Deinococcus–Thermus
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''Deinococcota'' (synonym, ''Deinococcus-Thermus'') is a
phylum In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below kingdom and above class. Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature f ...
of bacteria with a single class, ''Deinococci'', that are highly resistant to environmental hazards, also known as
extremophiles An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism that is able to live (or in some cases thrive) in extreme environments, i.e. environments that make survival challenging such as due to extreme temper ...
. 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.


Taxonomy

The phylum ''Deinococcota'' consists of a single class (''
Deinococci ''Deinococcota'' (synonym, ''Deinococcus-Thermus'') 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 ...
'') and two orders: * The ''
Deinococcales ''Deinococcota'' (synonym, ''Deinococcus-Thermus'') 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 ...
'' include two families (''
Deinococcaceae ''Deinococcus'' (from the el, δεινός, ''deinos'', "dreadful, strange" and κόκκος, ''kókkos'', "granule") is in the monotypic family Deinococcaceae, and one genus of three in the order Deinococcales of the bacterial phylum ''Deinococ ...
'' and'' Trueperaceae''), with three genera, ''
Deinococcus ''Deinococcus'' (from the el, δεινός, ''deinos'', "dreadful, strange" and κόκκος, ''kókkos'', "granule") is in the monotypic family Deinococcaceae, and one genus of three in the order Deinococcales of the bacterial phylum ''Deinococ ...
'', ''
Deinobacterium ''Deinobacterium'' is a genus in the ''Deinococcota'' phylum (Bacteria). Not to be confused with ''Deinobacter'', a disused name for '' Deinococcus''. Etymology The name ''Deinobacterium'' derives from: Greek adjective ''deinos (δεινός)'' ...
'' and ''
Truepera ''Truepera'' is one genus of bacteria in the family '' Trueperaceae'' from the phylum ''Deinococcota''. The following points accounts for its characteristics: * These strains form orange/red colonies and have spherical-shaped cells. * Optimum gro ...
''.Garrity GM, Holt JG. (2001) Phylum BIV. "Deinococcus–Thermus". In: Bergey’s manual of systematic bacteriology, pp. 395-420. Eds D. R. Boone, R. W. Castenholz. Springer-: New York.Garrity GM, Bell JA, Lilburn TG. (2005) Phylum BIV. The revised road map to the Manual. In: Bergey’s manual of systematic bacteriology, pp. 159-220. Eds Brenner DJ, Krieg NR, Staley JT, Garrity GM. Springer-: New York. ''
Truepera radiovictrix ''Truepera'' is one genus of bacteria in the family '' Trueperaceae'' from the phylum ''Deinococcota''. The following points accounts for its characteristics: * These strains form orange/red colonies and have spherical-shaped cells. * Optimum gro ...
'' is the earliest diverging member of the order. Within the order, ''
Deinococcus ''Deinococcus'' (from the el, δεινός, ''deinos'', "dreadful, strange" and κόκκος, ''kókkos'', "granule") is in the monotypic family Deinococcaceae, and one genus of three in the order Deinococcales of the bacterial phylum ''Deinococ ...
'' forms a distinct monophyletic cluster with respect to ''
Deinobacterium ''Deinobacterium'' is a genus in the ''Deinococcota'' phylum (Bacteria). Not to be confused with ''Deinobacter'', a disused name for '' Deinococcus''. Etymology The name ''Deinobacterium'' derives from: Greek adjective ''deinos (δεινός)'' ...
'' and ''
Truepera species ''Truepera'' is one genus of bacteria in the family '' Trueperaceae'' from the phylum ''Deinococcota''. The following points accounts for its characteristics: * These strains form orange/red colonies and have spherical-shaped cells. * Optimum gro ...
''. The genus includes several species that are resistant to radiation; they have become famous for their ability to eat nuclear waste and other toxic materials, survive in the vacuum of space and survive extremes of heat and cold. * The ''
Thermales ''Thermales'' is an order of bacteria belonging to the ''Deinococcota'' phylum. They are particularly resistant to heat, and live in the benthic zone of the Gulf of Mexico. Members of the order ''Thermales'' can be distinguished from all other ...
'' include several genera resistant to heat ('' Marinithermus'', ''
Meiothermus ''Meiothermus'' is a genus of ''Deinococcota'' bacteria. Members of ''Meiothermus'' can be reliably distinguished from other genera in the family '' Thermaceae'' as well as all other bacteria by the presence of three conserved signature indel ...
'', '' Oceanithermus'', ''
Thermus ''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 th ...
'', '' Vulcanithermus'', '' Rhabdothermus'') placed within a single family, ''
Thermaceae ''Thermales'' is an order of bacteria belonging to the ''Deinococcota'' phylum. They are particularly resistant to heat, and live in the benthic zone of the Gulf of Mexico. Members of the order ''Thermales'' can be distinguished from all other ...
''. Phylogenetic analyses demonstrate that within the ''
Thermales ''Thermales'' is an order of bacteria belonging to the ''Deinococcota'' phylum. They are particularly resistant to heat, and live in the benthic zone of the Gulf of Mexico. Members of the order ''Thermales'' can be distinguished from all other ...
'', ''
Meiothermus ''Meiothermus'' is a genus of ''Deinococcota'' bacteria. Members of ''Meiothermus'' can be reliably distinguished from other genera in the family '' Thermaceae'' as well as all other bacteria by the presence of three conserved signature indel ...
'' and ''
Thermus ''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 th ...
'' species form a monophyletic cluster, with respect to '' Marinithermus'', '' Oceanithermus'', '' Vulcanithermus'' and '' Rhabdothermus'' that branch as outgroups within the order. This suggests that ''
Meiothermus ''Meiothermus'' is a genus of ''Deinococcota'' bacteria. Members of ''Meiothermus'' can be reliably distinguished from other genera in the family '' Thermaceae'' as well as all other bacteria by the presence of three conserved signature indel ...
'' and ''
Thermus ''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 th ...
'' species are more closely related to one another relative to other genera within the order. '' Thermus aquaticus'' was important in the development of the polymerase chain reaction where repeated cycles of heating DNA to near boiling make it advantageous to use a thermo-stable DNA polymerase enzyme. Though these two groups evolved from a common ancestor, the two mechanisms of resistance appear to be largely independent.


Molecular signatures

Molecular signatures in the form of conserved signature indels (CSIs) and proteins (CSPs) have been found that are uniquely shared by all members belonging to the ''Deinococcota'' phylum. These CSIs and CSPs are distinguishing characteristics that delineate the unique phylum from all other bacterial organisms, and their exclusive distribution is parallel with the observed differences in physiology. CSIs and CSPs have also been found that support order and family-level taxonomic rankings within the phylum. Some of the CSIs found to support order level distinctions are thought to play a role in the respective
extremophilic An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism that is able to live (or in some cases thrive) in extreme environments, i.e. environments that make survival challenging such as due to extreme temper ...
characteristics. The CSIs found in DNA-directed RNA polymerase subunit beta and DNA topoisomerase I in ''
Thermales ''Thermales'' is an order of bacteria belonging to the ''Deinococcota'' phylum. They are particularly resistant to heat, and live in the benthic zone of the Gulf of Mexico. Members of the order ''Thermales'' can be distinguished from all other ...
'' species may be involved in thermophilicity, while those found in Excinuclease ABC, DNA gyrase, and DNA repair protein RadA in ''
Deinococcales ''Deinococcota'' (synonym, ''Deinococcus-Thermus'') 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 ...
'' species may be associated with radioresistance. Two CSPs that were found uniquely for all members belonging to the ''Deinococcus'' genus are well characterized and are thought to play a role in their characteristic radioresistant phenotype. These CSPs include the DNA damage repair protein PprA the single-stranded DNA-binding protein DdrB. Additionally, some genera within this group, including ''
Deinococcus ''Deinococcus'' (from the el, δεινός, ''deinos'', "dreadful, strange" and κόκκος, ''kókkos'', "granule") is in the monotypic family Deinococcaceae, and one genus of three in the order Deinococcales of the bacterial phylum ''Deinococ ...
'', ''
Thermus ''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 th ...
'', and ''
Meiothermus ''Meiothermus'' is a genus of ''Deinococcota'' bacteria. Members of ''Meiothermus'' can be reliably distinguished from other genera in the family '' Thermaceae'' as well as all other bacteria by the presence of three conserved signature indel ...
'', also have molecular signatures that demarcate them as individual genera, inclusive of their respective species, providing a means to distinguish them from the rest of the group and all other bacteria. CSIs have also been found specific for ''
Truepera radiovictrix ''Truepera'' is one genus of bacteria in the family '' Trueperaceae'' from the phylum ''Deinococcota''. The following points accounts for its characteristics: * These strains form orange/red colonies and have spherical-shaped cells. * Optimum gro ...
'' .


Phylogeny


Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) * Phylum Deinococcota Oren and Garrity 2021 ** Class Deinococci Garrity & Holt 2002 Oren, Parte & Garrity 2016 ex Cavalier-Smith 2020; "Thermi" Rinke et al. 2013; "Thermia" Cavalier-Smith 2020">Deinococcia" Oren, Parte & Garrity 2016 ex Cavalier-Smith 2020; "Thermi" Rinke et al. 2013; "Thermia" Cavalier-Smith 2020*** Order
Deinococcales ''Deinococcota'' (synonym, ''Deinococcus-Thermus'') 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 ...
Rainey et al. 1997 rueperales García-López et al. 2020**** Family
Deinococcaceae ''Deinococcus'' (from the el, δεινός, ''deinos'', "dreadful, strange" and κόκκος, ''kókkos'', "granule") is in the monotypic family Deinococcaceae, and one genus of three in the order Deinococcales of the bacterial phylum ''Deinococ ...
Brooks and Murray 1981 emend. Rainey et al. 1997 ***** Genus ''
Deinococcus ''Deinococcus'' (from the el, δεινός, ''deinos'', "dreadful, strange" and κόκκος, ''kókkos'', "granule") is in the monotypic family Deinococcaceae, and one genus of three in the order Deinococcales of the bacterial phylum ''Deinococ ...
'' Brooks and Murray 1981 emend. Rainey et al. 1997 ***** Genus ''
Deinobacterium ''Deinobacterium'' is a genus in the ''Deinococcota'' phylum (Bacteria). Not to be confused with ''Deinobacter'', a disused name for '' Deinococcus''. Etymology The name ''Deinobacterium'' derives from: Greek adjective ''deinos (δεινός)'' ...
'' Ekman et al. 2011 **** Family Trueperaceae Rainey et al. 2005 ***** Genus ''
Truepera ''Truepera'' is one genus of bacteria in the family '' Trueperaceae'' from the phylum ''Deinococcota''. The following points accounts for its characteristics: * These strains form orange/red colonies and have spherical-shaped cells. * Optimum gro ...
'' da Costa, Rainey and Albuquerque 2005 *** Order
Thermales ''Thermales'' is an order of bacteria belonging to the ''Deinococcota'' phylum. They are particularly resistant to heat, and live in the benthic zone of the Gulf of Mexico. Members of the order ''Thermales'' can be distinguished from all other ...
Rainey and Da Costa 2002 **** Family
Thermaceae ''Thermales'' is an order of bacteria belonging to the ''Deinococcota'' phylum. They are particularly resistant to heat, and live in the benthic zone of the Gulf of Mexico. Members of the order ''Thermales'' can be distinguished from all other ...
Da Costa and Rainey 2002 ***** Genus "'' Allomeiothermus''" Jiao et al. 2022 ***** Genus '' Calidithermus'' Raposo et al. 2019 ***** Genus '' Marinithermus'' Sako et al. 2003 ***** Genus ''
Meiothermus ''Meiothermus'' is a genus of ''Deinococcota'' bacteria. Members of ''Meiothermus'' can be reliably distinguished from other genera in the family '' Thermaceae'' as well as all other bacteria by the presence of three conserved signature indel ...
'' Nobre et al. 1996 emend. Albuquerque et al. 2009 ***** Genus '' Oceanithermus'' Miroshnichenko et al. 2003 emend. Mori et al. 2004 ***** Genus '' Rhabdothermus'' Steinsbu et al. 2011 ***** Genus ''
Thermus ''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 th ...
'' Brock and Freeze 1969 emend. Nobre et al. 1996 ***** Genus '' Vulcanithermus'' Miroshnichenko et al. 2003


Sequenced genomes

Currently there are 10 sequenced genomes of strains in this phylum. *''Deinococcus radiodurans'' R1 *''Thermus thermophilus'' HB27 *''Thermus thermophilus'' HB8 *''Deinococcus geothermalis'' DSM 11300 *''Deinococcus deserti'' VCD115 *''Meiothermus ruber'' DSM 1279 *''Meiothermus silvanus'' DSM 9946 *''Truepera radiovictrix'' DSM 17093 *''Oceanithermus profundus'' DSM 14977 The two ''Meiothermus'' species were sequenced under the auspices of the
Genomic Encyclopedia of Bacteria and Archaea Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dime ...
project (GEBA), which aims at sequencing organisms based on phylogenetic novelty and not on pathogenicity or notoriety.


See also

*
List of bacteria genera This article lists the genera of the bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI). However many taxonomic names are ...
*
List of bacterial orders This article lists the orders of the Bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S ...


References

{{DEFAULTSORT:Deinococcus-Thermus Bergey's volume 1 Polyextremophiles Bacteria phyla