List of Archaea genera: Difference between revisions
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{{short description|Wikipedia list article}} |
{{short description|Wikipedia list article}} |
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This article lists the [[genus (biology)|genera]] of the [[Archaea]]. 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/domain/archaea | title=Archaea | accessdate=2013-03-20 | publisher=[[List of Prokaryotic names with Standing in Nomenclature]] (LPSN)| accessdate=2021-06-27 }}</ref> and [[National Center for Biotechnology Information]] (NCBI)<ref>{{cite web |author = Sayers|display-authors = etal| url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2157 |title=Archaea |accessdate=2021-03-20 |publisher=[[National Center for Biotechnology Information]] (NCBI) taxonomy database}}</ref> |
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This article lists the [[genus (biology)|genera]] of the [[Archaea]]. |
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and the phylogeny is based on 16S rRNA-based LTP release 132 by [[The All-Species Living Tree Project]].<ref>[[All-Species Living Tree Project]].{{cite web | url=https://itol.embl.de/tree/37201229170412631528207598 | title=16S rRNA-based LTP release 132 | publisher=[[Silva Comprehensive Ribosomal RNA Database]] | accessdate=2020-08-20}}</ref> |
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== Phylogeny == |
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The following genus of the Archaea has not been assigned to a [[phylum (biology)|phylum]]: |
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[[National Center for Biotechnology Information]] (NCBI) taxonomy was initially used to decorate the genome tree via tax2tree. The 16S rRNA-based [[Greengenes]] taxonomy is used to supplement the taxonomy particularly in regions of the tree with no cultured representatives. [[List of Prokaryotic names with Standing in Nomenclature]] (LPSN) is used as the primary taxonomic authority for establishing naming priorities. Taxonomic ranks are normalised using phylorank and the taxonomy manually curated to remove polyphyletic groups.<ref name="pmid30148503">{{cite journal|last1=Parks|first1=DH|last2=Chuvochina|first2=M|last3=Waite|first3=DW|last4=Rinke|first4=C|last5=Skarshewski|first5=A|last6=Chaumeil|first6=PA|last7=Hugenholtz|first7=P|date=November 2018|title=A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.|journal=Nature Biotechnology|volume=36|issue=10|pages=996–1004|biorxiv=10.1101/256800|doi=10.1038/nbt.4229|pmid=30148503|s2cid=52093100}}</ref><ref>{{cite journal|last1=Parks|first1=DH|last2=Chuvochina|first2=M|last3=Chaumeil|first3=PA|last4=Rinke|first4=C|last5=Mussig|first5=AJ|last6=Hugenholtz|first6=P|date=September 2020|title=A complete domain-to-species taxonomy for Bacteria and Archaea.|url=https://www.researchgate.net/publication/340954053|journal=Nature Biotechnology|volume=38|issue=9|pages=1079–1086|biorxiv=10.1101/771964|doi=10.1038/s41587-020-0501-8|pmid=32341564|s2cid=216560589}}</ref><ref>{{cite journal|last1=Chaumeil|first1=PA|last2=Mussig|first2=AJ|last3=Hugenholtz|first3=P|last4=Parks|first4=DH|date=15 November 2019|title=GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.|journal=Bioinformatics|doi=10.1093/bioinformatics/btz848|pmc=7703759|pmid=31730192|doi-access=free}}</ref><ref>{{cite journal|last1=Almeida|first1=Alexandre|last2=Nayfach|first2=Stephen|last3=Boland|first3=Miguel|last4=Strozzi|first4=Francesco|last5=Beracochea|first5=Martin|last6=Shi|first6=Zhou Jason|last7=Pollard|first7=Katherine S.|last8=Sakharova|first8=Ekaterina|last9=Parks|first9=Donovan H.|last10=Hugenholtz|first10=Philip|last11=Segata|first11=Nicola|date=20 July 2020|title=A unified catalog of 204,938 reference genomes from the human gut microbiome|journal=Nature Biotechnology|doi=10.1038/s41587-020-0603-3|pmid=32690973|doi-access=free|last12=Kyrpides|first12=Nikos C.|last13=Finn|first13=Robert D.}}</ref><ref>{{cite journal|last1=Nayfach|first1=Stephen|last2=Roux|first2=Simon|last3=Seshadri|first3=Rekha|last4=Udwary|first4=Daniel|last5=Varghese|first5=Neha|last6=Schulz|first6=Frederik|last7=Wu|first7=Dongying|last8=Paez-Espino|first8=David|last9=Chen|first9=I-Min|last10=Huntemann|first10=Marcel|last11=Palaniappan|first11=Krishna|date=9 November 2020|title=A genomic catalog of Earth's microbiomes|journal=Nature Biotechnology|doi=10.1038/s41587-020-0718-6|doi-access=free|first15=Torben|last16=Kirton|first16=Edward|last17=Faria|last14=Reddy|last18=Edirisinghe|first18=Janaka N.|first19=Christopher S.|last20=Jungbluth|last24=Arkin|first20=Sean P.|last15=Nielsen|last21=Chivian|first21=Dylan|last22=Dehal|first22=Paramvir|last23=Wood-Charlson|first23=Elisha M.|last19=Henry|last28=Mouncey|first24=Adam P.|last29=Ivanova|first14=T. B. K.|first29=Natalia N.|last26=Visel|first26=Axel|last27=Woyke|first27=Tanja|first28=Nigel J.|last30=Kyrpides|first25=Susannah G.|last25=Tringe|first30=Nikos C.|last31=Eloe-Fadrosh|first31=Emiley A.|first13=Supratim|last13=Mukherjee|first12=Joshua|last12=Ladau|first17=José P.}}</ref> |
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Cladogram was taken from the [[Annotree]] website, which uses the GTDB release 05-RS95 (17 July 2020).<ref>{{cite journal |last1=Mendler|first1=K|last2=Chen|first2=H|last3=Parks|first3=DH|last4=Hug|first4=LA|last5=Doxey|first5=AC |date=2019 |title=AnnoTree: visualization and exploration of a functionally annotated microbial tree of life |journal=Nucleic Acids Research |volume=47 | pages=4442–4448 |url=http://annotree.uwaterloo.ca/app/ |doi=10.1093/nar/gkz246|doi-access=free}}</ref> |
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*[[Genus (biology)|Genus]] ''[[Halostagnicola]]'' |
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{{Clade|style=font-size:90%; line-height:90%|label1=[[Archaea]]| |
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{{clade |
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|label1="[[DPANN]]" |
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|1={{Clade |
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|1=[[Altiarchaeota]] |
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|2={{Clade |
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|label1="[[Diapherotrites]]" |
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|1={{Clade |
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|1=[[Iainarchaeaota]] |
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|2=[[Micrarchaeota]] |
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}} |
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|2={{Clade |
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|1=[[Undinarchaeota]] |
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|2={{Clade |
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|1={{Clade |
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|1=[[Aenigmarchaeota]] |
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|2={{Clade |
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|1=[[Huberarchaeaota]] |
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|2=[[Nanohaloarchaeota]] |
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}} |
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}} |
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|2=[[Nanoarchaeota]] |
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}} |
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}} |
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}} |
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}} |
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|2={{Clade |
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|label1="[[Proteoarchaeota]]" |
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|1={{Clade |
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|1="[[Thermoproteota]]" |
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|2="[[Asgardaeota]]" |
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}} |
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|label1="[[Euryarchaeota|Euryarchaeida]]" |
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|2={{Clade |
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|1={{Clade |
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|1=[[Hydrothermarchaeota]] |
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|2={{Clade |
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|1=[[Hadarchaeota]] |
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|2="[[Methanobacteriota]]" |
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}} |
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}} |
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|2={{Clade |
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|1="[[Thermoplasmatota]]" |
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|2="[[Halobacteriota]]" (Class II Methanogens) |
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}} |
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}} |
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}} |
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}} |
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}} |
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==Phylum "[[Altarchaeota]]"== |
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===Class "[[Altarchaeia]]"=== |
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====Order "[[Altarchaeales]]"==== |
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=====Family "Altarchaeaceae"===== |
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* "''Candidatus'' [[Altarchaeum]]" <small>corrig. Probst et al. 2014</small> |
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==Phylum "[[Iainarchaeota]]"== |
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This section lists the genera of Archaea within the [[Phylum (biology)|Phylum]] [[Crenarchaeota]]. |
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===Class "[[Iainarchaeia]]"=== |
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====Order "[[Iainarchaeales]]"==== |
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=====Family "[[Iainarchaeaceae]]"===== |
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* "''Candidatus'' [[Forterrea]]" <small>Probst & Banfield 2017</small> |
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* "''Candidatus'' [[Iainarchaeum]]" <small>Rinke et al. 2013</small> |
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==Phylum "[[Micrarchaeota]]"== |
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==Class Thermoprotei== |
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===Class "[[Micrarchaeia]]"=== |
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====Order [[Fermentimicrarchaeales]]==== |
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=====Family [[Fermentimicrarchaeaceae]]===== |
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* "''Candidatus'' [[Fermentimicrarchaeum]]" <small>Kadnikov et al. 2020</small> |
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====Order "[[Micrarchaeales]]"==== |
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=====Family "[[Micrarchaeaceae]]"===== |
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* "''Candidatus'' [[Mancarchaeum]]" <small>Golyshina et al. 2017</small> |
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* "''Candidatus'' [[Micrarchaeum]]" <small>Baker et al. 2010</small> |
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==Phylum "[[Undinarchaeota]]"== |
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This section lists the genera of Archaea within the [[Class (biology)|Class]] [[Thermoprotei]]. |
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===Class "[[Undinarchaeia]]"=== |
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====Order "[[Naiadarchaeales]]"==== |
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=====Family "[[Naiadarchaeaceae]]"===== |
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* "''Candidatus'' [[Naiadarchaeum]]" <small>Dombrowski et al. 2020</small> |
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===Order |
====Order "[[Undinarchaeales]]"==== |
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=====Family "[[Undinarchaeaceae]]"===== |
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* "''Candidatus'' [[Undinarchaeum]]" <small>Dombrowski et al. 2020</small> |
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==Phylum "[[Aenigmarchaeota|Aenigmatarchaeota]]"== |
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===Class "[[Aenigmatarchaeia]]"=== |
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====Order "[[Aenigmatarchaeales]]"==== |
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=====Family "[[Aenigmatarchaeaceae]]"===== |
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* "''Candidatus'' [[Aenigmatarchaeum]]" <small>corrig. Rinke et al. 2013</small> |
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==Phylum "[[Huberarchaeaota]]"== |
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This section lists the genera of Archaea within the [[Order (biology)|Order]] [[Caldisphaerales]]. |
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===Class "[[Huberarchaeia]]"=== |
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====Order "[[Huberarchaeales]]"==== |
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=====Family "[[Huberarchaeaceae]]"===== |
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* "''Candidatus'' [[Huberarchaeum]]" <small>corrig. Schwank et al. 2019</small> |
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==Phylum "[[Nanohaloarchaeota]]"== |
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====Family Caldisphaeraceae==== |
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===Class "[[Nanohalobia]]"=== |
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====Order "Nanohalobiales"==== |
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=====Family "Nanohalobiaceae"===== |
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* ?"''Candidatus'' [[Nanohalobium]]" <small>La Cono et al. 2020</small> |
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===Class "[[Nanohalarchaeia]]"=== |
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====Order "[[Nanohalarchaeales]]"==== |
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=====Family "[[Nanohalarchaeaceae]]"===== |
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* ?"''Candidatus'' [[Nanohalarchaeum]]" <small>corrig. Hamm et al. 2019</small> |
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===Class "[[Nanosalinia]]"=== |
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This section lists the genera of Archaea within the [[Family (biology)|Family]] [[Caldisphaeraceae]]. |
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====Order "[[Nanosalinales]]"==== |
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=====Family "[[Nanosalinaceae]]"===== |
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* ?"''Candidatus'' [[Nanopetraeus]]" <small>corrig. Crits‐Christoph et al. 2016</small> |
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* ?"''Candidatus'' [[Haloredivivus]]" <small>Ghai et al. 2011</small> |
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* "''Candidatus'' [[Nanosalina]]" <small>Narasingarao et al. 2012</small> |
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* "''Candidatus'' [[Nanosalinicola]]" <small>corrig. Narasingarao et al. 2012</small> |
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==Phylum "[[Nanoarchaeota]]"== |
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:*Genus ''[[Caldisphaera]]'' |
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===Class "[[Nanoarchaeia]]"=== |
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====Nanoarchaeia incertae sedis==== |
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* "[[Mamarchaeales]]" |
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* "[[Woesearchaeales]]" (DHVE-6) |
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* "[[Pacearchaeales]]" (DHVE-5, DUSEL-1) |
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* "[[Tiddalikarchaeales]]" <small>Vazquez-Campos et al. 2019</small> (LFWA-I) |
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* "[[Wiannamattarchaeales]]" <small>Vazquez-Campos et al. 2019</small> (LFWA-II, Eury4AB) |
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* "[[Gugararchaeales]]" <small>Vazquez-Campos et al. 2019</small> (LFWA-III, Eury4AA) |
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====Order |
====Order "[[Parvarchaeales]]"==== |
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=====Family "[[Parvarchaeaceae]]"===== |
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* "''Candidatus'' [[Parvarchaeum]]" <small>Baker et al. 2010</small> (ARMAN 4 & 5) |
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====Order "[[Nanoarchaeales]]"==== |
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This section lists the genera of Archaea within the Order [[Cenarchaeales]]. |
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=====Family "[[Nanoarchaeaceae]]"===== |
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* "[[Nanoarchaeum]]" <small>Huber et al. 2002</small> |
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=====Family "Nanopusillaceae"===== |
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* "''Candidatus'' [[Nanoclepta]]" <small>St. John et al. 2019</small> |
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* "''Candidatus'' [[Nanopusillus]]" <small>Wurch et al. 2016</small> |
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==Phylum "[[Asgardaeota]]"== |
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=====Family Cenarchaeaceae===== |
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===Class "[[Freyarchaeia]]"=== |
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===Class "[[Borrarchaeia]]"=== |
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This section lists the genera of Archaea within the Family [[Cenarchaeaceae]]. |
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====Order "[[Borrarchaeales]]"==== |
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=====Family "[[Borrarchaeaceae]]"===== |
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* ?"''Candidatus'' [[Borrarchaeum]]" <small>Liu et al. 2020</small> |
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===Class "[[Jordarchaeia]]"=== |
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:*Genus ''[[Cenarchaeum]]'' |
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====Order "[[Jordarchaeales]]"==== |
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=====Family "[[Jordarchaeaceae]]"===== |
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* ?"''Candidatus'' [[Jordarchaeum]]" <small>Sun et al. 2021</small> |
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===Class "[[Heimdallarchaeia]]"=== |
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====Order Desulfurococcales==== |
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====Class Incertae sedis==== |
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* "[[Gerdarchaeales]]" |
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* "[[Heimdallarchaeales]]" |
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====Order "[[Wukongarchaeales]]"==== |
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This section lists the genera of Archaea within the Order [[Desulfurococcales]]. |
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=====Family "[[Wukongarchaeaceae]]"===== |
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* "''Candidatus'' [[Wukongarchaeum]]" <small>Liu et al. 2020</small> |
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====Order "[[Hodarchaeales]]"==== |
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The following two genera of Desulfurococcales have not been assigned to a family: |
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=====Family "[[Hodarchaeaceae]]"===== |
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* "''Candidatus'' [[Hodarchaeum]]" <small>Liu et al. 2020</small> |
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====Order "[[Kariarchaeales]]"==== |
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*Genus ''[[Caldococcus]]'' |
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=====Family "[[Kariarchaeaceae]]"===== |
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*Genus ''[[Ignisphaera]]'' |
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* "''Candidatus'' [[Kariarchaeum]]" <small>Liu et al. 2020</small> |
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===Class "[[Lokiarchaeia]]"=== |
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=====Family Desulfurococcaceae===== |
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====Lokiarchaeia incertae sedis==== |
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* Order "[[Helarchaeales]]" |
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** Family "[[Helarchaeaceae]]" |
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* Order "[[Odinarchaeales]]"=== |
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** Family "[[Odinarchaeaceae]]" |
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====Order "[[Baldrarchaeales]]"==== |
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This section lists the genera of Archaea within the Family [[Desulfurococcaceae]]. |
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=====Family "[[Baldrarchaeaceae]]"===== |
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* "Candidatus Baldrarchaeum yapensis]]" <small>Liu et al. 2020</small> |
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====Order "[[Lokiarchaeales]]"==== |
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:*Genus ''[[Acidilobus]]'' |
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=====Family "[[Lokiarchaeaceae]]"===== |
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:*Genus ''[[Acidococcus]]'' |
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* "''Candidatus'' [[Lokiarchaeum]]" <small>corrig. Spang et al. 2015</small> |
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:*Genus ''[[Aeropyrum]]'' |
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* "''Candidatus'' [[Promethearchaeum]]" <small>corrig. Imachi, Nobu & Takai 2020</small> |
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:*Genus ''[[Desulfurococcus]]'' |
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:*Genus ''[[Ignicoccus]]'' |
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:*Genus ''[[Staphylothermus]]'' |
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:*Genus ''[[Stetteria]]'' |
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:*Genus ''[[Sulfophobococcus]]'' |
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:*Genus ''[[Thermodiscus]]'' |
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:*Genus ''[[Thermosphaera]]'' |
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=== |
===Class "[[Thorarchaeia]]"=== |
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====Order "[[Thorarchaeales]]"==== |
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=====Family "[[Thorarchaeaceae]]"===== |
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====Order "[[Hermodarchaeales]]"==== |
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This section lists the genera of Archaea within the Family [[Pyrodictiaceae]]. |
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=====Family "[[Hermodarchaeaceae]]"===== |
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* "''Candidatus'' [[Hermodarchaeum]]" <small>Liu et al. 2020</small> |
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====Order "[[Sifarchaeales]]"==== |
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:*Genus ''[[Geogemma]]'' |
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=====Family "[[Sifarchaeaceae]]"===== |
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:*Genus ''[[Hyperthermus]]'' |
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* "''Candidatus'' [[Sifarchaeotum]]" <small>Farag, Zhao & Biddle 2020</small> |
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:*Genus ''[[Pyrodictium]]'' |
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:*Genus ''[[Pyrolobus]]'' |
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==Phylum "[[Thermoproteota]]"== |
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====Order Nitrosopumilales==== |
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===Class "[[Korarchaeia]]"=== |
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Only environmental samples of the Korarchaeota have been studied. |
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===Class [[Thermoprotei]]=== |
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This section lists the genera of Archaea within the Order [[Nitrosopumilales]]. |
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====Order [[Caldisphaerales]]==== |
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=====Family [[Caldisphaeraceae]]===== |
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* Genus ''[[Caldisphaera]]'' |
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==== |
====Order [[Cenarchaeales]]==== |
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=====Family [[Cenarchaeaceae]]===== |
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* Genus ''[[Cenarchaeum]]'' |
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====Order [[Desulfurococcales]]==== |
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This section lists the genera of Archaea within the Family [[Nitrosopumilaceae]]. |
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* Genus ''[[Caldococcus]]'' |
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* Genus ''[[Ignisphaera]]'' |
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=====Family [[Desulfurococcaceae]]===== |
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:*Genus ''[[Nitrosopumilus]]'' (candidatus) |
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* Genus ''[[Acidilobus]]'' |
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* Genus ''[[Acidococcus]]'' |
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* Genus ''[[Aeropyrum]]'' |
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* Genus ''[[Desulfurococcus]]'' |
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* Genus ''[[Ignicoccus]]'' |
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* Genus ''[[Staphylothermus]]'' |
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* Genus ''[[Stetteria]]'' |
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* Genus ''[[Sulfophobococcus]]'' |
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* Genus ''[[Thermodiscus]]'' |
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* Genus ''[[Thermosphaera]]'' |
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==== |
=====Family [[Pyrodictiaceae]]===== |
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* Genus ''[[Geogemma]]'' |
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* Genus ''[[Hyperthermus]]'' |
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* Genus ''[[Pyrodictium]]'' |
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* Genus ''[[Pyrolobus]]'' |
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====Order [[Nitrosopumilales]]==== |
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This section lists the genera of Archaea within the Order [[Sulfolobales]]. |
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=====Family [[Nitrosopumilaceae]]===== |
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* Genus ''[[Nitrosopumilus]]'' (candidatus) |
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==== |
====Order [[Sulfolobales]]==== |
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=====Family [[Sulfolobaceae]]===== |
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* Genus ''[[Acidianus]]'' |
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* Genus ''[[Metallosphaera]]'' |
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* Genus ''[[Stygiolobus]]'' |
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* Genus ''[[Sulfolobus]]'' |
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* Genus ''[[Sulfurisphaera]]'' |
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====Order [[Thermoproteales]]==== |
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This section lists the genera of Archaea within the Family [[Sulfolobaceae]]. |
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=====Family [[Thermofilaceae]]===== |
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* Genus ''[[Thermofilum]]'' |
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=====Family [[Thermoproteaceae]]===== |
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:*Genus ''[[Acidianus]]'' |
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* Genus ''[[Caldivirga]]'' |
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* Genus ''[[Pyrobaculum]]'' |
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* Genus ''[[Thermocladium]]'' |
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* Genus ''[[Thermoproteus]]'' |
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* Genus ''[[Vulcanisaeta]]'' |
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====Order Thermoproteales==== |
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This section lists the genera of Archaea within the Order [[Thermoproteales]]. |
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=====Family Thermofilaceae===== |
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This section lists the genera of Archaea within the Family [[Thermofilaceae]]. |
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:*Genus ''[[Thermofilum]]'' |
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=====Family Thermoproteaceae===== |
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This section lists the genera of Archaea within the Family [[Thermoproteaceae]]. |
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:*Genus ''[[Caldivirga]]'' |
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:*Genus ''[[Pyrobaculum]]'' |
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:*Genus ''[[Thermocladium]]'' |
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:*Genus ''[[Thermoproteus]]'' |
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:*Genus ''[[Vulcanisaeta]]'' |
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==Phylum Euryarchaeota== |
==Phylum Euryarchaeota== |
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This section lists the genera of Archaea within the Phylum [[Euryarchaeota]]. |
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The following genus of the Euryarchaeota has not been assigned to a class: |
The following genus of the Euryarchaeota has not been assigned to a class: |
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*Genus ''[[Aciduliprofundum]]'' |
*Genus ''[[Aciduliprofundum]]'' |
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===Class Archaeoglobi=== |
===Class Archaeoglobi=== |
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This section lists the genera of Archaea within the Class [[Archaeoglobi]]. |
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====Order Archaeoglobales==== |
====Order Archaeoglobales==== |
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This section lists the genera of Archaea within the Order [[Archaeoglobales]]. |
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=====Family Archaeoglobaceae===== |
=====Family Archaeoglobaceae===== |
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This section lists the genera of Archaea within the Family [[Archaeoglobaceae]]. |
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:*Genus ''[[Archaeoglobus]]'' |
:*Genus ''[[Archaeoglobus]]'' |
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:*Genus ''[[Ferroglobus]]'' |
:*Genus ''[[Ferroglobus]]'' |
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Line 139: | Line 272: | ||
===Class Halobacteria=== |
===Class Halobacteria=== |
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This section lists the genera of Archaea within the Class [[Halobacteria]]. |
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====Order Halobacteriales==== |
====Order Halobacteriales==== |
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This section lists the genera of Archaea within the Order [[Halobacteriales]]. |
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=====Family Halobacteriaceae===== |
=====Family Halobacteriaceae===== |
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This section lists the genera of Archaea within the Family [[Halobacteriaceae]]. |
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:*Genus ''[[Haladaptatus]]'' |
:*Genus ''[[Haladaptatus]]'' |
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:*Genus ''[[Halalkalicoccus]]'' |
:*Genus ''[[Halalkalicoccus]]'' |
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Line 179: | Line 303: | ||
===Class Methanobacteria=== |
===Class Methanobacteria=== |
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This section lists the genera of Archaea within the Class [[Methanobacteria]]. |
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====Order Methanobacteriales==== |
====Order Methanobacteriales==== |
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This section lists the genera of Archaea within the Order [[Methanobacteriales]]. |
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The following two genera of the [[Methanomicrobiales]] have not been assigned to a family: |
The following two genera of the [[Methanomicrobiales]] have not been assigned to a family: |
||
*Genus ''[[Methanoregula]]'' (''candidatus'') |
*Genus ''[[Methanoregula]]'' (''candidatus'') |
||
*Genus ''[[Methanocalculus]]'' |
*Genus ''[[Methanocalculus]]'' |
||
=====Family Methanobacteriaceae===== |
=====Family Methanobacteriaceae===== |
||
This section lists the genera of Archaea within the Family [[Methanobacteriaceae]]. |
|||
:*Genus ''[[Methanobacterium]]'' |
:*Genus ''[[Methanobacterium]]'' |
||
:*Genus ''[[Methanobrevibacter]]'' |
:*Genus ''[[Methanobrevibacter]]'' |
||
Line 201: | Line 315: | ||
=====Family Methanothermaceae===== |
=====Family Methanothermaceae===== |
||
This section lists the genera of Archaea within the Family [[Methanothermaceae]]. |
|||
:*Genus ''[[Methanothermus]]'' |
:*Genus ''[[Methanothermus]]'' |
||
===Class Methanococci=== |
===Class Methanococci=== |
||
This section lists the genera of Archaea within the Class [[Methanococci]]. |
|||
====Order Methanococcales==== |
====Order Methanococcales==== |
||
This section lists the genera of Archaea within the Order [[Methanococcales]]. |
|||
=====Family Methanocaldococcaceae===== |
=====Family Methanocaldococcaceae===== |
||
This section lists the genera of Archaea within the Family [[Methanocaldococcaceae]]. |
|||
:*Genus ''[[Methanocaldococcus]]'' |
:*Genus ''[[Methanocaldococcus]]'' |
||
:*Genus ''[[Methanotorris]]'' |
:*Genus ''[[Methanotorris]]'' |
||
=====Family Methanococcaceae===== |
=====Family Methanococcaceae===== |
||
This section lists the genera of Archaea within the Family [[Methanococcaceae]]. |
|||
:*Genus ''[[Methanococcus]]'' |
:*Genus ''[[Methanococcus]]'' |
||
:*Genus ''[[Methanothermococcus]]'' |
:*Genus ''[[Methanothermococcus]]'' |
||
===Class Methanomicrobia=== |
===Class Methanomicrobia=== |
||
This section lists the genera of Archaea within the Class [[Methanomicrobia]]. |
|||
====Order Methanomicrobiales==== |
====Order Methanomicrobiales==== |
||
This section lists the genera of Archaea within the Order Methanomicrobiales. |
|||
=====Family Methanocorpusculaceae===== |
=====Family Methanocorpusculaceae===== |
||
This section lists the genera of Archaea within the Family [[Methanocorpusculaceae]]. |
|||
:*Genus ''[[Methanocorpusculum]]'' |
:*Genus ''[[Methanocorpusculum]]'' |
||
=====Family Methanomicrobiaceae===== |
=====Family Methanomicrobiaceae===== |
||
This section lists the genera of Archaea within the Family [[Methanomicrobiaceae]]. |
|||
:*Genus ''[[Methanoculleus]]'' |
:*Genus ''[[Methanoculleus]]'' |
||
:*Genus ''[[Methanofollis]]'' |
:*Genus ''[[Methanofollis]]'' |
||
Line 254: | Line 341: | ||
=====Family Methanospirillaceae===== |
=====Family Methanospirillaceae===== |
||
This section lists the genera of Archaea within the Family [[Methanospirillaceae]]. |
|||
:*Genus ''[[Methanospirillum]]'' |
:*Genus ''[[Methanospirillum]]'' |
||
====Order Methanosarcinales==== |
====Order Methanosarcinales==== |
||
This section lists the genera of Archaea within the Order [[Methanosarcinales]]. |
|||
=====Family Methanosaetaceae===== |
=====Family Methanosaetaceae===== |
||
This section lists the genera of Archaea within the Family [[Methanosaetaceae]]. |
|||
:*Genus ''[[Methanosaeta]]'' |
:*Genus ''[[Methanosaeta]]'' |
||
=====Family Methanosarcinaceae===== |
=====Family Methanosarcinaceae===== |
||
This section lists the genera of Archaea within the Family [[Methanosarcinaceae]]. |
|||
:*Genus ''[[Methanimicrococcus]]'' |
:*Genus ''[[Methanimicrococcus]]'' |
||
:*Genus ''[[Methanococcoides]]'' |
:*Genus ''[[Methanococcoides]]'' |
||
Line 283: | Line 358: | ||
===Class Methanopyri=== |
===Class Methanopyri=== |
||
This section lists the genera of Archaea within the Class [[Methanopyri]]. |
|||
====Order Methanopyrales==== |
====Order Methanopyrales==== |
||
This section lists the genera of Archaea within the Order [[Methanopyrales]]. |
|||
=====Family Methanopyraceae===== |
=====Family Methanopyraceae===== |
||
This section lists the genera of Archaea within the Family [[Methanopyraceae]]. |
|||
:*Genus ''[[Methanopyrus]]'' |
:*Genus ''[[Methanopyrus]]'' |
||
===Class Thermococci=== |
===Class Thermococci=== |
||
This section lists the genera of Archaea within the Class [[Thermococci]]. |
|||
====Order Thermococcales==== |
====Order Thermococcales==== |
||
This section lists the genera of Archaea within the Order [[Thermococcales]]. |
|||
=====Family Thermococcaceae===== |
=====Family Thermococcaceae===== |
||
This section lists the genera of Archaea within the Family [[Thermococcaceae]]. |
|||
:*Genus ''[[Palaeococcus]]'' |
:*Genus ''[[Palaeococcus]]'' |
||
:*Genus ''[[Pyrococcus]]'' |
:*Genus ''[[Pyrococcus]]'' |
||
Line 313: | Line 370: | ||
===Class Thermoplasmata=== |
===Class Thermoplasmata=== |
||
This section lists the genera of Archaea within the Class [[Thermoplasmata]]. |
|||
====Order Thermoplasmatales==== |
====Order Thermoplasmatales==== |
||
This section lists the genera of Archaea within the Order [[Thermoplasmatales]]. |
|||
=====Family Ferroplasmaceae===== |
=====Family Ferroplasmaceae===== |
||
This section lists the genera of Archaea within the Family [[Ferroplasmaceae]]. |
|||
:*Genus ''[[Ferroplasma]]'' |
:*Genus ''[[Ferroplasma]]'' |
||
=====Family Picrophilaceae===== |
=====Family Picrophilaceae===== |
||
This section lists the genera of Archaea within the Family [[Picrophilaceae]]. |
|||
:*Genus ''[[Picrophilus]]'' |
:*Genus ''[[Picrophilus]]'' |
||
=====Family Thermoplasmataceae===== |
=====Family Thermoplasmataceae===== |
||
This section lists the genera of Archaea within the Family [[Thermoplasmataceae]]. |
|||
:*Genus ''[[Thermoplasma]]'' |
:*Genus ''[[Thermoplasma]]'' |
||
== |
== References == |
||
{{reflist}} |
|||
This section lists the genera of Archaea within the Phylum [[Korarchaeota]]. |
|||
Only environmental samples of the Korarchaeota have been studied. |
|||
==Phylum Nanoarchaeota== |
|||
This section lists the genera of Archaea within the Phylum [[Nanoarchaeota]]. |
|||
The following genus of the Nanoarchaeota has not been assigned to a class: |
|||
*Genus ''[[Nanoarchaeum]]'' |
|||
[[Category:Archaea genera| ]] |
[[Category:Archaea genera| ]] |
Revision as of 19:41, 13 July 2021
This article lists the genera of the Archaea. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[1] and National Center for Biotechnology Information (NCBI)[2] and the phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project.[3]
Phylogeny
National Center for Biotechnology Information (NCBI) taxonomy was initially used to decorate the genome tree via tax2tree. The 16S rRNA-based Greengenes taxonomy is used to supplement the taxonomy particularly in regions of the tree with no cultured representatives. List of Prokaryotic names with Standing in Nomenclature (LPSN) is used as the primary taxonomic authority for establishing naming priorities. Taxonomic ranks are normalised using phylorank and the taxonomy manually curated to remove polyphyletic groups.[4][5][6][7][8]
Cladogram was taken from the Annotree website, which uses the GTDB release 05-RS95 (17 July 2020).[9]
Archaea |
| ||||||||||||||||||||||||
Phylum "Altarchaeota"
Class "Altarchaeia"
Order "Altarchaeales"
Family "Altarchaeaceae"
- "Candidatus Altarchaeum" corrig. Probst et al. 2014
Phylum "Iainarchaeota"
Class "Iainarchaeia"
Order "Iainarchaeales"
Family "Iainarchaeaceae"
- "Candidatus Forterrea" Probst & Banfield 2017
- "Candidatus Iainarchaeum" Rinke et al. 2013
Phylum "Micrarchaeota"
Class "Micrarchaeia"
Order Fermentimicrarchaeales
Family Fermentimicrarchaeaceae
- "Candidatus Fermentimicrarchaeum" Kadnikov et al. 2020
Order "Micrarchaeales"
Family "Micrarchaeaceae"
- "Candidatus Mancarchaeum" Golyshina et al. 2017
- "Candidatus Micrarchaeum" Baker et al. 2010
Phylum "Undinarchaeota"
Class "Undinarchaeia"
Order "Naiadarchaeales"
Family "Naiadarchaeaceae"
- "Candidatus Naiadarchaeum" Dombrowski et al. 2020
Order "Undinarchaeales"
Family "Undinarchaeaceae"
- "Candidatus Undinarchaeum" Dombrowski et al. 2020
Phylum "Aenigmatarchaeota"
Class "Aenigmatarchaeia"
Order "Aenigmatarchaeales"
Family "Aenigmatarchaeaceae"
- "Candidatus Aenigmatarchaeum" corrig. Rinke et al. 2013
Phylum "Huberarchaeaota"
Class "Huberarchaeia"
Order "Huberarchaeales"
Family "Huberarchaeaceae"
- "Candidatus Huberarchaeum" corrig. Schwank et al. 2019
Phylum "Nanohaloarchaeota"
Class "Nanohalobia"
Order "Nanohalobiales"
Family "Nanohalobiaceae"
- ?"Candidatus Nanohalobium" La Cono et al. 2020
Class "Nanohalarchaeia"
Order "Nanohalarchaeales"
Family "Nanohalarchaeaceae"
- ?"Candidatus Nanohalarchaeum" corrig. Hamm et al. 2019
Class "Nanosalinia"
Order "Nanosalinales"
Family "Nanosalinaceae"
- ?"Candidatus Nanopetraeus" corrig. Crits‐Christoph et al. 2016
- ?"Candidatus Haloredivivus" Ghai et al. 2011
- "Candidatus Nanosalina" Narasingarao et al. 2012
- "Candidatus Nanosalinicola" corrig. Narasingarao et al. 2012
Phylum "Nanoarchaeota"
Class "Nanoarchaeia"
Nanoarchaeia incertae sedis
- "Mamarchaeales"
- "Woesearchaeales" (DHVE-6)
- "Pacearchaeales" (DHVE-5, DUSEL-1)
- "Tiddalikarchaeales" Vazquez-Campos et al. 2019 (LFWA-I)
- "Wiannamattarchaeales" Vazquez-Campos et al. 2019 (LFWA-II, Eury4AB)
- "Gugararchaeales" Vazquez-Campos et al. 2019 (LFWA-III, Eury4AA)
Order "Parvarchaeales"
Family "Parvarchaeaceae"
- "Candidatus Parvarchaeum" Baker et al. 2010 (ARMAN 4 & 5)
Order "Nanoarchaeales"
Family "Nanoarchaeaceae"
- "Nanoarchaeum" Huber et al. 2002
Family "Nanopusillaceae"
- "Candidatus Nanoclepta" St. John et al. 2019
- "Candidatus Nanopusillus" Wurch et al. 2016
Phylum "Asgardaeota"
Class "Freyarchaeia"
Class "Borrarchaeia"
Order "Borrarchaeales"
Family "Borrarchaeaceae"
- ?"Candidatus Borrarchaeum" Liu et al. 2020
Class "Jordarchaeia"
Order "Jordarchaeales"
Family "Jordarchaeaceae"
- ?"Candidatus Jordarchaeum" Sun et al. 2021
Class "Heimdallarchaeia"
Class Incertae sedis
Order "Wukongarchaeales"
Family "Wukongarchaeaceae"
- "Candidatus Wukongarchaeum" Liu et al. 2020
Order "Hodarchaeales"
Family "Hodarchaeaceae"
- "Candidatus Hodarchaeum" Liu et al. 2020
Order "Kariarchaeales"
Family "Kariarchaeaceae"
- "Candidatus Kariarchaeum" Liu et al. 2020
Class "Lokiarchaeia"
Lokiarchaeia incertae sedis
- Order "Helarchaeales"
- Family "Helarchaeaceae"
- Order "Odinarchaeales"===
- Family "Odinarchaeaceae"
Order "Baldrarchaeales"
Family "Baldrarchaeaceae"
- "Candidatus Baldrarchaeum yapensis]]" Liu et al. 2020
Order "Lokiarchaeales"
Family "Lokiarchaeaceae"
- "Candidatus Lokiarchaeum" corrig. Spang et al. 2015
- "Candidatus Promethearchaeum" corrig. Imachi, Nobu & Takai 2020
Class "Thorarchaeia"
Order "Thorarchaeales"
Family "Thorarchaeaceae"
Order "Hermodarchaeales"
Family "Hermodarchaeaceae"
- "Candidatus Hermodarchaeum" Liu et al. 2020
Order "Sifarchaeales"
Family "Sifarchaeaceae"
- "Candidatus Sifarchaeotum" Farag, Zhao & Biddle 2020
Phylum "Thermoproteota"
Class "Korarchaeia"
Only environmental samples of the Korarchaeota have been studied.
Class Thermoprotei
Order Caldisphaerales
Family Caldisphaeraceae
- Genus Caldisphaera
Order Cenarchaeales
Family Cenarchaeaceae
- Genus Cenarchaeum
Order Desulfurococcales
- Genus Caldococcus
- Genus Ignisphaera
Family Desulfurococcaceae
- Genus Acidilobus
- Genus Acidococcus
- Genus Aeropyrum
- Genus Desulfurococcus
- Genus Ignicoccus
- Genus Staphylothermus
- Genus Stetteria
- Genus Sulfophobococcus
- Genus Thermodiscus
- Genus Thermosphaera
Family Pyrodictiaceae
- Genus Geogemma
- Genus Hyperthermus
- Genus Pyrodictium
- Genus Pyrolobus
Order Nitrosopumilales
Family Nitrosopumilaceae
- Genus Nitrosopumilus (candidatus)
Order Sulfolobales
Family Sulfolobaceae
- Genus Acidianus
- Genus Metallosphaera
- Genus Stygiolobus
- Genus Sulfolobus
- Genus Sulfurisphaera
Order Thermoproteales
Family Thermofilaceae
- Genus Thermofilum
Family Thermoproteaceae
- Genus Caldivirga
- Genus Pyrobaculum
- Genus Thermocladium
- Genus Thermoproteus
- Genus Vulcanisaeta
Phylum Euryarchaeota
The following genus of the Euryarchaeota has not been assigned to a class:
- Genus Aciduliprofundum
Class Archaeoglobi
Order Archaeoglobales
Family Archaeoglobaceae
- Genus Archaeoglobus
- Genus Ferroglobus
- Genus Geoglobus
Class Halobacteria
Order Halobacteriales
Family Halobacteriaceae
- Genus Haladaptatus
- Genus Halalkalicoccus
- Genus Haloalcalophilium
- Genus Haloarcula
- Genus Halobacterium
- Genus Halobaculum
- Genus Halobiforma
- Genus Halococcus
- Genus Haloferax
- Genus Halogeometricum
- Genus Halomicrobium
- Genus Halopiger
- Genus Haloplanus
- Genus Haloquadra
- Genus Halorhabdus
- Genus Halorubrum
- Genus Halosarcina
- Genus Halosimplex
- Genus Haloterrigena
- Genus Halovivax
- Genus Natrialba
- Genus Natrinema
- Genus Natronobacterium
- Genus Natronococcus
- Genus Natronolimnobius
- Genus Natronomonas
- Genus Natronorubrum
Class Methanobacteria
Order Methanobacteriales
The following two genera of the Methanomicrobiales have not been assigned to a family:
- Genus Methanoregula (candidatus)
- Genus Methanocalculus
Family Methanobacteriaceae
- Genus Methanobacterium
- Genus Methanobrevibacter
- Genus Methanosphaera
- Genus Methanothermobacter
Family Methanothermaceae
- Genus Methanothermus
Class Methanococci
Order Methanococcales
Family Methanocaldococcaceae
- Genus Methanocaldococcus
- Genus Methanotorris
Family Methanococcaceae
- Genus Methanococcus
- Genus Methanothermococcus
Class Methanomicrobia
Order Methanomicrobiales
Family Methanocorpusculaceae
- Genus Methanocorpusculum
Family Methanomicrobiaceae
- Genus Methanoculleus
- Genus Methanofollis
- Genus Methanogenium
- Genus Methanolacinia
- Genus Methanomicrobium
- Genus Methanoplanus
Family Methanospirillaceae
- Genus Methanospirillum
Order Methanosarcinales
Family Methanosaetaceae
- Genus Methanosaeta
Family Methanosarcinaceae
- Genus Methanimicrococcus
- Genus Methanococcoides
- Genus Methanohalobium
- Genus Methanohalophilus
- Genus Methanolobus
- Genus Methanomethylovorans
- Genus Methanosalsum
- Genus Methanosarcina
Class Methanopyri
Order Methanopyrales
Family Methanopyraceae
- Genus Methanopyrus
Class Thermococci
Order Thermococcales
Family Thermococcaceae
- Genus Palaeococcus
- Genus Pyrococcus
- Genus Thermococcus
Class Thermoplasmata
Order Thermoplasmatales
Family Ferroplasmaceae
- Genus Ferroplasma
Family Picrophilaceae
- Genus Picrophilus
Family Thermoplasmataceae
- Genus Thermoplasma
References
- ^ J.P. Euzéby. "Archaea". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.
- ^ Sayers; et al. "Archaea". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
- ^ All-Species Living Tree Project."16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database. Retrieved 2020-08-20.
- ^ Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004. bioRxiv 10.1101/256800. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
- ^ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.
- ^ Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics. doi:10.1093/bioinformatics/btz848. PMC 7703759. PMID 31730192.
- ^ Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco; Beracochea, Martin; Shi, Zhou Jason; Pollard, Katherine S.; Sakharova, Ekaterina; Parks, Donovan H.; Hugenholtz, Philip; Segata, Nicola; Kyrpides, Nikos C.; Finn, Robert D. (20 July 2020). "A unified catalog of 204,938 reference genomes from the human gut microbiome". Nature Biotechnology. doi:10.1038/s41587-020-0603-3. PMID 32690973.
- ^ Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I-Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T. B. K.; Nielsen, Torben; Kirton, Edward; Faria, José P.; Edirisinghe, Janaka N.; Henry, Christopher S.; Jungbluth, Sean P.; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M.; Arkin, Adam P.; Tringe, Susannah G.; Visel, Axel; Woyke, Tanja; Mouncey, Nigel J.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. doi:10.1038/s41587-020-0718-6.
- ^ Mendler, K; Chen, H; Parks, DH; Hug, LA; Doxey, AC (2019). "AnnoTree: visualization and exploration of a functionally annotated microbial tree of life". Nucleic Acids Research. 47: 4442–4448. doi:10.1093/nar/gkz246.