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130-403: The bathypelagic zone is characterized by a nearly constant temperature of approximately 4 °C (39 °F) and a salinity range of 33-35 g/kg. This region has little to no light because sunlight does not reach this deep in the ocean and bioluminescence is limited. The hydrostatic pressure in this zone ranges from 100-400 atmospheres (atm) due to the increase of 1 atm for every 10 m depth. It

260-456: A black lining able to keep the light from any bioluminescent fish prey which they have swallowed from attracting larger predators. 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 army as

390-651: 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. Among the anecdotes of navigation by bioluminescence is one recounted by the Apollo 13 astronaut Jim Lovell , who as a Navy pilot had found his way back to his aircraft carrier USS Shangri-La when his navigation systems failed. Turning off his cabin lights, he saw

520-515: A buffering agent in maintaining acid base homeostasis in the human body. Phosphates move quickly through plants and animals; however, the processes that move them through the soil or ocean are very slow, making the phosphorus cycle overall one of the slowest biogeochemical cycles. The global phosphorus cycle includes four major processes: In terrestrial systems, bioavailable P (‘reactive P’) mainly comes from weathering of phosphorus-containing rocks. The most abundant primary phosphorus-mineral in

650-401: 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 30 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

780-550: A drastic shift in anoxic conditions seen in both the Gulf of Mexico and the Baltic Sea . Some research suggests that when anoxic conditions arise from eutrophication due to excess phosphorus, this creates a positive feedback loop that releases more phosphorus from oceanic reserves, exacerbating the issue. This could possibly create a self-sustaining cycle of oceanic anoxia where the constant recovery of phosphorus keeps stabilizing

910-542: A given area. Prokaryote abundance can range from 0.03-2.3x105 cells ml, and have population turnover times that can range from 0.1–30 years. Archaea make up a larger portion of the total prokaryote cell abundance, and different groups have different growth needs, with some archaea groups for example utilizing amino acid groups more readily than others. Some archaea like Crenarchaeota have Crenarchaeota 16S rRNA and archaeal amoA gene abundances correlated to dissolved inorganic carbon (DIC) fixation . The utilization of DIC

1040-433: 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. The cookiecutter shark uses bioluminescence to camouflage its underside by counter-illumination, 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

1170-403: A longer, red wavelength. The dragonfish species which produce the red light also produce blue light in photophore on the dorsal area. The main function of this is to alert 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. Phosphorus cycle The phosphorus cycle

1300-430: A major influx of phosphorus due to increased agricultural use and other industrial applications, thus these organisms could theoretically store phosphorus and hold on to it until it could be recycled in terrestrial ecosystems which would have lost this excess phosphorus due to runoff. Wetlands are frequently applied to solve the issue of eutrophication. Nitrate is transformed in wetlands to free nitrogen and discharged to

1430-405: A majority are found in symbiotic relationships that involve fish, squids, crustaceans etc. as hosts. Most luminous bacteria inhabit the sea, dominated by Photobacterium and Vibrio . In the symbiotic relationship, bacterium benefit from having a source of nourishment and a refuge to grow. Hosts obtain these bacterial symbionts either from the environment, spawning , or the luminous bacterium

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1560-485: 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. 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

1690-408: A sharp increase in phosphorus concentration in solution, and phosphorus can be leached. In addition, reducing the soil causes a shift in phosphorus from resilient to more labile forms. This could eventually increase the potential for phosphorus loss. This is of particular concern for the environmentally sound management of such areas, where disposal of agricultural wastes has already become a problem. It

1820-426: A source of light during clandestine operations. 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. They also have organs on the head which produce red light; they are the only terrestrial organisms to emit light of this color. Aposematism is a widely used function of bioluminescence, providing

1950-399: A very slow and gradual time scale. Since the 1840s, when the technology to mine and extract phosphorus became more prevalent, approximately 110 teragrams of phosphorus has been added to the environment. This trend appears to be continuing in the future as from 1900-2022, the amount of phosphorus mined globally has increased 72-fold, with an expected annual increase of 4%. Most of this mining

2080-542: A warning that the creature concerned is unpalatable. It is suggested that many firefly larvae glow to repel predators; some millipedes glow for the same purpose. 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. The limpet Latia neritoides

2210-457: Is a way to classify organisms that have common ancestry. Some important groups of bacterial grazers include Rhizaria , Alveolata , Fungi , Stramenopiles , Amoebozoa , and Excavata (listed from most to least abundant), with the remaining composition classified as uncertain or other. Viruses influence biogeochemical cycling through the role they play in marine food webs . Their overall abundance can be up to two orders of magnitude lower than

2340-453: Is also a process that delivers carbon to the bathypelagic zone, however, it constitutes a substantially smaller portion of overall transport than POC delivery. DOC transport occurs most readily in regions with high rates of ventilation or ocean turnover, such as the interior of gyres or deep water formation sites along the thermohaline circulation . The region in the water column at which calcite dissolution begins to occur rapidly, known as

2470-695: Is believed that these conditions have been consistent for the past 8000 years. This ocean depth spans from the edge of the continental shelf down to the top of the abyssal zone , and along continental slope depths. The bathymetry of the bathypelagic zone consists of limited areas where the seafloor is in this depth range along the deepest parts of the continental margins , as well as seamounts and mid-ocean ridges . The continental slopes are mostly made up of accumulated sediment, while seamounts and mid-ocean ridges contain large areas of hard substrate that provide habitats for bathypelagic fishes and benthic invertebrates. Although currents at these depths are very slow,

2600-452: Is defined as substances that pass through a 0.45 μm filter . DIP consists mainly of orthophosphate (PO 4 ) and polyphosphate, while DOP consists of DNA and phosphoproteins . Particulate matter are the substances that get caught on a 0.45 μm filter and do not pass through. POP consists of both living and dead organisms, while PIP mainly consists of hydroxyapatite , Ca 5 (PO 4 ) 3 OH . Inorganic phosphorus comes in

2730-471: Is done to produce fertilizers which can be used on a global scale. However, at the rate humans are mining, the geological system can not quickly restore what is lost. Thus, researchers are examining ways to better recycle phosphorus in the environment, with one promising application including the use of microorganisms. Regardless, humans have had a profound impact on the phosphorus cycle with wide-reaching implications about food security , eutrophication , and

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2860-416: Is evolving with their host. Coevolutionary interactions are suggested as host organisms' anatomical adaptations have become specific to only certain luminous bacteria, to suffice ecological dependence of bioluminescence. Bioluminescence is widely studied amongst species located in the mesopelagic zone, but the benthic zone at mesopelagic depths has remained widely unknown. Benthic habitats at depths beyond

2990-419: Is expelled, distracting or repelling a potential predator, while the animal escapes to safety. The deep sea squid Octopoteuthis deletron may autotomize portions of its arms which are luminous and continue to twitch and flash, thus distracting a predator while the animal flees. Dinoflagellates may use bioluminescence for defense against predators . They shine when they detect a predator, possibly making

3120-546: 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. The most frequently encountered bioluminescent organisms may be the dinoflagellates in the surface layers of the sea, which are responsible for the sparkling luminescence sometimes seen at night in disturbed water. At least 18 genera of these phytoplankton exhibit luminosity. Luminescent dinoflagellate ecosystems are present in warm water lagoons and bays with narrow openings to

3250-404: Is limited in supply for plant growth. Phosphates move quickly through plants and animals; however, the processes that move them through the soil or ocean are very slow, making the phosphorus cycle overall one of the slowest biogeochemical cycles. Low-molecular-weight (LMW) organic acids are found in soils. They originate from the activities of various microorganisms in soils or may be exuded from

3380-411: Is mainly derived from weathering of rocks containing phosphorus which are then transported to the oceans in a dissolved form by river runoff. Due to a dramatic rise in mining for phosphorus, it is estimated that humans have increased the net storage of phosphorus in soil and ocean systems by 75%. This increase in phosphorus has led to more eutrophication in ocean waters as phytoplankton blooms have caused

3510-549: Is needed to explore this question, and may require revisions to our understanding of the global carbon cycle . Organic material from primary production in the epipelagic zone , and to a far lesser extent, organic inputs from terrestrial sources, make up a majority of the Particulate Organic Matter (POM) in the ocean. POM is delivered to the bathypelagic zone via sinking copepod fecal pellets and dead organisms; these parcels of organic matter fall through

3640-425: Is no conclusive evidence that the cockroaches are bioluminescent. 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 to other organisms in the deep ocean environment where red light has been filtered out by

3770-421: Is only produced in isolated and specific conditions. Therefore, the phosphorus cycle is primarily examined studying the movement of orthophosphate (PO 4 ) , the form of phosphorus that is most commonly seen in the environment, through terrestrial and aquatic ecosystems. Living organisms require phosphorus , a vital component of DNA , RNA , ATP , etc., for their proper functioning. Phosphorus also enters in

3900-406: Is prevalent in the pelagic zone such as counter-illumination may not be functional or relevant in the benthic realm. Bioluminescence in bathyal benthic species still remains poorly studied due to difficulties of the collection of species at these depths. Bioluminescence has several functions in different taxa. Steven Haddock et al. (2010) list as more or less definite functions in marine organisms

4030-450: Is produced in the epipelagic zone , with a small portion transported deeper into the ocean interior. This process, known as the biological pump , plays a large role in the sequestration of carbon from the atmosphere into the ocean. Organic carbon is primarily exported to the bathypelagic zone in the form of particulate organic carbon (POC) and dissolved organic carbon (DOC). POC is the largest component of organic carbon delivered to

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4160-582: Is regenerated from the oxidized (oxyluciferin) form, allowing it to recombine with aequorin, in preparation for a subsequent flash. Photoproteins are thus enzymes , but with unusual reaction kinetics. 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 . Overall, bioluminescence has arisen over 40 times in evolutionary history. In evolution , luciferins tend to vary little: one in particular, coelenterazine ,

4290-439: Is restricted by its rate of release during weathering. The release of phosphorus from apatite dissolution is a key control on ecosystem productivity. The primary mineral with significant phosphorus content, apatite [Ca 5 (PO 4 ) 3 OH] undergoes carbonation . Little of this released phosphorus is taken up by biota, as it mainly reacts with other soil minerals. This leads to phosphorus becoming unavailable to organisms in

4420-406: Is slowly lost in runoff . Low concentration of phosphorus in soils reduces plant growth and slows soil microbial growth, as shown in studies of soil microbial biomass . Soil microorganisms act as both sinks and sources of available phosphorus in the biogeochemical cycle. Short-term transformation of phosphorus is chemical, biological, or microbiological. In the long-term global cycle, however,

4550-518: Is that bioluminescence has evolved independently at least 40 times. 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, 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

4680-399: Is the biogeochemical cycle that involves the movement of phosphorus through the lithosphere , hydrosphere , and biosphere . Unlike many other biogeochemical cycles, the atmosphere does not play a significant role in the movement of phosphorus, because phosphorus and phosphorus-based materials do not enter the gaseous phase readily, as the main source of gaseous phosphorus, phosphine ,

4810-544: 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 synthesise coelenterazine: some of them obtain it through their diet. Conversely, luciferase enzymes vary widely and tend to be different in each species. Bioluminescence occurs widely among animals, especially in

4940-534: Is the only known bioluminescent terrestrial mollusk. 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. 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

5070-401: Is the only known freshwater gastropod that emits light. It produces greenish luminescent mucus which may have an anti-predator function. 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. Communication in the form of quorum sensing plays

5200-456: Is thought to be fueled by the oxidation of ammonium and is one form of chemoautotrophy. Based on regional variation and differences in prokaryote abundance, heterotrophic prokaryote production, and particulate organic carbon (POC) inputs to the bathypelagic zone. Research to quantify bacterial-consuming grazers, like heterotrophic eukaryotes , has been limited by difficulties in sampling. Oftentimes organisms do not survive being brought to

5330-420: Is used for camouflage by counterillumination , in which the animal matches the overhead environmental light as seen from below. In these animals, photoreceptors control the illumination to match the brightness of the background. 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

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5460-483: Is usually viewed as the most important process in controlling terrestrial P-bioavailability in the mineral soil. This process can lead to the low level of dissolved phosphorus concentrations in soil solution. Various physiological strategies are used by plants and microorganisms for obtaining phosphorus from this low level of phosphorus concentration. Soil phosphorus is usually transported to rivers and lakes and can then either be buried in lake sediments or transported to

5590-489: The diel vertical migration of mesopelagic species in that it is not driven by sunlight. Instead, the migration of bathypelagic organisms is driven by other factors, most of which remain unknown. Some research suggests the movement of species within the overlying pelagic region could prompt individual bathypelagic species to migrate, such as Sthenoteuthis sp. , a species of squid . In this particular example, Sthenoteuthis sp. appears to migrate individually over

5720-404: The firefly luciferase . Generically, this reaction can be described as: Instead of a luciferase, the jellyfish Aequorea victoria makes use of another type of protein called a photoprotein , in this case specifically aequorin . When calcium ions are added, rapid catalysis creates a brief flash quite unlike the prolonged glow produced by luciferase. In a second, much slower step, luciferin

5850-473: The lysocline , is typically located near the base bathypelagic zone at approximately 3,500 m depth, but varies among ocean basins. The lysocline lies below the saturation depth (the transition to undersaturated conditions with respect to calcium carbonate ) and above the carbonate compensation depth (below which there is no calcium carbonate preservation). In a supersaturated environment, the tests of calcite-forming organisms are preserved as they sink toward

5980-406: The mesopelagic zone , however, there is often high viral abundance found around deep-sea hydrothermal vents . The magnitude of their impacts on biological systems is demonstrated by the varying range of viral-to-prokaryote abundance ratios ranging from 1-223, this indicates that there are the same amount or more viruses than prokaryotes. Despite the lack of light, vision plays a role in life within

6110-478: The orthophosphate ion (PO 4 ) , consisting of a P atom and 4 oxygen atoms. On land most phosphorus is found in rocks and minerals. Phosphorus-rich deposits have generally formed in the ocean or from guano, and over time, geologic processes bring ocean sediments to land. Weathering of rocks and minerals release phosphorus in a soluble form where it is taken up by plants, and it is transformed into organic compounds. The plants may then be consumed by herbivores and

6240-506: The Oplophoridae family, uses its photophores to emit light, and can secrete a bioluminescent substance when in the presence of a predator. This secretory mechanism is common among prey fish. Many cephalopods , including at least 70 genera of squid , are bioluminescent. 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

6370-472: 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. 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. In

6500-512: The air.  Phosphorus is adsorbed by wetland soils which are taken up by the plants. Therefore, wetlands could help to reduce the concentration of nitrogen and phosphorus to remit eutrophication. However, wetland soils can only hold a limited amount of phosphorus. To remove phosphorus continually, it is necessary to add more new soils within the wetland from remnant plant stems, leaves, root debris, and undecomposable parts of dead algae, bacteria, fungi, and invertebrates. Nutrients are important to

6630-452: The amount of phosphorus that enters the cycle which has led to excessive nutrient intake in freshwater systems causing dramatic growth in algal populations. When these algae die, their putrefaction depletes the water of oxygen and can toxify the waters. Both these effects cause plant and animal death rates to increase as the plants take in and animals drink the poisonous water. Oceanic ecosystems gather phosphorus through many sources, but it

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6760-480: The animal's light organ. Bioluminescence is used in a variety of ways and for different purposes. The cirrate octopod Stauroteuthis syrtensis uses emits bioluminescence from its sucker like structures. These structures are believed to have evolved from what are more commonly known as octopus suckers. They do not have the same function as the normal suckers because they no longer have any handling or grappling ability due its evolution of photophores . The placement of

6890-496: The animals obtain it through their diet. Conversely, luciferases vary widely between different species. Bioluminescence has arisen over 40 times in evolutionary history . Both Aristotle and Pliny the Elder mentioned that damp wood sometimes gives off a glow. Many centuries later Robert Boyle showed that oxygen was involved in the process, in both wood and glowworms. It was not until the late nineteenth century that bioluminescence

7020-468: 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". Charles Darwin noticed bioluminescence in the sea, describing it in his Journal : While sailing in these latitudes on one very dark night,

7150-534: The atmosphere" was probably responsible. Daniel Pauly comments that Darwin "was lucky with most of his guesses, but not here", noting that biochemistry was too little known, and that the complex evolution of the marine animals involved "would have been too much for comfort". Bioluminescence attracted the attention of the United States Navy in the Cold War , since submarines in some waters can create

7280-489: The bathypelagic ecosystem is constrained by its lack of sunlight and primary producers , with limited production of microbial biomass via autotrophy. The trophic networks in this region rely on particulate organic matter (POM) that sinks from the epipelagic and mesopelagic water, and oxygen inputs from the thermohaline circulation . Despite these limitations, this open-ocean ecosystem is home to microbial organisms , fish , and nekton . A comprehensive understanding of

7410-433: The bathypelagic region and the properties that deliver organic carbon to the deep sea. The bathypelagic zone currently acts as a significant reservoir for carbon because of its sheer volume and the century to millennial timescales these waters are isolated from the atmosphere, this ocean zone plays an important role in moderating the effects of anthropogenic climate change. The burial of particulate organic carbon (POC) in

7540-498: The bathypelagic with bioluminescence a trait among both nektonic and planktonic organisms. In contrast to organisms in the water column, benthic organisms in this region tend to have limited to no bioluminescence . The bathypelagic zone contains sharks , squid , octopuses , and many species of fish, including deep-water anglerfish , gulper eel , amphipods , and dragonfish . The fish are characterized by weak muscles, soft skin, and slimy bodies. The adaptations of some of

7670-471: The bathypelagic zone; it primarily takes the form of fecal pellets and dead organisms that sink out of the surface waters and fall toward the ocean floor. Regions with higher primary productivity where particles are able to sink quickly, such as equatorial upwelling zones and the Arabian Sea , have the greatest amount of POC delivery to the bathypelagic zone. The vertical mixing of DOC-rich surface waters

7800-445: The biosphere. Phosphorus does enter the atmosphere in very small amounts when dust containing phosphorus is dissolved in rainwater and sea spray, but the element mainly remains on land and in rock and soil minerals. Phosphates which are found in fertilizers, sewage and detergents, can cause pollution in lakes and streams. Over-enrichment of phosphate in both fresh and inshore marine waters can lead to massive algae blooms . In fresh water,

7930-444: The chemical mechanisms or to prove what function the light serves. 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. The following functions are reasonably well established in the named organisms. In many animals of the deep sea, including several squid species, bacterial bioluminescence

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8060-416: The composition of phospholipids present in cell membranes . Plants assimilate phosphorus as phosphate and incorporate it into organic compounds . In animals , inorganic phosphorus in the form of apatite ( Ca 5 (PO 4 ) 3 (OH,F) ) is also a key component of bones , teeth ( tooth enamel ), etc. On the land, phosphorus gradually becomes less available to plants over thousands of years, since it

8190-450: The course of ~4–5 hours towards the surface and then form into groups. While in most regions migration patterns can be driven by predation , in this particular region, the migration patterns are not believed to result solely from predator-prey relations. Instead, these relations are commensalistic , with the species who remain in the bathypelagic benefitting from the POM mixing caused by

8320-464: The crust is apatite , which can be dissolved by natural acids generated by soil microbes and fungi, or by other chemical weathering reactions and physical erosion. The dissolved phosphorus is bioavailable to terrestrial organisms and plants and is returned to the soil after their decay. Phosphorus retention by soil minerals (e.g., adsorption onto iron and aluminum oxyhydroxides in acidic soils and precipitation onto calcite in neutral-to-calcareous soils)

8450-472: The dead insect thus assisting in the dispersal of both bacteria and nematodes. 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. Quantula striata

8580-560: The death and decay of these blooms leads to eutrophication . An example of this is the Canadian Experimental Lakes Area. Freshwater algal blooms are generally caused by excess phosphorus, while those that take place in saltwater tend to occur when excess nitrogen is added. However, it is possible for eutrophication to be due to a spike in phosphorus content in both freshwater and saltwater environments. Phosphorus occurs most abundantly in nature as part of

8710-757: 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. All bioluminescent organisms have in common that the reaction of a "luciferin" and oxygen is catalyzed by a luciferase to produce light. McElroy and Seliger proposed in 1962 that the bioluminescent reaction evolved to detoxify oxygen, in parallel with photosynthesis. Thuesen, Davis et al. showed in 2016 that bioluminescence has evolved independently 27 times within 14 fish clades across ray-finned fishes. The oldest of these appears to be Stomiiformes and Myctophidae. In sharks, bioluminescence has evolved only once. Genomic analysis of octocorals indicates that their ancestor

8840-695: The development of increased eye sensitivity and enhanced visual signals. 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. Rees et al. use 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 (e.g. H 2 O 2 and O 2 ). The functional shift from antioxidation to bioluminescence probably occurred when

8970-415: The dominant inorganic P species in nature, is oxidation state (P5+), certain microorganisms can use phosphonate and phosphite (P3+ oxidation state) as a P source by oxidizing it to orthophosphate. Recently, rapid production and release of reduced phosphorus compounds has provided new clues about the role of reduced P as a missing link in oceanic phosphorus. The availability of phosphorus in an ecosystem

9100-510: The downward flux of carbon from the surface oceans, overall, there will likely be less carbon sequestered to the bathypelagic region. Bioluminescence Bioluminescence is the production and emission of light by living organisms . 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 arthropods such as fireflies . In some animals,

9230-446: The eutrophic growth. Attempts to mitigate this problem using biological approaches are being investigated. One such approach involves using phosphorus accumulating organisms such as, Candidatus accumulibacter phosphatis , which are capable of effectively storing phosphorus in the form of phosphate in marine ecosystems. Essentially, this would alter how the phosphorus cycle exists currently in marine ecosystems. Currently, there has been

9360-417: The female lights up to attract males. The defense mechanisms for bioluminescent organisms can come in multiple forms; startling prey, counter-illumination, smoke screen or misdirection, distractive body parts, burglar alarm, sacrificial tag or warning coloration. The shrimp family Oplophoridae Dana use their bioluminescence as a way of startling the predator that is after them. Acanthephyra purpurea , within

9490-488: The fish that live there include small eyes and transparent skin. However, this zone is difficult for fish to live in since food is scarce; resulting in species evolving slow metabolic rates in order to conserve energy. Occasionally, large sources of organic matter from decaying organisms, such as whale falls , create a brief burst of activity by attracting organisms from different bathypelagic communities. Some bathypelagic species undergo vertical migration , which differs from

9620-434: 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 analyze

9750-444: The form of readily soluble orthophosphate . Particulate organic phosphorus occurs in suspension in living and dead protoplasm and is insoluble. Dissolved organic phosphorus is derived from the particulate organic phosphorus by excretion and decomposition and is soluble. The primary biological importance of phosphates is as a component of nucleotides , which serve as energy storage within cells ( ATP ) or when linked together, form

9880-459: The global phosphorus cycle primarily through the mining and subsequent transformation of phosphorus minerals for use in fertilizer and industrial products. Some phosphorus is also lost as effluent through the mining and industrial processes as well. Phosphorus is an essential nutrient for plants and animals. Phosphorus is a limiting nutrient for aquatic organisms. Phosphorus forms parts of important life-sustaining molecules that are very common in

10010-402: The glowing wake of the ship, and was able to fly to it and land safely. 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, and demonstrated that the process was related to

10140-517: The glowworm 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", and in 1854 Johann Florian Heller (1813–1871) identified strands ( hyphae ) of fungi as the source of light in dead wood. Tuckey , in his posthumous 1818 Narrative of the Expedition to the Zaire , described catching

10270-425: The growth and survival of living organisms and, hence, are essential for developing and maintaining healthy ecosystems. Humans have greatly influenced the phosphorus cycle by mining phosphate rock. For millennia, phosphorus was primarily brought into the environment by weathering phosphate-containing rocks, which would replenish the phosphorus normally lost to the environment through processes such as runoff, albeit on

10400-521: The inputs driving the microbial ecology in the bathypelagic zone is lacking due to limited observational data, but has been improving with advancements in deep-sea technology. A majority of our knowledge of ocean microbial activity comes from studies of the shallower regions of the ocean because it is easier to access, and it was previously assumed that deeper water did not have suitable physical conditions for diverse microbial communities. The bathypelagic zone receives inputs of organic material and POM from

10530-510: The laboratory, luciferase-based systems are used in genetic engineering and biomedical research. Researchers are also investigating the possibility of using bioluminescent systems for street and decorative lighting, and a bioluminescent plant has been created. 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. This experimental form of illumination avoided

10660-411: The later stage of weathering and soil development as it will precipitate into rocks. Available phosphorus is found in a biogeochemical cycle in the upper soil profile, while phosphorus found at lower depths is primarily involved in geochemical reactions with secondary minerals. Plant growth depends on the rapid root uptake of phosphorus released from dead organic matter in the biochemical cycle. Phosphorus

10790-439: The light is bacteriogenic, produced by symbiotic bacteria such as those from the genus Vibrio ; in others, it is autogenic, produced by the animals themselves. In a general sense, the principal chemical reaction in bioluminescence involves a light-emitting molecule and an enzyme , generally called luciferin and luciferase , respectively. Because these are generic names, luciferins and luciferases are often distinguished by

10920-553: The lure, they are bitten by the shark. 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. 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. However, doubt has been cast on this assertion, and there

11050-468: The major transfer is driven by tectonic movement over geologic time and weathering of phosphate containing rock such as apatite . Furthermore, phosphorus tends to be a limiting nutrient in aquatic ecosystems . However, as phosphorus enters aquatic ecosystems, it has the possibility to lead to over-production in the form of eutrophication , which can happen in both freshwater and saltwater environments. Human activities have caused major changes to

11180-463: The marine environment, use of luminescence for mate attraction is chiefly known among ostracods , small shrimp-like 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". A polychaete worm, the Bermuda fireworm creates a brief display, a few nights after the full moon, when

11310-403: The mesopelagic are also poorly understood due to the same constraints. Unlike the pelagic zone where the emission of light is undisturbed in the open sea, the occurrence of bioluminescence in the benthic zone is less common. It has been attributed to the blockage of emitted light by a number of sources such as the sea floor, and inorganic and organic structures. Visual signals and communication that

11440-401: The most sampled and researched due to their relatively easy access. However, more recently locations further offshore and at greater depths, such as ocean ridges and seamounts , are being increasingly studied due to advances in technology and laboratory methods, as well as collaboration with industry. The first discovery of communities subsisting off of the chemical energy in hydrothermal vents

11570-563: The necessity of using candles which risked sparking explosions of firedamp . 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 records that Robert Boyle experimented on these light sources, and showed that both they and

11700-450: The nucleic acids DNA and RNA . The double helix of our DNA is only possible because of the phosphate ester bridge that binds the helix. Besides making biomolecules, phosphorus is also found in bone and the enamel of mammalian teeth, whose strength is derived from calcium phosphate in the form of hydroxyapatite . It is also found in the exoskeleton of insects, and phospholipids (found in all biological membranes ). It also functions as

11830-422: The ocean via river runoff. Atmospheric phosphorus deposition is another important marine phosphorus source to the ocean. In surface seawater, dissolved inorganic phosphorus, mainly orthophosphate (PO 4 ), is assimilated by phytoplankton and transformed into organic phosphorus compounds. Phytoplankton cell lysis releases cellular dissolved inorganic and organic phosphorus to the surrounding environment. Some of

11960-413: The ocean's ability to do so will be negatively affected as atmospheric CO 2 concentrations continue to rise and global temperatures continue to warm. This will lead to changes such as deoxygenation , ocean acidification , temperature increase, and carbon sequestration decrease, among other physical and chemical alterations. These perturbations may have significant impacts on the organisms that dwell in

12090-402: The ocean. 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 . Bioluminescence is abundant in the pelagic zone, with the most concentration at depths devoid of light and surface waters at night. These organisms participate in diurnal vertical migration from the dark depths to

12220-441: The only unifying mechanism is the role of molecular oxygen ; often there is a concurrent release of carbon dioxide (CO 2 ). For example, the firefly luciferin/luciferase reaction requires magnesium and ATP and produces CO 2 , adenosine monophosphate (AMP) and pyrophosphate (PP) as waste products. Other cofactors may be required, such as calcium (Ca ) for the photoprotein aequorin , or magnesium (Mg ) ions and ATP for

12350-556: The open sea, including fish , jellyfish , comb jellies , crustaceans , and cephalopod molluscs; in some fungi and bacteria ; and in various terrestrial invertebrates, nearly all of which are beetles . In marine coastal habitats, about 2.5% of organisms are estimated to be bioluminescent, whereas in pelagic habitats in the eastern Pacific, about 76% of the main taxa of deep-sea animals have been found to be capable of producing light. More than 700 animal genera have been recorded with light-producing species. Most marine light-emission

12480-699: The organic phosphorus compounds can be hydrolyzed by enzymes synthesized by bacteria and phytoplankton and subsequently assimilated. The vast majority of phosphorus is remineralized within the water column, and approximately 1% of associated phosphorus carried to the deep sea by the falling particles is removed from the ocean reservoir by burial in sediments. A series of diagenetic processes act to enrich sediment pore water phosphorus concentrations, resulting in an appreciable benthic return flux of phosphorus to overlying bottom waters. These processes include Additionally, These processes are similar to phosphorus cycling in lakes and rivers. Although orthophosphate (PO 4 ),

12610-412: The overall availability of the nutrient. Other human processes can have detrimental effects on the phosphorus cycle, such as the repeated application of liquid hog manure in excess to crops. Applying biosolids may also increase available phosphorus in soil. In poorly drained soils or in areas where snowmelt can cause periodic waterlogging, reducing conditions can be attained in 7–10 days. This causes

12740-578: The oxidation of a specific compound, which he named luciferin , by an enzyme . 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 to produce light, were interchangeable between species, showing that all bioluminescent organisms had

12870-438: The past several decades, many aspects remain a mystery. One of the major areas of current research is focused on understanding carbon remineralization rates in the region. Prior studies have struggled to quantify the rates at which prokaryotes in this region remineralize carbon because previously developed techniques may not be adequate for this region, and indicate remineralization rates much higher than expected. Further work

13000-466: The phenomenon. Today, the two prevailing hypotheses (both concerning marine bioluminescence) are those put forth by Howard Seliger in 1993 and Rees et al. in 1998. 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 favored

13130-660: The phosphorus is either incorporated into their tissues or excreted. After death, the animal or plant decays, and phosphorus is returned to the soil where a large part of the phosphorus is transformed into insoluble compounds. Runoff may carry a small part of the phosphorus back to the ocean . Generally with time (thousands of years) soils become deficient in phosphorus leading to ecosystem retrogression. There are four major pools of phosphorus in freshwater ecosystems: dissolved inorganic phosphorus (DIP), dissolved organic phosphorus (DOP), particulate inorganic phosphorus (PIP) and particulate organic phosphorus (POP). Dissolved material

13260-434: The photophores are within the animals oral reach, which leads researchers to suggest that it uses it bioluminescence to capture and lure prey. 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. Click beetles emit an orange light from

13390-440: The predator itself more vulnerable by attracting the attention of predators from higher trophic levels. 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

13520-444: The rate of their degradation to generate free phosphate. There are various enzymes such as phosphatases , nucleases and phytase involved for the degradation. Some of the abiotic pathways in the environment studied are hydrolytic reactions and photolytic reactions. Enzymatic hydrolysis of organic phosphorus is an essential step in the biogeochemical phosphorus cycle, including the phosphorus nutrition of plants and microorganisms and

13650-444: The reflected glare of these livid flames, was not so utterly obscure, as over the rest of the heavens. Darwin also observed a luminous "jelly-fish of the genus Dianaea", noting 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." He guessed that "a disturbed electrical condition of

13780-429: The region. Our understanding of these biogeochemical processes has historically been limited due to the difficulty and cost of collecting samples from these ocean depths. Other technological challenges, such as measuring microbial activity under the pressure conditions experienced in the bathypelagic zone, have also restricted our knowledge of the region. Although scientific advancements have increased our understanding over

13910-400: The retainment of functional eyes for organisms to detect bioluminescence. Organisms often produce bioluminescence themselves, rarely do they generate it from outside phenomena. However, there are occasions where bioluminescence is produced by bacterial symbionts that have a symbiotic relationship with the host organism. Although many luminous bacteria in the marine environment are free-living,

14040-544: The roots of living plants. Several of those organic acids are capable of forming stable organo-metal complexes with various metal ions found in soil solutions. As a result, these processes may lead to the release of inorganic phosphorus associated with aluminum, iron, and calcium in soil minerals. The production and release of oxalic acid by mycorrhizal fungi explain their importance in maintaining and supplying phosphorus to plants. The availability of organic phosphorus to support microbial, plant and animal growth depends on

14170-497: The sea floor, resulting in sediments with relatively high amounts of CaCO 3 . However, as depth and pressure increase and temperature decreases, the solubility of calcium carbonate also increases, which results in more dissolution and less net transport to the deeper, underlying seafloor. As a result of this rapid change in dissolution rates, sediments in the bathypelagic region vary widely in CaCO 3 content and burial. The ecology of

14300-401: 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

14430-652: The seafloor, making them regions of interest for deep-sea mining . Many of the biogeochemical processes in the bathypelagic region are dependent upon the input of organic matter from the overlying epipelagic and mesopelagic zones. This organic material, sometimes called marine snow , sinks in the water column or is transported within downward convected water masses such as the Thermohaline Circulation . Hydrothermal vents also deliver heat and chemicals such as sulfide and methane . These chemicals can be utilized to sustain metabolism by organisms in

14560-484: The sediments and the biosphere. It can also be recycled from the sediments and the water system allowing it to stay in the environment. Antrhopogenic effects can also cause phosphorus to flow into aquatic ecosystems as seen in drainage water and runoff from fertilized soils on agricultural land. Additionally, eroded soils, which can be caused by deforestation and urbanization, can lead to more phosphorus and nitrogen being added to these aquatic ecosystems. These all increase

14690-456: The species or group, e.g. 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 11 different animal phyla , though in some of these,

14820-399: 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. While popular at first, Seliger's theory has been challenged, particularly on the biochemical and genetic evidence that Rees examines. What remains clear, however,

14950-411: The surface at night, dispersing the population of bioluminescent organisms across the pelagic water column. The dispersal of bioluminescence across different depths in the pelagic zone has been attributed to the selection pressures imposed by predation and the lack of places to hide in the open sea. In depths where sunlight never penetrates, often below 200m, the significance of bioluminescent is evident in

15080-442: The surface due to experiencing drastic pressure changes in a short amount of time. Work is underway to quantify cell abundance and biomass, but due to poor survival, it is difficult to get accurate counts. In more recent years there has been an effort to categorize the diversity of the eukaryotic assemblages in the bathypelagic zone using methods to assess the genetic compositions of microbial communities based on supergroups, which

15210-424: The surface ocean on the order of 1-3.6 Pg C/year. Prokaryote biomass in the bathypelagic is dependent and thus correlated with the amount of sinking POM and organic carbon availability. These essential organic carbon inputs for microbes typically decrease with depth as they are utilized while sinking to the bathypelagic. Microbial production varies over six orders of magnitude based on resource availability in

15340-676: The topography of seamounts interrupts the currents and creates eddies that retain plankton in the seamount region, thus increasing fauna nearby as well Hydrothermal vents are also a common feature in some areas of the bathypelagic zone and are primarily formed from the spreading of Earth's tectonic plates at mid-ocean ridges . As the bathypelagic region lacks light, these vents play an important role in global ocean chemical processes, thus supporting unique ecosystems that have adapted to utilize chemicals as energy, via chemoautotrophy , instead of sunlight, to sustain themselves. In addition, hydrothermal vents facilitate precipitation of minerals on

15470-552: The transfer of organic phosphorus from soil to bodies of water. Many organisms rely on the soil derived phosphorus for their phosphorus nutrition. Eutrophication is when waters are enriched by nutrients that lead to structural changes to the aquatic ecosystem such as algae bloom, deoxygenation, reduction of fish species. It does occur naturally, as when lakes age they become more productive due to increases in major limiting reagents such as nitrogen and phosphorus. For example, phosphorus can enter into lakes where it will accumulate in

15600-407: The twentieth and early twenty-first century was published recently. In 1932 E. N. Harvey was among the first to propose how bioluminescence could have evolved. 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

15730-632: The underlying sediments via the biological carbon pump , and the solubility pump of dissolved inorganic carbon (DIC) into the ocean interior via the thermohaline conveyor are key processes for removing excess atmospheric carbon. However, as atmospheric CO 2 concentrations and global temperatures continue to rise, the efficiency at which the bathypelagic will store and bury the influx of carbon will most likely decrease. While some regions may experience an increase in POC input, such as Arctic regions where increased periods of minimal sea ice coverage will increase

15860-404: The upward movement of another species. In addition, the vertical migrating species' timing bathypelagic appears linked to the lunar cycle . However, the exact indicators causing this timing are still unknown. This region is understudied due to a lack of data/observations and difficulty of access (i.e. cost, remote locations, extreme pressure). Historically in oceanography, continental margins were

15990-429: The water column and deliver organic carbon , nitrogen , and phosphorus , to organisms that live below the photic zone. These parcels are sometimes referred to as marine snow or ocean dandruff. This is also the dominant delivery mechanism of food to organisms in the bathypelagic zone because there is no sunlight for photosynthesis , with chemoautotrophy playing a more minor role as far as we know. As POM sinks through

16120-659: The water column, it is consumed by organisms which deplete it of nutrients. The size and density of these particles affect their likelihood of reaching organisms in the bathypelagic zone. Smaller parcels of POM often become aggregated together as they fall, which quickens their descent and prohibits their consumption by other organisms, increasing their likelihood of reaching lower depths. The density of these particles may be increased in some regions where minerals associated with some forms of phytoplankton, such as biogenic silica and calcium carbonate "ballast" resulting in more rapid transport to deeper depth. A majority of organic carbon

16250-487: The water column. These fish are able to utilize the longer wavelength to act as a spotlight for its prey that only they can see. The fish may also use this light to communicate with each other to find potential mates. The ability of the fish to see this light is explained by the presence of specialized rhodopsin pigment. The mechanism of light creation is through a suborbital photophore that utilizes gland cells which produce exergonic chemical reactions that produce light with

16380-449: The zooids, but each responds to the light produced by other individuals, and even to light from other nearby colonies. 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. Some bioluminous bacteria infect nematodes that parasitize Lepidoptera larvae. When these caterpillars die, their luminosity may attract predators to

16510-413: Was aboard an expedition in 1977 led by Jack Corliss , an oceanographer from Oregon State University . More recent advancements include remotely operated vehicles (ROVs), autonomous underwater vehicles (AUVs), and independent gliders and floats. The oceans act as a buffer for anthropogenic climate change due to their ability to take up atmospheric CO 2 and absorb heat from the atmosphere. However,

16640-575: Was another ten years before he discovered the chemical's structure and published his 1957 paper Crystalline Cypridina Luciferin . Shimomura, Martin Chalfie , 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. Harvey wrote a detailed historical account on all forms of luminescence in 1957. An updated book on bioluminescence covering also

16770-423: Was bioluminescent as long as 540 million years ago. 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. Because of the diversity of luciferin/luciferase combinations, there are very few commonalities in the chemical mechanism. From currently studied systems,

16900-437: Was properly investigated. The phenomenon is widely distributed among animal groups, especially in marine environments. On land it occurs in fungi, bacteria and some groups of invertebrates , including insects . The uses of bioluminescence by animals include counterillumination camouflage, mimicry of other animals, for example to lure prey, and signaling to other individuals of the same species, such as to attract mates. In

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