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Bioluminescent Bacteria
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. These 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 these 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 close to equally. Another possible reason bacteria use luminescence is for quorum sensing, an ability to regulate gene expression in response to bacterial cell density.

History
Records of bioluminescent bacteria have been around for thousands of years. They appear in folklore from many countries such as India and Scandanavia. Both Aristotle and Charles Darwin have described the phenomenon of the oceans glowing. Since its discovery less than 30 years ago, the luciferase enzyme and its regulatory gene, the lux gene, has led to major advances in molecular biology, through its use as a reporter gene. Luciferase was first purified by McElroy and Green in 1955. It was later discovered that there were two subunits to luciferase, called subunits α and β. The genes encoding these enzymes, luxA and luxB, respectively, were first isolated from the lux operon of Aliivibrio fisheri .

Use as a Laboratory Tool
After the discovery of the lux operon, the use of bioluminescent bacteria as a laboratory tool is claimed to have revolutionized the area of environmental microbiology. The applications of bioluminescent bacteria include biosensors for detection of contaminants, measurement of pollutant toxicity and monitoring of genetically engineered bacteria released into the environment. Biosensors, created by placing a lux gene construct under the control of an inducible promoter, can be used to determine the concentration of specific pollutants. Biosensors are also able to distinguish between pollutants that are bioavailable and those that are inert and unavailable. For example, Pseudomonas fluorescens has been genetically engineered to be capable of degrading salicylate and naphthalene, and is used as a biosensor to assess the bioavailability of salicylate and naphthalene. Biosensors can also be used as an indicator of cellular metabolic activity and to detect the presence of pathogens.

Evolution
The light-producing chemistry behind bioluminescence varies across the lineages of bioluminescent organisms. Based on this observation, bioluminescence is believed to have evolved independently at least 40 times. In bioluminescent bacteria, the reclassification of the members ofVibrio fischeri species group as a new genus, Aliivibrio, has led to increased interest in the evolutionary origins of bioluminescence . Among bacteria, the distribution of bioluminescent species is polyphyletic. For instance, while all species in the terrestrial genus Photorhabdus are luminescent, the genera Aliivibrio, Photobacterium, Shewanella and Vibrio contain both luminous and non-luminous species. Despite bioluminescence in bacteria not sharing a common origin, the bacteria share a common gene sequence. The appearance of the highly conserved lux operon in bacteria from very different ecological niches suggests a strong selective advantage despite the high energetic costs of producing light. DNA repair is thought to be the initial selective advantage for light production in bacteria. Consequently, the lux operon may have been lost in bacteria that evolved more efficient DNA repair systems but retained in those where visible light became a selective advantage. The evolution of quorum sensing is believed to have afforded further selective advantage for light production. Quorum sensing allows bacteria to conserve energy by ensuring that they do not synthesize light-producing chemicals unless a sufficient concentration is present to be visible.

Bacterial groups that exhibit bioluminescence
All bacterial species that have been reported to posses bioluminescence belong to the families Vibrionaceae, Shewanellaceae, or Enterobacteriaceae, all of which are assigned to the class Gammaproteobacteria. (List from Dunlap and Henryk (2013), "Luminous Bacteria", The Prokaryotes )

Distribution
Bioluminescent bacteria are most abundant in marine environments during spring blooms when there are high nutrient concentrations. These light-emitting organisms are found mainly in coastal waters near the outflow of rivers, such as in the northern Adriatic Sea, Gulf of Trieste, northwestern part of the Caspian Sea, coast of Africa and many more. Bioluminescent bacteria are also found in freshwater and terrestrial environments but are less distributed than in seawater environments. They are found globally, as free-living, symbiotic or parasitic forms and possibly as opportunistic pathogens. Factors that affect the distribution of bioluminescent bacteria include temperature, salinity, nutrient concentration, pH level and solar radiation. For example, Aliivibrio fischeri grows favourably in environments that have temperatures between 5 to 30°C and pH that is less than 6.8, whereas Photobacterium phosphoreum thrive in conditions that have temperatures between 5 to 25°C and pH that is less than 7.0.

Genetic Diversity
All bioluminescent bacteria share a common gene sequence: the lux operon characterized by the luxCDABE gene organization. LuxAB codes for luciferase while luxCDE code for a fatty acid reductase complex that is responsible for synthesizing aldehydes for the bioluminescent reaction. Despite this common gene organization, variations, such as the presence of other lux genes, can be observed among species. Based on similarities in gene content and organization, the lux operon can be organized into four distinct types: the Aliivibrio/Shewanella type, the Photobacterium type, theVibrio/Candidatus Photodesmus type, and the Photorhabdus type. While this organization follows the genera level classification for members of Vibrionaceae (Aliivibrio, Photobacterium, and Vibrio), its evolutionary history is not known.

With the exception of the Photorhabdus operon type, all variants of the lux operon contain the flavin reductase-encoding luxG gene. Most of the Aliivibrio/Shewanella type operons contain additional luxI/luxR regulatory genes that are used for autoinduction during quorum sensing. The Photobacterum operon type is characterized by the presence of rib genes that code for riboflavin, and forms the lux-rib operon. TheVibrio/Candidatus Photodesmus operon type differs from both the Aliivibrio/Shewanella and the Photobacterium operon types in that the operon has no regulatory genes directly associated with it.

Mechanism
The enzyme luciferase is needed to produce bioluminescence. All bacterial luciferases are approximately 80 KDa heterodimers containing two subunits: α and β. The α subunit is responsible for light emission. The luxA and luxB genes encode for the α and β subunits, respectively. In most bioluminescent bacteria, the luxA and luxB genes are flanked upstream by luxC and luxD and downstream by luxE.

The bioluminescent reaction is as follows:

FMNH2 + O2 + R-CHO -> FMN + H2O + R-COOH + Light (~ 495 nm)

Molecular oxygen reacts with FMNH2 (reduced flavin mononucleotide) and a long-chain aldehyde to produce FMN (flavin mononucleotide), water and a corresponding fatty acid. The blue-green light emission of bioluminescence, such as that produced by Photobacterium phosphoreum and Vibro harveyi, results from this reaction. Because light emission involves expending six ATP molecules for each photon, it is an energetically expensive process. For this reason, light emission is not constitutively expressed in bioluminescent bacteria; it is expressed only when physiologically necessary.

Quorum Sensing
Bioluminescence in bacteria can be regulated through a phenomenon known as autoinduction or quorum sensing. Quorom sensing is a form of cell-to-cell communication that alters gene expression in response to cell density. Autoinducer is a diffusible pheromone produced constitutively by bioluminescent bacteria and serves as an extracellular signalling molecule. When the concentration of autoinducer secreted by bioluminescent cells in the environment reaches a threshold (above 107 cells per mL), it induces the expression of luciferase and other enzymes involved in bioluminescence. Bacteria are able to estimate their density by sensing the level of autoinducer in the environment and regulate their bioluminescence such that it is expressed only when there is a sufficiently high cell population. A sufficiently high cell population ensures that the bioluminescence produced by the cells will be visible in the environment.

A well known example of quorum sensing is that between Aliivibrio fischeri and its host. This process is regulated by LuxI and LuxR, encoded by luxI and luxR respectively. LuxI is autoinducer synthase that produces autoinducer (AI) while LuxR functions as both a receptor and transcription factor for the lux operon. When LuxR binds AI, LuxR-AI complex activates transcription of the lux operon and induces the expression of luciferase. Using this system, A. fischeri has shown that bioluminescence is expressed only when the bacteria are host-associated and have reached sufficent cell densities.

Another example of quorum sensing by bioluminescent bacteria is by Vibrio harveyi, which are known to be free-living. Unlike Aliivibrio fischeri, V. harveyi do not possess the luxI/luxR regulatory genes and therefore have a different mechanism of quorum sensing regulation. Instead, they use the system known as three-channel quorum sensing system.

Role
The uses of bioluminescence and its biological and ecological significance for animals, including host organisms for bacteria symbiosis, have been widely studied. Its benefits for bacteria, however, still remain unclear.

One explanation for the role of bacterial bioluminescence is from the biochemical aspect. Several studies have shown the biochemical roles of the luminescence pathway. It can function as an alternate pathway for electron flow under low oxygen concentration, which can be advantageous when no fermentable substrate is available. In this process, light emission is a side product of the metabolism.

Evidence also suggests that bacterial luciferase contributes to the resistance of oxidative stress. In laboratory culture, luxA and luxB mutants of Vibrio harveyi, which lacked luciferase activity, showed impairment of growth under high oxidative stress compared to wild type. The luxD mutants, which had an unaffected luciferase but were unable to produce luminescence, showed little or no difference. This suggests that luciferase mediates the detoxification of reactive oxygen.

Bacterial bioluminescence has also been proposed to be a source of internal light in photoreactivation, a DNA repair process carried out by photolyase. Experiments have shown that non-luminescent V. harveyi mutants are more sensitive to UV irradiation, suggesting the existence of a bioluminescent-mediated DNA repair system.

Another hypothesis, called the “bait hypothesis”, is that bacterial bioluminescence functions to attract predators who will assist in their dispersal. They are either directly ingested by fish or indirectly ingested by zooplankton which will eventually be consumed by higher trophic levels. The aim of this is ultimately for passage into the fish gut, a nutrient-rich environment where they survive digestion and can divide, get excreted, and continue their cycle. Experiments using luminescent Photobacterium leiognathi and non-luminescent mutants have shown that luminescence attract zooplankton and fish, thus supporting this hypothesis.

Symbiosis with other organisms
The symbiotic relationship between the Hawaiian bobtail squid Euprymna scolopes and marine gram-negative bacterium Aliivibrio fischeri has been well studied. The two organisms exhibit a mutualistic relationship in which bioluminescence produced by A. fischeri help attract pray to the squid, while the nutrient-rich host tissue provides A. fischeri with a protected environment. Bioluminescence provided by A. fischeri also aids in the defence of E. scolopes during its nighttime foraging activity by helping 'E. scolopes' camouflage. Following bacterial colonization, the specialized organs of the squid undergo developmental changes and a relationship becomes established. The squid expels 90% of the bacterial population each morning because following environmental illumination, it no longer needs to produce bioluminescence, and any bioluminescence produced would be futile in the daylight. This expulsion benefits the bacteria by aiding in their dissemination. A single expulsion by one bobtail squid produces enough bacterial symbionts to fill 10,000m3 of seawater at a concentration that is comparable to what is found in coastal waters. Thus, in at least some habitats, the symbiotic relationship between 'A. fischeri' and 'E. scolopes' plays a key role in determining the abundance and distribution of 'E. scolopes. There is a higher abundance of 'A. fischeri in the vicinity of a population of E. scolopes and this abundance markedly decreases with increasing distance from the host’s habitat.

Bioluminescent Photobacterium species also engage in mutually beneficial associations with fish and squid. P. kishitanii, P. leiogathi, and P. mandapamensis live in dense populations in the light organs of marine fish and squid, and are provided with nutrients and oxygen for reproduction and light production. In turn, the host animals are provided with bioluminescence that aid in sex-specific signaling, predator avoidance, locating or attracting prey, and schooling.

Article
Bioluminescent bacteria

History

 * How and when was it originally found?
 * Why are people interested in it? What is the significance?

Use as Laboratory Tool

 * How are they used as tool in laboratory.
 * By changing the regulation of the lux operon and adding it to other bacteria it is possible to use genetically modified bacteria to detect contaminants, measure pollution and monitor the bacteria after release   . Observing the amount of light that is given off by the bacteria and seeing how it changes do the level of pollutions. In this way allows for both the lethal concentration to be determined and to see the effect of lower concentrations on the organism. Sub lethal concentrations will result in decreased luminescence corresponding to the amount of decrease in metabolism that the concentration of pollution is causing.

Mechanism
Luciferase
 * How do they make bioluminescence?

Genetic Diversity

 * Is there any genetic diversity or classification?

Organisms that Possess Bioluminescence

 * Bacterial species or groups

Role

 * Why do they have this trait?
 * Significance as better survival of individuals?

Symbiosis

 * What kind of symbiosis can we see?
 * Specific examples of bacteria and its symbiot?

Ecological Relation

 * Any significance at ecological level?

-organisms (symbiosis)

-citations for what is there

-celular level breakdown (luciferase) (BLAST??)

-ecological significace (roles in reproduction)

-genetics _ different types of lucerin

-ecological role that is played at a comunity level?

-scientific history (discovery and uses in science)

-images with captions

-statistical figures maybe?

Bioluminescent bacteria

Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity (2010)
https://www.ncbi.nlm.nih.gov/pubmed/20448176

Review on bioluminescence, relatively new, not limited to bacterial.

Bacterial bioluminescence: its control and ecological significance (1979)
https://www.ncbi.nlm.nih.gov/pubmed/396467

Classical view of bacterial bioluminescence, still very helpful with a lot of content. Need to be careful about the names of bacteria here, since many of them have changed in past years.

Bioluminescence in the Sea (2010)

Haddock, Steven H.d., Mark A. Moline, and James F. Case. "Bioluminescence in the Sea."Annual Review of Marine Science 2.1 (2010): 443-93. Web.

Understanding the significance of bioluminescence in marine communities.

Bacterial Bioluminescence (1977)

Hastings, J. W., and K. H. Nealson. "Bacterial Bioluminescence." Annual Review of Microbiology 31.1 (1977): 549-95. Web.

Facts and descriptions on various aspects of bacterial bioluminescence.