Bioluminescence

@article{crossref1952bioluminescence,
    title = "Bioluminescence",
    year = "1952",
    journal = "AIBS Bulletin",
    url = "https://doi.org/10.1093/aibsbulletin/2.2.13-b",
    doi = "10.1093/aibsbulletin/2.2.13-b",
    number = "2",
    pages = "13-13",
    volume = "2"
}

Relative spectral emission curves are available for the lights of many invertebrate animals, but none exists for fish. It seems likely that many bony fish use their photophores to signal to one another. Information about the spectral composition of fish luminescence is desirable to permit comparisons with the spectral sensitivities of fish eyes, to enable calculations to be made of luminous intensities, and to allow estimates to be made of the rate of attenuation of such lights in sea water. To further these ends, measurements were made of the spectral composition of the luminescence of the lantern-fish, Myctophum punctatum.

@article{doi101017s0025315400013072,
    author = "Nicol, J. A. C.",
    title = "Spectral composition of the light of the Lantern-fish, Myctophum punctatum",
    year = "1960",
    journal = "Journal of the Marine Biological Association of the United Kingdom",
    abstract = "Relative spectral emission curves are available for the lights of many invertebrate animals, but none exists for fish. It seems likely that many bony fish use their photophores to signal to one another. Information about the spectral composition of fish luminescence is desirable to permit comparisons with the spectral sensitivities of fish eyes, to enable calculations to be made of luminous intensities, and to allow estimates to be made of the rate of attenuation of such lights in sea water. To further these ends, measurements were made of the spectral composition of the luminescence of the lantern-fish, Myctophum punctatum.",
    url = "https://doi.org/10.1017/s0025315400013072",
    doi = "10.1017/s0025315400013072",
    openalex = "W2159549031"
}

The problem of how a fish can make itself invisible in the natural light-conditions in an aquatic environment is discussed with particular reference to the silvery surfaces of fish. In fish which we have examined, the silvery surfaces are of two types: (1) an argenteum which consists of long thin crystals of guanine whose reflecting surfaces are approximately parallel with the surface of the fish; (2) layers of guanine crystals lying either on the inner surfaces of the scales or in the subdermis—these crystals are not, in general, orientated with their reflecting surfaces parallel with the surfaces of the fish, and are much broader than those of the argenteum. Methods are described by which the orientation of the crystal planes with respect to the planes of the scales on which they lie can be determined. The orientation of the crystals of type 2 in different parts of the body is described for the horse mackerel, Trachurus trachurus (L.), and for the bleak, Alburnus alburnus (L.). For the bleak it is shown that although the planes of the crystals are often very much inclined with respect to the planes of the scales, the long axes of the crystals are always approximately parallel with the planes of scales. The inclination of the crystals, therefore, is away from the scales across their short axes. Measurements of the light transmitted by silvery scales of the bleak show that they reflect light strongly when this falls obliquely on the crystals which they contain and that they are most transparent to light which strikes the scales in a direction perpendicular to the reflecting planes of the crystals.

@article{doi101017s0025315400016520,
    author = "Denton, E. J. and Nicol, J. A. C.",
    title = "Studies on reflexion of light from silvery surfaces of fishes, with special reference to the bleak, Alburnus alburnus",
    year = "1965",
    journal = "Journal of the Marine Biological Association of the United Kingdom",
    abstract = "The problem of how a fish can make itself invisible in the natural light-conditions in an aquatic environment is discussed with particular reference to the silvery surfaces of fish. In fish which we have examined, the silvery surfaces are of two types: (1) an argenteum which consists of long thin crystals of guanine whose reflecting surfaces are approximately parallel with the surface of the fish; (2) layers of guanine crystals lying either on the inner surfaces of the scales or in the subdermis—these crystals are not, in general, orientated with their reflecting surfaces parallel with the surfaces of the fish, and are much broader than those of the argenteum. Methods are described by which the orientation of the crystal planes with respect to the planes of the scales on which they lie can be determined. The orientation of the crystals of type 2 in different parts of the body is described for the horse mackerel, Trachurus trachurus (L.), and for the bleak, Alburnus alburnus (L.). For the bleak it is shown that although the planes of the crystals are often very much inclined with respect to the planes of the scales, the long axes of the crystals are always approximately parallel with the planes of scales. The inclination of the crystals, therefore, is away from the scales across their short axes. Measurements of the light transmitted by silvery scales of the bleak show that they reflect light strongly when this falls obliquely on the crystals which they contain and that they are most transparent to light which strikes the scales in a direction perpendicular to the reflecting planes of the crystals.",
    url = "https://doi.org/10.1017/s0025315400016520",
    doi = "10.1017/s0025315400016520",
    openalex = "W2076259803"
}

@article{denton1970on1,
    author = "Denton, E. J. and Nicol, J. A. C. and Gilpin-Brown, J. B. and Wright, P. G",
    title = {On the "filters" of mesopelagic fish and on a fish emitting red light and especially sensitive to red light},
    year = "1970",
    journal = "Journal of Physiology, v. 208, p. 72P",
    note = {talkorigins\_source = {true}; raw\_reference = {Denton, E. J., Nicol, J. A. C., Gilpin-Brown, J. B., and Wright, P. G., 1970, On the "filters" of mesopelagic fish and on a fish emitting red light and especially sensitive to red light: Journal of Physiology, v. 208, p. 72P.}}
}

The features of the vertical distribution of meso- and bathypelagic fishes are poorly known. Much of our present knowledge is based upon data collected on the early, major expeditions (i.e. Brauer, 1906; Murray & Hjort, 1912; Jespersen, 1915; Jespersen & Tåning, 1926; Norman, 1929, 1930; Regan & Trewavas, 1929, 1930; Benin, 1934, 1937; Ege 1934 1948, 1953, 1957; Bertelsen, 1951; Parr, 1960; Ebeling, 1962; Ebeling & Weed, 1963; Nafpaktitis, 1968). Fishing depths were not accurately determined, the depth of net generally being calculated from the length of wire out and the wire angle to the water surface. Closing nets were infrequently used. From these reports a general appreciation of vertical distributions has been possible. More recently, distribution studies mostly made in restricted areas using open nets with depths more accurately determined indicate a limited vertical distribution for each species (Aron, 1962; Pearcy, 1964; Pearcy & Laurs, 1966; Lavenberg & Ebeling, 1967; Paxton, 1967).

@article{doi101017s0025315400005920,
    author = "Badcock, J.",
    title = "The Vertical Distribution of Mesopelagic Fishes Collected on the SOND Cruise",
    year = "1970",
    journal = "Journal of the Marine Biological Association of the United Kingdom",
    abstract = "The features of the vertical distribution of meso- and bathypelagic fishes are poorly known. Much of our present knowledge is based upon data collected on the early, major expeditions (i.e. Brauer, 1906; Murray \& Hjort, 1912; Jespersen, 1915; Jespersen \& Tåning, 1926; Norman, 1929, 1930; Regan \& Trewavas, 1929, 1930; Benin, 1934, 1937; Ege 1934 1948, 1953, 1957; Bertelsen, 1951; Parr, 1960; Ebeling, 1962; Ebeling \& Weed, 1963; Nafpaktitis, 1968). Fishing depths were not accurately determined, the depth of net generally being calculated from the length of wire out and the wire angle to the water surface. Closing nets were infrequently used. From these reports a general appreciation of vertical distributions has been possible. More recently, distribution studies mostly made in restricted areas using open nets with depths more accurately determined indicate a limited vertical distribution for each species (Aron, 1962; Pearcy, 1964; Pearcy \& Laurs, 1966; Lavenberg \& Ebeling, 1967; Paxton, 1967).",
    url = "https://doi.org/10.1017/s0025315400005920",
    doi = "10.1017/s0025315400005920",
    openalex = "W2112989721",
    references = "doi101017s0025315400005749, doi101038174869b0, doi1010381981244a0, doi10108000222932908673038, doi1010970001069419550400000011, doi101126science15137161399, doi101126science1603831991, doi1011639789004611191, doi102307201400, openalexw1568910078"
}

@article{openalexw2466257108,
    author = "Ej, Denton and Jb, Gilpin-Brown and Pg, Wright",
    title = "On the 'filters' in the photophores of mesopelagic fish and on a fish emitting red light and especially sensitive to red light.",
    year = "1970",
    journal = "PubMed",
    openalex = "W2466257108"
}

The angular distributions of luminescent light produced by two oceanic fish, Argyropelecus affinis and Chauliodus sloani, were measured in two vertical planes, one containing the antero-posterior axis of the fish and the other at right angles to this axis. These distributions of light were of the kind required to match, over a wide range of angles of viewing, the external daylight field in the ocean. These observations give strong support to the hypothesis that the function of many photophores is to give camouflage.

@article{denton1972the,
    author = "Denton, Eric James and Gilpin-Brown, J. B. and Wright, P. G.",
    title = "The angular distribution of the light produced by some mesopelagic fish in relation to their camouflage",
    year = "1972",
    journal = "Proceedings of the Royal Society of London. Series B. Biological Sciences",
    abstract = "The angular distributions of luminescent light produced by two oceanic fish, Argyropelecus affinis and Chauliodus sloani, were measured in two vertical planes, one containing the antero-posterior axis of the fish and the other at right angles to this axis. These distributions of light were of the kind required to match, over a wide range of angles of viewing, the external daylight field in the ocean. These observations give strong support to the hypothesis that the function of many photophores is to give camouflage.",
    url = "https://doi.org/10.1098/rspb.1972.0071",
    doi = "10.1098/rspb.1972.0071",
    number = "1067",
    openalex = "W2117282057",
    pages = "145-158",
    volume = "182",
    references = "doi101016014663135690003x, doi101017s0025315400005920, doi101017s0025315400016544, doi1010381981244a0, doi101038scientificamerican017164, doi101093bioscience1610752a, doi1010970001069419550400000011, doi103402tellusav12i39393, openalexw2417215454, openalexw2466257108"
}

@inproceedings{denton1972the2,
    author = "Denton, E. J. and Nicol, J. A. C. and Gilpin-Brown, J. B. and Wright, P. G",
    title = "The angular distribution of the light produced by some mesopelagic fish in relation to their camouflage",
    year = "1972",
    booktitle = "Proceedings of the Royal Society, London B, v. 182, p. 145-158",
    note = "talkorigins\_source = {true}; raw\_reference = {Denton, E. J., Nicol, J. A. C., Gilpin-Brown, J. B., and Wright, P. G., 1972, The angular distribution of the light produced by some mesopelagic fish in relation to their camouflage: Proceedings of the Royal Society, London B, v. 182, p. 145-158.}"
}

@article{lawry1974lantern,
    author = "LAWRY, JAMES V.",
    title = "Lantern Fish compare Downwelling Light and Bioluminescence",
    year = "1974",
    journal = "Nature",
    url = "https://doi.org/10.1038/247155a0",
    doi = "10.1038/247155a0",
    number = "5437",
    openalex = "W2035729676",
    pages = "155-157",
    volume = "247",
    references = "denton1972the, doi101017s0025315400013072, doi1010381981244a0, doi10108010236247209386904, doi101098rstb19700037, doi101126science15137161399, doi101126science1603831991, doi101139f67047, doi101139f68040, doi101139f70088"
}

@article{doi101038265179a0,
    author = "Case, J. F. and Warner, Jon A. and Barnes, Anthony T. and Lowenstine, M.R.",
    title = "Bioluminescence of lantern fish (Myctophidae) in response to changes in light intensity",
    year = "1977",
    journal = "Nature",
    url = "https://doi.org/10.1038/265179a0",
    doi = "10.1038/265179a0",
    openalex = "W2039817809",
    references = "doi1010381981244a0, lawry1974lantern"
}

@book{herring1978bioluminescence3,
    author = "Herring, P. J",
    title = "Bioluminescence in Action",
    year = "1978",
    publisher = "London, Academic Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Herring, P. J., 1978, Bioluminescence in Action: London, Academic Press.}"
}

The mesopelagic shrimp Sergestes similis emits ventrally directed bioluminescence that closely matches the intensity of downward-directed illumination and is able to rapidly modify its light output to match changes in background intensity. Masking experiments show that the photoreceptors involved are the compound eyes or adjacent tissues. Light emission originates from modified portions of the hepatopancreas and is similar to oceanic light in angular distribution and spectral characteristics. Normally oriented animals respond minimally to upward-directed light.

@article{doi101126science20343851109,
    author = "Warner, Jon A. and Latz, Michael I. and Case, James F.",
    title = "Cryptic Bioluminescence in a Midwater Shrimp",
    year = "1979",
    journal = "Science",
    abstract = "The mesopelagic shrimp Sergestes similis emits ventrally directed bioluminescence that closely matches the intensity of downward-directed illumination and is able to rapidly modify its light output to match changes in background intensity. Masking experiments show that the photoreceptors involved are the compound eyes or adjacent tissues. Light emission originates from modified portions of the hepatopancreas and is similar to oceanic light in angular distribution and spectral characteristics. Normally oriented animals respond minimally to upward-directed light.",
    url = "https://doi.org/10.1126/science.203.4385.1109",
    doi = "10.1126/science.203.4385.1109",
    openalex = "W2031735107"
}

Two species of mesopelagic squid greatly altered the color of their bioluminescence during counterillumination. The color change was triggered by changes in water temperature corresponding to those normally encountered by these vertically migrating animals. These squid can probably conceal themselves under the different colors of downwelling light that they encounter in their day and night habitats.

@article{young1980bioluminescence,
    author = "Young, Richard Edward and Mencher, Frederick M.",
    title = "Bioluminescence in Mesopelagic Squid: Diel Color Change During Counterillumination",
    year = "1980",
    journal = "Science",
    abstract = "Two species of mesopelagic squid greatly altered the color of their bioluminescence during counterillumination. The color change was triggered by changes in water temperature corresponding to those normally encountered by these vertically migrating animals. These squid can probably conceal themselves under the different colors of downwelling light that they encounter in their day and night habitats.",
    url = "https://doi.org/10.1126/science.208.4449.1286",
    doi = "10.1126/science.208.4449.1286",
    number = "4449",
    openalex = "W2086541670",
    pages = "1286-1288",
    volume = "208",
    references = "denton1972the, doi1010079783642664687, doi101007bf00389215, doi1010160198014980900229, doi101017s0025315400013072, doi101111j146979981978tb03932x, doi101126science20343851109"
}

ABSTRACT Leiognathids are shallow-water, Indo-West Pacific fishes that have a circumeso-phageal, bacterial light organ. Visual observations of living fishes revealed a mottled ventral luminescence pattern, which was analyzed both behaviorally and morphologically. In behavioral experiments, these fishes responded to increases in intensity of downwelling light with increases in the intensity of ventral luminescence. However, while the absolute luminescence levels tracked the ambient light levels, they did not increase in direct proportion to those of increasing downwelling light; luminescence levels were closer to the intensity of downwelling light at low light levels. The tissues that intervene between the internal light organ and the external environment are responsible for the observed mottled pattern of the ventral luminescence. Furthermore, these tissues, which have been incorporated into the light organ system, are involved in the control of the intensity, spectral quality and angular distribution of the fish’s luminescence. The spectral peak of the bacterial luminescence from whole fish (500 nm) was shifted about 10 nm towards the green relative to the spectral peak of cultured light organ symbionts (485–490nm). The luminescence had the greatest intensity of outward expression at an angle of 20–25° from the ventral midline and was undetectable dorsally. The ventral illumination behavior of leiognathids, with their associated morphology, is compared and contrasted with the counterillumination systems that have been described in a number of mesopelagic fishes, shrimps and squids.

@article{doi101242jeb1561119,
    author = "McFall‐Ngai, Margaret and Morin, James G.",
    title = "Camouflage by Disruptive Illumination in Leiognathids, A Family of Shallow-Water, Bioluminescent Fishes",
    year = "1991",
    journal = "Journal of Experimental Biology",
    abstract = "ABSTRACT Leiognathids are shallow-water, Indo-West Pacific fishes that have a circumeso-phageal, bacterial light organ. Visual observations of living fishes revealed a mottled ventral luminescence pattern, which was analyzed both behaviorally and morphologically. In behavioral experiments, these fishes responded to increases in intensity of downwelling light with increases in the intensity of ventral luminescence. However, while the absolute luminescence levels tracked the ambient light levels, they did not increase in direct proportion to those of increasing downwelling light; luminescence levels were closer to the intensity of downwelling light at low light levels. The tissues that intervene between the internal light organ and the external environment are responsible for the observed mottled pattern of the ventral luminescence. Furthermore, these tissues, which have been incorporated into the light organ system, are involved in the control of the intensity, spectral quality and angular distribution of the fish’s luminescence. The spectral peak of the bacterial luminescence from whole fish (500 nm) was shifted about 10 nm towards the green relative to the spectral peak of cultured light organ symbionts (485–490nm). The luminescence had the greatest intensity of outward expression at an angle of 20–25° from the ventral midline and was undetectable dorsally. The ventral illumination behavior of leiognathids, with their associated morphology, is compared and contrasted with the counterillumination systems that have been described in a number of mesopelagic fishes, shrimps and squids.",
    url = "https://doi.org/10.1242/jeb.156.1.119",
    doi = "10.1242/jeb.156.1.119",
    openalex = "W2342903842",
    references = "doi1010381981244a0, doi101098rspb19850051, openalexw2466257108, young1980bioluminescence"
}

Many deep-sea species, particularly crustaceans, cephalopods, and fish, use photophores to illuminate their ventral surfaces and thus disguise their silhouettes from predators viewing them from below. This strategy has several potential limitations, two of which are examined here. First, a predator with acute vision may be able to detect the individual photophores on the ventral surface. Second, a predator may be able to detect any mismatch between the spectrum of the bioluminescence and that of the background light. The first limitation was examined by modeling the perceived images of the counterillumination of the squid Abralia veranyi and the myctophid fish Ceratoscopelus maderensis as a function of the distance and visual acuity of the viewer. The second limitation was addressed by measuring downwelling irradiance under moonlight and starlight and then modeling underwater spectra. Four water types were examined: coastal water at a depth of 5 m and oceanic water at 5, 210, and 800 m. The appearance of the counterillumination was more affected by the visual acuity of the viewer than by the clarity of the water, even at relatively large distances. Species with high visual acuity (0.11 degrees resolution) were able to distinguish the individual photophores of some counterilluminating signals at distances of several meters, thus breaking the camouflage. Depth and the presence or absence of moonlight strongly affected the spectrum of the background light, particularly near the surface. The increased variability near the surface was partially offset by the higher contrast attenuation at shallow depths, which reduced the sighting distance of mismatches. This research has implications for the study of spatial resolution, contrast sensitivity, and color discrimination in deep-sea visual systems.

@article{doi1023071543624,
    author = "Johnsen, Sönke and Widder, Edith A. and Mobley, Curtis D.",
    title = "Propagation and Perception of Bioluminescence: Factors Affecting Counterillumination as a Cryptic Strategy",
    year = "2004",
    journal = "Biological Bulletin",
    abstract = "Many deep-sea species, particularly crustaceans, cephalopods, and fish, use photophores to illuminate their ventral surfaces and thus disguise their silhouettes from predators viewing them from below. This strategy has several potential limitations, two of which are examined here. First, a predator with acute vision may be able to detect the individual photophores on the ventral surface. Second, a predator may be able to detect any mismatch between the spectrum of the bioluminescence and that of the background light. The first limitation was examined by modeling the perceived images of the counterillumination of the squid Abralia veranyi and the myctophid fish Ceratoscopelus maderensis as a function of the distance and visual acuity of the viewer. The second limitation was addressed by measuring downwelling irradiance under moonlight and starlight and then modeling underwater spectra. Four water types were examined: coastal water at a depth of 5 m and oceanic water at 5, 210, and 800 m. The appearance of the counterillumination was more affected by the visual acuity of the viewer than by the clarity of the water, even at relatively large distances. Species with high visual acuity (0.11 degrees resolution) were able to distinguish the individual photophores of some counterilluminating signals at distances of several meters, thus breaking the camouflage. Depth and the presence or absence of moonlight strongly affected the spectrum of the background light, particularly near the surface. The increased variability near the surface was partially offset by the higher contrast attenuation at shallow depths, which reduced the sighting distance of mismatches. This research has implications for the study of spatial resolution, contrast sensitivity, and color discrimination in deep-sea visual systems.",
    url = "https://doi.org/10.2307/1543624",
    doi = "10.2307/1543624",
    openalex = "W2142081438",
    references = "denton1972the, doi1010079789401706193, doi1010160022519371901895, doi101016s0042698998002624, doi101017s1464793103006420, doi101038415609a, doi101098rspb19850051, doi101364ao32007484, openalexw1507653370, openalexw1564498658, openalexw1658472922, young1980bioluminescence"
}

Mesopelagic fishes occur in all the world’s oceans, but their abundance and consequently their ecological significance remains uncertain. The current global estimate based on net sampling prior to 1980 suggests a global abundance of one gigatonne (109 t) wet weight. Here we report novel evidence of efficient avoidance of such sampling by the most common myctophid fish in the Northern Atlantic, i.e. Benthosema glaciale. We reason that similar avoidance of nets may explain consistently higher acoustic abundance estimates of mesopelagic fish from different parts of the world’s oceans. It appears that mesopelagic fish abundance may be underestimated by one order of magnitude, suggesting that the role of mesopelagic fish in the oceans might need to be revised.

@article{doi103354meps09785,
    author = "Kaartvedt, Stein and Staby, Arved and Aksnes, DL",
    title = "Efficient trawl avoidance by mesopelagic fishes causes large underestimation of their biomass",
    year = "2012",
    journal = "Marine Ecology Progress Series",
    abstract = "Mesopelagic fishes occur in all the world’s oceans, but their abundance and consequently their ecological significance remains uncertain. The current global estimate based on net sampling prior to 1980 suggests a global abundance of one gigatonne (109 t) wet weight. Here we report novel evidence of efficient avoidance of such sampling by the most common myctophid fish in the Northern Atlantic, i.e. Benthosema glaciale. We reason that similar avoidance of nets may explain consistently higher acoustic abundance estimates of mesopelagic fish from different parts of the world’s oceans. It appears that mesopelagic fish abundance may be underestimated by one order of magnitude, suggesting that the role of mesopelagic fish in the oceans might need to be revised.",
    url = "https://doi.org/10.3354/meps09785",
    doi = "10.3354/meps09785",
    openalex = "W2034941158",
    references = "doi101017s1464793103006420"
}

We report the discovery of light organs (photophores) adjacent to the dorsal defensive spines of a small deep-sea lanternshark (Etmopterus spinax). Using a visual modeling based on in vivo luminescence recordings we show that this unusual light display would be detectable by the shark's potential predators from several meters away. We also demonstrate that the luminescence from the spine-associated photophores (SAPs) can be seen through the mineralized spines, which are partially translucent. These results suggest that the SAPs function, either by mimicking the spines' shape or by shining through them, as a unique visual deterrent for predators. This conspicuous dorsal warning display is a surprising complement to the ventral luminous camouflage (counterillumination) of the shark.

@article{doi101038srep01308,
    author = "Claes, Julien M. and Dean, Mason N. and Nilsson, Dan-Eric and Hart, Nathan S. and Mallefet, Jérôme",
    title = "A deepwater fish with ‘lightsabers’ – dorsal spine-associated luminescence in a counterilluminating lanternshark",
    year = "2013",
    journal = "Scientific Reports",
    abstract = "We report the discovery of light organs (photophores) adjacent to the dorsal defensive spines of a small deep-sea lanternshark (Etmopterus spinax). Using a visual modeling based on in vivo luminescence recordings we show that this unusual light display would be detectable by the shark's potential predators from several meters away. We also demonstrate that the luminescence from the spine-associated photophores (SAPs) can be seen through the mineralized spines, which are partially translucent. These results suggest that the SAPs function, either by mimicking the spines' shape or by shining through them, as a unique visual deterrent for predators. This conspicuous dorsal warning display is a surprising complement to the ventral luminous camouflage (counterillumination) of the shark.",
    url = "https://doi.org/10.1038/srep01308",
    doi = "10.1038/srep01308",
    openalex = "W1965517630",
    references = "doi101016jcub201108012, doi101016jcub201110014, doi101016jcub201202031, doi101093beheco141103, doi101098rspb19850051, doi101126science1174269, doi101139z97838, doi1011426102, doi101146annurevmarine120308081028, openalexw1511461941"
}

With a current estimate of ~1,000 million tons, mesopelagic fishes likely dominate the world total fishes biomass. However, recent acoustic observations show that mesopelagic fishes biomass could be significantly larger than the current estimate. Here we combine modelling and a sensitivity analysis of the acoustic observations from the Malaspina 2010 Circumnavigation Expedition to show that the previous estimate needs to be revised to at least one order of magnitude higher. We show that there is a close relationship between the open ocean fishes biomass and primary production, and that the energy transfer efficiency from phytoplankton to mesopelagic fishes in the open ocean is higher than what is typically assumed. Our results indicate that the role of mesopelagic fishes in oceanic ecosystems and global ocean biogeochemical cycles needs to be revised as they may be respiring ~10% of the primary production in deep waters.

@article{doi101038ncomms4271,
    author = "Irigoien, Xabier and Klevjer, Thor A. and Røstad, Anders and Martínez, Udane and Boyra, Guillermo and Acuña, José Luis and Bode, Antonio and Echevarrı́a, Fidel and González-Gordillo, J. Ignacio and Hernández‐León, Santiago and Agustı́, Susana and Aksnes, Dag L. and Duarte, Carlos M. and Kaartvedt, Stein",
    title = "Large mesopelagic fishes biomass and trophic efficiency in the open ocean",
    year = "2014",
    journal = "Nature Communications",
    abstract = "With a current estimate of \textasciitilde 1,000 million tons, mesopelagic fishes likely dominate the world total fishes biomass. However, recent acoustic observations show that mesopelagic fishes biomass could be significantly larger than the current estimate. Here we combine modelling and a sensitivity analysis of the acoustic observations from the Malaspina 2010 Circumnavigation Expedition to show that the previous estimate needs to be revised to at least one order of magnitude higher. We show that there is a close relationship between the open ocean fishes biomass and primary production, and that the energy transfer efficiency from phytoplankton to mesopelagic fishes in the open ocean is higher than what is typically assumed. Our results indicate that the role of mesopelagic fishes in oceanic ecosystems and global ocean biogeochemical cycles needs to be revised as they may be respiring \textasciitilde 10\% of the primary production in deep waters.",
    url = "https://doi.org/10.1038/ncomms4271",
    doi = "10.1038/ncomms4271",
    openalex = "W2099984711",
    references = "doi1010160304380092900168, doi101017cbo9780511623370, doi101038374255a0, doi10108010618600199610474713, doi1011111467988400145, doi101111j16000587200906299x, doi101111j20070906759005171x, doi101126science166390172, doi101357002224007781567621, doi1023073996, doi104319lo19974210001"
}

@incollection{björn2015bioluminescence,
    author = "Björn, Lars Olof and Ghiradella, Helen",
    title = "Bioluminescence",
    year = "2015",
    booktitle = "Photobiology",
    url = "https://doi.org/10.1007/978-1-4939-1468-5\_26",
    doi = "10.1007/978-1-4939-1468-5\_26",
    pages = "399-413"
}

Abstract Acoustic survey methods are useful to estimate the distribution, abundance, and biomass of mesopelagic fish, a key component of open ocean ecosystems. However, mesopelagic fish pose several challenges for acoustic biomass estimation based on their small size, wide depth range, mixed aggregations, and length-dependent acoustic reflectance, which differentiate them from the larger epipelagic and neritic fish for which these methods were developed. Foremost, there is a strong effect of depth on swimbladder resonance, so acoustic surveys of mesopelagic fish must incorporate depth-stratification. Additionally, the 1–3 cm juveniles of many species are not only more abundant, but can also be stronger acoustic backscatterers than the larger adults that comprise most of the biomass. The dominant species in terms of biomass may thus be weak acoustic backscatters. Failure to properly incorporate depth, the full size distribution, and certain less-abundant species into mesopelagic acoustic analyses could lead to errors in estimated biomass of up to three orders of magnitude. Thus, thorough validation, or “ground-truthing ”, of the species composition, depth structure, population size distribution, capture efficiency of the sampling device, and acoustic properties of the fish present is critical for credible acoustic estimates of mesopelagic fish biomass. This is not insurmountable, but requires more ancillary data than is usually collected.

@article{doi101093icesjmsfsv023,
    author = "Davison, Peter C. and Koslow, J. Anthony and Kloser, Rudy",
    title = "Acoustic biomass estimation of mesopelagic fish: backscattering from individuals, populations, and communities",
    year = "2015",
    journal = "ICES Journal of Marine Science",
    abstract = "Abstract Acoustic survey methods are useful to estimate the distribution, abundance, and biomass of mesopelagic fish, a key component of open ocean ecosystems. However, mesopelagic fish pose several challenges for acoustic biomass estimation based on their small size, wide depth range, mixed aggregations, and length-dependent acoustic reflectance, which differentiate them from the larger epipelagic and neritic fish for which these methods were developed. Foremost, there is a strong effect of depth on swimbladder resonance, so acoustic surveys of mesopelagic fish must incorporate depth-stratification. Additionally, the 1–3 cm juveniles of many species are not only more abundant, but can also be stronger acoustic backscatterers than the larger adults that comprise most of the biomass. The dominant species in terms of biomass may thus be weak acoustic backscatters. Failure to properly incorporate depth, the full size distribution, and certain less-abundant species into mesopelagic acoustic analyses could lead to errors in estimated biomass of up to three orders of magnitude. Thus, thorough validation, or “ground-truthing ”, of the species composition, depth structure, population size distribution, capture efficiency of the sampling device, and acoustic properties of the fish present is critical for credible acoustic estimates of mesopelagic fish biomass. This is not insurmountable, but requires more ancillary data than is usually collected.",
    url = "https://doi.org/10.1093/icesjms/fsv023",
    doi = "10.1093/icesjms/fsv023",
    openalex = "W2042361955"
}

Despite appearing featureless to our eyes, the open ocean is a highly variable environment for polarization-sensitive viewers. Dynamic visual backgrounds coupled with predator encounters from all possible directions make this habitat one of the most challenging for camouflage. We tested open-ocean crypsis in nature by collecting more than 1500 videopolarimetry measurements from live fish from distinct habitats under a variety of viewing conditions. Open-ocean fish species exhibited camouflage that was superior to that of both nearshore fish and mirrorlike surfaces, with significantly higher crypsis at angles associated with predator detection and pursuit. Histological measurements revealed that specific arrangements of reflective guanine platelets in the fish's skin produce angle-dependent polarization modifications for polarocrypsis in the open ocean, suggesting a mechanism for natural selection to shape reflectance properties in this complex environment.

@article{doi101126scienceaad5284,
    author = "Brady, Parrish and Gilerson, Alexander and Kattawar, George W. and Sullivan, James M. and Twardowski, Michael and Dierssen, Heidi M. and Gao, Meng and Travis, Kort and Etheredge, Robert Ian and Tonizzo, Alberto and Ibrahim, Amir and Carrizo, Carlos and Gu, Yalong and Russell, Brandon and Mislinski, Kathryn and Zhao, Shulei and Cummings, Molly E.",
    title = "Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments",
    year = "2015",
    journal = "Science",
    abstract = "Despite appearing featureless to our eyes, the open ocean is a highly variable environment for polarization-sensitive viewers. Dynamic visual backgrounds coupled with predator encounters from all possible directions make this habitat one of the most challenging for camouflage. We tested open-ocean crypsis in nature by collecting more than 1500 videopolarimetry measurements from live fish from distinct habitats under a variety of viewing conditions. Open-ocean fish species exhibited camouflage that was superior to that of both nearshore fish and mirrorlike surfaces, with significantly higher crypsis at angles associated with predator detection and pursuit. Histological measurements revealed that specific arrangements of reflective guanine platelets in the fish's skin produce angle-dependent polarization modifications for polarocrypsis in the open ocean, suggesting a mechanism for natural selection to shape reflectance properties in this complex environment.",
    url = "https://doi.org/10.1126/science.aad5284",
    doi = "10.1126/science.aad5284",
    openalex = "W2290428086",
    references = "doi101146annurevmarine010213135018"
}

Bioluminescence (BL) is a spectacular phenomenon involving light emission by live organisms. It is caused by the oxidation of a small organic molecule, luciferin, with molecular oxygen, which is catalysed by the enzyme luciferase. In nature, there are approximately 30 different BL systems, of which only 9 have been studied to various degrees in terms of their reaction mechanisms. A vast range of in vitro and in vivo analytical techniques have been developed based on BL, including tests for different analytes, immunoassays, gene expression assays, drug screening, bioimaging of live organisms, cancer studies, the investigation of infectious diseases and environmental monitoring. This review aims to cover the major existing applications for bioluminescence in the context of the diversity of luciferases and their substrates, luciferins. Particularly, the properties and applications of d-luciferin, coelenterazine, bacterial, Cypridina and dinoflagellate luciferins and their analogues along with their corresponding luciferases are described. Finally, four other rarely studied bioluminescent systems (those of limpet Latia, earthworms Diplocardia and Fridericia and higher fungi), which are promising for future use, are also discussed.

@article{doi101039c6cs00296j,
    author = "Kaskova, Zinaida M. and Tsarkova, Aleksandra S. and Yampolsky, Ilia V.",
    title = "1001 lights: luciferins, luciferases, their mechanisms of action and applications in chemical analysis, biology and medicine",
    year = "2016",
    journal = "Chemical Society Reviews",
    abstract = "Bioluminescence (BL) is a spectacular phenomenon involving light emission by live organisms. It is caused by the oxidation of a small organic molecule, luciferin, with molecular oxygen, which is catalysed by the enzyme luciferase. In nature, there are approximately 30 different BL systems, of which only 9 have been studied to various degrees in terms of their reaction mechanisms. A vast range of in vitro and in vivo analytical techniques have been developed based on BL, including tests for different analytes, immunoassays, gene expression assays, drug screening, bioimaging of live organisms, cancer studies, the investigation of infectious diseases and environmental monitoring. This review aims to cover the major existing applications for bioluminescence in the context of the diversity of luciferases and their substrates, luciferins. Particularly, the properties and applications of d-luciferin, coelenterazine, bacterial, Cypridina and dinoflagellate luciferins and their analogues along with their corresponding luciferases are described. Finally, four other rarely studied bioluminescent systems (those of limpet Latia, earthworms Diplocardia and Fridericia and higher fungi), which are promising for future use, are also discussed.",
    url = "https://doi.org/10.1039/c6cs00296j",
    doi = "10.1039/c6cs00296j",
    openalex = "W2518749305",
    references = "doi1011426102"
}

Bioluminescence is primarily a marine phenomenon with 80% of metazoan bioluminescent genera occurring in the world's oceans. Here we show that bioluminescence has evolved repeatedly and is phylogenetically widespread across ray-finned fishes. We recover 27 independent evolutionary events of bioluminescence, all among marine fish lineages. This finding indicates that bioluminescence has evolved many more times than previously hypothesized across fishes and the tree of life. Our exploration of the macroevolutionary patterns of bioluminescent lineages indicates that the present day diversity of some inshore and deep-sea bioluminescent fish lineages that use bioluminescence for communication, feeding, and reproduction exhibit exceptional species richness given clade age. We show that exceptional species richness occurs particularly in deep-sea fishes with intrinsic bioluminescent systems and both shallow water and deep-sea lineages with luminescent systems used for communication.

@article{doi101371journalpone0155154,
    author = "Davis, Matthew P. and Sparks, John S. and Smith, William L.",
    title = "Repeated and Widespread Evolution of Bioluminescence in Marine Fishes",
    year = "2016",
    journal = "PLoS ONE",
    abstract = "Bioluminescence is primarily a marine phenomenon with 80\% of metazoan bioluminescent genera occurring in the world's oceans. Here we show that bioluminescence has evolved repeatedly and is phylogenetically widespread across ray-finned fishes. We recover 27 independent evolutionary events of bioluminescence, all among marine fish lineages. This finding indicates that bioluminescence has evolved many more times than previously hypothesized across fishes and the tree of life. Our exploration of the macroevolutionary patterns of bioluminescent lineages indicates that the present day diversity of some inshore and deep-sea bioluminescent fish lineages that use bioluminescence for communication, feeding, and reproduction exhibit exceptional species richness given clade age. We show that exceptional species richness occurs particularly in deep-sea fishes with intrinsic bioluminescent systems and both shallow water and deep-sea lineages with luminescent systems used for communication.",
    url = "https://doi.org/10.1371/journal.pone.0155154",
    doi = "10.1371/journal.pone.0155154",
    openalex = "W2417326502",
    references = "doi101002bio1170010303, doi101073pnas0811087106, doi101073pnas1206625109, doi10108010635150490522232, doi101093bioinformaticsbtm538, doi101093molbevmsn083, doi101093nargkf436, doi101111j001438202001tb00826x, doi101126science1174269, doi101146annurevmarine120308081028, doi101186147121487214, doi101186s1286201504466"
}

Bioluminescence is a fascinating phenomenon occurring in numerous animal taxa in the ocean. The reef dwelling splitfin flashlight fish (Anomalops katoptron) can be found in large schools during moonless nights in the shallow water of coral reefs and in the open surrounding water. Anomalops katoptron produce striking blink patterns with symbiotic bacteria in their sub-ocular light organs. We examined the blink frequency in A. katoptron under various laboratory conditions. During the night A. katoptron swims in schools roughly parallel to their conspecifics and display high blink frequencies of approximately 90 blinks/minute with equal on and off times. However, when planktonic prey was detected in the experimental tank, the open time increased compared to open times in the absence of prey and the frequency decreased to 20% compared to blink frequency at night in the absence of planktonic prey. During the day when the school is in a cave in the reef tank the blink frequency decreases to approximately 9 blinks/minute with increasing off-times of the light organ. Surprisingly the non-luminescent A. katoptron with non-functional light organs displayed the same blink frequencies and light organ open/closed times during the night and day as their luminescent conspecifics. In the presence of plankton non-luminescent specimens showed no change in the blink frequency and open/closed times compared to luminescent A. katoptron. Our experiments performed in a coral reef tank show that A. katoptron use bioluminescent illumination to detect planktonic prey and that the blink frequency of A. katoptron light organs follow an exogenous control by the ambient light.

@article{doi101371journalpone0170489,
    author = "Hellinger, Jens and Jägers, Peter and Donner, Marcel and Sutt, Franziska and Mark, Melanie D. and Senen, Budiono and Tollrian, Ralph and Herlitze, Stefan",
    title = "The Flashlight Fish Anomalops katoptron Uses Bioluminescent Light to Detect Prey in the Dark",
    year = "2017",
    journal = "PLoS ONE",
    abstract = "Bioluminescence is a fascinating phenomenon occurring in numerous animal taxa in the ocean. The reef dwelling splitfin flashlight fish (Anomalops katoptron) can be found in large schools during moonless nights in the shallow water of coral reefs and in the open surrounding water. Anomalops katoptron produce striking blink patterns with symbiotic bacteria in their sub-ocular light organs. We examined the blink frequency in A. katoptron under various laboratory conditions. During the night A. katoptron swims in schools roughly parallel to their conspecifics and display high blink frequencies of approximately 90 blinks/minute with equal on and off times. However, when planktonic prey was detected in the experimental tank, the open time increased compared to open times in the absence of prey and the frequency decreased to 20\% compared to blink frequency at night in the absence of planktonic prey. During the day when the school is in a cave in the reef tank the blink frequency decreases to approximately 9 blinks/minute with increasing off-times of the light organ. Surprisingly the non-luminescent A. katoptron with non-functional light organs displayed the same blink frequencies and light organ open/closed times during the night and day as their luminescent conspecifics. In the presence of plankton non-luminescent specimens showed no change in the blink frequency and open/closed times compared to luminescent A. katoptron. Our experiments performed in a coral reef tank show that A. katoptron use bioluminescent illumination to detect planktonic prey and that the blink frequency of A. katoptron light organs follow an exogenous control by the ambient light.",
    url = "https://doi.org/10.1371/journal.pone.0170489",
    doi = "10.1371/journal.pone.0170489",
    openalex = "W2586945288",
    references = "doi101007bf00163984, doi101007bf00300175, doi101007bf00428634, doi101038srep01308, doi101038srep04328, doi101126science1174269, doi101146annurevmarine120308081028, doi101242jeb012880, doi101371journalpone0155154, doi1018900012965820010822177icacia20co2, doi1018900903131"
}

Abstract The mesopelagic community is important for downward oceanic carbon transportation and is a potential food source for humans. Estimates of global mesopelagic fish biomass vary substantially (between 1 and 20 Gt). Here, we develop a global mesopelagic fish biomass model using daytime 38 kHz acoustic backscatter from deep scattering layers. Model backscatter arises predominantly from fish and siphonophores but the relative proportions of siphonophores and fish, and several of the parameters in the model, are uncertain. We use simulations to estimate biomass and the variance of biomass determined across three different scenarios; S1, where all fish have gas-filled swimbladders, and S2 and S3, where a proportion of fish do not. Our estimates of biomass ranged from 1.8 to 16 Gt (25–75% quartile ranges), and median values of S1 to S3 were 3.8, 4.6, and 8.3 Gt, respectively. A sensitivity analysis shows that for any given quantity of fish backscatter, the fish swimbladder volume, its size distribution and its aspect ratio are the parameters that cause most variation (i.e. lead to greatest uncertainty) in the biomass estimate. Determination of these parameters should be prioritized in future studies, as should determining the proportion of backscatter due to siphonophores.

@article{doi101093icesjmsfsy037,
    author = "Proud, Roland and Handegard, Nils Olav and Kloser, Rudy and Cox, Martin J. and Brierley, Andrew S.",
    title = "From siphonophores to deep scattering layers: uncertainty ranges for the estimation of global mesopelagic fish biomass",
    year = "2018",
    journal = "ICES Journal of Marine Science",
    abstract = "Abstract The mesopelagic community is important for downward oceanic carbon transportation and is a potential food source for humans. Estimates of global mesopelagic fish biomass vary substantially (between 1 and 20 Gt). Here, we develop a global mesopelagic fish biomass model using daytime 38 kHz acoustic backscatter from deep scattering layers. Model backscatter arises predominantly from fish and siphonophores but the relative proportions of siphonophores and fish, and several of the parameters in the model, are uncertain. We use simulations to estimate biomass and the variance of biomass determined across three different scenarios; S1, where all fish have gas-filled swimbladders, and S2 and S3, where a proportion of fish do not. Our estimates of biomass ranged from 1.8 to 16 Gt (25–75\% quartile ranges), and median values of S1 to S3 were 3.8, 4.6, and 8.3 Gt, respectively. A sensitivity analysis shows that for any given quantity of fish backscatter, the fish swimbladder volume, its size distribution and its aspect ratio are the parameters that cause most variation (i.e. lead to greatest uncertainty) in the biomass estimate. Determination of these parameters should be prioritized in future studies, as should determining the proportion of backscatter due to siphonophores.",
    url = "https://doi.org/10.1093/icesjms/fsy037",
    doi = "10.1093/icesjms/fsy037",
    openalex = "W2800543464",
    references = "doi101016jtree201303008, doi103389fmars201600181"
}

BACKGROUND: In the darkness of the ocean, an impressive number of taxa have evolved the capability to emit light. Many mesopelagic organisms emit a dim ventral glow that matches with the residual environmental light in order to camouflage themselves (counterillumination function). Sharks use their luminescence mainly for this purpose. Specific lateral marks have been observed in Etmopteridae sharks (one of the two known luminous shark families) suggesting an inter/intraspecific recognition. Conversely, dorsal luminescence patterns are rare within these deep-sea organisms. RESULTS: have dorsal luminescence patterns. These dorsal patterns consist of specific lines of luminous organs, called photophores, on the rostrum, dorsal area and at periphery of the spine. This dorsal light seems to be in contrast with the counterilluminating role of ventral photophores. However, skin photophores surrounding the defensive dorsal spines show a precise pattern supporting an aposematism function for this bioluminescence. Using in situ imaging, morphological and histological analysis, we reconstructed the dorsal light emission pattern on these species, with an emphasis on the photogenic skin associated with the spine. Analyses of video footage validated, for the first time, the defensive function of the dorsal spines. Finally, we did not find evidence that Etmopteridae possess venomous spine-associated glands, present in Squalidae and Heterondontidae, via MRI and CT scans. CONCLUSION: This work highlights for the first time a species-specific luminous dorsal pattern in three deep-sea lanternsharks. We suggest an aposematic use of luminescence to reveal the presence of the dorsal spines. Despite the absence of venom apparatus, the defensive use of spines is documented for the first time in situ by video recordings.

@article{doi101186s4085101901262,
    author = "Duchatelet, Laurent and Pinte, Nicolas and Tomita, Taketeru and Sato, Keiichi and Mallefet, Jérôme",
    title = "Etmopteridae bioluminescence: dorsal pattern specificity and aposematic use",
    year = "2019",
    journal = "Zoological Letters",
    abstract = "BACKGROUND: In the darkness of the ocean, an impressive number of taxa have evolved the capability to emit light. Many mesopelagic organisms emit a dim ventral glow that matches with the residual environmental light in order to camouflage themselves (counterillumination function). Sharks use their luminescence mainly for this purpose. Specific lateral marks have been observed in Etmopteridae sharks (one of the two known luminous shark families) suggesting an inter/intraspecific recognition. Conversely, dorsal luminescence patterns are rare within these deep-sea organisms. RESULTS: have dorsal luminescence patterns. These dorsal patterns consist of specific lines of luminous organs, called photophores, on the rostrum, dorsal area and at periphery of the spine. This dorsal light seems to be in contrast with the counterilluminating role of ventral photophores. However, skin photophores surrounding the defensive dorsal spines show a precise pattern supporting an aposematism function for this bioluminescence. Using in situ imaging, morphological and histological analysis, we reconstructed the dorsal light emission pattern on these species, with an emphasis on the photogenic skin associated with the spine. Analyses of video footage validated, for the first time, the defensive function of the dorsal spines. Finally, we did not find evidence that Etmopteridae possess venomous spine-associated glands, present in Squalidae and Heterondontidae, via MRI and CT scans. CONCLUSION: This work highlights for the first time a species-specific luminous dorsal pattern in three deep-sea lanternsharks. We suggest an aposematic use of luminescence to reveal the presence of the dorsal spines. Despite the absence of venom apparatus, the defensive use of spines is documented for the first time in situ by video recordings.",
    url = "https://doi.org/10.1186/s40851-019-0126-2",
    doi = "10.1186/s40851-019-0126-2",
    openalex = "W2937650742",
    references = "doi101038srep04328, doi101186s1286201504466"
}

Schooling fishes, like flocking birds and swarming insects, display remarkable behavioral coordination. While over 25% of fish species exhibit schooling behavior, nighttime schooling has rarely been observed or reported. This is due to vision being the primary modality for schooling, which is corroborated by the fact that most fish schools disperse at critically low light levels. Here we report on a large aggregation of the bioluminescent flashlight fish Anomalops katoptron that exhibited nighttime schooling behavior during multiple moon phases, including the new moon. Data were recorded with a suite of low-light imaging devices, including a high-speed, high-resolution scientific complementary metal-oxide-semiconductor (sCMOS) camera. Image analysis revealed nighttime schooling using synchronized bioluminescent flashing displays, and demonstrated that school motion synchrony exhibits correlation with relative swim speed. A computer model of flashlight fish schooling behavior shows that only a small percentage of individuals need to exhibit bioluminescence in order for school cohesion to be maintained. Flashlight fish schooling is unique among fishes, in that bioluminescence enables schooling in conditions of no ambient light. In addition, some members can still partake in the school while not actively exhibiting their bioluminescence. Image analysis of our field data and model demonstrate that if a small percentage of fish become motivated to change direction, the rest of the school follows. The use of bioluminescence by flashlight fish to enable schooling in shallow water adds an additional ecological application to bioluminescence and suggests that schooling behavior in mesopelagic bioluminescent fishes may be also mediated by luminescent displays.

@article{doi101371journalpone0219852,
    author = "Gruber, David F. and Phillips, Brennan and O’Brien, Rory and Boominathan, Vivek and Veeraraghavan, Ashok and Vasan, Ganesh and O’Brien, Peter and Pieribone, Vincent A. and Sparks, John S.",
    title = "Bioluminescent flashes drive nighttime schooling behavior and synchronized swimming dynamics in flashlight fish",
    year = "2019",
    journal = "PLoS ONE",
    abstract = "Schooling fishes, like flocking birds and swarming insects, display remarkable behavioral coordination. While over 25\% of fish species exhibit schooling behavior, nighttime schooling has rarely been observed or reported. This is due to vision being the primary modality for schooling, which is corroborated by the fact that most fish schools disperse at critically low light levels. Here we report on a large aggregation of the bioluminescent flashlight fish Anomalops katoptron that exhibited nighttime schooling behavior during multiple moon phases, including the new moon. Data were recorded with a suite of low-light imaging devices, including a high-speed, high-resolution scientific complementary metal-oxide-semiconductor (sCMOS) camera. Image analysis revealed nighttime schooling using synchronized bioluminescent flashing displays, and demonstrated that school motion synchrony exhibits correlation with relative swim speed. A computer model of flashlight fish schooling behavior shows that only a small percentage of individuals need to exhibit bioluminescence in order for school cohesion to be maintained. Flashlight fish schooling is unique among fishes, in that bioluminescence enables schooling in conditions of no ambient light. In addition, some members can still partake in the school while not actively exhibiting their bioluminescence. Image analysis of our field data and model demonstrate that if a small percentage of fish become motivated to change direction, the rest of the school follows. The use of bioluminescence by flashlight fish to enable schooling in shallow water adds an additional ecological application to bioluminescence and suggests that schooling behavior in mesopelagic bioluminescent fishes may be also mediated by luminescent displays.",
    url = "https://doi.org/10.1371/journal.pone.0219852",
    doi = "10.1371/journal.pone.0219852",
    openalex = "W2969004747",
    references = "doi101371journalpone0170489"
}

@article{kaartvedt2019herding,
    author = "Kaartvedt, S and Røstad, A and Opdal, AF and Aksnes, DL",
    title = "Herding mesopelagic fish by light",
    year = "2019",
    journal = "Marine Ecology Progress Series",
    url = "https://doi.org/10.3354/meps13079",
    doi = "10.3354/meps13079",
    openalex = "W2963936192",
    pages = "225-231",
    volume = "625",
    references = "doi101016jpocean201305013, doi101017cbo9781139168212, doi101017s1464793103006420, doi101038ncomms4271, doi101038ngeo1837, doi101038srep19873, doi101093icesjmsfsv023, doi101093icesjmsfsy037, doi101139f02076, doi103354meps09785"
}

@misc{cornils2020bioluminescence,
    author = "Cornils, B.",
    title = "bioluminescence",
    year = "2020",
    booktitle = "Catalysis from A to Z",
    url = "https://doi.org/10.1002/9783527809080.cataz01966",
    doi = "10.1002/9783527809080.cataz01966"
}

Though mesopelagic fish respond to natural light (e.g., diurnal vertical migration), few studies have looked at how they respond to artificial light and if artificial lights could be used in commercial operations to improve catchability of mesopelagic fish. Here we present a preliminary study on how mesopelagic organisms respond to blue and green spotlights, as well as red and white diffuse lights in Masfjorden (Norway; max depth of 480 m). The response of organisms in each of the three sound scattering layers (SSLs) was observed when a) artificial lights were positioned in a layer or b) moved with a constant speed (generally 0.03 ms−1) towards a layer. The artificial lights were attached to a rig with a self-contained echosounder, which recorded the vertical and horizontal avoidance of organisms in each SSL to different artificial lights. Net hauls (MIC-net) and video footage confirmed that Maurolicus muelleri and siphonophores were present in the upper layer (100–150 m), while Benthosema glaciale were present in the deeper layers (∼200 m and ∼300 m to seabed). Our findings suggest that M. muelleri (SSL1) horizontally avoid blue spotlight and white diffuse light, while B. glaciale (SSL2 and SSL3) mainly avoid the same lights downwards and can be herded downwards over 250 m. Though this study should be regarded as preliminary, the observed avoidance/herding response suggests artificial lights could be applied to improve existing fish capture methods for mesopelagic fish.

@article{doi101016jaaf202005002,
    author = "Underwood, Melanie J. and Utne-Palm, Anne Christine and Øvredal, Jan Tore and Bjordal, Åsmund",
    title = "The response of mesopelagic organisms to artificial lights",
    year = "2020",
    journal = "Aquaculture and Fisheries",
    abstract = "Though mesopelagic fish respond to natural light (e.g., diurnal vertical migration), few studies have looked at how they respond to artificial light and if artificial lights could be used in commercial operations to improve catchability of mesopelagic fish. Here we present a preliminary study on how mesopelagic organisms respond to blue and green spotlights, as well as red and white diffuse lights in Masfjorden (Norway; max depth of 480 m). The response of organisms in each of the three sound scattering layers (SSLs) was observed when a) artificial lights were positioned in a layer or b) moved with a constant speed (generally 0.03 ms−1) towards a layer. The artificial lights were attached to a rig with a self-contained echosounder, which recorded the vertical and horizontal avoidance of organisms in each SSL to different artificial lights. Net hauls (MIC-net) and video footage confirmed that Maurolicus muelleri and siphonophores were present in the upper layer (100–150 m), while Benthosema glaciale were present in the deeper layers (∼200 m and ∼300 m to seabed). Our findings suggest that M. muelleri (SSL1) horizontally avoid blue spotlight and white diffuse light, while B. glaciale (SSL2 and SSL3) mainly avoid the same lights downwards and can be herded downwards over 250 m. Though this study should be regarded as preliminary, the observed avoidance/herding response suggests artificial lights could be applied to improve existing fish capture methods for mesopelagic fish.",
    url = "https://doi.org/10.1016/j.aaf.2020.05.002",
    doi = "10.1016/j.aaf.2020.05.002",
    openalex = "W3041631003",
    references = "kaartvedt2019herding"
}

This review presents a synthesis of shark bioluminescence knowledge. Up to date, bioluminescent sharks are found only in Squaliformes, and specifically in Etmopteridae, Dalatiidae and Somniosidae families. The state-of-the-art knowledge about the evolution, ecological functions, histological structure, the associated squamation and physiological control of the photogenic organs of these elusive deep-sea sharks is presented. Special focus is given to their unique and singular hormonal luminescence control mechanism. In this context, the implication of the photophore-associated extraocular photoreception—which complements the visual adaptations of bioluminescent sharks to perceive residual downwelling light and luminescence in dim light environment—in the hormonally based luminescence control is depicted in detail. Similarities and differences between shark families are highlighted and support the hypothesis of an evolutionary unique ancestral appearance of luminescence in elasmobranchs. Finally, potential areas for future research on shark luminescence are presented.

@article{doi103390oceans2040047,
    author = "Duchatelet, Laurent and Claes, Julien M. and Delroisse, Jérôme and Flammang, Patrick and Mallefet, Jérôme",
    title = "Glow on Sharks: State of the Art on Bioluminescence Research",
    year = "2021",
    journal = "Oceans",
    abstract = "This review presents a synthesis of shark bioluminescence knowledge. Up to date, bioluminescent sharks are found only in Squaliformes, and specifically in Etmopteridae, Dalatiidae and Somniosidae families. The state-of-the-art knowledge about the evolution, ecological functions, histological structure, the associated squamation and physiological control of the photogenic organs of these elusive deep-sea sharks is presented. Special focus is given to their unique and singular hormonal luminescence control mechanism. In this context, the implication of the photophore-associated extraocular photoreception—which complements the visual adaptations of bioluminescent sharks to perceive residual downwelling light and luminescence in dim light environment—in the hormonally based luminescence control is depicted in detail. Similarities and differences between shark families are highlighted and support the hypothesis of an evolutionary unique ancestral appearance of luminescence in elasmobranchs. Finally, potential areas for future research on shark luminescence are presented.",
    url = "https://doi.org/10.3390/oceans2040047",
    doi = "10.3390/oceans2040047",
    openalex = "W4200532068",
    references = "doi101007bf02101634, doi101034j160007492000130203x, doi101039c6cs00296j, doi101073pnas2133521100, doi101126science1174269, doi101139g03040, doi101146annurevcellbio141197, doi101146annurevmarine120308081028, doi101152physrev1998783687, doi1012019780203491317"
}

We assessed the activity and swimming patterns of mesopelagic fishes in the Red Sea using bottom-moored, upward-facing echosounders deployed at 555 and 700 m depth. The vertically migrating mesopelagic scattering layer descended close to the bottom during daytime. This permitted assessment of behavior at mesopelagic depths by applying acoustic target tracking for individuals traversing the acoustic beam. Swimming activity did not fit the notion of torpid behavior in the daytime habitat. The fishes were moving continuously, with a prevailing downward direction before noon and upward after, though individuals were swimming in both directions at all times. They moreover were swimming horizontally at estimated speeds of ∼2.1 cm s −1, suggesting ∼0.5–1 body length s −1, intermittently turning. High activity at high temperatures suggests high respiration at depth, considered a key element for the active carbon pump. • We analyzed in situ mesopelagic fish swimming behavior in the lower twilight zone. • We present swimming speeds and activity obtained from stationary acoustics. • We found considerable activity of migrating mesopelagic fish at daytime depths. • Our findings challenge a common notion of torpid daytime behaviour. • High activity at warm temperatures suggests high respiration at depth.

@article{doi101016jdsr2022103897,
    author = "Sobradillo, B and Christiansen, Svenja and Røstad, Anders and Kaartvedt, Stein",
    title = "Individual daytime swimming of mesopelagic fishes in the world's warmest twilight zone",
    year = "2022",
    journal = "Deep Sea Research Part I Oceanographic Research Papers",
    abstract = "We assessed the activity and swimming patterns of mesopelagic fishes in the Red Sea using bottom-moored, upward-facing echosounders deployed at 555 and 700 m depth. The vertically migrating mesopelagic scattering layer descended close to the bottom during daytime. This permitted assessment of behavior at mesopelagic depths by applying acoustic target tracking for individuals traversing the acoustic beam. Swimming activity did not fit the notion of torpid behavior in the daytime habitat. The fishes were moving continuously, with a prevailing downward direction before noon and upward after, though individuals were swimming in both directions at all times. They moreover were swimming horizontally at estimated speeds of ∼2.1 cm s −1, suggesting ∼0.5–1 body length s −1, intermittently turning. High activity at high temperatures suggests high respiration at depth, considered a key element for the active carbon pump. • We analyzed in situ mesopelagic fish swimming behavior in the lower twilight zone. • We present swimming speeds and activity obtained from stationary acoustics. • We found considerable activity of migrating mesopelagic fish at daytime depths. • Our findings challenge a common notion of torpid daytime behaviour. • High activity at warm temperatures suggests high respiration at depth.",
    url = "https://doi.org/10.1016/j.dsr.2022.103897",
    doi = "10.1016/j.dsr.2022.103897",
    openalex = "W4306173671",
    references = "kaartvedt2019herding"
}

Mesopelagic fishes and invertebrates contribute to the biological carbon pump (BCP) through direct and indirect effects on the gravitational, diffusive, and migrant (active) fluxes. Here, we analyzed the effect of these organisms on total carbon export and sequestration using an idealized depth-resolved food-web model. We constrained a baseline scenario with observations from the Red Sea where mesopelagic fishes perform extensive diel vertical migration (DVM), presumably making them particularly important in carbon export. Our results are consistent with previous studies suggesting that mesopelagic fishes fuel a hotspot of heterotrophic activity in the mesopelagic zone of the Red Sea. While the supply of new nutrients to the euphotic zone is of first order in framing total carbon export and sequestration, we found 2 modulating effects of fish DVM. First, DVM enhances carbon sequestration because active carbon flux attenuates less than the gravitational and diffusive fluxes, and also because migrators fuel the gravitational flux deep into the mesopelagic zone. Secondly, through microbial food-web cascades, fish predation affects the relative contribution of the active and the passive fluxes with non-linear, less intuitive consequences for carbon export and sequestration. These food-web cascades involve a surprisingly large variation in the depth of the euphotic zone that is associated with a ‘diatom nutrient trap’ at the bottom of the euphotic zone.

@article{doi103354meps14373,
    author = "Aksnes, DL and Løtvedt, AS and Lindemann, Christian and Calleja, María Ll. and Morán, XAG and Kaarvedt, S and Thingstad, T. Frede",
    title = "Effects of migrating mesopelagic fishes on the biological carbon pump",
    year = "2023",
    journal = "Marine Ecology Progress Series",
    abstract = "Mesopelagic fishes and invertebrates contribute to the biological carbon pump (BCP) through direct and indirect effects on the gravitational, diffusive, and migrant (active) fluxes. Here, we analyzed the effect of these organisms on total carbon export and sequestration using an idealized depth-resolved food-web model. We constrained a baseline scenario with observations from the Red Sea where mesopelagic fishes perform extensive diel vertical migration (DVM), presumably making them particularly important in carbon export. Our results are consistent with previous studies suggesting that mesopelagic fishes fuel a hotspot of heterotrophic activity in the mesopelagic zone of the Red Sea. While the supply of new nutrients to the euphotic zone is of first order in framing total carbon export and sequestration, we found 2 modulating effects of fish DVM. First, DVM enhances carbon sequestration because active carbon flux attenuates less than the gravitational and diffusive fluxes, and also because migrators fuel the gravitational flux deep into the mesopelagic zone. Secondly, through microbial food-web cascades, fish predation affects the relative contribution of the active and the passive fluxes with non-linear, less intuitive consequences for carbon export and sequestration. These food-web cascades involve a surprisingly large variation in the depth of the euphotic zone that is associated with a ‘diatom nutrient trap’ at the bottom of the euphotic zone.",
    url = "https://doi.org/10.3354/meps14373",
    doi = "10.3354/meps14373",
    openalex = "W4384484673",
    references = "kaartvedt2019herding"
}

In the dark, expansive habitat of the deep sea, the production of light through bioluminescence is commonly used among a wide range of taxa. In decapod crustaceans, bioluminescence is only known in shrimps (Dendrobranchiata and Caridea) and may occur in different modes, including luminous secretions that are used to deter predators and/or from specialised light organs called photophores that function by providing camouflage against downwelling light. Photophores exhibit an extensive amount of morphological variation across decapod families: they may be internal (of hepatic origin) or embedded in surface tissues (dermal), and may possess an external lens, suggesting independent origins and multiple functions. Within Dendrobranchiata, we report bioluminescence in Sergestidae, Aristeidae, and Solenoceridae, and speculate that it may also be found in Acetidae, Luciferidae, Sicyonellidae, Benthesicymidae, and Penaeidae. Within Caridea, we report bioluminescence in Acanthephyridae, Oplophoridae, Pandalidae, and new observations for Pasiphaeidae. This comprehensive review includes historic taxonomic literature and recent studies investigating bioluminescence in all midwater and deep benthic shrimp families. Overall, we report known or suspected bioluminescence in 157 species across 12 families of decapod shrimps, increasing previous records of bioluminescent species by 65%. Mounting evidence from personal observations and the literature allow us to speculate the presence of light organs in several families thought to lack bioluminescence, making this phenomenon much more common than previously reported. We provide a detailed discussion of light organ morphology and function within each group and indicate future directions that will contribute to a better understanding of how deep-sea decapods use the language of light.

@article{doi101111brv13093,
    author = "Collins, Stormie B and Bracken‐Grissom, Heather D.",
    title = "The language of light: a review of bioluminescence in deep‐sea decapod shrimps",
    year = "2024",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "In the dark, expansive habitat of the deep sea, the production of light through bioluminescence is commonly used among a wide range of taxa. In decapod crustaceans, bioluminescence is only known in shrimps (Dendrobranchiata and Caridea) and may occur in different modes, including luminous secretions that are used to deter predators and/or from specialised light organs called photophores that function by providing camouflage against downwelling light. Photophores exhibit an extensive amount of morphological variation across decapod families: they may be internal (of hepatic origin) or embedded in surface tissues (dermal), and may possess an external lens, suggesting independent origins and multiple functions. Within Dendrobranchiata, we report bioluminescence in Sergestidae, Aristeidae, and Solenoceridae, and speculate that it may also be found in Acetidae, Luciferidae, Sicyonellidae, Benthesicymidae, and Penaeidae. Within Caridea, we report bioluminescence in Acanthephyridae, Oplophoridae, Pandalidae, and new observations for Pasiphaeidae. This comprehensive review includes historic taxonomic literature and recent studies investigating bioluminescence in all midwater and deep benthic shrimp families. Overall, we report known or suspected bioluminescence in 157 species across 12 families of decapod shrimps, increasing previous records of bioluminescent species by 65\%. Mounting evidence from personal observations and the literature allow us to speculate the presence of light organs in several families thought to lack bioluminescence, making this phenomenon much more common than previously reported. We provide a detailed discussion of light organ morphology and function within each group and indicate future directions that will contribute to a better understanding of how deep-sea decapods use the language of light.",
    url = "https://doi.org/10.1111/brv.13093",
    doi = "10.1111/brv.13093",
    openalex = "W4396672731",
    references = "denton1972the, doi101007bf00396920, doi101017s1464793103006420, doi101038s41598020612849, doi101038srep04328, doi101093acprofoso97801995811390010001, doi101093icb452234, doi101098rspb20190079, doi101111brv12672, doi101126science1174269, doi101146annurevmarine120308081028, doi101371journalpone0170489, doi103390life14040432, openalexw1923423279"
}

Although there are thousands of marine bioluminescent species, very little is known about the effects of artificial light at night (ALAN) on these organisms, particularly those living near the sea surface, such as dinoflagellates. These organisms have a circadian clock that influences their rhythmic physiology, including processes like photosynthesis and nitrogen metabolism, which help regulate marine carbon and nitrogen cycles, respectively. The purpose of this study is to partially address this knowledge gap and research the effects of light pollution on the bioluminescent dinoflagellate Pyrocystis lunula through a series of experiments aimed at verifying the consequences due to changes in the normal day-night circadian cycle and exposure to different types of light source, colors, and light intensities. The response variable was the Corrected Total Algal Bioluminescence, which was recorded with a digital camera and then calculated with the ImageJ software. Results show that dinoflagellates do not appear to be susceptible to slight changes in the light/dark cycle. However, a total absence of light and darkness leads to a drastic inhibition of their bioluminescence, particularly under white LED or incandescent artificial light and with a light intensity of 100 lux or higher.

@article{doi1015359revmar1625,
    author = "Bari, Davide Di",
    title = "Natural light vs artificial light. Effects of light pollution on the bioluminescence of dinoflagellate Pyrocystis lunula",
    year = "2024",
    journal = "Revista Ciencias Marinas y Costeras",
    abstract = "Although there are thousands of marine bioluminescent species, very little is known about the effects of artificial light at night (ALAN) on these organisms, particularly those living near the sea surface, such as dinoflagellates. These organisms have a circadian clock that influences their rhythmic physiology, including processes like photosynthesis and nitrogen metabolism, which help regulate marine carbon and nitrogen cycles, respectively. The purpose of this study is to partially address this knowledge gap and research the effects of light pollution on the bioluminescent dinoflagellate Pyrocystis lunula through a series of experiments aimed at verifying the consequences due to changes in the normal day-night circadian cycle and exposure to different types of light source, colors, and light intensities. The response variable was the Corrected Total Algal Bioluminescence, which was recorded with a digital camera and then calculated with the ImageJ software. Results show that dinoflagellates do not appear to be susceptible to slight changes in the light/dark cycle. However, a total absence of light and darkness leads to a drastic inhibition of their bioluminescence, particularly under white LED or incandescent artificial light and with a light intensity of 100 lux or higher.",
    url = "https://doi.org/10.15359/revmar.16-2.5",
    doi = "10.15359/revmar.16-2.5",
    openalex = "W4405368692",
    references = "doi10100797814615871493, doi101016jhal200808006, doi101016jjenvman201106029, doi101016jtree201009007, doi101038s41598018246306, doi101039c9qm00716d, doi101111j13652664201202212x, doi101126sciadv1600377, doi101146annurevmarine120308081028, doi1015359revmar1625, doi103390life14040432, doi105751es03685150413"
}

Although there are thousands of marine bioluminescent species, very little is known about the effects of artificial light at night (ALAN) on these organisms, particularly those living near the sea surface, such as dinoflagellates. These organisms have a circadian clock that influences their rhythmic physiology, including processes like photosynthesis and nitrogen metabolism, which help regulate marine carbon and nitrogen cycles, respectively. The purpose of this study is to partially address this knowledge gap and research the effects of light pollution on the bioluminescent dinoflagellate Pyrocystis lunula through a series of experiments aimed at verifying the consequences due to changes in the normal day-night circadian cycle and exposure to different types of light source, colors, and light intensities. The response variable was the Corrected Total Algal Bioluminescence, which was recorded with a digital camera and then calculated with the ImageJ software. Results show that dinoflagellates do not appear to be susceptible to slight changes in the light/dark cycle. However, a total absence of light and darkness leads to a drastic inhibition of their bioluminescence, particularly under white LED or incandescent artificial light and with a light intensity of 100 lux or higher.

@article{doi1015359revmar1652,
    author = "Bari, Davide Di",
    title = "Natural light vs artificial light. Effects of light pollution on the bioluminescence of dinoflagellate Pyrocystis lunula",
    year = "2024",
    journal = "Revista Ciencias Marinas y Costeras",
    abstract = "Although there are thousands of marine bioluminescent species, very little is known about the effects of artificial light at night (ALAN) on these organisms, particularly those living near the sea surface, such as dinoflagellates. These organisms have a circadian clock that influences their rhythmic physiology, including processes like photosynthesis and nitrogen metabolism, which help regulate marine carbon and nitrogen cycles, respectively. The purpose of this study is to partially address this knowledge gap and research the effects of light pollution on the bioluminescent dinoflagellate Pyrocystis lunula through a series of experiments aimed at verifying the consequences due to changes in the normal day-night circadian cycle and exposure to different types of light source, colors, and light intensities. The response variable was the Corrected Total Algal Bioluminescence, which was recorded with a digital camera and then calculated with the ImageJ software. Results show that dinoflagellates do not appear to be susceptible to slight changes in the light/dark cycle. However, a total absence of light and darkness leads to a drastic inhibition of their bioluminescence, particularly under white LED or incandescent artificial light and with a light intensity of 100 lux or higher.",
    url = "https://doi.org/10.15359/revmar.16.5.2",
    doi = "10.15359/revmar.16.5.2",
    openalex = "W4405288151",
    references = "doi10100797814615871493, doi101016jhal200808006, doi101016jjenvman201106029, doi101016jtree201009007, doi101038s41598018246306, doi101039c9qm00716d, doi101111j13652664201202212x, doi101126sciadv1600377, doi101146annurevmarine120308081028, doi1015359revmar1625, doi103390life14040432, doi105751es03685150413"
}

Bioluminescence is the production of visible light by an organism. This phenomenon is particularly widespread in marine animals, especially in the deep sea. While the luminescent status of numerous marine animals has been recently clarified thanks to advancements in deep-sea exploration technologies and phylogenetics, that of others has become more obscure due to dramatic changes in systematics (themselves triggered by molecular phylogenies). Here, we combined a comprehensive literature review with unpublished data to establish a catalogue of marine luminescent animals. Inventoried animals were identified to species level in over 97% of the cases and were associated with a score reflecting the robustness of their luminescence record. While luminescence capability has been established in 695 genera of marine animals, luminescence reports from 99 additional genera need further confirmation. Altogether, these luminescent and potentially luminescent genera encompass 9405 species, of which 2781 are luminescent, 136 are potentially luminescent (e.g., suggested luminescence in those species needs further confirmation), 99 are non-luminescent, and 6389 have an unknown luminescent status. Comparative analyses reveal new insights into the occurrence of luminescence among marine animal groups and highlight promising research areas. This work will provide a solid foundation for future studies related to the field of marine bioluminescence.

@article{doi103390life14040432,
    author = "Claes, Julien M. and Haddock, Steven H. D. and Coubris, Constance and Mallefet, Jérôme",
    title = "Systematic Distribution of Bioluminescence in Marine Animals: A Species-Level Inventory",
    year = "2024",
    journal = "Life",
    abstract = "Bioluminescence is the production of visible light by an organism. This phenomenon is particularly widespread in marine animals, especially in the deep sea. While the luminescent status of numerous marine animals has been recently clarified thanks to advancements in deep-sea exploration technologies and phylogenetics, that of others has become more obscure due to dramatic changes in systematics (themselves triggered by molecular phylogenies). Here, we combined a comprehensive literature review with unpublished data to establish a catalogue of marine luminescent animals. Inventoried animals were identified to species level in over 97\% of the cases and were associated with a score reflecting the robustness of their luminescence record. While luminescence capability has been established in 695 genera of marine animals, luminescence reports from 99 additional genera need further confirmation. Altogether, these luminescent and potentially luminescent genera encompass 9405 species, of which 2781 are luminescent, 136 are potentially luminescent (e.g., suggested luminescence in those species needs further confirmation), 99 are non-luminescent, and 6389 have an unknown luminescent status. Comparative analyses reveal new insights into the occurrence of luminescence among marine animal groups and highlight promising research areas. This work will provide a solid foundation for future studies related to the field of marine bioluminescence.",
    url = "https://doi.org/10.3390/life14040432",
    doi = "10.3390/life14040432",
    openalex = "W4393161018",
    references = "denton1972the, doi101002bio1170010303, doi101038ncomms4271, doi101038s41586023059366, doi101038srep45750, doi101039b713328f, doi101126science1174269, doi101146annurevmarine120308081028, doi101371journalpone0051629, doi101371journalpone0155154, doi103390oceans2040047"
}

@article{balasubramanian2025bioluminescence,
    author = "Balasubramanian, Chirag and Raghavan, Farheen",
    title = "Bioluminescence mechanisms and ecological functions in mesopelagic fish species",
    year = "2025",
    journal = "International Journal of Biology Sciences",
    url = "https://doi.org/10.33545/26649926.2025.v7.i11b.677",
    doi = "10.33545/26649926.2025.v7.i11b.677",
    number = "11",
    openalex = "W7154596507",
    pages = "89-91",
    volume = "7"
}

Light functions as the universal language in the deep sea (>200 m). Both bioluminescent emissions and downwelling light sources dimly illuminate the water column and can drive sensory system evolution. In pelagic environments, vertically migrating animals can experience drastic changes to their lighting environment across depth, subjecting them to unique selective pressures, possibly to distinguish between changes in ambient light and bioluminescent sources. Here we show that visual opsin diversity across a group of variable vertical migrators -bioluminescent deep-sea shrimp belonging to the Superfamily Oplophoroidea- is higher among species who migrate to shallower waters with more variable light conditions. Further, we provide evidence for adaptive visual evolution among species who have evolved an additional mode of bioluminescence (photophores), including positive selection for a putative mid-wavelength sensitive opsin that may facilitate light source discrimination. Diversification of this opsin appears to play an important role in the visual ecologies of photophore-bearing shrimp with its diversification in Oplophoroidea likely playing a critical role in the fitness and evolutionary success of this group.

@article{doi101038s4200302507450z,
    author = "DeLeo, Danielle M. and Bracken‐Grissom, Heather D.",
    title = "Bioluminescence and environmental light drive the visual evolution of deep-sea shrimp (Oplophoroidea)",
    year = "2025",
    journal = "Communications Biology",
    abstract = "Light functions as the universal language in the deep sea (>200 m). Both bioluminescent emissions and downwelling light sources dimly illuminate the water column and can drive sensory system evolution. In pelagic environments, vertically migrating animals can experience drastic changes to their lighting environment across depth, subjecting them to unique selective pressures, possibly to distinguish between changes in ambient light and bioluminescent sources. Here we show that visual opsin diversity across a group of variable vertical migrators -bioluminescent deep-sea shrimp belonging to the Superfamily Oplophoroidea- is higher among species who migrate to shallower waters with more variable light conditions. Further, we provide evidence for adaptive visual evolution among species who have evolved an additional mode of bioluminescence (photophores), including positive selection for a putative mid-wavelength sensitive opsin that may facilitate light source discrimination. Diversification of this opsin appears to play an important role in the visual ecologies of photophore-bearing shrimp with its diversification in Oplophoroidea likely playing a critical role in the fitness and evolutionary success of this group.",
    url = "https://doi.org/10.1038/s42003-025-07450-z",
    doi = "10.1038/s42003-025-07450-z",
    openalex = "W4407364255",
    references = "doi101111brv13093"
}

Bioluminescent symbioses in marine animals, particularly cephalopods and fishes, representremarkable models of convergent evolution and microbe-host interaction. These luminouspartnerships, such as Euprymna scolopes with Vibrio fischeri and ponyfishes withPhotobacterium- enable ecological functions like predator evasion, camouflage viacounterillumination, and mating communication. This review synthesizes current knowledge ofhost-microbe specificity, quorum sensing, and light-organ anatomy across taxa. The conserved luxoperon is playing a central role in bacterial light production, while hosts employ adaptations likespectral filtering and muscular shutters to regulate bioluminescence. Circadian rhythms furthersynchronize emission with behavior and environment. Despite growing insight, knowledge gapsremain in symbiont acquisition, evolutionary transitions, and resilience to ocean warming,acidification, and pollution. We highlight future research directions, including CRISPR-enabledfunctional genomics, eDNA surveys, and cross-species colonization experiments to uncovermechanisms of specificity and adaptation. Bioluminescent symbioses not only illuminateecological and evolutionary dynamics but also inspire applications in biosensing, bioimaging, andmarine environmental monitoring. Protecting these systems is critical, as environmental stressthreatens to disrupt their delicate balance and broader ecosystem functions.

@misc{doi1031230osfion5bv8v1,
    author = "Akther, Hasna",
    title = "Convergent Evolution of Bioluminescent Symbioses in Fish and Cephalopods: Mechanisms, Host Specificity, and Ecological Roles",
    year = "2025",
    abstract = "Bioluminescent symbioses in marine animals, particularly cephalopods and fishes, representremarkable models of convergent evolution and microbe-host interaction. These luminouspartnerships, such as Euprymna scolopes with Vibrio fischeri and ponyfishes withPhotobacterium- enable ecological functions like predator evasion, camouflage viacounterillumination, and mating communication. This review synthesizes current knowledge ofhost-microbe specificity, quorum sensing, and light-organ anatomy across taxa. The conserved luxoperon is playing a central role in bacterial light production, while hosts employ adaptations likespectral filtering and muscular shutters to regulate bioluminescence. Circadian rhythms furthersynchronize emission with behavior and environment. Despite growing insight, knowledge gapsremain in symbiont acquisition, evolutionary transitions, and resilience to ocean warming,acidification, and pollution. We highlight future research directions, including CRISPR-enabledfunctional genomics, eDNA surveys, and cross-species colonization experiments to uncovermechanisms of specificity and adaptation. Bioluminescent symbioses not only illuminateecological and evolutionary dynamics but also inspire applications in biosensing, bioimaging, andmarine environmental monitoring. Protecting these systems is critical, as environmental stressthreatens to disrupt their delicate balance and broader ecosystem functions.",
    url = "https://doi.org/10.31230/osf.io/n5bv8\_v1",
    doi = "10.31230/osf.io/n5bv8\_v1",
    openalex = "W4413015655",
    references = "doi101007s0022700312853, doi101038nrd3013, doi101038nrmicro957, doi1011112041210x12034, doi101111bij12701, doi101126science1174269, doi101128mr4344965181979, doi101128mr5511231421991, doi101146annurevbioeng4111901093336, doi101146annurevmicro091313103654, doi103390life14040432"
}

Treatment of Mycobacterium abscessus pulmonary disease (Mabs-PD) is a growing global health challenge. The lack of bactericidal antibiotics effective at therapeutically relevant concentrations underscores an urgent need for drug discovery. Targeting cell wall synthesis is a promising strategy for drug discovery, as exemplified by the clinical success of broad-spectrum β-lactam antibiotics. Here, we employ a bioluminescence-based whole-cell assay optimized to identify compounds that disrupt both cell wall synthesis and oxidative phosphorylation. A focused drug library screen against Mabs reveals a chemically tractable naphthalen-1-ylmethanamine scaffold with potent bactericidal activity. The optimized derivative GM47-1 targets MmpL3, compromises cell wall integrity, induces ATP leakage, and uncouples respiration. Further chemical optimization yields a derivative with nanomolar minimum inhibitory concentration, bactericidal activity against intracellular Mabs, and efficacy in a zebrafish infection model. Together, these findings identify a promising scaffold for therapeutic development and demonstrate the utility of this bioluminescence-based platform for discovering bactericidal agents against Mabs.

@article{doi101016jcelrep2026117311,
    author = "Singh, Samsher and Sorayah, Ria and Chen, Yushu and Mulholland, Claire V and Daher, Wassim and Pee, Carmen J E and Tan, Casandra Ai Zhu and Wee, Denise and Chen, Zhuoyan and Oehlers, Stefan H and Kline, Kimberly A and Chng, Shu Sin and Berney, Michael and Kremer, Laurent and Moraski, Garrett and Pethe, Kevin",
    title = "A bioluminescence-based chemical screen identifies a bactericidal naphthalen-1-ylmethanamine scaffold targeting MmpL3 in Mycobacterium abscessus.",
    year = "2026",
    journal = "Cell reports",
    abstract = "Treatment of Mycobacterium abscessus pulmonary disease (Mabs-PD) is a growing global health challenge. The lack of bactericidal antibiotics effective at therapeutically relevant concentrations underscores an urgent need for drug discovery. Targeting cell wall synthesis is a promising strategy for drug discovery, as exemplified by the clinical success of broad-spectrum β-lactam antibiotics. Here, we employ a bioluminescence-based whole-cell assay optimized to identify compounds that disrupt both cell wall synthesis and oxidative phosphorylation. A focused drug library screen against Mabs reveals a chemically tractable naphthalen-1-ylmethanamine scaffold with potent bactericidal activity. The optimized derivative GM47-1 targets MmpL3, compromises cell wall integrity, induces ATP leakage, and uncouples respiration. Further chemical optimization yields a derivative with nanomolar minimum inhibitory concentration, bactericidal activity against intracellular Mabs, and efficacy in a zebrafish infection model. Together, these findings identify a promising scaffold for therapeutic development and demonstrate the utility of this bioluminescence-based platform for discovering bactericidal agents against Mabs.",
    url = "https://pubmed.ncbi.nlm.nih.gov/42030156/",
    doi = "10.1016/j.celrep.2026.117311",
    pmid = "42030156"
}

The sensitive detection of microorganisms in complex samples, such as herbal medicines, was significantly hampered by severe matrix interference and low target abundance. While magnetic separation and microfluidics offered enrichment capabilities, existing platforms often struggled to achieve efficient, parallel enrichment of both specific pathogens and total aerobic microbes. To address this critical gap, we developed an integrated microfluidic platform featuring a custom dot-array magnetic field that enabled highly efficient and parallel enrichment of multiple bacterial targets. A dual-mechanism capture strategy was implemented, utilizing immunomagnetic beads (IMBs) for the specific isolation of Salmonella paratyphi B (S. paratyphi B) and Escherichia coli (E. coli), and cationic polymer-modified beads for the broad-spectrum capture of aerobic bacteria. Following enrichment, captured viable bacteria were rapidly quantified via ATP bioluminescence. The system demonstrated high sensitivity, with limits of detection of 49 CFU mL-1 for S. paratyphi B, 60 CFU mL-1 for E. coli, and 55 CFU mL-1 for aerobic bacteria, and exhibited a strong linear response (R2 > 0.99) across a wide dynamic range (103-107 CFU mL-1). Successful application in spiked licorice samples confirmed the platform's practicality and reliability for the rapid, multiplexed detection of microbial contaminants in complex herbal products, offering a powerful tool for quality and safety monitoring.

@article{doi101039d6ay00153j,
    author = "Zhang, Chunyan and Chen, Chengjian and Zhang, Weifei and Zheng, Jiayu and Wulan, Tuya and Feng, Xuanlin and Wu, Zhisheng and Li, Nan",
    title = "A dot-array magnetic enrichment strategy for rapid, multiplexed detection of viable bacteria via ATP bioluminescence.",
    year = "2026",
    journal = "Analytical methods: advancing methods and applications",
    abstract = "The sensitive detection of microorganisms in complex samples, such as herbal medicines, was significantly hampered by severe matrix interference and low target abundance. While magnetic separation and microfluidics offered enrichment capabilities, existing platforms often struggled to achieve efficient, parallel enrichment of both specific pathogens and total aerobic microbes. To address this critical gap, we developed an integrated microfluidic platform featuring a custom dot-array magnetic field that enabled highly efficient and parallel enrichment of multiple bacterial targets. A dual-mechanism capture strategy was implemented, utilizing immunomagnetic beads (IMBs) for the specific isolation of Salmonella paratyphi B (S. paratyphi B) and Escherichia coli (E. coli), and cationic polymer-modified beads for the broad-spectrum capture of aerobic bacteria. Following enrichment, captured viable bacteria were rapidly quantified via ATP bioluminescence. The system demonstrated high sensitivity, with limits of detection of 49 CFU mL-1 for S. paratyphi B, 60 CFU mL-1 for E. coli, and 55 CFU mL-1 for aerobic bacteria, and exhibited a strong linear response (R2 > 0.99) across a wide dynamic range (103-107 CFU mL-1). Successful application in spiked licorice samples confirmed the platform's practicality and reliability for the rapid, multiplexed detection of microbial contaminants in complex herbal products, offering a powerful tool for quality and safety monitoring.",
    url = "https://pubmed.ncbi.nlm.nih.gov/42037523/",
    doi = "10.1039/d6ay00153j",
    pmid = "42037523"
}