Gammaproteobacteria

Currently there are many different classifications based on different approaches, like NCBI (National Center for Biotechnology Information)  based on genomic, LPSN (List of Prokaryotic names with Standing in Nomenclature) , ARB-Silva Database[8] based on ribosomal RNA, or a multiprotein approach. It is still very difficult to resolve the phylogeny of this bacterial class.[9]

Here, it is reported a clade based on a set of 356 protein families for the class of Gammaproteobacteria.

A number of bacteria have been described as members of the Gammaproteobacteria, but have not yet been assigned an order or family. These include bacteria of the genera Alkalimarinus, Alkalimonas, Arenicella, Gallaecimonas, Ignatzschineria, Litorivivens, Marinicella, Methylohalomonas, Methylonatrum, Plasticicumulans, Pseudohongiella, Sedimenticola, Thiohalobacter, Thiohalomonas, Thiohalorhabdus, Thiolapillus, and Wohlfahrtiimonas.[11]

Gammaproteobacteria, especially the orders Alteromonadales and Vibrionales, are fundamental in marine and coastal ecosystems because they are the major groups involved in the nutrients cycling[12] and despite their fame as pathogens, they find application in a huge number of fields, such as bioremediation and biosynthesis.

Gammaproteobacteria can be used as a microbial fuel cell (MFC)[13] element that applies their ability to dissimilate various metals.[14] The produced energy could be collected as one of the most environmentally friendly and sustainable energy production systems.[15] They are also used as biological methane filters.[16]

Phototrophic purple sulfur bacteria are used in wastewater treatment processes[17] and the ability of some Gammaproteobacteria (e.g. the genus Alcanivorax[18]) to bioremediate oil is becoming increasingly important to degrade crude oil after oil spills.[19] Some species from the family Chromatiaceae are notable because might be involved in the production of vitamin B12.[20] Another application of some Gammaproteobacteria is their ability to synthesize Poly-b-hydroxyalkanoate (PHA)[21] which is a polymer that is used in the production of biodegradable plastics. Also lots of Gammaproteobacteria species are able to generate secondary metabolites with antibacterial properties.[22]

Gammaproteobacteria are widely distributed and abundant in various ecosystems such as soil, freshwater lakes and rivers, oceans and salt lakes. For example, Gammaproteobacteria constitute about 6–20% (average of 14%) of bacterioplankton in different oceans;[23] plus, current researches have revealed their worldwide propagation in deep-sea and coastal sediments.[24] In seawater, Bacterial community composition could be shaped by miscellaneous environmental parameters, such as phosphorus, total organic carbon contents, salinity, and pH,[25] and the higher is the soil pH, the higher is the relative abundance of Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria.[26] The relative abundance of Betaproteobacteria and Gammaproteobacteria is also positively correlated to the dissolved organic carbon (DOC) concentration, which is a key environmental parameter shaping bacterial community composition.[27] Gammaproteobacteria are also key players in the dark carbon fixation in coastal sediments, which are the largest carbon sink on Earth and the majority of these bacteria have not been cultured yet.[28] The deep-sea hydrothermal system is one of the most extreme environments on Earth. Almost all vent-endemic animals are strongly associated with the primary production of the endo- and/or episymbiotic chemoautotrophic microorganisms.[29] Analyses of the both symbiotic and free-living microbial communities in the various deep-sea hydrothermal environments have revealed a predominance in biomass of members of the Gammaproteobacteria.[30]

Gammaproteobacteria have a wide diversity, metabolic versatility, and functional redundancy in the hydrothermal sediments, and they are responsible for the important organic carbon turnover and nitrogen and sulfur cycling processes.[31] Anoxic hydrothermal fluids contain several reduced compounds such as H2, CH4, and reduced metal ions in addition to H2S. It has been proposed that hydrogen sulfide-oxidizing and oxygen- reducing chemoautotrophs potentially sustain the primary production in these unique ecosystems.[32] In the last decades, it has been found that orders belonging to Gammaproteobacteria, like Pseudomonas, Moraxella, are able to degrade different types of plastics and these microbes might have a key role in plastic biodegradation.[33]

In the class of Gammaproteobacteria there is a wide diversity of metabolisms.

Some groups are nitrite-oxidizers[34] and ammonia oxidizers like the members of  Nitrosococcus - with the exception of Nitrosococcus mobilis -  and they are also obligate halophilic bacteria. [35]

Among Gammaproteobacteria there are chemoautotrophic sulfur-oxidizing groups, like Thiotrichales, which are found as microbial biofilm filamentous communities in the Tor Caldara shallow-water gas vent in the Tyrrhenian sea .[36] Moreover, thanks to 16S rRNA gene analysis, different sulfide oxidizers in the Gammaporteobacteria class have been detected, and the most important among them are Beggiatoa,Thioploca and Thiomargarita; besides, large amounts of hydrogen sulfide are produced by sulfate-reducing bacteria in organic-rich coastal sediments.[37]

Marine Gammaproteobacteria also include aerobic anoxygenic phototrophic bacteria (AAP) that use bacteriochlorophyll to support the electron transport chain. They are believed to be an essential community in the oceans and are also well spread all around. [38]

Another type of metabolism carried out by Gammaproteobacteria is the oxidation of Methane, carried out by the order Methylococcales. They metabolize methane as sole energy source and are very important in the global carbon cycle. They are found in any site where methane sources are, like gas reserves, soils, wastewaters.   [39]

Purple sulfur bacteria are anoxygenic phototrophic iron‐oxidizers and they are part of the genus[40] Acidithiobacillus but, there are also two strains of Thiodictyon (Chromatiales order) -strain L7 and strain F4- and few species within the genus Thermomonas (order Lysobacter) that carry out the same metabolism.[41]

In this class, there are numerous genera of obligate and generalist hydrocarbonclastic bacteria. The obligate hydrocarbonoclastic bacteria (OHCB) share the ability to utilize hydrocarbons almost exclusively as a carbon source and until now they have been found only in the marine environment. The genera carrying out this metabolism are Alcanivorax, Oleiphilus, Oleispira, Thalassolitus, Cycloclasticus and Neptunomonas. Subsequently, additional species such as Polycyclovorans, Algiphilus of the order Xanthomonadales and Porticoccus hydrocarbonoclasticus of the order Cellvibrionales that were isolated from phytoplankton. Groups of aerobic “generalist” hydrocarbon degraders can utilize hydrocarbons and nonhydrocarbon substrates as source of carbon and energy and are members within the genera Acinetobacter, Colwellia, Glaciecola, Halomonas, Marinobacter, Marinomonas, Methylomonas, Pseudoalteromonas, Pseudomonas, Rhodanobacter, Shewanella, Stenotrophomonas, and Vibrio.[42]

The most frequent pathway to synthesize glucose among Gammaporteobacteria members is Calvin–Benson–Bassham (CBB) cycle but, a minority of species of this class may use the rTCA cycle.[43] Thioflavicoccus mobilis (free living gammaproteobacteria) and "Candidatus Endoriftia persephone" (symbiont of the giant tubeworm Riftia pachyptila), present the possibility of using the rTCA cycle in addition to the CBB cycle. It has been showed that some species of Gammaproteobacteria may express two different carbon fixation pathways simultaneously.[44]

Symbiosis is a close and a long-term biological interaction between two different biological organisms. A large number of Gammaproteobacteria are able to join in a close endosymbiosis with various species. Evidence for this can be found in a wide variety of ecological niches: on the ground[45][46] underground,[47] or deep on the ocean floor.[48] On the land, it has been reported that Gammaproteobacteria species have been isolated from Robinia pseudoacacia[49] and other plants,[50][51] while in the deep sea a sulfur-oxidizing gammaproteobacteria was found in a hydrothermal vent chimney;[52] by entering into symbiotic relationships in deep sea areas, sulfur-oxidizing chemolithotrophic microbes receive additional organic hydrocarbons in hydrothermal ecosystems. Some Gammaproteobacteria are symbiotic with geothermic ocean vent-downwelling animals[53], and in addition, Gammaproteobacteria can have complex relationships with other species that live around thermal springs,[54] for example, with the shrimp Rimicaris exoculata living from hydrothermal vents on the Mid-Atlantic Ridge.

Regarding the endosymbionts, most of them lack many of their family characteristics due to significant genome reduction.[55][56]

Gammaproteobacteria comprise several medically and scientifically important groups of bacteria, such as the Enterobacteriaceae, Vibrionaceae, and Pseudomonadaceae. A number of important human pathogens belong to this class, e.g. Salmonella spp. (enteritis and typhoid fever), Yersinia pestis (plague), Vibrio cholerae (cholera), Pseudomonas aeruginosa (lung infections in hospitalized or cystic fibrosis patients), and Escherichia coli (food poisoning).There are also plant pathogens such as Xanthomonas axonopodis pv. citri (citrus canker), Pseudomonas syringae pv. actinidiae (kiwifruit Psa outbreak), and Xylella fastidiosa. Also in the marine environment we can found pathogens that belong to Gammaproteobacteria class, such as several species in genus Vibrio, that can infect different marine organisms, such as fish, shrimp, corals or oysters,[57] and species of Salmonella that can also infect grey seals (Halichoerus grypus).[58]

Below there is the description of some of the most famous human pathogens belonging to the class Gammaproteobacteria.[59]

• E. coli is the most well known microorganism and it can have pathogenic and non pathogenic strains, and it is the most common responsible for human diseases. For example, among all the pathogens belonging to the genus Escherichia, the strain E. coli O157:H7 is transmitted to humans by ingesting contaminated water, beef or vegetables that have not been properly sanitized and it is responsible of the hemorrhagic enteritis
• In the genus Salmonella we can found two most important pathogens: Salmonella typhi and Salmonella paratyphi. We can found the Salmonella in a wide variety of animals, reptile included and it can induce the Typhoid fever that is a severe gastroenteritis, usually accompanied by a high fever.
• The most known pathogens in genus Yersinia are Yersinia pestis that caused in past three major plague pandemic: the Justinian Plague, the Black Death and the Modern Plague.[60] This disease can be diffused by infected fleas, through direct contact with infected materials or by inhalation and can be very severe in people. We have mainly 3 forms: bubonic plague, septicemic plague and Pneumonic plague.
• In Pseudomonadaceae family there is the genus Pseudomonas, which can grow as biofilms and contains an excreted exopolysaccharide that can interfere with the disinfection of colonized surfaces. The most common microbe that belong to Pseudomonas genus is Pseudomonas aeruginosa,[61] that can induce serious infections include malignant external otitis, endophthalmitis, endocarditis, meningitis, pneumonia, and septicemia.
• In the order Vibrionales and in the family of Vibrionaceae there is the genus Vibrio. Many species of genus Vibrio are pathogens not only for human but also for fish and crustaceans. The most known disease of this genus is cholera, caused by the species Vibrio cholerae. Cholera is a waterborne disease and is particularly associated with poverty and poor sanitation.[62] Be

sides V. cholerae, in genus Vibrio there is also Vibrio parahaemolyticus that can infect human through the consumption of raw or under cooked shellfish, contaminated food, and exposure of wounds to warm seawater, and it can induct, in the most of the cases, gastroenteritis, but it can cause also wound infections and septicemia.[63]

• Betaproteobacteria
• Proteobacteria

• Gammaproteobacteria at the US National Library of Medicine Medical Subject Headings (MeSH)