Bioluminescence

Bioluminescence is the production and emission of light by a living organism. It is a form of chemiluminescence. Bioluminescence occurs widely in marine vertebrates and invertebrates, as well as in some fungi, microorganisms including some bioluminescent bacteria and terrestrial invertebrates such as fireflies. In some animals, the light is bacteriogenic, produced by symbiotic organisms such as Vibrio bacteria; in others, it is autogenic, produced by the animals themselves.

In a general sense, the principal chemical reaction in bioluminescence involves some light-emitting molecule and an enzyme, generally called the luciferin and the luciferase, respectively. Because these are generic names, the luciferins and luciferases are often distinguished by including the species or group, i.e. Firefly luciferin. In all characterized cases, the enzyme catalyzes the oxidation of the luciferin.

In some species, the luciferase requires other cofactors, such as calcium or magnesium ions, and sometimes also the energy-carrying molecule adenosine triphosphate (ATP). In evolution, luciferins vary little: one in particular, coelenterazine, is found in eleven different animal (phyla), though in some of these, the animals obtain it through their diet. Conversely, luciferases vary widely between different species, and consequently bioluminescence has arisen over forty times in evolutionary history.

Both Aristotle and Pliny the Elder mentioned that damp wood sometimes gives off a glow and many centuries later Robert Boyle showed that oxygen was involved in the process, both in wood and in glow-worms. It was not until the late nineteenth century that bioluminescence was properly investigated. The phenomenon is widely distributed among animal groups, especially in marine environments where dinoflagellates cause phosphorescence in the surface layers of water. On land it occurs in fungi, bacteria and some groups of invertebrates, including insects.

The uses of bioluminescence by animals include counter-illumination camouflage, mimicry of other animals, for example to lure prey, and signalling to other individuals of the same species, such as to attract mates. In the laboratory, luciferase-based systems are used in genetic engineering and for biomedical research. Other researchers are investigating the possibility of using bioluminescent systems for street and decorative lighting, and a bioluminescent plant has been created.[1]

Photinus pyralis Firefly glowing
Flying and glowing firefly, Photinus pyralis
Lampyris Noctiluca (firefly) mating
Male and female of the species Lampyris noctiluca mating. The female of this species has no wings, she's a larviforme, unlike the male species.

History

Before the development of the safety lamp for use in coal mines, dried fish skins were used in Britain and Europe as a weak source of light.[2] This experimental form of illumination avoided the necessity of using candles which risked sparking explosions of firedamp.[3] Another safe source of illumination in mines was bottles containing fireflies.[4] In 1920, the American zoologist E. Newton Harvey published a monograph, The Nature of Animal Light, summarizing early work on bioluminescence. Harvey notes that Aristotle mentions light produced by dead fish and flesh, and that both Aristotle and Pliny the Elder (in his Natural History) mention light from damp wood. He also records that Robert Boyle experimented on these light sources, and showed that both they and the glow-worm require air for light to be produced. Harvey notes that in 1753, J. Baker identified the flagellate Noctiluca "as a luminous animal" "just visible to the naked eye",[5] and in 1854 Johann Florian Heller (1813–1871) identified strands (hyphae) of fungi as the source of light in dead wood.[6]

Tuckey, in his posthumous 1818 Narrative of the Expedition to the Zaire, described catching the animals responsible for luminescence. He mentions pellucids, crustaceans (to which he ascribes the milky whiteness of the water), and cancers (shrimps and crabs). Under the microscope he described the "luminous property" to be in the brain, resembling "a most brilliant amethyst about the size of a large pin's head".[7]

Charles Darwin noticed bioluminescence in the sea, describing it in his Journal:

While sailing in these latitudes on one very dark night, the sea presented a wonderful and most beautiful spectacle. There was a fresh breeze, and every part of the surface, which during the day is seen as foam, now glowed with a pale light. The vessel drove before her bows two billows of liquid phosphorus, and in her wake she was followed by a milky train. As far as the eye reached, the crest of every wave was bright, and the sky above the horizon, from the reflected glare of these livid flames, was not so utterly obscure, as over the rest of the heavens.[8]

Darwin also observed a luminous "jelly-fish of the genus Dianaea"[8] and noted that "When the waves scintillate with bright green sparks, I believe it is generally owing to minute crustacea. But there can be no doubt that very many other pelagic animals, when alive, are phosphorescent."[8] He guessed that "a disturbed electrical condition of the atmosphere"[8] was probably responsible. Daniel Pauly comments that Darwin "was lucky with most of his guesses, but not here",[9] noting that biochemistry was too little known, and that the complex evolution of the marine animals involved "would have been too much for comfort".[9]

Aequorea4
Osamu Shimomura isolated the photoprotein aequorin and its cofactor coelenterazine from the crystal jelly Aequorea victoria in 1961.[10]

Bioluminescence attracted the attention of the United States Navy in the Cold War, since submarines in some waters can create a bright enough wake to be detected; a German submarine was sunk in the First World War, having been detected in this way. The navy was interested in predicting when such detection would be possible, and hence guiding their own submarines to avoid detection.[11]

Among the anecdotes of navigation by bioluminescence, the Apollo 13 astronaut Jim Lovell recounted how as a navy pilot he had found his way back to his aircraft carrier USS Shangri-La when his navigation systems failed. Turning off his cabin lights, he saw the glowing wake of the ship, and was able to fly to it and land safely.[12]

The French pharmacologist Raphaël Dubois carried out work on bioluminescence in the late nineteenth century. He studied click beetles (Pyrophorus) and the marine bivalve mollusc Pholas dactylus. He refuted the old idea that bioluminescence came from phosphorus,[13][a] and demonstrated that the process was related to the oxidation of a specific compound, which he named luciferin, by an enzyme.[15] He sent Harvey siphons from the mollusc preserved in sugar. Harvey had become interested in bioluminescence as a result of visiting the South Pacific and Japan and observing phosphorescent organisms there. He studied the phenomenon for many years. His research aimed to demonstrate that luciferin, and the enzymes that act on it is to produce light, were interchangeable between species, showing that all bioluminescent organisms had a common ancestor. However, he found this hypothesis to be false, with different organisms having major differences in the composition of their light-producing proteins. He spent the next thirty years purifying and studying the components, but it fell to the young Japanese chemist Osamu Shimomura to be the first to obtain crystalline luciferin. He used the sea firefly Vargula hilgendorfii, but it was another ten years before he discovered the chemical's structure and was able to publish his 1957 paper Crystalline Cypridina Luciferin.[16] More recently, Martin Chalfie, Osamu Shimomura and Roger Y. Tsien won the 2008 Nobel Prize in Chemistry for their 1961 discovery and development of green fluorescent protein as a tool for biological research.[17]

Harvey wrote a detailed historical account on all forms of luminescence in 1957.[18] An updated book on bioluminescence covering also the twentieth and early twenty-first century was published recently.[19]

[20]

In 2016, deep sea bioluminescent corals were captured for the first time in color HD Video. [21]

Evolution

E. N. Harvey (1932) was among the first to propose how bioluminescence could have evolved.[22] In this early paper, he suggested that proto-bioluminescence could have arisen from respiratory chain proteins that hold fluorescent groups. This hypothesis has since been disproven, but it did lead to considerable interest in the origins of the phenomenon. Today, the two prevailing hypotheses (both concerning marine bioluminescence) are the ones put forth by Seliger (1993) and Rees et al. (1998).[23][24]

Seliger's theory identifies luciferase enzymes as the catalyst for the evolution of bioluminescent systems. It suggests that the original purpose of luciferases was as mixed-function oxygenases. As the early ancestors of many species moved into deeper and darker waters natural selection applied forces that favored the development of increased eye sensitivity and enhanced visual signals.[25] If selection were to favor a mutation in the oxygenase enzyme required for the breakdown of pigment molecules (molecules often associated with spots used to attract a mate or distract a predator) it could have eventually resulted in external luminescence in tissues.[23]

Rees et al. (1998) uses evidence gathered from the marine luciferin coelenterazine to suggest that selection acting on luciferins may have arisen from pressures to protect oceanic organisms from potentially deleterious reactive oxygen species (ROS) (e.g. H2O2 and O2 ). The functional shift from antioxidation to bioluminescence probably occurred when the strength of selection for antioxidation defense decreased as early species moved further down the water column. At greater depths exposure to ROS is significantly lower, as is the endogenous production of ROS through metabolism.[24]

While popular at first, Seliger's theory has been challenged, particularly on the biochemical and genetic evidence that Rees examines. What remains clear, however, is that bioluminescence has evolved independently at least 40 times.[26] Bioluminescence in fish began at least by the Cretaceous period. About 1,500 fish species are known to be bioluminescent; the capability evolved independently at least 27 times. Of these 27 occasions, 17 involved the taking up of bioluminous bacteria from the surrounding water while in the others, the intrinsic light evolved through chemical synthesis. These fish have become surprisingly diverse in the deep ocean and control their light with the help of their nervous system, using it not just to lure prey or hide from predators, but also for communication.[27][28]

Chemical mechanism

Firefly Luciferase Crystal Structure.rsh
Protein structure of the luciferase of the firefly Photinus pyralis. The enzyme is a much larger molecule than luciferin.

Bioluminescence is a form of chemiluminescence where light energy is released by a chemical reaction. This reaction involves a light-emitting pigment, the luciferin, and a luciferase, the enzyme component.[29] Because of the diversity of luciferin/luciferase combinations, there are very few commonalities in the chemical mechanism. From currently studied systems, the only unifying mechanism is the role of molecular oxygen, though many examples have a concurrent release of carbon dioxide. For example, the firefly luciferin/luciferase reaction requires magnesium and ATP and produces carbon dioxide (CO2), adenosine monophosphate (AMP) and pyrophosphate (PP) as waste products. Other cofactors may be required for the reaction, such as calcium (Ca2+) for the photoprotein aequorin, or magnesium (Mg2+) ions and ATP for the firefly luciferase.[30] Generically, this reaction could be described as:

Coelenterazine
Coelenterazine is a luciferin found in many different marine phyla from comb jellies to vertebrates. Like all luciferins, it is oxidised to produce light.

Instead of a luciferase, the jellyfish Aequorea victoria makes use of another type of protein called a photoprotein, in this case specifically aequorin.[31] When calcium ions are added, the rapid catalysis creates a brief flash quite unlike the prolonged glow produced by luciferase. In a second, much slower, step luciferin is regenerated from the oxidised (oxyluciferin) form, allowing it to recombine with aequorin, in readiness for a subsequent flash. Photoproteins are thus enzymes, but with unusual reaction kinetics.[32] Furthermore, some of the blue light released by aequorin in contact with calcium ions is absorbed by a green fluorescent protein, which in turn releases green light in a process called resonant energy transfer.[33]

Overall, bioluminescence has arisen over forty times in evolutionary history.[29] In evolution, luciferins tend to vary little: one in particular, coelenterazine, is the light emitting pigment for nine phyla (groups of very different organisms), including polycystine radiolaria, Cercozoa (Phaeodaria), protozoa, comb jellies, cnidaria including jellyfish and corals, crustaceans, molluscs, arrow worms and vertebrates (ray-finned fish). Not all these organisms synthesize coelenterazine: some of them obtain it through their diet.[29] Conversely, luciferase enzymes vary widely and tend to be different in each species.[29]

Distribution

Bioluminescent dinoflagellates 2
Huge numbers of bioluminescent dinoflagellates creating phosphorescence in breaking waves

Bioluminescence occurs widely among animals, especially in the open sea, including fish, jellyfish, comb jellies, crustaceans, and cephalopod molluscs; in some fungi and bacteria; and in various terrestrial invertebrates including insects. About 76% of the main taxa of deep-sea animals produce light.[34] Most marine light-emission is in the blue and green light spectrum. However, some loose-jawed fish emit red and infrared light, and the genus Tomopteris emits yellow light.[29][35]

The most frequently encountered bioluminescent organisms may be the dinoflagellates present in the surface layers of the sea, which are responsible for the sparkling phosphorescence sometimes seen at night in disturbed water. At least eighteen genera exhibit luminosity.[29] A different effect is the thousands of square miles of the ocean which shine with the light produced by bioluminescent bacteria, known as mareel or the milky seas effect.[36]

Non-marine bioluminescence is less widely distributed, the two best-known cases being in fireflies and glow worms. Other invertebrates including insect larvae, annelids and arachnids possess bioluminescent abilities. Some forms of bioluminescence are brighter (or exist only) at night, following a circadian rhythm.

Uses in nature

Bioluminescence has several functions in different taxa. Steven Haddock et al. (2010) list as more or less definite functions in marine organisms the following: defensive functions of startle, counterillumination (camouflage), misdirection (smoke screen), distractive body parts, burglar alarm (making predators easier for higher predators to see), and warning to deter settlers; offensive functions of lure, stun or confuse prey, illuminate prey, and mate attraction/recognition. It is much easier for researchers to detect that a species is able to produce light than to analyse the chemical mechanisms or to prove what function the light serves.[29] In some cases the function is unknown, as with species in three families of earthworm (Oligochaeta), such as Diplocardia longa where the coelomic fluid produces light when the animal moves.[37] The following functions are reasonably well established in the named organisms.

Counterillumination camouflage

Squid Counterillumination
Principle of counterillumination camouflage in firefly squid, Watasenia scintillans. When seen from below by a predator, the bioluminescence helps to match the squid's brightness and colour to the sea surface above.

In many animals of the deep sea, including several squid species, bacterial bioluminescence is used for camouflage by counterillumination, in which the animal matches the overhead environmental light as seen from below.[38] In these animals, photoreceptors control the illumination to match the brightness of the background.[38] These light organs are usually separate from the tissue containing the bioluminescent bacteria. However, in one species, Euprymna scolopes, the bacteria are an integral component of the animal's light organ.[39]

Attraction

A fungus gnat from New Zealand, Arachnocampa luminosa, lives in the predator-free environment of caves and its larvae emit bluish-green light.[40] They dangle silken threads that glow and attract flying insects, and wind in their fishing-lines when prey becomes entangled.[41] The bioluminescence of the larvae of another fungus gnat from North America which lives on streambanks and under overhangs has a similar function. Orfelia fultoni builds sticky little webs and emits light of a deep blue colour. It has an inbuilt biological clock and, even when kept in total darkness, turns its light on and off in a circadian rhythm.[42]

Fireflies use light to attract mates. Two systems are involved according to species; in one, females emit light from their abdomens to attract males; in the other, flying males emit signals to which the sometimes sedentary females respond.[37][43] Click beetles emit an orange light from the abdomen when flying and a green light from the thorax when they are disturbed or moving about on the ground. The former is probably a sexual attractant but the latter may be defensive.[37] Larvae of the click beetle Pyrophorus nyctophanus live in the surface layers of termite mounds in Brazil. They light up the mounds by emitting a bright greenish glow which attracts the flying insects on which they feed.[37]

In the marine environment, use of luminescence for mate attraction is chiefly known among ostracods, small shrimplike crustaceans, especially in the family Cyprididae. Pheromones may be used for long-distance communication, with bioluminescence used at close range to enable mates to "home in".[29] A polychaete worm, the Bermuda fireworm creates a brief display, a few nights after the full moon, when the female lights up to attract males.[44]

Defence

Many cephalopods, including at least 70 genera of squid, are bioluminescent.[29] Some squid and small crustaceans use bioluminescent chemical mixtures or bacterial slurries in the same way as many squid use ink. A cloud of luminescent material is expelled, distracting or repelling a potential predator, while the animal escapes to safety.[29] The deep sea squid Octopoteuthis deletron may autotomise portions of its arms which are luminous and continue to twitch and flash, thus distracting a predator while the animal flees.[29]

Dinoflagellates may use bioluminescence for defence against predators. They shine when they detect a predator, possibly making the predator itself more vulnerable by attracting the attention of predators from higher trophic levels.[29] Grazing copepods release any phytoplankton cells that flash, unharmed; if they were eaten they would make the copepods glow, attracting predators, so the phytoplankton's bioluminescence is defensive. The problem of shining stomach contents is solved (and the explanation corroborated) in predatory deep-sea fishes: their stomachs have a black lining able to keep the light from any bioluminescent fish prey which they have swallowed from attracting larger predators.[9]

The sea-firefly is a small crustacean living in sediment. At rest it emits a dull glow but when disturbed it darts away leaving a cloud of shimmering blue light to confuse the predator. During World War II it was gathered and dried for use by the Japanese military as a source of light during clandestine operations.[16]

The larvae of railroad worms (Phrixothrix) have paired photic organs on each body segment, able to glow with green light; these are thought to have a defensive purpose.[45] They also have organs on the head which produce red light; they are the only terrestrial organisms to emit light of this colour.[46]

Warning

Aposematism is a widely used function of bioluminescence, providing a warning that the creature concerned is unpalatable. It is suggested that many firefly larvae glow to repel predators; millipedes glow for the same purpose.[47] Some marine organisms are believed to emit light for a similar reason. These include scale worms, jellyfish and brittle stars but further research is needed to fully establish the function of the luminescence. Such a mechanism would be of particular advantage to soft-bodied cnidarians if they were able to deter predation in this way.[29] The limpet Latia neritoides is the only known freshwater gastropod that emits light. It produces greenish luminescent mucus which may have an anti-predator function.[48] The marine snail Hinea brasiliana uses flashes of light, probably to deter predators. The blue-green light is emitted through the translucent shell, which functions as an efficient diffuser of light.[49]

Communication

Tunicate off Atauro island
Pyrosoma, a colonial tunicate; each individual zooid in the colony flashes a blue-green light.

Communication in the form of quorum sensing plays a role in the regulation of luminescence in many species of bacteria. Small extracellularly secreted molecules stimulate the bacteria to turn on genes for light production when cell density, measured by concentration of the secreted molecules, is high.[29]

Pyrosomes are colonial tunicates and each zooid has a pair of luminescent organs on either side of the inlet siphon. When stimulated by light, these turn on and off, causing rhythmic flashing. No neural pathway runs between the zooids, but each responds to the light produced by other individuals, and even to light from other nearby colonies.[50] Communication by light emission between the zooids enables coordination of colony effort, for example in swimming where each zooid provides part of the propulsive force.[51]

Some bioluminous bacteria infect nematodes that parasitize Lepidoptera larvae. When these caterpillars die, their luminosity may attract predators to the dead insect thus assisting in the dispersal of both bacteria and nematodes.[37] A similar reason may account for the many species of fungi that emit light. Species in the genera Armillaria, Mycena, Omphalotus, Panellus, Pleurotus and others do this, emitting usually greenish light from the mycelium, cap and gills. This may attract night-flying insects and aid in spore dispersal, but other functions may also be involved.[37]

Quantula striata is the only known bioluminescent terrestrial mollusc. Pulses of light are emitted from a gland near the front of the foot and may have a communicative function, although the adaptive significance is not fully understood.[52]

Mimicry

Bioluminescence is used by a variety of animals to mimic other species. Many species of deep sea fish such as the anglerfish and dragonfish make use of aggressive mimicry to attract prey. They have an appendage on their heads called an esca that contains bioluminescent bacteria able to produce a long-lasting glow which the fish can control. The glowing esca is dangled or waved about to lure small animals to within striking distance of the fish.[29][53]

The cookiecutter shark uses bioluminescence to camouflage its underside by counterillumination, but a small patch near its pectoral fins remains dark, appearing as a small fish to large predatory fish like tuna and mackerel swimming beneath it. When such fish approach the lure, they are bitten by the shark.[54][55]

Female Photuris fireflies sometimes mimic the light pattern of another firefly, Photinus, to attract its males as prey. In this way they obtain both food and the defensive chemicals named lucibufagins, which Photuris cannot synthesize.[56]

South American giant cockroaches of the genus Lucihormetica were believed to be the first known example of defensive mimicry, emitting light in imitation of bioluminescent, poisonous click beetles.[57] However, doubt has been cast on this assertion, and there is no conclusive evidence that the cockroaches are bioluminescent.[58][59]

Malacosteus niger cam
Flashing of photophores of black dragonfish, Malacosteus niger, showing red fluorescence

Illumination

While most marine bioluminescence is green to blue, some deep sea barbeled dragonfishes in the genera Aristostomias, Pachystomias and Malacosteus emit a red glow. This adaptation allows the fish to see red-pigmented prey, which are normally invisible in the deep ocean environment where red light has been filtered out by the water column.[60]

The black dragonfish (also called the northern stoplight loosejaw) Malacosteus niger is believed to be one of the only fish to produce a red glow. Its eyes, however, are insensitive to this wavelength; it has an additional retinal pigment which fluoresces blue-green when illuminated. This alerts the fish to the presence of its prey. The additional pigment is thought to be assimilated from chlorophyll derivatives found in the copepods which form part of its diet.[61]

Biotechnology

Biology and medicine

Bioluminescent organisms are a target for many areas of research. Luciferase systems are widely used in genetic engineering as reporter genes, each producing a different colour by fluorescence,[62][63] and for biomedical research using bioluminescence imaging.[64][65][66] For example, the firefly luciferase gene was used as early as 1986 for research using transgenic tobacco plants.[67] Vibrio bacteria symbiose with marine invertebrates such as the Hawaiian bobtail squid (Euprymna scolopes), are key experimental models for bioluminescence.[68][69] Bioluminescent activated destruction is an experimental cancer treatment.[70] See also optogenetics which involves the use of light to control cells in living tissue, typically neurons, that have been genetically modified to express light-sensitive ion channels, and also see biophoton, a photon of non-thermal origin in the visible and ultraviolet spectrum emitted from a biological system.

Light production

The structures of photophores, the light producing organs in bioluminescent organisms, are being investigated by industrial designers. Engineered bioluminescence could perhaps one day be used to reduce the need for street lighting, or for decorative purposes if it becomes possible to produce light that is both bright enough and can be sustained for long periods at a workable price.[11][71][72] The gene that makes the tails of fireflies glow has been added to mustard plants. The plants glow faintly for an hour when touched, but a sensitive camera is needed to see the glow.[73] University of Wisconsin–Madison is researching the use of genetically engineered bioluminescent E. coli bacteria, for use as bioluminescent bacteria in a light bulb.[74] In 2011, Philips launched a microbial system for ambience lighting in the home.[75][76] An iGEM team from Cambridge (England) has started to address the problem that luciferin is consumed in the light-producing reaction by developing a genetic biotechnology part that codes for a luciferin regenerating enzyme from the North American firefly; this enzyme "helps to strengthen and sustain light output".[77] In 2016, Glowee, a French company started selling bioluminescent lights, targeting shop fronts and municipal street signs as their main markets.[78] France has a law that forbids retailers and offices from illuminating their windows between 1 and 7 in the morning in order to minimise energy consumption and pollution.[79][80] Glowee hoped their product would get around this ban. They used bacteria called Aliivibrio fischeri which glow in the dark, but the maximum lifetime of their product was three days.[78]

See also

Notes

  1. ^ However, the name 'phosphorus', as used in the 17th century, did not necessarily mean the modern element; any substance that glowed by itself could be given this name, meaning "light bearer".[14]

References

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Further reading

  • Victor Benno Meyer-Rochow (2009) Bioluminescence in Focus – a collection of illuminating essays Research Signpost: ISBN 978-81-308-0357-9
  • Shimomura, Osamu (2006). Bioluminescence: Chemical Principles and Methods. Word Scientific Publishing. ISBN 981-256-801-8.
  • Lee, John (2016). "Bioluminescence, the Nature of the Light." The University of Georgia Libraries. http://hdl.handle.net/10724/20031
  • Wilson, T.; Hastings, J.W. (1998). "Bioluminescence". Annual Review of Cell and Developmental Biology. 14: 197–230. doi:10.1146/annurev.cellbio.14.1.197. PMID 9891783.
  • Anctil, Michel (2018). Luminous Creatures: The History and Science of Light Production in Living Organisms. McGill-Queen's University Press. ISBN 978-0-7735-5312-5

External links

Counter-illumination

Counter-illumination is a method of active camouflage seen in marine animals such as firefly squid and midshipman fish, and in military prototypes, producing light to match their backgrounds in both brightness and wavelength.

Marine animals of the mesopelagic (mid-water) zone tend to appear dark against the bright water surface when seen from below. They can camouflage themselves, often from predators but also from their prey, by producing light with bioluminescence photophores on their downward-facing surfaces, reducing the contrast of their silhouettes against the background. The light may be produced by the animals themselves, or by symbiotic bacteria, often Aliivibrio fischeri. Counter-illumination differs from countershading, which uses only pigments such as melanin to reduce the appearance of shadows. It is one of the dominant types of aquatic camouflage, along with transparency and silvering. All three methods make animals in open water resemble their environment.

Counter-illumination has not so far come into widespread military use, but during the Second World War it was trialled in ships in the Canadian Diffused lighting camouflage project, and in aircraft in the American Yehudi lights project.

Deep sea creature

The term deep sea creature refers to organisms that live below the photic zone of the ocean. These creatures must survive in extremely harsh conditions, such as hundreds of bars of pressure, small amounts of oxygen, very little food, no sunlight, and constant, extreme cold. Most creatures have to depend on food floating down from above.

These creatures live in very demanding environments, such as the abyssal or hadal zones, which, being thousands of meters below the surface, are almost completely devoid of light. The water is between 3 and 10 degrees Celsius and has low oxygen levels. Due to the depth, the pressure is between 20 and 1,000 bars. Creatures that live hundreds or even thousands of meters deep in the ocean have adapted to the high pressure, lack of light, and other factors.

Dinoflagellate

The dinoflagellates (Greek δῖνος dinos "whirling" and Latin flagellum "whip, scourge") are a classification subgroup of algae. They are a large group of flagellate eukaryotes that constitute the phylum Dinoflagellata. Most are marine plankton, but they also are common in freshwater habitats. Their populations are distributed depending on sea surface temperature, salinity, or depth. Many dinoflagellates are known to be photosynthetic, but a large fraction of these are in fact mixotrophic, combining photosynthesis with ingestion of prey (phagotrophy). In terms of number of species, dinoflagellates are one of the largest groups of marine eukaryotes, although this group is substantially smaller than diatoms. Some species are endosymbionts of marine animals and play an important part in the biology of coral reefs. Other dinoflagellates are unpigmented predators on other protozoa, and a few forms are parasitic (for example, Oodinium and Pfiesteria). Some dinoflagellates produce resting stages, called dinoflagellate cysts or dinocysts, as part of their lifecycles.

Dinoflagellates are considered to be protists, with their own division, Dinoflagellata.About 1,555 species of free-living marine dinoflagellates are currently described. Another estimate suggests about 2,000 living species, of which more than 1,700 are marine (free-living, as well as benthic) and about 220 are from fresh water. The latest estimates suggest a total of 2,294 living dinoflagellate species, which includes marine, freshwater, and parasitic dinoflagellates.A bloom of certain dinoflagellates can result in a visible coloration of the water colloquially known as red tide, which can cause shellfish poisoning if humans eat contaminated shellfish. Some dinoflagellates also exhibit bioluminescence—primarily emitting blue-green light.

Firefly

The Lampyridae are a family of insects in the beetle order Coleoptera. They are winged soft-bodied beetles, commonly called fireflies or lightning bugs for their conspicuous use of bioluminescence during twilight to attract mates or prey. Fireflies produce a "cold light", with no infrared or ultraviolet frequencies. This chemically produced light from the lower abdomen may be yellow, green, or pale red, with wavelengths from 510 to 670 nanometers. Some species such as the dimly glowing "blue ghost" of the Eastern US are commonly thought to emit blue light (<490 nanometers), however this is a false perception of their truly green emission light due to the Purkinje effect.About 2,100 species of fireflies are found in temperate and tropical climates. Many are in marshes or in wet, wooded areas where their larvae have abundant sources of food. Some species are called "glowworms" in Eurasia and elsewhere. The form of the insect which emits light varies from species to species. Sometimes it is the larvae which emit light, sometimes a larviform female, sometimes the eggs emit light. (In the glow worm found in the UK, Lampyris noctiluca, it is the female that is most easily noticed.) In the Americas, "glow worm" also refers to the related Phengodidae. In New Zealand and Australia the term "glow worm" is in use for the luminescent larvae of the fungus gnat Arachnocampa. In many species of fireflies, both male and female fireflies have the ability to fly, but in some species, the females are flightless.

Foxfire

Foxfire, also called fairy fire or chimpanzee fire, is the bioluminescence created by some species of fungi present in decaying wood. The bluish-green glow is attributed to a luciferase, an oxidative enzyme, which emits light as it reacts with a luciferin. The phenomenon has been known since ancient times, with its source determined in 1823.

Gippsland Lakes

The Gippsland Lakes are a network of lakes, marshes and lagoons in east Gippsland, Victoria, Australia covering an area of about 354 square kilometres (137 sq mi). The largest of the lakes are Lake Wellington (Gunai language: Murla), Lake King and Lake Victoria. The lakes are collectively fed by the Avon, Thomson, Latrobe, Mitchell, Nicholson and Tambo rivers.

Glowworm

Glowworm or glow-worm is the common name for various groups of insect larvae and adult larviform females that glow through bioluminescence. They include members of the families Elateridae, Lampyridae, Phengodidae, and Rhagophthalmidae among beetles; as well as members of the genera Arachnocampa, Keroplatus, and Orfelia among keroplatid fungus gnats.

List of bioluminescent fungus species

Found largely in temperate and tropical climates, currently there are known more than 75 species of bioluminescent fungi, all of which are members of the order Agaricales (Basidiomycota) with one exceptional ascomycete belonging to the order Xylariales. All known bioluminescent Agaricales are mushroom-forming, white-spored agarics that belong to four distinct evolutionary lineages. The Omphalotus lineage (comprising the genera Omphalotus and Neonothopanus) contains 12 species, the Armillaria lineage has 10 known species, while the Mycenoid lineage (Mycena, Panellus, Prunulus, Roridomyces) has more than 50 species. The recently discovered Lucentipes lineage contains two species, Mycena lucentipes and Gerronema viridilucens, which belong to a family that has not yet been formally named. Armillaria mellea is the most widely distributed of the luminescent fungi, found across Asia, Europe, North America, and South Africa.Bioluminescent fungi emit a greenish light at a wavelength of 520–530 nm. The light emission is continuous and occurs only in living cells. No correlation of fungal bioluminescence with cell structure has been found. Bioluminescence may occur in both mycelia and fruit bodies, as in Panellus stipticus and Omphalotus olearius, or only in mycelia and young rhizomorphs, as in Armillaria mellea. In Roridomyces roridus luminescence occurs only in the spores, while in Collybia tuberosa, it is only in the sclerotia.Although the biochemistry of fungal bioluminescence has not fully been characterized, the preparation of bioluminescent, cell-free extracts has allowed researchers to characterize the in vitro requirements of fungal bioluminescence. Experimental data suggest that a two-stage mechanism is required. In the first, a light-emitting substance (called "luciferin") is reduced by a soluble reductase enzyme at the expense of NAD(P)H. In the second stage, reduced luciferin is oxidized by an insoluble luciferase that releases the energy in the form of bluish-green light. Conditions that affect the growth of fungi, such as pH, light and temperature, have been found to influence bioluminescence, suggesting a link between metabolic activity and fungal bioluminescence.All bioluminescent fungi share the same enzymatic mechanism, suggesting that there is a bioluminescent pathway that arose early in the evolution of the mushroom-forming Agaricales. All known luminescent species are white rot fungi capable of breaking down lignin, found in abundance in wood. Bioluminescence is an oxygen-dependent metabolic process because it provides antioxidant protection against the potentially damaging effects of reactive oxygen species produced during wood decay. The physiological and ecological function of fungal bioluminescence has not been established with certainty. It has been suggested that in the dark beneath closed tropical forest canopies, bioluminescent fruit bodies may be at an advantage by attracting grazing animals (including insects and other arthropods) that could help disperse their spores. Conversely, where mycelium (and vegetative structures like rhizomorphs and sclerotia) are the bioluminescent tissues, the argument has been made that light emission could deter grazing.The following list of bioluminescent mushrooms is based on a 2008 literature survey by Dennis Desjardin and colleagues, in addition to accounts of several new species published since then.

List of light sources

This is a list of sources of light, including both natural and artificial processes that emit light. This article focuses on sources that produce wavelengths from about 390 to 700 nanometers, called visible light.

Luciferase

Luciferase is a generic term for the class of oxidative enzymes that produce bioluminescence, and is usually distinguished from a photoprotein. The name was first used by Raphaël Dubois who invented the words luciferin and luciferase, for the substrate and enzyme, respectively. Both words are derived from the Latin word lucifer – meaning lightbringer.

Luciferases are widely used in biotechnology, for microscopy and as reporter genes, for many of the same applications as fluorescent proteins. However, unlike fluorescent proteins, luciferases do not require an external light source, but do require addition of luciferin, the consumable substrate.

Luciferin

Luciferin (from the Latin lucifer, "light-bringer") is a generic term for the light-emitting compound found in organisms that generate bioluminescence. Luciferins typically undergo an enzyme-catalysed oxidation and the resulting excited state intermediate emits light upon decaying to its ground state. This may refer to molecules that are substrates for both luciferases and photoproteins.

Milky seas effect

Milky seas, also called mareel, is a luminous phenomenon in the ocean in which large areas of seawater (up to 6,000 sq mi or 16,000 km2) appear to glow brightly enough at night to be seen by satellites orbiting Earth. Modern science only tentatively attributes this effect to bioluminescent bacteria or dinoflagellates, causing the sea to uniformly display an eerie blue glow at night. However, no modern research proves that bioluminescent bacteria are capable of illuminating the ocean from horizon to horizon and for days at a time, as described in mariners' tales for centuries (notably appearing in chapter 23 of Jules Verne's Twenty Thousand Leagues Under the Sea). In fact, the effect has not been rigorously documented nor thoroughly explained, even in modern times.

Mycetophilidae

The Mycetophilidae are a family of small flies, forming the bulk of those species known as fungus gnats. About 3000 described species are placed in 150 genera, but the true number of species is undoubtedly much higher. They are generally found in the damp habitats favoured by their host fungi and sometimes form dense swarms.Adults of this family can usually be separated from other small flies by the strongly humped thorax, well-developed coxae, and often spinose legs, but identification within the family between genera and species generally requires close study of microscopic features such as subtle differences in wing venation and variation in chaetotaxy and genitalia. The terrestrial larvae usually feed on fungi, especially the fruiting bodies, but also spores and hyphae, but some species have been recorded on mosses and liverworts. The larvae of some species, while still being associated with fungi, are at least partly predatory.

Noctiluca scintillans

Noctiluca scintillans, commonly known as the sea sparkle, and also published as Noctiluca miliaris, is a free-living, marine-dwelling species of dinoflagellate that exhibits bioluminescence when disturbed (popularly known as mareel). Its bioluminescence is produced throughout the cytoplasm of this single-celled protist, by a luciferin-luciferase reaction in thousands of spherically shaped organelles, called scintillons.

Photophore

A photophore is a glandular organ that appears as luminous spots on various marine animals, including fish and cephalopods. The organ can be simple, or as complex as the human eye; equipped with lenses, shutters, color filters and reflectors. The bioluminescence can variously be produced from compounds during the digestion of prey, from specialized mitochondrial cells in the organism, called photocytes ("light producing" cells), or, similarly, associated with symbiotic bacteria in the organism that is cultured.

The character of photophores is important in the identification of deep sea fishes. Photophores on fish are used for attracting food or for camouflage from predators by counter-illumination.

Photophores are found on some cephalopods, including firefly squid, the sparkling enope or firefly squid, which can create impressive light displays.

Ruakuri Cave

Ruakuri Cave is the longest cave in the Waitomo area of New Zealand. It was first discovered by local Māori between 400 and 500 years ago. The name Ruakuri, or "den of dogs" was created when wild dogs were discovered making their home in the cave entrance some 300 years later. The cave entrance was used by the Maori as an urupa or burial site. It is this sacred area that has now been protected with the construction of the impressive spiral drum entrance some distance away.

Ruakuri is the only wheelchair-accessible cave in the Southern Hemisphere. It is well known for its spiritual links to Māori and its unusual limestone formations and caverns.Major features of the Ruakuri Cave include Holdens Cavern (named after James Holden who first opened the cave to the public), The Drum Passage, The Pretties and The Ghost Passage.

The cave was open to the public from 1904 until 1988, when it was closed due to a legal and financial dispute. It was reopened in 2005.Inside there is a dynamic natural environment, with glowworms, limestone formations, underground rivers, and hidden waterfalls.

Squaliformes

The Squaliformes are an order of sharks that includes about 126 species in seven families.

Members of the order have two dorsal fins, which usually possess spines,they usually have a sharp head, no anal fin or nictitating membrane, and five to seven gill slits. In most other respects, however, they are quite variable in form and size. Most species of the squaliform order live in a saltwater or brackish waters, They are found worldwide, from northern to tropical waters, and from shallow coastal seas to the open ocean.All members of the family Eptomeridae and Dalatiidae and Zameus squamulosus possess photophores, luminous organs, and exhibit intrinsic bioluminescence . Bioluminescence evolved once in Squaliformes, approximately 111-153 million years ago, and helped the Squaliformes radiate and adapt to the deep sea. The common ancestor of Dalatiidae, Etmopteridae, Somniosidae, and Oxynotidae possessed a luminous organ and used bioluminescence for camouflage by counterillumination . Counterillumination is an active form of camouflage in which an organism emits light to match the intensity of downwelling light to hide from predators below. Currently, bioluminescence provides different functions for Squaliformes based on the family. Dalatiidae and Zameus squamulosus possess simple photophores and use bioluminescence for ventral counter-illumination. Etmopteridae possess more complex photophores and utilize bioluminescence for ventral counter illumination as well as species recognition .

Tomales Bay

Tomales Bay is a long, narrow inlet of the Pacific Ocean in Marin County in northern California in the United States. It is approximately 15 miles (25 km) long and averages nearly 1.0 miles (1.6 km) wide, effectively separating the Point Reyes Peninsula from the mainland of Marin County. It is located approximately 30 miles (48 km) northwest of San Francisco. The bay forms the eastern boundary of Point Reyes National Seashore. Tomales Bay is recognized for protection by the California Bays and Estuaries Policy. On its northern end it opens out onto Bodega Bay, which shelters it from the direct current of the Pacific. The bay is formed along a submerged portion of the San Andreas Fault.

Oyster farming is a major industry on the bay. The two largest producers are Tomales Bay Oyster Company and Hog Island Oyster Company, both of which retail oysters to the public and have picnic grounds on the east shore. Hillsides east of Tomales Bay are grazed by cows belonging to local dairies. There is also grazing land west of the bay, on farms and ranches leased from Point Reyes National Seashore.

The bay sees significant amounts of water sports including sailing, kayaking, fishing and motor boating. Watercraft may be launched on Tomales Bay from the public boat ramp at Nick's Cove, north of Marshall. There is a $5 fee. The sand bar at the mouth of Tomales Bay is notoriously dangerous, with a long history of small-boat accidents.

The California Office of Environmental Health Hazard Assessment (OEHHA) has developed a safe eating advisory for fish caught here, based on levels of mercury or PCBs found in local species.Of special interest is the bioluminescence that can be seen from June to November.Towns bordering Tomales Bay include Inverness, Inverness Park, Point Reyes Station, and Marshall. Additional hamlets include Nick's Cove, Spengers, Duck Cove, Shallow Beach, and Vilicichs. Dillon Beach lies just to the north of the mouth of the bay, and Tomales just to the east.

Torrey Pines State Beach

Torrey Pines State Beach is a coastal beach located in the San Diego, California community of Torrey Pines, and is located south of Del Mar and north of La Jolla. Coastal erosion from the adjacent Torrey Pines State Reserve makes for a picturesque landscape. It is a local favorite among surfers and remains a quintessential Southern California beach. Occurrences of bioluminescence have been noted.The beach is at the bottom of 300 foot sandstone cliffs of white and golden stone, with a greenish layer sometimes visible at the very bottom. At the north end of the beach the cliffs ends and Los Peñasquitos Lagoon, a salt marsh estuary, empties into the ocean. A county highway crosses the entrance, with limited free parking along the beach.

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