@article{doi10130674d7173a2b2111d78648000102c1865d,
    author = "Stockman, R. N. Ginsburg K. W.",
    title = "The Production of Lime Mud by Algae in South Florida",
    year = "1967",
    journal = "Journal of Sedimentary Research",
    abstract = "We have made estimates of the annual production of fine aragonite mud (14 age determinations of subsurface samples. Considering only production within the areas of maximum mud accumulation, we calculated that since the areas were flooded by rising sea level 4000 to 10,000 years ago, the present rate of production by Penicillus sp. could account for all the fine aragonite mud in the inner Florida Reef Tract and one,third of the same material in northeastern Florida Bay. The production of aragonite mud by Penicillus sp. provides a base line for evaluating the production of other similar algae. In the reef tract and the southeastern and western margins of Florida Bay, two other related green algae together are more abundant than Penicillus sp, in northeastern Florida Bay, one alga is more abundant than Penicillus. Another source of fine lime mud is the biological and mechanical breakdown of resistant skeletons, mollusks, algae, corals, etc. This breakdown gives recognizable skeletal silt (15-62mu), but appreciable finer particles (",
    url = "https://doi.org/10.1306/74d7173a-2b21-11d7-8648000102c1865d",
    doi = "10.1306/74d7173a-2b21-11d7-8648000102c1865d",
    openalex = "W2159278218"
}

@article{doi101111j1469185x1969tb00609x,
    author = "Stoddart, D. R.",
    title = "ECOLOGY AND MORPHOLOGY OF RECENT CORAL REEFS",
    year = "1969",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Summary 1. The classical ‘coral reef problem’ concerned the geological relationships of reefs as major topographical features; modern coral studies consider reefs both as complex biological systems of high productivity and as geological structures forming a framework for and being modified by coral growth. 2. Deep borings in reefs have conclusively confirmed the general arguments of Darwin, that oceanic reefs developed by progressive subsidence of their foundations. Darwin failed to take account of Pleistocene changes in sea level and their effect on the present surface features of reefs. Daly's alternative ‘glacial control theory’ was based on false assumptions concerning marine erosion rates during glacial periods, but if sea level during the Holocene was higher than at present, as Daly also supposed, the effects on reef features would be profound. 3. Reefs are complex biological systems in tropical seas, dominated by scleractinian corals. Coral faunas are larger and more diverse in the Indo‐Pacific than in the Atlantic. Hermatypic corals are restricted to shallow water by the light requirements of their symbiotic algae, but temperature is a major control of worldwide distributions. Temperature, salinity and sediment tolerances of corals are wider than formerly supposed, and corals can survive brief emersion except when it coincides with heavy rainfall. Water turbulence is an important ecological control, but difficult to measure. 4. The trophic status of corals is still unclear, but in spite of their anatomical and physiological specialization as carnivores it is likely that they derive some nutrient substances from zooxanthellae. Suggestions that filamentous algae in coral heads play a major part in the economy of the corals have not been supported by later work, but biomass pyramids constructed on the basis by Odum and Odum remain the only ones available. Most reefs are apparently autotrophic, with 1500–3500 g. Carbon being fixed per m. 2 per year. 5. Few animals eat corals, which may account for their success. Important predators are fish and the echinoderm Acanthaster. Quantitative estimates of biogenic erosion of organic skeletons on reefs are high. Fish affect not only corals but other invertebrates, algae and marine phanerogams. 6. Corals may be killed by ‘dark water’, intense rain or river floodwaters, earth movements, human interference and especially hurricanes. Reef recovery after hurricanes may take 10–20 years. 7. In addition to fringing, barrier and atoll reefs, intermediate types are recognised. The main types may consist of linear reefs or faros. Smaller lagoon reefs include pinnacles, patches and platforms, and submerged knolls. Complex cellular or mesh reef patterns are also found. 8. Reefs are conspicuously zoned, both laterally in response to changing exposure to waves to form windward and leeward reefs, and transversely, as a result of steep environmental gradients across reef flats from sea to lagoon. Topographic and ecological zones may be characterized by particular coral species, but these vary widely from reef to reef. A major distinction can be made between reefs with and without algal ridges, which are common on open‐ocean trade‐wind reefs, in the Indo‐Pacific, but are absent on Caribbean reefs and on Indo‐Pacific reefs in more sheltered waters. gorgonians are common on Caribbean reefs, alcyonaceans in the Indo‐Pacific. 9. Much of the difficulty in comparing reefs stems from the lack of uniformity in surveying methods. Problems of describing the complex three‐dimensional patterns of organisms on reefs have yet to be solved, and hence little progress has been made in explanation of these patterns. Explanation in terms of simple environmental controls is inadequate. 10. Understanding the distribution of corals is made more difficult both by taxo‐nomic problems and by the plasticity of growth form in different situations. 11. Growth of corals and reefs may be estimated by measuring the growth of individual colonies, measuring rates of calcium carbonate deposition in the skeleton, measuring topographic change on the reef and deducing net rates of reef growth from geological evidence. Massive corals may increase in diameter by 1 cm./year, branches of branching corals may increase in length by 10 cm./year. Study of deposition rates shows variation within colonies, between species, in light and dark, and seasonally. Rates of reef growth extrapolated from colony measurements reach 2–5 cm./year, and contrast with figures as low as 0–02 cm/year averaged over 70 million years from borehole data. Both colony growth rates and geological data suggest worldwide variations in rates of reef growth. 12. In spite of clear evidence of long‐continued subsidence, present surface features of reefs, often only thinly veneered by modern corals, have been much affected by recent sea level fluctuations. Many slightly raised reefs at 2–10 m. above sea level date at 90–160 thousand years B.P.; there is evidence for a sea level at about the present level at 30–35 thousand years B.P.; and controversy continues over whether sea level has stood higher than the present at any time since the last sea level rise began about 20,000 years ago. Evidence from many reefs suggests a slightly higher sea level in the last 4000 years, but on other reefs such evidence is lacking. 13. Several reef features (submerged terraces, groove‐spur systems, algal ridge, reef flat, reef blocks and reef islands) have been interpreted either as relict features dating from a higher sea level in the last 5000 years, or contemporary features developed in response to present processes. In some cases the evidence is equivocal; in others it is clear that diverse features are being grouped together under the same name. If such features are referable to a higher sea level, this may have been of last Interglacial or even Interstadial age rather than Holocene. 14. A reef consists of a rigid framework defining several major depositional environments within and around it. Sediments are of biological, mainly skeletal origin, except in unusual environments such as the Bahama Banks. The characteristics of sediments derived from organisms depend partly on the breakdown patterns of particular skeletons, partly on transportation and sorting processes. Fine sediments may be either detrital, or physicochemical precipitates. 15. Organisms affect sediments after deposition, by disturbance, transportation and probably comminution. Fish and holothurians have been studied in detail. 16. While new theories of coral reefs are proposed from time to time, the need is less for new theories than for standardised procedures to ensure comparability of reef studies and the identification of variations in reefs both on local and regional scales. While reefs as biological systems adjust relatively rapidly to changes, reefs as geological systems adjust much more slowly. Because of the magnitude and recency of Pleistocene fluctuations in sea level, many biological features of reefs are out of phase with inherited geological features, and this had led to much controversy.",
    url = "https://doi.org/10.1111/j.1469-185x.1969.tb00609.x",
    doi = "10.1111/j.1469-185x.1969.tb00609.x",
    openalex = "W2172280477",
    references = "doi1010160025322764900489, doi1010160079194661900040, doi101016s0065288108604381, doi101086626295, doi101086626809, doi1023071929924, doi1023071942181, doi1023071943285, doi104319lo1956120102, openalexw3126336940, openalexw574363047"
}

@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"
}

@article{doi101126science1774045270,
    author = "Knutson, D W and Buddemeier, Robert W. and Smith, Stephen V.",
    title = "Coral Chronometers: Seasonal Growth Bands in Reef Corals",
    year = "1972",
    journal = "Science",
    abstract = "Autoradiagraphs and x-radiographs have been made of vertical sections through the centers of reef corals from Eniwetok. Radioactivity bands in the coral structure are caused by strontium-90 and are related to specific series of nuclear tests, thus making possible calculation of long-term growth rates. These data indicate that the cyclic variations in radial density revealed by x-radiography are annual.",
    url = "https://doi.org/10.1126/science.177.4045.270",
    doi = "10.1126/science.177.4045.270",
    openalex = "W2004026365",
    references = "chave1972carbonate"
}

@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{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"
}

@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"
}

@article{doi101007bf00302170,
    author = "Szmant, Alina M.",
    title = "Reproductive ecology of Caribbean reef corals",
    year = "1986",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/bf00302170",
    doi = "10.1007/bf00302170",
    openalex = "W2011426613",
    references = "doi101111j1469185x1969tb00609x, doi1023071942565"
}

@article{doi1023073514476,
    author = "Hallock, Pamela and Schlager, Wolfgang",
    title = "Nutrient Excess and the Demise of Coral Reefs and Carbonate Platforms",
    year = "1986",
    journal = "Palaios",
    abstract = "Growth rates of corals on Holocene reefs indicate that carbonate platforms should easily keep pace with long-term subsidence and sea-level changes, yet drowned reefs and platforms are common in the geologic record. Recognition of the negative influence of nutrients on reef communities provides a clue to that paradox. The primary carbonate-sediment producers of the coral reef community are highly adapted to nutrient-deficient environments. Input of nitrates and phosphates stimulates growth of plankton, which reduces water transparency, limiting depth ranges of zooxanthellate corals and calcareous algae and thereby reducing carbonate production. Higher nutrient concentrations and plankton densities also stimulate growth of fleshy algae and ahermatypic suspension-feeding animals in the benthos. Besides displacing hermatypic algae and corals, many of these fastgrowing competitors are bioeroders that actively destroy thze reefal structure. Because rates of carbonate production and bioerosion are similar, even modest increases in nutrient availability can shift a reef community from net production to net erosion. In the geologic record, drowned reefs and carbonate platforms typically exhibit evidence of nondeposition, bioerosion, and reduced redox potential, which indicate excess nutrient availability during drowning. Drowned reefs overlain by shales are possible victims of nutrients in terrestrial runoff that suppressed reef growth before arrival of siliciclastic sediments. Other drowned platforms may have succumbed during rapid pulses of sea-level rise that flooded previously subaerial platforms. Nutrients in the soils of the flooding platform were mixed into surface waters, suppressing reef growth. The reef drowned if submergence proceeded beyond the critical depth before the excess nutrients were exported from the system. Other mechanisms for reef drowning by excess nutrients include changes in local or regional upwelling patterns or mid-ocean overturn.",
    url = "https://doi.org/10.2307/3514476",
    doi = "10.2307/3514476",
    openalex = "W2327706037",
    references = "doi101038187123a0, doi101144gsjgs13620175"
}

@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{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"
}

@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"
}

@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"
}

@article{doi104319lo1997425part21119,
    author = "Lapointe, Brian E.",
    title = "Nutrient thresholds for bottom‐up control of macroalgal blooms on coral reefs in Jamaica and southeast Florida",
    year = "1997",
    journal = "Limnology and Oceanography",
    abstract = "During the past two decades coral reefs in the greater Caribbean area have been altered by phase shifts away from corals and toward macroalgae or algal turfs. This study tested the hypothesis that because the phase shift on reefs in Jamaica and southeast Florida involved frondose macroalgae, bottom‐up control via nutrient enrichment must be a causal factor. The approach was multifaceted and included measurement of near‐bottom nutrient concentrations, salinity, nutrient enrichment bioassays, alkaline phosphatase assays, tissue C: N: P ratios, and tissue 15 N: 14 N (δ 15 N) ratios. In both locations, concentrations of dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP) exceeded nutrient thresholds (∼1.0 µ M DIN, 0.1 µ M SRP) noted to sustain macroalgal blooms on Caribbean coral reefs. High seawater DIN: SRP ratios, alkaline phosphatase activity, and tissue C: P and N: P ratios of macroalgae on the carbonate‐rich Jamaican reef suggested SRP limitation of productivity compared to lower values of these variables on siliciclastic reefs in Florida that suggested DIN limitation. This pattern was corroborated experimentally when SRP enrichment increased P max (photosynthetic capacity at light saturation) of the chlorophyte Chaetomorpha linum in Jamaica compared to DIN enrichment that increased a (the photosynthetic efficiency under low irradiance) of the deeper growing chlorophyte Codium isthmocladum in southeast Florida. Increased DIN concentrations were associated with reduced salinity on both reefs, indicating submarine groundwater discharge was a significant source of DIN. Elevated δ 15 N values of C. isthmocladum tissue further pointed to wastewater DIN as a source of nitrogen contributing to the blooms in southeast Florida.",
    url = "https://doi.org/10.4319/lo.1997.42.5\_part\_2.1119",
    doi = "10.4319/lo.1997.42.5\_part\_2.1119",
    openalex = "W2105082791"
}

@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{doi101007s003380050213,
    author = "McCook, Laurence J.",
    title = "Macroalgae, nutrients and phase shifts on coral reefs: scientific issues and management consequences for the Great Barrier Reef",
    year = "1999",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/s003380050213",
    doi = "10.1007/s003380050213",
    openalex = "W1999306630"
}

@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"
}

@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"
}

@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"
}

@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{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"
}

@article{doi101126science1058635,
    author = "Bellwood, David R. and Hughes, Terry P.",
    title = "Regional-Scale Assembly Rules and Biodiversity of Coral Reefs",
    year = "2001",
    journal = "Science",
    abstract = "Tropical reef fishes and corals exhibit highly predictable patterns of taxonomic composition across the Indian and Pacific Oceans. Despite steep longitudinal and latitudinal gradients in total species richness, the composition of these key taxa is constrained within a remarkably narrow range of values. Regional-scale variation in reef biodiversity is best explained by large-scale patterns in the availability of shallow-water habitat. Once habitat area is accounted for, there is surprisingly little residual effect of latitude or longitude. Low-diversity regions are most vulnerable to human impacts such as global warming, underscoring the urgent need for integrated management at multinational scales.",
    url = "https://doi.org/10.1126/science.1058635",
    doi = "10.1126/science.1058635",
    openalex = "W1999174996",
    references = "doi101007s003380050220, doi101111j155856461999tb03769x, doi101126science2314734129"
}

@book{openalexw253507229,
    author = "Spalding, Mark and Ravilious, Corinna and Green, Edmund P.",
    title = "World atlas of coral reefs",
    year = "2001",
    abstract = "Coral reefs are one of the most biologically diverse habitats in the world, host to an extraordinary variety of marine plants and animals. They are also one of the world's most fragile and endangered ecosystems. The growth of mass tourism, combined with the boom in popularity of scuba diving, has brought these spectacular ecosystems to public attention across the planet. Coral reefs provide essential fish habitat, support endangered and threatened species, and harbor protected marine mammals and turtles. They are a significant source of food, provide income and employment through tourism and marine recreation, and offer countless other benefits to humans, including supplying compounds for pharmaceuticals. Yet coral reefs around the world are rapidly being degraded by a number of human activities, such as overfishing, coastal development, and the introduction of sewage, fertilizer, and sediment. World Atlas of Coral Reefs provides the first detailed and definitive account of the current state of our planet's coral reefs. With its wealth of authoritative and up-to-date information, the finest maps available, and detailed descriptive texts and images by leading experts, this full-color volume will be a critical resource for anyone interested in these vital environments. World Atlas of Coral Reefs contains eighty-four full-page newly researched and drawn color maps, together with more than two hundred color photos illustrating reefs, reef animals, and images taken from space by NASA astronauts during the 2000 and 2001 space shuttle flights. The authors provide a wealth of information on the geography, biodiversity, and human uses of coral reefs, as well as details about the threats to their existence. Prepared at the UNEP-World Conservation Monitoring Centre in Cambridge, England--the United Nations office responsible for providing authoritative information on the condition of global biodiversity--the Atlas will be a critical tool for scientists, students, policymakers, and planners at local, national, and international levels alike. Publication of the World Atlas of Coral Reefs is supported by international institutions including the United Nations Environment Programme; The Marine Aquarium Council, The International Coral Reef Initiative; ICLARM--The World Fish Center; the Professional Association of Diving Instructors, and the Aventis Foundation.",
    openalex = "W253507229"
}

@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{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"
}

@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"
}

@article{doi101126science1095733,
    author = "Little, Angela F. and van Oppen, Madeleine J. H. and Willis, Bette L.",
    title = "Flexibility in Algal Endosymbioses Shapes Growth in Reef Corals",
    year = "2004",
    journal = "Science",
    abstract = "The relation between corals and their algal endosymbionts has been a key to the success of scleractinian (stony) corals as modern reef-builders, but little is known about early stages in the establishment of the symbiosis. Here, we show that initial uptake of zooxanthellae by juvenile corals during natural infection is nonspecific (a potentially adaptive trait); the association is flexible and characterized by a change in (dominant) zooxanthella strains over time; and growth rates of experimentally infected coral holobionts are partly contingent on the zooxanthella strain harbored, with clade C–infected juveniles growing two to three times as fast as those infected with clade D.",
    url = "https://doi.org/10.1126/science.1095733",
    doi = "10.1126/science.1095733",
    openalex = "W2123619757"
}

@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{doi101126science1119861,
    author = "Roberts, J. Murray and Wheeler, Andrew J. and Freiwald, André",
    title = "Reefs of the Deep: The Biology and Geology of Cold-Water Coral Ecosystems",
    year = "2006",
    journal = "Science",
    abstract = "Coral reefs are generally associated with shallow tropical seas; however, recent deep-ocean exploration using advanced acoustics and submersibles has revealed unexpectedly widespread and diverse coral ecosystems in deep waters on continental shelves, slopes, seamounts, and ridge systems around the world. Advances reviewed here include the use of corals as paleoclimatic archives and their biogeological functioning, biodiversity, and biogeography. Threats to these fragile, long-lived, and rich ecosystems are mounting: The impacts of deep-water trawling are already widespread, and effects of ocean acidification are potentially devastating.",
    url = "https://doi.org/10.1126/science.1119861",
    doi = "10.1126/science.1119861",
    openalex = "W2137258492"
}

@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"
}

@article{doi101007s003380080418z,
    author = "Perry, Chris T. and Spencer, Tom and Kench, Paul S.",
    title = "Carbonate budgets and reef production states: a geomorphic perspective on the ecological phase-shift concept",
    year = "2008",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/s00338-008-0418-z",
    doi = "10.1007/s00338-008-0418-z",
    openalex = "W2072549492",
    references = "doi101016s0025326x99002374"
}

@article{doi101126science1159196,
    author = "Carpenter, Kent E. and Abrar, Muhammad and Aeby, Greta S. and Aronson, Richard B. and Banks, Stuart and Bruckner, Andrew W. and Chiriboga, Angel I. and Cortés, Jorge and Delbeek, J. Charles and DeVantier, Lyndon and Edgar, Graham J. and Edwards, Alasdair J. and Fenner, Douglas and Guzmán, Héctor M. and Hoeksema, Bert W. and Hodgson, Gregor and Johan, Ofri and Licuanan, Wilfredo Y. and Livingstone, Suzanne R. and Lovell, Edward R. and Moore, Jennifer and Obura, David O. and Ochavillo, Domingo and Polidoro, Beth and Precht, William F. and Quibilan, Miledel Christine C. and Reboton, Clarissa and Richards, Zoe T. and Rogers, Alex D. and Sanciangco, Jonnell C. and Sheppard, Anne and Sheppard, Charles and Smith, Jennifer E. and Stuart, Simon N. and Turak, Emre and Veron, J. E. N. and Wallace, Carden C. and Weil, Ernesto and Wood, Elizabeth",
    title = "One-Third of Reef-Building Corals Face Elevated Extinction Risk from Climate Change and Local Impacts",
    year = "2008",
    journal = "Science",
    abstract = "The conservation status of 845 zooxanthellate reef-building coral species was assessed by using International Union for Conservation of Nature Red List Criteria. Of the 704 species that could be assigned conservation status, 32.8\% are in categories with elevated risk of extinction. Declines in abundance are associated with bleaching and diseases driven by elevated sea surface temperatures, with extinction risk further exacerbated by local-scale anthropogenic disturbances. The proportion of corals threatened with extinction has increased dramatically in recent decades and exceeds that of most terrestrial groups. The Caribbean has the largest proportion of corals in high extinction risk categories, whereas the Coral Triangle (western Pacific) has the highest proportion of species in all categories of elevated extinction risk. Our results emphasize the widespread plight of coral reefs and the urgent need to enact conservation measures.",
    url = "https://doi.org/10.1126/science.1159196",
    doi = "10.1126/science.1159196",
    openalex = "W2153213062",
    references = "doi101126science1085706"
}

@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"
}

@article{doi101371journalpone0003039,
    author = "Graham, Nicholas A. J. and McClanahan, Tim R. and MacNeil, M. Aaron and Wilson, Shaun K. and Polunin, Nicholas and Jennings, Simon and Chabanet, Pascale and Clark, Susan and Spalding, Mark and Letourneur, Yves and Bigot, Lionel and Galzin, René and Öhman, Marcus and Garpe, Kajsa and Edwards, Alasdair J. and Sheppard, Charles",
    title = "Climate Warming, Marine Protected Areas and the Ocean-Scale Integrity of Coral Reef Ecosystems",
    year = "2008",
    journal = "PLoS ONE",
    abstract = "Coral reefs have emerged as one of the ecosystems most vulnerable to climate variation and change. While the contribution of a warming climate to the loss of live coral cover has been well documented across large spatial and temporal scales, the associated effects on fish have not. Here, we respond to recent and repeated calls to assess the importance of local management in conserving coral reefs in the context of global climate change. Such information is important, as coral reef fish assemblages are the most species dense vertebrate communities on earth, contributing critical ecosystem functions and providing crucial ecosystem services to human societies in tropical countries. Our assessment of the impacts of the 1998 mass bleaching event on coral cover, reef structural complexity, and reef associated fishes spans 7 countries, 66 sites and 26 degrees of latitude in the Indian Ocean. Using Bayesian meta-analysis we show that changes in the size structure, diversity and trophic composition of the reef fish community have followed coral declines. Although the ocean scale integrity of these coral reef ecosystems has been lost, it is positive to see the effects are spatially variable at multiple scales, with impacts and vulnerability affected by geography but not management regime. Existing no-take marine protected areas still support high biomass of fish, however they had no positive affect on the ecosystem response to large-scale disturbance. This suggests a need for future conservation and management efforts to identify and protect regional refugia, which should be integrated into existing management frameworks and combined with policies to improve system-wide resilience to climate variation and change.",
    url = "https://doi.org/10.1371/journal.pone.0003039",
    doi = "10.1371/journal.pone.0003039",
    openalex = "W1994387974"
}

@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"
}

@article{doi1010292008gb003286,
    author = "Tribollet, Aline and Godinot, Claire and Atkinson, M. J. and Langdon, Chris",
    title = "Effects of elevated p CO 2 on dissolution of coral carbonates by microbial euendoliths",
    year = "2009",
    journal = "Global Biogeochemical Cycles",
    abstract = "Eight‐month‐old blocks of the coral Porites lobata colonized by natural Hawaiian euendolithic and epilithic communities were experimentally exposed to two different aqueous p CO 2 treatments, 400 ppmv and 750 ppmv, for 3 months. The chlorophyte Ostreobium quekettii dominated communities at the start and at the end of the experiment (65–90\%). There were no significant differences in the relative abundance of euendolithic species, nor were there any differences in bioeroded area at the surface of blocks (27\%) between p CO 2 treatments. The depth of penetration of filaments of O. quekettii was, however, significantly higher under 750 ppmv (1.4 mm) than under 400 ppmv (1 mm). Consequently, rates of carbonate dissolution measured under elevated p CO 2 were 48\% higher than under ambient p CO 2 (0.46 kg CaCO 3 dissolved m −2 a −1 versus 0.31 kg m −2 a −1). Thus, biogenic dissolution of carbonates by euendoliths in coral reefs may be a dominant mechanism of carbonate dissolution in a more acidic ocean.",
    url = "https://doi.org/10.1029/2008gb003286",
    doi = "10.1029/2008gb003286",
    openalex = "W2095091888",
    references = "doi101016s0025326x99002374"
}

@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"
}

@article{doi105194bg616712009,
    author = "Maier, Cornelia and Hegeman, J. and Weinbauer, Markus G. and Gattuso, Jean‐Pierre",
    title = "Calcification of the cold-water coral Lophelia pertusa, under ambient and reduced pH",
    year = "2009",
    journal = "Biogeosciences",
    abstract = "Abstract. The cold-water coral Lophelia pertusa is one of the few species able to build reef-like structures and a 3-dimensional coral framework in the deep oceans. Furthermore, deep cold-water coral bioherms may be among the first marine ecosystems to be affected by ocean acidification. Colonies of L. pertusa were collected during a cruise in 2006 to cold-water coral bioherms of the Mingulay reef complex (Hebrides, North Atlantic). Shortly after sample collection onboard these corals were labelled with calcium-45. The same experimental approach was used to assess calcification rates and how those changed due to reduced pH during a cruise to the Skagerrak (North Sea) in 2007. The highest calcification rates were found in youngest polyps with up to 1\% d−1 new skeletal growth and average rates of 0.11±0.02\% d−1±S.E.). Lowering pH by 0.15 and 0.3 units relative to the ambient level resulted in calcification being reduced by 30 and 56\%. Lower pH reduced calcification more in fast growing, young polyps (59\% reduction) than in older polyps (40\% reduction). Thus skeletal growth of young and fast calcifying corallites suffered more from ocean acidification. Nevertheless, L. pertusa exhibited positive net calcification (as measured by 45Ca incorporation) even at an aragonite saturation state (Ωa) below 1.",
    url = "https://doi.org/10.5194/bg-6-1671-2009",
    doi = "10.5194/bg-6-1671-2009",
    openalex = "W2171829412",
    references = "doi101016s0921818198000356, doi1010291999gb001195, doi1010292004gb002247, doi1010292004jc002576, doi1010292006gl027207, doi1010292006gl028554, doi101038nature04095, doi101038nature07051, doi101093icb391160, doi101126science1119861"
}

@article{doi101111j13652486201002204x,
    author = "Kiessling, Wolfgang and Simpson, Carl",
    title = "On the potential for ocean acidification to be a general cause of ancient reef crises",
    year = "2010",
    journal = "Global Change Biology",
    abstract = "Anthropogenic rise in the carbon dioxide concentration in the atmosphere leads to global warming and acidification of the oceans. Ocean acidification (OA) is harmful to many organisms but especially to those that build massive skeletons of calcium carbonate, such as reef corals. Here, we test the recent suggestion that OA leads not only to declining calcification of reef corals and reduced growth rates of reefs but may also have been a trigger of ancient reef crises and mass extinctions in the sea. We analyse the fossil record of biogenic reefs and marine organisms to (1) assess the timing and intensity of ancient reef crises, (2) check which reef crises were concurrent with inferred pulses of carbon dioxide concentrations and (3) evaluate the correlation between reef crises and mass extinctions and their selectivity in terms of inferred physiological buffering. We conclude that four of five global metazoan reef crises in the last 500 Myr were probably at least partially governed by OA and rapid global warming. However, only two of the big five mass extinctions show geological evidence of OA.",
    url = "https://doi.org/10.1111/j.1365-2486.2010.02204.x",
    doi = "10.1111/j.1365-2486.2010.02204.x",
    openalex = "W2100073969",
    references = "doi1011302007242401, doi101146annurevecolsys35021103105715, doi105194bg616712009"
}

@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{doi101111j13652486201102523x,
    author = "Perry, Chris T. and Kench, Paul S. and Smithers, S and Riegl, Bernhard and Yamano, Hiroya and O’Leary, Michael",
    title = "Implications of reef ecosystem change for the stability and maintenance of coral reef islands",
    year = "2011",
    journal = "Global Change Biology",
    abstract = "Abstract Coral reef islands are among the most vulnerable environments on Earth to climate change because they are low lying and largely constructed from unconsolidated sediments that can be readily reworked by waves and currents. These sediments derive entirely from surrounding coral reef and reef flat environments and are thus highly sensitive to ecological transitions that may modify reef community composition and productivity. How such modifications – driven by anthropogenic disturbances and on‐going and projected climatic and environmental change – will impact reef island sediment supply and geomorphic stability remains a critical but poorly resolved question. Here, we review the unique ecological–geomorphological linkages that underpin this question and, using different scenarios of environmental change for which reef sediment production responses can be projected, explore the likely resilience of different island types. In general, sand‐dominated islands are likely to be less resilient than those dominated by rubble grade material. However, because different islands typically have different dominant sediment constituents (usually either coral, benthic foraminifera or H alimeda) and because these respond differently to individual ecological disturbances, island resilience is likely to be highly variable. Islands composed of coral sands are likely to undergo major morphological change under most near‐future ecological change scenarios, while those dominated by H alimeda may be more resilient. Islands composed predominantly of benthic foraminifera (a common state through the P acific region) are likely to exhibit varying degrees of resilience depending upon the precise combination of ecological disturbances faced. The study demonstrates the critical need for further research bridging the ecological–geomorphological divide to understand: (1) sediment production responses to different ecological and environmental change scenarios; and (2) dependant landform vulnerability.",
    url = "https://doi.org/10.1111/j.1365-2486.2011.02523.x",
    doi = "10.1111/j.1365-2486.2011.02523.x",
    openalex = "W2114408276",
    references = "doi101016s0025326x99002374"
}

@article{doi101111j13652486201102583x,
    author = "Form, Armin and Riebesell, Ulf",
    title = "Acclimation to ocean acidification during long‐term CO 2 exposure in the cold‐water coral L ophelia pertusa",
    year = "2011",
    journal = "Global Change Biology",
    abstract = "Abstract Ocean acidity has increased by 30\% since preindustrial times due to the uptake of anthropogenic CO 2 and is projected to rise by another 120\% before 2100 if CO 2 emissions continue at current rates. Ocean acidification is expected to have wide‐ranging impacts on marine life, including reduced growth and net erosion of coral reefs. Our present understanding of the impacts of ocean acidification on marine life, however, relies heavily on results from short‐term CO 2 perturbation studies. Here, we present results from the first long‐term CO 2 perturbation study on the dominant reef‐building cold‐water coral L ophelia pertusa and relate them to results from a short‐term study to compare the effect of exposure time on the coral's responses. Short‐term (1 week) high CO 2 exposure resulted in a decline of calcification by 26–29\% for a pH decrease of 0.1 units and net dissolution of calcium carbonate. In contrast, L. pertusa was capable to acclimate to acidified conditions in long‐term (6 months) incubations, leading to even slightly enhanced rates of calcification. Net growth is sustained even in waters sub‐saturated with respect to aragonite. Acclimation to seawater acidification did not cause a measurable increase in metabolic rates. This is the first evidence of successful acclimation in a coral species to ocean acidification, emphasizing the general need for long‐term incubations in ocean acidification research. To conclude on the sensitivity of cold‐water coral reefs to future ocean acidification further ecophysiological studies are necessary which should also encompass the role of food availability and rising temperatures.",
    url = "https://doi.org/10.1111/j.1365-2486.2011.02583.x",
    doi = "10.1111/j.1365-2486.2011.02583.x",
    openalex = "W2132881865",
    references = "doi105194bg616712009"
}

@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"
}

@article{doi101007s0033801209014,
    author = "Perry, Chris T. and Edinger, Evan and Kench, Paul S. and Murphy, Gary N. and Smithers, S and Steneck, Robert S. and Mumby, Peter J.",
    title = "Estimating rates of biologically driven coral reef framework production and erosion: a new census-based carbonate budget methodology and applications to the reefs of Bonaire",
    year = "2012",
    journal = "Coral Reefs",
    url = "https://doi.org/10.1007/s00338-012-0901-4",
    doi = "10.1007/s00338-012-0901-4",
    openalex = "W2090226803",
    references = "doi101016s0025326x99002374"
}

@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"
}

@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"
}

@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"
}

@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"
}

@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"
}

@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"
}

@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"
}

@article{doi101126science1241981,
    author = "de Goeij, Jasper M. and van Oevelen, Dick and Vermeij, Mark J. A. and Osinga, Ronald and Middelburg, Jack J. and de Goeij, Anton F.P.M. and Admiraal, Wim",
    title = "Surviving in a Marine Desert: The Sponge Loop Retains Resources Within Coral Reefs",
    year = "2013",
    journal = "Science",
    abstract = {Ever since Darwin's early descriptions of coral reefs, scientists have debated how one of the world's most productive and diverse ecosystems can thrive in the marine equivalent of a desert. It is an enigma how the flux of dissolved organic matter (DOM), the largest resource produced on reefs, is transferred to higher trophic levels. Here we show that sponges make DOM available to fauna by rapidly expelling filter cells as detritus that is subsequently consumed by reef fauna. This "sponge loop" was confirmed in aquarium and in situ food web experiments, using (13)C- and (15)N-enriched DOM. The DOM-sponge-fauna pathway explains why biological hot spots such as coral reefs persist in oligotrophic seas--the reef's paradox--and has implications for reef ecosystem functioning and conservation strategies.},
    url = "https://doi.org/10.1126/science.1241981",
    doi = "10.1126/science.1241981",
    openalex = "W2109476731"
}

@article{doi101016jcosust201311029,
    author = "D’Angelo, Cecilia and Wiedenmann, Jörg",
    title = "Impacts of nutrient enrichment on coral reefs: new perspectives and implications for coastal management and reef survival",
    year = "2014",
    journal = "Current Opinion in Environmental Sustainability",
    abstract = "Anthropogenic nutrient enrichment is often associated with coral reef decline. Consequently, there is a large consent that increased nutrient influxes in reef waters have negative longterm consequences for corals. However, the mechanisms by which dissolved inorganic nutrients can disturb corals and their symbiotic algae are subject to controversial debate. Herein, we discuss recent studies that demonstrate how nutrient enrichment affects the heat and light stress tolerance of corals and their bleaching susceptibility. We integrate direct and indirect effects of nutrient enrichment on corals in a model that explains why healthy coral reefs can exist over a rather broad range of natural nutrient environments at the lower end of the concentration scale and that anthropogenic nutrient enrichment can disturb the finely balanced processes via multiple pathways. We conceptualise that corals can suffer from secondary negative nutrient effects due to the alteration of their natural nutrient environment by increased phytoplankton loads. In this context, we suggest that phytoplankton represents a likely vector that can translate nutrients effects, induced for instance by coastal run-off, into nutrient stress on coral reefs in considerable distance to the site of primary nutrient enrichment. The presented synthesis of the literature suggests that the effects of nutrient enrichment and eutrophication beyond certain thresholds are negative for the physiological performance of the coral individual and for ecosystem functioning. Hence, the immediate implementation of knowledge-based nutrient management strategies is crucial for coral reef survival.",
    url = "https://doi.org/10.1016/j.cosust.2013.11.029",
    doi = "10.1016/j.cosust.2013.11.029",
    openalex = "W1974182285",
    references = "doi101016s0025326x99002374"
}

@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"
}

@article{doi101126science1251336,
    author = "Palumbi, Stephen R. and Barshis, Daniel J. and Traylor‐Knowles, Nikki and Bay, Rachael A.",
    title = "Mechanisms of reef coral resistance to future climate change",
    year = "2014",
    journal = "Science",
    abstract = "Reef corals are highly sensitive to heat, yet populations resistant to climate change have recently been identified. To determine the mechanisms of temperature tolerance, we reciprocally transplanted corals between reef sites experiencing distinct temperature regimes and tested subsequent physiological and gene expression profiles. Local acclimatization and fixed effects, such as adaptation, contributed about equally to heat tolerance and are reflected in patterns of gene expression. In less than 2 years, acclimatization achieves the same heat tolerance that we would expect from strong natural selection over many generations for these long-lived organisms. Our results show both short-term acclimatory and longer-term adaptive acquisition of climate resistance. Adding these adaptive abilities to ecosystem models is likely to slow predictions of demise for coral reef ecosystems.",
    url = "https://doi.org/10.1126/science.1251336",
    doi = "10.1126/science.1251336",
    openalex = "W2051481587"
}

@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"
}

@article{doi103389fmars201500037,
    author = "Cathalot, Cécile and van Oevelen, Dick and Cox, Tom J. S. and Kutti, Tina and Lavaleye, Marc and Duineveld, Gerard and Meysman, Filip J. R.",
    title = "Cold-water coral reefs and adjacent sponge grounds: hotspots of benthic respiration and organic carbon cycling in the deep sea",
    year = "2015",
    journal = "Frontiers in Marine Science",
    abstract = "Cold-water coral reefs and adjacent sponge grounds are distributed widely in the deep ocean, where only a small fraction of the surface productivity reaches the seafloor as detritus. It remains elusive how these hotspots of biodiversity can thrive in such a food-limited environment, as data on energy flow and organic carbon utilization are critically lacking. Here we report in situ community respiration rates for cold-water coral and sponge ecosystems obtained by the non-invasive aquatic Eddy Correlation technique. Oxygen uptake rates over coral reefs and adjacent sponge grounds in the Træna Coral Field (Norway) were 9-20 times higher than those of the surrounding soft sediments. These high respiration rates indicate strong organic matter consumption, and hence suggest a local focusing onto these ecosystems of the downward flux of organic matter that is exported from the surface ocean. Overall, our results show that coral reefs and adjacent sponge grounds are hotspots of carbon processing in the food-limited deep ocean, and that these deep-sea ecosystems play a more prominent role in marine biogeochemical cycles than previously recognized.",
    url = "https://doi.org/10.3389/fmars.2015.00037",
    doi = "10.3389/fmars.2015.00037",
    openalex = "W1916037364",
    references = "doi105194bg616712009"
}

@article{doi101371journalpone0158094,
    author = "Guannel, Greg and Arkema, Katie K. and Ruggiero, Peter and Verutes, Gregory M.",
    title = "The Power of Three: Coral Reefs, Seagrasses and Mangroves Protect Coastal Regions and Increase Their Resilience",
    year = "2016",
    journal = "PLoS ONE",
    abstract = "Natural habitats have the ability to protect coastal communities against the impacts of waves and storms, yet it is unclear how different habitats complement each other to reduce those impacts. Here, we investigate the individual and combined coastal protection services supplied by live corals on reefs, seagrass meadows, and mangrove forests during both non-storm and storm conditions, and under present and future sea-level conditions. Using idealized profiles of fringing and barrier reefs, we quantify the services supplied by these habitats using various metrics of inundation and erosion. We find that, together, live corals, seagrasses, and mangroves supply more protection services than any individual habitat or any combination of two habitats. Specifically, we find that, while mangroves are the most effective at protecting the coast under non-storm and storm conditions, live corals and seagrasses also moderate the impact of waves and storms, thereby further reducing the vulnerability of coastal regions. Also, in addition to structural differences, the amount of service supplied by habitats in our analysis is highly dependent on the geomorphic setting, habitat location and forcing conditions: live corals in the fringing reef profile supply more protection services than seagrasses; seagrasses in the barrier reef profile supply more protection services than live corals; and seagrasses, in our simulations, can even compensate for the long-term degradation of the barrier reef. Results of this study demonstrate the importance of taking integrated and place-based approaches when quantifying and managing for the coastal protection services supplied by ecosystems.",
    url = "https://doi.org/10.1371/journal.pone.0158094",
    doi = "10.1371/journal.pone.0158094",
    openalex = "W2474682767",
    references = "doi101016joceaneng200907018, doi101038ncomms2409"
}

@article{doi101111gcb13647,
    author = "van Oppen, Madeleine J. H. and Gates, Ruth D. and Blackall, Linda L. and Cantin, Neal E. and Chakravarti, Leela J. and Chan, Wing Yan and Cormick, Craig and Crean, Angela J. and Damjanovic, Katarina and Epstein, Hannah E. and Harrison, Peter L. and Jones, Thomas A. and Miller, Margaret W. and Pears, Rachel and Peplow, Lesa M. and Raftos, David A. and Schaffelke, Britta and Stewart, Kristen and Torda, Gergely and Wachenfeld, David and Weeks, Andrew R. and Putnam, Hollie M.",
    title = "Shifting paradigms in restoration of the world's coral reefs",
    year = "2017",
    journal = "Global Change Biology",
    abstract = "Many ecosystems around the world are rapidly deteriorating due to both local and global pressures, and perhaps none so precipitously as coral reefs. Management of coral reefs through maintenance (e.g., marine-protected areas, catchment management to improve water quality), restoration, as well as global and national governmental agreements to reduce greenhouse gas emissions (e.g., the 2015 Paris Agreement) is critical for the persistence of coral reefs. Despite these initiatives, the health and abundance of corals reefs are rapidly declining and other solutions will soon be required. We have recently discussed options for using assisted evolution (i.e., selective breeding, assisted gene flow, conditioning or epigenetic programming, and the manipulation of the coral microbiome) as a means to enhance environmental stress tolerance of corals and the success of coral reef restoration efforts. The 2014-2016 global coral bleaching event has sharpened the focus on such interventionist approaches. We highlight the necessity for consideration of alternative (e.g., hybrid) ecosystem states, discuss traits of resilient corals and coral reef ecosystems, and propose a decision tree for incorporating assisted evolution into restoration initiatives to enhance climate resilience of coral reefs.",
    url = "https://doi.org/10.1111/gcb.13647",
    doi = "10.1111/gcb.13647",
    openalex = "W2594335126",
    references = "doi101038ncomms2409, doi101073pnas1422301112, doi101890es15001211"
}

@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"
}

@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{doi101073pnas1708001115,
    author = "Cinner, Joshua E. and Maire, Eva and Huchery, Cindy and MacNeil, M. Aaron and Graham, Nicholas A. J. and Mora, Camilo and McClanahan, Tim R. and Barnes, Michele L. and Kittinger, John N. and Hicks, Christina C. and D’Agata, Stéphanie and Hoey, Andrew S. and Gurney, Georgina G. and Feary, David A. 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 and Hardt, Marah J. and Beger, Maria and Friedlander, Alan M. 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, Charlotte and Tupper, Mark and Ferse, Sebastian C. A. and Sumaila, U. Rashid and Pardede, Shinta and Mouillot, David",
    title = "Gravity of human impacts mediates coral reef conservation gains",
    year = "2018",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {Coral reefs provide ecosystem goods and services for millions of people in the tropics, but reef conditions are declining worldwide. Effective solutions to the crisis facing coral reefs depend in part on understanding the context under which different types of conservation benefits can be maximized. Our global analysis of nearly 1,800 tropical reefs reveals how the intensity of human impacts in the surrounding seascape, measured as a function of human population size and accessibility to reefs ("gravity"), diminishes the effectiveness of marine reserves at sustaining reef fish biomass and the presence of top predators, even where compliance with reserve rules is high. Critically, fish biomass in high-compliance marine reserves located where human impacts were intensive tended to be less than a quarter that of reserves where human impacts were low. Similarly, the probability of encountering top predators on reefs with high human impacts was close to zero, even in high-compliance marine reserves. However, we find that the relative difference between openly fished sites and reserves (what we refer to as conservation gains) are highest for fish biomass (excluding predators) where human impacts are moderate and for top predators where human impacts are low. Our results illustrate critical ecological trade-offs in meeting key conservation objectives: reserves placed where there are moderate-to-high human impacts can provide substantial conservation gains for fish biomass, yet they are unlikely to support key ecosystem functions like higher-order predation, which is more prevalent in reserve locations with low human impacts.},
    url = "https://doi.org/10.1073/pnas.1708001115",
    doi = "10.1073/pnas.1708001115",
    openalex = "W2809574340",
    references = "doi101038nature18607"
}

@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"
}

@article{doi101126scienceaar3320,
    author = "Lamb, Joleah B. and Willis, Bette L. and Fiorenza, Evan A. and Couch, Courtney S. and Howard, Robert and Rader, Douglas N. and True, James and Kelly, Lisa A. and Ahmad, Awaludinnoer and Jompa, Jamaluddin and Harvell, C. Drew",
    title = "Plastic waste associated with disease on coral reefs",
    year = "2018",
    journal = "Science",
    abstract = "Plastic waste can promote microbial colonization by pathogens implicated in outbreaks of disease in the ocean. We assessed the influence of plastic waste on disease risk in 124,000 reef-building corals from 159 reefs in the Asia-Pacific region. The likelihood of disease increases from 4\% to 89\% when corals are in contact with plastic. Structurally complex corals are eight times more likely to be affected by plastic, suggesting that microhabitats for reef-associated organisms and valuable fisheries will be disproportionately affected. Plastic levels on coral reefs correspond to estimates of terrestrial mismanaged plastic waste entering the ocean. We estimate that 11.1 billion plastic items are entangled on coral reefs across the Asia-Pacific and project this number to increase 40\% by 2025. Plastic waste management is critical for reducing diseases that threaten ecosystem health and human livelihoods.",
    url = "https://doi.org/10.1126/science.aar3320",
    doi = "10.1126/science.aar3320",
    openalex = "W2785173370",
    references = "doi101038nature21707"
}

@article{doi101146annurevmarine010318095300,
    author = "Bruno, John F. and Côté, Isabelle M. and Toth, Lauren T.",
    title = "Climate Change, Coral Loss, and the Curious Case of the Parrotfish Paradigm: Why Don't Marine Protected Areas Improve Reef Resilience?",
    year = "2019",
    journal = "Annual Review of Marine Science",
    abstract = "Scientists have advocated for local interventions, such as creating marine protected areas and implementing fishery restrictions, as ways to mitigate local stressors to limit the effects of climate change on reef-building corals. However, in a literature review, we find little empirical support for the notion of managed resilience. We outline some reasons for why marine protected areas and the protection of herbivorous fish (especially parrotfish) have had little effect on coral resilience. One key explanation is that the impacts of local stressors (e.g., pollution and fishing) are often swamped by the much greater effect of ocean warming on corals. Another is the sheer complexity (including numerous context dependencies) of the five cascading links assumed by the managed-resilience hypothesis. If reefs cannot be saved by local actions alone, then it is time to face reef degradation head-on, by directly addressing anthropogenic climate change-the root cause of global coral decline.",
    url = "https://doi.org/10.1146/annurev-marine-010318-095300",
    doi = "10.1146/annurev-marine-010318-095300",
    openalex = "W2908138043",
    references = "doi101038ncomms2409"
}

@article{tortolerolangarica2019accelerated,
    author = "Tortolero-Langarica, J.J. Adolfo and Rodríguez-Troncoso, Alma P. and Cupul-Magaña, Amílcar L. and Alarcón-Ortega, Lucy C. and Santiago-Valentín, Jeimy D.",
    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",
    pages = "89-97",
    volume = "128",
    references = "doi101016jecss200809003, doi101016jpocean200603009, doi101071mf99078, doi101098rspb20090339, doi101126science1152509, doi101126science1204794, doi101126science2845411118, doi101126scienceaan8048, doi101371journalpone0000711, doi103354meps007207"
}

@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{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"
}

@article{doi103389fmars202000514,
    author = "Mies, Miguel and Francini‐Filho, Ronaldo B. and Zilberberg, Carla and Garrido, Amana G. and Longo, Guilherme Ortigara and Laurentino, Eduarda and Güth, Arthur Z. and Sumida, Paulo Yukio Gomes and Banha., Thomás Nei Soto",
    title = "South Atlantic Coral Reefs Are Major Global Warming Refugia and Less Susceptible to Bleaching",
    year = "2020",
    journal = "Frontiers in Marine Science",
    abstract = "Mass coral bleaching has increased in intensity and frequency and has severely impacted shallow tropical reefs worldwide. Although extensive investigation has been conducted on the resistance and resilience of coral reefs in the Indo-Pacific and Caribbean, the unique reefs of the South Atlantic remain largely unassessed. Here we compiled primary and literature data for reefs from three biogeographical regions: Indo-Pacific, Caribbean and South Atlantic and performed comparative analyses to investigate whether the latter may be more resistant to bleaching. Our findings show that South Atlantic corals display critical features that make them less susceptible to mass coral bleaching: (i) deeper bathymetric distribution, as species have a mean maximum depth of occurrence of 70 m; (ii) higher tolerance to turbidity, as nearly 60\% of species are found in turbid conditions; (iii) higher tolerance to nutrient enrichment, as nitrate concentration in the South Atlantic is naturally elevated; (iv) higher morphological resistance, as massive growth forms are dominant and comprise two thirds of species; and (v) more flexible symbiotic associations, as 75\% of corals and 60\% of symbiont phylotypes are generalists. Such features were associated with occurrence of fewer bleaching episodes with coral mortality in the South Atlantic, approximately 60\% less than the Indo-Pacific and 50\% less than the Caribbean. In addition, no mass coral mortality episodes associated with the three global mass bleaching events have been reported for the South Atlantic, which suffered considerably less bleaching. These results show that South Atlantic reefs display several remarkable features for withstanding thermal stress. Together with a historic experience of lower heat stress, our findings may explain why climate change impacts in this region have been less intense. Given the large extension and latitudinal distribution of South Atlantic coral reefs and communities, the region may be recognized as a major refugium and likely to resist climate change impacts more effectively than Indo-Pacific and Caribbean reefs.",
    url = "https://doi.org/10.3389/fmars.2020.00514",
    doi = "10.3389/fmars.2020.00514",
    openalex = "W3034843423",
    references = "doi101126sciadv1501252"
}

@article{céspedesrodríguez2021gross,
    author = "Céspedes-Rodríguez, EC and Londoño-Cruz, E",
    title = "Gross calcium carbonate production in Eastern Tropical Pacific coral reefs (Gorgona Island, Colombia)",
    year = "2021",
    journal = "Marine Ecology Progress Series",
    abstract = "The production and accumulation of carbonate reef framework is the positive component of reef development. The main organisms participating in this process are corals and crustose coralline algae (CCA) because their combined calcareous skeletons construct and help to consolidate reef frameworks. We assessed the contribution (i.e. gross production) of corals and CCA to the calcium carbonate (CaCO 3) budget of the 2 largest and most developed reefs of Gorgona Island (Pacific coast of Colombia). On each zone (back reef [BR], reef flat [RP], reef front [RF], and reef slope [RS]) of these reefs, we measured substrate rugosity, coral (Pocillopora spp.) and CCA cover, colony density for corals, skeletal density for CCA, and growth rates for the estimation of CaCO 3 production rates. Pocillopora spp. corals contributed 93.1\% of the total carbonate production, while CCA supplied the remaining 6.9\%. CaCO 3 production was higher at Playa Blanca reef, although CaCO 3 production in the RF of La Azufrada (12.31 kg m -2 yr -1) was higher in comparison to the RF at Playa Blanca (8.45 kg m -2 yr -1). Otherwise, CaCO 3 production was higher in all other reef zones (BR, RP, RS) of Playa Blanca, although only significantly higher in the BR (2.25 kg m -2 yr -1 at Playa Blanca against 0.29 kg m -2 yr -1 at La Azufrada). The RF contributed the most CaCO 3, mainly due to its high live coral cover and rapid coral growth. Although the contribution of CCA is low, they are key for reef stability. CaCO 3 production rates reported here (2.86 and 3.80 kg m -2 yr -1 in La Azufrada and Playa Blanca, respectively) are within the limits reported for Eastern Tropical Pacific reefs, and raise hope for the continued existence of coral reefs in an era of increasing threats to this ecosystem.",
    url = "https://doi.org/10.3354/meps13643",
    doi = "10.3354/meps13643",
    openalex = "W3121727345",
    pages = "37-46",
    volume = "665",
    references = "doi10100797894017749944, doi101007s003380050220, doi101016s0025326x99002374, doi101038nature02691, doi101038nature18607, doi101038nature21707, doi101093icb391146, doi101093icesjmsfsn048, doi101126science1085706, doi1023071942565"
}

@article{doi101038s41467021247773,
    author = "Johnson, Maggie D. and Scott, Jarrod J. and Leray, Matthieu and Lucey, Noelle and Bravo, Lucia M. Rodriguez and Wied, William L. and Altieri, Andrew H.",
    title = "Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef",
    year = "2021",
    journal = "Nature Communications",
    abstract = "Loss of oxygen in the global ocean is accelerating due to climate change and eutrophication, but how acute deoxygenation events affect tropical marine ecosystems remains poorly understood. Here we integrate analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered benthic community composition and microbial assemblages in a shallow tropical reef ecosystem. Conditions associated with the event precipitated coral bleaching and mass mortality, causing a 50\% loss of live coral and a shift in the benthic community that persisted a year later. Conversely, the unique taxonomic and functional profile of hypoxia-associated microbes rapidly reverted to a normoxic assemblage one month after the event. The decoupling of ecological trajectories among these major functional groups following an acute event emphasizes the need to incorporate deoxygenation as an emerging stressor into coral reef research and management plans to combat escalating threats to reef persistence.",
    url = "https://doi.org/10.1038/s41467-021-24777-3",
    doi = "10.1038/s41467-021-24777-3",
    openalex = "W3070971032",
    references = "doi101038s4155802007379"
}

@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"
}

@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"
}

@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{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"
}

@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"
}

@misc{doi107287peerj14586v01reviews1,
    title = {Peer Review \#1 of "Spatiotemporal variability of oxygen concentration in coral reefs of Gorgona Island (Eastern Tropical Pacific) and its effect on the coral Pocillopora capitata (v0.1)"},
    year = "2023",
    abstract = "Dissolved oxygen concentration (DO) is one of the main factors limiting benthic species distribution.Due to ocean warming and eutrophication, the ocean is deoxygenating.In the Eastern Tropical Pacific (ETP), deep waters with low DO (20 m depth and coincide with the deepest bathymetric distribution of scattered colonies of Pocillopora.Because DO concentrations in coral reefs of Gorgona island were comparably low to other coral reefs in the Eastern Tropical Pacific, and the hypoxic threshold of P. capitata was close to the minimum DO record on reefs, hypoxic events could represent a threat if conditions that promote eutrophication (and consequently hypoxia) increase.",
    url = "https://doi.org/10.7287/peerj.14586v0.1/reviews/1",
    doi = "10.7287/peerj.14586v0.1/reviews/1",
    openalex = "W4318591813",
    references = "céspedesrodríguez2021gross, doi101002sim1545, doi101016jmarpolbul200411028, doi101016jpocean200603008, doi101038nature21399, doi101073pnas0803833105, doi101093icb391146, doi101126science1153847, doi101126scienceaan8048, doi101146annurevmarine010908163855, doi103389fmars201700158"
}

@misc{doi107287peerj14586v01reviews2,
    title = {Peer Review \#2 of "Spatiotemporal variability of oxygen concentration in coral reefs of Gorgona Island (Eastern Tropical Pacific) and its effect on the coral Pocillopora capitata (v0.1)"},
    year = "2023",
    abstract = "Dissolved oxygen concentration (DO) is one of the main factors limiting benthic species distribution.Due to ocean warming and eutrophication, the ocean is deoxygenating.In the Eastern Tropical Pacific (ETP), deep waters with low DO (20 m depth and coincide with the deepest bathymetric distribution of scattered colonies of Pocillopora.Because DO concentrations in coral reefs of Gorgona island were comparably low to other coral reefs in the Eastern Tropical Pacific, and the hypoxic threshold of P. capitata was close to the minimum DO record on reefs, hypoxic events could represent a threat if conditions that promote eutrophication (and consequently hypoxia) increase.",
    url = "https://doi.org/10.7287/peerj.14586v0.1/reviews/2",
    doi = "10.7287/peerj.14586v0.1/reviews/2",
    openalex = "W4318591823",
    references = "céspedesrodríguez2021gross, doi101002sim1545, doi101016jmarpolbul200411028, doi101016jpocean200603008, doi101038nature21399, doi101073pnas0803833105, doi101093icb391146, doi101126science1153847, doi101126scienceaan8048, doi101146annurevmarine010908163855, doi103389fmars201700158"
}

@misc{doi107287peerj14586v02reviews1,
    title = {Peer Review \#1 of "Spatiotemporal variability of oxygen concentration in coral reefs of Gorgona Island (Eastern Tropical Pacific) and its effect on the coral Pocillopora capitata (v0.2)"},
    year = "2023",
    abstract = "Dissolved oxygen concentration (DO) is one of the main factors limiting benthic species distribution.Due to ocean warming and eutrophication, the ocean is deoxygenating.In the Eastern Tropical Pacific (ETP), deep waters with low DO (20 m depth and coincide with the deepest bathymetric distribution of scattered colonies of Pocillopora.Because DO concentrations in coral reefs of Gorgona island were comparably low to other coral reefs in the Eastern Tropical Pacific, and the hypoxic threshold of P. capitata was close to the minimum DO record on reefs, hypoxic events could represent a threat if conditions that promote eutrophication (and consequently hypoxia) increase.",
    url = "https://doi.org/10.7287/peerj.14586v0.2/reviews/1",
    doi = "10.7287/peerj.14586v0.2/reviews/1",
    openalex = "W4318591815",
    references = "céspedesrodríguez2021gross, doi101002sim1545, doi101016jmarpolbul200411028, doi101016jpocean200603008, doi101038nature21399, doi101073pnas0803833105, doi101093icb391146, doi101126science1153847, doi101126scienceaan8048, doi101146annurevmarine010908163855, doi103389fmars201700158"
}

@article{doi107717peerj14586,
    author = "Castrillón-Cifuentes, Ana Lucia and Zapata, Fernando A. and Giraldo, Alan and Wild, Christian",
    title = "Spatiotemporal variability of oxygen concentration in coral reefs of Gorgona Island (Eastern Tropical Pacific) and its effect on the coral Pocillopora capitata",
    year = "2023",
    journal = "PeerJ",
    abstract = "was close to the minimum DO record on reefs, hypoxic events could represent a threat if conditions that promote eutrophication (and consequently hypoxia) increase.",
    url = "https://doi.org/10.7717/peerj.14586",
    doi = "10.7717/peerj.14586",
    openalex = "W4318066501",
    references = "céspedesrodríguez2021gross, doi101002sim1545, doi101016jmarpolbul200411028, doi101016jpocean200603008, doi101038nature21399, doi101073pnas0803833105, doi101093icb391146, doi101126science1153847, doi101126scienceaan8048, doi101146annurevmarine010908163855, doi103389fmars201700158"
}

@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"
}

@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"
}

@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"
}

@article{doi1010881755131514101012009,
    author = "Badriana, Mochamad Riam and Nur, A A and Hidayatullah, A I and Oktaviani, Dian and Widyananto, Prastyo Abi and Park, Hae‐Sim and Hutahean, A A",
    title = "Water quality assessment in Indonesia coral reef garden Buleleng site area, Bali",
    year = "2024",
    journal = "IOP Conference Series Earth and Environmental Science",
    abstract = "Abstract The Indonesia Coral Reef Garden (ICRG) program is announced as a coral reef restoration program and has 5 site areas including in Buleleng, Bali. A plantation program has been done by 2020 but it is necessary to monitor and study regarding the water quality surrounding the restoration area. A field survey in Buleleng was carried out on 6-7 October 2022 to measure ocean parameters both physical and chemical characteristics that are suitable for coral life. The bathymetry result at Buleleng varied significantly from shallow to deeper water depth. Many corals are found in the shallow area with the natural coral meanwhile the restoration coral was put in more than 3 m depth. In the study, the sea condition of temperature, salinity, pH, turbidity, and DO is 28.52 -29.66 °C, 33.6 - 33.9 ‰, 8.0 - 8.13,1.04 -1.78 FTU, and 4.27 - 4.85 mg/L, respectively. Based on the conformity of water quality, the water condition is good for coral growth. Heavy metal detected in sample water has low levels compared to marine biota threshold in the national standard.",
    url = "https://doi.org/10.1088/1755-1315/1410/1/012009",
    doi = "10.1088/1755-1315/1410/1/012009",
    openalex = "W4404618440",
    references = "doi107717peerj14586"
}

@article{doi101111gbi12590,
    author = "Piller, Werner E and Harzhauser, Mathias",
    title = "Nubecularia-coralline algal-serpulid-microbial bioherms of the Paratethys Sea-Distribution and paleoecological significance (upper Serravallian, upper Sarmatian, Middle Miocene).",
    year = "2024",
    journal = "Geobiology",
    abstract = "Nubecularia bioherms represent unique bioconstructions that are restricted to the upper Serravallian of the Paratethys and have been reported since the 19th century. They occur in the Central Paratethys in the late Sarmatian and the Eastern Paratethys in the Bessarabian both regional stages of the respective Paratethyan areas. In this study, several locations in the Vienna and Styrian basins of the Central Paratethys were studied out of which four localities were documented in detail (Wolfsthal, Maustrenk, St. Margarethen-Zollhaus, Vienna-Ruzickagasse) to reconstruct their sedimentary setting, their internal composition, and their indications of environmental parameters. The detailed studies included logging of outcrop sections, petrographic, facies and biotic analyses of polished slabs and thin sections and also cathodoluminescence analyses. These concluded that these bioconstructions are not only composed of the foraminifer Nubecularia but represent a complex mixture and interrelationships of Nubecularia, serpulids and microbial carbonate. Four boundstone types can be differentiated: Nubecularia boundstone, Nubecularia-coralline algal boundstone, stromatolitic/thrombolitic boundstone and serpulid-nubeculariid-microbial boundstone. The first 3 types are characteristic of specific localities; the fourth type occurs in all studied locations and represents the terminal association on top of the three other types. The three basal boundstones are predominantly of columnar growth form irrespective of dominance of Nubecularia, coralline algae or microbial carbonate, and the terminal boundstone is widely irregularly organized. The general depositional environment is characterized by cross-bedded oolitic grainstones with abundant quartz grains, miliolid foraminifers and mollusks. Intercalated are microbial carbonates mostly stromatolites but also thrombolites. This indicates a general high water energy environment interrupted by more calm periods when the microbial carbonate was built. The 3 basal types of bioconstructions are interpreted to reflect decreasing food supply and/or oxygenation from Nubecularia over Nubecularia-coralline algal to stromatolitic/thrombolitic boundstone. The serpulid-nubeculariid-microbial boundstone reflects an internal succession with a decrease of the same parameters. Water depth is considered very shallow ranging from 0 to a few meters, and salinity was normal marine to hypersaline. The reconstructed paleoenvironment with dominating oolite shoals and seagrass meadows was not restricted to the Central Paratethys but extended over the entire Paratethys and represented the largest oolite facies area of the entire Cenozoic!",
    url = "https://pubmed.ncbi.nlm.nih.gov/38468508/",
    doi = "10.1111/gbi.12590",
    pmid = "38468508"
}

@article{doi103354meps14661,
    author = "Cabral-Tena, RA and Tortolero-Langarica, JJA and Carricart-Ganivet, JP and Rodríguez‐Troncoso, Alma Paola and Cruz-Ortega, Israel and Cupul‐Magaña, Amilcar Leví and Balart, Eduardo F. and Reyes‐Bonilla, Héctor and López‐Pérez, Andrés",
    title = "Sex-associated differences in sclerochronology and sensitivity to thermal stress in Caribbean and eastern Pacific reef-building corals",
    year = "2024",
    journal = "Marine Ecology Progress Series",
    abstract = "The density banding patterns of the skeletons of massive reef-building corals can be used as historical records of their growth, life history, and environmental conditions. By analyzing these patterns, it is possible to estimate growth parameters such as skeletal density, extension rate, and calcification rate. The responses of stony corals to environmental stress depend on the amount of energy available for high-energetic metabolic processes, including skeletal calcification and sexual reproduction. The sex of a colony may also influence its calcification rate and resistance to environmental stressors like thermal anomalies. Here, we review and summarize the literature that focuses on sex-associated differences in coral calcification rates between male and female colonies and then we examine their differential responses to changes in sea surface temperature (SST) in Porites panamensis, P. lobata, Pavona gigantea, Siderastrea siderea, Montastraea cavernosa, Dichocoenia stokesi, and Dengrogyra cylindrus from the eastern Pacific and Caribbean regions through a reanalysis of published data. Differences in the calcification rates between sexes were due to the energy available for calcification and the strategy employed for skeletal growth. Female corals exhibited lower calcification rates than male colonies in all coral species. The results reveal that overall, the calcification rate was negatively related to SST when the data of both sexes were pooled. However, when data were analyzed separately by sex, only the calcification rate of females was significantly dependent on SST. These findings highlight the implications for paleoenvironmental reconstructions using coral skeletons and the potential disparities in the populations of gonochoric corals.",
    url = "https://doi.org/10.3354/meps14661",
    doi = "10.3354/meps14661",
    openalex = "W4400985534",
    references = "doi101111gbi12491"
}

@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"
}

@article{doi107717peerj18095,
    author = "Long, Ying and Sinutok, Sutinee and Buapet, Pimchanok and Yucharoen, Mathinee",
    title = "Unraveling the physiological responses of morphologically distinct corals to low oxygen",
    year = "2024",
    journal = "PeerJ",
    abstract = "Background: Low oxygen in marine environments, intensified by climate change and local pollution, poses a substantial threat to global marine ecosystems, especially impacting vulnerable coral reefs and causing metabolic crises and bleaching-induced mortality. Yet, our understanding of the potential impacts in tropical regions is incomplete. Furthermore, uncertainty surrounds the physiological responses of corals to hypoxia and anoxia conditions. Methods:). We measured and compared photosynthetic efficiency, Symbiodiniaceae density, chlorophyll concentration, respiratory rates, primary production, and calcification across the various treatments. Results:, exposed to anoxia, experienced mortality with tissue loss within 24 hours. This study underscores species-specific variations in susceptibility associated with different morphologies under low oxygen conditions. The results demonstrate the substantial impact of deoxygenation on coral growth and health, with the compounded challenges of climate change and coastal pollution exacerbating oxygen availability, leading to increasingly significant implications for coral ecosystems.",
    url = "https://doi.org/10.7717/peerj.18095",
    doi = "10.7717/peerj.18095",
    openalex = "W4402751852",
    references = "doi103389fmars20231212717"
}

@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{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"
}

@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"
}

@article{doi1012692ijb2735261,
    author = "{Angelo A. Responte, Jonalyn B. Galorio, Mary Dorothy Anne Y. Seno, Immanuel N. Galorio, Frence Eliza E. Elecho}",
    title = "Spatial and tidal profiles of seawater properties, and their relation to coral cover of selected reefs in Iligan City, Lanao Del Norte, Philippines",
    year = "2025",
    journal = "International Journal of Biosciences (IJB)",
    abstract = "A hydrographic investigation was conducted in coral reefs along the coast of Iligan bay to evaluate the influence of tides to the spatial distribution of water parameters and determine the relation of the water parameters to the coral cover in the area. Water samples were collected at 0m, 5m and 8m using 1.5L Niskin bottle and water parameters were immediately measured using calibrated handheld meters on board. Coral assessment was done using Photo-transect technique and estimation of hard coral cover was done using Coral Point Count with Excel Extensions (CPCe). Salinity increased with depth and values were higher at high tide. The observed suboptimal salinity may account for the poor cover of hard corals. Temperature was highest at the surface and decreases with depth in both tides. Reef1 had the coldest waters in both tides, warmest at the farthest reefs 3 and 4 from the estuary. Dissolved oxygen decreases with depth in both tides and higher during high tide. At low tide, pH was highest at surface; at high tide pH highest at 5m. At low tide pH was highest at reef1, and lowest at reef4. During high tide pH was uniform at 8.1 in all four reefs. Temperature, pH and dissolved oxygen were within the ideal range for optimum growth and coral reef development. Therefore, the observed poor coral cover was not associated with the status of these parameters.",
    url = "https://doi.org/10.12692/ijb/27.3.52-61",
    doi = "10.12692/ijb/27.3.52-61",
    openalex = "W4414443861",
    references = "doi107717peerj14586"
}

@article{oliveira2025calcium,
    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",
    url = "https://doi.org/10.1016/j.marenvres.2025.107218",
    doi = "10.1016/j.marenvres.2025.107218",
    openalex = "W4410250628",
    pages = "107218",
    volume = "209",
    references = "doi10100797894017328402, doi101016s0012825202001046, doi101016s0025326x99002374, doi101038nature04095, doi101038ncomms2409, doi101093icb391146, doi101111j13652699201102613x, doi101126sciadv1501252, doi101126scienceaan8048, doi103389fmars201700158"
}

@article{doi1034133olar0137,
    author = "Zhang, F and Song, Zhongchang and Su, Yingnan and Liu, Chichi C. and Fang, Xuwen and Sun, Shengyao and Xiao, Wupeng and Ou, Wenzhan and Zhang, Yu",
    title = "Acoustic Characteristics and Seasonal Variations of Photosynthetic Sounds in Coral Reefs of Dongshan Island, China",
    year = "2026",
    journal = "Ocean-Land-Atmosphere Research",
    abstract = "The acoustic contributions of primary producers to ocean soundscapes are poorly understood compared to those of marine animals. This study investigated acoustic signals generated by photosynthetic bubbles produced by algae in a coral reef ecosystem on Dongshan Island, China. Using continuous passive acoustic monitoring (PAM), we recorded bubble sounds and applied a Python-based code to extract candidate signals, which were then classified using a trained neural network. Subsequent analysis revealed distinct seasonal patterns in signal rates, with the highest in summer (103.2 pulses/30 min), followed by spring (60.4) and winter (41.3). Data from autumn (4.2) were considerably lower and were excluded from interseasonal comparisons because the recorder was deployed far from the reef. The highest rates of acoustic detection often occurred at night. We ascribed this phenomenon to the production of bubbles of comparable sizes via other processes and to the delayed detachment of photosynthetic bubbles, modulated by additional rhythmic factors. We developed a ridge regression model using environmental parameters to examine photosynthetic events during the day, showing that signals directly related to photosynthesis peaked around midday and were positively correlated with dissolved oxygen (DO) concentrations on most sampled days, thereby partly supporting the predictive model. This work may advance research on assessing ebullitive oxygen fluxes from primary producers and offers a novel, noninvasive tool for the rapid, continuous monitoring of ecosystem health.",
    url = "https://doi.org/10.34133/olar.0137",
    doi = "10.34133/olar.0137",
    openalex = "W7129031454",
    references = "doi107717peerj14586"
}