Aliivibrio fischeri
Aliivibrio fischeri (also called Vibrio fischeri) is a Gram-negative, rod-shaped bacterium found globally in marine environments. This species has bioluminescent properties, and is found predominantly in symbiosis with various marine animals, such as the Hawaiian bobtail squid. It is heterotrophic, oxidase-positive, and motile by means of a single polar flagella. Free-living "A. fischeri" cells survive on decaying organic matter. The bacterium is a key research organism for examination of microbial bioluminescence, quorum sensing, and bacterial-animal symbiosis. It is named after Bernhard Fischer, a German microbiologist. Ribosomal RNA comparison led to the reclassification of  this species from genus "Vibrio" to the newly created "Aliivibrio" in 2007. However, the name change is not generally accepted by most researchers, who still publish "Vibrio fischeri" (see Google Scholar for 2018-2019). Genome. The genome for "A. fischeri" was completely sequenced in 2004 and consists of two chromosomes, one smaller and one larger. Chromosome 1 has 2.9 million base pairs (Mbp) and chromosome 2 has 1.3 Mbp, bringing the total genome to 4.2 Mbp. "A. fischeri" has the lowest G+C content of 27 "Vibrio" species, but is still most closely related to the higher-pathogenicity species such as  V. cholerae. The genome for "A. fischeri" also carries mobile genetic elements. Ecology. "A. fischeri" are globally distributed in temperate and subtropical marine environments. They can be found free-floating in oceans, as well as associated with marine animals, sediment, and decaying matter. "A. fischeri" have been most studied as symbionts of marine animals, including squids in the genus "Euprymna" and "Sepiola", where "A. fischeri" can be found in the squids' light organs. This relationship has been best characterized in the Hawaiian Bobtail Squid ("Euprymna scolopes"), where "A. fischeri" is the only species of bacteria inhabiting the squid's light  organ. Symbiosis with the Hawaiian Bobtail Squid. "A. fischeri" colonization of the light organ of the Hawaiian Bobtail Squid is currently studied as a simple model for mutualistic symbiosis, as it contains only two species and "A. fischeri" can be cultured in a lab and genetically modified. This mutualistic symbiosis functions primarily due to "A. fischeri" bioluminescence. "A. fischeri" colonizes the light organ of the Hawaiian Bobtail Squid and luminesces at night, providing the squid with counter-illumination camouflage, which prevents the squid from casting a shadow on the ocean floor. "A. fischeri c"olonization occurs in juvenile squids and induces  morphological changes the squids light organ. Interestingly, certain morphological changes made by "A. fischeri" do not occur when the microbe cannot luminescence, indicating that bioluminescence (described below) is truly essential for symbiosis. In the process of colonization, ciliated cells within the animals' photophores (light-producing organs) selectively draw in the symbiotic bacteria. These cells promote the growth of the symbionts and actively reject any competitors. The bacteria cause these cells to die off once the light organ is sufficiently colonized. The light organs of certain squid contain reflective plates that intensify and direct the light produced, due to proteins  known as reflectins. They regulate the light for counter-illumination camouflage, requiring the intensity to match that of the sea surface above. Sepiolid squid expel 90% of the symbiotic bacteria in their light organ each morning in a process known as "venting". Venting is thought to provide the source from which newly hatched squid are colonized by "A. fischeri". Bioluminescence. The bioluminescence of "A. fischeri" is caused by transcription of the "lux" operon, which is induced through population-dependent quorum sensing. The population of "A. fischeri" needs to reach an optimal level to activate the "lux" operon and stimulate light  production. The circadian rhythm controls light expression, where luminescence is much brighter during the day and dimmer at night, as required for camouflage. The bacterial luciferin-luciferase system is encoded by a set of genes labelled the "lux" operon. In "A. fischeri", five such genes ("luxCDABEG") have been identified as active in the emission of visible light, and two genes ("luxR" and "luxI") are involved in regulating the operon. Several external and intrinsic factors appear to either induce or inhibit the transcription of this gene set and produce or suppress light emission. "A. fischeri" is one of many species of  bacteria that commonly form symbiotic relationships with marine organisms. Marine organisms contain bacteria that use bioluminescence so they can find mates, ward off predators, attract prey, or communicate with other organisms. In return, the organism the bacteria are living within provides the bacteria with a nutrient-rich environment. The "lux" operon is a 9-kilobase fragment of the "A. fischeri" genome that controls bioluminescence through the catalytic activity of the enzyme luciferase. This operon has a known gene sequence of "luxCDAB(F)E", where "luxA" and "luxB" code for the protein subunits of the luciferase enzyme, and the "luxCDE" codes for a  fatty acid reductase complex that makes the fatty acids necessary for the luciferase mechanism." luxC "codes for the enzyme acyl-reductase, "luxD" codes for acyl-transferase, and "luxE" makes the proteins needed for the enzyme acyl-protein synthetase. Luciferase produces blue/green light through the oxidation of reduced flavin mononucleotide and a long-chain aldehyde by diatomic oxygen. The reaction is summarized as: The reduced flavin mononucleotide (FMNH) is provided by the "fre" gene, also referred to as "luxG". In "A. fischeri", it is directly next to "luxE" (giving "luxCDABE-fre") from 1042306 to 1048745 To generate the aldehyde needed  in the reaction above, three additional enzymes are needed. The fatty acids needed for the reaction are pulled from the fatty acid biosynthesis pathway by acyl-transferase. Acyl-transferase reacts with acyl-ACP to release R-COOH, a free fatty acid. R-COOH is reduced by a two-enzyme system to an aldehyde. The reaction is: Quorum Sensing. One primary system that controls bioluminescence through regulation of the "lux" operon is quorum sensing, a conserved system across many microbial species that regulates gene expression in response to bacterial concentration. Quorum sensing functions through the production of an autoinducer, usually a  small organic molecule, by individual cells. As cell populations increase, levels of autoinducers increase, and specific proteins that regulate transcription of genes bind to these autoinducers and alter gene expression. This system allows microbial cells to "communicate" amongst each other and coordinate behaviors like luminescence, which require large amounts of cells to produce an effect. In "A. fischeri", there are two primary quorum sensing systems, each of which respond to slightly different environments. The first system is commonly referred to as the "lux" system, as it is encoded within the "lux" operon, and uses the autoinducer 3OC6-HSL. The protein  LuxI synthesizes this signal, which is subsequently released from the cell. This signal, 3OC6-HSL, then binds to the protein LuxR, which regulates the expression of many different genes, but is most known for upregulation of genes involved in luminescence. The second system, commonly referred to as the "ain" system, uses the autoinducer C8-HSL, which is produced by the protein AinS. Similar to the "lux" system, the autoinducer C8-HSL increases activation of LuxR. In addition, C8-HSL binds to another transcriptional regulator, LitR, giving the "ain" and "lux" systems of quorum sensing slightly different genetic targets within the  cell. The different genetic targets of the "ain" and "lux" systems are essential, because these two systems respond to different cellular environments. The "ain" system regulates transcription in response to intermediate cell density cell environments, producing lower levels of luminescence and even regulating metabolic processes like the acetate switch. On the other hand, the "lux" quorum sensing system occurs in response to high cell density, producing high levels of luminescence and regulating the transcription of other genes, including QsrP, RibB, and AcfA. Both of the "ain" and "lux" quorum sensing systems are essential for colonization of the squid and regulate  multiple colonization factors in the bacteria. Natural transformation. Natural bacterial transformation is an adaptation for transferring DNA from one individual cell to another. Natural transformation, including the uptake and incorporation of exogenous DNA into the recipient genome, has been demonstrated in "A. fischeri". This process requires induction by chitohexaose and is likely regulated by genes "tfoX" and "tfoY". Natural transformation of "A. fischeri" facilitates rapid transfer of mutant genes across strains and provides a useful tool for experimental genetic manipulation in this species. State microbe status. In 2014, Hawaiian State Senator Glenn Wakai submitted SB3124 proposing "Aliivibrio fischeri" as the  state microbe of Hawaii. The bill was in competition with a bill to make "Flavobacterium akiainvivens" the state microbe, but neither passed. In 2017, legislation similar to the original 2013 "F. akiainvivens" bill was submitted in the Hawaii House of Representatives by Isaac Choy and in the Hawaii Senate by Brian Taniguchi.