ecology for living in warm and oligotrophic oceans, especially for reef-building corals and larger reefdwelling benthic foraminifera. As a consequence of global warming, bleaching may be a global threat to algal symbiont-bearing marine calcifying organisms under conditions of high temperature and light intensity. If CO 2 is dissolved in seawater, the partial pressure of CO 2 in seawater (pCO 2) and dissolved inorganic carbon (DIC) increases while pH and the saturation state of carbonate minerals decreases without any change in total alkalinity. Generally, marine calcifying organisms show decreases in calcification rates in response to acidified seawater. However, the response often differs depending on situations, species, and life-cycle stage. Some benthic foraminifera showed a positive response to low pH conditions. The Acropora digitifera coral calcification of adult branches was not reduced markedly at higher pCO 2 conditions, although calcification tended to decrease versus pCO 2 in both aposymbiotic and symbiotic polyps. New analytical technologies help identify important constraints on calcification processes. Based upon Ca isotopes, the transport path of Ca 2+ and the degree of its activity would predominantly control the carbonate precipitation rate. Visualization of the extracellular pH distribution shows that proton pumping produces the high internal pH and large internal-external pH gap in association with foraminiferal calcification. From the perspective of a long-term change in the Earth's surface environment, foraminifera seem to be more adaptive and robust than corals in coping with ocean warming and acidification but it is necessary to further understand the mechanisms underlying variations in sensitivity to heat stress and acidified seawater for future prediction. Since CO 2 is more soluble in lower temperature seawater, ocean acidification is more critical in the polar and high-latitude},
    url = "https://doi.org/10.1186/s40645-018-0239-9",
    doi = "10.1186/s40645-018-0239-9",
    openalex = "W2911999993",
    references = "doi101371journalpone0190872, doi101666110271"
}

Abstract Globally, many coral reefs have fallen into negative carbonate budget states, where biological erosion exceeds carbonate production. The compounding effects of urbanization and climate change have caused reductions in coral cover and shifts in community composition that may limit the ability of reefs to maintain rates of vertical accretion in line with rising sea levels. Here we report on coral reef carbonate budget surveys across seven coral reefs in Singapore, which persist under chronic turbidity and in highly disturbed environmental conditions, with less than 20% light penetration to 2 m depth. Results show that mean net carbonate budgets across Singapore’s reefs were relatively low, at 0.63 ± 0.27 kg CaCO 3 m −2 yr −1 (mean ± 1 SE) with a range from − 1.56 to 1.97, compared with the mean carbonate budgets across the Indo-Pacific of 1.4 ± 0.15 kg CaCO 3 m −2 yr −1, and isolated Indian Ocean reefs pre-2016 bleaching (~ 3.7 kg CaCO 3 m −2 yr −1). Of the seven reefs surveyed, only one reef had a net negative, or erosional budget, due to near total loss of coral cover (< 5% remaining coral). Mean gross carbonate production on Singapore’s reefs was dominated by stress-tolerant and generalist species, with low-profile morphologies, and was ~ 3 kg m −2 yr −1 lower than on reefs with equivalent coral cover elsewhere in the Indo-Pacific. While overall these reefs are maintaining and adding carbonate structure, their mean vertical accretion potential is below both current rates of sea level rise (1993–2010), and future predictions under RCP 4.5 and RCP 8.5 scenarios. This is likely to result in an increase of 0.2–0.6 m of water above Singapore’s reefs in the next 80 yr, further narrowing the depth range over which these reefs can persist.

@article{doi101007s00338020019533,
    author = "Januchowski‐Hartley, Fraser A. and Bauman, Andrew G. and Morgan, Kyle M. and Seah, Jovena C. L. and Huang, Danwei and Todd, Peter A.",
    title = "Accreting coral reefs in a highly urbanized environment",
    year = "2020",
    journal = "Coral Reefs",
    abstract = "Abstract Globally, many coral reefs have fallen into negative carbonate budget states, where biological erosion exceeds carbonate production. The compounding effects of urbanization and climate change have caused reductions in coral cover and shifts in community composition that may limit the ability of reefs to maintain rates of vertical accretion in line with rising sea levels. Here we report on coral reef carbonate budget surveys across seven coral reefs in Singapore, which persist under chronic turbidity and in highly disturbed environmental conditions, with less than 20\% light penetration to 2 m depth. Results show that mean net carbonate budgets across Singapore’s reefs were relatively low, at 0.63 ± 0.27 kg CaCO 3 m −2 yr −1 (mean ± 1 SE) with a range from − 1.56 to 1.97, compared with the mean carbonate budgets across the Indo-Pacific of 1.4 ± 0.15 kg CaCO 3 m −2 yr −1, and isolated Indian Ocean reefs pre-2016 bleaching (\textasciitilde\ 3.7 kg CaCO 3 m −2 yr −1). Of the seven reefs surveyed, only one reef had a net negative, or erosional budget, due to near total loss of coral cover (< 5\% remaining coral). Mean gross carbonate production on Singapore’s reefs was dominated by stress-tolerant and generalist species, with low-profile morphologies, and was \textasciitilde\ 3 kg m −2 yr −1 lower than on reefs with equivalent coral cover elsewhere in the Indo-Pacific. While overall these reefs are maintaining and adding carbonate structure, their mean vertical accretion potential is below both current rates of sea level rise (1993–2010), and future predictions under RCP 4.5 and RCP 8.5 scenarios. This is likely to result in an increase of 0.2–0.6 m of water above Singapore’s reefs in the next 80 yr, further narrowing the depth range over which these reefs can persist.",
    url = "https://doi.org/10.1007/s00338-020-01953-3",
    doi = "10.1007/s00338-020-01953-3",
    openalex = "W3027316033",
    references = "doi101007s00338019018522"
}

@article{doi101007s0033802001966y,
    author = "Burt, John A. and Camp, Emma F. and Enochs, Ian C. and Johansen, Jacob L. and Morgan, Kyle M. and Riegl, Bernhard and Hoey, Andrew S.",
    title = "Insights from extreme coral reefs in a changing world",
    year = "2020",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/s00338-020-01966-y",
    doi = "10.1007/s00338-020-01966-y",
    openalex = "W3035397619",
    references = "doi101038s4155802007379, doi101111oik05946, doi103389fmars201800004"
}

@article{doi101007s003430209253z,
    author = "Zheng, Xinqing and Li, Yuanchao and Liang, Jilin and Lin, Rongcheng and Wang, Daoru",
    title = "Performance of ecological restoration in an impaired coral reef in the Wuzhizhou Island, Sanya, China",
    year = "2020",
    journal = "Journal of Oceanology and Limnology",
    url = "https://doi.org/10.1007/s00343-020-9253-z",
    doi = "10.1007/s00343-020-9253-z",
    openalex = "W3022718742",
    references = "doi1010029781118223246, doi101007bf00301691, doi101016jecoleng201901002, doi101016jmarpolbul200411028, doi101016s0921800999000099, doi101021es0482583, doi101111j14610248201201861x, doi101126science1085706, doi103354meps062185, doi105343bms20111143, openalexw2297370949, tortolerolangarica2019accelerated"
}

Predicting the bleaching responses of corals is crucial in light of frequent heat stress events to manage further losses of biodiversity and ecosystem functioning, especially for reefs impacted by urbanisation. We examined if the coral cover and community at various Singapore sites changed during the 2016 global coral bleaching event. Bleaching prevalence varied widely among sites in June 2016, and was best explained by site and coral species. While some sites were minimally impacted, others registered significant decreases in coral cover and community changes persisting till March 2017, when normal colouration was mostly regained by corals. Bleaching susceptibility was associated with larger corallites in hermaphrodites and smaller corallites in gonochores (probably due to the cost of maintaining dual sexual functions in hermaphrodites), and with increasing proximity between polyps (likely because thermal damage would be less contained among polyps with greater physiological integration). However, bleaching resilience-the capacity to regain baseline pigmentation-was poorly explained by the traits studied. Our findings suggest that the interplay between local conditions and species composition strongly affects bleaching outcomes on urbanised reefs, and underscore the utility of coral traits for predicting bleaching responses to help in formulating appropriate management strategies.

@article{doi101016jmarpolbul2020111111,
    author = "Ng, Chin Soon Lionel and Huang, Danwei and Toh, Kok Ben and Sam, Shu Qin and Kikuzawa, Yuichi Preslie and Toh, Tai Chong and Taira, Daisuke and Chan, Yong Kit Samuel and Hung, Ling Zi Tracy and Sim, Wan Ting and Rashid, Ahmad Rafiuddin and Afiq‐Rosli, Lutfi and Ng, Ngan Kee and Chou, Loke Ming",
    title = "Responses of urban reef corals during the 2016 mass bleaching event",
    year = "2020",
    journal = "Marine Pollution Bulletin",
    abstract = "Predicting the bleaching responses of corals is crucial in light of frequent heat stress events to manage further losses of biodiversity and ecosystem functioning, especially for reefs impacted by urbanisation. We examined if the coral cover and community at various Singapore sites changed during the 2016 global coral bleaching event. Bleaching prevalence varied widely among sites in June 2016, and was best explained by site and coral species. While some sites were minimally impacted, others registered significant decreases in coral cover and community changes persisting till March 2017, when normal colouration was mostly regained by corals. Bleaching susceptibility was associated with larger corallites in hermaphrodites and smaller corallites in gonochores (probably due to the cost of maintaining dual sexual functions in hermaphrodites), and with increasing proximity between polyps (likely because thermal damage would be less contained among polyps with greater physiological integration). However, bleaching resilience-the capacity to regain baseline pigmentation-was poorly explained by the traits studied. Our findings suggest that the interplay between local conditions and species composition strongly affects bleaching outcomes on urbanised reefs, and underscore the utility of coral traits for predicting bleaching responses to help in formulating appropriate management strategies.",
    url = "https://doi.org/10.1016/j.marpolbul.2020.111111",
    doi = "10.1016/j.marpolbul.2020.111111",
    openalex = "W3016106172",
    references = "doi101007s00338019018522"
}

@article{doi101038s4155802007379,
    author = "Hughes, David and Alderdice, Rachel and Cooney, Christopher and Kühl, Michael and Pernice, Mathieu and Voolstra, Christian R. and Suggett, David J.",
    title = "Coral reef survival under accelerating ocean deoxygenation",
    year = "2020",
    journal = "Nature Climate Change",
    url = "https://doi.org/10.1038/s41558-020-0737-9",
    doi = "10.1038/s41558-020-0737-9",
    openalex = "W3014480380",
    references = "doi101016jcellsig201201008, doi101016jgloenvcha201404002, doi101016jmolcel200804009, doi101016s0092867401005074, doi101016s0967065397848259, doi101038nature22901, doi101038nrm3028, doi101126science1153213, doi101126science1156401, doi101126scienceaam7240, doi101130g322301, doi103389fmars201700158, doi103389fmars201800004"
}

Abstract The combined accelerated footprint of climate change and enhanced anthropogenic pressures and the poor outcomes of many traditional management activities raise the needs for active reef restoration tactics (targeting coral mariculture/transplantation), backed by ecological engineering approaches. These approaches include, among others, the use of ecosystem engineer species, which, through modifications in their physical or biological properties, they create new habitats characterized by novel biodiversity (through either autogeny or allogeny engineering acts). Only a small number of studies on coral reef restoration have discussed/mentioned “ecological engineering” or “coral reef engineering”. Examining reef restoration publications (2016–2019; 145 publications) reveals only 39 (26.9%) dealing with ecological engineering aspects, with 10 classes of “applications” (26 publications) and 4 classes of “properties” (n = 13). Ecological engineering “applications” incorporate all aspects of reef restoration, while the ecological engineering “properties” deal with assisted genetics, coral chimerism, aqua-culturing reef-dwelling organisms, and the consideration of life history parameters of maricultured/transplanted key species. Yet, many ecological engineering applications focus on particular coral species, addressing their specific community issues, while only few address the needs of the entire ecosystem/landscape restoration. It is concluded that rather than trying to return ecosystems to historic states, ecological engineering should shift towards creating novel ecosystems not existed before.

@article{doi101093icesjmsfsaa022,
    author = "Rinkevich, Baruch",
    title = "Ecological engineering approaches in coral reef restoration",
    year = "2020",
    journal = "ICES Journal of Marine Science",
    abstract = "Abstract The combined accelerated footprint of climate change and enhanced anthropogenic pressures and the poor outcomes of many traditional management activities raise the needs for active reef restoration tactics (targeting coral mariculture/transplantation), backed by ecological engineering approaches. These approaches include, among others, the use of ecosystem engineer species, which, through modifications in their physical or biological properties, they create new habitats characterized by novel biodiversity (through either autogeny or allogeny engineering acts). Only a small number of studies on coral reef restoration have discussed/mentioned “ecological engineering” or “coral reef engineering”. Examining reef restoration publications (2016–2019; 145 publications) reveals only 39 (26.9\%) dealing with ecological engineering aspects, with 10 classes of “applications” (26 publications) and 4 classes of “properties” (n = 13). Ecological engineering “applications” incorporate all aspects of reef restoration, while the ecological engineering “properties” deal with assisted genetics, coral chimerism, aqua-culturing reef-dwelling organisms, and the consideration of life history parameters of maricultured/transplanted key species. Yet, many ecological engineering applications focus on particular coral species, addressing their specific community issues, while only few address the needs of the entire ecosystem/landscape restoration. It is concluded that rather than trying to return ecosystems to historic states, ecological engineering should shift towards creating novel ecosystems not existed before.",
    url = "https://doi.org/10.1093/icesjms/fsaa022",
    doi = "10.1093/icesjms/fsaa022",
    openalex = "W3009701001",
    references = "doi101007978146124018114, doi101016jecoleng200410003, doi101016jecoleng201901002, doi101038nature21708, doi101073pnas091092998, doi101073pnas1208909109, doi1011111365243513331, doi101111j13652664200901751x, doi101126science1255641, doi1023073545850, doi103354meps07815, tortolerolangarica2019accelerated"
}

BACKGROUND: The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for microalgal endosymbionts and bacteria) is a potential mechanism that may assist corals to thrive in warm waters. The northern Red Sea experiences extreme temperatures anomalies, yet corals in this area rarely bleach suggesting possible refugia to climate change. However, the coral microbiome composition, and how it relates to the capacity to thrive in warm waters in this region, is entirely unknown. RESULTS: We investigated microbiomes for six coral species (Porites nodifera, Favia favus, Pocillopora damicornis, Seriatopora hystrix, Xenia umbellata, and Sarcophyton trocheliophorum) from five sites in the northern Red Sea spanning 4° of latitude and summer mean temperature ranges from 26.6 °C to 29.3 °C. A total of 19 distinct dinoflagellate endosymbionts were identified as belonging to three genera in the family Symbiodiniaceae (Symbiodinium, Cladocopium, and Durusdinium). Of these, 86% belonged to the genus Cladocopium, with notably five novel types (19%). The endosymbiont community showed a high degree of host-specificity despite the latitudinal gradient. In contrast, the diversity and composition of bacterial communities of the surface mucus layer (SML)-a compartment particularly sensitive to environmental change-varied significantly between sites, however for any given coral was species-specific. CONCLUSION: The conserved endosymbiotic community suggests high physiological plasticity to support holobiont productivity across the different latitudinal regimes. Further, the presence of five novel algal endosymbionts suggests selection of certain genotypes (or genetic adaptation) within the semi-isolated Red Sea. In contrast, the dynamic composition of bacteria associated with the SML across sites may contribute to holobiont function and broaden the ecological niche. In doing so, SML bacterial communities may aid holobiont local acclimatization (or adaptation) by readily responding to changes in the host environment. Our study provides novel insight about the selective and endemic nature of coral microbiomes along the northern Red Sea refugia.

@article{doi101186s4016801907765,
    author = "Osman, Eslam O. and Suggett, David J. and Voolstra, Christian R. and Pettay, D. Tye and Clark, Dave R. and Pogoreutz, Claudia and Sampayo, Eugenia M. and Warner, Mark E. and Smith, David J.",
    title = "Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities",
    year = "2020",
    journal = "Microbiome",
    abstract = "BACKGROUND: The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for microalgal endosymbionts and bacteria) is a potential mechanism that may assist corals to thrive in warm waters. The northern Red Sea experiences extreme temperatures anomalies, yet corals in this area rarely bleach suggesting possible refugia to climate change. However, the coral microbiome composition, and how it relates to the capacity to thrive in warm waters in this region, is entirely unknown. RESULTS: We investigated microbiomes for six coral species (Porites nodifera, Favia favus, Pocillopora damicornis, Seriatopora hystrix, Xenia umbellata, and Sarcophyton trocheliophorum) from five sites in the northern Red Sea spanning 4° of latitude and summer mean temperature ranges from 26.6 °C to 29.3 °C. A total of 19 distinct dinoflagellate endosymbionts were identified as belonging to three genera in the family Symbiodiniaceae (Symbiodinium, Cladocopium, and Durusdinium). Of these, 86\% belonged to the genus Cladocopium, with notably five novel types (19\%). The endosymbiont community showed a high degree of host-specificity despite the latitudinal gradient. In contrast, the diversity and composition of bacterial communities of the surface mucus layer (SML)-a compartment particularly sensitive to environmental change-varied significantly between sites, however for any given coral was species-specific. CONCLUSION: The conserved endosymbiotic community suggests high physiological plasticity to support holobiont productivity across the different latitudinal regimes. Further, the presence of five novel algal endosymbionts suggests selection of certain genotypes (or genetic adaptation) within the semi-isolated Red Sea. In contrast, the dynamic composition of bacteria associated with the SML across sites may contribute to holobiont function and broaden the ecological niche. In doing so, SML bacterial communities may aid holobiont local acclimatization (or adaptation) by readily responding to changes in the host environment. Our study provides novel insight about the selective and endemic nature of coral microbiomes along the northern Red Sea refugia.",
    url = "https://doi.org/10.1186/s40168-019-0776-5",
    doi = "10.1186/s40168-019-0776-5",
    openalex = "W3004497505",
    references = "doi103389fmars201800004"
}

Coral reef ecosystems have suffered an unprecedented loss of habitat-forming hard corals in recent decades. While marine conservation has historically focused on passive habitat protection, demand for and interest in active restoration has been growing in recent decades. However, a disconnect between coral restoration practitioners, coral reef managers and scientists has resulted in a disjointed field where it is difficult to gain an overview of existing knowledge. To address this, we aimed to synthesise the available knowledge in a comprehensive global review of coral restoration methods, incorporating data from the peer-reviewed scientific literature, complemented with grey literature and through a survey of coral restoration practitioners. We found that coral restoration case studies are dominated by short-term projects, with 60% of all projects reporting less than 18 months of monitoring of the restored sites. Similarly, most projects are relatively small in spatial scale, with a median size of restored area of 100 m2. A diverse range of species are represented in the dataset, with 229 different species from 72 coral genera. Overall, coral restoration projects focused primarily on fast-growing branching corals (59% of studies), and report survival between 60 and 70%. To date, the relatively young field of coral restoration has been plagued by similar 'growing pains' as ecological restoration in other ecosystems. These include 1) a lack of clear and achievable objectives, 2) a lack of appropriate and standardised monitoring and reporting and, 3) poorly designed projects in relation to stated objectives. Mitigating these will be crucial to successfully scale up projects, and to retain public trust in restoration as a tool for resilience based management. Finally, while it is clear that practitioners have developed effective methods to successfully grow corals at small scales, it is critical not to view restoration as a replacement for meaningful action on climate change.

@article{doi101371journalpone0226631,
    author = "Boström‐Einarsson, Lisa and Babcock, Russell C. and Bayraktarov, Elisa and Ceccarelli, Daniela M. and Cook, Nathan and Ferse, Sebastian C. A. and Hancock, Boze and Harrison, Peter L. and Hein, Margaux Y. and Shaver, Elizabeth C. and Smith, Adam and Suggett, David J. and Stewart‐Sinclair, Phoebe J. and Vardi, Tali and McLeod, Ian",
    title = "Coral restoration – A systematic review of current methods, successes, failures and future directions",
    year = "2020",
    journal = "PLoS ONE",
    abstract = "Coral reef ecosystems have suffered an unprecedented loss of habitat-forming hard corals in recent decades. While marine conservation has historically focused on passive habitat protection, demand for and interest in active restoration has been growing in recent decades. However, a disconnect between coral restoration practitioners, coral reef managers and scientists has resulted in a disjointed field where it is difficult to gain an overview of existing knowledge. To address this, we aimed to synthesise the available knowledge in a comprehensive global review of coral restoration methods, incorporating data from the peer-reviewed scientific literature, complemented with grey literature and through a survey of coral restoration practitioners. We found that coral restoration case studies are dominated by short-term projects, with 60\% of all projects reporting less than 18 months of monitoring of the restored sites. Similarly, most projects are relatively small in spatial scale, with a median size of restored area of 100 m2. A diverse range of species are represented in the dataset, with 229 different species from 72 coral genera. Overall, coral restoration projects focused primarily on fast-growing branching corals (59\% of studies), and report survival between 60 and 70\%. To date, the relatively young field of coral restoration has been plagued by similar 'growing pains' as ecological restoration in other ecosystems. These include 1) a lack of clear and achievable objectives, 2) a lack of appropriate and standardised monitoring and reporting and, 3) poorly designed projects in relation to stated objectives. Mitigating these will be crucial to successfully scale up projects, and to retain public trust in restoration as a tool for resilience based management. Finally, while it is clear that practitioners have developed effective methods to successfully grow corals at small scales, it is critical not to view restoration as a replacement for meaningful action on climate change.",
    url = "https://doi.org/10.1371/journal.pone.0226631",
    doi = "10.1371/journal.pone.0226631",
    openalex = "W3003324864",
    references = "doi101016jecss200809003, doi101126scienceaan8048"
}

The escalating rate at which coral communities are declining globally requires urgent intervention and new approaches to reef management to reduce and halt further coral loss. For reef systems with limited natural larval supply, the introduction of large numbers of competent coral larvae directly to natural reef substrata provides a potentially useful approach to replenish adult coral populations. While few experiments have tested this approach, only one experiment has demonstrated its long-term success to date. Given the differences in life-history traits among corals, and different sensitivities of larvae to abiotic and biotic factors, coupled with the dynamic nature of post-settlement survivorship and recruitment processes, trials of the larval enhancement technique with larvae of different coral species are needed to test the broader applicability and viability of this approach. Accordingly, in this paper we examine the applicability of the larval enhancement technique to restore a population of Acropora loripes in the Bolinao-Anda Reef Complex, Pangasinan, northwestern Philippines. Larvae were cultured ex situ following spawning of collected A. loripes colonies in June 2014. Competent larvae were transported to degraded reef areas and approximately 300,000 larvae were introduced in each of three 6 × 4 m plots directly on the reef. Fine mesh enclosures retained the larvae inside each treatment plot for five days. Three adjacent 6 × 4 m plots that served as controls were also covered with mesh enclosures, but no larvae were introduced. Each plot contained ten 10 × 10 cm conditioned settlement tiles cut from dead tabulate Acropora that were used to quantify initial larval settlement. After allowing larval settlement for five days, mean settlement on tiles from the larval enhancement plots that were monitored under stereomicroscopes was significantly higher (27.8 ± 6.7 spat per tile) than in control plots, in which not a single recruit was recorded. Post-settlement survivorship and growth of spat and coral recruits on tiles and reef substrata inside the experimental plots were monitored periodically for 35 months. After 35 months, the mean size of each of the remaining 47 A. loripes coral colonies surviving on the reef substrata was 438.1 ± 5.4 cm3, with a mean diameter of 7.9 ± 0.6 cm. The average production cost for each of the surviving A. loripes colonies at 35 months was USD 35.20. These colonies are expected to spawn and contribute to the natural larval pool when they become reproductively mature, thereby enhancing natural coral recovery in the area. This study demonstrates that mass coral larval enhancement can be successfully used for restoring populations of coral species with different life-history traits, and the techniques can rapidly increase larval recruitment rates on degraded reef areas, hence catalysing the regeneration of declining coral populations.

@article{doi101371journalpone0242847,
    author = "dela Cruz, Dexter W. and Harrison, Peter L.",
    title = "Enhancing coral recruitment through assisted mass settlement of cultured coral larvae",
    year = "2020",
    journal = "PLoS ONE",
    abstract = "The escalating rate at which coral communities are declining globally requires urgent intervention and new approaches to reef management to reduce and halt further coral loss. For reef systems with limited natural larval supply, the introduction of large numbers of competent coral larvae directly to natural reef substrata provides a potentially useful approach to replenish adult coral populations. While few experiments have tested this approach, only one experiment has demonstrated its long-term success to date. Given the differences in life-history traits among corals, and different sensitivities of larvae to abiotic and biotic factors, coupled with the dynamic nature of post-settlement survivorship and recruitment processes, trials of the larval enhancement technique with larvae of different coral species are needed to test the broader applicability and viability of this approach. Accordingly, in this paper we examine the applicability of the larval enhancement technique to restore a population of Acropora loripes in the Bolinao-Anda Reef Complex, Pangasinan, northwestern Philippines. Larvae were cultured ex situ following spawning of collected A. loripes colonies in June 2014. Competent larvae were transported to degraded reef areas and approximately 300,000 larvae were introduced in each of three 6 × 4 m plots directly on the reef. Fine mesh enclosures retained the larvae inside each treatment plot for five days. Three adjacent 6 × 4 m plots that served as controls were also covered with mesh enclosures, but no larvae were introduced. Each plot contained ten 10 × 10 cm conditioned settlement tiles cut from dead tabulate Acropora that were used to quantify initial larval settlement. After allowing larval settlement for five days, mean settlement on tiles from the larval enhancement plots that were monitored under stereomicroscopes was significantly higher (27.8 ± 6.7 spat per tile) than in control plots, in which not a single recruit was recorded. Post-settlement survivorship and growth of spat and coral recruits on tiles and reef substrata inside the experimental plots were monitored periodically for 35 months. After 35 months, the mean size of each of the remaining 47 A. loripes coral colonies surviving on the reef substrata was 438.1 ± 5.4 cm3, with a mean diameter of 7.9 ± 0.6 cm. The average production cost for each of the surviving A. loripes colonies at 35 months was USD 35.20. These colonies are expected to spawn and contribute to the natural larval pool when they become reproductively mature, thereby enhancing natural coral recovery in the area. This study demonstrates that mass coral larval enhancement can be successfully used for restoring populations of coral species with different life-history traits, and the techniques can rapidly increase larval recruitment rates on degraded reef areas, hence catalysing the regeneration of declining coral populations.",
    url = "https://doi.org/10.1371/journal.pone.0242847",
    doi = "10.1371/journal.pone.0242847",
    openalex = "W3109303908",
    references = "doi101093icesjmsfsaa022"
}

Competitive interactions between corals and macroalgae play an important role in determining benthic community structure on coral reefs. While it is known that macroalgae may negatively affect corals, the relative influence of contact- versus water-mediated macroalgal interactions on corals—such as via an influence on coral-associated microbiomes—is less well understood. Further, the impacts of macroalgae on corals that have persisted in a heavily urbanized reef system have not been explored previously. We examined the effects of the macroalgae Lobophora sp. and Hypnea pannosa on the physiology and microbiome of three Indo-Pacific coral species (Merulina ampliata, Montipora stellata, and Pocillopora acuta) collected from Singapore’s highly urbanized reefs, and compared how these effects varied between direct contact and water-mediated interactions. Direct contact by Lobophora sp. caused visible tissue bleaching and reduced Fv/Fm in all three coral species, while direct contact by H. pannosa only led to slight, but significant, suppression of coral Fv/Fm. No detrimental effects on coral physiology were observed when corals were in close proximity to the macroalgae or when in direct contact with algal mimics. However, both direct contact and water-mediated interactions with Lobophora sp. and H. pannosa altered the prokaryotic community structures in M. stellata. For M. ampliata and P. acuta, the changes in their microbiomes in response to algal treatments were more strongly influenced by the source reefs from which the coral colonies were collected. In particular, coral colonies collected from Kusu Island had proportionately more initial abundances of potentially pathogenic bacteria in their microbiomes than those collected from Pulau Satumu; nevertheless, coral fragments from Kusu Island had the same physiological responses to macroalgal interactions as corals from Pulau Satumu. Overall, our results reveal that, for the species tested, the coral microbiomes were sensitive to both direct contact and water-mediated interactions with macroalgae, while coral physiology was only compromised when in direct contact. Further, the presence of high levels of potentially pathogenic bacteria in some of the coral samples did not lead to the corals being more susceptible to impacts from macroalgae.

@article{doi103389fmars201900831,
    author = "Fong, Jenny and Deignan, Lindsey K. and Bauman, Andrew G. and Steinberg, Peter D. and McDougald, Diane and Todd, Peter A.",
    title = "Contact- and Water-Mediated Effects of Macroalgae on the Physiology and Microbiome of Three Indo-Pacific Coral Species",
    year = "2020",
    journal = "Frontiers in Marine Science",
    abstract = "Competitive interactions between corals and macroalgae play an important role in determining benthic community structure on coral reefs. While it is known that macroalgae may negatively affect corals, the relative influence of contact- versus water-mediated macroalgal interactions on corals—such as via an influence on coral-associated microbiomes—is less well understood. Further, the impacts of macroalgae on corals that have persisted in a heavily urbanized reef system have not been explored previously. We examined the effects of the macroalgae Lobophora sp. and Hypnea pannosa on the physiology and microbiome of three Indo-Pacific coral species (Merulina ampliata, Montipora stellata, and Pocillopora acuta) collected from Singapore’s highly urbanized reefs, and compared how these effects varied between direct contact and water-mediated interactions. Direct contact by Lobophora sp. caused visible tissue bleaching and reduced Fv/Fm in all three coral species, while direct contact by H. pannosa only led to slight, but significant, suppression of coral Fv/Fm. No detrimental effects on coral physiology were observed when corals were in close proximity to the macroalgae or when in direct contact with algal mimics. However, both direct contact and water-mediated interactions with Lobophora sp. and H. pannosa altered the prokaryotic community structures in M. stellata. For M. ampliata and P. acuta, the changes in their microbiomes in response to algal treatments were more strongly influenced by the source reefs from which the coral colonies were collected. In particular, coral colonies collected from Kusu Island had proportionately more initial abundances of potentially pathogenic bacteria in their microbiomes than those collected from Pulau Satumu; nevertheless, coral fragments from Kusu Island had the same physiological responses to macroalgal interactions as corals from Pulau Satumu. Overall, our results reveal that, for the species tested, the coral microbiomes were sensitive to both direct contact and water-mediated interactions with macroalgae, while coral physiology was only compromised when in direct contact. Further, the presence of high levels of potentially pathogenic bacteria in some of the coral samples did not lead to the corals being more susceptible to impacts from macroalgae.",
    url = "https://doi.org/10.3389/fmars.2019.00831",
    doi = "10.3389/fmars.2019.00831",
    openalex = "W3002839732",
    references = "doi101007s00338019018522"
}

. While comprehensive long-term studies are required, direct transplantation methodologies of coral micro-fragments are emerging as time-effective and affordable restoration tools to mitigate anthropogenic and climate change impacts in remote and marginal reefs.

@article{doi103390ijerph17186574,
    author = "Tortolero‐Langarica, J. J. Adolfo and Rodríguez‐Troncoso, Alma Paola and Cupul‐Magaña, Amilcar Leví and Rinkevich, Baruch",
    title = "Micro-Fragmentation as an Effective and Applied Tool to Restore Remote Reefs in the Eastern Tropical Pacific",
    year = "2020",
    journal = "International Journal of Environmental Research and Public Health",
    abstract = ". While comprehensive long-term studies are required, direct transplantation methodologies of coral micro-fragments are emerging as time-effective and affordable restoration tools to mitigate anthropogenic and climate change impacts in remote and marginal reefs.",
    url = "https://doi.org/10.3390/ijerph17186574",
    doi = "10.3390/ijerph17186574",
    openalex = "W3084327467",
    references = "doi101016jecoleng201901002, doi101016jpocean200603009, doi101038s4158601800412, doi101038s4158601807769, doi101126science1204794, doi101126science1232310, doi101126scienceaaa4216, doi101371journalpone0000711, doi101371journalpone0033353, doi101371journalpone0226631, doi103354meps007207, tortolerolangarica2019accelerated"
}

Maintaining coral reef ecosystems is a social imperative, because so many people depend on coral reefs for food production, shoreline protection, and livelihoods. The survival of reefs this century, however, is threatened by the mounting effects of climate change. Climate mitigation is the foremost and essential action to prevent coral reef ecosystem collapse. Without it, reefs will become extremely diminished within the next 20–30 years. Even with strong climate mitigation, however, existing conservation measures such as marine protected areas and fisheries management are no longer sufficient to sustain the ecosystem and many additional and innovative actions to increase reef resilience must also be taken. In this paper we assess the suite of protections and actions in terms of their potential to be effective according to a set of criteria that include effectiveness, readiness, co-benefits and disbenefits. Even with the best scientific innovation, saving coral reefs will require a well-funded, well-designed, and rapidly executed strategy with political and social commitments at the level of other grand challenges.

@article{doi101016jbiocon2021109107,
    author = "Kleypas, Joan A. and Allemand, Denis and Anthony, Kenneth R. N. and Baker, Andrew C. and Beck, Michael W. and Hale, Lynne Zeitlin and Hilmi, Nathalie and Hoegh‐Guldberg, Ove and Hughes, Terry P. and Kaufman, Les and Kayanne, Hajime and Magnan, Alexandre and Mcleod, Elizabeth and Mumby, Peter J. and Palumbi, Stephen R. and Richmond, Robert H. and Rinkevich, Baruch and Steneck, Robert S. and Voolstra, Christian R. and Wachenfeld, David and Gattuso, Jean‐Pierre",
    title = "Designing a blueprint for coral reef survival",
    year = "2021",
    journal = "Biological Conservation",
    abstract = "Maintaining coral reef ecosystems is a social imperative, because so many people depend on coral reefs for food production, shoreline protection, and livelihoods. The survival of reefs this century, however, is threatened by the mounting effects of climate change. Climate mitigation is the foremost and essential action to prevent coral reef ecosystem collapse. Without it, reefs will become extremely diminished within the next 20–30 years. Even with strong climate mitigation, however, existing conservation measures such as marine protected areas and fisheries management are no longer sufficient to sustain the ecosystem and many additional and innovative actions to increase reef resilience must also be taken. In this paper we assess the suite of protections and actions in terms of their potential to be effective according to a set of criteria that include effectiveness, readiness, co-benefits and disbenefits. Even with the best scientific innovation, saving coral reefs will require a well-funded, well-designed, and rapidly executed strategy with political and social commitments at the level of other grand challenges.",
    url = "https://doi.org/10.1016/j.biocon.2021.109107",
    doi = "10.1016/j.biocon.2021.109107",
    openalex = "W3156335823",
    references = "doi101093icesjmsfsaa022"
}

@article{doi101016jmarenvres2021105322,
    author = "Ng, Chin Soon Lionel and Chan, Yong Kit Samuel and Nguyen, Nhung and Kikuzawa, Yuichi Preslie and Sam, Shu Qin and Toh, Tai Chong and Mock, Aidan Yong Jie and Chou, Loke Ming and Huang, Danwei",
    title = "Coral community composition and carbonate production in an urbanized seascape",
    year = "2021",
    journal = "Marine Environmental Research",
    url = "https://doi.org/10.1016/j.marenvres.2021.105322",
    doi = "10.1016/j.marenvres.2021.105322",
    openalex = "W3151681122",
    references = "doi101007s00338019018522"
}

@article{doi101016jmarpolbul2021112849,
    author = "Fong, Jenny and Todd, Peter A.",
    title = "Spatio-temporal dynamics of coral–macroalgal interactions and their impacts on coral growth on urbanised reefs",
    year = "2021",
    journal = "Marine Pollution Bulletin",
    url = "https://doi.org/10.1016/j.marpolbul.2021.112849",
    doi = "10.1016/j.marpolbul.2021.112849",
    openalex = "W3195311448",
    references = "doi101007s00338019018522"
}

@article{doi101016joneear202108016,
    author = "Eddy, Tyler D. and Lam, Vicky W. Y. and Reygondeau, Gabriel and Cisneros‐Montemayor, Andrés M. and Greer, Krista and Palomares, Maria Lourdes D. and Bruno, John F. and Ota, Yoshitaka and Cheung, William W. L.",
    title = "Global decline in capacity of coral reefs to provide ecosystem services",
    year = "2021",
    journal = "One Earth",
    url = "https://doi.org/10.1016/j.oneear.2021.08.016",
    doi = "10.1016/j.oneear.2021.08.016",
    openalex = "W3199321815",
    references = "doi101038nature18607, doi101126scienceaan8048"
}

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.

@article{doi101038s4146702126543x,
    author = "Dubé, Caroline and Ziegler, Maren and Mercière, Alexandre and Boissin, Émilie and Planes, Serge and Bourmaud, Chloé A.-F. and Voolstra, Christian R.",
    title = "Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition",
    year = "2021",
    journal = "Nature Communications",
    abstract = "Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.",
    url = "https://doi.org/10.1038/s41467-021-26543-x",
    doi = "10.1038/s41467-021-26543-x",
    openalex = "W3209179210",
    references = "doi1010022015gl063488"
}

Abstract Long-term coral reef resilience to multiple stressors depends on their ability to maintain positive calcification rates. Estimates of coral ecosystem calcification and organic productivity provide insight into the environmental drivers and temporal changes in reef condition. Here, we analyse global spatiotemporal trends and drivers of coral reef calcification using a meta-analysis of ecosystem-scale case studies. A linear mixed effects regression model was used to test whether ecosystem-scale calcification is related to seasonality, methodology, calcifier cover, year, depth, wave action, latitude, duration of data collection, coral reef state, Ω ar, temperature and organic productivity. Global ecosystem calcification estimated from changes in seawater carbonate chemistry was driven primarily by depth and benthic calcifier cover. Current and future declines in coral cover will significantly affect the global reef carbonate budget, even before considering the effects of sub-lethal stressors on calcification rates. Repeatedly studied reefs exhibited declining calcification of 4.3 ± 1.9% per year (x̄ = 1.8 ± 0.7 mmol m −2 d −1 yr −1), and increasing organic productivity at 3.0 ± 0.8 mmol m −2 d −1 per year since 1970. Therefore, coral reef ecosystems are experiencing a shift in their essential metabolic processes of calcification and photosynthesis, and could become net dissolving worldwide around 2054.

@article{doi101038s4324702100168w,
    author = "Davis, Kay L. and Colefax, Andrew P. and Tucker, James P. and Kelaher, Brendan P. and Santos, Isaac R.",
    title = "Global coral reef ecosystems exhibit declining calcification and increasing primary productivity",
    year = "2021",
    journal = "Communications Earth \& Environment",
    abstract = "Abstract Long-term coral reef resilience to multiple stressors depends on their ability to maintain positive calcification rates. Estimates of coral ecosystem calcification and organic productivity provide insight into the environmental drivers and temporal changes in reef condition. Here, we analyse global spatiotemporal trends and drivers of coral reef calcification using a meta-analysis of ecosystem-scale case studies. A linear mixed effects regression model was used to test whether ecosystem-scale calcification is related to seasonality, methodology, calcifier cover, year, depth, wave action, latitude, duration of data collection, coral reef state, Ω ar, temperature and organic productivity. Global ecosystem calcification estimated from changes in seawater carbonate chemistry was driven primarily by depth and benthic calcifier cover. Current and future declines in coral cover will significantly affect the global reef carbonate budget, even before considering the effects of sub-lethal stressors on calcification rates. Repeatedly studied reefs exhibited declining calcification of 4.3 ± 1.9\% per year (x̄ = 1.8 ± 0.7 mmol m −2 d −1 yr −1), and increasing organic productivity at 3.0 ± 0.8 mmol m −2 d −1 per year since 1970. Therefore, coral reef ecosystems are experiencing a shift in their essential metabolic processes of calcification and photosynthesis, and could become net dissolving worldwide around 2054.",
    url = "https://doi.org/10.1038/s43247-021-00168-w",
    doi = "10.1038/s43247-021-00168-w",
    openalex = "W3168530769",
    references = "doi1010022016jc012326, doi101371journalpone0190872"
}

emissions.

@article{doi101073pnas2015265118,
    author = "Cornwall, Christopher E. and Comeau, Steeve and Kornder, Niklas A. and Perry, Chris T. and van Hooidonk, Ruben and DeCarlo, Thomas M. and Pratchett, Morgan S. and Anderson, Kristen D. and Browne, Nicola K. and Carpenter, R. C. and Díaz-Pulido, Guillermo and D’Olivo, Juan Pablo and Doo, Steve S. and Figueiredo, Joana and Fortunato, Sofia and Kennedy, Emma and Lantz, Coulson A. and McCulloch, Malcolm T. and González‐Rivero, Manuel and Schoepf, Verena and Smithers, S and Lowe, Ryan",
    title = "Global declines in coral reef calcium carbonate production under ocean acidification and warming",
    year = "2021",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "emissions.",
    url = "https://doi.org/10.1073/pnas.2015265118",
    doi = "10.1073/pnas.2015265118",
    openalex = "W3161219580",
    references = "doi101038ncomms2409, doi101126scienceaao1118"
}

Abstract The capacity of coral reefs to provide ecosystem services is widely recognized, but this ability depends on continued carbonate production within the coral community. The Islas Marías archipelago (21° 29.5′ N–106° 15′ W) is subject to minimal anthropic pressures. This archipelago serves as a model to study the influence of environmental variables [e.g., sea surface temperature (SST), upwelling periods, El Niño‐Southern Oscillation (ENSO) events, and pH] on the structure of the coral community. The aim of this study was to evaluate the growth parameters, ecological volume, and CaCO 3 production of Pocillopora corals, which comprise the dominant genus in the Eastern Tropical Pacific (ETP). During an annual period (2016–2017), 10 colonies were stained with alizarin red and height, major diameter, and minor diameter measurements were recorded. Live coral cover, the annual extension rate (cm/year), skeletal density (g/cm 3), the calcification rate (g/cm 2 year −1), ecological volume (cm −3), and carbonate production (kg m −2 year −1) were also calculated. The average extension rate (± SD), skeletal density, and the calcification rate were 1.86 ± 0.31 cm/year, 2.28 ± 0.34 g CaCO 3 cm −3, and 4.34 ± 1.28 g CaCO 3 cm −2 year −1, respectively. The average live coral coverage was 3.19 ± 3.17%, and the relative cover of Pocillopora corals was 65%. Ecological volume increased 140.6 ± 84.28% with respect to the initial volume, and the average production of CaCO 3 was 0.46 ± 0.41 kg CaCO 3 m −2 year −1. This study shows evidence of low growth rates, low generation of three‐dimensionality, and low CaCO 3 production in the study area when compared to other sites in the ETP. These results are relevant because they indicate compromised long‐term maintenance and reef development in Islas Marías, which may result in low reef functionality and compromise the stability of reef‐associated biodiversity and ecosystem services.

@article{doi101111maec12678,
    author = "González‐Pabón, María A. and Tortolero‐Langarica, J. J. Adolfo and Calderón‐Aguilera, Luis E. and Solana‐Arellano, Elena and Rodríguez‐Troncoso, Alma Paola and Cupul‐Magaña, Amilcar Leví and Cabral‐Tena, Rafael A.",
    title = "Low calcification rate, structural complexity, and calcium carbonate production of Pocillopora corals in a biosphere reserve of the central Mexican Pacific",
    year = "2021",
    journal = "Marine Ecology",
    abstract = "Abstract The capacity of coral reefs to provide ecosystem services is widely recognized, but this ability depends on continued carbonate production within the coral community. The Islas Marías archipelago (21° 29.5′ N–106° 15′ W) is subject to minimal anthropic pressures. This archipelago serves as a model to study the influence of environmental variables [e.g., sea surface temperature (SST), upwelling periods, El Niño‐Southern Oscillation (ENSO) events, and pH] on the structure of the coral community. The aim of this study was to evaluate the growth parameters, ecological volume, and CaCO 3 production of Pocillopora corals, which comprise the dominant genus in the Eastern Tropical Pacific (ETP). During an annual period (2016–2017), 10 colonies were stained with alizarin red and height, major diameter, and minor diameter measurements were recorded. Live coral cover, the annual extension rate (cm/year), skeletal density (g/cm 3), the calcification rate (g/cm 2 year −1), ecological volume (cm −3), and carbonate production (kg m −2 year −1) were also calculated. The average extension rate (± SD), skeletal density, and the calcification rate were 1.86 ± 0.31 cm/year, 2.28 ± 0.34 g CaCO 3 cm −3, and 4.34 ± 1.28 g CaCO 3 cm −2 year −1, respectively. The average live coral coverage was 3.19 ± 3.17\%, and the relative cover of Pocillopora corals was 65\%. Ecological volume increased 140.6 ± 84.28\% with respect to the initial volume, and the average production of CaCO 3 was 0.46 ± 0.41 kg CaCO 3 m −2 year −1. This study shows evidence of low growth rates, low generation of three‐dimensionality, and low CaCO 3 production in the study area when compared to other sites in the ETP. These results are relevant because they indicate compromised long‐term maintenance and reef development in Islas Marías, which may result in low reef functionality and compromise the stability of reef‐associated biodiversity and ecosystem services.",
    url = "https://doi.org/10.1111/maec.12678",
    doi = "10.1111/maec.12678",
    openalex = "W3199876163",
    references = "doi101016jcub201807008, doi101016jecoleng201901002, doi101016jecoser201207005, doi101016s0921800999000099, doi101038387253a0, doi101038nmeth2089, doi101038s4158601800412, doi101071mf99078, doi101073pnas1208909109, doi10108001621459199510476572, doi101126science19943351302, doi103390ijerph17186574, tortolerolangarica2019accelerated"
}

Coral reef restoration is a rapidly growing movement galvanized by the accelerating degradation of the world's tropical coral reefs. The need for concerted and collaborative action focused on the recovery of coral reef ecosystems coalesced in the creation of the Coral Restoration Consortium (CRC) in 2017. In March 2020, the CRC leadership team met for a biennial review of international coral reef restoration efforts and a discussion of perceived knowledge and implementation bottlenecks that may impair scalability and efficacy. Herein we present six priorities wherein the CRC will foster scientific advancement and collaboration to: (1) increase restoration efficiency, focusing on scale and cost‐effectiveness of deployment; (2) scale up larval‐based coral restoration efforts, emphasizing recruit health, growth, and survival; (3) ensure restoration of threatened coral species proceeds within a population‐genetics management context; (4) support a holistic approach to coral reef ecosystem restoration; (5) develop and promote the use of standardized terms and metrics for coral reef restoration; and (6) support coral reef restoration practitioners working in diverse geographic locations. These priorities are not exhaustive nor do we imply that accomplishing these tasks alone will be sufficient to restore coral reefs globally; rather these are topics where we feel the CRC community of practice can make timely and significant contributions to facilitate the growth of coral reef restoration as a practical conservation strategy. The goal for these collective actions is to provide tangible, local‐scale advancements in reef condition that offset declines resulting from local and global stressors including climate change.

@article{doi101111rec13498,
    author = "Vardi, Tali and Hoot, Whitney C. and Levy, Jessica and Shaver, Elizabeth C. and Winters, R. Scott and Banaszak, Anastazia T. and Baums, Iliana B. and Chamberland, Valérie F. and Cook, Nathan and Gulko, David and Hein, Margaux Y. and Kaufman, Les and Loewe, Michelle and Lundgren, Petra and Lustic, Caitlin and MacGowan, Petra and Matz, Mikhail V. and McGonigle, Miles L. and McLeod, Ian and Moore, Jennifer and Moore, Tom and Pivard, Sandrine and Pollock, F. Joseph and Rinkevich, Baruch and Suggett, David J. and Suleiman, Samuel and Viehman, T. Shay and Villalobos, Tatiana and Weis, Virginia M. and Wolke, Chelsea and Montoya-Maya, PH",
    title = "Six priorities to advance the science and practice of coral reef restoration worldwide",
    year = "2021",
    journal = "Restoration Ecology",
    abstract = "Coral reef restoration is a rapidly growing movement galvanized by the accelerating degradation of the world's tropical coral reefs. The need for concerted and collaborative action focused on the recovery of coral reef ecosystems coalesced in the creation of the Coral Restoration Consortium (CRC) in 2017. In March 2020, the CRC leadership team met for a biennial review of international coral reef restoration efforts and a discussion of perceived knowledge and implementation bottlenecks that may impair scalability and efficacy. Herein we present six priorities wherein the CRC will foster scientific advancement and collaboration to: (1) increase restoration efficiency, focusing on scale and cost‐effectiveness of deployment; (2) scale up larval‐based coral restoration efforts, emphasizing recruit health, growth, and survival; (3) ensure restoration of threatened coral species proceeds within a population‐genetics management context; (4) support a holistic approach to coral reef ecosystem restoration; (5) develop and promote the use of standardized terms and metrics for coral reef restoration; and (6) support coral reef restoration practitioners working in diverse geographic locations. These priorities are not exhaustive nor do we imply that accomplishing these tasks alone will be sufficient to restore coral reefs globally; rather these are topics where we feel the CRC community of practice can make timely and significant contributions to facilitate the growth of coral reef restoration as a practical conservation strategy. The goal for these collective actions is to provide tangible, local‐scale advancements in reef condition that offset declines resulting from local and global stressors including climate change.",
    url = "https://doi.org/10.1111/rec.13498",
    doi = "10.1111/rec.13498",
    openalex = "W3200599911",
    references = "doi101093icesjmsfsaa022"
}

Coral reefs were traditionally perceived as productive hot spots in oligotrophic waters. While modern evidence indicates that many coral reef food webs are heavily subsidized by planktonic production, the pathways through which this occurs remain unresolved. We used the analytical power of carbon isotope analysis of essential amino acids to distinguish between alternative carbon pathways supporting four key reef predators across an oceanic atoll. This technique separates benthic versus planktonic inputs, further identifying two distinct planktonic pathways (nearshore reef-associated plankton and offshore pelagic plankton), and revealing that these reef predators are overwhelmingly sustained by offshore pelagic sources rather than by reef sources (including reef-associated plankton). Notably, pelagic reliance did not vary between species or reef habitats, emphasizing that allochthonous energetic subsidies may have system-wide importance. These results help explain how coral reefs maintain exceptional productivity in apparently nutrient-poor tropical settings, but also emphasize their susceptibility to future ocean productivity fluctuations.

@article{doi101126sciadvabf3792,
    author = "Skinner, Christina and Mill, Aileen C. and Fox, Michael D. and Newman, Steven P. and Zhu, Yiou and Kuhl, Alison and Polunin, Nicholas",
    title = "Offshore pelagic subsidies dominate carbon inputs to coral reef predators",
    year = "2021",
    journal = "Science Advances",
    abstract = "Coral reefs were traditionally perceived as productive hot spots in oligotrophic waters. While modern evidence indicates that many coral reef food webs are heavily subsidized by planktonic production, the pathways through which this occurs remain unresolved. We used the analytical power of carbon isotope analysis of essential amino acids to distinguish between alternative carbon pathways supporting four key reef predators across an oceanic atoll. This technique separates benthic versus planktonic inputs, further identifying two distinct planktonic pathways (nearshore reef-associated plankton and offshore pelagic plankton), and revealing that these reef predators are overwhelmingly sustained by offshore pelagic sources rather than by reef sources (including reef-associated plankton). Notably, pelagic reliance did not vary between species or reef habitats, emphasizing that allochthonous energetic subsidies may have system-wide importance. These results help explain how coral reefs maintain exceptional productivity in apparently nutrient-poor tropical settings, but also emphasize their susceptibility to future ocean productivity fluctuations.",
    url = "https://doi.org/10.1126/sciadv.abf3792",
    doi = "10.1126/sciadv.abf3792",
    openalex = "W3132099018",
    references = "doi101371journalpone0190872"
}

BACKGROUND: Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillopora and Porites, and investigated whether this technique can benefit coral heat resistance while modifying the bacterial microbiome. Initially, heat-tolerant donors were identified in the wild. We then used fresh homogenates made from coral donor tissues to inoculate conspecific, heat-susceptible recipients and documented their bleaching responses and microbiomes by 16S rRNA gene metabarcoding. RESULTS: Recipients of both coral species bleached at lower rates compared to the control group when exposed to short-term heat stress (34 °C). One hundred twelve (Pocillopora sp.) and sixteen (Porites sp.) donor-specific bacterial species were identified in the microbiomes of recipients indicating transmission of bacteria. The amplicon sequence variants of the majority of these transmitted bacteria belonged to known, putatively symbiotic bacterial taxa of corals and were linked to the observed beneficial effect on the coral stress response. Microbiome dynamics in our experiments support the notion that microbiome community evenness and dominance of one or few bacterial species, rather than host-species identity, were drivers for microbiome stability in a holobiont context. CONCLUSIONS: Our results suggest that coral recipients likely favor the uptake of putative bacterial symbionts, recommending to include these taxonomic groups in future coral probiotics screening efforts. Our study suggests a scenario where these donor-specific bacterial symbionts might have been more efficient in supporting the recipients to resist heat stress compared to the native symbionts present in the control group. These findings urgently call for further experimental investigation of the mechanisms of action underlying the beneficial effect of CMT and for field-based long-term studies testing the persistence of the effect. Video abstract.

@article{doi101186s40168021010536,
    author = "Doering, Talisa and Wall, Marlene and Putchim, Lalita and Rattanawongwan, Tipwimon and Schroeder, Roman and Hentschel, Ute and Roik, Anna",
    title = "Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues",
    year = "2021",
    journal = "Microbiome",
    abstract = "BACKGROUND: Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillopora and Porites, and investigated whether this technique can benefit coral heat resistance while modifying the bacterial microbiome. Initially, heat-tolerant donors were identified in the wild. We then used fresh homogenates made from coral donor tissues to inoculate conspecific, heat-susceptible recipients and documented their bleaching responses and microbiomes by 16S rRNA gene metabarcoding. RESULTS: Recipients of both coral species bleached at lower rates compared to the control group when exposed to short-term heat stress (34 °C). One hundred twelve (Pocillopora sp.) and sixteen (Porites sp.) donor-specific bacterial species were identified in the microbiomes of recipients indicating transmission of bacteria. The amplicon sequence variants of the majority of these transmitted bacteria belonged to known, putatively symbiotic bacterial taxa of corals and were linked to the observed beneficial effect on the coral stress response. Microbiome dynamics in our experiments support the notion that microbiome community evenness and dominance of one or few bacterial species, rather than host-species identity, were drivers for microbiome stability in a holobiont context. CONCLUSIONS: Our results suggest that coral recipients likely favor the uptake of putative bacterial symbionts, recommending to include these taxonomic groups in future coral probiotics screening efforts. Our study suggests a scenario where these donor-specific bacterial symbionts might have been more efficient in supporting the recipients to resist heat stress compared to the native symbionts present in the control group. These findings urgently call for further experimental investigation of the mechanisms of action underlying the beneficial effect of CMT and for field-based long-term studies testing the persistence of the effect. Video abstract.",
    url = "https://doi.org/10.1186/s40168-021-01053-6",
    doi = "10.1186/s40168-021-01053-6",
    openalex = "W3159082718",
    references = "doi101038s41467019109695, doi103389fmars201800004"
}

Increasing evidence suggests that coral reefs exposed to elevated turbidity may be more resilient to climate change impacts and serve as an important conservation hotspot. However, logistical difficulties in studying turbid environments have led to poor representation of these reef types within the scientific literature, with studies using different methods and definitions to characterize turbid reefs. Here we review the geological origins and growth histories of turbid reefs from the Holocene (past), their current ecological and environmental states (present), and their potential responses and resilience to increasing local and global pressures (future). We classify turbid reefs using new descriptors based on their turbidity regime (persistent, fluctuating, transitional) and sources of sediment input (natural versus anthropogenic). Further, by comparing the composition, function and resilience of two of the most studied turbid reefs, Paluma Shoals Reef Complex, Australia (natural turbidity) and Singapore reefs (anthropogenic turbidity), we found them to be two distinct types of turbid reefs with different conservation status. As the geographic range of turbid reefs is expected to increase due to local and global stressors, improving our understanding of their responses to environmental change will be central to global coral reef conservation efforts.

@article{doi103390d13060251,
    author = "Zweifler, Adi and O’Leary, Michael and Morgan, Kyle M. and Browne, Nicola K.",
    title = "Turbid Coral Reefs: Past, Present and Future—A Review",
    year = "2021",
    journal = "Diversity",
    abstract = "Increasing evidence suggests that coral reefs exposed to elevated turbidity may be more resilient to climate change impacts and serve as an important conservation hotspot. However, logistical difficulties in studying turbid environments have led to poor representation of these reef types within the scientific literature, with studies using different methods and definitions to characterize turbid reefs. Here we review the geological origins and growth histories of turbid reefs from the Holocene (past), their current ecological and environmental states (present), and their potential responses and resilience to increasing local and global pressures (future). We classify turbid reefs using new descriptors based on their turbidity regime (persistent, fluctuating, transitional) and sources of sediment input (natural versus anthropogenic). Further, by comparing the composition, function and resilience of two of the most studied turbid reefs, Paluma Shoals Reef Complex, Australia (natural turbidity) and Singapore reefs (anthropogenic turbidity), we found them to be two distinct types of turbid reefs with different conservation status. As the geographic range of turbid reefs is expected to increase due to local and global stressors, improving our understanding of their responses to environmental change will be central to global coral reef conservation efforts.",
    url = "https://doi.org/10.3390/d13060251",
    doi = "10.3390/d13060251",
    openalex = "W3170581537",
    references = "doi101007s00338019018522, doi101111oik05946"
}

@article{doi101016jecoleng2022106558,
    author = "Xia, Jingquan and Zhu, Wentao and Liu, Xiangbo and Ren, Yuxiao and Huang, Jianzhong and Zhu, Ming and Wu, Zhong-qi-yue and Wang, Aimin and Li, Xiubao",
    title = "The effect of two types of grid transplantation on coral growth and the in-situ ecological restoration in a fragmented reef of the South China Sea",
    year = "2022",
    journal = "Ecological Engineering",
    url = "https://doi.org/10.1016/j.ecoleng.2022.106558",
    doi = "10.1016/j.ecoleng.2022.106558",
    openalex = "W4210672228",
    references = "doi101007s003430209253z"
}

The world’s coral reefs are threatened by the cumulative impacts of global climate change and local stressors. Driven largely by a desire to understand the interactions between corals and their symbiotic microorganisms, and to use this knowledge to eventually improve coral health, interest in coral microbiology and the coral microbiome has increased in recent years. In this review, we summarize the role of the coral microbiome in maintaining a healthy metaorganism by providing nutrients, support for growth and development, protection against pathogens, and mitigation of environmental stressors. We explore the concept of coral microbiome engineering, that is, precise and controlled manipulation of the coral microbiome to aid and enhance coral resilience and tolerance in the changing oceans. Although coral microbiome engineering is clearly in its infancy, several recent breakthroughs indicate that such engineering is an effective tool for restoration and preservation of these valuable ecosystems. To assist with identifying future research targets, we have reviewed the common principles of microbiome engineering and its applications in improving human health and agricultural productivity, drawing parallels to where coral microbiome engineering can advance in the not-too-distant future. Finally, we end by discussing the challenges faced by researchers and practitioners in the application of microbiome engineering in coral reefs and provide recommendations for future work.

@article{doi101016jeng202207010,
    author = "Li, Jie and Yang, Qingsong and Dong, Junde and Sweet, Michael and Zhang, Ying and Liu, Cong and Zhang, Yanying and Tang, Xiaoyu and Zhang, Wenqian and Zhang, Si",
    title = "Microbiome Engineering: A Promising Approach to Improve Coral Health",
    year = "2022",
    journal = "Engineering",
    abstract = "The world’s coral reefs are threatened by the cumulative impacts of global climate change and local stressors. Driven largely by a desire to understand the interactions between corals and their symbiotic microorganisms, and to use this knowledge to eventually improve coral health, interest in coral microbiology and the coral microbiome has increased in recent years. In this review, we summarize the role of the coral microbiome in maintaining a healthy metaorganism by providing nutrients, support for growth and development, protection against pathogens, and mitigation of environmental stressors. We explore the concept of coral microbiome engineering, that is, precise and controlled manipulation of the coral microbiome to aid and enhance coral resilience and tolerance in the changing oceans. Although coral microbiome engineering is clearly in its infancy, several recent breakthroughs indicate that such engineering is an effective tool for restoration and preservation of these valuable ecosystems. To assist with identifying future research targets, we have reviewed the common principles of microbiome engineering and its applications in improving human health and agricultural productivity, drawing parallels to where coral microbiome engineering can advance in the not-too-distant future. Finally, we end by discussing the challenges faced by researchers and practitioners in the application of microbiome engineering in coral reefs and provide recommendations for future work.",
    url = "https://doi.org/10.1016/j.eng.2022.07.010",
    doi = "10.1016/j.eng.2022.07.010",
    openalex = "W4294570635",
    references = "doi101093icesjmsfsaa022"
}

, with a significant difference (threefold) between reef zones (shallow vs deep), highlighting the higher carbonate production at deep-reef sites. Coral cover, carbonate production and sclerocronological characteristics showed a decrease rate (between 30 and 60%) associated with thermal anomaly events such as La Niña (2010-2011) and El Niño (2014-2016), with positive sights of recovery (twofold) during the following years 2017-2018. This study provides evidence that massive Pavona and branching Pocillopora corals are key reef-building species at Islas Marias archipelago, due to their capability of sustaining live coral coverage and carbonate through thermal disturbance periods. Revealing, that corals at mid-water depths (>10 m) may significantly contribute to the long-term stability of biogenic reef-framework, and geo-ecological functionality of the eastern tropical Pacific reefs.

@article{doi101111gbi12491,
    author = "Tortolero‐Langarica, J. J. Adolfo and Rodríguez‐Troncoso, Alma Paola and Cupul‐Magaña, Amilcar Leví and Morales-de-Anda, Diana and Caselle, Jennifer E. and Carricart‐Ganivet, Juan P.",
    title = "Coral calcification and carbonate production in the eastern tropical Pacific: The role of branching and massive corals in the reef maintenance",
    year = "2022",
    journal = "Geobiology",
    abstract = ", with a significant difference (threefold) between reef zones (shallow vs deep), highlighting the higher carbonate production at deep-reef sites. Coral cover, carbonate production and sclerocronological characteristics showed a decrease rate (between 30 and 60\%) associated with thermal anomaly events such as La Niña (2010-2011) and El Niño (2014-2016), with positive sights of recovery (twofold) during the following years 2017-2018. This study provides evidence that massive Pavona and branching Pocillopora corals are key reef-building species at Islas Marias archipelago, due to their capability of sustaining live coral coverage and carbonate through thermal disturbance periods. Revealing, that corals at mid-water depths (>10 m) may significantly contribute to the long-term stability of biogenic reef-framework, and geo-ecological functionality of the eastern tropical Pacific reefs.",
    url = "https://doi.org/10.1111/gbi.12491",
    doi = "10.1111/gbi.12491",
    openalex = "W4221084184",
    references = "céspedesrodríguez2021gross, doi101016jcub201807008, doi101016jpocean200603009, doi101016jpocean200603012, doi101038nature22901, doi101038s4158601800412, doi101098rspb20090339, doi101111j1469185x200800058x, doi101126science1152509, doi101126science1232310, doi101126science1251336, doi103390ijerph17186574"
}

Thermal refugia underpin climate-smart management of coral reefs, but whether current thermal refugia will remain so under future warming is uncertain. We use statistical downscaling to provide the highest resolution thermal stress projections (0.01°/1 km, >230,000 reef pixels) currently available for coral reefs and identify future refugia on locally manageable scales. Here, we show that climate change will overwhelm current local-scale refugia, with declines in global thermal refugia from 84% of global coral reef pixels in the present-day climate to 0.2% at 1.5°C, and 0% at 2.0°C of global warming. Local-scale oceanographic features such as upwelling and strong ocean currents only rarely provide future thermal refugia. We confirm that warming of 1.5°C relative to pre-industrial levels will be catastrophic for coral reefs. Focusing management efforts on thermal refugia may only be effective in the short-term. Promoting adaptation to higher temperatures and facilitating migration will instead be needed to secure coral reef survival.

@article{doi101371journalpclm0000004,
    author = "Dixon, Adele M. and Forster, Piers and Heron, Scott F. and Stoner, Anne M. K. and Beger, Maria",
    title = "Future loss of local-scale thermal refugia in coral reef ecosystems",
    year = "2022",
    journal = "PLOS Climate",
    abstract = "Thermal refugia underpin climate-smart management of coral reefs, but whether current thermal refugia will remain so under future warming is uncertain. We use statistical downscaling to provide the highest resolution thermal stress projections (0.01°/1 km, >230,000 reef pixels) currently available for coral reefs and identify future refugia on locally manageable scales. Here, we show that climate change will overwhelm current local-scale refugia, with declines in global thermal refugia from 84\% of global coral reef pixels in the present-day climate to 0.2\% at 1.5°C, and 0\% at 2.0°C of global warming. Local-scale oceanographic features such as upwelling and strong ocean currents only rarely provide future thermal refugia. We confirm that warming of 1.5°C relative to pre-industrial levels will be catastrophic for coral reefs. Focusing management efforts on thermal refugia may only be effective in the short-term. Promoting adaptation to higher temperatures and facilitating migration will instead be needed to secure coral reef survival.",
    url = "https://doi.org/10.1371/journal.pclm.0000004",
    doi = "10.1371/journal.pclm.0000004",
    openalex = "W4210539223",
    references = "doi103389fmars201800004"
}

Coral growth is an important metric of coral health and underpins reef-scale functional attributes such as structural complexity and calcium carbonate production. There persists, however, a paucity of growth data for most reef-building regions, especially for coral species whose skeletal architecture prevents the use of traditional methods such as coring and Alizarin staining. We used structure-from-motion photogrammetry to quantify a range of colony-scale growth metrics for six coral species in the Mexican Caribbean and present a newly developed workflow to measure colony volume change over time. Our results provide the first growth metrics for two species that are now major space occupiers on Caribbean reefs, Agaricia agaricites and Agaricia tenuifolia. We also document higher linear extension, volume increase and calcification rates within back reef compared to fore reef environments for four other common species: Orbicella faveolata, Porites astreoides, Siderastrea siderea and Pseudodiploria strigosa. Linear extension rates in our study were lower than those obtained via computed tomography (CT) scans of coral cores from the same sites, as the photogrammetry method averages growth in all dimensions, while the CT method depicts growth only along the main growth axis (upwards). The comparison of direct volume change versus potential volume increase calculated from linear extension emphasizes the importance of assessing whole colony growth to improve calcification estimates. The method presented here provides an approach that can generate accurate calcification estimates alongside a range of other whole-colony growth metrics in a non-invasive way.

@article{doi101371journalpone0277546,
    author = "Lange, Ines D. and Molina‐Hernández, Ana and Medellín‐Maldonado, Francisco and Perry, Chris T. and Álvarez‐Filip, Lorenzo",
    title = "Structure-from-motion photogrammetry demonstrates variability in coral growth within colonies and across habitats",
    year = "2022",
    journal = "PLoS ONE",
    abstract = "Coral growth is an important metric of coral health and underpins reef-scale functional attributes such as structural complexity and calcium carbonate production. There persists, however, a paucity of growth data for most reef-building regions, especially for coral species whose skeletal architecture prevents the use of traditional methods such as coring and Alizarin staining. We used structure-from-motion photogrammetry to quantify a range of colony-scale growth metrics for six coral species in the Mexican Caribbean and present a newly developed workflow to measure colony volume change over time. Our results provide the first growth metrics for two species that are now major space occupiers on Caribbean reefs, Agaricia agaricites and Agaricia tenuifolia. We also document higher linear extension, volume increase and calcification rates within back reef compared to fore reef environments for four other common species: Orbicella faveolata, Porites astreoides, Siderastrea siderea and Pseudodiploria strigosa. Linear extension rates in our study were lower than those obtained via computed tomography (CT) scans of coral cores from the same sites, as the photogrammetry method averages growth in all dimensions, while the CT method depicts growth only along the main growth axis (upwards). The comparison of direct volume change versus potential volume increase calculated from linear extension emphasizes the importance of assessing whole colony growth to improve calcification estimates. The method presented here provides an approach that can generate accurate calcification estimates alongside a range of other whole-colony growth metrics in a non-invasive way.",
    url = "https://doi.org/10.1371/journal.pone.0277546",
    doi = "10.1371/journal.pone.0277546",
    openalex = "W4309138813",
    references = "doi101007s00338019018522"
}

The worldwide decline of coral reefs has renewed interest in coral communities at the edge of environmental limits because they have the potential to serve as resilience hotspots and climate change refugia, and can provide insights into how coral reefs might function in future ocean conditions. These coral communities are often referred to as marginal or extreme but few definitions exist and usage of these terms has therefore been inconsistent. This creates significant challenges for categorising these often poorly studied communities and synthesising data across locations. Furthermore, this impedes our understanding of how coral communities can persist at the edge of their environmental limits and the lessons they provide for future coral reef survival. Here, we propose that marginal and extreme coral communities are related but distinct and provide a novel conceptual framework to redefine them. Specifically, we define coral reef extremeness solely based on environmental conditions (i.e., large deviations from optimal conditions in terms of mean and/or variance) and marginality solely based on ecological criteria (i.e., altered community composition and/or ecosystem functioning). This joint but independent assessment of environmental and ecological criteria is critical to avoid common pitfalls where coral communities existing outside the presumed optimal conditions for coral reef development are automatically considered inferior to coral reefs in more traditional settings. We further evaluate the differential potential of marginal and extreme coral communities to serve as natural laboratories, resilience hotspots and climate change refugia, and discuss strategies for their conservation and management as well as priorities for future research. Our new classification framework provides an important tool to improve our understanding of how corals can persist at the edge of their environmental limits and how we can leverage this knowledge to optimise strategies for coral reef conservation, restoration and management in a rapidly changing ocean.

@article{doi101016jscitotenv2023163688,
    author = "Schoepf, Verena and Baumann, Justin H. and Barshis, Daniel J. and Browne, Nicola K. and Camp, Emma F. and Comeau, Steeve and Cornwall, Christopher E. and Guzmán, Héctor M. and Riegl, Bernhard and Rodolfo-Metalpa, Riccardo and Sommer, Brigitte",
    title = "Corals at the edge of environmental limits: A new conceptual framework to re-define marginal and extreme coral communities",
    year = "2023",
    journal = "The Science of The Total Environment",
    abstract = "The worldwide decline of coral reefs has renewed interest in coral communities at the edge of environmental limits because they have the potential to serve as resilience hotspots and climate change refugia, and can provide insights into how coral reefs might function in future ocean conditions. These coral communities are often referred to as marginal or extreme but few definitions exist and usage of these terms has therefore been inconsistent. This creates significant challenges for categorising these often poorly studied communities and synthesising data across locations. Furthermore, this impedes our understanding of how coral communities can persist at the edge of their environmental limits and the lessons they provide for future coral reef survival. Here, we propose that marginal and extreme coral communities are related but distinct and provide a novel conceptual framework to redefine them. Specifically, we define coral reef extremeness solely based on environmental conditions (i.e., large deviations from optimal conditions in terms of mean and/or variance) and marginality solely based on ecological criteria (i.e., altered community composition and/or ecosystem functioning). This joint but independent assessment of environmental and ecological criteria is critical to avoid common pitfalls where coral communities existing outside the presumed optimal conditions for coral reef development are automatically considered inferior to coral reefs in more traditional settings. We further evaluate the differential potential of marginal and extreme coral communities to serve as natural laboratories, resilience hotspots and climate change refugia, and discuss strategies for their conservation and management as well as priorities for future research. Our new classification framework provides an important tool to improve our understanding of how corals can persist at the edge of their environmental limits and how we can leverage this knowledge to optimise strategies for coral reef conservation, restoration and management in a rapidly changing ocean.",
    url = "https://doi.org/10.1016/j.scitotenv.2023.163688",
    doi = "10.1016/j.scitotenv.2023.163688",
    openalex = "W4366993230",
    references = "doi101038s4324702300766w"
}

Abstract Understanding the drivers of net coral reef calcium carbonate production is increasingly important as ocean warming, acidification, and other anthropogenic stressors threaten the maintenance of coral reef structures and the services these ecosystems provide. Despite intense research effort on coral reef calcium carbonate production, the inclusion of a key reef forming/accreting calcifying group, the crustose coralline algae, remains challenging both from a theoretical and practical standpoint. While corals are typically the primary reef builders of contemporary reefs, crustose coralline algae can contribute equally. Here, we combine several sets of data with numerical and theoretical modelling to demonstrate that crustose coralline algae carbonate production can match or even exceed the contribution of corals to reef carbonate production. Despite their importance, crustose coralline algae are often inaccurately recorded in benthic surveys or even entirely missing from coral reef carbonate budgets. We outline several recommendations to improve the inclusion of crustose coralline algae into such carbonate budgets under the ongoing climate crisis.

@article{doi101038s4324702300766w,
    author = "Cornwall, Christopher E. and Carlot, Jérémy and Branson, Oscar and Courtney, Travis A. and Harvey, Ben P. and Perry, Chris T. and Andersson, Andreas J. and Díaz-Pulido, Guillermo and Johnson, Maggie D. and Kennedy, Emma and Krieger, Erik C. and Mallela, Jennie and McCoy, Sophie J. and Nugues, Maggy M. and Quinter, Evan and Ross, Claire L. and Ryan, Emma and Saderne, Vincent and Comeau, Steeve",
    title = "Crustose coralline algae can contribute more than corals to coral reef carbonate production",
    year = "2023",
    journal = "Communications Earth \& Environment",
    abstract = "Abstract Understanding the drivers of net coral reef calcium carbonate production is increasingly important as ocean warming, acidification, and other anthropogenic stressors threaten the maintenance of coral reef structures and the services these ecosystems provide. Despite intense research effort on coral reef calcium carbonate production, the inclusion of a key reef forming/accreting calcifying group, the crustose coralline algae, remains challenging both from a theoretical and practical standpoint. While corals are typically the primary reef builders of contemporary reefs, crustose coralline algae can contribute equally. Here, we combine several sets of data with numerical and theoretical modelling to demonstrate that crustose coralline algae carbonate production can match or even exceed the contribution of corals to reef carbonate production. Despite their importance, crustose coralline algae are often inaccurately recorded in benthic surveys or even entirely missing from coral reef carbonate budgets. We outline several recommendations to improve the inclusion of crustose coralline algae into such carbonate budgets under the ongoing climate crisis.",
    url = "https://doi.org/10.1038/s43247-023-00766-w",
    doi = "10.1038/s43247-023-00766-w",
    openalex = "W4362665706",
    references = "doi101007bf00428135, doi101016s0022098105800061, doi101038ncomms2409, doi101038s415860180194z, doi101073pnas2015265118, doi101086283381, doi101098rspb20090339, doi101146annureves17110186001421, doi101371journalpone0025026, doi1023071933661"
}

Rapidly changing conditions alter disturbance patterns, highlighting the need to better understand how the transition from pulse disturbances to more persistent stress will impact ecosystem dynamics. We conducted a global analysis of the impacts of 11 types of disturbances on reef integrity using the rate of change of coral cover as a measure of damage. Then, we evaluated how the magnitude of the damage due to thermal stress, cyclones, and diseases varied among tropical Atlantic and Indo-Pacific reefs and whether the cumulative impact of thermal stress and cyclones was able to modulate the responses of reefs to future events. We found that reef damage largely depends on the condition of a reef before a disturbance, disturbance intensity, and biogeographic region, regardless of the type of disturbance. Changes in coral cover after thermal stress events were largely influenced by the cumulative stress of past disturbances and did not depend on disturbance intensity or initial coral cover, which suggests that an ecological memory is present within coral communities. In contrast, the effect of cyclones (and likely other physical impacts) was primarily modulated by the initial reef condition and did not appear to be influenced by previous impacts. Our findings also underscore that coral reefs can recover if stressful conditions decrease, yet the lack of action to reduce anthropogenic impacts and greenhouse gas emissions continues to trigger reef degradation. We uphold that evidence-based strategies can guide managers to make better decisions to prepare for future disturbances.

@article{doi101111gcb16686,
    author = "González‐Barrios, F. Javier and Estrada‐Saldívar, Nuria and Pérez‐Cervantes, Esmeralda and Secaira‐Fajardo, Fernando and Álvarez‐Filip, Lorenzo",
    title = "Legacy effects of anthropogenic disturbances modulate dynamics in the world's coral reefs",
    year = "2023",
    journal = "Global Change Biology",
    abstract = "Rapidly changing conditions alter disturbance patterns, highlighting the need to better understand how the transition from pulse disturbances to more persistent stress will impact ecosystem dynamics. We conducted a global analysis of the impacts of 11 types of disturbances on reef integrity using the rate of change of coral cover as a measure of damage. Then, we evaluated how the magnitude of the damage due to thermal stress, cyclones, and diseases varied among tropical Atlantic and Indo-Pacific reefs and whether the cumulative impact of thermal stress and cyclones was able to modulate the responses of reefs to future events. We found that reef damage largely depends on the condition of a reef before a disturbance, disturbance intensity, and biogeographic region, regardless of the type of disturbance. Changes in coral cover after thermal stress events were largely influenced by the cumulative stress of past disturbances and did not depend on disturbance intensity or initial coral cover, which suggests that an ecological memory is present within coral communities. In contrast, the effect of cyclones (and likely other physical impacts) was primarily modulated by the initial reef condition and did not appear to be influenced by previous impacts. Our findings also underscore that coral reefs can recover if stressful conditions decrease, yet the lack of action to reduce anthropogenic impacts and greenhouse gas emissions continues to trigger reef degradation. We uphold that evidence-based strategies can guide managers to make better decisions to prepare for future disturbances.",
    url = "https://doi.org/10.1111/gcb.16686",
    doi = "10.1111/gcb.16686",
    openalex = "W4327753871",
    references = "doi101007s003430209253z"
}

Coral reef ecosystems worldwide are facing significant damage due to climate change and human disturbances. Consequently, restoration actions have been implemented to repair degraded reef areas. However, many restoration efforts have been hindered by severe environmental conditions, which can hamper restoration success and create challenges in developing cost‐effective coral reef restoration methods. To address this, we conducted a study to test a low‐cost reef restoration tool known as “framed reef modules” (FRMs), specifically aiming to mitigate the impacts of typhoons. We measured the growth rates (after 300 days) and survivorship (after 400 days) of Acropora hyacinthus and A. microphthalma fragments located at different distances from substrates (H0, H10, H30, and H45). The FRMs were exposed to multiple typhoons, and despite the harsh conditions, they remained undamaged. For comparison, we also examined basalt grid plates buried in gravel. After 400 days, the H45 FRMs showed the highest survival rates (A. hyacinthus 86% and A. microphthalma 90%) compared to H30 FRMs (A. hyacinthus 80% and A. microphthalma 84%), H10 FRMs (A. hyacinthus 4% and A. microphthalma 24%), and H0 FRMs (A. hyacinthus 3% and A. microphthalma 22%). It was found that transplanted corals with a height of at least 30 cm from the substrate demonstrated resilience against impacts caused by macroalgae, turf algae, and sedimentation rates. This study showed the effectiveness of an ecological engineering approach using FRMs to enhance the three‐dimensional complexity of restored reefs and rehabilitate coral reefs damaged by typhoons. Furthermore, this method offered reduced costs and improved reef resilience.

@article{doi101111rec13997,
    author = "Liu, Xiangbo and Zhu, Wentao and Chen, Ruimei and Rinkevich, Baruch and Shafir, Shai and Xia, Jingquan and Zhu, Ming and Chen, Rouwen and Wang, Aimin and Li, Xiubao",
    title = "Framed reef modules: a new and cost‐effective tool for coral restoration",
    year = "2023",
    journal = "Restoration Ecology",
    abstract = "Coral reef ecosystems worldwide are facing significant damage due to climate change and human disturbances. Consequently, restoration actions have been implemented to repair degraded reef areas. However, many restoration efforts have been hindered by severe environmental conditions, which can hamper restoration success and create challenges in developing cost‐effective coral reef restoration methods. To address this, we conducted a study to test a low‐cost reef restoration tool known as “framed reef modules” (FRMs), specifically aiming to mitigate the impacts of typhoons. We measured the growth rates (after 300 days) and survivorship (after 400 days) of Acropora hyacinthus and A. microphthalma fragments located at different distances from substrates (H0, H10, H30, and H45). The FRMs were exposed to multiple typhoons, and despite the harsh conditions, they remained undamaged. For comparison, we also examined basalt grid plates buried in gravel. After 400 days, the H45 FRMs showed the highest survival rates (A. hyacinthus 86\% and A. microphthalma 90\%) compared to H30 FRMs (A. hyacinthus 80\% and A. microphthalma 84\%), H10 FRMs (A. hyacinthus 4\% and A. microphthalma 24\%), and H0 FRMs (A. hyacinthus 3\% and A. microphthalma 22\%). It was found that transplanted corals with a height of at least 30 cm from the substrate demonstrated resilience against impacts caused by macroalgae, turf algae, and sedimentation rates. This study showed the effectiveness of an ecological engineering approach using FRMs to enhance the three‐dimensional complexity of restored reefs and rehabilitate coral reefs damaged by typhoons. Furthermore, this method offered reduced costs and improved reef resilience.",
    url = "https://doi.org/10.1111/rec.13997",
    doi = "10.1111/rec.13997",
    openalex = "W4386010602",
    references = "doi101007s003430209253z, doi103390ijerph17186574"
}

The degradation of coral reefs during the last decades has turned attention toward management and restoration interventions. This study seeks to operationalize coral gardening of Pocillopora spp. fragments in low profile bottom‐anchored nurseries and to compare survival and growth patterns between sites, time, and fragment size in the southern Mexican Pacific. After 357 days, fragments showed high survival (96.4%), growth rates (4.35 cm/year), and an increase in coral coverage from 3.62 ± 1.3% (mean ± SD) to 17.42 ± 4.8% (approximately 480%). Coral growth rate did not show differences between sites (pseudo‐ F [1,635] = 0.21, p = 0.63), but corals grew more significantly during the upwelling season in the Gulf of Tehuantepec. According to linear and local regression analysis, the extension rate in nurseries was significantly higher when corals were smaller (<7 cm in diameter) being of relevance for operationalizing coral gardening from donor colonies; nevertheless, coral shrinkage (13.1%), when corals were smaller (i.e. during the early phases of the coral gardening protocol), calls for precaution and close monitoring. Operationalizing coral gardening of Pocillopora spp. fragments, including successful metrics in upwelling areas, are relevant for reef restoration in the eastern tropical Pacific; nevertheless, lessons regarding shrinkage and differential growth rates related to coral size should also be considered.

@article{doi101111rec14006,
    author = "García‐Medrano, Diego and López‐Pérez, Andrés and Guendulain-García, Sergio D. and Valencia‐Méndez, Omar and Granja‐Fernández, Rebeca and González‐Mendoza, Tania and Torres‐Hernández, Pablo",
    title = "Gardening Pocillopora spp. fragments and their potential for rebuilding reef systems in the southern Mexican Pacific",
    year = "2023",
    journal = "Restoration Ecology",
    abstract = "The degradation of coral reefs during the last decades has turned attention toward management and restoration interventions. This study seeks to operationalize coral gardening of Pocillopora spp. fragments in low profile bottom‐anchored nurseries and to compare survival and growth patterns between sites, time, and fragment size in the southern Mexican Pacific. After 357 days, fragments showed high survival (96.4\%), growth rates (4.35 cm/year), and an increase in coral coverage from 3.62 ± 1.3\% (mean ± SD) to 17.42 ± 4.8\% (approximately 480\%). Coral growth rate did not show differences between sites (pseudo‐ F [1,635] = 0.21, p = 0.63), but corals grew more significantly during the upwelling season in the Gulf of Tehuantepec. According to linear and local regression analysis, the extension rate in nurseries was significantly higher when corals were smaller (<7 cm in diameter) being of relevance for operationalizing coral gardening from donor colonies; nevertheless, coral shrinkage (13.1\%), when corals were smaller (i.e. during the early phases of the coral gardening protocol), calls for precaution and close monitoring. Operationalizing coral gardening of Pocillopora spp. fragments, including successful metrics in upwelling areas, are relevant for reef restoration in the eastern tropical Pacific; nevertheless, lessons regarding shrinkage and differential growth rates related to coral size should also be considered.",
    url = "https://doi.org/10.1111/rec.14006",
    doi = "10.1111/rec.14006",
    openalex = "W4386752661",
    references = "doi101002aqc558, doi10100797894017749945, doi101007s003380050220, doi101016jecoleng201808017, doi101016jecoleng201901002, doi101016jjembe200801024, doi101073pnas1208909109, doi10108001621459198810478639, doi101371journalpone0000711, doi101371journalpone0226631, doi103354meps08554, tortolerolangarica2019accelerated"
}

Introduction: The 1997-98 El Niño event caused massive coral bleaching and mortality in the Central Mexican Pacific (CMP). Punta de Mita alone used to harbor more than 30 % of the coral coverage in this region, with a mono-specific Pocillopora coverage. The 1997-1998 ENSO event caused massive coral mortality reducing live coral coverage to < 5 %. Despite being considered a coral region unlikely to recover, recent restoration efforts have been implemented to rehabilitate the coral community. Objective: To assess coral recovery by analyzing the coral growth and survival rates of branching Pocillopora species at Punta de Mita. Methods: Healthy coral fragments of opportunity were re-attached to the natural substrata using zip ties and measured considering their growth in terms of maximum length and width (cm) to determine their annual extension rates. Results: After 50 weeks, corals duplicated their size, with a mean growth of ~ 4 cm year-1. After 100 weeks (2 years), corals triplicated their size, increasing on average 8–9 cm in each diameter. Conclusions: Successful coral reef restoration activities in the Central Mexican Pacific are the result of Pocillopora’s physiological processes, such as fast growth rates, and recent life-history traits, like the ability to cope with thermal anomalies, which enable them to thrive in a dynamic region severely affected by natural and anthropogenic perturbations. Indeed, a region considered unlikely to recover has regained its live coral cover from < 5 % in 1998 up to 15 % in 20 years. This demonstrates the importance of assisting natural coral recovery with restoration efforts, especially in coral locations that, despite environmental perturbations, have proven to be resilient and may become coral refugia areas under the current climate change scenario.

@article{doi1015517revbioltropv71is154795,
    author = "Martínez-Castillo, Violeta and Rodríguez‐Troncoso, Alma Paola and Tortolero‐Langarica, J. J. Adolfo and Cupul‐Magaña, Amilcar Leví",
    title = "Active restoration efforts in the Central Mexican Pacific as a strategy for coral reef recovery",
    year = "2023",
    journal = "Revista de Biología Tropical",
    abstract = "Introduction: The 1997-98 El Niño event caused massive coral bleaching and mortality in the Central Mexican Pacific (CMP). Punta de Mita alone used to harbor more than 30 \% of the coral coverage in this region, with a mono-specific Pocillopora coverage. The 1997-1998 ENSO event caused massive coral mortality reducing live coral coverage to < 5 \%. Despite being considered a coral region unlikely to recover, recent restoration efforts have been implemented to rehabilitate the coral community. Objective: To assess coral recovery by analyzing the coral growth and survival rates of branching Pocillopora species at Punta de Mita. Methods: Healthy coral fragments of opportunity were re-attached to the natural substrata using zip ties and measured considering their growth in terms of maximum length and width (cm) to determine their annual extension rates. Results: After 50 weeks, corals duplicated their size, with a mean growth of \textasciitilde\ 4 cm year-1. After 100 weeks (2 years), corals triplicated their size, increasing on average 8–9 cm in each diameter. Conclusions: Successful coral reef restoration activities in the Central Mexican Pacific are the result of Pocillopora’s physiological processes, such as fast growth rates, and recent life-history traits, like the ability to cope with thermal anomalies, which enable them to thrive in a dynamic region severely affected by natural and anthropogenic perturbations. Indeed, a region considered unlikely to recover has regained its live coral cover from < 5 \% in 1998 up to 15 \% in 20 years. This demonstrates the importance of assisting natural coral recovery with restoration efforts, especially in coral locations that, despite environmental perturbations, have proven to be resilient and may become coral refugia areas under the current climate change scenario.",
    url = "https://doi.org/10.15517/rev.biol.trop..v71is1.54795",
    doi = "10.15517/rev.biol.trop..v71is1.54795",
    openalex = "W4367856319",
    references = "doi101111gbi12491, doi101111maec12678"
}

Background. Coral reefs provide several important geo-ecological functions essential for the sustainability of coastal human communities. However, during the last 50 years, reef ecosystems are experiencing rapid degradation caused by natural and anthropogenic disturbances. One consequence of the above has been the reduction in the carbonate production rate and the structural complexity of these systems. Particularly, the loss of key coral species in the construction of reefs has compromised the functionality of the ecosystem. Objective. In this study we used an adaptation of the ReefBudget methodology to measure the calcium carbonate budget in the reef of La Entrega, Oaxaca, Mexico. Methods. Six transects were carried out to estimate the abundance of eroding fish (25 x 4 m), sea urchins (25 x 2 m) and the composition of the benthos. Results. When carrying out the corresponding calculations, it was found that in La Entrega 13.72 kg m-2 year-1 (commonly referred as “G”) are produced, the endobioerosion (including erosion by sponges) calculated was 5.65 G. The sea urchin erosion is 0.12 G and that of fish is 0.73 G; the resulting net carbonate budget was 7.21 G. The accretion rate (vertical reef growth) at La Entrega reef was 7.07 mm yr-1. We consider it important to mention that the reef patch at La Entrega is relatively small (approximately 324 x 233 m) compared to formations in the Caribbean or Indo-Pacific regions. Conclusions. Net production at La Entrega is higher than estimated for most Caribbean reefs (2-4 G) but lower than that of the Indo-Pacific (5-14 G). Differences in the balance between regions are mainly associated with differences in the abundances of builder species in each region. According to what was modeled in this work, the La Entrega reef patch presents a sufficient accretion rate to deal with a possible rise in sea level under the RCP 4.5 and 2.6 scenarios (4 and 7 mm, respectively).

@article{doi1024275hthl7067,
    author = "Cabral‐Tena, Rafael A. and Laboratorio de Arrecifes y Biodiversidad/Departamento de Ecología Marina, Centro de Investigación Cientifica y de Educación Superior Ensenada, Baja California.",
    title = "Carbonate Budget in the reef-patch of La Entrega, Oaxaca. Southern Mexican Pacific",
    year = "2023",
    journal = "Hidrobiológica",
    abstract = "Background. Coral reefs provide several important geo-ecological functions essential for the sustainability of coastal human communities. However, during the last 50 years, reef ecosystems are experiencing rapid degradation caused by natural and anthropogenic disturbances. One consequence of the above has been the reduction in the carbonate production rate and the structural complexity of these systems. Particularly, the loss of key coral species in the construction of reefs has compromised the functionality of the ecosystem. Objective. In this study we used an adaptation of the ReefBudget methodology to measure the calcium carbonate budget in the reef of La Entrega, Oaxaca, Mexico. Methods. Six transects were carried out to estimate the abundance of eroding fish (25 x 4 m), sea urchins (25 x 2 m) and the composition of the benthos. Results. When carrying out the corresponding calculations, it was found that in La Entrega 13.72 kg m-2 year-1 (commonly referred as “G”) are produced, the endobioerosion (including erosion by sponges) calculated was 5.65 G. The sea urchin erosion is 0.12 G and that of fish is 0.73 G; the resulting net carbonate budget was 7.21 G. The accretion rate (vertical reef growth) at La Entrega reef was 7.07 mm yr-1. We consider it important to mention that the reef patch at La Entrega is relatively small (approximately 324 x 233 m) compared to formations in the Caribbean or Indo-Pacific regions. Conclusions. Net production at La Entrega is higher than estimated for most Caribbean reefs (2-4 G) but lower than that of the Indo-Pacific (5-14 G). Differences in the balance between regions are mainly associated with differences in the abundances of builder species in each region. According to what was modeled in this work, the La Entrega reef patch presents a sufficient accretion rate to deal with a possible rise in sea level under the RCP 4.5 and 2.6 scenarios (4 and 7 mm, respectively).",
    url = "https://doi.org/10.24275/hthl7067",
    doi = "10.24275/hthl7067",
    openalex = "W4387347209",
    references = "doi101111maec12678"
}

Vital fluorescence staining of calcium-containing structures in calcifying organisms is a powerful tool for the study of biocalcification. The main dyes used in this field have green or red fluorescence, which may be overlapped with the fluorescence of chlorophyll and other organic substances. We synthesized a novel coumarin-based fluorescent dye QA2 that stains calcium carbonate and calcium phosphate. The fluorescence of this dye depends from environment, it is enhanced in non-polar medium with a shift of the emission maximum to the blue spectrum region. Small vaterite and calcium phosphate particles adsorb QA2 on the surface and exhibit predominantly green fluorescence, while low surface area calcite crystals are stained in bulk and show additional intense blue fluorescence. The ability of the QA2 dye to generate blue fluorescence of calcium carbonate may be useful for tracking calcium carbonate formation at living organisms in the presence of green and red fluorescent organic substances.

@article{doi1031951265835182023a6244,
    author = "S.N., S.N. Zelinskiy and E.N., E.N. Danilovtseva and Strelova, Mariya S. and V.A., V.A. Pal’shin and V.V., V.V. Annenkov",
    title = "Coumarin-based acid dye for fluorescent staining of calcium carbonate particles",
    year = "2023",
    journal = "Limnology and Freshwater Biology",
    abstract = "Vital fluorescence staining of calcium-containing structures in calcifying organisms is a powerful tool for the study of biocalcification. The main dyes used in this field have green or red fluorescence, which may be overlapped with the fluorescence of chlorophyll and other organic substances. We synthesized a novel coumarin-based fluorescent dye QA2 that stains calcium carbonate and calcium phosphate. The fluorescence of this dye depends from environment, it is enhanced in non-polar medium with a shift of the emission maximum to the blue spectrum region. Small vaterite and calcium phosphate particles adsorb QA2 on the surface and exhibit predominantly green fluorescence, while low surface area calcite crystals are stained in bulk and show additional intense blue fluorescence. The ability of the QA2 dye to generate blue fluorescence of calcium carbonate may be useful for tracking calcium carbonate formation at living organisms in the presence of green and red fluorescent organic substances.",
    url = "https://doi.org/10.31951/2658-3518-2023-a-6-244",
    doi = "10.31951/2658-3518-2023-a-6-244",
    openalex = "W4390354100",
    references = "doi101111maec12678"
}

Over the past decade, there has been increasing interest in marine restoration, requiring a consideration of various approaches for optimal success. Artificial reefs (ARs) have been employed for marine restoration and fisheries management, but their effectiveness in restoring ecosystems lacks well-defined ecological criteria and empirical evidence. A systematic review of the literature on ARs articles between 1990–2020, a meta-analysis of their effectiveness based on the similarity of species composition with reference natural reefs (NRs), as well as bias risk analyses were carried out. Research on ARs primarily focused production of marine communities (n = 168). There are important information gaps regarding socioeconomic aspects; design, materials, and disposal in the selected habitats; legal, management, and planning aspects considering long-term monitoring. Regarding effectiveness, few articles (n = 13) allowed comparisons between ARs and NRs, highlighting the need to apply proper reference sites in AR implementations. Meta-analysis showed that ARs are not similar to reference NRs (p = 0.03, common effect and p = 0.05 random effect models). However, a high index of heterogeneity (88%) suggests that this relation may be influenced by factors other than the reef type. Thus, further analysis can disguise variables conditioning this AR–NR similarity as a measure of restoration for degraded marine ecosystems.

@article{doi103390environments10070121,
    author = "Bracho-Villavicencio, Carolina and Matthews-Cascón, Helena and Rossi, Sérgio",
    title = "Artificial Reefs around the World: A Review of the State of the Art and a Meta-Analysis of Its Effectiveness for the Restoration of Marine Ecosystems",
    year = "2023",
    journal = "Environments",
    abstract = "Over the past decade, there has been increasing interest in marine restoration, requiring a consideration of various approaches for optimal success. Artificial reefs (ARs) have been employed for marine restoration and fisheries management, but their effectiveness in restoring ecosystems lacks well-defined ecological criteria and empirical evidence. A systematic review of the literature on ARs articles between 1990–2020, a meta-analysis of their effectiveness based on the similarity of species composition with reference natural reefs (NRs), as well as bias risk analyses were carried out. Research on ARs primarily focused production of marine communities (n = 168). There are important information gaps regarding socioeconomic aspects; design, materials, and disposal in the selected habitats; legal, management, and planning aspects considering long-term monitoring. Regarding effectiveness, few articles (n = 13) allowed comparisons between ARs and NRs, highlighting the need to apply proper reference sites in AR implementations. Meta-analysis showed that ARs are not similar to reference NRs (p = 0.03, common effect and p = 0.05 random effect models). However, a high index of heterogeneity (88\%) suggests that this relation may be influenced by factors other than the reef type. Thus, further analysis can disguise variables conditioning this AR–NR similarity as a measure of restoration for degraded marine ecosystems.",
    url = "https://doi.org/10.3390/environments10070121",
    doi = "10.3390/environments10070121",
    openalex = "W4384525613",
    references = "doi101093icesjmsfsaa022"
}

Coral reefs are three-dimensional biogenic structures that provide habitat for plenty of marine organisms; yet, coral reefs are deteriorating worldwide. Hence, it is essential to identify suitable substitutes for such coral services. This study examines reef fishes’ behavior and reactions to three-dimensional-printed (3DP) corals based on scanned Stylophora pistillata, as well as modified 3DP models. In particular, fishes’ unresponsiveness to the color, shape, morphology, and material of 3DP models both in vitro and in situ experiments was investigated. Coral reef fishes responded to the 3DP corals and demonstrated their usage in a range of services. Moreover, a greater number of fish species interacted more with 3DP models than they did with live corals. Furthermore, specific reef fish species, such as Sea Goldies (Pseudanthias squamipinnis), showed a preference for specific 3DP coral color, and other species demonstrated preferences for specific 3DP model shapes. The current study results show that three-dimensional-printed coral models can substitute for live corals for certain types of reef fish services.

@article{doi103390jmse11040882,
    author = "Oren, Asa and Berman, Ofer and Neri, Reem and Tarazi, Ezri and Parnas, Haim and Lotan, Offri and Zoabi, Majeed and Josef, Noam and Shashar, Nadav",
    title = "Three-Dimensional-Printed Coral-like Structures as a Habitat for Reef Fish",
    year = "2023",
    journal = "Journal of Marine Science and Engineering",
    abstract = "Coral reefs are three-dimensional biogenic structures that provide habitat for plenty of marine organisms; yet, coral reefs are deteriorating worldwide. Hence, it is essential to identify suitable substitutes for such coral services. This study examines reef fishes’ behavior and reactions to three-dimensional-printed (3DP) corals based on scanned Stylophora pistillata, as well as modified 3DP models. In particular, fishes’ unresponsiveness to the color, shape, morphology, and material of 3DP models both in vitro and in situ experiments was investigated. Coral reef fishes responded to the 3DP corals and demonstrated their usage in a range of services. Moreover, a greater number of fish species interacted more with 3DP models than they did with live corals. Furthermore, specific reef fish species, such as Sea Goldies (Pseudanthias squamipinnis), showed a preference for specific 3DP coral color, and other species demonstrated preferences for specific 3DP model shapes. The current study results show that three-dimensional-printed coral models can substitute for live corals for certain types of reef fish services.",
    url = "https://doi.org/10.3390/jmse11040882",
    doi = "10.3390/jmse11040882",
    openalex = "W4366772108",
    references = "doi103390ijerph17186574"
}

Introduction: Hermatypic corals have the capacity to construct the physical reef-framework and maintain the balance of coral reef functionality. However, in the past three decades, coral communities have been menaced by natural and anthropic pressures, resulting in an abrupt coral cover decline, and slow natural recovery. To mitigate coral reef collapse, assisted restoration techniques has been implemented and improved worldwide, However, the long-term effects of such interventions on ecological attributes have been scarcely reported. Objective: This study evaluated the effect of assisted coral intervention on calcium carbonate production (kg CaCO3 m-2 yr-1) and ecological volume (cm3) yielded by branching and massive corals from the central Mexican Pacific. Methods: We used colony size, extension rate, and skeletal density measurements of direct outplanted Pocillopora and Pavona coral species to calculate coral carbonate production, ecological volume, and model their long-term potential. Results: Coral carbonate produced after one-year of outplanting increased by 42 % (1.17 kg CaCO3 m-2 yr-1), where Pocillopora spp. and Pavona clavus corals contribute with 0.97 and 0.20 kg CaCO3 m-2 yr-1, respectively. The ecological volume also increased by 384 cm3 for Pocillopora and 56 cm3 for Pavona after one year period. Furthermore, the results suggest that long-term coral restoration actions (10 years) have the potential to significantly increase carbonate production. Conclusions: our data indicate that coral restoration initiatives have the potential to help mitigate the current low calcium carbonate production of Mexican Pacific reefs and may significantly contribute to the long-term maintenance of reef-framework based on ecological engineering tools, such initiatives represent essential functional properties related to reef ecosystem services provision.

@article{tortolerolangarica2023the,
    author = "Tortolero-Langarica, J. J. Adolfo and Rodríguez-Troncoso, Alma P. and Alvarez-Filip, Lorenzo and Cupul-Magaña, Amílcar L. and Carricart-Ganivet, Juan P.",
    title = "The contribution of assisted coral restoration to calcium carbonate production in Eastern Pacific reefs",
    year = "2023",
    journal = "Revista de Biología Tropical",
    abstract = "Introduction: Hermatypic corals have the capacity to construct the physical reef-framework and maintain the balance of coral reef functionality. However, in the past three decades, coral communities have been menaced by natural and anthropic pressures, resulting in an abrupt coral cover decline, and slow natural recovery. To mitigate coral reef collapse, assisted restoration techniques has been implemented and improved worldwide, However, the long-term effects of such interventions on ecological attributes have been scarcely reported. Objective: This study evaluated the effect of assisted coral intervention on calcium carbonate production (kg CaCO3 m-2 yr-1) and ecological volume (cm3) yielded by branching and massive corals from the central Mexican Pacific. Methods: We used colony size, extension rate, and skeletal density measurements of direct outplanted Pocillopora and Pavona coral species to calculate coral carbonate production, ecological volume, and model their long-term potential. Results: Coral carbonate produced after one-year of outplanting increased by 42 \% (1.17 kg CaCO3 m-2 yr-1), where Pocillopora spp. and Pavona clavus corals contribute with 0.97 and 0.20 kg CaCO3 m-2 yr-1, respectively. The ecological volume also increased by 384 cm3 for Pocillopora and 56 cm3 for Pavona after one year period. Furthermore, the results suggest that long-term coral restoration actions (10 years) have the potential to significantly increase carbonate production. Conclusions: our data indicate that coral restoration initiatives have the potential to help mitigate the current low calcium carbonate production of Mexican Pacific reefs and may significantly contribute to the long-term maintenance of reef-framework based on ecological engineering tools, such initiatives represent essential functional properties related to reef ecosystem services provision.",
    url = "https://doi.org/10.15517/rev.biol.trop..v71is1.54849",
    doi = "10.15517/rev.biol.trop..v71is1.54849",
    number = "S1",
    openalex = "W4367856271",
    pages = "e54849",
    volume = "71",
    references = "doi10100797894007011449, doi101007s0033801209014, doi101016jpocean200603004, doi101016jpocean200603012, doi101038nature22901, doi1011111365243513247, doi101111gbi12491, doi101111maec12678, doi101126scienceaaa4216, doi101371journalpone0003039, doi101371journalpone0009278, doi101371journalpone0226631"
}

Abstract Coral calcification is critical for reef growth and highly dependent on environmental conditions. Yet, little is known about how corals calcify under sub-optimal conditions (e.g., turbid waters, high nutrients, sedimentation) or coral growth in understudied regions such as the Colombian Caribbean. We therefore assessed the calcification and linear extension rates of five coral species across an inshore-to-offshore gradient in the Colombian Caribbean. A suite of environmental variables (temperature, light intensity, visibility, pH, nutrients) measured during the rainy season (May – November 2022) demonstrated more sub-optimal conditions inshore compared to offshore. Across all species, calcification rates were 59% and 37% lower inshore compared to the offshore and midshore sites, respectively. Across all sites, massive corals calcified up to 92% more than branching species but were more susceptible to heat stress and sub-optimal inshore conditions. However, branching species had reduced survival due to extreme climatic events (i.e., bleaching, hurricanes). A comparison with published rates for the wider Caribbean revealed that massive species in the Colombian Caribbean grow up to 11 times more than those in the wider Caribbean while branching species generally have similar growth rates, but this finding may have been influenced by fragment size and/or heat stress. Our findings indicate that present-day environmental conditions, coupled with more frequent extreme climatic events, will favor massive over branching species in midshore areas of the Colombian Caribbean. This suggests a possible shift towards faster calcifying massive species in future coral communities, possibly exacerbating the ongoing regional decline in branching species over the last decades.

@article{doi101007s00227024045115,
    author = "gel. Bravo, M. A. and Schoepf, Verena",
    title = "Growth rates of five coral species across a strong environmental gradient in the Colombian Caribbean",
    year = "2024",
    journal = "Marine Biology",
    abstract = "Abstract Coral calcification is critical for reef growth and highly dependent on environmental conditions. Yet, little is known about how corals calcify under sub-optimal conditions (e.g., turbid waters, high nutrients, sedimentation) or coral growth in understudied regions such as the Colombian Caribbean. We therefore assessed the calcification and linear extension rates of five coral species across an inshore-to-offshore gradient in the Colombian Caribbean. A suite of environmental variables (temperature, light intensity, visibility, pH, nutrients) measured during the rainy season (May – November 2022) demonstrated more sub-optimal conditions inshore compared to offshore. Across all species, calcification rates were 59\% and 37\% lower inshore compared to the offshore and midshore sites, respectively. Across all sites, massive corals calcified up to 92\% more than branching species but were more susceptible to heat stress and sub-optimal inshore conditions. However, branching species had reduced survival due to extreme climatic events (i.e., bleaching, hurricanes). A comparison with published rates for the wider Caribbean revealed that massive species in the Colombian Caribbean grow up to 11 times more than those in the wider Caribbean while branching species generally have similar growth rates, but this finding may have been influenced by fragment size and/or heat stress. Our findings indicate that present-day environmental conditions, coupled with more frequent extreme climatic events, will favor massive over branching species in midshore areas of the Colombian Caribbean. This suggests a possible shift towards faster calcifying massive species in future coral communities, possibly exacerbating the ongoing regional decline in branching species over the last decades.",
    url = "https://doi.org/10.1007/s00227-024-04511-5",
    doi = "10.1007/s00227-024-04511-5",
    openalex = "W4402049667",
    references = "doi101111rec14006"
}

Abstract Function-based studies have opened a new chapter in our understanding of coral reefs. Unfortunately, we are opening this chapter as the world’s reefs rapidly transform. In this context, one of the most important roles of function-based studies is to inform coral reef conservation. At this critical juncture, we have a chance to reflect on where we have come from, and where we are going, in coral reef functional ecology, with specific consideration of what this means for our approaches to conserving reefs. As focal examples, we examine the role of corals on reefs, and the practice of culling crown-of-thorns starfish, from a functional perspective. We also consider how the papers in this special issue build on our current understanding. Ultimately, we highlight how robust scientific investigation, based on an understanding of ecosystem functions, will be key in helping us navigate reefs through the current coral reef crisis.

@article{doi101007s0033802402474z,
    author = "Bellwood, David R. and Brandl, Simon J. and McWilliam, Mike and Streit, Robert P. and Yan, Helen F. and Tebbett, Sterling B.",
    title = "Studying functions on coral reefs: past perspectives, current conundrums, and future potential",
    year = "2024",
    journal = "Coral Reefs",
    abstract = "Abstract Function-based studies have opened a new chapter in our understanding of coral reefs. Unfortunately, we are opening this chapter as the world’s reefs rapidly transform. In this context, one of the most important roles of function-based studies is to inform coral reef conservation. At this critical juncture, we have a chance to reflect on where we have come from, and where we are going, in coral reef functional ecology, with specific consideration of what this means for our approaches to conserving reefs. As focal examples, we examine the role of corals on reefs, and the practice of culling crown-of-thorns starfish, from a functional perspective. We also consider how the papers in this special issue build on our current understanding. Ultimately, we highlight how robust scientific investigation, based on an understanding of ecosystem functions, will be key in helping us navigate reefs through the current coral reef crisis.",
    url = "https://doi.org/10.1007/s00338-024-02474-z",
    doi = "10.1007/s00338-024-02474-z",
    openalex = "W4392129275",
    references = "doi101038s4324702300766w"
}

Abstract Understanding and incorporating stakeholders' perceptions is fundamental to effectively managing marine protected areas (MPAs). Islas Marietas National Park (IMNP), an ecologically important coral reef ecosystem in the Central Mexican Pacific (CMP), has experienced major fluctuations in tourism pressures, environmental health, and regulatory changes in the past decade, which has led to efforts in its monitoring and restoration; however, limited research has been conducted to understand stakeholders’ perceptions of the social-ecological system. The present study integrates ecological attributes of the park, primarily changes in live coral cover (LCC), and stakeholders’ perceptions of the coral reef ecosystem to determine how users and tourism operators perceive the ecological changes in the area. It employs a mixed-methods approach, including ecological markers such as changes in live coral cover from 2012 to 2022 and recent surveys collected from tourism stakeholders. The results show that while live coral cover increased from 12.11 ± 6.21% in 2012 to 25.29 ± 15.00%, tourists and tourism operators perceive a decrease and degradation of the natural environment. In addition, tourists perceive a major ecological decline than tourism operators, and this perception is not correlated with their age range. Perceptions of environmental health do not align with the health status assessed by ecological monitoring, and the lack of awareness of ecological recovery at IMNP may hinder management efforts’ continued and expanded success. Therefore, developing more effective communication initiatives, citizen involvement, and education is important for conserving and managing coral communities in the park.

@article{doi101007s44289024000149,
    author = "Burroughs, Carina and Rodríguez‐Troncoso, Alma Paola",
    title = "Contrasts in ecological assessment and tourism sector perceptions of coral reefs: a case study at Islas Marietas National Park",
    year = "2024",
    journal = "Discover Oceans",
    abstract = "Abstract Understanding and incorporating stakeholders' perceptions is fundamental to effectively managing marine protected areas (MPAs). Islas Marietas National Park (IMNP), an ecologically important coral reef ecosystem in the Central Mexican Pacific (CMP), has experienced major fluctuations in tourism pressures, environmental health, and regulatory changes in the past decade, which has led to efforts in its monitoring and restoration; however, limited research has been conducted to understand stakeholders’ perceptions of the social-ecological system. The present study integrates ecological attributes of the park, primarily changes in live coral cover (LCC), and stakeholders’ perceptions of the coral reef ecosystem to determine how users and tourism operators perceive the ecological changes in the area. It employs a mixed-methods approach, including ecological markers such as changes in live coral cover from 2012 to 2022 and recent surveys collected from tourism stakeholders. The results show that while live coral cover increased from 12.11 ± 6.21\% in 2012 to 25.29 ± 15.00\%, tourists and tourism operators perceive a decrease and degradation of the natural environment. In addition, tourists perceive a major ecological decline than tourism operators, and this perception is not correlated with their age range. Perceptions of environmental health do not align with the health status assessed by ecological monitoring, and the lack of awareness of ecological recovery at IMNP may hinder management efforts’ continued and expanded success. Therefore, developing more effective communication initiatives, citizen involvement, and education is important for conserving and managing coral communities in the park.",
    url = "https://doi.org/10.1007/s44289-024-00014-9",
    doi = "10.1007/s44289-024-00014-9",
    openalex = "W4399953693",
    references = "doi1010022017rg000560, doi1010029781394260645, doi101016c20130114110, doi101016jecoleng201901002, doi101016jgloenvcha201307020, doi101016jgloenvcha201404002, doi101038nature18607, doi101073pnas1121215109, doi101126science1152509, doi101126science1204794, doi102167jost7100, tortolerolangarica2019accelerated"
}

Substrate stabilisation can be used to enhance coral recruitment where mobile rubble beds have formed post-disturbance. We trialled gabion-like ‘reef bags’, biodegradable coconut-fibre coir mesh bags filled with coral rubble at Pinnacle Bay and Bait Reef on the Great Barrier Reef. Most coir remained intact during the first 12 months, but had completely biodegraded after 2 years, leaving behind the experimental rubble mounds. After approximately 2 years, fish abundance was higher above mounds compared to surrounding rubble. After approximately 3 years, rubble stability and binding was also higher in rubble mounds than in surrounding rubble at Pinnacle Bay, but not at Bait Reef (although binding did increase in Bait Reef mounds over this time). The increased stability and binding did not, however, translate to significantly higher coral recruitment on rubble mounds in either location. The placement of these reef bags in terms of depth, reef zone, sediment load and competition appears crucial. Future trials should consider the size and interlocked-ness of rubble, the size of reef bags, larger mesh hole sizes, the number of layers of coir, and include unbagged mounds. • Coir mesh bags stabilised rubble into 3D mounds for 1 year, biodegrading afterwards. • Fish abundance was higher above rubble mounds compared to surrounding rubble. • Binding increased in rubble mounds but not in surrounding rubble. • The bags stabilise rubble without introducing foreign materials into the environment. • Coral recruitment may be hindered by thick mesh with small holes.

@article{doi101016jecoleng2024107433,
    author = "Kenyon, Tania M. and Jones, C. M. and Rissik, David and Brassil, W. and Callaghan, David P. and Mattocks, Neil and Baldock, Tom E.",
    title = "Bio-degradable ‘reef bags’ used for rubble stabilisation and their impact on rubble stability, binding, coral recruitment and fish occupancy",
    year = "2024",
    journal = "Ecological Engineering",
    abstract = "Substrate stabilisation can be used to enhance coral recruitment where mobile rubble beds have formed post-disturbance. We trialled gabion-like ‘reef bags’, biodegradable coconut-fibre coir mesh bags filled with coral rubble at Pinnacle Bay and Bait Reef on the Great Barrier Reef. Most coir remained intact during the first 12 months, but had completely biodegraded after 2 years, leaving behind the experimental rubble mounds. After approximately 2 years, fish abundance was higher above mounds compared to surrounding rubble. After approximately 3 years, rubble stability and binding was also higher in rubble mounds than in surrounding rubble at Pinnacle Bay, but not at Bait Reef (although binding did increase in Bait Reef mounds over this time). The increased stability and binding did not, however, translate to significantly higher coral recruitment on rubble mounds in either location. The placement of these reef bags in terms of depth, reef zone, sediment load and competition appears crucial. Future trials should consider the size and interlocked-ness of rubble, the size of reef bags, larger mesh hole sizes, the number of layers of coir, and include unbagged mounds. • Coir mesh bags stabilised rubble into 3D mounds for 1 year, biodegrading afterwards. • Fish abundance was higher above rubble mounds compared to surrounding rubble. • Binding increased in rubble mounds but not in surrounding rubble. • The bags stabilise rubble without introducing foreign materials into the environment. • Coral recruitment may be hindered by thick mesh with small holes.",
    url = "https://doi.org/10.1016/j.ecoleng.2024.107433",
    doi = "10.1016/j.ecoleng.2024.107433",
    openalex = "W4404198882",
    references = "doi103389fmars20231298411"
}

Coral reefs provide a multitude of ecosystem functions owing to the high levels of biodiversity they host. Coral species, as the foundation of shallow-water reefs, differ in their contributions toward the functioning of the ecosystem due in part to the disparate phylogenetic histories of scleractinian lineages. Understanding the spatial patterns and temporal trajectories of these biodiversity facets, as well as their interrelationships, is critical for more targeted conservation strategies in the face of widespread habitat degradation and climate change. Here, we analyse long-term benthic data spanning 1986 through 2020 on coral reefs in Singapore, which have been impacted by decades of urbanisation-related and thermal stressors, to test for differences between coral biodiversity facets—specifically, taxonomic, phylogenetic (evolutionary relatedness between species), and functional (occupancy of functional trait space) richness and diversity. Analyses show that taxonomic and phylogenetic richness and diversity measures increased over the 35-year period despite declines during major bleaching events. Yet, while taxonomic and phylogenetic diversity increased, functional richness and diversity declined over the same period. Community-weighted trait measures indicate a shift towards dominance of more stress-tolerant traits such as slower growth rates, smaller corallite sizes, and massive colony forms. Together, these trends highlight the effects of chronic urban stressors alongside major bleaching events impacting reef assemblages. Critically, such assemblage shifts and functional diversity declines were masked by increasing taxonomic diversity, which is most commonly assessed, and could erode ecosystem resilience. The temporal decoupling of the biodiversity facets examined here underscore the need for more comprehensive monitoring of reefs through a combination of trait-based approaches alongside traditional field surveys at finer taxonomic resolution.

@article{doi101016jecolind2024112143,
    author = "Chan, Yong Kit Samuel and Ng, Chin Soon Lionel and Tun, Karenne and Chou, Loke Ming and Huang, Danwei",
    title = "Decadal decline of functional diversity despite increasing taxonomic and phylogenetic diversity of coral reefs under chronic urbanisation stress",
    year = "2024",
    journal = "Ecological Indicators",
    abstract = "Coral reefs provide a multitude of ecosystem functions owing to the high levels of biodiversity they host. Coral species, as the foundation of shallow-water reefs, differ in their contributions toward the functioning of the ecosystem due in part to the disparate phylogenetic histories of scleractinian lineages. Understanding the spatial patterns and temporal trajectories of these biodiversity facets, as well as their interrelationships, is critical for more targeted conservation strategies in the face of widespread habitat degradation and climate change. Here, we analyse long-term benthic data spanning 1986 through 2020 on coral reefs in Singapore, which have been impacted by decades of urbanisation-related and thermal stressors, to test for differences between coral biodiversity facets—specifically, taxonomic, phylogenetic (evolutionary relatedness between species), and functional (occupancy of functional trait space) richness and diversity. Analyses show that taxonomic and phylogenetic richness and diversity measures increased over the 35-year period despite declines during major bleaching events. Yet, while taxonomic and phylogenetic diversity increased, functional richness and diversity declined over the same period. Community-weighted trait measures indicate a shift towards dominance of more stress-tolerant traits such as slower growth rates, smaller corallite sizes, and massive colony forms. Together, these trends highlight the effects of chronic urban stressors alongside major bleaching events impacting reef assemblages. Critically, such assemblage shifts and functional diversity declines were masked by increasing taxonomic diversity, which is most commonly assessed, and could erode ecosystem resilience. The temporal decoupling of the biodiversity facets examined here underscore the need for more comprehensive monitoring of reefs through a combination of trait-based approaches alongside traditional field surveys at finer taxonomic resolution.",
    url = "https://doi.org/10.1016/j.ecolind.2024.112143",
    doi = "10.1016/j.ecolind.2024.112143",
    openalex = "W4398155037",
    references = "doi101007s00338019018522"
}

1. There is an increased need for habitat models of coral reefs to aid active interventions and restoration efforts rather than just map reef habitat extent. Habitat models provide the base layer for connectivity estimates among coral populations, to identify sites with likely increased coral survival and reduced project costs. We present a spatial modelling method to better identify coral reef habitats for coral recruitment and survival. 2. We demonstrate these methods for an offshore reef cluster in North Western Australia that has lost live coral as a result of successive bleaching events. This isolated set of reefs has high levels of coral self-recruitment, which makes them a good test for methods that underpin spatial optimisation of coral restoration locations. 3. Our method uses satellite derived, multiscale depth and rugosity metrics to model habitat classes, and applies randomForest cross-validated variable importance to optimally select a subset of these metrics that best model each habitat. Our approach produces improved models compared to existing object-based segmentation methods by overcoming a bias toward larger single-scale homogenous reef features. 4. Our method produces robust models of target reef recruitment habitats with encrusting and juvenile corals with crustose coralline algae but also models of habitats that are not desirable as recruitment habitat such as turf algae, sand, and rubble. All these models meet or exceed accepted accuracy benchmarks (accuracy and AUC values >0.8 on blind hold-out data used for validation and kappa values >0.6). 5. These models are specifically designed to support coral restoration including prime coral recruitment habitats with a mixture of crustose coralline encrusting and juvenile corals. 6. We demonstrate how spatially explicit model validation can identify locations within the target area where models are most and least supported, providing valuable additional insights into planning targeted survey efforts to reduce spatial uncertainty, and targeted restoration interventions that have the highest probability of success. 7. Our method has broad utility due to the widely and freely available Sentinel 2 remote sensing data cover for most reef systems globally, and field data collected with a simple drop camera system and classified with via the ReefCloud open access image classification system. It also has potential for adaption and refinement using other finer scale commercial remote sensing satellite data that can be used to drive digital elevation models including Planet Labs Skysat and Worldview 3 data. • Remote sensing model identifies coral recruitment habitats for reef conservation. • Uses machine learning to map habitats using depth, rugosity, and band values. • Maps desirable (e.g., CCA, juvenile corals) and undesirable (e.g., sand) habitats. • Spatial validation accuracy guides field surveys and restoration sites. • Applicable globally using open Sentinel 2 data and simple camera setups.

@article{doi101016jrse2024114231,
    author = "Radford, Ben and Puotinen, Marji and Sahin, Defne and Boutros, Nader and Wyatt, Mathew and Gilmour, James",
    title = "A remote sensing model for coral recruitment habitat",
    year = "2024",
    journal = "Remote Sensing of Environment",
    abstract = "1. There is an increased need for habitat models of coral reefs to aid active interventions and restoration efforts rather than just map reef habitat extent. Habitat models provide the base layer for connectivity estimates among coral populations, to identify sites with likely increased coral survival and reduced project costs. We present a spatial modelling method to better identify coral reef habitats for coral recruitment and survival. 2. We demonstrate these methods for an offshore reef cluster in North Western Australia that has lost live coral as a result of successive bleaching events. This isolated set of reefs has high levels of coral self-recruitment, which makes them a good test for methods that underpin spatial optimisation of coral restoration locations. 3. Our method uses satellite derived, multiscale depth and rugosity metrics to model habitat classes, and applies randomForest cross-validated variable importance to optimally select a subset of these metrics that best model each habitat. Our approach produces improved models compared to existing object-based segmentation methods by overcoming a bias toward larger single-scale homogenous reef features. 4. Our method produces robust models of target reef recruitment habitats with encrusting and juvenile corals with crustose coralline algae but also models of habitats that are not desirable as recruitment habitat such as turf algae, sand, and rubble. All these models meet or exceed accepted accuracy benchmarks (accuracy and AUC values >0.8 on blind hold-out data used for validation and kappa values >0.6). 5. These models are specifically designed to support coral restoration including prime coral recruitment habitats with a mixture of crustose coralline encrusting and juvenile corals. 6. We demonstrate how spatially explicit model validation can identify locations within the target area where models are most and least supported, providing valuable additional insights into planning targeted survey efforts to reduce spatial uncertainty, and targeted restoration interventions that have the highest probability of success. 7. Our method has broad utility due to the widely and freely available Sentinel 2 remote sensing data cover for most reef systems globally, and field data collected with a simple drop camera system and classified with via the ReefCloud open access image classification system. It also has potential for adaption and refinement using other finer scale commercial remote sensing satellite data that can be used to drive digital elevation models including Planet Labs Skysat and Worldview 3 data. • Remote sensing model identifies coral recruitment habitats for reef conservation. • Uses machine learning to map habitats using depth, rugosity, and band values. • Maps desirable (e.g., CCA, juvenile corals) and undesirable (e.g., sand) habitats. • Spatial validation accuracy guides field surveys and restoration sites. • Applicable globally using open Sentinel 2 data and simple camera setups.",
    url = "https://doi.org/10.1016/j.rse.2024.114231",
    doi = "10.1016/j.rse.2024.114231",
    openalex = "W4399555952",
    references = "doi101038s4324702300766w"
}

@article{doi101016jscitotenv2024172897,
    author = "Zhu, Wentao and Zhao, He and Ke, Jingzhao and Zhang, Junling and Liu, Xiangbo and Zhou, Yinyin and Chen, Rouwen and Wang, Aimin and Li, Xiubao",
    title = "Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater",
    year = "2024",
    journal = "The Science of The Total Environment",
    url = "https://doi.org/10.1016/j.scitotenv.2024.172897",
    doi = "10.1016/j.scitotenv.2024.172897",
    openalex = "W4396521061",
    references = "doi101007s003430209253z"
}

, whereas control plots exhibited net erosive states. Staghorn restoration plots sustained positive net carbonate production at a threshold of ~ 2.96% coral cover. However, bleaching, storms, and disease challenge these reefs, highlighting the need for restoration strategies that enhance resilience to environmental stressors. Establishing Acroporid aggregations through outplanting, alongside climate adaptation strategies, could foster reef habitat growth and enhance the recovery of ecosystem services.

@article{doi101038s41598024767998,
    author = "Esplandiu, Emily and Morris, John T. and Enochs, Ian C. and Besemer, Nicole and Lirman, Diego",
    title = "Enhancing reef carbonate budgets through coral restoration",
    year = "2024",
    journal = "Scientific Reports",
    abstract = ", whereas control plots exhibited net erosive states. Staghorn restoration plots sustained positive net carbonate production at a threshold of \textasciitilde\ 2.96\% coral cover. However, bleaching, storms, and disease challenge these reefs, highlighting the need for restoration strategies that enhance resilience to environmental stressors. Establishing Acroporid aggregations through outplanting, alongside climate adaptation strategies, could foster reef habitat growth and enhance the recovery of ecosystem services.",
    url = "https://doi.org/10.1038/s41598-024-76799-8",
    doi = "10.1038/s41598-024-76799-8",
    openalex = "W4404240930",
    references = "doi103389fmars20231298411, tortolerolangarica2023the"
}

Coral reefs are among the most sensitive ecosystems affected by ocean warming and acidification, and are predicted to collapse over the next few decades. Reefs are predicted to shift from net accreting calcifier-dominated systems with exceptionally high biodiversity to net eroding algal-dominated systems with dramatically reduced biodiversity. Here, we present a two-year experimental study examining the responses of entire mesocosm coral reef communities to warming (+2 °C), acidification (-0.2 pH units), and combined future ocean (+2 °C, -0.2 pH) treatments. Contrary to modeled projections, we show that under future ocean conditions, these communities shift structure and composition yet persist as novel calcifying ecosystems with high biodiversity. Our results suggest that if climate change is limited to Paris Climate Agreement targets, coral reefs could persist in an altered state rather than collapse.

@article{doi101073pnas2407112121,
    author = "Jury, Christopher P. and Bahr, Keisha D. and Cros, Annick and Dobson, Kerri L. and Freel, Evan B. and Graham, Andrew T. and McLachlan, Rowan H. and Nelson, Craig E. and Price, James and de Souza, Mariana Rocha and Shizuru, Leah E. K. and Smith, Celia M. and Sparagon, Wesley J. and Squair, Cheryl and Timmers, Molly A. and Vicente, Jan and Webb, Maryann K. and Yamase, Nicole H. and Grottoli, Andréa G. and Toonen, Robert J.",
    title = "Experimental coral reef communities transform yet persist under mitigated future ocean warming and acidification",
    year = "2024",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Coral reefs are among the most sensitive ecosystems affected by ocean warming and acidification, and are predicted to collapse over the next few decades. Reefs are predicted to shift from net accreting calcifier-dominated systems with exceptionally high biodiversity to net eroding algal-dominated systems with dramatically reduced biodiversity. Here, we present a two-year experimental study examining the responses of entire mesocosm coral reef communities to warming (+2 °C), acidification (-0.2 pH units), and combined future ocean (+2 °C, -0.2 pH) treatments. Contrary to modeled projections, we show that under future ocean conditions, these communities shift structure and composition yet persist as novel calcifying ecosystems with high biodiversity. Our results suggest that if climate change is limited to Paris Climate Agreement targets, coral reefs could persist in an altered state rather than collapse.",
    url = "https://doi.org/10.1073/pnas.2407112121",
    doi = "10.1073/pnas.2407112121",
    openalex = "W4403863195",
    references = "doi101038s4324702300766w"
}

Coral reefs are increasingly impacted by climate-induced warming events. However, there is limited empirical evidence on the variation in the response of shallow coral reef communities to thermal stress across depths. Here, we assess depth-dependent changes in coral reef benthic communities following successive marine heatwaves from 2015 to 2017 across a 5-25 m depth gradient in the remote Chagos Archipelago, Central Indian Ocean. Our analyses show an overall decline in hard and soft coral cover and an increase in crustose coralline algae, sponge and reef pavement following successive marine heatwaves on the remote reef system. Our findings indicate that the changes in benthic communities in response to elevated seawater temperatures varied across depths. We found greater changes in benthic group cover at shallow depths (5-15 m) compared with deeper zones (15-25 m). The loss of hard coral cover was better predicted by initial thermal stress, while the loss of soft coral was associated with repeated thermal stress following successive warming events. Our study shows that benthic communities extending to 25 m depth were impacted by successive marine heatwaves, supporting concerns about the resilience of shallow coral reef communities to increasingly severe climate-driven warming events.

@article{doi101098rsos231246,
    author = "Pilly, Sivajyodee Sannassy and Roche, Ronan and Richardson, Laura E. and Turner, John R.",
    title = "Depth variation in benthic community response to repeated marine heatwaves on remote Central Indian Ocean reefs",
    year = "2024",
    journal = "Royal Society Open Science",
    abstract = "Coral reefs are increasingly impacted by climate-induced warming events. However, there is limited empirical evidence on the variation in the response of shallow coral reef communities to thermal stress across depths. Here, we assess depth-dependent changes in coral reef benthic communities following successive marine heatwaves from 2015 to 2017 across a 5-25 m depth gradient in the remote Chagos Archipelago, Central Indian Ocean. Our analyses show an overall decline in hard and soft coral cover and an increase in crustose coralline algae, sponge and reef pavement following successive marine heatwaves on the remote reef system. Our findings indicate that the changes in benthic communities in response to elevated seawater temperatures varied across depths. We found greater changes in benthic group cover at shallow depths (5-15 m) compared with deeper zones (15-25 m). The loss of hard coral cover was better predicted by initial thermal stress, while the loss of soft coral was associated with repeated thermal stress following successive warming events. Our study shows that benthic communities extending to 25 m depth were impacted by successive marine heatwaves, supporting concerns about the resilience of shallow coral reef communities to increasingly severe climate-driven warming events.",
    url = "https://doi.org/10.1098/rsos.231246",
    doi = "10.1098/rsos.231246",
    openalex = "W4393227654",
    references = "doi101038s4324702300766w"
}

Coral reefs play a crucial role in supporting over half a billion human livelihoods through their contributions to fisheries, tourism, and coastal protection. In light of substantial global declines in coral cover and the deterioration of reef habitats due to climate change and other human‐driven influences, the urgency of coral reef restoration has escalated to help preserve their vital ecosystem services. Comprehending the economic costs associated with existing and potential future coral restoration approaches has become time‐sensitive. The median cost of coral reef restoration is estimated to be 400,000 USD/ha (at base year 2010). This estimate comes with limitations due to its reliance on reported project costs associated with various techniques. Here we look to standardize expenses through uniform costing of reported efforts based on the time invested to estimate specific per‐unit costs for restoration methods. We complement literature‐extracted values with independent estimates based on real‐world operations. Using this approach, we decipher comparative costs of different nursery and outplanting approaches and identify incorporated dependencies. To gain insights into the impact of labor costs on global coral reef restoration expenditures, we examine variations in the costs of labor in two coral reef regions. Overall, our data‐based approach identifies limitations within the most commonly practiced restoration pathways, opportunities to reduce operational costs, and points toward priorities for future research and development.

@article{doi101111rec14326,
    author = "Schmidt‐Roach, Sebastian and Knorr, Travis G. and Roch, Cassandra and Klaus, Rebecca and Klepac, Courtney and Klein, Shannon G. and Duarte, Carlos M.",
    title = "Cost‐efficiency and effectiveness of coral restoration pathways",
    year = "2024",
    journal = "Restoration Ecology",
    abstract = "Coral reefs play a crucial role in supporting over half a billion human livelihoods through their contributions to fisheries, tourism, and coastal protection. In light of substantial global declines in coral cover and the deterioration of reef habitats due to climate change and other human‐driven influences, the urgency of coral reef restoration has escalated to help preserve their vital ecosystem services. Comprehending the economic costs associated with existing and potential future coral restoration approaches has become time‐sensitive. The median cost of coral reef restoration is estimated to be 400,000 USD/ha (at base year 2010). This estimate comes with limitations due to its reliance on reported project costs associated with various techniques. Here we look to standardize expenses through uniform costing of reported efforts based on the time invested to estimate specific per‐unit costs for restoration methods. We complement literature‐extracted values with independent estimates based on real‐world operations. Using this approach, we decipher comparative costs of different nursery and outplanting approaches and identify incorporated dependencies. To gain insights into the impact of labor costs on global coral reef restoration expenditures, we examine variations in the costs of labor in two coral reef regions. Overall, our data‐based approach identifies limitations within the most commonly practiced restoration pathways, opportunities to reduce operational costs, and points toward priorities for future research and development.",
    url = "https://doi.org/10.1111/rec.14326",
    doi = "10.1111/rec.14326",
    openalex = "W4404430499",
    references = "doi103389fmars20231298411, doi103390ijerph17186574"
}

Coral carbonate production is fundamental to reef accretion and, consequently, the preservation of essential reef ecosystem services, such as wave attenuation and sustained reef biodiversity. However, the unprecedented loss of coral reefs from anthropogenic impacts has put these valuable ecosystem services at risk. To counteract this loss, active rehabilitation of degraded reef sites has accelerated globally. A variety of restoration practices exist, tailored to local site needs and reef types. For sites where there is a significant unconsolidated substrate, Mars Assisted Reef Restoration System (MARRS, or “Reef Stars”) has been utilised to contribute toward rubble stabilisation and reef accretion. However, the effect of the Reef Stars on the local carbonate budgets and structural complexity has not been assessed. For that purpose, we assess coral cover and reef complexity through a census-based approach to identify the contribution of carbonate producers and eroders alongside studying coral skeletal properties to estimate current carbonate budgets on a rehabilitated site compared to natural unrehabilitated reef and rubble patches on the mid-Great Barrier Reef. Our research identified positive ecological processes and ecological functions such as increased carbonate budget, coral cover and structural complexity at the restored site compared to the non-intervened reef and rubble patches. In general, no impacts on skeletal rigour relative to this active reef restoration were found for two key coral species and the Acropora rubble for most of the skeletal traits. However, Pocillopora damicornis hardness seemed to decrease on the restored site compared to the other sites, demonstrating different performances of coral species during restoration activities that should be considered to maximise return-on-effort of restoration activities. Overall, our data demonstrate that consideration of carbonate budgets is important for measuring success of coral restoration initiatives and that coral restoration can be a relevant tool to recover lost local carbonate budgets.

@article{doi103389fmars20231298411,
    author = "Lendo, C. Isabel Nuñez and Suggett, David J. and Boote, Chloë and McArdle, Alicia and Nicholson, Freda and Fisher, Eric E. and Smith, David J. and Camp, Emma F.",
    title = "Carbonate budgets induced by coral restoration of a Great Barrier Reef site following cyclone damage",
    year = "2024",
    journal = "Frontiers in Marine Science",
    abstract = "Coral carbonate production is fundamental to reef accretion and, consequently, the preservation of essential reef ecosystem services, such as wave attenuation and sustained reef biodiversity. However, the unprecedented loss of coral reefs from anthropogenic impacts has put these valuable ecosystem services at risk. To counteract this loss, active rehabilitation of degraded reef sites has accelerated globally. A variety of restoration practices exist, tailored to local site needs and reef types. For sites where there is a significant unconsolidated substrate, Mars Assisted Reef Restoration System (MARRS, or “Reef Stars”) has been utilised to contribute toward rubble stabilisation and reef accretion. However, the effect of the Reef Stars on the local carbonate budgets and structural complexity has not been assessed. For that purpose, we assess coral cover and reef complexity through a census-based approach to identify the contribution of carbonate producers and eroders alongside studying coral skeletal properties to estimate current carbonate budgets on a rehabilitated site compared to natural unrehabilitated reef and rubble patches on the mid-Great Barrier Reef. Our research identified positive ecological processes and ecological functions such as increased carbonate budget, coral cover and structural complexity at the restored site compared to the non-intervened reef and rubble patches. In general, no impacts on skeletal rigour relative to this active reef restoration were found for two key coral species and the Acropora rubble for most of the skeletal traits. However, Pocillopora damicornis hardness seemed to decrease on the restored site compared to the other sites, demonstrating different performances of coral species during restoration activities that should be considered to maximise return-on-effort of restoration activities. Overall, our data demonstrate that consideration of carbonate budgets is important for measuring success of coral restoration initiatives and that coral restoration can be a relevant tool to recover lost local carbonate budgets.",
    url = "https://doi.org/10.3389/fmars.2023.1298411",
    doi = "10.3389/fmars.2023.1298411",
    openalex = "W4391261256",
    references = "doi101007s003380000086, doi1010160026080085900515, doi101016jecoleng201901002, doi101038nature21707, doi101038s4158601800412, doi101046j14610248200100203x, doi101073pnas1208909109, doi101093biomet5234591, doi101098rspb20090339, doi101126science1086050, doi101126science1149345, tortolerolangarica2019accelerated"
}

Significant threats to the long-term persistence of coral reefs have accelerated the adoption of coral propagation and out-planting approaches. However, how materials commonly used for propagation structures could potentially affect coral-associated bacterial communities remains untested. Here, we examined the impact of metal propagation structures on coral-associated bacterial communities. Fragments of the coral species Acropora millepora were grown on aluminium, sand/epoxy-coated steel (Reef Stars), and uncoated steel (rebar) structures. After 6 months, the functional and taxonomic profiles of coral-associated bacterial communities of propagated corals and reef colonies were characterised using amplicon (16S rRNA gene) and shotgun metagenomic sequencing. No differences in the phylogenetic structure or functional profile of coral-associated bacterial communities were observed between propagated corals and reef colonies. However, specific genes and pathways (e.g., lipid, nucleotide, and carbohydrate metabolism) were overrepresented in corals grown on different materials, and different taxa were indicative of the materials. These findings indicate that coral propagation on different materials may lead to differences in the individual bacterial taxa and functional potential of coral-associated bacterial communities, but how these contribute to changed holobiont fitness presents a key question to be addressed.

@article{doi103389fmars20241366971,
    author = "Strudwick, Paige and Suggett, David J. and Seymour, Justin R. and DeMaere, Matthew Z. and Grima, Amanda and Edmondson, John and McArdle, Alicia and Nicholson, Freda and Camp, Emma F.",
    title = "Assessing how metal reef restoration structures shape the functional and taxonomic profile of coral-associated bacterial communities",
    year = "2024",
    journal = "Frontiers in Marine Science",
    abstract = "Significant threats to the long-term persistence of coral reefs have accelerated the adoption of coral propagation and out-planting approaches. However, how materials commonly used for propagation structures could potentially affect coral-associated bacterial communities remains untested. Here, we examined the impact of metal propagation structures on coral-associated bacterial communities. Fragments of the coral species Acropora millepora were grown on aluminium, sand/epoxy-coated steel (Reef Stars), and uncoated steel (rebar) structures. After 6 months, the functional and taxonomic profiles of coral-associated bacterial communities of propagated corals and reef colonies were characterised using amplicon (16S rRNA gene) and shotgun metagenomic sequencing. No differences in the phylogenetic structure or functional profile of coral-associated bacterial communities were observed between propagated corals and reef colonies. However, specific genes and pathways (e.g., lipid, nucleotide, and carbohydrate metabolism) were overrepresented in corals grown on different materials, and different taxa were indicative of the materials. These findings indicate that coral propagation on different materials may lead to differences in the individual bacterial taxa and functional potential of coral-associated bacterial communities, but how these contribute to changed holobiont fitness presents a key question to be addressed.",
    url = "https://doi.org/10.3389/fmars.2024.1366971",
    doi = "10.3389/fmars.2024.1366971",
    openalex = "W4395669366",
    references = "doi103389fmars20231298411"
}

The decline of coral reefs has increased interest in ecological restoration. Due to the scarcity of coral gardening projects in the Eastern Tropical Pacific, improving our understanding of such techniques is key. We report the results of coral gardening using the branching Pocillopora spp. and massive coral species (Pavona gigantea, Pavona clavus and Porites lobata) in an upwelling area in Costa Rica. We examined whether nursery type influenced Pocillopora spp. survival and growth, and how environmental conditions shaped restoration. We monitored the survival and growth of Pocillopora spp. fragments (n = 334) and microfragments of massive species (P. gigantea [n = 148], P. clavus [n = 37], P. lobata [n = 66]) over 11 months. Survival at the end of the gardening period was 51% for Pocillopora spp., 59% for P. clavus, 55% for P. gigantea, and 17% for P. lobata, with a decline after a cease in maintenance caused by the COVID-19 lockdown. Pocillopora spp. fragments in the floating nurseries exhibited higher growth (7.52 ± 1.98 and 6.64 ± 2.91 cm yr -1) than in the A-frame (4.16 ± 2.35 cm yr -1), which suggests the benefits of suspending fragments. For massive microfragments coral growth was 1.92-4.66 cm 2 yr -1 and were affected by pigmentation loss, causing partial tissue loss and mortality. Our results point towards acclimation to local conditions, and show the need to develop site-specific cost-efficient gardening techniques for massive species, allowing for a multi-species approach to ensure long-term ecosystem recovery.

@article{doi103389fmars20241400026,
    author = "Fabregat-Malé, Sònia and Mena-González, Sebastián and Quesada‐Perez, Fabio and Alvarado, Juan José",
    title = "Testing the feasibility of coral nurseries in an upwelling area in the North Pacific of Costa Rica",
    year = "2024",
    journal = "Frontiers in Marine Science",
    abstract = "The decline of coral reefs has increased interest in ecological restoration. Due to the scarcity of coral gardening projects in the Eastern Tropical Pacific, improving our understanding of such techniques is key. We report the results of coral gardening using the branching Pocillopora spp. and massive coral species (Pavona gigantea, Pavona clavus and Porites lobata) in an upwelling area in Costa Rica. We examined whether nursery type influenced Pocillopora spp. survival and growth, and how environmental conditions shaped restoration. We monitored the survival and growth of Pocillopora spp. fragments (n = 334) and microfragments of massive species (P. gigantea [n = 148], P. clavus [n = 37], P. lobata [n = 66]) over 11 months. Survival at the end of the gardening period was 51\% for Pocillopora spp., 59\% for P. clavus, 55\% for P. gigantea, and 17\% for P. lobata, with a decline after a cease in maintenance caused by the COVID-19 lockdown. Pocillopora spp. fragments in the floating nurseries exhibited higher growth (7.52 ± 1.98 and 6.64 ± 2.91 cm yr -1) than in the A-frame (4.16 ± 2.35 cm yr -1), which suggests the benefits of suspending fragments. For massive microfragments coral growth was 1.92-4.66 cm 2 yr -1 and were affected by pigmentation loss, causing partial tissue loss and mortality. Our results point towards acclimation to local conditions, and show the need to develop site-specific cost-efficient gardening techniques for massive species, allowing for a multi-species approach to ensure long-term ecosystem recovery.",
    url = "https://doi.org/10.3389/fmars.2024.1400026",
    doi = "10.3389/fmars.2024.1400026",
    openalex = "W4402141618",
    references = "doi101111gbi12491, doi101111rec14006"
}

Sexually propagated scleractinian corals are in high demand for coral reef restoration. However, for threatened reef-building corals, many of the molecular mechanisms related to their reproduction remain largely unknown, which forms a major bottleneck in the large-scale cultivation of sexually reproducing corals. In this study, we analyzed the proteomic signatures of red eggs and spermatozoa from the ecologically significant coral Galaxea fascicularis, using a data-independent acquisition mass spectrometry (DIA-MS) method. A total of 7741 and 7279 proteins from mature red eggs and spermatozoa were identified, respectively. Among these proteins, 596 proteins were spermatozoa-specific and 1056 were egg-specific. Additionally, a total of 4413 differentially abundant proteins (DAPs) were identified, among which 3121 proteins were up-regulated in red eggs and 1292 proteins were up-regulated in spermatozoa. Furthermore, anenrichment analyses showed that DAPs identified in red eggs were mainly involved in the progesterone-mediated oocyte maturation pathway and lectin pathway; and DAPs detected in spermatozoa were mainly involved in the insulin secretion pathway and metabolic pathways for the generation of energy. This result will contribute to the discovery of the intrinsic regulation pathway of gamete maturation and fertilization. Furthermore, at least 57 proteins associated with gamete maturation and reproduction were identified, including the red fluorescent protein (RFP), vitellogenin proteins (VG), the egg protein (EP), the testis-specific serine/threonine-protein kinase family (TSSKs), and the EF-hand Ca2+-binding protein family (EFHC1 and EFHC2). Particularly, the third yolk protein EUPHY was reported for the first time in G. fascicularis. In conclusion, this study unveiled groundbreaking molecular insights into coral sexual reproduction, paving the way for more effective conservation and sustainable development of coral reef ecosystems

@article{doi103390jmse12122341,
    author = "Zhou, Yinyin and Ke, Jingzhao and Zheng, Lingyu and Mo, Shaoyang and Liu, Xiangbo and Zhao, He and Zhu, Wentao and Li, Xiubao",
    title = "Data-Independent Acquisition-Based Quantitative Proteomics Analysis of Fertile Red Eggs and Spermatozoa in Hermatypic Coral Galaxea fascicularis: Revealing Key Proteins Related to Gamete Maturation and Fertilization",
    year = "2024",
    journal = "Journal of Marine Science and Engineering",
    abstract = "Sexually propagated scleractinian corals are in high demand for coral reef restoration. However, for threatened reef-building corals, many of the molecular mechanisms related to their reproduction remain largely unknown, which forms a major bottleneck in the large-scale cultivation of sexually reproducing corals. In this study, we analyzed the proteomic signatures of red eggs and spermatozoa from the ecologically significant coral Galaxea fascicularis, using a data-independent acquisition mass spectrometry (DIA-MS) method. A total of 7741 and 7279 proteins from mature red eggs and spermatozoa were identified, respectively. Among these proteins, 596 proteins were spermatozoa-specific and 1056 were egg-specific. Additionally, a total of 4413 differentially abundant proteins (DAPs) were identified, among which 3121 proteins were up-regulated in red eggs and 1292 proteins were up-regulated in spermatozoa. Furthermore, anenrichment analyses showed that DAPs identified in red eggs were mainly involved in the progesterone-mediated oocyte maturation pathway and lectin pathway; and DAPs detected in spermatozoa were mainly involved in the insulin secretion pathway and metabolic pathways for the generation of energy. This result will contribute to the discovery of the intrinsic regulation pathway of gamete maturation and fertilization. Furthermore, at least 57 proteins associated with gamete maturation and reproduction were identified, including the red fluorescent protein (RFP), vitellogenin proteins (VG), the egg protein (EP), the testis-specific serine/threonine-protein kinase family (TSSKs), and the EF-hand Ca2+-binding protein family (EFHC1 and EFHC2). Particularly, the third yolk protein EUPHY was reported for the first time in G. fascicularis. In conclusion, this study unveiled groundbreaking molecular insights into coral sexual reproduction, paving the way for more effective conservation and sustainable development of coral reef ecosystems",
    url = "https://doi.org/10.3390/jmse12122341",
    doi = "10.3390/jmse12122341",
    openalex = "W4405640276",
    references = "doi101007s003430209253z"
}

Abstract Calcium carbonate production constitutes one of the core processes that drive coral reef ecosystem functioning and can be assessed using in-water or image-based survey methods, which have not previously been compared. This study compares carbonate production estimates from in-water ReefBudget surveys and image-based CoralNet analyses in Puerto Rico, Indonesia, and Chagos Archipelago. Methods were compared for different regions (Western Atlantic and Indo-Pacific), reef settings (low and high coral cover), CoralNet calcification versions (v1 and v2), and input metrics (regional vs. local coral growth rates). We show similar gross carbonate production estimates between methods, indicating that area-normalised scaling of calcification rates and assumptions about colony size and rugosity employed in CoralNet produce comparable estimates to ReefBudget surveys. Divergences in carbonate production estimates are potentially driven by differences in survey methods (reef contour measurements vs. planar imagery) and survey effort, which affect calcifier cover estimates, particularly at low coral cover sites. Local versus regional growth rate comparisons suggest site-specific factors can influence accuracy more than method choice. Our findings suggest that image-based methods can allow rapid reef-scale calcification estimates from photo or video imagery. These methods, combined with machine learning substrate classification algorithms, can estimate both benthic cover and carbonate production over larger reef areas and can be applied to historically collect benthic cover data to track carbonate production trends. We encourage researchers to recognise situation-specific differences in methodologies and select the one most suitable for their specific study site, required level of accuracy, and time constraints for fieldwork and image analysis.

@article{doi101007s00338025026201,
    author = "Pilly, Sivajyodee Sannassy and Townsend, Joseph E. and Alisa, Cut Aja Gita and Razak, Tries B. and Roche, Ronan and Turner, John R. and Chan, Stephen and Kriegman, David and Andersson, Andreas J. and Perry, Chris T. and Lange, Ines D. and Courtney, Travis A.",
    title = "Quantifying coral reef carbonate budgets: a comparison between ReefBudget and CoralNet",
    year = "2025",
    journal = "Coral Reefs",
    abstract = "Abstract Calcium carbonate production constitutes one of the core processes that drive coral reef ecosystem functioning and can be assessed using in-water or image-based survey methods, which have not previously been compared. This study compares carbonate production estimates from in-water ReefBudget surveys and image-based CoralNet analyses in Puerto Rico, Indonesia, and Chagos Archipelago. Methods were compared for different regions (Western Atlantic and Indo-Pacific), reef settings (low and high coral cover), CoralNet calcification versions (v1 and v2), and input metrics (regional vs. local coral growth rates). We show similar gross carbonate production estimates between methods, indicating that area-normalised scaling of calcification rates and assumptions about colony size and rugosity employed in CoralNet produce comparable estimates to ReefBudget surveys. Divergences in carbonate production estimates are potentially driven by differences in survey methods (reef contour measurements vs. planar imagery) and survey effort, which affect calcifier cover estimates, particularly at low coral cover sites. Local versus regional growth rate comparisons suggest site-specific factors can influence accuracy more than method choice. Our findings suggest that image-based methods can allow rapid reef-scale calcification estimates from photo or video imagery. These methods, combined with machine learning substrate classification algorithms, can estimate both benthic cover and carbonate production over larger reef areas and can be applied to historically collect benthic cover data to track carbonate production trends. We encourage researchers to recognise situation-specific differences in methodologies and select the one most suitable for their specific study site, required level of accuracy, and time constraints for fieldwork and image analysis.",
    url = "https://doi.org/10.1007/s00338-025-02620-1",
    doi = "10.1007/s00338-025-02620-1",
    openalex = "W4408532796",
    references = "doi103389fmars20231298411"
}

Fish are a key group in any coral community, and their assemblage varies with differences in habitat structure among reefs, as well as with seasonal and interannual environmental fluctuations that influence community structure and ecosystem functioning. Long-term monitoring, combined with taxonomic and functional indexes, can provide valuable information on the effects of local and regional environmental fluctuations on any biological group. This study evaluated the decadal (2013–2022) variability of fish assemblage and their function in a Natural Protected Area composed of a coral community distributed along two islands, using diurnal visual censuses along belt transects (5 transects/site/season/year) in a 3–13 m depth range. The results showed higher values of species richness, functional richness, evenness, and redundancy on Isla Redonda, which also exhibited the highest observed diversity of benthic components, suggesting a potential association between benthic diversity and fish assemblage structure. Throughout the decade, fish assemblages exhibited clear temporal trends influenced by seasonal cycles, large-scale climatic events, and habitat changes. Especially during the El Niño 2015–2016 event, an abnormal increase in temperatures led to marked shifts in species composition and a decline in the abundance of schooling planktivorous species, such as Apogon pacificus. This was followed by a reduction in species richness in 2018, primarily due to habitat homogenization resulting from a decline in benthic diversity. The loss of benthic diversity and more frequent extreme meteorological events will likely disrupt species interactions, affecting coexistence, resource use, and long-term community stability. Although connectivity between islands currently acts as a buffer, this could be compromised if environmental conditions deteriorate (e.g., natural and anthropogenic stressors), causing a significant decline in the reef’s health and provision of ecosystem services.

@article{doi101007s44396025000158,
    author = "de Alba-Guzmán, Cassandra and Rodríguez‐Troncoso, Alma Paola and Cupul‐Magaña, Amilcar Leví and Rodríguez‐Zaragoza, Fabián A. and Cabral‐Tena, Rafael A. and Tortolero‐Langarica, J. J. Adolfo",
    title = "Decadal changes in the fish assemblage structure and function within an insular coral community",
    year = "2025",
    journal = "Discover Ecology",
    abstract = "Fish are a key group in any coral community, and their assemblage varies with differences in habitat structure among reefs, as well as with seasonal and interannual environmental fluctuations that influence community structure and ecosystem functioning. Long-term monitoring, combined with taxonomic and functional indexes, can provide valuable information on the effects of local and regional environmental fluctuations on any biological group. This study evaluated the decadal (2013–2022) variability of fish assemblage and their function in a Natural Protected Area composed of a coral community distributed along two islands, using diurnal visual censuses along belt transects (5 transects/site/season/year) in a 3–13 m depth range. The results showed higher values of species richness, functional richness, evenness, and redundancy on Isla Redonda, which also exhibited the highest observed diversity of benthic components, suggesting a potential association between benthic diversity and fish assemblage structure. Throughout the decade, fish assemblages exhibited clear temporal trends influenced by seasonal cycles, large-scale climatic events, and habitat changes. Especially during the El Niño 2015–2016 event, an abnormal increase in temperatures led to marked shifts in species composition and a decline in the abundance of schooling planktivorous species, such as Apogon pacificus. This was followed by a reduction in species richness in 2018, primarily due to habitat homogenization resulting from a decline in benthic diversity. The loss of benthic diversity and more frequent extreme meteorological events will likely disrupt species interactions, affecting coexistence, resource use, and long-term community stability. Although connectivity between islands currently acts as a buffer, this could be compromised if environmental conditions deteriorate (e.g., natural and anthropogenic stressors), causing a significant decline in the reef’s health and provision of ecosystem services.",
    url = "https://doi.org/10.1007/s44396-025-00015-8",
    doi = "10.1007/s44396-025-00015-8",
    openalex = "W4417107400",
    references = "doi101007s44289024000149, doi101111rec14006"
}

Benthic biogenic habitats are crucial for coastal marine ecosystems, supporting food and shelter for a large range of marine species, but they are increasingly threatened by increasing anthropogenic impacts. While large-scale monitoring data are increasingly available, tools to describe benthic habitat changes in standardised and yet finely resolved manner are still needed. The aim of this study was to define reef benthic habitat states and explore their spatial and temporal variability on a global scale using an innovative clustering pipeline. For this purpose, we used substrate cover data collected along 6554 transects worldwide by citizen scientists contributing to the Reef Life Survey program. We applied an innovative clustering pipeline that combines three algorithms — Uniform Manifold Approximation and Projection (UMAP) for dimension reduction; Hierarchical Density-Based Spatial Clustering of Applications with Noise (HDBSCAN) — to identify benthic habitat states and Shapley values to interpret the clusters identified. This unsupervised pipeline identified 17 distinct clusters worldwide, representing typical temperate and tropical benthic habitats such as large canopy forming algae and branching corals, respectively, as well as transitional states between different habitat states. Temporal site-specific analyses further demonstrated the pipeline's effectiveness in capturing fine-scale habitat dynamics. By providing a standardised, scalable approach, this work enables consistent tracking of benthic habitat changes across spatial and temporal scales worldwide. This study also showcases the potential of integrating the UMAP-HDBSCAN pipeline with Shapley values for clustering noisy ecological data from citizen science initiatives. • UMAP-HDBSCAN pipeline defines 17 nuances benthic habitat states globally. • SHAP values uncover benthic habitats by explaining discovered cluster compositions. • Reveals habitat transitions and potential regime shifts across benthic ecosystems. • UMAP-HDBSCAN pipeline enables tracking of spatio-temporal benthic habitat changes. • Adaptable workflow for clustering noisy ecological data in diverse research contexts.

@article{doi101016jecoinf2025103058,
    author = "Violet, Clément and Boyé, Aurélien and Dubois, Sophie and Edgar, Graham J. and Oh, Elizabeth and Stuart‐Smith, Rick D. and Marzloff, Martin P.",
    title = "Leveraging citizen science to classify and track benthic habitat states: An unsupervised UMAP-HDBSCAN pipeline applied to the global reef life survey dataset",
    year = "2025",
    journal = "Ecological Informatics",
    abstract = "Benthic biogenic habitats are crucial for coastal marine ecosystems, supporting food and shelter for a large range of marine species, but they are increasingly threatened by increasing anthropogenic impacts. While large-scale monitoring data are increasingly available, tools to describe benthic habitat changes in standardised and yet finely resolved manner are still needed. The aim of this study was to define reef benthic habitat states and explore their spatial and temporal variability on a global scale using an innovative clustering pipeline. For this purpose, we used substrate cover data collected along 6554 transects worldwide by citizen scientists contributing to the Reef Life Survey program. We applied an innovative clustering pipeline that combines three algorithms — Uniform Manifold Approximation and Projection (UMAP) for dimension reduction; Hierarchical Density-Based Spatial Clustering of Applications with Noise (HDBSCAN) — to identify benthic habitat states and Shapley values to interpret the clusters identified. This unsupervised pipeline identified 17 distinct clusters worldwide, representing typical temperate and tropical benthic habitats such as large canopy forming algae and branching corals, respectively, as well as transitional states between different habitat states. Temporal site-specific analyses further demonstrated the pipeline's effectiveness in capturing fine-scale habitat dynamics. By providing a standardised, scalable approach, this work enables consistent tracking of benthic habitat changes across spatial and temporal scales worldwide. This study also showcases the potential of integrating the UMAP-HDBSCAN pipeline with Shapley values for clustering noisy ecological data from citizen science initiatives. • UMAP-HDBSCAN pipeline defines 17 nuances benthic habitat states globally. • SHAP values uncover benthic habitats by explaining discovered cluster compositions. • Reveals habitat transitions and potential regime shifts across benthic ecosystems. • UMAP-HDBSCAN pipeline enables tracking of spatio-temporal benthic habitat changes. • Adaptable workflow for clustering noisy ecological data in diverse research contexts.",
    url = "https://doi.org/10.1016/j.ecoinf.2025.103058",
    doi = "10.1016/j.ecoinf.2025.103058",
    openalex = "W4407025889",
    references = "doi101038s4324702300766w"
}

@article{doi101016jjenvman2025128166,
    author = "Reguero, B.G. and Gaido, C. and Storlazzi, CD and McNulty, V.P. and Perez, D.I. and Beck, Mw",
    title = "Where to restore and conserve? A regional benefit cost analysis of coral reef protection and restoration for coastal flood resilience",
    year = "2025",
    journal = "Journal of Environmental Management",
    url = "https://doi.org/10.1016/j.jenvman.2025.128166",
    doi = "10.1016/j.jenvman.2025.128166",
    openalex = "W7116793658",
    references = "doi103389fmars20231298411"
}

Understanding species' susceptibility to environmental stressors is crucial for conservation planning, but such data are unavailable for many subtropical corals. We therefore conducted 1-month laboratory experiments to determine the heat stress susceptibility of eight species from subtropical areas by exposing them to 32 °C (treatment) or 25 °C (control). Four species (Dipsastraea rotumana, Echinophyllia aspera, Pavona decussata, and Platygyra carnosa) survived the whole experiment, although bleaching occurred after one to two weeks of exposure. The heat exposure caused total mortality in the other four species: on day 2 in Acropora solitaryensis, day 7 in Acropora digitifera, day 9 in Acropora pruinosa, and day 17 in Montipora peltiformis. These results suggest that repeated heatwaves may cause changes in coral communities by causing disproportionally high mortality of heat-sensitive species. Coral species tested in this study, collected from subtropical reefs previously thought to be refuges for coral reefs under global warming, demonstrated greater susceptibility to heat stress than their tropical counterparts. This raises concerns about the persistence of coral reefs as sea surface temperatures continue to rise.

@article{doi101016jmarenvres2025107132,
    author = "Yeung, Yip Hung and Zhang, Yanjie and Xie, James Y. and Qiu, Jian‐Wen",
    title = "Laboratory experiments revealed different bleaching susceptibilities to heat stress in eight species of subtropical urban corals",
    year = "2025",
    journal = "Marine Environmental Research",
    abstract = "Understanding species' susceptibility to environmental stressors is crucial for conservation planning, but such data are unavailable for many subtropical corals. We therefore conducted 1-month laboratory experiments to determine the heat stress susceptibility of eight species from subtropical areas by exposing them to 32 °C (treatment) or 25 °C (control). Four species (Dipsastraea rotumana, Echinophyllia aspera, Pavona decussata, and Platygyra carnosa) survived the whole experiment, although bleaching occurred after one to two weeks of exposure. The heat exposure caused total mortality in the other four species: on day 2 in Acropora solitaryensis, day 7 in Acropora digitifera, day 9 in Acropora pruinosa, and day 17 in Montipora peltiformis. These results suggest that repeated heatwaves may cause changes in coral communities by causing disproportionally high mortality of heat-sensitive species. Coral species tested in this study, collected from subtropical reefs previously thought to be refuges for coral reefs under global warming, demonstrated greater susceptibility to heat stress than their tropical counterparts. This raises concerns about the persistence of coral reefs as sea surface temperatures continue to rise.",
    url = "https://doi.org/10.1016/j.marenvres.2025.107132",
    doi = "10.1016/j.marenvres.2025.107132",
    openalex = "W4409199311",
    references = "doi101016jrsma2023103289"
}

@article{doi101016jmarenvres2025107169,
    author = "Zhu, Wentao and Zhang, Junling and Zhao, He and Liu, Xiangbo and Ke, Jingzhao and Wang, Aimin and Li, Xiubao",
    title = "Relative importance of microbial abundance and taxonomic types in driving the processes and functions of coral reef seawater in the Wuzhizhou Island",
    year = "2025",
    journal = "Marine Environmental Research",
    url = "https://doi.org/10.1016/j.marenvres.2025.107169",
    doi = "10.1016/j.marenvres.2025.107169",
    openalex = "W4409628379",
    references = "doi101007s003430209253z"
}

Corals, as primary calcifiers, play a vital role in synthesizing calcium carbonate (CaCO3) to build their skeletons, contributing to the formation of complex benthic habitats that support high biodiversity and marine productivity. However, coral habitats have dramatically declined worldwide due to ocean warming and acidification. Interestingly, the subtropical Southwestern Atlantic (SWA) has emerged as a potential refuge, where corals like Mussismilia hispida exhibit resilience to thermal anomalies. In this study, we estimate CaCO3 production by M. hispida in subtropical SWA reefs, revealing an average growth rate of 4.3 ± 1 mm/year and a CaCO3 production rate of 1.31 ± 0.3 kg. m-2. year-1. These values are comparable to tropical reef systems, suggesting that M. hispida contributes significantly to carbonate production, even in higher latitude environments. Moreover, despite experiencing one of the most intense thermal anomalies recorded, colony abundance (i.e., ind. m-2) and carbonate production remained stable, emphasizing the potential of the region as a climate refuge. While many tropical reefs act as net CO2 sources due to the release of CO2 during calcification, SWA subtropical reefs present lower coverage of corals. They are dominated by algae and other primary producers, acting as an important potential carbon sink through photosynthesis and long-term storage of carbon over centuries as mineralized CaCO3. Thus, we provide evidence that M. hispida, by producing ∼170 tons. year-1 of CaCO3 in the subtropical reefs of the Alcatrazes Archipelago, acts as a key player in carbon sequestration and CaCO3 production in higher latitude SWA areas.

@article{doi101016jmarenvres2025107218,
    author = "Oliveira, L S and Sanches, Fábio H C and Silva, M A and Longo, P A S and Laurino, Ivan R A and Motta, Fabio Dos Santos and Pereira-Filho, Guilherme H",
    title = "Calcium carbonate production by the massive coral Mussismilia hispida in subtropical reefs of the Southwestern Atlantic.",
    year = "2025",
    journal = "Marine environmental research",
    abstract = "Corals, as primary calcifiers, play a vital role in synthesizing calcium carbonate (CaCO3) to build their skeletons, contributing to the formation of complex benthic habitats that support high biodiversity and marine productivity. However, coral habitats have dramatically declined worldwide due to ocean warming and acidification. Interestingly, the subtropical Southwestern Atlantic (SWA) has emerged as a potential refuge, where corals like Mussismilia hispida exhibit resilience to thermal anomalies. In this study, we estimate CaCO3 production by M. hispida in subtropical SWA reefs, revealing an average growth rate of 4.3 ± 1 mm/year and a CaCO3 production rate of 1.31 ± 0.3 kg. m-2. year-1. These values are comparable to tropical reef systems, suggesting that M. hispida contributes significantly to carbonate production, even in higher latitude environments. Moreover, despite experiencing one of the most intense thermal anomalies recorded, colony abundance (i.e., ind. m-2) and carbonate production remained stable, emphasizing the potential of the region as a climate refuge. While many tropical reefs act as net CO2 sources due to the release of CO2 during calcification, SWA subtropical reefs present lower coverage of corals. They are dominated by algae and other primary producers, acting as an important potential carbon sink through photosynthesis and long-term storage of carbon over centuries as mineralized CaCO3. Thus, we provide evidence that M. hispida, by producing ∼170 tons. year-1 of CaCO3 in the subtropical reefs of the Alcatrazes Archipelago, acts as a key player in carbon sequestration and CaCO3 production in higher latitude SWA areas.",
    url = "https://pubmed.ncbi.nlm.nih.gov/40373644/",
    doi = "10.1016/j.marenvres.2025.107218",
    openalex = "W4410250628",
    pmid = "40373644",
    references = "doi10100797894017328402, doi101016s0012825202001046, doi101016s0025326x99002374, doi101038nature04095, doi101038ncomms2409, doi101093icb391146, doi101111j13652699201102613x, doi101126sciadv1501252, doi101126scienceaan8048, doi103389fmars201700158"
}

Calcifying organisms support key geo-ecological functions in shallow tropical and temperate reefs worldwide, including creating habitat structure, producing sediments, and supporting reef accretion. These functions depend on the carbonate budget: the balance between calcium carbonate production and erosion. While carbonate budgets are well characterized in tropical coral reefs, the carbonate budgets of temperate rocky reefs, and their variability across spatiotemporal scales, remain much less well understood. Here, we quantify the carbonate budget of a seaweed-dominated rocky reef ecosystem within the world's largest cool-water carbonate depositional system. We first measured the seasonal and annual calcification rates of key calcifying groups (mobile invertebrates, corals, and coralline algae) across depths of 5, 10 and 18 m at two sites. Using a census-based approach, we then estimated how reef-scale gross carbonate production and erosion varied over depth. Crustose coralline algae exhibited calcification rates similar to those recorded in tropical studies, but their calcification was 2-7 times lower than that of corals. At the reef scale, gross carbonate production ranged from 9 to 2369 g CaCO3 m-2 yr-1, and was dominated by crustose and articulated coralline algae at shallow depths (68-96 % of the total production, 5-10 m depth), with corals becoming the principal contributors (58-62 %) at greater depths. Mobile invertebrates (gastropods and sea urchins) were minor contributors to carbonate production overall (1-3 %). Sea urchins entirely drove bioerosion however, which was relatively low (8-114 g CaCO3 m-2 yr-1) and increased with depth. Although the average net carbonate production in the studied temperate reefs (216-671 g CaCO3 m-2 yr-1) is relatively low compared to that of healthy coral reefs in the region (1400-3880 g CaCO3 m-2 yr-1), the vast expanses of seaweed-dominated rocky reefs in the study area and globally suggest that these ecosystems may play an underappreciated role in cool-water and global carbonate production. Indeed, preliminary estimates suggest that carbonate production across Australia's temperate Great Southern Reef could be comparable to tropical systems renowned for their high carbonate production such as the Great Barrier Reef.

@article{doi101016jmarenvres2025107416,
    author = "Pessarrodona, Albert and Attlan, Océane and Wernberg, Thomas",
    title = "Significant carbonate production on a temperate reef system in southwestern Australia.",
    year = "2025",
    journal = "Marine environmental research",
    abstract = "Calcifying organisms support key geo-ecological functions in shallow tropical and temperate reefs worldwide, including creating habitat structure, producing sediments, and supporting reef accretion. These functions depend on the carbonate budget: the balance between calcium carbonate production and erosion. While carbonate budgets are well characterized in tropical coral reefs, the carbonate budgets of temperate rocky reefs, and their variability across spatiotemporal scales, remain much less well understood. Here, we quantify the carbonate budget of a seaweed-dominated rocky reef ecosystem within the world's largest cool-water carbonate depositional system. We first measured the seasonal and annual calcification rates of key calcifying groups (mobile invertebrates, corals, and coralline algae) across depths of 5, 10 and 18 m at two sites. Using a census-based approach, we then estimated how reef-scale gross carbonate production and erosion varied over depth. Crustose coralline algae exhibited calcification rates similar to those recorded in tropical studies, but their calcification was 2-7 times lower than that of corals. At the reef scale, gross carbonate production ranged from 9 to 2369 g CaCO3 m-2 yr-1, and was dominated by crustose and articulated coralline algae at shallow depths (68-96 \% of the total production, 5-10 m depth), with corals becoming the principal contributors (58-62 \%) at greater depths. Mobile invertebrates (gastropods and sea urchins) were minor contributors to carbonate production overall (1-3 \%). Sea urchins entirely drove bioerosion however, which was relatively low (8-114 g CaCO3 m-2 yr-1) and increased with depth. Although the average net carbonate production in the studied temperate reefs (216-671 g CaCO3 m-2 yr-1) is relatively low compared to that of healthy coral reefs in the region (1400-3880 g CaCO3 m-2 yr-1), the vast expanses of seaweed-dominated rocky reefs in the study area and globally suggest that these ecosystems may play an underappreciated role in cool-water and global carbonate production. Indeed, preliminary estimates suggest that carbonate production across Australia's temperate Great Southern Reef could be comparable to tropical systems renowned for their high carbonate production such as the Great Barrier Reef.",
    url = "https://pubmed.ncbi.nlm.nih.gov/40769114/",
    doi = "10.1016/j.marenvres.2025.107416",
    openalex = "W4412987784",
    pmid = "40769114",
    references = "doi101016jmarenvres2025107218, doi1010292010gl046474, doi10102993gb02524, doi101071mf15232, doi101098rstb20130269, doi101126scienceaad8745, doi101146annureves17110186001421, doi1023071933661, doi1032614rj2017066, doi103354meps10573, openalexw171744082"
}

@article{doi101016jmarenvres2025107661,
    author = "Hong, Miao and Duan, Xiaowei and Chen, Yimeng and Wang, Jianjia and Zhou, Xijie and Wang, Ge and Zhang, Jingjing and Liu, Senkai and Shi, Wenjie and Luo, Zhaohe and Zheng, Xinqing",
    title = "Multi-marker eDNA metabarcoding reveals more abundant coral biodiversity in a subtropical coastal reef ecosystem",
    year = "2025",
    journal = "Marine Environmental Research",
    url = "https://doi.org/10.1016/j.marenvres.2025.107661",
    doi = "10.1016/j.marenvres.2025.107661",
    openalex = "W4415679189",
    references = "doi101016jrsma2023103289"
}

-aminobenzoic acid (ODPABA). The total concentrations (∑8OUVFs) in coral tissues and macroalgae were found to be 4.3-52.0 and 8.0-29.0 ng/g dry weight (dw), respectively. The bioaccumulation factors (BAFs) for BPs (including BP-1, BP-3, and BP-8) and OC in coral tissues were higher than those in macroalgae, while the BAFs for 4-MBC and ODPABA were relatively lower. Preliminary risk assessment results indicated that, in the worst-case scenario, more than 65 and 84% of coral samples had BP-3 concentrations exceeding the thresholds for causing coral larval bleaching and mortality, respectively. At the same time, 99% of the macroalgae samples showed ODPABA concentrations exceeding the thresholds related to their growth inhibition. Therefore, BP-3 and ODPABA posed significant ecological risks to corals and macroalgae, subsequently threatening the health and stability of the coral reef ecosystem.

@article{doi101021acsest4c11463,
    author = "Lyu, Lina and Li, Jie and Huang, Qinyu and Liu, Qing and Yang, Cheng and Dong, Junde and Su, Hongfei and Zhang, Si",
    title = "Exploring the Hidden Threat of Organic UV Filters to Corals and Macroalgae in Coral Reef Ecosystem from Luhuitou, Sanya, China",
    year = "2025",
    journal = "Environmental Science \& Technology",
    abstract = "-aminobenzoic acid (ODPABA). The total concentrations (∑8OUVFs) in coral tissues and macroalgae were found to be 4.3-52.0 and 8.0-29.0 ng/g dry weight (dw), respectively. The bioaccumulation factors (BAFs) for BPs (including BP-1, BP-3, and BP-8) and OC in coral tissues were higher than those in macroalgae, while the BAFs for 4-MBC and ODPABA were relatively lower. Preliminary risk assessment results indicated that, in the worst-case scenario, more than 65 and 84\% of coral samples had BP-3 concentrations exceeding the thresholds for causing coral larval bleaching and mortality, respectively. At the same time, 99\% of the macroalgae samples showed ODPABA concentrations exceeding the thresholds related to their growth inhibition. Therefore, BP-3 and ODPABA posed significant ecological risks to corals and macroalgae, subsequently threatening the health and stability of the coral reef ecosystem.",
    url = "https://doi.org/10.1021/acs.est.4c11463",
    doi = "10.1021/acs.est.4c11463",
    openalex = "W4408678979",
    references = "doi101007s003430209253z"
}

Coral restoration is gaining popularity as part of a continuum of approaches addressing the widespread, recurring mass mortality events of corals that-together with elevated and chronic mortality, slower growth and recruitment failure-threaten the persistence of coral reefs worldwide. However, the monetary costs associated with broad-scale coral restoration are massive, making widespread implementation challenging, especially with the lack of coordinated and ecologically informed planning. By combining a comprehensive dataset documenting the success of coral restoration with current and forecasted environmental, ecological and climate data, we highlight how such a coordinated and ecologically informed approach is not forthcoming, despite the extent of previous and ongoing efforts. We show that: (1) restoration sites tend to be disproportionally close to human settlements and therefore more vulnerable to local anthropogenic impacts; (2) the immediate outcomes of restoration do not appear to be influenced by relevant ecological and environmental predictors such as cumulative impact; and (3) most restored localities have a high and severe bleaching risk by the middle of this century, with more than half of recently restored sites already affected. Our findings highlight the need for the coral reef community to reinforce joint development of restoration guidelines that go beyond local objectives, with attention to ocean warming trends and their long-term impacts on coral resilience and restoration success.

@article{doi101038s4155902502667x,
    author = "Mulà, Clelia and Bradshaw, Corey J. A. and Cabeza, Mar and Manca, Federica and Montano, Simone and Strona, Giovanni",
    title = "Restoration cannot be scaled up globally to save reefs from loss and degradation",
    year = "2025",
    journal = "Nature Ecology \& Evolution",
    abstract = "Coral restoration is gaining popularity as part of a continuum of approaches addressing the widespread, recurring mass mortality events of corals that-together with elevated and chronic mortality, slower growth and recruitment failure-threaten the persistence of coral reefs worldwide. However, the monetary costs associated with broad-scale coral restoration are massive, making widespread implementation challenging, especially with the lack of coordinated and ecologically informed planning. By combining a comprehensive dataset documenting the success of coral restoration with current and forecasted environmental, ecological and climate data, we highlight how such a coordinated and ecologically informed approach is not forthcoming, despite the extent of previous and ongoing efforts. We show that: (1) restoration sites tend to be disproportionally close to human settlements and therefore more vulnerable to local anthropogenic impacts; (2) the immediate outcomes of restoration do not appear to be influenced by relevant ecological and environmental predictors such as cumulative impact; and (3) most restored localities have a high and severe bleaching risk by the middle of this century, with more than half of recently restored sites already affected. Our findings highlight the need for the coral reef community to reinforce joint development of restoration guidelines that go beyond local objectives, with attention to ocean warming trends and their long-term impacts on coral resilience and restoration success.",
    url = "https://doi.org/10.1038/s41559-025-02667-x",
    doi = "10.1038/s41559-025-02667-x",
    openalex = "W4409268111",
    references = "doi103389fmars20231298411"
}

and drove significant increases in structural complexity. There was no measurable impact of restoring slower-growing, massive corals on reef-accretion potential inshore; however, whereas the severe 2023 coral-bleaching event immediately following our study caused near-complete mortality of A. cervicornis, 59% of massive corals survived, highlighting potential trade-offs between coral growth and survival on future restoration efficacy. We conclude that although restoration can produce rapid, small-scale increases in reef-accretion potential, there remain important uncertainties about how and whether ecosystem-scale benefits of restoration on important geo-ecological reef functions can persist long term.

@article{doi101038s41598025048183,
    author = "Toth, Lauren T. and Johnson, Selena A. Kupfner and Lyons, E. and Spadaro, Jason and Stathakopoulos, Anastasios and Bloomer, Sierra and Mallon, Jennifer and Jenkins, Connor M. and Williams, Sara D. and Combs, Ian R. and Craig, Zachary and Muller, Erinn M.",
    title = "Coral restoration can drive rapid increases in reef accretion potential",
    year = "2025",
    journal = "Scientific Reports",
    abstract = "and drove significant increases in structural complexity. There was no measurable impact of restoring slower-growing, massive corals on reef-accretion potential inshore; however, whereas the severe 2023 coral-bleaching event immediately following our study caused near-complete mortality of A. cervicornis, 59\% of massive corals survived, highlighting potential trade-offs between coral growth and survival on future restoration efficacy. We conclude that although restoration can produce rapid, small-scale increases in reef-accretion potential, there remain important uncertainties about how and whether ecosystem-scale benefits of restoration on important geo-ecological reef functions can persist long term.",
    url = "https://doi.org/10.1038/s41598-025-04818-3",
    doi = "10.1038/s41598-025-04818-3",
    openalex = "W4412937695",
    references = "doi101007s003380120984y, doi101016jecoleng201901002, doi101016joneear202108016, doi101038ncomms2409, doi101038srep39666, doi101098rspb20090339, doi1011111365243513331, doi101371journalpone0226631, doi1021932005723, doi103389fmars20231298411, doi105479si007756301531, tortolerolangarica2019accelerated"
}

The sensitivity of coral reefs to climate change is well established. As the oceans warm and acidify, the calcification of coral reefs declines with net calcium carbonate dissolution projected under even moderate emissions trajectories. The impact of this on the global carbon cycle is however yet to be accounted for. Here, we use a synthesis of the sensitivity of coral reef calcification to climate change, alongside reef distribution products to estimate alkalinity and dissolved inorganic carbon fluxes resulting from reductions in reef calcification. Using a global ocean biogeochemical model, we simulate the impact on ocean carbon uptake under different emissions scenarios, accounting for uncertainty in present-day calcification rates. Reductions in net coral reef carbonate production can enhance the ocean carbon sink by up to 1.25 GtCO2 y-1 by midcentury (0.48 GtCO2 y-1 median estimate) with cumulative ocean carbon uptake up to 13% greater by 2300 (7% median estimate). Our findings indicate that accounting for the coral reef feedback in projections will increase estimates of the remaining carbon budget associated with global warming thresholds, as well as the likelihood that net zero emissions can be achieved without negative emissions.

@article{doi101073pnas2501562122,
    author = "Kwiatkowski, Lester and Planchat, Alban and Pyolle, Marc and Torres, Olivier and Bouttes, Nathaelle and Comte, Adrien and Bopp, Laurent",
    title = "Declining coral calcification to enhance twenty-first-century ocean carbon uptake by gigatonnes.",
    year = "2025",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    abstract = "The sensitivity of coral reefs to climate change is well established. As the oceans warm and acidify, the calcification of coral reefs declines with net calcium carbonate dissolution projected under even moderate emissions trajectories. The impact of this on the global carbon cycle is however yet to be accounted for. Here, we use a synthesis of the sensitivity of coral reef calcification to climate change, alongside reef distribution products to estimate alkalinity and dissolved inorganic carbon fluxes resulting from reductions in reef calcification. Using a global ocean biogeochemical model, we simulate the impact on ocean carbon uptake under different emissions scenarios, accounting for uncertainty in present-day calcification rates. Reductions in net coral reef carbonate production can enhance the ocean carbon sink by up to 1.25 GtCO2 y-1 by midcentury (0.48 GtCO2 y-1 median estimate) with cumulative ocean carbon uptake up to 13\% greater by 2300 (7\% median estimate). Our findings indicate that accounting for the coral reef feedback in projections will increase estimates of the remaining carbon budget associated with global warming thresholds, as well as the likelihood that net zero emissions can be achieved without negative emissions.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12167964/",
    doi = "10.1073/pnas.2501562122",
    openalex = "W4410948292",
    pmcid = "PMC12167964",
    pmid = "40455984",
    references = "doi101007s105840110156z, doi1010179781009157896007, doi1010292019ms002010, doi10102992jc00188, doi101071mf99078, doi101126science1152509, doi101126science26551781547, doi105194bg1734392020, doi105194essd1448112022, doi105194gmd1335712020"
}

Climate-driven shifts in the abundance and distribution of habitat-forming species are transforming how ecosystems produce and cycle carbon, nutrients and energy. Temperate kelp forests are increasingly being replaced by tropical or warm-affinity habitat-forming species like turf seaweeds and corals, i.e. 'tropicalized'. These changes can have cascading effects on associated species such as calcifying organisms, which contribute to sediment generation and carbon cycling via the production of calcium carbonate. This study quantified carbonate production and erosion across a temperate kelp forest and three tropicalized reef states following the 2011 marine heatwave: kelp-turf mix, warmer affinity seaweeds and coral-turf dominance. Results show that gross carbonate production was the highest in coral-turf reefs (1.85 ± 0.65 kg m-2 yr-1), lowest in warmer affinity seaweed reefs (0.04 ± 0.02 kg m-2 yr-1) and intermediate in temperate kelp forests (0.60 ± 0.19 kg m-2 yr-1). These differences were linked to the abundance of corals in coral-turf state and scarce calcifying algae in the warmer affinity seaweed state. Bioerosion played a moderate role in the overall budget, but the dominant bioeroders differed between habitats: urchins in temperate reefs contributed 80% less than parrotfishes in tropicalized reefs. Overall, tropicalization can either increase or decrease carbonate availability, depending on the dominant habitat formers. These shifts may significantly impact inorganic carbon cycling and the structural and functional integrity of coastal reef ecosystems.

@article{doi101098rspb20252578,
    author = "Attlan, Océane and Wernberg, Thomas and Wood, Georgina and Pessarrodona, Albert",
    title = "Diverging carbonate budgets following tropicalization of temperate reefs.",
    year = "2025",
    journal = "Proceedings. Biological sciences",
    abstract = "Climate-driven shifts in the abundance and distribution of habitat-forming species are transforming how ecosystems produce and cycle carbon, nutrients and energy. Temperate kelp forests are increasingly being replaced by tropical or warm-affinity habitat-forming species like turf seaweeds and corals, i.e. 'tropicalized'. These changes can have cascading effects on associated species such as calcifying organisms, which contribute to sediment generation and carbon cycling via the production of calcium carbonate. This study quantified carbonate production and erosion across a temperate kelp forest and three tropicalized reef states following the 2011 marine heatwave: kelp-turf mix, warmer affinity seaweeds and coral-turf dominance. Results show that gross carbonate production was the highest in coral-turf reefs (1.85 ± 0.65 kg m-2 yr-1), lowest in warmer affinity seaweed reefs (0.04 ± 0.02 kg m-2 yr-1) and intermediate in temperate kelp forests (0.60 ± 0.19 kg m-2 yr-1). These differences were linked to the abundance of corals in coral-turf state and scarce calcifying algae in the warmer affinity seaweed state. Bioerosion played a moderate role in the overall budget, but the dominant bioeroders differed between habitats: urchins in temperate reefs contributed 80\% less than parrotfishes in tropicalized reefs. Overall, tropicalization can either increase or decrease carbonate availability, depending on the dominant habitat formers. These shifts may significantly impact inorganic carbon cycling and the structural and functional integrity of coastal reef ecosystems.",
    url = "https://pubmed.ncbi.nlm.nih.gov/41538033/",
    doi = "10.1098/rspb.2025.2578",
    openalex = "W7117327002",
    pmid = "41538033",
    references = "doi101016jmarenvres2025107416, doi101038nature12857, doi101093icb391146, doi101098rspb20140846, doi101126science1132294, doi101126science1165283, doi101126science1824116975, doi101126scienceaad8745, doi101126scienceaai9214, doi1023073545860, doi1032614rj2017066"
}

Climate change and human activities threaten coral reefs, requiring effective restoration. This study assessed the growth and calcification rates of transplanted corals by examining skeletal characteristics, conducted in the Coral Fragmentation (CF), Natural Reef (NA), Coral Nursery (CN), and Coral Restoration (CR) areas on Wuzhizhou Island, Hainan. Samples of Acropora hyacinthus and A. microphthalma were collected from each area in April 2024, with CR samples including corals transplanted for 1, 2, and 3 years using the Framed Reef Module. Results indicated that while Fv/Fm values remained consistent among samples, significant differences in symbiont density and biomass suggest variations in symbiont adaptation. Extended transplantation significantly influenced both the ecological volume (EV) and calcification rates of transplanted corals. Specifically, A. hyacinthus and A. microphthalma demonstrated significant increases in EV of 267.78 and 271.70%, respectively, when comparing corals transplanted for 3 years to those transplanted for only 1 year. Additionally, the calcification rates of these species showed a marked increase over time, with A. hyacinthus achieving a rate of (9.24 ± 2.70 g CaCO 3 cm −2 yr −1) in the 3‐year transplants, compared to (5.02 ± 1.86 g CaCO 3 cm −2 yr −1) for the 1‐year transplants. Similarly, A. microphthalma exhibited a calcification rate of (9.06 ± 2.62 g CaCO 3 cm −2 yr −1) for 3‐year transplants, compared to (4.24 ± 2.18 g CaCO 3 cm −2 yr −1) for 1‐year transplants. Survival rates for both species fell below 70% due to 2023 thermal stress, highlighting their vulnerability. Although extended transplantation boosts coral growth, challenges like thermal stress hinder restoration success. This study provides insights to improve coral resilience in the face of climate change.

@article{doi101111rec70107,
    author = "Zhao, He and Zhang, Junling and Liu, Xiangbo and Yang, Pei and Ke, Jingzhao and Zhu, Wentao and Wang, Aimin and Liu, Xiangbo",
    title = "Coral transplantation increases ecological volume and calcification rate of Acropora species on Wuzhizhou Island: evidence from coral growth, physiology, and skeletal characteristics",
    year = "2025",
    journal = "Restoration Ecology",
    abstract = "Climate change and human activities threaten coral reefs, requiring effective restoration. This study assessed the growth and calcification rates of transplanted corals by examining skeletal characteristics, conducted in the Coral Fragmentation (CF), Natural Reef (NA), Coral Nursery (CN), and Coral Restoration (CR) areas on Wuzhizhou Island, Hainan. Samples of Acropora hyacinthus and A. microphthalma were collected from each area in April 2024, with CR samples including corals transplanted for 1, 2, and 3 years using the Framed Reef Module. Results indicated that while Fv/Fm values remained consistent among samples, significant differences in symbiont density and biomass suggest variations in symbiont adaptation. Extended transplantation significantly influenced both the ecological volume (EV) and calcification rates of transplanted corals. Specifically, A. hyacinthus and A. microphthalma demonstrated significant increases in EV of 267.78 and 271.70\%, respectively, when comparing corals transplanted for 3 years to those transplanted for only 1 year. Additionally, the calcification rates of these species showed a marked increase over time, with A. hyacinthus achieving a rate of (9.24 ± 2.70 g CaCO 3 cm −2 yr −1) in the 3‐year transplants, compared to (5.02 ± 1.86 g CaCO 3 cm −2 yr −1) for the 1‐year transplants. Similarly, A. microphthalma exhibited a calcification rate of (9.06 ± 2.62 g CaCO 3 cm −2 yr −1) for 3‐year transplants, compared to (4.24 ± 2.18 g CaCO 3 cm −2 yr −1) for 1‐year transplants. Survival rates for both species fell below 70\% due to 2023 thermal stress, highlighting their vulnerability. Although extended transplantation boosts coral growth, challenges like thermal stress hinder restoration success. This study provides insights to improve coral resilience in the face of climate change.",
    url = "https://doi.org/10.1111/rec.70107",
    doi = "10.1111/rec.70107",
    openalex = "W4411356580",
    references = "doi101111maec12678"
}

Abstract Introduction Coral reefs face escalating threats from the synergic effects of natural and anthropogenic stressors, challenging traditional conservation strategies and prompting the emergence of direct intervention approaches for coral reef restoration. Coral reef restoration efforts in the Eastern Tropical Pacific, particularly in the Mexican Pacific (MP), face unique challenges due to environmental factors and infrequent interventions. Objective This review examines procedural aspects and the effectiveness of active restoration efforts along MP reefs, emphasizing coral gardening's adaptability, assisted propagation's affordability, artificial substrata's potential, micro‐fragmentation's promise, and ecological engineering approaches. Results From 2010 to 2023, restoration interventions in the MP increased by 180%, primarily targeting the branching coral genus Pocillopora, using asexual recruits and micro‐fragments. Most studies indicate regional and local environmental variability has influenced survival, growth rates, and self‐attachment success. While early intervention assessments reported high fragment survival rates (>60%) and significant growth (up to a two‐fold increase), there is now a shift toward evaluating ecological metrics such as coral cover, species assemblages, carbonate production, and overall ecosystem functionality, which are currently under assessment in the region. Conclusions Restoration programs should be tailored to site‐specific characteristics. Their effectiveness depends on biological and ecological metrics, but comprehensive evaluations must also incorporate social and economic factors. Achieving lasting success requires transitioning to cost‐effective, scalable, and sustainable restoration programs while addressing the root causes of reef decline (environmental degradation) and enhancing coral resilience.

@article{doi101111rec70176,
    author = "Tortolero‐Langarica, J. J. Adolfo and Rodríguez‐Troncoso, Alma Paola and Nava, Héctor",
    title = "Advances in coral reef restoration in the Mexican Pacific: active interventions and scaling approaches",
    year = "2025",
    journal = "Restoration Ecology",
    abstract = "Abstract Introduction Coral reefs face escalating threats from the synergic effects of natural and anthropogenic stressors, challenging traditional conservation strategies and prompting the emergence of direct intervention approaches for coral reef restoration. Coral reef restoration efforts in the Eastern Tropical Pacific, particularly in the Mexican Pacific (MP), face unique challenges due to environmental factors and infrequent interventions. Objective This review examines procedural aspects and the effectiveness of active restoration efforts along MP reefs, emphasizing coral gardening's adaptability, assisted propagation's affordability, artificial substrata's potential, micro‐fragmentation's promise, and ecological engineering approaches. Results From 2010 to 2023, restoration interventions in the MP increased by 180\%, primarily targeting the branching coral genus Pocillopora, using asexual recruits and micro‐fragments. Most studies indicate regional and local environmental variability has influenced survival, growth rates, and self‐attachment success. While early intervention assessments reported high fragment survival rates (>60\%) and significant growth (up to a two‐fold increase), there is now a shift toward evaluating ecological metrics such as coral cover, species assemblages, carbonate production, and overall ecosystem functionality, which are currently under assessment in the region. Conclusions Restoration programs should be tailored to site‐specific characteristics. Their effectiveness depends on biological and ecological metrics, but comprehensive evaluations must also incorporate social and economic factors. Achieving lasting success requires transitioning to cost‐effective, scalable, and sustainable restoration programs while addressing the root causes of reef decline (environmental degradation) and enhancing coral resilience.",
    url = "https://doi.org/10.1111/rec.70176",
    doi = "10.1111/rec.70176",
    openalex = "W4416052351",
    references = "doi101111rec14006"
}

Coral reefs are among the most valuable ecosystems on Earth, providing major benefits to human societies and hosting a wide variety of species. Today, these ecosystems are threatened by a combination of local and global factors that overcome the natural capacity of coral reefs for regeneration. Therefore, active restoration methods have been developed and conducted to help coral reefs recover faster than before. The construction of artificial reefs, which are artificial structures that are deliberately submerged in aquatic environments and whose characteristics mimic those of natural reefs, is a marine restoration strategy. These strategies have the potential to increase the ecological value of degraded sites in both the short term and long term by providing additional habitats for coral growth and acting as future hubs for coral larval dispersal. However, the success of artificial reefs in achieving these objectives depends largely on the materials used to construct them. Concrete, plastics, metals and wood, which are the major materials found in modern reefs, suffer from substantial drawbacks that limit the ability to reach restoration goals. In this short study, we discuss innovations that have been developed to overcome the drawbacks of modern artificial reefs to encourage the creation of a new generation of artificial reefs that can substantially contribute to active coral reef restoration.

@article{doi101186s44315025000475,
    author = "Ozanam, Baptiste and Romans, Pascal and Lami, Raphaël",
    title = "Choosing the right substrate to restore coral reefs through artificial reef construction: a mini-review",
    year = "2025",
    journal = "Blue Biotechnology",
    abstract = "Coral reefs are among the most valuable ecosystems on Earth, providing major benefits to human societies and hosting a wide variety of species. Today, these ecosystems are threatened by a combination of local and global factors that overcome the natural capacity of coral reefs for regeneration. Therefore, active restoration methods have been developed and conducted to help coral reefs recover faster than before. The construction of artificial reefs, which are artificial structures that are deliberately submerged in aquatic environments and whose characteristics mimic those of natural reefs, is a marine restoration strategy. These strategies have the potential to increase the ecological value of degraded sites in both the short term and long term by providing additional habitats for coral growth and acting as future hubs for coral larval dispersal. However, the success of artificial reefs in achieving these objectives depends largely on the materials used to construct them. Concrete, plastics, metals and wood, which are the major materials found in modern reefs, suffer from substantial drawbacks that limit the ability to reach restoration goals. In this short study, we discuss innovations that have been developed to overcome the drawbacks of modern artificial reefs to encourage the creation of a new generation of artificial reefs that can substantially contribute to active coral reef restoration.",
    url = "https://doi.org/10.1186/s44315-025-00047-5",
    doi = "10.1186/s44315-025-00047-5",
    openalex = "W4416375180",
    references = "doi103389fmars20231298411"
}

Marine heatwaves (MHWs) are increasingly affecting tropical seas, causing mass coral bleaching and mortality in the wider Caribbean (WC) and eastern tropical Pacific (ETP). This leads to significant coral loss, reduced biodiversity, and impaired ecological functions. Climate models forecast a troubling future for Latin American coral reefs, but downscaled projections for the WC and ETP remain limited. Understanding regional temperature thresholds that threaten coral reef futures and restoration efforts is critical. Our goals included analyzing historical trends in July–August–September–October (JASO) temperature anomalies and exploring future projections at subregional and country levels. From 1940 to 2023, JASO air and ocean temperature anomalies showed significant increases. Projections indicate that even under optimistic scenario 4.5, temperatures may exceed the +1.5 °C air threshold beyond pre-industrial levels by the 2040s and the +1.0 °C ocean threshold beyond historical annual maximums by the 2030s, resulting in severe coral bleaching and mortality. Business-as-usual scenario 8.5 suggests conditions will become intolerable for coral conservation and restoration by the 2030s, with decadal warming trends largely surpassing historical rates, under unbearable conditions for corals. The immediate development of regional and local adaptive coral reef conservation and restoration plans, along with climate change adaptation and mitigation strategies, is essential to provide time for optimistic scenarios to materialize.

@article{doi103390atmos16050575,
    author = "Hernández‐Delgado, Edwin A. and Rodríguez-González, Yanina M.",
    title = "Runaway Climate Across the Wider Caribbean and Eastern Tropical Pacific in the Anthropocene: Threats to Coral Reef Conservation, Restoration, and Social–Ecological Resilience",
    year = "2025",
    journal = "Atmosphere",
    abstract = "Marine heatwaves (MHWs) are increasingly affecting tropical seas, causing mass coral bleaching and mortality in the wider Caribbean (WC) and eastern tropical Pacific (ETP). This leads to significant coral loss, reduced biodiversity, and impaired ecological functions. Climate models forecast a troubling future for Latin American coral reefs, but downscaled projections for the WC and ETP remain limited. Understanding regional temperature thresholds that threaten coral reef futures and restoration efforts is critical. Our goals included analyzing historical trends in July–August–September–October (JASO) temperature anomalies and exploring future projections at subregional and country levels. From 1940 to 2023, JASO air and ocean temperature anomalies showed significant increases. Projections indicate that even under optimistic scenario 4.5, temperatures may exceed the +1.5 °C air threshold beyond pre-industrial levels by the 2040s and the +1.0 °C ocean threshold beyond historical annual maximums by the 2030s, resulting in severe coral bleaching and mortality. Business-as-usual scenario 8.5 suggests conditions will become intolerable for coral conservation and restoration by the 2030s, with decadal warming trends largely surpassing historical rates, under unbearable conditions for corals. The immediate development of regional and local adaptive coral reef conservation and restoration plans, along with climate change adaptation and mitigation strategies, is essential to provide time for optimistic scenarios to materialize.",
    url = "https://doi.org/10.3390/atmos16050575",
    doi = "10.3390/atmos16050575",
    openalex = "W4410298624",
    references = "doi103390ijerph17186574"
}

The last few decades have seen the emergence of coral restoration projects as an alternative to counter the rapid degradation of coral reefs, given the ecological and economic significance of these reefs. Although these projects have successfully increased coral cover with low mortality and high growth rates of the colonies, there has been limited understanding of the health status of the restored colonies and their impact on the marine fauna of the reef. To address this knowledge gap, a study was conducted comparing the physical and physiological traits of natural and restored Pocillopora colonies, along with the diversity and composition of associated reef fishes, five to six years after coral fragments were implanted on a rocky-coral reef in the southern part of the Gulf of California, Mexico. The study revealed that the restored colonies exhibited similar characteristics in terms of morphology and physiology to the natural ones, leading to similar reef fish diversity and composition. The findings suggest that coral restoration programs, employing simple methods such as fragmentation, not only increase coral cover but also provide a suitable habitat for associated marine fauna, allowing for the recovery of the reef community and its functionality.

@article{doi105343bms20240107,
    author = "Torres, María Marínez and Olivier, Damien and Reyes‐Bonilla, Héctor",
    title = "Evaluation of a coral restoration program in the Gulf of California: similar characteristics between restored and natural coral colonies lead to the same reef fish composition",
    year = "2025",
    journal = "Bulletin of Marine Science",
    abstract = "The last few decades have seen the emergence of coral restoration projects as an alternative to counter the rapid degradation of coral reefs, given the ecological and economic significance of these reefs. Although these projects have successfully increased coral cover with low mortality and high growth rates of the colonies, there has been limited understanding of the health status of the restored colonies and their impact on the marine fauna of the reef. To address this knowledge gap, a study was conducted comparing the physical and physiological traits of natural and restored Pocillopora colonies, along with the diversity and composition of associated reef fishes, five to six years after coral fragments were implanted on a rocky-coral reef in the southern part of the Gulf of California, Mexico. The study revealed that the restored colonies exhibited similar characteristics in terms of morphology and physiology to the natural ones, leading to similar reef fish diversity and composition. The findings suggest that coral restoration programs, employing simple methods such as fragmentation, not only increase coral cover but also provide a suitable habitat for associated marine fauna, allowing for the recovery of the reef community and its functionality.",
    url = "https://doi.org/10.5343/bms.2024.0107",
    doi = "10.5343/bms.2024.0107",
    openalex = "W4409875865",
    references = "doi101111rec14006"
}

into the sediment carbon reservoir. These findings, reported for the first time, demonstrate the significant carbon sequestration potential of coral reef ecosystems, in which SCS reefs were used as an example, and provide critical insights into the role of corals and reef-dwelling fish in coral reef carbon cycling. These findings further highlight the necessity of biodiversity conservation amid increasingly severe global changes, specifically to maintain the carbon sequestration function and stability of coral reef ecosystems.

@article{doi101002advs202520612,
    author = "Chen, Yiting and Zhou, Wenliang and Qiu, Lan and Lai, Han and Huang, Mingpan and Li, Qian and Yu, Wen and Qian, Pei‐Yuan and Wei, Fuwen",
    title = "Corals and Reef‐Dwelling Fish Regulate Carbon Storage and Cycling Processes in Coral Reef Ecosystems",
    year = "2026",
    journal = "Advanced Science",
    abstract = "into the sediment carbon reservoir. These findings, reported for the first time, demonstrate the significant carbon sequestration potential of coral reef ecosystems, in which SCS reefs were used as an example, and provide critical insights into the role of corals and reef-dwelling fish in coral reef carbon cycling. These findings further highlight the necessity of biodiversity conservation amid increasingly severe global changes, specifically to maintain the carbon sequestration function and stability of coral reef ecosystems.",
    url = "https://doi.org/10.1002/advs.202520612",
    doi = "10.1002/advs.202520612",
    openalex = "W7154728503",
    references = "doi101073pnas2501562122"
}

@article{doi101007s0034302551042,
    author = "Liu, Xiangbo and Chen, Ruimei and Lin, Xiaoyu and Zhao, He and Zhang, Junling and Zhu, Wentao and Zhou, Yinyin and Wang, Aimin and Li, XiuBao",
    title = "From rubble to reef: ecological transformation in volcanic rock-assisted coral restoration",
    year = "2026",
    journal = "Journal of Oceanology and Limnology",
    url = "https://doi.org/10.1007/s00343-025-5104-2",
    doi = "10.1007/s00343-025-5104-2",
    openalex = "W7118074032",
    references = "doi101016jrsma2023103289"
}

@article{doi101016jenvres2026123775,
    author = "Yang, Bo and Yang, Bo and Yang, Bin and Yang, Bin and Xie, Lei and Kang, Zenjun and Mo, Xiaorong and Li, Qin and Zhou, Jiaodi and Huang, Haifang and Yan, Tingting and Xu, Cheng",
    title = "Coral mucus input promotes sedimentary organic matter degradation: Evidence from a typical coral reef area, northern South China Sea",
    year = "2026",
    journal = "Environmental Research",
    url = "https://doi.org/10.1016/j.envres.2026.123775",
    doi = "10.1016/j.envres.2026.123775",
    openalex = "W7123591220",
    references = "doi101016jrsma2023103289"
}

@article{doi101016jrsma2026104984,
    author = "de Lavôr, Larissa Fernandes and Souza, Maria Cecília Silva and Massei, Karina and dos Santos Souza, Alexandre and do Amaral Vaz Manso, Valdir and de Miranda Lopes Neumann, Virgínio Henrique and Vianna, Pedro and da Silva Moura, Christianne Maria and Silva, N. and da Silva, Richarde Marques and dos Santos Ferreira, Rogério and da Costa Silva, Jefferson and Mishra, Manoranjan and Santos, Celso Augusto Guimarães",
    title = "Influence of coral reef morphology on wave climate and sea-level rise projections along a reef-protected beach in Northeast Brazil",
    year = "2026",
    journal = "Regional Studies in Marine Science",
    url = "https://doi.org/10.1016/j.rsma.2026.104984",
    doi = "10.1016/j.rsma.2026.104984",
    openalex = "W7154486541",
    references = "doi101038s41598025048183"
}

Abstract Carbonate mineral production and dissolution regulate atmospheric carbon dioxide (CO 2) concentrations via modulation of the ocean alkalinity content. The anthropogenic rise in atmospheric CO 2 reduces calcification rates and enhances calcium carbonate dissolution, which increases ocean alkalinity, counteracts acidification, and stimulates ocean CO 2 uptake. However, carbonate dissolution takes place primarily in the deep ocean, so this feedback is slow, maintaining ocean CO 2 uptake over millennial timescales. Here, we present evidence that seawater alkalinity on the continental shelf is increasing on annual‐decadal timescales, at a rate that is orders of magnitude faster than the deep ocean feedback. Biogeochemical model analyses suggest this fast feedback results from calcium carbonate dissolution in the shelf seafloor driven by increasing atmospheric CO 2 concentrations. Extrapolating these results to the global continental shelf suggests that shelf carbonate dissolution has been accelerating since the 1800s and may account for up to 10% of the missing ∼0.3 Pg C yr −1 in ocean model carbon budgets.

@article{doi1010292025av001865,
    author = "van de Velde, Sebastiaan and Vervoort, Pam and Smith, Robert O. and Law, Cliff and Currie, Kim",
    title = "Anthropogenically Stimulated Carbonate Dissolution in the Global Shelf Seafloor Is Potentially an Important and Fast Climate Feedback",
    year = "2026",
    journal = "AGU Advances",
    abstract = "Abstract Carbonate mineral production and dissolution regulate atmospheric carbon dioxide (CO 2) concentrations via modulation of the ocean alkalinity content. The anthropogenic rise in atmospheric CO 2 reduces calcification rates and enhances calcium carbonate dissolution, which increases ocean alkalinity, counteracts acidification, and stimulates ocean CO 2 uptake. However, carbonate dissolution takes place primarily in the deep ocean, so this feedback is slow, maintaining ocean CO 2 uptake over millennial timescales. Here, we present evidence that seawater alkalinity on the continental shelf is increasing on annual‐decadal timescales, at a rate that is orders of magnitude faster than the deep ocean feedback. Biogeochemical model analyses suggest this fast feedback results from calcium carbonate dissolution in the shelf seafloor driven by increasing atmospheric CO 2 concentrations. Extrapolating these results to the global continental shelf suggests that shelf carbonate dissolution has been accelerating since the 1800s and may account for up to 10\% of the missing ∼0.3 Pg C yr −1 in ocean model carbon budgets.",
    url = "https://doi.org/10.1029/2025av001865",
    doi = "10.1029/2025av001865",
    openalex = "W7125481116",
    references = "doi101073pnas2501562122"
}

@article{doi101073pnas2521543123,
    author = "Camacho, Alejandro E. and Dana, David A. and Matz, Mikhail V.",
    title = "Coral species from another ocean may be the only way to save Caribbean reefs",
    year = "2026",
    journal = "Proceedings of the National Academy of Sciences",
    url = "https://doi.org/10.1073/pnas.2521543123",
    doi = "10.1073/pnas.2521543123",
    openalex = "W7125488797",
    references = "doi101038s41598025048183"
}

Introduction: The Reef Functional Index (RFI) is a tool used to analyze the physical functionality of coral assemblages based on morpho-functional traits that support their geo-ecological roles. This tool has been applied to assess the effects of active restoration on coral reefs under varying levels of stress. However, to date, it has not been used to analyze long-term assisted recovery through restoration activities. Objective: This study evaluated the historical trajectory of physical functionality over the long term (2012–2023) in six coral reef communities within the Islas Marietas National Park (PNIM), considering that active restoration efforts have been in place since 2014, using the RFI as a metric. Methods: The RFI was used as an indicator of physical functionality to assess temporal changes in reef condition throughout the analysis period. The percentage of natural change and change subsidized by restoration was calculated for both RFI and live coral cover (LCC). Results: RFI values revealed that although coral communities in the PNIM had, by 2023, regained LCC levels exceeding those recorded in 1997, physical functionality had not yet been fully restored. Restoration activities have contributed to approaching historical functional values, even under the impact of various natural stressors; however, spatial analysis at the island and site level indicated that recovery has not been uniform. Conclusions: The findings highlight the need to review and adapt restoration strategies, emphasizing greater efforts in sites where coral functionality remains below pre-disturbance levels. Additionally, the results demonstrate that the RFI is a valuable tool for evaluating the long-term success of coral restoration and identifying potential areas of opportunity in degraded reef sites.

@article{doi10155173s8sp047,
    author = "Muñoz-Alfaro, Adahara and Rodríguez‐Troncoso, Alma Paola and Cupul‐Magaña, Amilcar Leví and Tortolero‐Langarica, J. J. Adolfo and Cabral-Tena, Rafael Andrés",
    title = "Historical analysis of the recovery of physical functionality in a coral reef community following the implementation of active restoration practices",
    year = "2026",
    journal = "Revista de Biología Tropical",
    abstract = "Introduction: The Reef Functional Index (RFI) is a tool used to analyze the physical functionality of coral assemblages based on morpho-functional traits that support their geo-ecological roles. This tool has been applied to assess the effects of active restoration on coral reefs under varying levels of stress. However, to date, it has not been used to analyze long-term assisted recovery through restoration activities. Objective: This study evaluated the historical trajectory of physical functionality over the long term (2012–2023) in six coral reef communities within the Islas Marietas National Park (PNIM), considering that active restoration efforts have been in place since 2014, using the RFI as a metric. Methods: The RFI was used as an indicator of physical functionality to assess temporal changes in reef condition throughout the analysis period. The percentage of natural change and change subsidized by restoration was calculated for both RFI and live coral cover (LCC). Results: RFI values revealed that although coral communities in the PNIM had, by 2023, regained LCC levels exceeding those recorded in 1997, physical functionality had not yet been fully restored. Restoration activities have contributed to approaching historical functional values, even under the impact of various natural stressors; however, spatial analysis at the island and site level indicated that recovery has not been uniform. Conclusions: The findings highlight the need to review and adapt restoration strategies, emphasizing greater efforts in sites where coral functionality remains below pre-disturbance levels. Additionally, the results demonstrate that the RFI is a valuable tool for evaluating the long-term success of coral restoration and identifying potential areas of opportunity in degraded reef sites.",
    url = "https://doi.org/10.15517/3s8sp047",
    doi = "10.15517/3s8sp047",
    openalex = "W7155104838",
    references = "doi101007s44289024000149"
}

Introduction: The genus Pocillopora comprises coral species distributed throughout tropical and subtropical regions. In the Central Mexican Pacific region, Pocillopora verrucosa is the main reef-building species. In response to the recent decline in coral coverage, restoration protocols have been implemented over the past decade. However, to date, no genetic diversity records are available as potential markers to evaluate the effect of assisted recruitment on site dynamics in the area. Objective: Determine the genetic diversity of P. verrucosa in an insular (Islas Marietas National Park) and a coastal (Punta de Mita) restoration site within the Central Mexican Pacific. Methods: A 2 cm2 fragment from 15 colonies per site was collected. Mitochondrial markers for the COI and ATP6 genes were amplified. A total of 40 sequences of the COI (n = 19) and ATP6 (n = 21) genes were obtained, and the haplotype and nucleotide diversity were determined. Results: For the COI gene, two haplotypes shared between the sites were identified, with H1 being the most abundant. For the ATP6 gene, one exclusive haplotype was detected in Islas Marietas National Park, and one more abundant haplotype was shared between the two sites. The AMOVA results revealed a homogeneous pattern with Fst values of 0.21603 (p < 0.10655) for COI and Fst = 0.04174 (p < 0.3753) for ATP6. Conclusions: The low genetic diversity suggests that, as previously reported, asexual reproduction has been the predominant mode throughout the site’s history, and that the assisted propagation implemented may promote the maintenance of the individuals that have historically shown resistance to thermal stressors. However, it is essential to explore alternative propagation techniques in future restoration initiatives, as the long-term success of restoration also relies on reducing the vulnerability of these ecosystems to future environmental stressors.

@article{doi1015517h7pzq822,
    author = "Rodríguez, María Teresa Macedo and Bautista‐Guerrero, Eric and Santiago-Valentín, Jeimy Denisse and Cupul‐Magaña, Amilcar Leví and Troncoso, Alma Paola Rodríguez",
    title = "Identifying resilient individuals of Pocillopora verrucosa (Ellis \& Solander, 1786): insights from diversity assessments for coral restoration",
    year = "2026",
    journal = "Revista de Biología Tropical",
    abstract = "Introduction: The genus Pocillopora comprises coral species distributed throughout tropical and subtropical regions. In the Central Mexican Pacific region, Pocillopora verrucosa is the main reef-building species. In response to the recent decline in coral coverage, restoration protocols have been implemented over the past decade. However, to date, no genetic diversity records are available as potential markers to evaluate the effect of assisted recruitment on site dynamics in the area. Objective: Determine the genetic diversity of P. verrucosa in an insular (Islas Marietas National Park) and a coastal (Punta de Mita) restoration site within the Central Mexican Pacific. Methods: A 2 cm2 fragment from 15 colonies per site was collected. Mitochondrial markers for the COI and ATP6 genes were amplified. A total of 40 sequences of the COI (n = 19) and ATP6 (n = 21) genes were obtained, and the haplotype and nucleotide diversity were determined. Results: For the COI gene, two haplotypes shared between the sites were identified, with H1 being the most abundant. For the ATP6 gene, one exclusive haplotype was detected in Islas Marietas National Park, and one more abundant haplotype was shared between the two sites. The AMOVA results revealed a homogeneous pattern with Fst values of 0.21603 (p < 0.10655) for COI and Fst = 0.04174 (p < 0.3753) for ATP6. Conclusions: The low genetic diversity suggests that, as previously reported, asexual reproduction has been the predominant mode throughout the site’s history, and that the assisted propagation implemented may promote the maintenance of the individuals that have historically shown resistance to thermal stressors. However, it is essential to explore alternative propagation techniques in future restoration initiatives, as the long-term success of restoration also relies on reducing the vulnerability of these ecosystems to future environmental stressors.",
    url = "https://doi.org/10.15517/h7pzq822",
    doi = "10.15517/h7pzq822",
    openalex = "W7155038580",
    references = "doi101007s44289024000149, doi101111rec14006"
}