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Gammaproteobacteria
The Class Gammaproteobacteria belongs to the Proteobacteria phylum and contains about 250 genera, which makes it the most genera-rich taxa of the Prokaryotes.[1] Several medically, ecologically, and scientifically important groups of bacteria belong to this class. It is composed by all Gram-negative microbes and is the most phylogenetically and physiologically diverse class of Proteobacteria.[2] The word Gammaproteobacteria comes from three Greek words: the Greek letter "gamma" (?) meaning "changeable", the word proteakos () "little stick", and , that means "bacterium", so it means "changeable little stick bacterium". The name refers to Proteus, the Greek sea god who could change his shape.[3] These microorganisms can live in several terrestrial and marine environments, in which they play various important roles, including extreme environments like the hydrothermal vents. They generally have different shapes, like rods, curved rods, cocci, spirilla, and filaments[4] and include free living bacteria, biofilm formers, commensals and symbionts,[5] some also have the distinctive trait of being bioluminescent.[6] Metabolisms found in the different genera are very different; there are both aerobic and anaerobic (obligate or facultative) species, chemolithoautotrophics, chemoorganotrophics, photoautotrophs and heterotrophs.[7]
Phylogeny of Gammaproteobacteria after[10] 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.)
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]
Ecology
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]
Metabolism
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]
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
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]
Pathogens
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]
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^T. Gutierrez - 2019 - Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK
^Koppenhagen VB, Schlingmann G, Schaer W, Dresow. Moo-young M, Vezina C, Singh K (eds.). "Extracellular metabolites from phototrophic bacteria as possible intermediates in the biosynthesis of vitamin B12". Fermentation Products. Pergamon: 247-252. ISBN978-0-08-025385-5.
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^Broszat M, Nacke H, Blasi R, Siebe C, Huebner J, Daniel R, Grohmann E. 2014. Wastewater irrigation increases the abundance of potentially harmful Gammaproteobacteria in soils in Mezquital Valley, Mexico. Appl Environ Microbiol.
^Jiang H, Dong H, Ji S, Ye Y, Wu N (2007-09-26). "Microbial Diversity in the Deep Marine Sediments from the Qiongdongnan Basin in South China Sea". Geomicrobiology Journal. 24 (6): 505-517. doi:10.1080/01490450701572473. S2CID130552094.
^Stewart FJ, Newton IL, Cavanaugh CM (September 2005). "Chemosynthetic endosymbioses: adaptations to oxic-anoxic interfaces". Trends in Microbiology. 13 (9): 439-48. doi:10.1016/j.tim.2005.07.007. PMID16054816.
^Cesar Mota, Jennifer Ridenoure, Jiayang Cheng, Francis L. de los Reyes, High levels of nitrifying bacteria in intermittently aerated reactors treating high ammonia wastewater. FEMS Microbiology Ecology, Volume 54, Issue 3, November 2005, Pages 391-400
^Sabine Lenk, Julia Arnds, Katrice Zerjatke, Niculina Musat, Rudolf Amann and Marc Mußmann* Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany. Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment. (2011)
^Sabrina Hedrich,Michael Schlomann and D. Barrie Johnson. The iron-oxidizing proteobacteria. School of Biological Sciences, College of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, UK 2 Interdisciplinary Ecological Center, TU Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany. (2011)
^Terry J. McGenity, Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes, 2019 143-152; 181-189; 191-205.
^Kikuchi Y, Hosokawa T, Nikoh N, Fukatsu T (February 2012). "Gut symbiotic bacteria in the cabbage bugs Eurydema rugosa and Eurydema dominulus (Heteroptera: Pentatomidae)". Applied Entomology and Zoology. 47 (1): 1-8. doi:10.1007/s13355-011-0081-7. S2CID14943700.
^Shiraishi A, Matsushita N, Hougetsu T (August 2010). "Nodulation in black locust by the Gammaproteobacteria Pseudomonas sp. and the Betaproteobacteria Burkholderia sp". Systematic and Applied Microbiology. 33 (5): 269-74. doi:10.1016/j.syapm.2010.04.005. PMID20542651.
^Ghosh PK, De TK, Maiti TK (2015-04-01). "Ascorbic acid production in root, nodule and Enterobacter spp. (Gammaproteobacteria) isolated from root nodule of the legume Abrus precatorius L.". Biocatalysis and Agricultural Biotechnology. 4 (2): 127-134. doi:10.1016/j.bcab.2014.11.006.
^Benhizia Y, Benhizia H, Benguedouar A, Muresu R, Giacomini A, Squartini A (August 2004). "Gamma proteobacteria can nodulate legumes of the genus Hedysarum". Systematic and Applied Microbiology. 27 (4): 462-8. doi:10.1078/0723202041438527. PMID15368852.