Deep sea fish

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Anglerfish which lives in the bathypelagic zone.[[1]]

Description of the Niche

Where located?

While the concept of deep sea fish may be a bit variable in terms of the depth they inhabit, it is usually understood that deep sea fishes are those living in the bathypelagic, abyssopelagic and demersal zone. Bathypelagic species, such as the angler fishes, inhabit the deeper part of the pelagic zone, lives from from 1,000 m down to around 4,000 m, while abyssopelagic species live from 4,000 m down to above the ocean floor. Demersal species occupy the bottom of the ocean floor and are divided into benthic and benthopelagic species. Benthic fishes are those that spend most of their time on the bottom such as the rays and flatfishes, while benthopelgic fishes are those that swim habitually near the ocean floor such as the squalid sharks (family Squalidae) and smoothheads (family Alepocephalidae).(2)

Physical Conditions?

The conditions of the deep sea are extreme and the species inhabiting the area are challenged with adapting to these conditions. The most challenging is perhaps the high hydrostatic pressure. For each 10m increase in depth, the pressure increases by 1atm (~0.101MPa). The average pressure below 1000m is near 380atm while the maximum may reach up to 1100atm. In addition to the high pressure, the temperature in deep sea is very low, typically in the range of 2-4°C. Lack of sunlight is another condition these animals are challenged with affecting their vision as well as the photosynthetic production below ~100m. Due to these extreme conditions, the deep sea species are expected to possess well adapted biochemical systems. Also, for the same reason, the bacteria that inhabit the organs of these species are mostly extremophiles such as barophiles and psychrophiles.(1)

Influence of adjacent communities?

Hydrothermal vent is one community that may influence deep sea fishes. Although the water temperatures of hydrothermal vents are near 400°C, this area is very productive biologically hosting communities such as chemosynthetic archaea. Because of its high temperature and toxicity of its fluid, deep sea fishes adapted to the cold temperature may not survive around this community.(1)


One of the most fascinating characteristics of deep sea fish is their ability to luminesce under certain conditions. Bioluminescence is essentially the ability of organisms to emit a glowing, visible light. It occurs almost everywhere, but is most prevalent in oceans, sometimes exhibiting the “milky sea” effect, where a large group of bioluminescent bacteria can glow in large proportions, even able to be seen via satellite. Furthermore, in the oceans, bioluminescence is often found in both shallow water and deep water, but it is most common in the upper 1000 m of the pelagic habitat, with 14 marine phyla exhibiting bioluminescence. (12) The deep water fish evolved to be able to utilize light producing microbes to cope with the harsh conditions of their environment. They have developed a symbiotic relationship with bioluminescent bacteria, with specialized organs that provide bioluminescent bacteria with sufficient food and a safe place to live. In return, fish can use the bacteria to emit a light to aid in camouflage, hunting, and attracting mates. On a larger scale, luminescent bacteria have even provided for strategies for treating cystic fibrosis and preventing antibiotic resistant bacteria infections. (8)

Bioluminescent Bacteria

As mentioned above, bioluminescent bacteria and deep sea fish maintain a symbiotic relationship to give the fish a source of light. Bioluminescent bacteria are classified in the genera Vibrio and Photomicrobium, and look like curved rods usually 1-3 microns long, with a motile flagella. They survive in seawater, fish digestive tracts, the outside of decaying fish, and their symbiotic relationship is most commonly found in angler fish, flashlight fish, and the bobtail squid. (11)

Biochemistry and Quorum Sensing

How do they make light?

FMNH2 + O2 + RCHO --> FMN + RCOOH + H2O + Light (8)

This reaction involves the oxidation of substrate luciferin in the presence of an catalytic enzyme luciferase. LuxA and LuxB catalyze the luciferase reaction, using oxygen and a reduced flavin mononucleotide to oxidize a long chain aldehyde RCHO. It results in the production of light and and inactive oxyluciferin, ATP used as energy to produce more luciferin. Sometimes luciferin and luciferase are bound together in a single molecule called “photoprotein”, which can be triggered by calcium ions to produce light. Most of the energy produced is emitted as light rather than heat, and the creation of light occurs only when organisms are present in high cell densities. (15)

Quorum sensing is the cell to cell communication that takes place in this light production process, and quorum is the minimum number of cells required in order to take an action between cells. Therefore quorum sensing allows the bacteria to regulate gene expression according to the density of a certain cell around it. It allows for the prevention of premature initiation of a process, and does not allow the cell to take action until it reaches the confidence factor. (14) The molecule that is accumulated and sensed is an autoinducer, LuxI in bioluminescent bacteria, and it is excreted by the cell into the medium, where it accumulates until it reaches the minimum concentration. Once at the threshold concentration, it diffuses back into the cell, binding to the regulatory molecule LuxR. This new complex activates transcription of the luciferase gene, resulting in a luminescence. (8)


Three kinds of single celled marine organisms produce light: bacteria, dinoflagellates, radiolarians, all with different luciferins. Individual bacteria do not luminesce; in order for a glowing effect, there needs a large group of luminescent bacteria, because luciferase production turned on only when the accumulation in the environment reaches a critical concentration of an autoinducer released by the bacteria. Though luminescent bacteria are also found freely flowing in the ocean, they more commonly found as symbionts in the light organs of fish (11)

Deep Sea Shrimp spitting bioluminescence in defense.[[2]]

Deep Sea Shrimp spitting bioluminescence in defense.[[3]]

Use by fish

Many species of fish use luminescent bacteria as symbionts as their source of light: shallow water species utilize bacteria better in warm temperature conditions, while deep sea fish bacteria are better accustomed to cold temperatures. Most of these fish have photophores that open into the gut, and their symbionts are extracellular. For example, the flashlight fish uses its light organ as a "flashlight" to help it see in the dark. Deep sea anglerfishes however, have photophores that open to the sea water via pores. Because bacteria perpetually grow, the photophores must be occluded in order to turn off the luminescence. These fish use their hanging bioluminescent appendages as bait to lure prey towards them. Another fish, the deep sea shrimp, can spit bioluminescence to distract a predator for defense. Most fish synthesize their own luciferin, and a few must take it in their diet. Almost all produce a blue light, and some produce both blue and red (12)

Species of Bioluminescent bacteria

Bioluminescent bacteria can be divided into two genres, Vibrio and Photobacteria. The most common three are Vibrio fischeri, Vibrio harveyi, and Photobacterium phosphoreum. These bacteria, as mentioned above, all exhibit similar characteristics in terms of their use of quorum sensing, and the luciferase reaction. (16)

Vibrio fischeri

Vibrio fischeri contain some squids and fishes, and are the most well-known species of bioluminescent bacteria. As mentioned above, they are a very quorum–sensitive species, only being activated when a certain threshold limit is reached. The autoinducer in Vibrio fischeri is N-(3-oxohexanoyl)homoserine lactone: when a certain extracellular concentration of this autoinducer is reached, it triggers the LuxR to express the genes for luciferase and to eventually glow. Vibrio fischeri maintain a symbiotic relationship with a small Hawaiian squid, which provides for a safe environment for the bacteria, while receiving aid in hunting at night. (9)

Vibrio Harveyi

Vibrio Harveyi is more apparent as a free-flowing bacteria in the ocean, rather than living in deep sea organisms as vibrio fischeri are in deep sea fish and squid. They do however exhibit harmful pathogen characteristics towards fish and invertebrates, as they can cause a wide variety of infections and diseases in these organisms. They are also the cause of the “milky sea” effect, mentioned above. (15)

Photobacterium Phosphoreum

Photobacterium Phosphoreum is the other bioluminescent bacteria that are often present in deep sea organisms, surviving in the light organs, usually the gut, of deep sea fishes. It carries similar properties as Vibriro fischeri in terms of its symbiotic relationship with the host organism, its reaction to create light, and its use of quorum sensing.(11)

Current Research

One of the major ongoing concerns right now involving deep sea fishes is the threat brought upon these communities by human activities. For example, many deep seas are found beyond the exclusive economic zone of individual nations on the High seas, which are an open access to all nations for fishing activities. Due to these over-exploited and unregulated activities, deep sea is under multiple threats including climate change, acidification, and possible extinction of some species. While it has been previously viewed that deep sea was protective from the effects of surface driven cycles and impacts, modern research shows that this may not be true after all. During the study done approximately 4 years ago, it was found that increasing fresh water input from terrestrial sources may disrupt thermohaline circulation, changing ocean circulation patterns as well as the temperature and the density. As more threats to the deep sea communities are discovered recently, we still lack sound scientific basis for restoring the habitats and protecting them. Thus, it is believed that more research needs to be conducted to solve some of the problems.(7)

Another recent research involves quorum sensing in Vibrio harveyi. A bioluminescent bacteria, Vibrio harveyi is considered to be deadly to many cultured animals. In order to find the cure for some of this bacterial causing diseases, since quorum sensing is involved pathological events such as biofilm formation and and bacterial virulence, researches involving quorum sensing inhibitors are being conducted. Autoinducer-2(AI-2) mediates the quorum sensing in both gram positive and gram negative bacteria. This molecule exists in complex with boric acid with complex F being the biologically active form of V. harveyi. This complex binds to the LuxP receptor in V. harveyi triggering cascade of events that lead to quorum sensing and bioluminescence. Hence, in order to inhibit this activity, the research involves mimicking of the boric acid complex (F) with structurally similar compound boronic acid. By binding this molecule to the LuxP site, antagonizing of the bacterial quorum sensing can be made possible. In conclusion, after screening 50 boronic acid compounds for their ability to inhibit quorum sensing activity, the result showed that several phenylboronic acids exhibited AI-2 inhibition effect. This can be a very useful tool as well as a good lead to future researches.(6)

Since the first discovery by the mariners around 17th century, there has been many speculations and questions raised about the "milky seas". Milky sea, a continuous and substancial light emission from the surface of the ocean, has been the subject of a study in terms of what causes the light emission. Marine bioluminescent organisms emit light as brief flashes (milliseconds or seconds) or discontinuous bursts lasting for minutes at most and cannot be responsible for the prolonged emission of light by the "milky seas". Bioluminescent bacteria seemed like an unlike source of light also since it was thought that the autoinducer of quorum sensing cannot accumulate at required concentration in the open ocean. However, in recent studies, through the use of satellite it has been shown that the light does come from the bioluminescent bacteria such as Vibrio harveyi. Due to the complexity more researches are necessary in order to fully understand this "milky sea" effect.(5)


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2. Gordon, J.D.M. "Deep-Sea Fishes". Scottish Association for Marine Science 2001. p.687-693.

3. Nakayama, A., Yano Y., and Yoshida K. "New Method for Isolating Barophiles from Intestinal Contentsof Deep-Sea Fishes Retrieved from the Abyssal Zone". APPLIED AND ENVIRONMENTAL MICROBIOLOGY 1994. Vol.60 No.11. p.4210-4212.

4. Marc, J.E.C., Maarel, V.D., Artz, R., Haanstra, R., and Forney, L. "Association of Marine Archaea with the Digestive Tracts of Two Marine Fish Species". APPLIED AND ENVIRONMENTAL MICROBIOLOGY 1998. Vol. 64 No.8. p.2894-2898.

5. Elvidege, C., Haddock, S., Lee, T., Miller, S. "Detection of a Bioluminescent Milky Sea from Space". Proceedings of the National Academy of Sciences of the United States of America 2005. Vol.102 No.40. p.14181-14184.

6. Ni, Nanting; Chou, Han-Ting; Wang, Junfeng; Li, Minyong; Lu, Chung-Dar; Tai, Phang C.; Wang, Binghe. "Identification of boronic acids as antagonists of bacterial quorum sensing in Vibrio harveyi". Biochemical and Biophysical Research Communications 2008. Vol.369 No.2. p.590-594.

7. Davies, A.J., Hall-Spencer, J., Roberts, J.M. "Preserving deep-sea natural heritage: Emerging issues in offshore conservation and management". Biological Conservation 2007. Vol.138 No.3-4. p. 299-312.

8. "Bioluminescent Bacteria." Bioluminescent Bacteria. Cornell University Biology Department. 29 Aug. 2008 <>.

9. Butler, David, and Nehring. Biology/Bimm101 recombinant DNA Techniques. San Diego, CA: UCSD Soft Reserves, 2007. 21-22.

10. Danyluk, Bo Ena, Waldemar Uchman, Piotr Konieczny, and Agnieszka Bilska. "An Objective Method to assess bioluminescent properties of selected bacterial strains." Technology of Agricultural University of Poznan: 5-16.

11. F. L. Thompson, T. Iida, J. Swings, “ Biodiversity of Vibrios”. Microbiol Mol Biol Rev. September 2004. Volume 68. Issue 3. p. 403-431

12. Haddock, Steven. "The Bioluminescence Web Page." The Bioluminescence Web Page. 1997. Monterey Bay Aquarium Research Institute. 29 Aug. 2008 <>.

13. Herring, P. J., and E. A. Widder. "Bioluminescence." UCSD Encyclopedia of Ocean Sciences. 2001. UCSD. 29 Aug. 2008 <>.

14. Larsen, Rachel. "Regulation of Gene Expression." UCSD, San Diego. 22 Aug. 2008.

15. Lightner, D. V. Diseases of cultured penaeid shrimp. CRC Handbook of Mariculture, Crustacean Aquaculture. 1993 pp. 393–486.

16. Madanecki, Piotr. "Luminescent Bacteria." Luminescent Bacteria. 23 1998. 29 Aug. 2008 <>.

17. Slonczewski, Joan L., John W. Foster, and Kathy M. Gillen. Microbiology : An Evolving Science. Boston: W. W. Norton & Company, Incorporated, 2008. 378-79.

Edited by Hoo Sup Lee and Ryul Devin Park, student of Rachel Larsen