User:Battloglio/sandbox

Read more about the course assignments here here or by visiting our University webpage here

The Class Gammaproteobacteria belongs to the Proteobacteria phylum and contains about 250 genera, which makes it the most genera-rich taxa of the Prokaryotes. Several medically, ecologically, and scientifically important groups of bacteria belong to this class.

The word Gammaproteobacteria comes from three Greek words: the Greek letter "gamma" (γ) meaning "changeable", the word proteakos (πρωτεϊκός) "little stick", and βακτήριον, that means bacterium. The name is referred to Proteus, the Greek sea god who could change his shape. This group is composed by all Gram-negative microbes and is the most phylogenetically and physiologically diverse class of Proteobacteria. These microorganisms can live in several terrestrial and marine environments, in which they play various important roles, including extreme environments like the hydrotermal vents. They generally have different shapes, like rods, curved rods, cocci, spirilla, and filaments and include free living bacteria, biofilm formers, commensals and symbionts (e.g. Beggioatoa sp.), some also have the distinctive trait of being bioluminescent. Metabolisms found in the different genera are very different; there are both aerobic and anaerobic (obligate or facultative) species, chemolithoautotrophics, chemoorganotrophics, photoautotrophs and heterotrophs.

Phylogeny
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 based on ribosomal RNA, or a multiprotein approach. It is still very difficult to resolve the phylogeny of this bacterial class.

Here, it is reported a clade based on 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.

Significance and applications
Gammaproteobacteria, especially the orders Alteromonadales and the Vibrionales, are fundamental in marine and coastal ecosystems because they are the major groups involved in the nutrients cycling.

Gammaproteobacteria, despite their fame as pathogens, find their application in a huge number of areas, such as bioremediation and biosynthesis.

Gammaproteobacteria can be used as a microbial fuel cell(MFC) element that applies their ability to dissimilate various metals. This energy could be collected as one of the most environmentally friendly and sustainable energy production systems. They are also used as biological methane filters. Phototrophic purple sulfur bacteria are used in wastewater treatment processes and the ability of some gammaproteobacteria (e.g. the genus Alcanivorax ) to bioremediate oil is becoming increasingly important to degrade crude oil after oil spills by microbial activity.

Some species of Gammaproteobacterias from the family Chromatiaceae are notable because might be involved for the production of vitamin B12.

An important aspect of the application is the ability of some gammaproteobacteria to synthesize Poly-b-hydroxyalkanoate (PHA). This is a polymer that is used for the production of biodegradable plastics. Also lots of Gammaproteobacteria species are able to generate secondary metabolites with antibacterial properties.

Ecology
Gammaproteobacteria, as the second diverse bacterial class, are widely distributed and abundant in various ecosystems such as soil, freshwater lakes and rivers, oceans and salt lakes. For example, Gammaproteobacteria constituted about 6–20% (average of 14%) of bacterioplankton in different oceans. And current researches have revealed their worldwide propagation in deep-sea and coastal sediments.

In seawater Bacterial community composition could be shaped by miscellaneous environmental parameters, such as salinity, pH, phosphorus and total organic carbon contents. The relative abundance of Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria increases with increasing soil pH.

The dissolved organic carbon (DOC) concentration is one key environmental parameter shaping bacterial community composition. The relative abundance of Betaproteobacteria and Gammaproteobacteria was positively correlated with DOC.

Marine sediments are the largest carbon sink on Earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, by the Gammaproteobacteria, which have not been cultured yet.

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. 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.

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. 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.

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.

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

The members of  Nitrosococcus - with the exception of Nitrosococcus mobilis - are ammonia oxidizers and obligate halophilic bacteria.

Among Gammaproteobacteria there 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.

Large amounts of hydrogen sulfide are produced by sulfate-reducing bacteria in organic-rich coastal sediments (Jørgensen, 1982). (No link)

Thanks 16S rRNA gene analysis have been detected different specialist sulfide oxidizers in the Gammaporteobacteria class, of which the most important are present in the order of Thiotrichales, such as  Beggiatoa,Thioploca and Thiomargarita.

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.

Another type of metabolism carried out by Gammaproteobacteria is the methanogenesis, 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.

Another group of Gammaproteobacteria are Purple sulfur bacteria and they are anoxygenic phototrophic iron‐oxidizers and they are part of the genus 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).

In the class of Gammaproteobacteria 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 enviroment. The genera carring 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 non-hydrocarbon substrates a 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.

Most frequent pathway to synthesize glucose among Gammaporteobacteria members is Calvin–Benson–Bassham (CBB) cycle, but in addition some species of the Gammaproteobacteria class may use the rTCA cycle, as shown in studies. 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. This researches showed that some species of Gammaproteobacteria may express two different carbon fixation pathways simultaneously.

Symbiosis
Symbiosis is a close and 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, underground , or deep on the ocean floor.

It has been reported that Gammaproteobacteria species have been isolated from Robinia pseudoacacia and other plants.

A sulfur-oxidizing gammaproteobacterium was found in a hydrothermal vent chimney. By entering into symbiotic relationships in deep sea areas, sulfur-oxidizing chemolithotrophic microbes receive additional organic hydrocarbons in hydrothermal ecosystems. Some Gammaproteobacteria are arsymbiotic with geothermic ocean vent-dwelling animals.

In addition, Gammaproteobacteria can have complex relationships with other species that live around thermal springs. For example, with the shrimp Rimicaris exoculata living from hydrothermal vents on the Mid-Atlantic Ridge.

In general, most endosymbionts lack many of their family characteristics due to significant genome reduction.

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, and species of Salmonella that can also infect grey seals (Halichoerus grypus). Below are described some of the most famous human pathogens belonging to the class Gammaproteobacteria.

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 include and 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. 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 that can grow as biofilms and contains an excreted exopolysaccharide that can infect several the surfaces. The most common microbe that belong in Pseudomonas genus is Pseudomonas aeruginosa, 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 ; Besides 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.