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List of Archaea genera

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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]

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.[3][4][5][6][7]

Cladogram was taken from the GTDB release 07-RS207 (8th April 2022).[8][9][10] The position of clades with a "question mark" are based on the additional phylogeny of the 16S rRNA-based LTP_12_2021 by The All-Species Living Tree Project.[11][12][13]

Archaea

Phylum "Altarchaeota"

Class "Altarchaeia"

Order "Altarchaeales"

  • Family "Altarchaeaceae" corrig. Probst et al. 2014

Phylum "Iainarchaeota"

Class "Iainarchaeia"

Order 0-14-0-20-30-16

  • Family CSSED10-239
    • "Candidatus Forterrea" Probst & Banfield 2017

Order "Iainarchaeales"

  • Family "Iainarchaeaceae" Rinke et al. 2020

Phylum "Micrarchaeota"

Phylogeny of Micrarchaeota[8][9][10]
"Norongarragalinales"

"Ca. Norongarragalina"

"Micrarchaeales"
"Burarchaeales"

"Ca. Burarchaeum"

"Fermentimicrarchaeales"

"Ca. Fermentimicrarchaeum"

"Gugararchaeales"

"Ca. Gugararchaeum"

"Anstonellales"

Class "Micrarchaeia"

Order "Norongarragalinales"

  • Family "Norongarragalinaceae" Vázquez-Campos et al. 2021

Order "Micrarchaeales"

  • Family "Micrarchaeaceae" Vázquez-Campos et al. 2021

Order "Burarchaeales"

  • Family "Burarchaeaceae" Vázquez-Campos et al. 2021

Order "Fermentimicrarchaeales"

  • Family "Fermentimicrarchaeaceae" Kadnikov et al. 2020 (Sv326)

Order "Gugararchaeales"

  • Family "Gugararchaeaceae" Vázquez-Campos et al. 2021

Order "Anstonellales"

  • Family "Anstonellaceae" Vázquez-Campos et al. 2021
    • "Candidatus Anstonella" Vázquez-Campos et al. 2021
  • Family "Bilamarchaeaceae" Vázquez-Campos et al. 2021

Phylum "Undinarchaeota"

Class "Undinarchaeia"

Order "Undinarchaeales"

  • Family "Naiadarchaeaceae" Dombrowski et al. 2020
  • Family "Undinarchaeaceae" Dombrowski et al. 2020

Phylum "Huberarchaeaota"

Class "Huberarchaeia"

Order "Huberarchaeales"

  • Family "Huberarchaeaceae" Rinke et al. 2020

Phylum "Aenigmatarchaeota"

Class "Aenigmatarchaeia"

Order "Aenigmatarchaeales"

  • Family "Aenigmatarchaeaceae" corrig. Rinke et al. 2020

Phylum "Nanohalarchaeota"

Phylogeny of Nanohalobiaceae[8][9][10]

"Candidatus Nanosalinicola"

"Candidatus Nanosalina"

"Candidatus Nanohalobium"

Class "Nanohalarchaeia"

Order "Nanohalarchaeales"

  • Family "Nanohalarchaeaceae"

Class "Nanohalobiia"

Order "Nanohalobiales"

  • Family "Nanohalobiaceae" La Cono et al. 2020

Phylum "Nanoarchaeota"

Phylogeny of "Nanoarchaeota"[8][9][10]
"Nanoarchaeia"
"Nanoarchaeales"
"Nanoarchaeaceae"

"Nanoarchaeum"

"Nanopusillaceae"

"Ca. Nanoclepta"

"Ca. Nanopusillus"

"Tiddalikarchaeales"

"Ca. Tiddalikarchaeum"

"Parvarchaeales"

"Ca. Parvarchaeum"

Class Nanobdellia

Order Nanobdellales

  • Family Nanobdellaceae Kato et al. 2022

Class "Nanoarchaeia"

Nanoarchaeia incertae sedis

Order "Tiddalikarchaeales"

  • Family "Tiddalikarchaeaceae" Vázquez-Campos et al. 2021

Order "Parvarchaeales"

  • Family "Acidifodinimicrobiaceae" Luo et al. 2020
  • Family "Parvarchaeaceae" Rinke et al. 2020

Order "Nanoarchaeales"

  • Family "Nanoarchaeaceae" Huber et al. 2011
  • Family "Nanopusillaceae" Huber et al. 2011

Phylum "Asgardaeota"

Phylogeny of Asgardaeota[8][9][10]

Class "Tyrarchaeia"

Class "Sifarchaeia"

Order "Borrarchaeales"

  • Family "Borrarchaeaceae" Liu et al. 2020

Order "Sifarchaeales"

  • Family "Sifarchaeaceae" Sun et al. 2021
    • "Candidatus Sifarchaeum" corrig. Farag, Zhao & Biddle 2020

Class "Wukongarchaeia"

Order "Wukongarchaeales"

  • Family "Wukongarchaeaceae" Liu et al. 2020

Class "Heimdallarchaeia"

Heimdallarchaeia Incertae sedis

Order "Hodarchaeales"

  • Family "Hodarchaeaceae" Liu et al. 2020

Order "Kariarchaeales"

  • Family "Kariarchaeaceae" Liu et al. 2020

Class "Freyrarchaeia"

Class "Friggarchaeia"

Class "Gefionarchaeia"

Class "Idunnarchaeia"

Class "Jordarchaeia"

Order "Jordarchaeales"

  • Family "Jordarchaeaceae" Sun et al. 2021

Class "Odinarchaeia"

Order "Odinarchaeales"

  • Family "Odinarchaeaceae" Tamarit et al. 2022

Class "Baldrarchaeia"

Order "Baldrarchaeales"

  • Family "Baldrarchaeaceae" Liu et al. 2020

Class "Thorarchaeia"

Order "Thorarchaeales"

Class "Hermodarchaeia"

Order "Hermodarchaeales"

  • Family "Hermodarchaeaceae" Liu et al. 2020

Class "Lokiarchaeia"

Order "Helarchaeales"

Order "Sigynarchaeales"

Order "Lokiarchaeales"

  • Family "Lokiarchaeaceae" Vanwonterghem et al. 2016
    • "Candidatus Lokiarchaeum" corrig. Spang et al. 2015 (MBGB, DSAG)
  • Family "MK-D1"

Phylum "Thermoproteota"

Phylogeny of Thermoproteota[8][9][10]

Thermoproteota Incertae sedis

Class "Korarchaeia"

Order "Korarchaeales"

Class Nitrososphaeria_A

Order "Caldarchaeales"

  • Family "Caldarchaeaceae" Rinke et al. 2020

Class Nitrososphaeria

Nitrososphaeria Incertae sedis

Order "Geothermarchaeales"

Order "Conexivisphaerales"

  • Family "Conexivisphaeraceae" Kato et al. 2021 (THSC Group)

Order Nitrososphaerales

Phylogeny of Nitrososphaerales[8][9][10]

Class "Methanomethylicia"

Order "Methanohydrogenicales"

  • Family "Methanohydrogenicaceae" Berghuis et al. 2019

Order "Methanomediales"

  • Family "Methanomediaceae" Berghuis et al. 2019

Order "Methanomethylarchaeales"

  • Family "Methanomethylarchaeceae" corrig. Hua et al. 2019

Order "Methanomethylovorales"

  • Family "Methanomethylovoraceae" Hua et al. 2019

Order "Nezhaarchaeales"

Order "Methanomethylicales"

  • Family "Candidatus Methanomethylicaceae" corrig. Vanwonterghem et al. 2016

Class Thermoproteia

Thermoproteia Incertae sedis

Order Thermofilales

Order Thermoproteales

Phylogeny of Thermoproteales[8][9][10]
Thermoproteaceae
"Thermocladiaceae"

Order Sulfolobales

Phylogeny of Sulfolobales[8][9][10]

Phylum "Hadarchaeota"

Class "Persephonarchaeia"

Class "Hadarchaeia"

Order "Hadarchaeales"

Phylum Methanobacteriota_B

Phylogeny of Thermococci[8][9][10]
"Acherontia"
"Methanofastidiales"
"Methanofastidiosaceae"

"Ca. Methanofastidiosum"

Thermococcales
Thermococcaceae
Thermococci

Class "Theionarchaeia"

Class Thermococci

Order "Methanofastidiosales"

  • Family "Methanofastidiosaceae" Rinke et al. 2020

Order Thermococcales

Phylum Methanobacteriota_A

Phylogeny of Methanobacteriota_A[8][9][10]

Class Methanopyri

Order Methanopyrales

Class Methanococci

Order Methanococcales

Phylum "Hydrothermarchaeota"

Class "Hydrothermarchaeia"

Order "Hydrothermarchaeales"

  • Family "Hydrothermarchaeaceae" Chuvochina et al. 2019

Phylum "Methanobacteriota"

Phylogeny of Methanobacteriota[8][9][10]

Methanothermus {Methanothermaceae}

Methanothermobacter species-group 2 {Methanothermobacteraceae_A}

"Methanothermobacteraceae"

Methanothermobacter

Methanobacteriaceae

Methanobrevibacter

Methanobacterium species-group 2

Class Methanobacteria

Order Tepidaquicellales

  • Family "Tepidaquicellaceae" corrig. Kadnikov et al. 2020

Order Methanobacteriales

Phylum "Thermoplasmatota"

Phylogeny of Thermoplasmatota[8][9][10]

Class "Izemarchaea"

Order "Thermoprofundales"

  • (MBG-D, E2)

Class "Pontarchaea"

Order MGIII

  • (MGIII High GC)
  • (MGIII Low GC)

Class "Poseidoniia"

Order "Poseidoniales"

  • Family "Poseidoniaceae" corrig. Rinke et al. 2019
  • Family "Thalassarchaeaceae" corrig. Rinke et al. 2019

Class Thermoplasmata

Order "Lunaplasmatales"

  • Family "Lunaplasmataceae" Zinke et al. 2021

Order "Proteinoplasmatales"

Order "Sysuiplasmatales"

  • Family "Sysuiplasmataceae" Yuan et al. 2021

Order "Gimiplasmatales"

  • Family "Gimiplasmataceae" Hu et al. 2020

Order Methanomassiliicoccales

Phylogeny of Methanomassiliicoccales[8][9][10]
Methanomassiliicoccaceae

Methanomassiliicoccus

Methanomethylophilaceae"

"Candidatus Methanospyradousia"

"Candidatus Methanomethylophilus"

"Candidatus Methanogranum"

"Candidatus Methanoplasma"

Order PWKY01

Order "Aciduliprofundales"

  • Family "Aciduliprofundaceae" Rinke et al. 2020

Order Thermoplasmatales

Phylogeny of Thermoplasmatales[8][9][10]

Phylum "Halobacteriota"

Phylogeny of Halobacteriota[8][9][10]
"Syntropharchaeia"

"Syntropharchaeales"

"Methanocellia"

Methanocellales

"Methanosarcinia"

"Methanotrichales"

Methanosarcinales_A

Methanosarcinales

"Methanomicrobia"

Methanomicrobiales

Halobacteriota incertae sedis

Order "Methanoflorentales"

  • Family "Methanoflorentaceae" Mondav et al. 2014

Class "Methanoliparia"

Order "Methanoliparales"

Class Archaeoglobi

Order Archaeoglobales

Phylogeny of Archaeoglobales[8][9][10]

Class "Syntropharchaeia"

Order "Methanophagales"

  • Family "Methanophagaceae" Chadwick et al. 2022

Order "Syntropharchaeales"

  • Family "Syntropharchaeaceae" corrig. (ANME-2 cluster)

Class "Methanocellia"

Order Methanocellales

  • Family Methanocellaceae Sakai et al. 2008

Class "Methanosarcinia"

Order "Methanotrichales"

  • Family Methanotrichaceae Akinyemi et al. 2021

Order Methanosarcinales_A

  • Family Methermicoccaceae Cheng et al. 2007

Order Methanosarcinales

Phylogeny of Methanosarcinales[8][9][10]

Class Methanomicrobia

Order "Alkanophagales"

Order Methanomicrobiales

Phylogeny of Methanomicrobiales[8][9][10]

Class "Hikarchaeia"

Order "Hikarchaeales"

  • Family "Hikarchaeaceae" Martijn et al. 2020 (MG-IV)

Class "Methanonatronarchaeia"

Order "Methanonatronarchaeales"

  • Family "Methanohalarchaeaceae" Sorokin et al. 2018
  • Family Methanonatronarchaeaceae Sorokin et al. 2018

Class Halobacteria

Order Halobacteriales

Phylogeny of Halobacteriales[8][9][10]
Phylogeny of Natrialbaceae[8][9][10]
Phylogeny of Haloferacaceae[8][9][10]

See also

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. ^ 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.
  4. ^ 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.
  5. ^ 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.
  6. ^ 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. 39 (1): 105–114. doi:10.1038/s41587-020-0603-3. PMC 7801254. PMID 32690973.
  7. ^ Nayfach, Stephen; et al. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. 39 (4): 499–509. doi:10.1038/s41587-020-0718-6. PMC 8041624. PMID 33169036.
  8. ^ a b c d e f g h i j k l m n o p q r s t u v "GTDB release 07-RS207". Genome Taxonomy Database. Retrieved 20 June 2022.
  9. ^ a b c d e f g h i j k l m n o p q r s t u v "ar53_r207.sp_label". Genome Taxonomy Database. Retrieved 20 June 2022.
  10. ^ a b c d e f g h i j k l m n o p q r s t u v "Taxon History". Genome Taxonomy Database. Retrieved 20 June 2022.
  11. ^ "The LTP". Retrieved 23 February 2021.
  12. ^ "LTP_all tree in newick format". Retrieved 23 February 2021.
  13. ^ "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
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