Gammaproteobacteria

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Gammaproteobacteria
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Vibrio cholerae
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Domain: Bacteria
Phylum: Pseudomonadota
Class: Gammaproteobacteria
Garrity et al. 2005
Orders
Synonyms
  • "Chromatiia" Cavalier-Smith 2020

Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota (synonym Proteobacteria). It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. [1] Several medically, ecologically, and scientifically important groups of bacteria belong to this class. All members of this class are Gram-negative. It is the most phylogenetically and physiologically diverse class of the Pseudomonadota. [2]

Contents

Members of Gammaproteobacteria live in several terrestrial and marine environments, in which they play various important roles, including in extreme environments such as hydrothermal vents. They can have different shapes, rods, curved rods, cocci, spirilla, and filaments, [3] and include free living bacteria, biofilm formers, commensals and symbionts; [4] some also have the distinctive trait of being bioluminescent. [5] Diverse metabolisms are found in Gammaproteobacteria; there are both aerobic and anaerobic (obligate or facultative) species, chemolithoautotrophics, chemoorganotrophics, photoautotrophs and heterotrophs. [6]

Etymology

The element "gamma" (third letter of the Greek alphabet) indicates that this is Class III in Bergey's Manual of Systematic Bacteriology (Vol. II, page 1). Proteus refers to the Greek sea god who could change his shape. Bacteria (Greek βακτήριον; "rod" "little stick"), in terms of etymological history, refers to Bacillus (rod-shaped bacteria), but in this case is "useful in the interim while the phylogenetic data are being integrated into formal bacterial taxonomy." [7]

Phylogeny

Currently, many different classifications are based on different approaches, such as the National Center for Biotechnology Information, based on genomic, 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. [4]

The following molecular phylogeny of Gammaproteobacteria is based on a set of 356 protein families.

Phylogeny of Gammaproteobacteria

Betaproteobacteria

Gammaproteobacteria
Phylogeny of Gammaproteobacteria after [4] Not all orders are monophyletic, consequently families or genera are shown for the Pseudomonadales, Oceanospirillales, and Alteromonadales. In the case of singleton orders, the genus is shown. (In bacterial taxonomy, orders have the suffix -ales, while families have -aceae.)

A number of genera in Gammaproteobacteria have not yet been assigned to an order or family. These include Alkalimonas , Gallaecimonas , Ignatzschineria , Litorivivens , Marinicella , Plasticicumulans , Pseudohongiella , Sedimenticola , Thiohalobacter , Thiohalorhabdus , Thiolapillus , and Wohlfahrtiimonas . [9]

Significance and applications

Gammaproteobacteria, especially the orders Alteromonadales and Vibrionales, are fundamental in marine and coastal ecosystems because they are the major groups involved in nutrient cycling. [10] 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) [11] element that applies their ability to dissimilate various metals. [12] The produced energy could be collected as one of the most environmentally friendly and sustainable energy production systems. [13] They are also used as biological methane filters. [14]

Phototrophic purple sulfur bacteria are used in wastewater treatment processes. [15] The ability of some Gammaproteobacteria (e.g. the genus Alcanivorax [16] ) to bioremediate oil is increasingly important for degrading crude oil after oil spills. [17] Some species from the family Chromatiaceae are notable because they may be involved in the production of vitamin B12. [18] Some Gammaproteobacteria are used to synthesize poly-b-hydroxyalkanoate (PHA), [19] which is a polymer that is used in the production of biodegradable plastics. Many Gammaproteobacteria species are able to generate secondary metabolites with antibacterial properties. [20]

Ecology

Gammaproteobacteria are widely distributed and abundant in various ecosystems such as soil, freshwater lakes and rivers, oceans and salt lakes. For example, they constitute about 6–20% (average of 14%) of bacterioplankton in different oceans, [21] and they are distributed world-wide in both deep-sea and coastal sediments. [22] In seawater, bacterial community composition could be shaped by environmental parameters such as phosphorus availability, total organic carbon, salinity, and pH. [23] In soil, higher pH is correlated with higher relative abundance of Alphaproteobacteria , Betaproteobacteria and Gammaproteobacteria. [24] 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. [25] 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. [26] 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. [27] Analyses of both the symbiotic and free-living microbial communities in the various deep-sea hydrothermal environments have revealed a predominance in biomass of members of the Gammaproteobacteria. [28]

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. [29] Anoxic hydrothermal fluids contain several reduced compounds such as H2, CH4, and reduced metal ions in addition to H2S. Chemoautotrophs that oxidize hydrogen sulfide and reduce oxygen potentially sustain the primary production in these unique ecosystems. [30] 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. [31]

Metabolism

Gammaproteobacteria are metabolically diverse, employing a variety of electron donors for respiration and biosynthesis.

Some groups are nitrite-oxidizers [32] and ammonia oxidizers like the members of Nitrosococcus (with the exception of Nitrosococcus mobilis) and they are also obligate halophilic bacteria. [33]

Others are chemoautotrophic sulfur-oxidizers, like  Thiotrichales , which are found in communities such as filamentous microbial biofilms in the Tor Caldara shallow-water gas vent in the Tyrrhenian Sea. [34] 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. [35]

Marine Gammaproteobacteria include aerobic anoxygenic phototrophic bacteria (AAP) that use bacteriochlorophyll to support the electron transport chain. They are believed to be a widespread and essential community in the oceans. [36]

Methanotrophs, such as the order  Methylococcales, metabolize methane as sole energy source and are very important in the global carbon cycle. They are found in any site with methane sources, like gas reserves, soils, and wastewater. [37]

Purple sulfur bacteria are anoxygenic phototrophs that oxidize sulfur, [38] but potentially also other substrates like iron. [39] They are represented by members of two families, Chromatiaceae (e.g. Allochromatium , Chromatium , Thiodicyton ) and Ectothiorhodospiraceae (e.g. Ectothiorhodospira). [38] A few species within the genus Thermomonas (order Lysobacter) carry out the same metabolism. [40]

Numerous genera are obligate or generalist hydrocarbonclasts. The obligate hydrocarbonoclastic bacteria (OHCB) use hydrocarbons almost exclusively as a carbon source; until now[ when? ] they have been found only in the marine environment. Examples include Alcanivorax , Oleiphilus , Oleispira , Thalassolitus, Cycloclasticus and Neptunomonas, and some species of Polycyclovorans , Algiphilus (order Xanthomonadales ), and Porticoccus hydrocarbonoclasticus (order Cellvibrionales ) that were isolated from phytoplankton. In contrast, aerobic “generalist” hydrocarbon degraders can use either hydrocarbons or nonhydrocarbon substrates as sources of carbon and energy; examples are found in the genera Acinetobacter , Colwellia , Glaciecola , Halomonas , Marinobacter , Marinomonas , Methylomonas , Pseudoalteromonas , Pseudomonas , Rhodanobacter , Shewanella , Stenotrophomonas , and Vibrio . [41]

The most widespread pathway for carbon fixation among Gammaproteobacteria is the Calvin–Benson–Bassham (CBB) cycle, although a minority may use the rTCA cycle. [42] Thioflavicoccus mobilis (a free living species) and "Candidatus Endoriftia persephone" (symbiont of the giant tubeworm Riftia pachyptila ) may use the rTCA cycle in addition to the CBB cycle, and may express these two different pathways simultaneously. [43]

Symbiosis

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, [44] [45] within plants, [46] or deep on the ocean floor. [47] On the land, it has been reported that Gammaproteobacteria species have been isolated from Robinia pseudoacacia [48] and other plants, [49] [50] while in the deep sea a sulfur-oxidizing gammaproteobacteria was found in a hydrothermal vent chimney; [51] 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, [52] and in addition, Gammaproteobacteria can have complex relationships with other species that live around thermal springs, [53] 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. [54] [55]

Pathogens

Gammaproteobacteria include several medically and scientifically important groups of bacteria, such as the families Enterobacteriaceae , Vibrionaceae , and Pseudomonadaceae . A number of human pathogens belong to this class, including Yersinia pestis , Vibrio cholerae , Pseudomonas aeruginosa , Escherichia coli , and some species of Salmonella . The class also contains plant pathogens such as Xanthomonas axonopodis pv. citri (citrus canker), Pseudomonas syringae pv. actinidiae (kiwifruit Psa outbreak), and Xylella fastidiosa. In the marine environment, several species from this class can infect different marine organisms, such as species in the genus Vibrio which affect fish, shrimp, corals or oysters, [56] and species of Salmonella which affect grey seals (Halichoerus grypus). [57] [58]

See also

Related Research Articles

<span class="mw-page-title-main">Pseudomonadota</span> Phylum of Gram-negative bacteria

Pseudomonadota is a major phylum of Gram-negative bacteria. Currently, they are considered the predominant phylum within the realm of bacteria. They are naturally found as pathogenic and free-living (non-parasitic) genera. The phylum comprises six classes Acidithiobacillia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria. The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence.

<i>Riftia</i> Giant tube worm (species of annelid)

Riftia pachyptila, commonly known as the giant tube worm and less commonly known as the giant beardworm, is a marine invertebrate in the phylum Annelida related to tube worms commonly found in the intertidal and pelagic zones. R. pachyptila lives on the floor of the Pacific Ocean near hydrothermal vents. The vents provide a natural ambient temperature in their environment ranging from 2 to 30 °C, and this organism can tolerate extremely high hydrogen sulfide levels. These worms can reach a length of 3 m, and their tubular bodies have a diameter of 4 cm (1.6 in).

<span class="mw-page-title-main">Sulfur cycle</span> Biogeochemical cycle of sulfur

The important sulfur cycle is a biogeochemical cycle in which the sulfur moves between rocks, waterways and living systems. It is important in geology as it affects many minerals and in life because sulfur is an essential element (CHNOPS), being a constituent of many proteins and cofactors, and sulfur compounds can be used as oxidants or reductants in microbial respiration. The global sulfur cycle involves the transformations of sulfur species through different oxidation states, which play an important role in both geological and biological processes. Steps of the sulfur cycle are:

<span class="mw-page-title-main">Sulfur-reducing bacteria</span> Microorganisms able to reduce elemental sulfur to hydrogen sulfide

Sulfur-reducing bacteria are microorganisms able to reduce elemental sulfur (S0) to hydrogen sulfide (H2S). These microbes use inorganic sulfur compounds as electron acceptors to sustain several activities such as respiration, conserving energy and growth, in absence of oxygen. The final product of these processes, sulfide, has a considerable influence on the chemistry of the environment and, in addition, is used as electron donor for a large variety of microbial metabolisms. Several types of bacteria and many non-methanogenic archaea can reduce sulfur. Microbial sulfur reduction was already shown in early studies, which highlighted the first proof of S0 reduction in a vibrioid bacterium from mud, with sulfur as electron acceptor and H
2 as electron donor. The first pure cultured species of sulfur-reducing bacteria, Desulfuromonas acetoxidans, was discovered in 1976 and described by Pfennig Norbert and Biebel Hanno as an anaerobic sulfur-reducing and acetate-oxidizing bacterium, not able to reduce sulfate. Only few taxa are true sulfur-reducing bacteria, using sulfur reduction as the only or main catabolic reaction. Normally, they couple this reaction with the oxidation of acetate, succinate or other organic compounds. In general, sulfate-reducing bacteria are able to use both sulfate and elemental sulfur as electron acceptors. Thanks to its abundancy and thermodynamic stability, sulfate is the most studied electron acceptor for anaerobic respiration that involves sulfur compounds. Elemental sulfur, however, is very abundant and important, especially in deep-sea hydrothermal vents, hot springs and other extreme environments, making its isolation more difficult. Some bacteria – such as Proteus, Campylobacter, Pseudomonas and Salmonella – have the ability to reduce sulfur, but can also use oxygen and other terminal electron acceptors.

<span class="mw-page-title-main">Iron-oxidizing bacteria</span> Bacteria deriving energy from dissolved iron

Iron-oxidizing bacteria are chemotrophic bacteria that derive energy by oxidizing dissolved iron. They are known to grow and proliferate in waters containing iron concentrations as low as 0.1 mg/L. However, at least 0.3 ppm of dissolved oxygen is needed to carry out the oxidation.

<i>Beggiatoa</i> Genus of bacteria

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<span class="mw-page-title-main">Zetaproteobacteria</span> Class of bacteria

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<i>Olavius algarvensis</i> Species of annelid worm

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Sulfurimonas is a bacterial genus within the class of Campylobacterota, known for reducing nitrate, oxidizing both sulfur and hydrogen, and containing Group IV hydrogenases. This genus consists of four species: Sulfurimonas autorophica, Sulfurimonas denitrificans, Sulfurimonas gotlandica, and Sulfurimonas paralvinellae. The genus' name is derived from "sulfur" in Latin and "monas" from Greek, together meaning a “sulfur-oxidizing rod”. The size of the bacteria varies between about 1.5-2.5 μm in length and 0.5-1.0 μm in width. Members of the genus Sulfurimonas are found in a variety of different environments which include deep sea-vents, marine sediments, and terrestrial habitats. Their ability to survive in extreme conditions is attributed to multiple copies of one enzyme. Phylogenetic analysis suggests that members of the genus Sulfurimonas have limited dispersal ability and its speciation was affected by geographical isolation rather than hydrothermal composition. Deep ocean currents affect the dispersal of Sulfurimonas spp., influencing its speciation. As shown in the MLSA report of deep-sea hydrothermal vents Campylobacterota, Sulfurimonas has a higher dispersal capability compared with deep sea hydrothermal vent thermophiles, indicating allopatric speciation.

<span class="mw-page-title-main">Microbial oxidation of sulfur</span>

Microbial oxidation of sulfur is the oxidation of sulfur by microorganisms to build their structural components. The oxidation of inorganic compounds is the strategy primarily used by chemolithotrophic microorganisms to obtain energy to survive, grow and reproduce. Some inorganic forms of reduced sulfur, mainly sulfide (H2S/HS−) and elemental sulfur (S0), can be oxidized by chemolithotrophic sulfur-oxidizing prokaryotes, usually coupled to the reduction of oxygen (O2) or nitrate (NO3−). Anaerobic sulfur oxidizers include photolithoautotrophs that obtain their energy from sunlight, hydrogen from sulfide, and carbon from carbon dioxide (CO2).

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<span class="mw-page-title-main">Marine microbiome</span>

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Ann Patricia Wood is a retired British biochemist and bacteriologist who specialized in the ecology, taxonomy and physiology of sulfur-oxidizing chemolithoautotrophic bacteria and how methylotrophic bacteria play a role in the degradation of odour causing compounds in the human mouth, vagina and skin. The bacterial genus Annwoodia was named to honor her contributions to microbial research in 2017.

<span class="mw-page-title-main">Sponge microbiomes</span>

Sponge microbiomes are diverse communities of microorganisms in symbiotic association with marine sponges as their hosts. These microorganisms include bacteria, archaea, fungi, viruses, among others. The sponges have the ability to filter seawater and recycle nutrients while providing a safe habitat to many microorganisms, which provide the sponge host with fixed nitrogen and carbon, and stimulates the immune system. Together, a sponge and its microbiome form a holobiont, with a single sponge often containing more than 40 bacterial phyla, making sponge microbial environments a diverse and dense community. Furthermore, individual holobionts work hand in hand with other near holobionts becoming a nested ecosystem, affecting the environment at multiple scales.

References

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