Wikipedia

List of Archaea genera

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] However, in the List provided below, GTDB has precedence unless otherwise noted.

Phylogeny edit

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 08-RS214 (28th April 2023).[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 "Microcaldota" edit

Class "Microcaldia" edit

Order "Microcaldales" edit

  • Family "Microcaldaceae" Sakai et al. 2022

Phylum "Undinarchaeota" edit

Class "Undinarchaeia" edit

Order "Undinarchaeales" edit

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

Phylum "Altarchaeota" edit

Class "Altarchaeia" edit

Order "Altarchaeales" edit

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

Phylum "Iainarchaeota" edit

Class "Iainarchaeia" edit

Order "Forterreales" edit

  • Family "Forterreaceae" Pallen, Rodriguez-R & Alikhan 2022
    • "Candidatus Forterrea" Probst & Banfield 2017

Order "Iainarchaeales" edit

  • Family "Iainarchaeaceae" Rinke et al. 2020

Phylum "Micrarchaeota" edit

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

"Ca. Norongarragalina"

"Micrarchaeales"
"Micrarchaeaceae"
"Anstonellales"
"Anstonellaceae"

"Ca. Anstonella"

"Bilamarchaeaceae"

"Ca. Bilamarchaeum"

"Fermentimicrarchaeales"

"Ca. Fermentimicrarchaeum"

"Burarchaeales"

"Ca. Burarchaeum"

"Gugararchaeales"

"Ca. Gugararchaeum"

Class "Micrarchaeia" edit

Order "Norongarragalinales" edit

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

Order "Micrarchaeales" edit

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

Order "Anstonellales" edit

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

Order "Fermentimicrarchaeales" edit

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

Order "Burarchaeales" edit

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

Order "Gugararchaeales" edit

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

Phylum "Huberarchaeaota" edit

Class "Huberarchaeia" edit

Order "Huberarchaeales" edit

  • Family "Huberarchaeaceae" Rinke et al. 2020

Phylum "Aenigmatarchaeota" edit

Class "Aenigmatarchaeia" edit

Order "Aenigmatarchaeales" edit

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

Phylum "Nanohalarchaeota" edit

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

"Candidatus Nanosalinicola"

"Candidatus Nanosalina"

"Candidatus Nanohalobium"

Class "Nanohalarchaeia" edit

Order "Nanohalarchaeales" edit

  • Family "Nanohalarchaeaceae"

Class "Nanohalobiia" edit

Order "Nanohalobiales" edit

  • Family "Nanoanaerosalinaceae" Zhao et al. 2022
  • Family "Nanohalalkaliarchaeaceae" La Cono et al. 2020
  • Family "Nanohalobiaceae" La Cono et al. 2020

Phylum "Nanoarchaeota" edit

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

"Nanoarchaeum"

"Nanopusillaceae"

"Ca. Nanoclepta"

"Ca. Nanopusillus"

"Tiddalikarchaeales"

"Ca. Tiddalikarchaeum"

"Parvarchaeales"

"Ca. Parvarchaeum"

Class "Nanoarchaeia" edit

Nanoarchaeia incertae sedis edit

Order "Nanoarchaeales" edit

  • Family "Nanoarchaeaceae" Huber et al. 2011
  • Family "Nanopusillaceae" Huber et al. 2011
    • Nanobdella Kato et al. 2022
    • "Candidatus Nanoclepta" St. John et al. 2019
    • "Candidatus Nanopusillus" Wurch et al. 2016 ["Candidatus Nanobsidianus" Castelle et al. 2015]

Order "Tiddalikarchaeales" edit

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

Order "Parvarchaeales" edit

Phylum "Asgardaeota" edit

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

Asgardaeota incertae sedis edit

  • Class "Asgardarchaeia"
    • Order "Asgardarchaeales"
      • Family "Asgardarchaeaceae" Eme et al. 2023
  • Class "Balderarchaeia"
    • Order "Balderarchaeales"
      • Family "Balderarchaeaceae" Xie et al. 2022
  • Class "Freyrarchaeia"
    • Order "Freyrarchaeales"
  • Class "Njordarchaeia"
    • Order "Njordarchaeales"
  • Class "Tyrarchaeia"
    • Order "Tyrarchaeales"
      • Family "Tyrarchaeaceae" Xie et al. 2022

Class "Sifarchaeia" edit

Order "Borrarchaeales" edit

  • Family "Borrarchaeaceae" Liu et al. 2021

Order "Sifarchaeales" edit

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

Class "Wukongarchaeia" edit

Order "Wukongarchaeales" edit

  • Family "Wukongarchaeaceae" Liu et al. 2021

Class "Heimdallarchaeia" edit

Order "Hodarchaeales" edit

  • Family "Hodarchaeaceae" Liu et al. 2021

Order "Gerdarchaeales" edit

Order "Kariarchaeales" edit

  • Family "Kariarchaeaceae" Liu et al. 2021

Order "Heimdallarchaeales" edit

Class "Jordarchaeia" edit

Order "Jordarchaeales" edit

  • Family "Jordarchaeaceae" Sun et al. 2021

Class "Baldrarchaeia" edit

Order "Baldrarchaeales" edit

  • Family "Baldrarchaeaceae" corrig. Liu et al. 2021

Class "Thorarchaeia" edit

Order "Thorarchaeales" edit

Class "Odinarchaeia" edit

Order "Odinarchaeales" edit

  • Family "Odinarchaeaceae" Tamarit et al. 2022

Class "Hermodarchaeia" edit

Order "Hermodarchaeales" edit

  • Family "Hermodarchaeaceae" corrig. Liu et al. 2021

Class "Lokiarchaeia" edit

Order "Helarchaeales" edit

Order "Sigynarchaeales" edit

Order "Lokiarchaeales" edit

In GTDB as order CR-4

  • Family "Lokiarchaeaceae" Vanwonterghem et al. 2016
    • ?"Candidatus Lokiarchaeum" corrig. Spang et al. 2015 (MBGB, DSAG)
  • Family "Prometheoarchaeaceae" Pallen, Rodriguez-R & Alikhan 2022[17] ("MK-D1")

Phylum "Thermoproteota" edit

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

Thermoproteota Incertae sedis edit

Class "Korarchaeia" edit

Order "Korarchaeales" edit

Class "Bathyarchaeia" edit

Order "Bathyarchaeales" edit

  • Family "Bathyarchaeaceae" Khomyakova et al. 2023

Order "Hecatellales" edit

  • Family "Hecatellaceae" Rinke et al. 2020

MCG6 edit

Class Nitrososphaeria_A edit

Order "Caldarchaeales" edit

Phylogeny of Nitrososphaeria_A[8][9][10]
"Caldarchaeales"
"Caldarchaeaceae"

"Ca. Calditenuis"

"Wolframiiraptoraceae"
  • Family "Caldarchaeaceae" Rinke et al. 2020

Class Nitrososphaeria edit

Nitrososphaeria Incertae sedis edit

Order "Geothermarchaeales" edit

Order "Conexivisphaerales" edit

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

Order Nitrososphaerales edit

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

Class "Culexarchaeia" edit

Order "Culexarchaeles" edit

  • Family "Culexarchaeaceae" Kohtz et al. 2022 ["Methanomediaceae" Berghuis et al. 2019]
    • ?"Candidatus Culexarchaeum" Kohtz et al. 2022 ["Candidatus Methanomedium" Berghuis et al. 2019]
  • Family "Culexmicrobiaceae" Kohtz et al. 2022

Class "Methanomethylicia" edit

Methanomethylicia incertae sedis edit

  • Order "Methanohydrogenicales"
    • Family "Methanohydrogenicaceae" Berghuis et al. 2019
  • Order "Methanomethylarchaeales"
    • Family "Methanomethylarchaeceae" corrig. Hua et al. 2019
  • Order "Methanomethylovorales"
    • Family "Methanomethylovoraceae" Hua et al. 2019

Order "Nezhaarchaeales" edit

Order "Methanomethylicales" edit

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

Class Thermoproteia edit

Order "Gearchaeales" edit

Order Thermofilales edit

Order Thermoproteales edit

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

Class "Sulfolobia" edit

Order "Marsarchaeales" edit

Order Sulfolobales edit

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

Phylum "Hadarchaeota" edit

Class "Persephonarchaeia" edit

Class "Hadarchaeia" edit

Order "Hadarchaeales" edit

  • Family "Hadarchaeaceae" Chuvochina et al. 2019 ex Chuvochina et al. 2023

Phylum Methanobacteriota_B edit

Phylogeny of Methanobacteriota_B[8][9][10]
Thermococci
"Methanofastidiales"

"Ca. Methanofastidiosum"

"Methanofastidiosaceae"
Thermococcales
Thermococcaceae

Class "Theionarchaeia" edit

Class Thermococci edit

Order "Methanofastidiosales" edit

  • Family "Methanofastidiosaceae" Rinke et al. 2020

Order Thermococcales edit

Phylum "Hydrothermarchaeota" edit

Class "Hydrothermarchaeia" edit

Order "Hydrothermarchaeales" edit

  • Family "Hydrothermarchaeaceae" Chuvochina et al. 2019 ex Chuvochina et al. 2023

Phylum "Methanobacteriota" edit

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

Class Methanopyri edit

Order Methanopyrales edit

Class Methanococci edit

Order Methanococcales edit

Class Methanobacteria edit

Order Methanobacteriales edit

Phylum "Thermoplasmatota" edit

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

Thermoplasmatota incertae sedis edit

Order "Yaplasmatales" edit

Class "Izemarchaea" edit

Order "Thermoprofundales" edit

  • (MBG-D, E2)

Class "Poseidoniia" edit

Order MGIII edit

Order "Poseidoniales" edit

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

Class Thermoplasmata edit

Order "Lunaplasmatales" edit

  • Family "Lunaplasmataceae" Zinke et al. 2021

Order "Natronoplasmatales" edit

Phylogeny of Natronoplasmatales[8][9][10]

"Candidatus Haladaptiplasma"

"Candidatus Natronoplasma"

"Candidatus Saliniplasma"

Order "Proteinoplasmatales" edit

  • (SG8-5)

Order "Gimiplasmatales" edit

  • Family "Gimiplasmataceae" Hu et al. 2020

Order "Sysuiplasmatales" edit

  • Family "Sysuiplasmataceae" Yuan et al. 2021

Order Methanomassiliicoccales edit

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

Methanomassiliicoccus

Methanomethylophilaceae"

"Candidatus Methanarcanum"

"Candidatus Methanomethylophilus"

"Candidatus Methanogranum"

"Candidatus Methanoplasma"

Order "Aciduliprofundales" edit

  • Family "Aciduliprofundaceae" Rinke et al. 2020

Order Thermoplasmatales edit

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

Phylum "Halobacteriota" edit

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

"Methanoliparales"

"Syntropharchaeia"

"Syntropharchaeales"

"Methanocellia"

Methanocellales

"Methanosarcinia"
"Methanosarcinia_A"

Methanosarcinales_A

"Methanomicrobia"

Methanomicrobiales

Halobacteriota incertae sedis edit

Order "Methanoflorentales" edit

  • Family "Methanoflorentaceae" Mondav et al. 2014

Class Archaeoglobi edit

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

Order "Mnemosynellales" edit

  • Family "Mnemosynellaceae" Adam et al. 2022

Order Archaeoglobales edit

Class "Methanoliparia" edit

Order "Methanoliparales" edit

Class "Syntropharchaeia" edit

Order "Methanophagales" edit

  • Family ?"Veteromethanophagaceae" Vulcano et al. 2022
  • Family "Methanophagaceae" Chadwick et al. 2022
  • Family "Methanoxibalbaceae" Laso-Pérez et al. 2022

Order "Syntropharchaeales" edit

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

Class "Methanocellia" edit

Order Methanocellales edit

  • Family Methanocellaceae Sakai et al. 2008

Class "Methanosarcinia" edit

Order Methanotrichales edit

Order Methanosarcinales edit

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

Class Methanosarcinia A edit

Order Methanosarcinales_A edit

  • Family Methermicoccaceae Cheng et al. 2007

Class Methanomicrobia edit

Order "Alkanophagales" edit

  • Family "Alkanophagaceae"

Order Methanomicrobiales edit

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

Class "Hikarchaeia" edit

Order "Hikarchaeales" edit

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

Class "Methanonatronarchaeia" edit

Order "Methanonatronarchaeales" edit

Class Halobacteria edit

Phylogeny of Halobacteria[8][9][10]
Halobacteriales

Order "Halorutilales" edit

  • Family "Halorutilaceae" Durán-Viseras et al. 2023

Order Halobacteriales edit

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

See also edit

References edit

  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. 36 (6): 1925–1927. 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 w "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  9. ^ a b c d e f g h i j k l m n o p q r s t u v w "ar53_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  10. ^ a b c d e f g h i j k l m n o p q r s t u v w "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
  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.
  14. ^ a b c Ruize Xie, Yinzhao Wang, Danyue Huang, Jialin Hou, Liuyang Li, Haining Hu, Xiaoxiao Zhao, Fengping Wang: Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes. In: Science China Life Sciences, vol. 65, p. 818–829, April 2022. doi:10.1007/s11427-021-1969-6, PMID 34378142. Epub: Aug. 6, 2021. Along with:Njordarchaeota, a new candidate for a sister group to eukaryotes. EurekAlert!, Oct. 20, 2021.
  15. ^ LPSN: Order "Candidatus Freyrarchaeales"
  16. ^ LPSN: Order "Candidatus Njordarchaeales"
  17. ^ a b c Fabai Wu, Daan R. Speth, Alon Philosof, Antoine Crémière, Aditi Narayanan, Roman A. Barco, Stephanie A. Connon, Jan P. Amend, Igor A. Antoshechkin, Victoria J. Orphan: Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes. In: Nature Microbiology volume 7, p. 200–212, Jan 13, 2022. doi:10.1038/s41564-021-01039-y, PMID 35027677, PMC 8813620. See also Extended Data Fig. 2.
  18. ^ LPSN: Family "Candidatus Sigynarchaeaceae"
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