Bioluminescence in the context of Deep sea fish

The aphotic zone (aphotic from Greek prefix ἀ- + φῶς "without light") is the portion of a lake or ocean where there is little or no sunlight. It is formally defined as the depths beyond which less than 1 percent of sunlight penetrates. Above the aphotic zone is the photic zone, which consists of the euphotic zone and the disphotic zone. The euphotic zone is the layer of water in which there is enough light for net photosynthesis to occur. The disphotic zone, also known as the twilight zone, is the layer of water with enough light for predators to see but not enough for the rate of photosynthesis to be greater than the rate of respiration.

The depth at which less than one percent of sunlight reaches begins the aphotic zone. While most of the ocean's biomass lives in the photic zone, the majority of the ocean's water lies in the aphotic zone. Bioluminescence is more abundant than sunlight in this zone. Most food in this zone comes from dead organisms sinking to the bottom of the lake or ocean from overlying waters.

Camouflage is the use of any combination of materials, coloration, or illumination for concealment, either by making animals or objects hard to see, or by disguising them as something else. Examples include the leopard's spotted coat, the battledress of a modern soldier, and the leaf-mimic katydid's wings. A third approach, motion dazzle, confuses the observer with a conspicuous pattern, making the object visible but momentarily harder to locate. The majority of camouflage methods aim for crypsis, often through a general resemblance to the background, high contrast disruptive coloration, eliminating shadow, and countershading. In the open ocean, where there is no background, the principal methods of camouflage are transparency, silvering, and countershading, while the ability to produce light is among other things used for counter-illumination on the undersides of cephalopods such as squid. Some animals, such as chameleons and octopuses, are capable of actively changing their skin pattern and colours, whether for camouflage or for signalling. It is possible that some plants use camouflage to evade being eaten by herbivores.

Military camouflage was spurred by the increasing range and accuracy of firearms in the 19th century. In particular the replacement of the inaccurate musket with the rifle made personal concealment in battle a survival skill. In the 20th century, military camouflage developed rapidly, especially during the World War I. On land, artists such as André Mare designed camouflage schemes and observation posts disguised as trees. At sea, merchant ships and troop carriers were painted in dazzle patterns that were highly visible, but designed to confuse enemy submarines as to the target's speed, range, and heading. During and after World War II, a variety of camouflage schemes were used for aircraft and for ground vehicles in different theatres of war. The use of radar since the mid-20th century has largely made camouflage for fixed-wing military aircraft obsolete.

Holoplankton are organisms that are planktic (they live in the water column and cannot swim against a current) for their entire life cycle. Holoplankton can be contrasted with meroplankton, which are planktic organisms that spend part of their life cycle in the benthic zone. Examples of holoplankton include some diatoms, radiolarians, some dinoflagellates, foraminifera, amphipods, krill, copepods, and salps, as well as some gastropod mollusk species. Holoplankton dwell in the pelagic zone as opposed to the benthic zone. Holoplankton include both phytoplankton and zooplankton and vary in size. The most common plankton are protists.

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 bioluminescent 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.

Active camouflage, adaptive camouflage, or chameleonizing is camouflage that adapts, often rapidly, to the surroundings of an object such as an animal or military vehicle. In theory, active camouflage could provide perfect concealment from visual detection.

Active camouflage occurs in several groups of animals, including reptiles on land, and cephalopod molluscs and flatfish in the sea. Animals achieve active camouflage both by color change and (among marine animals such as squid) by counter-illumination, with the use of bioluminescence.

Armillaria mellea, commonly known as honey fungus, is an edible basidiomycete fungus in the genus Armillaria. It is a plant pathogen and part of a cryptic species complex of closely related and morphologically similar species. It causes Armillaria root rot in many plant species and produces mushrooms around the base of trees it has infected. The symptoms of infection appear in the crowns of infected trees as discoloured foliage, reduced growth, dieback of the branches and death. The mycelium is capable of producing light via bioluminescence.

The mushroom is widely distributed in temperate regions of the Northern Hemisphere. It typically grows on hardwoods but may be found around and on other living and dead wood or in open areas.

Aggressive mimicry is a form of mimicry in which predators, parasites, or parasitoids share similar signals, using a harmless model, allowing them to avoid being correctly identified by their prey or host. Zoologists have repeatedly compared this strategy to a wolf in sheep's clothing. In its broadest sense, aggressive mimicry could include various types of exploitation, as when an orchid exploits a male insect by mimicking a sexually receptive female (see pseudocopulation), but will here be restricted to forms of exploitation involving feeding. For example, indigenous Australians who dress up as and imitate kangaroos when hunting would not be considered aggressive mimics, nor would a human angler, though they are undoubtedly practising self-decoration camouflage. Treated separately is molecular mimicry, which shares some similarity; for instance a virus may mimic the molecular properties of its host, allowing it access to its cells. An alternative term, Peckhamian mimicry, has been suggested (after George and Elizabeth Peckham), but it is seldom used.

Aggressive mimicry is opposite in principle to defensive mimicry, where the mimic generally benefits from being treated as harmful. The mimic may resemble its own prey, or some other organism which is beneficial or at least not harmful to the prey. The model, i.e. the organism being 'imitated', may experience increased or reduced fitness, or may not be affected at all by the relationship. On the other hand, the signal receiver inevitably suffers from being tricked, as is the case in most mimicry complexes.

Armillaria is a genus of fungi that includes the A. mellea species ('honey fungus') that live on trees and woody shrubs. It includes about 10 species formerly categorized summarily as A. mellea. Armillaria sp. are long-lived and form the largest living fungi in the world. The largest known specimen (an A. ostoyae) covers more than 3.4 square miles (8.8 km) in Oregon and is estimated to be 2,500 years old. Some species of Armillaria display bioluminescence.

Armillaria can be a destructive forest pathogen. It causes "white rot" root disease. As it feeds on dead plant material, it can kill its host with little negative effect to itself.

Chemiluminescence (also chemoluminescence) is the emission of light (luminescence) as the result of a chemical reaction, i.e. a chemical reaction results in a flash or glow of light. A standard example of chemiluminescence in the laboratory setting is the luminol test. Here, blood is indicated by luminescence upon contact with iron in hemoglobin. When chemiluminescence takes place in living organisms, the phenomenon is called bioluminescence. A light stick emits light by chemiluminescence.

Malacology, from Ancient Greek μαλακός (malakós), meaning "soft", and λόγος (lógos), meaning "study", is the branch of invertebrate zoology that deals with the study of the Mollusca (molluscs or mollusks), the second-largest phylum of animals in terms of described species after the arthropods. Mollusks include snails and slugs, clams, and cephalopods, along with numerous other kinds, many of which have shells.

Fields within malacological research include studies of mollusk taxonomy, ecology and evolution. Several subdivisions of malacology exist, including conchology, devoted to the study of mollusk shells, limacology, the study of gastropods, and teuthology, the study of cephalopods such as octopus, squid, and cuttlefish. Applied malacology studies medical, veterinary, and agricultural applications, for example the study of mollusks as vectors of schistosomiasis and other diseases.

Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota (synonym Proteobacteria). It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically important groups of bacteria belong to this class. All members of this class are Gram-negative. It is the most phylogenetically and physiologically diverse class of the Pseudomonadota.

Members of Gammaproteobacteria live in several terrestrial and marine environments, in which they play various important roles, including in extreme environments such as hydrothermal vents. They can have different shapes, rods, curved rods, cocci, spirilla, and filaments, and include free living bacteria, biofilm formers, commensals and symbionts; some also have the distinctive trait of being bioluminescent. Diverse metabolisms are found in Gammaproteobacteria; there are both aerobic and anaerobic (obligate or facultative) species, chemolithoautotrophics, chemoorganotrophics, photoautotrophs and heterotrophs.

Las Cabezas de San Juan (Spanish for 'the San Juan capes' or 'headlands'), officially Cabo San Juan (Cape San Juan in English), is a coastal area and nature reserve located in the northeastern corner of the main island of Puerto Rico, particularly in the Cabezas barrio of the municipality of Fajardo. The reserve is famous for its biodiversity, with its bioluminescent lagoon (Laguna Grande, one of the three year-round bioluminescent bodies of water in the territory and one of seven in the Caribbean), its coral reefs, and its subtropical dry and mangrove forests, and for its history, particularly for its lighthouse and its role during the Puerto Rico campaign of the Spanish–American War.

Bioluminescent bacteria are light-producing bacteria that are predominantly present in sea water, marine sediments, the surface of decomposing fish and in the gut of marine animals. While not as common, bacterial bioluminescence is also found in terrestrial and freshwater bacteria. Bioluminescent bacteria may be free-living (such as Vibrio harveyi) or in symbiosis with animals such as the Hawaiian Bobtail squid (Aliivibrio fischeri) or terrestrial nematodes (Photorhabdus luminescens). The host organisms provide bioluminescent bacteria a safe home and sufficient nutrition. In exchange, the hosts use the light produced by the bacteria for camouflage, prey and/or mate attraction. Bioluminescent bacteria have evolved symbiotic relationships with other organisms in which both participants benefit each other equally. Bacteria also use luminescence reaction for quorum sensing, an ability to regulate gene expression in response to bacterial cell density.

Cyclothone is a genus containing 13 extant species of bioluminescent fish, commonly known as 'bristlemouths' or 'bristlefishes' due to their shared characteristic of sharp, bristle-like teeth. These fishes typically grow to around 1–3 inches (25–76 mm), though some can be larger. These deep-sea fish are most commonly found in the mesopelagic zone of the ocean, mostly at depths of over 300 meters (1,000 feet), and many species have bioluminescence.

Cyclothone is believed to be the most abundant fish genus on Earth, with estimates that there are up to a quadrillion individuals (10, or one million billion in the short scale) within the current global population. They are so abundant that they are also believed to be the most abundant genus of vertebrate on earth.

The veiled anglemouth, Cyclothone microdon, is a bristlemouth of the family Gonostomatidae, abundant in all the world's oceans at depths of 300–2,500 meters (980–8,200 feet). Its length is 10–15 cm (4–6 in) though the largest known specimen is 7.6 cm (3.0 in). It gets its name from its circular mouth, filled with small teeth: the name "cyclothone" means in a circle or around and "microdon" means small teeth. The International Union for Conservation of Nature (IUCN) has assessed the veiled anglemouth is of Least Concern due to its abundance in most oceans and the little effect human impact has on its population growth. Some of the veiled anglemouth's physical features include a brown to black body with a radiating, or expansive, bioluminescent pigment over its head and fins.

A photophore is a specialized anatomical structure found in a variety of organisms that emits light through the process of bioluminescence. This light may be produced endogenously by the organism itself (non-symbiotic) or generated through a mutualistic relationship with bioluminescent bacteria (symbiotic), resulting in light production on a glandular organ of animals. Light organs are most commonly found in marine animals, including many species of fish and cephalopods. The organ can be simple, or as complex as the human eye, equipped with lenses, shutters, color filters, and reflectors; unlike an eye, however, it is optimized to produce light, not absorb it.

In the context of developmental biology, light organs form through precise genetic regulation and, in some cases, microbial colonization during specific stages of an organism's life cycle. They play a crucial evolutionary role in enabling species to adapt to low-light or dark environments, particularly in the deep sea.

The Lampyridae are a family of elateroid beetles with more than 2,400 described species, many of which are light-emitting. They are soft-bodied beetles commonly called fireflies, lightning bugs, or glowworms for their conspicuous production of light, mainly during twilight, to attract mates. The type species is Lampyris noctiluca, the common glow-worm of Europe. Light production in the Lampyridae is thought to have originated as a warning signal that the larvae were distasteful. This ability to create light was then co-opted as a mating signal and, in a further development, adult female fireflies of the genus Photuris mimic the flash pattern of the Photinus beetle to trap their males as prey.

Fireflies are found in temperate and tropical climates. Many live in marshes or in wet, wooded areas where their larvae have abundant sources of food. Although all fireflies nominally glow as larvae, only some species produce light in their adult stage, and the location of the light organ varies among species and between sexes of the same species. Fireflies have attracted human attention since classical antiquity; their presence has been taken to signify a wide variety of conditions in different cultures and is especially appreciated aesthetically in Japan, where parks are set aside for this specific purpose.

Glowworm is any member of various groups of insect larvae and adult larviform females that glow through bioluminescence. They include the European common glow-worm and other members of the Lampyridae, but bioluminescence also occurs in the families Elateridae, Phengodidae and Rhagophthalmidae among beetles; as well as members of the genera Arachnocampa, Keroplatus and Orfelia among keroplatid fungus gnats.