Deinococcus | |
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A tetrad of D. radiodurans | |
Scientific classification | |
Domain: | Bacteria |
Phylum: | Deinococcota |
Class: | Deinococci |
Order: | Deinococcales |
Family: | Deinococcaceae Brooks and Murray 1981 |
Genus: | Deinococcus Rainey et al. 1997 |
Type species | |
Deinococcus radiodurans Raj et al. 1960 ex Brooks and Murray 1981 | |
Species | |
See text. | |
Synonyms | |
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Deinococcus (from the Greek : δεινός, deinos, "dreadful, strange" and κόκκος, kókkos, "granule" [1] ) is in the monotypic family Deinococcaceae, and one genus [2] of three in the order Deinococcales [3] [4] of the bacterial phylum Deinococcota highly resistant to environmental hazards. These bacteria have thick cell walls that give them Gram-positive stains, but they include a second membrane and so are closer in structure to Gram-negative bacteria. Deinococcus survive when their DNA is exposed to high doses of gamma and UV radiation. Whereas other bacteria change their structure in the presence of radiation, such as by forming endospores, Deinococcus tolerate it without changing their cellular form and do not retreat into a hardened structure. They are also characterized by the presence of the carotenoid pigment deinoxanthin that give them their pink color. They are usually isolated according to these two criteria. In August 2020, scientists reported that bacteria from Earth, particularly Deinococcus bacteria, were found to survive for three years in outer space, based on studies conducted on the International Space Station. These findings support the notion of panspermia, the hypothesis that life exists throughout the Universe, distributed in various ways, including space dust, meteoroids, asteroids, comets, planetoids or contaminated spacecraft. [5] [6]
Members of Deinococcus can be distinguished from all other bacteria through molecular signatures known as conserved signature indels (CSIs) and proteins (CSPs). An earlier study on Deinococcus identified nine CSIs and 58 CSPs which were exclusively shared by members of this genus. [7] Some of the identified CSPs such as the DNA damage repair protein PprA and the single-stranded DNA-binding protein DdrB are thought to have functional roles in the DNA repair mechanism and radioresistance phenotype of Deinococcus. [7]
In a more recent work focused on DNA repair proteins an additional 22 CSIs were identified as specific to this genus, including a 30 amino acid insert in the UvrA1 protein that is suggested to play in a role in the resistance ability of Deinococcus species against radiation and oxidation damage. [8]
The uvrA1 gene in Deinococcus was found to form a novel genetic linkage with the genes of the proteins dCSP-1 (a transmembrane protein found only in Deinococcus species), DsbA and DsbB. The latter two proteins play a central role in the formation of disulfide bonds in proteins via oxidation-reduction of cysteine rich motifs (CXXC). [9] The above cluster of genes forms a novel operon unique to Deinococcus species and the encoded proteins are predicted to function together to combat against DNA damage caused by reactive oxidative species from radiation. [8]
The 30 aa CSI present in UvrA1 and another 5-7 aa CSI present in DsbA are located on surface loops of the proteins. The surface exposed loops/patches formed by these CSIs are thought to mediate protein-protein interactions with the transmembrane protein dCSP-1, thus facilitating a sequence of electron transfers that ultimately ameliorates oxidative damage. [8]
Although all species of the genus Deinococcus are related by definition, they exhibit substantial differences across their genomes. Most species appear to have about 3,000 genes, but only a fraction of them are shared in other species. For example, a 3-species comparison among D. radiodurans , D. deserti , and D. geothermalis shows that about two thirds of each genome is shared by all three species, but close to a third is specific and only found in one of the species (see figure). Once more genomes are included in such comparisons, the core genome will almost certainly be much smaller. [10]
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [11] and National Center for Biotechnology Information (NCBI). [12] As of August 2011 [update] , there were 47 species of Deinococcus described
16S rRNA based LTP_08_2023 [13] [14] [15] | 120 marker proteins based GTDB 08-RS214 [16] [17] [18] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Species incertae sedis:
The Aquificota phylum is a diverse collection of bacteria that live in harsh environmental settings. The name Aquificota 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.
Deinococcota is a phylum of bacteria with a single class, Deinococci, that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria.
Thermus is a genus of thermophilic bacteria. It is one of several bacteria belonging to the Deinococcota phylum. Thermus species can be distinguished from other genera in the family Thermaceae as well as all other bacteria by the presence of eight conserved signature indels (CSIs) found in proteins such as adenylate kinase and replicative DNA helicase as well as 14 conserved signature proteins (CSPs) that are exclusively shared by members of this genus.
Halomonadaceae is a family of halophilic Pseudomonadota.
Rubrobacter is a genus of Actinomycetota. It is radiotolerant and may rival Deinococcus radiodurans in this regard.
Arcanobacterium is a genus of bacteria. They are gram-positive, non–acid fast, nonmotile, facultatively anaerobic, and non–endospore forming. They are widely distributed in nature in the microbiota of animals and are mostly innocuous. Some can cause disease in humans and other animals. As with various species of a microbiota, they usually are not pathogenic but can occasionally opportunistically capitalize on atypical access to tissues or weakened host defenses.
Deinococcus radiodurans is a bacterium, an extremophile and one of the most radiation-resistant organisms known. It can survive cold, dehydration, vacuum, and acid, and therefore is known as a polyextremophile. The Guinness Book Of World Records listed it as the world's toughest known bacterium.
Dehalococcoidia is a class of Chloroflexota, a phylum of Bacteria. It is also known as the DHC group.
Polynucleobacter is a genus of bacteria, originally established by Heckmann and Schmidt (1987) to exclusively harbor obligate endosymbionts of ciliates belonging to the genus Euplotes.
Tepidimonas ignava is a gram-negative, slightly thermophilic, motile bacterium with a single polar flagellum from the genus Tepidimonas, which was isolated from the hot spring at São Pedro do Sul in central Portugal.
Exiguobacterium is a genus of bacilli and a member of the low GC phyla of Bacillota. Collins et al. first described the genus Exiguobacterium with the characterization of E. aurantiacum strain DSM6208T from an alkaline potato processing plant. It has been found in areas covering a wide range of temperatures (-12 °C—55 °C) including glaciers in Greenland and hot springs in Yellowstone, and has been isolated from ancient permafrost in Siberia. This ability to survive in varying temperature extremes makes them an important area of study. Some strains in addition to dynamic thermal adaption are also halotolerant, can grow within a wide range of pH values (5-11), tolerate high levels of UV radiation, and heavy metal stress.
Deinococcus ficus strain CC-FR2-10T is a recently discovered gram-positive bacteria which plays a role in the production of nitrogen fertilizer. It was originally isolated from a Ficus plant, hence its name.
Dehalogenimonas lykanthroporepellens is an anaerobic, Gram-negative bacteria in the phylum Chloroflexota isolated from a Superfund site in Baton Rouge, Louisiana. It is useful in bioremediation for its ability to reductively dehalogenate chlorinated alkanes.
Deinococcus frigens is a species of low temperature and drought-tolerating, UV-resistant bacteria from Antarctica. It is Gram-positive, non-motile and coccoid-shaped. Its type strain is AA-692. Individual Deinococcus frigens range in size from 0.9-2.0 μm and colonies appear orange or pink in color. Liquid-grown cells viewed using phase-contrast light microscopy and transmission electron microscopy on agar-coated slides show that isolated D. frigens appear to produce buds. Comparison of the genomes of Deiococcus radiodurans and D. frigens have predicted that no flagellar assembly exists in D. frigens.
Deinococcus deserti is a Gram-negative, rod-shaped bacterium that belongs to the Deinococcaceae, a group of extremely radiotolerant bacteria. D. deserti and other Deinococcaceae exhibit an extraordinary ability to withstand ionizing radiation.
Dyadobacter is a genus of gram negative rod-shaped bacteria belonging to the family Spirosomaceae in the phylum Bacteroidota. Typical traits of the genus include yellow colony colour, positive flexirubin test and non-motile behaviours. They possess an anaerobic metabolism, can utilise a broad range of carbon sources, and test positive for peroxide catalase activity. The type species is Dyadobacter fermentans, which was isolated from surface sterilised maize leaves,.
Rhodoluna is a Gram-positive, non-spore-forming and non-motile genus of bacteria from the family of Microbacteriaceae. The type strain of the only species Rhodoluna lacicola encodes an actinorhodopsin, which is a light-diven proton pump enabling light energy conversion, potentially resulting in a mixotrophic physiology. The type strain of R. lacicola was isolated from Lake Tai in China. The type strain MWH-Ta8 is remarkable for its very small cell size ultramicrobacterium and its small genome size of only 1.4 Mbp. The type strain has a planktonic lifestyle, that is freely floating the water column of aquatic systems. Currently, the genus Rhodoluna contains two described species.
The Temperatibacteraceae are a family of bacteria.
Schleiferiaceae is a family of bacteria in the order Flavobacteriales.
Holophagae is a class of Acidobacteriota.