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{{short description|Wikipedia list article}}
{{short description|Wikipedia list article}}
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>
This article lists the [[genus (biology)|genera]] of the [[Archaea]].
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>


== Phylogeny ==
The following genus of the Archaea has not been assigned to a [[phylum (biology)|phylum]]:
[[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>


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>
*[[Genus (biology)|Genus]] ''[[Halostagnicola]]''


{{Clade|style=font-size:90%; line-height:90%|label1=[[Archaea]]|
{{clade
|label1="[[DPANN]]"
|1={{Clade
|1=[[Altiarchaeota]]
|2={{Clade
|label1="[[Diapherotrites]]"
|1={{Clade
|1=[[Iainarchaeaota]]
|2=[[Micrarchaeota]]
}}
|2={{Clade
|1=[[Undinarchaeota]]
|2={{Clade
|1={{Clade
|1=[[Aenigmarchaeota]]
|2={{Clade
|1=[[Huberarchaeaota]]
|2=[[Nanohaloarchaeota]]
}}
}}
|2=[[Nanoarchaeota]]
}}
}}
}}
}}
|2={{Clade
|label1="[[Proteoarchaeota]]"
|1={{Clade
|1="[[Thermoproteota]]"
|2="[[Asgardaeota]]"
}}
|label1="[[Euryarchaeota|Euryarchaeida]]"
|2={{Clade
|1={{Clade
|1=[[Hydrothermarchaeota]]
|2={{Clade
|1=[[Hadarchaeota]]
|2="[[Methanobacteriota]]"
}}
}}
|2={{Clade
|1="[[Thermoplasmatota]]"
|2="[[Halobacteriota]]" (Class II Methanogens)
}}
}}
}}
}}
}}


==Phylum "[[Altarchaeota]]"==
===Class "[[Altarchaeia]]"===
====Order "[[Altarchaeales]]"====
=====Family "Altarchaeaceae"=====
* "''Candidatus'' [[Altarchaeum]]" <small>corrig. Probst et al. 2014</small>


==Phylum "[[Iainarchaeota]]"==
This section lists the genera of Archaea within the [[Phylum (biology)|Phylum]] [[Crenarchaeota]].
===Class "[[Iainarchaeia]]"===
====Order "[[Iainarchaeales]]"====
=====Family "[[Iainarchaeaceae]]"=====
* "''Candidatus'' [[Forterrea]]" <small>Probst & Banfield 2017</small>
* "''Candidatus'' [[Iainarchaeum]]" <small>Rinke et al. 2013</small>


==Phylum "[[Micrarchaeota]]"==
==Class Thermoprotei==
===Class "[[Micrarchaeia]]"===
====Order [[Fermentimicrarchaeales]]====
=====Family [[Fermentimicrarchaeaceae]]=====
* "''Candidatus'' [[Fermentimicrarchaeum]]" <small>Kadnikov et al. 2020</small>


====Order "[[Micrarchaeales]]"====
=====Family "[[Micrarchaeaceae]]"=====
* "''Candidatus'' [[Mancarchaeum]]" <small>Golyshina et al. 2017</small>
* "''Candidatus'' [[Micrarchaeum]]" <small>Baker et al. 2010</small>


==Phylum "[[Undinarchaeota]]"==
This section lists the genera of Archaea within the [[Class (biology)|Class]] [[Thermoprotei]].
===Class "[[Undinarchaeia]]"===
====Order "[[Naiadarchaeales]]"====
=====Family "[[Naiadarchaeaceae]]"=====
* "''Candidatus'' [[Naiadarchaeum]]" <small>Dombrowski et al. 2020</small>


===Order Caldisphaerales===
====Order "[[Undinarchaeales]]"====
=====Family "[[Undinarchaeaceae]]"=====
* "''Candidatus'' [[Undinarchaeum]]" <small>Dombrowski et al. 2020</small>


==Phylum "[[Aenigmarchaeota|Aenigmatarchaeota]]"==
===Class "[[Aenigmatarchaeia]]"===
====Order "[[Aenigmatarchaeales]]"====
=====Family "[[Aenigmatarchaeaceae]]"=====
* "''Candidatus'' [[Aenigmatarchaeum]]" <small>corrig. Rinke et al. 2013</small>


==Phylum "[[Huberarchaeaota]]"==
This section lists the genera of Archaea within the [[Order (biology)|Order]] [[Caldisphaerales]].
===Class "[[Huberarchaeia]]"===
====Order "[[Huberarchaeales]]"====
=====Family "[[Huberarchaeaceae]]"=====
* "''Candidatus'' [[Huberarchaeum]]" <small>corrig. Schwank et al. 2019</small>


==Phylum "[[Nanohaloarchaeota]]"==
====Family Caldisphaeraceae====
===Class "[[Nanohalobia]]"===
====Order "Nanohalobiales"====
=====Family "Nanohalobiaceae"=====
* ?"''Candidatus'' [[Nanohalobium]]" <small>La Cono et al. 2020</small>


===Class "[[Nanohalarchaeia]]"===
====Order "[[Nanohalarchaeales]]"====
=====Family "[[Nanohalarchaeaceae]]"=====
* ?"''Candidatus'' [[Nanohalarchaeum]]" <small>corrig. Hamm et al. 2019</small>


===Class "[[Nanosalinia]]"===
This section lists the genera of Archaea within the [[Family (biology)|Family]] [[Caldisphaeraceae]].
====Order "[[Nanosalinales]]"====
=====Family "[[Nanosalinaceae]]"=====
* ?"''Candidatus'' [[Nanopetraeus]]" <small>corrig. Crits‐Christoph et al. 2016</small>
* ?"''Candidatus'' [[Haloredivivus]]" <small>Ghai et al. 2011</small>
* "''Candidatus'' [[Nanosalina]]" <small>Narasingarao et al. 2012</small>
* "''Candidatus'' [[Nanosalinicola]]" <small>corrig. Narasingarao et al. 2012</small>


==Phylum "[[Nanoarchaeota]]"==
:*Genus ''[[Caldisphaera]]''
===Class "[[Nanoarchaeia]]"===
====Nanoarchaeia incertae sedis====
* "[[Mamarchaeales]]"
* "[[Woesearchaeales]]" (DHVE-6)
* "[[Pacearchaeales]]" (DHVE-5, DUSEL-1)
* "[[Tiddalikarchaeales]]" <small>Vazquez-Campos et al. 2019</small> (LFWA-I)
* "[[Wiannamattarchaeales]]" <small>Vazquez-Campos et al. 2019</small> (LFWA-II, Eury4AB)
* "[[Gugararchaeales]]" <small>Vazquez-Campos et al. 2019</small> (LFWA-III, Eury4AA)


====Order Cenarchaeales====
====Order "[[Parvarchaeales]]"====
=====Family "[[Parvarchaeaceae]]"=====
* "''Candidatus'' [[Parvarchaeum]]" <small>Baker et al. 2010</small> (ARMAN 4 & 5)


====Order "[[Nanoarchaeales]]"====
This section lists the genera of Archaea within the Order [[Cenarchaeales]].
=====Family "[[Nanoarchaeaceae]]"=====
* "[[Nanoarchaeum]]" <small>Huber et al. 2002</small>
=====Family "Nanopusillaceae"=====
* "''Candidatus'' [[Nanoclepta]]" <small>St. John et al. 2019</small>
* "''Candidatus'' [[Nanopusillus]]" <small>Wurch et al. 2016</small>


==Phylum "[[Asgardaeota]]"==
=====Family Cenarchaeaceae=====
===Class "[[Freyarchaeia]]"===


===Class "[[Borrarchaeia]]"===
This section lists the genera of Archaea within the Family [[Cenarchaeaceae]].
====Order "[[Borrarchaeales]]"====
=====Family "[[Borrarchaeaceae]]"=====
* ?"''Candidatus'' [[Borrarchaeum]]" <small>Liu et al. 2020</small>


===Class "[[Jordarchaeia]]"===
:*Genus ''[[Cenarchaeum]]''
====Order "[[Jordarchaeales]]"====
=====Family "[[Jordarchaeaceae]]"=====
* ?"''Candidatus'' [[Jordarchaeum]]" <small>Sun et al. 2021</small>


===Class "[[Heimdallarchaeia]]"===
====Order Desulfurococcales====
====Class Incertae sedis====
* "[[Gerdarchaeales]]"
* "[[Heimdallarchaeales]]"


====Order "[[Wukongarchaeales]]"====
This section lists the genera of Archaea within the Order [[Desulfurococcales]].
=====Family "[[Wukongarchaeaceae]]"=====
* "''Candidatus'' [[Wukongarchaeum]]" <small>Liu et al. 2020</small>


====Order "[[Hodarchaeales]]"====
The following two genera of Desulfurococcales have not been assigned to a family:
=====Family "[[Hodarchaeaceae]]"=====
* "''Candidatus'' [[Hodarchaeum]]" <small>Liu et al. 2020</small>


====Order "[[Kariarchaeales]]"====
*Genus ''[[Caldococcus]]''
=====Family "[[Kariarchaeaceae]]"=====
*Genus ''[[Ignisphaera]]''
* "''Candidatus'' [[Kariarchaeum]]" <small>Liu et al. 2020</small>


===Class "[[Lokiarchaeia]]"===
=====Family Desulfurococcaceae=====
====Lokiarchaeia incertae sedis====
* Order "[[Helarchaeales]]"
** Family "[[Helarchaeaceae]]"
* Order "[[Odinarchaeales]]"===
** Family "[[Odinarchaeaceae]]"


====Order "[[Baldrarchaeales]]"====
This section lists the genera of Archaea within the Family [[Desulfurococcaceae]].
=====Family "[[Baldrarchaeaceae]]"=====
* "Candidatus Baldrarchaeum yapensis]]" <small>Liu et al. 2020</small>


====Order "[[Lokiarchaeales]]"====
:*Genus ''[[Acidilobus]]''
=====Family "[[Lokiarchaeaceae]]"=====
:*Genus ''[[Acidococcus]]''
* "''Candidatus'' [[Lokiarchaeum]]" <small>corrig. Spang et al. 2015</small>
:*Genus ''[[Aeropyrum]]''
* "''Candidatus'' [[Promethearchaeum]]" <small>corrig. Imachi, Nobu & Takai 2020</small>
:*Genus ''[[Desulfurococcus]]''
:*Genus ''[[Ignicoccus]]''
:*Genus ''[[Staphylothermus]]''
:*Genus ''[[Stetteria]]''
:*Genus ''[[Sulfophobococcus]]''
:*Genus ''[[Thermodiscus]]''
:*Genus ''[[Thermosphaera]]''


=====Family Pyrodictiaceae=====
===Class "[[Thorarchaeia]]"===
====Order "[[Thorarchaeales]]"====
=====Family "[[Thorarchaeaceae]]"=====


====Order "[[Hermodarchaeales]]"====
This section lists the genera of Archaea within the Family [[Pyrodictiaceae]].
=====Family "[[Hermodarchaeaceae]]"=====
* "''Candidatus'' [[Hermodarchaeum]]" <small>Liu et al. 2020</small>


====Order "[[Sifarchaeales]]"====
:*Genus ''[[Geogemma]]''
=====Family "[[Sifarchaeaceae]]"=====
:*Genus ''[[Hyperthermus]]''
* "''Candidatus'' [[Sifarchaeotum]]" <small>Farag, Zhao & Biddle 2020</small>
:*Genus ''[[Pyrodictium]]''
:*Genus ''[[Pyrolobus]]''


==Phylum "[[Thermoproteota]]"==
====Order Nitrosopumilales====
===Class "[[Korarchaeia]]"===
Only environmental samples of the Korarchaeota have been studied.


===Class [[Thermoprotei]]===
This section lists the genera of Archaea within the Order [[Nitrosopumilales]].
====Order [[Caldisphaerales]]====
=====Family [[Caldisphaeraceae]]=====
* Genus ''[[Caldisphaera]]''


=====Family Nitrosopumilaceae=====
====Order [[Cenarchaeales]]====
=====Family [[Cenarchaeaceae]]=====
* Genus ''[[Cenarchaeum]]''


====Order [[Desulfurococcales]]====
This section lists the genera of Archaea within the Family [[Nitrosopumilaceae]].
* Genus ''[[Caldococcus]]''
* Genus ''[[Ignisphaera]]''


=====Family [[Desulfurococcaceae]]=====
:*Genus ''[[Nitrosopumilus]]'' (candidatus)
* Genus ''[[Acidilobus]]''
* Genus ''[[Acidococcus]]''
* Genus ''[[Aeropyrum]]''
* Genus ''[[Desulfurococcus]]''
* Genus ''[[Ignicoccus]]''
* Genus ''[[Staphylothermus]]''
* Genus ''[[Stetteria]]''
* Genus ''[[Sulfophobococcus]]''
* Genus ''[[Thermodiscus]]''
* Genus ''[[Thermosphaera]]''


====Order Sulfolobales====
=====Family [[Pyrodictiaceae]]=====
* Genus ''[[Geogemma]]''
* Genus ''[[Hyperthermus]]''
* Genus ''[[Pyrodictium]]''
* Genus ''[[Pyrolobus]]''


====Order [[Nitrosopumilales]]====
This section lists the genera of Archaea within the Order [[Sulfolobales]].
=====Family [[Nitrosopumilaceae]]=====
* Genus ''[[Nitrosopumilus]]'' (candidatus)


=====Family Sulfolobaceae=====
====Order [[Sulfolobales]]====
=====Family [[Sulfolobaceae]]=====
* Genus ''[[Acidianus]]''
* Genus ''[[Metallosphaera]]''
* Genus ''[[Stygiolobus]]''
* Genus ''[[Sulfolobus]]''
* Genus ''[[Sulfurisphaera]]''


====Order [[Thermoproteales]]====
This section lists the genera of Archaea within the Family [[Sulfolobaceae]].
=====Family [[Thermofilaceae]]=====
* Genus ''[[Thermofilum]]''


=====Family [[Thermoproteaceae]]=====
:*Genus ''[[Acidianus]]''
:*Genus ''[[Metallosphaera]]''
* Genus ''[[Caldivirga]]''
:*Genus ''[[Stygiolobus]]''
* Genus ''[[Pyrobaculum]]''
:*Genus ''[[Sulfolobus]]''
* Genus ''[[Thermocladium]]''
:*Genus ''[[Sulfurisphaera]]''
* Genus ''[[Thermoproteus]]''
* Genus ''[[Vulcanisaeta]]''

====Order Thermoproteales====

This section lists the genera of Archaea within the Order [[Thermoproteales]].

=====Family Thermofilaceae=====

This section lists the genera of Archaea within the Family [[Thermofilaceae]].

:*Genus ''[[Thermofilum]]''

=====Family Thermoproteaceae=====

This section lists the genera of Archaea within the Family [[Thermoproteaceae]].

:*Genus ''[[Caldivirga]]''
:*Genus ''[[Pyrobaculum]]''
:*Genus ''[[Thermocladium]]''
:*Genus ''[[Thermoproteus]]''
:*Genus ''[[Vulcanisaeta]]''


==Phylum Euryarchaeota==
==Phylum Euryarchaeota==

This section lists the genera of Archaea within the Phylum [[Euryarchaeota]].

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:

*Genus ''[[Aciduliprofundum]]''
*Genus ''[[Aciduliprofundum]]''


===Class Archaeoglobi===
===Class Archaeoglobi===

This section lists the genera of Archaea within the Class [[Archaeoglobi]].

====Order Archaeoglobales====
====Order Archaeoglobales====

This section lists the genera of Archaea within the Order [[Archaeoglobales]].

=====Family Archaeoglobaceae=====
=====Family Archaeoglobaceae=====

This section lists the genera of Archaea within the Family [[Archaeoglobaceae]].

:*Genus ''[[Archaeoglobus]]''
:*Genus ''[[Archaeoglobus]]''
:*Genus ''[[Ferroglobus]]''
:*Genus ''[[Ferroglobus]]''
Line 139: Line 272:


===Class Halobacteria===
===Class Halobacteria===

This section lists the genera of Archaea within the Class [[Halobacteria]].

====Order Halobacteriales====
====Order Halobacteriales====

This section lists the genera of Archaea within the Order [[Halobacteriales]].

=====Family Halobacteriaceae=====
=====Family Halobacteriaceae=====

This section lists the genera of Archaea within the Family [[Halobacteriaceae]].

:*Genus ''[[Haladaptatus]]''
:*Genus ''[[Haladaptatus]]''
:*Genus ''[[Halalkalicoccus]]''
:*Genus ''[[Halalkalicoccus]]''
Line 179: Line 303:


===Class Methanobacteria===
===Class Methanobacteria===

This section lists the genera of Archaea within the Class [[Methanobacteria]].

====Order Methanobacteriales====
====Order Methanobacteriales====

This section lists the genera of Archaea within the Order [[Methanobacteriales]].

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]]''


==Phylum Korarchaeota==
== 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"

Phylum "Iainarchaeota"

Class "Iainarchaeia"

Order "Iainarchaeales"

Family "Iainarchaeaceae"

Phylum "Micrarchaeota"

Class "Micrarchaeia"

Order Fermentimicrarchaeales

Family Fermentimicrarchaeaceae

Order "Micrarchaeales"

Family "Micrarchaeaceae"

Phylum "Undinarchaeota"

Class "Undinarchaeia"

Order "Naiadarchaeales"

Family "Naiadarchaeaceae"

Order "Undinarchaeales"

Family "Undinarchaeaceae"

Phylum "Aenigmatarchaeota"

Class "Aenigmatarchaeia"

Order "Aenigmatarchaeales"

Family "Aenigmatarchaeaceae"

Phylum "Huberarchaeaota"

Class "Huberarchaeia"

Order "Huberarchaeales"

Family "Huberarchaeaceae"

Phylum "Nanohaloarchaeota"

Class "Nanohalobia"

Order "Nanohalobiales"

Family "Nanohalobiaceae"

Class "Nanohalarchaeia"

Order "Nanohalarchaeales"

Family "Nanohalarchaeaceae"

Class "Nanosalinia"

Order "Nanosalinales"

Family "Nanosalinaceae"

Phylum "Nanoarchaeota"

Class "Nanoarchaeia"

Nanoarchaeia incertae sedis

Order "Parvarchaeales"

Family "Parvarchaeaceae"

Order "Nanoarchaeales"

Family "Nanoarchaeaceae"
Family "Nanopusillaceae"

Phylum "Asgardaeota"

Class "Freyarchaeia"

Class "Borrarchaeia"

Order "Borrarchaeales"

Family "Borrarchaeaceae"

Class "Jordarchaeia"

Order "Jordarchaeales"

Family "Jordarchaeaceae"

Class "Heimdallarchaeia"

Class Incertae sedis

Order "Wukongarchaeales"

Family "Wukongarchaeaceae"

Order "Hodarchaeales"

Family "Hodarchaeaceae"

Order "Kariarchaeales"

Family "Kariarchaeaceae"

Class "Lokiarchaeia"

Lokiarchaeia incertae sedis

Order "Baldrarchaeales"

Family "Baldrarchaeaceae"
  • "Candidatus Baldrarchaeum yapensis]]" Liu et al. 2020

Order "Lokiarchaeales"

Family "Lokiarchaeaceae"

Class "Thorarchaeia"

Order "Thorarchaeales"

Family "Thorarchaeaceae"

Order "Hermodarchaeales"

Family "Hermodarchaeaceae"

Order "Sifarchaeales"

Family "Sifarchaeaceae"

Phylum "Thermoproteota"

Class "Korarchaeia"

Only environmental samples of the Korarchaeota have been studied.

Class Thermoprotei

Order Caldisphaerales

Family Caldisphaeraceae

Order Cenarchaeales

Family Cenarchaeaceae

Order Desulfurococcales

Family Desulfurococcaceae
Family Pyrodictiaceae

Order Nitrosopumilales

Family Nitrosopumilaceae

Order Sulfolobales

Family Sulfolobaceae

Order Thermoproteales

Family Thermofilaceae
Family Thermoproteaceae

Phylum Euryarchaeota

The following genus of the Euryarchaeota has not been assigned to a class:

Class Archaeoglobi

Order Archaeoglobales

Family Archaeoglobaceae

Class Halobacteria

Order Halobacteriales

Family Halobacteriaceae

Class Methanobacteria

Order Methanobacteriales

The following two genera of the Methanomicrobiales have not been assigned to a family:

Family Methanobacteriaceae
Family Methanothermaceae

Class Methanococci

Order Methanococcales

Family Methanocaldococcaceae
Family Methanococcaceae

Class Methanomicrobia

Order Methanomicrobiales

Family Methanocorpusculaceae
Family Methanomicrobiaceae
Family Methanospirillaceae

Order Methanosarcinales

Family Methanosaetaceae
Family Methanosarcinaceae

Class Methanopyri

Order Methanopyrales

Family Methanopyraceae

Class Thermococci

Order Thermococcales

Family Thermococcaceae

Class Thermoplasmata

Order Thermoplasmatales

Family Ferroplasmaceae
Family Picrophilaceae
Family Thermoplasmataceae

References

  1. ^ J.P. Euzéby. "Archaea". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.
  2. ^ Sayers; et al. "Archaea". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  3. ^ All-Species Living Tree Project."16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database. Retrieved 2020-08-20.
  4. ^ 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.
  5. ^ 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.
  6. ^ 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.
  7. ^ 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.
  8. ^ 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.
  9. ^ 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.
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