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Direct |volume=1 |pages=19 |year=2006 |pmid=16834776 |pmc=1586193 |doi=10.1186/1745-6150-1-19 |doi-access=free }}</ref> * "Xenobacteria" }} '''''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]].<ref name="pmid18076002">{{cite journal|vauthors=Griffiths E, Gupta RS |title=Identification of signature proteins that are distinctive of the ''Deinococcus–Thermus'' phylum |journal=Int. Microbiol. |volume=10 |issue=3 |pages=201–8 |date=September 2007 |pmid=18076002 |url=http://www.im.microbios.org/1003/1003201.pdf |url-status=dead |archive-url=https://web.archive.org/web/20110614000738/http://www.im.microbios.org/1003/1003201.pdf |archive-date=2011-06-14 }}</ref> 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.<ref name="pmid21717204">{{cite journal |vauthors=Gupta RS|title=Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes |journal=Antonie van Leeuwenhoek |volume=100 |issue=2 |pages=171–182|year=2011 |pmid=21717204 |doi=10.1007/s10482-011-9616-8|pmc=3133647}}</ref><ref name="pmid24535491">{{cite journal |vauthors= Campbell C, Sutcliffe IC, Gupta RS |title= Comparative proteome analysis of ''Acidaminococcus intestini'' supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria |journal= Arch Microbiol |volume=196 |issue=4 |pages=307–310 |year=2014 |pmid=24535491 |doi=10.1007/s00203-014-0964-4|bibcode= 2014ArMic.196..307C |s2cid= 10721294 |url= http://nrl.northumbria.ac.uk/16439/1/AOMI-D-14-00009.pdf }}</ref><ref name="pmid20637628">{{cite journal |vauthors=Sutcliffe IC|title=A phylum level perspective on bacterial cell envelope architecture |journal=Trends Microbiol |volume=18 |issue=10 |pages=464–470 |year=2010 |pmid=20637628 |doi=10.1016/j.tim.2010.06.005 }}</ref> ==Taxonomy== The phylum ''Deinococcota'' consists of a single class (''[[Deinococci]]'') and two orders: * The ''[[Deinococcales]]'' include two families (''[[Deinococcaceae]]'' and'' [[Trueperaceae]]''), with three genera, ''[[Deinococcus]]'', ''[[Deinobacterium]]'' and ''[[Truepera]]''.<ref name="pmid15927420">{{cite journal |vauthors=Albuquerque L, Simões C, Nobre MF et al. |title=Truepera radiovictrix gen. nov., sp. nov., a new radiation resistant species and the proposal of Trueperaceae fam. nov. |journal=FEMS Microbiol Lett |volume=247 |issue=2 |pages=161–169 |year=2005 |pmid=15927420 |doi=10.1016/j.femsle.2005.05.002 |doi-access=free }}</ref><ref name=Garrity1>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.</ref><ref name=Garrity2>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.</ref> ''[[Truepera radiovictrix]]'' is the earliest diverging member of the order.<ref name="pmid15927420"/> Within the order, ''[[Deinococcus]]'' forms a distinct monophyletic cluster with respect to ''[[Deinobacterium]]'' and ''[[Truepera species]]''.<ref name="pmid27506333">{{cite journal |vauthors=Ho J, Adeolu M, Khadka B, Gupta RS |title= Identification of distinctive molecular traits that are characteristic of the phylum "''Deinococcus–Thermus''" and distinguish its main constituent groups |journal= Syst Appl Microbiol |volume=39 |issue=7 |pages=453–463 |year=2016 |pmid=27506333 |doi=10.1016/j.syapm.2016.07.003 }}</ref> 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.<ref name="pmid10470044">{{cite journal |vauthors=Battista JR, Earl AM, Park MJ |title= Why is ''Deinococcus radiodurans'' so resistant to ionizing radiation? |journal= Trends Microbiol |volume= 7|issue=9 |pages= 362–5|year=1999 |pmid=10470044 |doi=10.1016/S0966-842X(99)01566-8}}</ref> * The ''[[Thermales]]'' include several genera resistant to heat (''[[Marinithermus]]'', ''[[Meiothermus]]'', ''[[Oceanithermus]]'', ''[[Thermus]]'', ''[[Vulcanithermus]]'', ''[[Rhabdothermus]]'') placed within a single family, ''[[Thermaceae]]''.<ref name=Garrity1 /><ref name=Garrity2/><ref>{{cite web |url=http://www.bacterio.cict.fr/classifphyla.html#DeinococcusThermus |title= Classification of bacteria|website=www.bacterio.cict.fr |archive-url=https://web.archive.org/web/20130127030659/http://www.bacterio.cict.fr/classifphyla.html |archive-date=2013-01-27}}</ref> Phylogenetic analyses demonstrate that within the ''[[Thermales]]'', ''[[Meiothermus]]'' and ''[[Thermus]]'' species form a monophyletic cluster, with respect to ''[[Marinithermus]]'', ''[[Oceanithermus]]'', ''[[Vulcanithermus]]'' and ''[[Rhabdothermus]]'' that branch as outgroups within the order.<ref name="pmid27506333"/> This suggests that ''[[Meiothermus]]'' and ''[[Thermus]]'' 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.<ref name="pmid 2530914">{{cite journal |vauthors= Nelson RM, Long GL |title=A general method of site-specific mutagenesis using a modification of the Thermus aquaticus |journal=Anal Biochem |volume=180 |issue=1 |pages=147–151 |year=1989 |pmid=2530914|doi=10.1016/0003-2697(89)90103-6}}</ref> Though these two groups evolved from a common ancestor, the two mechanisms of resistance appear to be largely independent.<ref name="pmid27506333"/><ref name="pmid16242020">{{cite journal |vauthors=Omelchenko MV, Wolf YI, Gaidamakova EK |display-authors=etal |title=Comparative genomics of ''Thermus thermophilus'' and ''Deinococcus radiodurans'': Divergent routes of adaptation to thermophily and radiation resistance |journal=BMC Evol. Biol. |volume=5 |pages=57 |year=2005 |issue=1 |pmid=16242020 |pmc=1274311 |doi=10.1186/1471-2148-5-57 |doi-access=free |bibcode=2005BMCEE...5...57O }}</ref> ==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.<ref name="pmid18076002"/><ref name="pmid27506333"/> These [[conserved signature indels|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]] characteristics.<ref name="pmid27506333"/> The CSIs found in [[DNA-directed RNA polymerase]] subunit beta and [[Type I topoisomerase|DNA topoisomerase I]] in ''[[Thermales]]'' species may be involved in [[thermophile|thermophilicity]],<ref name="pmid 10499798">{{cite journal |vauthors= Zhang G, Campbell EA, Minakhin L, Richter C, Severinov K, Darst SA |title=Crystal structure of ''Thermus aquaticus'' core RNA polymerase at 3.3 A resolution |journal=Cell |volume=98 |issue=6|pages=811–824 |year=1999|pmid=10499798|doi=10.1016/S0092-8674(00)81515-9|s2cid=15695915 |doi-access=free }}</ref> while those found in [[Excinuclease]] ABC, [[DNA gyrase]], and [[DNA repair|DNA repair protein RadA]] in ''[[Deinococcales]]'' species may be associated with [[radioresistance]].<ref name="pmid 15454524">{{cite journal |vauthors= Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, Battista JR |title= Analysis of ''Deinococcus radiodurans'''s transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance |journal=Genetics |volume=168 |issue=1|pages=21–23 |year=2004|pmid=15454524|doi=10.1534/genetics.104.029249| url=http://www.genetics.org/content/168/1/21.long |pmc=1448114}}</ref> 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.<ref name="pmid27506333"/> These CSPs include the DNA damage repair protein PprA the single-stranded DNA-binding protein DdrB. Additionally, some genera within this group, including ''[[Deinococcus]]'', ''[[Thermus]]'', and ''[[Meiothermus]]'', 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.<ref name="pmid27506333"/> CSIs have also been found specific for ''[[Truepera radiovictrix]]'' . ==Phylogeny== {{Technical|section|date=January 2024}} {{see also|Bacterial taxonomy}} {| class="wikitable" |- ! colspan=1 | 16S rRNA based [[The All-Species Living Tree Project|LTP]]_08_2023<ref name=LTP>{{cite web|title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=20 November 2023}}</ref><ref>{{cite web|title=LTP_all tree in newick format|url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_08_2023.ntree |access-date=20 November 2023}}</ref><ref>{{cite web|title=LTP_08_2023 Release Notes| url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_08_2023_release_notes.pdf |access-date=20 November 2023}}</ref> ! colspan=1 | 120 marker proteins based [[Genome Taxonomy Database|GTDB]] 08-RS214<ref name="about">{{cite web |title=GTDB release 08-RS214 |url=https://gtdb.ecogenomic.org/about#4%7C |website=[[Genome Taxonomy Database]]|access-date=10 May 2023}}</ref><ref name="tree">{{cite web |title=bac120_r214.sp_label |url=https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/bac120_r214.sp_labels.tree |website=[[Genome Taxonomy Database]]|access-date=10 May 2023}}</ref><ref name="taxon_history">{{cite web |title=Taxon History |url=https://gtdb.ecogenomic.org/taxon_history/ |website=[[Genome Taxonomy Database]]|access-date=10 May 2023}}</ref> |- | style="vertical-align:top| {{Clade | style=font-size:90%;line-height:80% |label1="Deinococcia" |1={{clade |1={{clade |label1=[[Thermales]] |1={{clade |label1=[[Thermaceae]] |1={{clade |1={{clade |1=''[[Allomeiothermus]]'' |2={{clade |1=''[[Calidithermus]]'' |2=''[[Meiothermus]]'' }} }} |2={{clade |1={{clade |1=''[[Rhabdothermus]]'' |2=''[[Vulcanithermus]]'' }} |2={{clade |1=''[[Oceanithermus]]'' |2={{clade |1=''[[Marinithermus]]'' |2=''[[Thermus]]'' }} }} }} }} }} }} |2={{clade |label1=Trueperales |1={{clade |label1=Trueperaceae |1=''[[Truepera]]'' }} |label2=[[Deinococcales]] |2={{clade |label1=[[Deinococcaceae]] |1={{clade |1=''[[Deinobacterium]]'' |2=''[[Deinococcus]]'' }} }} }} }} }} | {{clade|style=font-size:90%;line-height:80%;width:500px |label1="Deinococcia" |1={{Clade |label1=[[Deinococcales]] |1={{Clade |1={{clade |label1="Marinithermaceae" |1={{clade |1=''[[Marinithermus]]'' |2=''[[Oceanithermus]]'' }} |label2=[[Thermaceae]] |2={{clade |1={{clade |1=''[[Allomeiothermus]]'' |2={{clade |1=''[[Calidithermus]]'' |2=''[[Meiothermus]]'' }} }} |2=''[[Thermus]]'' }} }} |2={{clade |label1=Trueperaceae |1=''[[Truepera]]'' |label2=[[Deinococcaceae]] |2={{clade |1={{clade |1=''[[Deinobacterium]]'' |2=''Deinococcus'' species-group 2 }} |2=''[[Deinococcus]]'' }} }} }} }} }} |} ==Taxonomy== The currently accepted taxonomy is based on the [[List of Prokaryotic names with Standing in Nomenclature]] (LPSN)<ref>{{cite web |author = J.P. Euzéby | url=https://lpsn.dsmz.de/phylum/deinococcota |title=''Deinococcota'' | access-date=2022-01-22|publisher=[[List of Prokaryotic names with Standing in Nomenclature]] (LPSN)}}</ref> and [[National Center for Biotechnology Information]] (NCBI)<ref>{{cite web |author = Sayers| url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=1297&lvl=6&lin=f&keep=1&srchmode=1&unlock |title=Deinococcus-Thermus |access-date=2016-03-20 |publisher=[[National Center for Biotechnology Information]] (NCBI) taxonomy database |display-authors=etal}}</ref> * Phylum '''Deinococcota''' <small>Oren and Garrity 2021</small> ** Class '''Deinococci''' <small>Garrity & Holt 2002</small> ["Deinococcia" <small>Oren, Parte & Garrity 2016 ex Cavalier-Smith 2020</small>; "Thermi" <small>Rinke et al. 2013</small>; "Thermia" <small>Cavalier-Smith 2020</small>] *** Order '''[[Deinococcales]]''' <small>Rainey et al. 1997</small> [Trueperales <small>García-López et al. 2020</small>] **** Family [[Deinococcaceae]] <small>Brooks and Murray 1981 emend. Rainey et al. 1997</small> ***** Genus ''[[Deinococcus]]'' <small>Brooks and Murray 1981 emend. Rainey et al. 1997</small> ***** Genus ''[[Deinobacterium]]'' <small>Ekman et al. 2011</small> **** Family [[Trueperaceae]] <small>Rainey et al. 2005</small> ***** Genus ''[[Truepera]]'' <small>da Costa, Rainey and Albuquerque 2005</small> *** Order '''[[Thermales]]''' <small>Rainey and Da Costa 2002</small> **** Family [[Thermaceae]] <small>Da Costa and Rainey 2002</small> ***** Genus ''[[Allomeiothermus]]'' <small>Jiao et al. 2023</small> ***** Genus ''[[Calidithermus]]'' <small>Raposo et al. 2019</small> ***** Genus ''[[Marinithermus]]'' <small>Sako et al. 2003</small> ***** Genus ''[[Meiothermus]]'' <small>Nobre et al. 1996 emend. Albuquerque et al. 2009</small> ***** Genus ''[[Oceanithermus]]'' <small>Miroshnichenko et al. 2003 emend. Mori et al. 2004</small> ***** Genus ''[[Rhabdothermus]]'' <small>Steinsbu et al. 2011</small> ***** Genus ''[[Thermus]]'' <small>Brock and Freeze 1969 emend. Nobre et al. 1996</small> ***** Genus ''[[Vulcanithermus]]'' <small>Miroshnichenko et al. 2003</small> ==Sequenced genomes== Currently there are 10 sequenced genomes of strains in this phylum.<ref>{{Cite web | url=https://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_taxtree.html |title = Microbial Genomes}}</ref> *''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]] project (GEBA), which aims at sequencing organisms based on phylogenetic novelty and not on pathogenicity or notoriety.<ref>{{Cite journal | doi = 10.1038/nature08656 | title = A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea | first30 = D. | last30 = Bruce | first29 = P. | last29 = Chain | first28 = S. | last28 = Gronow | first27 = E. | last27 = Lang | first26 = C. | last26 = Kerfeld | first25 = S. | last25 = Lucas | first24 = J. F. | last24 = Cheng | first23 = F. | last23 = Chen | first22 = C. | last22 = Han | first21 = A. | last21 = Copeland | first20 = M. | last20 = Nolan | first19 = A. | last19 = Lapidus | first18 = M. | last18 = Singer | first17 = A. | last17 = Zemla | first16 = P. | last16 = d'Haeseleer | first15 = I. J. | last15 = Anderson | first14 = S. | last14 = Spring | first13 = A. | last13 = Lykidis | first12 = A. | last12 = Pati | year = 2009 | first11 = S. D. | last1 = Wu | last11 = Hooper | first1 = D. | last2 = Hugenholtz | first2 = P. | first10 = B. J. | last3 = Mavromatis | first3 = K. | last4 = Pukall | first4 = R. D. | last5 = Dalin | last10 = Tindall | first5 = E. | last6 = Ivanova | first6 = N. N. | last7 = Kunin | first7 = V. | pmc = 3073058 | last8 = Goodwin | first8 = L. | last9 = Wu | first9 = M. | journal = Nature | volume = 462 | pages = 1056–1060 | pmid = 20033048 | issue = 7276 |bibcode = 2009Natur.462.1056W }}</ref> ==See also== * [[List of bacteria genera]] * [[List of bacterial orders]] ==References== {{Reflist}} {{Portal bar|Biology}} {{Extremophile}} {{Bacteria classification}} {{Life on Earth}} {{Taxonbar|from2=Q134886|from1=Q3021316}} {{DEFAULTSORT:Deinococcus-Thermus}} [[Category:Deinococcota| ]] [[Category:Polyextremophiles]] [[Category:Bacteria phyla]] </textarea><div class="templatesUsed"><div class="mw-templatesUsedExplanation"><p><span id="templatesused">Pages transcluded onto the current version of this page<span class="posteditwindowhelplinks"> (<a href="/wiki/Help:Transclusion" title="Help:Transclusion">help</a>)</span>:</span> </p></div><ul> <li><a href="/wiki/Template:;" title="Template:;">Template:;</a> (<a 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