Epsilonproteobacteria

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Epsilonproteobacteria
ARS Campylobacter jejuni.jpg
Campylobacter
Scientific classification
Domain: Bacteria
Phylum: Proteobacteria
Class:Epsilonproteobacteria
Orders

Epsilonproteobacteria are a class of Proteobacteria. [1] All species of this class are, like all Proteobacteria, Gram-negative.

Proteobacteria phylum of Gram-negative bacteria

Proteobacteria is a major phylum of gram-negative bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia, Legionellales and many other notable genera. Others are free-living (non-parasitic) and include many of the bacteria responsible for nitrogen fixation.

In biology, a species ( ) is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined. While these definitions may seem adequate, when looked at more closely they represent problematic species concepts. For example, the boundaries between closely related species become unclear with hybridisation, in a species complex of hundreds of similar microspecies, and in a ring species. Also, among organisms that reproduce only asexually, the concept of a reproductive species breaks down, and each clone is potentially a microspecies.

Contents

The Epsilonproteobacteria consist of few known genera, mainly the curved to spirilloid Wolinella spp., Helicobacter spp., and Campylobacter spp. Most of the known species inhabit the digestive tracts of animals and serve as symbionts (Wolinella spp. in cattle) or pathogens (Helicobacter spp. in the stomach, Campylobacter spp. in the duodenum).

The genus Wolinella is a member of the Campylobacterales order of Bacteria. The order Campylobacterales includes human pathogens such as Helicobacter pylori and Campylobacter jejuni.

<i>Helicobacter</i> genus of bacteria

Helicobacter is a genus of Gram-negative bacteria possessing a characteristic helical shape. They were initially considered to be members of the genus Campylobacter, but in 1989, Goodwin et al. published sufficient reasons to justify the new genus name Helicobacter. The genus Helicobacter contains about 35 species.

<i>Campylobacter</i> genus of bacteria

Campylobacter is a genus of Gram-negative bacteria. Campylobacter typically appear comma- or s-shaped, and are motile.

Numerous environmental sequences and isolates of Epsilonproteobacteria have also been recovered from hydrothermal vents and cold seep habitats. Examples of isolates include Sulfurimonas autotrophica, [2] Sulfurimonas paralvinellae, [3] Sulfurovum lithotrophicum [4] and Nautilia profundicola . [5] A member of the class Epsilonproteobacteria occurs as an endosymbiont in the large gills of the deepwater sea snail Alviniconcha hessleri . [6]

Hydrothermal vent A fissure in a planets surface from which geothermally heated water issues

A hydrothermal vent is a fissure on the seafloor from which geothermally heated water issues. Hydrothermal vents are commonly found near volcanically active places, areas where tectonic plates are moving apart at spreading centers, ocean basins, and hotspots. Hydrothermal deposits are rocks and mineral ore deposits formed by the action of hydrothermal vents.

Cold seep Ocean floor area where hydrogen sulfide, methane and other hydrocarbon-rich fluid seepage occurs

A cold seep is an area of the ocean floor where hydrogen sulfide, methane and other hydrocarbon-rich fluid seepage occurs, often in the form of a brine pool. Cold does not mean that the temperature of the seepage is lower than that of the surrounding sea water. On the contrary, its temperature is often slightly higher. The "cold" is relative to the very warm conditions of a hydrothermal vent. Cold seeps constitute a biome supporting several endemic species.

Sulfurimonas is a bacterial genus within the class of Epsilonproteobacteria, 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 Epsilonproteobacteria, Sulfurimonas has a higher dispersal capability compared with deep sea hydrothermal vent thermophiles, indicating allopatric speciation.

The Epsilonproteobacteria found at deep-sea hydrothermal vents characteristically exhibit chemolithotrophy, meeting their energy needs by oxidizing reduced sulfur, formate, or hydrogen coupled to the reduction of nitrate or oxygen. [7] Autotrophic Epsilonproteobacteria use the reverse Krebs cycle to fix carbon dioxide into biomass, a pathway originally thought to be of little environmental significance. The oxygen sensitivity of this pathway is consistent with their microaerophilic or anaerobic niche in these environments, and their likely evolution in the Mesoproterozoic oceans, [8] which are thought to have been sulfidic with low levels of oxygen available from cyanobacterial photosynthesis. [9]

The Mesoproterozoic Era is a geologic era that occurred from 1,600 to 1,000 million years ago. The Mesoproterozoic was the first period of Earth's history of which a fairly definitive geological record survives. Continents existed during the preceding era, but little is known about them. The continental masses of the Mesoproterozoic were more or less the same ones that exist today.

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [10] and National Center for Biotechnology Information (NCBI) [11] and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project [12]

National Center for Biotechnology Information database arm of the US National Library of Medicine

The National Centre for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.

The All-Species Living Tree Project collaboration between various academic groups/institutes

'The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria and Archaea. At one stage, 23S sequences were also collected, but this has since stopped.


   Nautiliaceae


Thioreductor micantisoli Nakagawa et al.2005




Caminibacter Alain et al.2002




Lebetimonas acidiphila Takai et al.2005



Nautilia Miroshnichenko et al.2002







Nitratiruptor tergarcus Nakagawa et al.2


   Campylobacterales


Hydrogenimonas thermophila Takai et al.2004




? Sulfuricurvum kujiense Kodama and Watanabe 2004



? Thiovulum majus Hinze 1913





Nitratifractor salsuginis Nakagawa et al.2005



Sulfurovum lithotrophicum Inagaki et al.2004




Sulfurimonas Inagaki et al.2003 emend. Takai et al.2006




   Helicobacteraceae


Wolinella Tanner et al.1981



Helicobacter Goodwin et al.1989 emend. Vandamme et al.1991



   Campylobacteraceae


?Candidatus Thioturbo danicus Muyzer et al. 2005



Arcobacter Vandamme et al.1991 emend. Vandamme et al.1992




Sulfurospirillum Schumacher et al.1993 emend. Luijten et al.2003



Campylobacter Sebald and Véron 1963 emend. Vandamme et al.2010









Notes:

Related Research Articles

The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. The name 'Aquificae' was given to this phylum based on an early genus identified within this group, Aquifex, which is able to produce water by oxidizing hydrogen. They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods. They are true bacteria as opposed to the other inhabitants of extreme environments, the Archaea.

Halopiger is a genus of archaeans in the family Halobacteriaceae that have high tolerance to salinity.

Nautilia profundicola is a Gram-negative chemolithoautotrophic epsilonproteobacterium found around hydrothermal vents in the deep ocean. It was first discovered in 1999 on the East Pacific Rise at depth of 2,500 metres (8,200 ft), on the surface of the polychaete worm Alvinella pompejana. Nautilia profundicola lives symbiotically on the dorsal hairs of A. pompejana but they may also form biofilms and live independently on the walls of hydrothermal vents. The ability of N. profundicola to survive in an anaerobic environment rich in sulfur, H2 and CO2 of varying temperature makes it a useful organism to study, as these are the conditions that are theorized to have prevailed around the time of the earliest life on earth.

Sulfurovum is a genus within the Epsilonproteobacteria which was first described in 2004 with the isolation and description of the type species Sulfurovum lithotrophicum from Okinawa trough hydrothermal sediments. Named for their ability to oxidize sulfur and their egg-like shape, cells are gram-negative, coccoid to short rods. Mesophilic chemolithoautotrophic growth occurs by oxidation of sulfur compounds coupled to the reduction of nitrate or molecular oxygen.

Sulfurovum lithotrophicum is a species of bacteria, the type species of its genus. It is a sulfur-oxidizing chemolithoautotroph within the ε-Proteobacteria isolated from Okinawa Trough hydrothermal sediments. It is mesophilic and also oxidises thiosulfate. It is a Gram-negative, non-motile and coccoid to oval-shaped bacterium. The type strain is 42BKTT.

The Nautiliaceae are a family of bacteria placed in an order to itself, Nautiliales, or in the order Campylobacterales. The members of the family are all thermophilic. They are:

Palaeococcus ferrophilus is a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. It cells are irregular cocci and motile with multiple polar flagella.

Methylocella tundrae is a species of bacterium. It is notable for oxidising methane. Its cells are aerobic, Gram-negative, non-motile, dinitrogen-fixing rods. Strain T4T is the type strain.

Sulfurimonas autotrophica is a sulfur- and thiosulfate-oxidizing ε-proteobacterium. It is mesophilic, and its cells are short rods, each being motile by means of a single polar flagellum. Its genome has been sequenced.

Sulfurimonas paralvinellae is a hydrogen- and sulfur-oxidizing ε-proteobacterium. It is a mesophilic chemolithoautotroph.

Persephonella guaymasensis is a thermophilic, hydrogen-oxidizing microaerophile first isolated from a deep-sea hydrothermal vent. It is strictly chemolithoautotrophic, microaerophilic, motile, 2-4 micrometres in size, rod-shaped, Gram-negative and non-sporulating. Its type strain is EX-H2T.

Nautilia lithotrophica is a thermophilic sulfur-reducing epsilon-proteobacterium isolated from a deep-sea hydrothermal vent. It is strictly anaerobic, with type strain 525T.

Caminibacter profundus is a species of moderately thermophilic, microaerobic to anaerobic, chemolithoautotrophic bacterium. It is a Gram-negative, non-motile rod, with type strain CRT.

Deferribacter desulfuricans is a species of sulfur-, nitrate- and arsenate-reducing thermophile first isolated from a deep-sea hydrothermal vent. It is an anaerobic, heterotrophic thermophile with type strain SSM1T.

Lebetimonas is a genus of bacteria from the family Nautiliaceae.

Lebetimonas acidiphila is a thermophilic, acidophilic, hydrogen-oxidizing and motile bacterium from the genus of Lebetimonas. To observe growth there temperature should be between 30 to 68 degrees celsius.

Nautilia abyssi is a thermophilic, sulfur-reducing and strictly anaerobic bacterium from the genus of Nautilia which has been isolated from a hydrothermal chimney from the East Pacific Rise.

Nautilia nitratireducens is a Gram-negative thermophilic, chemosynthetic, anaerobic bacterium from the genus of Nautilia which has been isolated from a hydrothermal vent from the East Pacific Rise.

References

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