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List of Archaea genera

From Wikipedia, the free encyclopedia

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

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

Cladogram was taken from the GTDB release 09-RS220 (24th April 2024).[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

Archaea incertae sedis

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  • Family "Afararchaeaceae" Baker et al. 2024
  • Family "Asbonarchaeaceae" Baker et al. 2024
  • Family "Chewarchaeaceae" Baker et al. 2024

Phylum "Microcaldota"

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Class "Microcaldia"

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Order "Microcaldales"

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  • Family "Microcaldaceae" Sakai et al. 2022

Phylum "Undinarchaeota"

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Class "Undinarchaeia"

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Order "Undinarchaeales"

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

Phylum "Altarchaeota"

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Class "Altarchaeia"

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Order "Altarchaeales"

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

Phylum "Iainarchaeota"

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Class "Iainarchaeia"

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Order "Forterreales"

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

Order "Iainarchaeales"

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  • Family "Iainarchaeaceae" Rinke et al. 2020

Phylum "Micrarchaeota"

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

"Ca. Norongarragalina"

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

"Ca. Anstonella"

"Bilamarchaeaceae"

"Ca. Bilamarchaeum"

"Gugararchaeales"

"Ca. Gugararchaeum"

"Burarchaeales"

"Ca. Burarchaeum"

"Fermentimicrarchaeales"

"Ca. Fermentimicrarchaeum"

Class "Micrarchaeia"

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Order "Norongarragalinales"

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

Order "Micrarchaeales"

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

Order "Anstonellales"

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

Order "Fermentimicrarchaeales"

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

Order "Burarchaeales"

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

Order "Gugararchaeales"

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

Phylum "Huberarchaeaota"

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Class "Huberarchaeia"

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Order "Huberarchaeales"

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  • Family "Huberarchaeaceae" Rinke et al. 2020

Phylum "Aenigmatarchaeota"

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Class "Aenigmatarchaeia"

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Order "Aenigmatarchaeales"

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

Phylum "Nanohalarchaeota"

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Phylogeny of Nanohalobiales[8][9][10]
"Nanoanaerosalinaceae"

"Candidatus Nanoanaerosalina"

"Nanohalalkaliarchaeaceae"

"Candidatus Nanohalalkaliarchaeum"

"Nanohalobiaceae"

"Candidatus Nanosalinicola"

"Candidatus Nanosalina"

"Candidatus Nanohalobium"

Class "Nanohalarchaeia"

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Order "Nanohydrothermales"

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  • Family "Nanohydrothermaceae" Xie et al. 2022

Order "Nucleotidisoterales"

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  • Family "Nanosalenecaceae" Xie et al. 2022
  • Family "Nucleotidisoteraceae" Xie et al. 2022
  • Family "Nucleotidivindicaceae" Xie et al. 2022

Order "Nanohalarchaeales"

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Class "Nanohalobiia"

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Order "Nanohalobiales"

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

Phylum Nanobdellota

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Phylogeny of Nanobdellota[8][9][10]
Nanobdellia
Nanobdellales
"Nanoarchaeaceae"

"Nanoarchaeum"

Nanobdellaceae
"Tiddalikarchaeales"

"Ca. Tiddalikarchaeum"

"Jingweiarchaeales"

"Ca. Jingweiarchaeum"

"JAPDLS01"

"Ca. Haiyanarchaeum"

"Parvarchaeales"
"Parvarchaeaceae"

Class Nanobdellia

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Nanobdellia incertae sedis

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Order JAPDLS01

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  • Family "Haiyanarchaeaceae" Rao et al. 2023

Order "Jingweiarchaeales"

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  • Family "Jingweiarchaeaceae" Rao et al. 2023

Order Nanobdellales

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  • Family "Nanoarchaeaceae" Huber et al. 2011
  • Family Nanobdellaceae Kato et al. 2022 ["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"

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

Order "Parvarchaeales"

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Phylum Promethearchaeota

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Phylogeny of Promethearchaeota[8][9][10]

Promethearchaeota incertae sedis

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  • Class "Asgardarchaeia"
    • Order "Asgardarchaeales"
      • Family "Asgardarchaeaceae" Eme et al. 2023 ex Tamarit et al. 2024
  • Class "Balderarchaeia"
    • Order "Balderarchaeales"
      • Family "Balderarchaeaceae" (sic) Xie et al. 2022
  • Class "Tyrarchaeia"
    • Order "Tyrarchaeales"
      • Family "Tyrarchaeaceae" Xie et al. 2022

Class "Thorarchaeia"

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Order "Thorarchaeales"

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Class "Njordarchaeia"

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Order "Njordarchaeales"

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Class "Sifarchaeia"

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Order "Borrarchaeales"

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  • Family "Borrarchaeaceae" Liu et al. 2021

Order "Sifarchaeales"

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

Class "Wukongarchaeia"

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Order "Wukongarchaeales"

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  • Family "Wukongarchaeaceae" Liu et al. 2021

Class "Heimdallarchaeia"

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Order "Hodarchaeales"

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  • Family "Hodarchaeaceae" Liu et al. 2021

Order "Gerdarchaeales"

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Order "Heimdallarchaeales"

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  • Family "Kariarchaeaceae" Liu et al. 2021
  • Family "Heimdallarchaeaceae" ?Wu et al. 2022

Class "Odinarchaeia"

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Order "Odinarchaeales"

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  • Family "Odinarchaeaceae" Tamarit et al. 2022

Class "Jordarchaeia"

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Order "Jordarchaeales"

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  • Family "Freyrarchaeaceae" Xie et al. 2022
  • Family "Jordarchaeaceae" Sun et al. 2021

Class "Baldrarchaeia"

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Order "Baldrarchaeales"

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

Class "Hermodarchaeia"

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Order "Hermodarchaeales"

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

Class Promethearchaeia

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Order "Helarchaeales"

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Order Promethearchaeales

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In GTDB as order CR-4

Phylogeny of Promethearchaeales[8][9][10]
"Sigynarchaeaceae"

"Candidatus Sigynarchaeum"

Promethearchaeaceae

Promethearchaeum

"Candidatus Harpocratesius"

"Candidatus Lokiarchaeum"

Phylum Thermoproteota

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

Thermoproteota Incertae sedis

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Class JANJXX01

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Order "Panguiarchaeales"

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  • Family "Panguiarchaeaceae" Qu et al. 2023

Class "Korarchaeia"

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Order "Korarchaeales"

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Class "Bathyarchaeia"

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Order "Hecatellales"

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  • Family "Hecatellaceae" Rinke et al. 2020

Order "Bathyarchaeales"

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  • Family "Bathyarchaeaceae" Khomyakova et al. 2023
  • Family "Bathycorpusculaceae" Loh & Brune 2023 [UBA233]

Class Nitrososphaeria_A

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Order "Caldarchaeales"

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

"Ca. Calditenuis"

"Caldarchaeaceae"
"Wolframiiraptoraceae"
  • Family "Calditenuaceae" Balbay et al. 2023
  • Family "Caldarchaeaceae" Rinke et al. 2020

Class Nitrososphaeria

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Nitrososphaeria Incertae sedis

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Order "Geothermarchaeales"

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Order "Conexivisphaerales"

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

Order Nitrososphaerales

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

Class "Methanomethylicia"

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Methanomethylicia incertae sedis

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  • 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"

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Order "Culexarchaeles"

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  • 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

Order "Methanomethylicales"

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Class Thermoproteia

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Order "Gearchaeales"

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  • Family "Gearchaeaceae" corrig.

Order Thermofilales

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Order Thermoproteales

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

Class "Sulfolobia"

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Order "Marsarchaeales"

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Order Sulfolobales

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

Phylum Methanobacteriota_A

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

Class "Methanococcia"

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Order Methanococcales

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Phylum "Hadarchaeota"

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Class "Persephonarchaeia"

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Class "Hadarchaeia"

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Order "Hadarchaeales"

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  • Family "Cerberiarchaeaceae" Benito Merino et al. 2024
  • Family "Hadarchaeaceae" Chuvochina et al. 2019 ex Chuvochina et al. 2023

Phylum Methanobacteriota_B

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

"Ca. Methanofastidiosum"

"Methanofastidiosaceae"
Thermococcales
Thermococcaceae

Class "Theionarchaeia"

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Class Thermococci

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Order "Methanofastidiosales"

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  • Family "Methanofastidiosaceae" Rinke et al. 2020

Order Thermococcales

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Phylum "Hydrothermarchaeota"

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Class "Hydrothermarchaeia"

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Order "Hydrothermarchaeales"

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  • Family BMS3B
  • Family "Hydrothermarchaeaceae" Chuvochina et al. 2019 ex Chuvochina et al. 2023

Phylum "Methanobacteriota"

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

Methanothermobacter species-group 2

"Methanothermobacteraceae"

Methanothermobacter

Methanobacteriaceae

Methanobacterium species-group 3

Methanobacterium species-group 2

Methanobacteriales

Class Methanopyri

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Order Methanopyrales

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Class Methanobacteria

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Order Methanobacteriales

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Phylum Thermoplasmatota

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

Thermoplasmatota incertae sedis

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Class "Izemarchaea"

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Order "Thermoprofundales"

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  • (MBG-D, E2)

Class "Poseidoniia"

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Order MGIII

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Order "Poseidoniales"

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

Class Thermoplasmata

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Order "Lunaplasmatales"

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  • Family "Lunaplasmataceae" Zinke et al. 2021

Order "Proteinoplasmatales"

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  • (SG8-5)

Order "Yaplasmatales"

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  • (RBG-16-68-12)

Order "Gimiplasmatales"

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  • Family "Gimiplasmataceae" Hu et al. 2020

Order "Sysuiplasmatales"

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  • Family "Sysuiplasmataceae" Yuan et al. 2021

Order Methanomassiliicoccales

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

Order "Halarchaeoplasmatales"

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Phylogeny of Halarchaeoplasmatales[8][9][10]

"Candidatus Haladaptiplasma"

"Candidatus Natronoplasma"

"Candidatus Saliniplasma"

Order "Aciduliprofundales"

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  • Family "Aciduliprofundaceae" Rinke et al. 2020

Order Thermoplasmatales

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

Phylum Halobacteriota

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

Halobacteriota incertae sedis

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Order "Methanoflorentales"

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  • Family "Methanoflorentaceae" Mondav et al. 2014

Class Methanomicrobia

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Order Methanomicrobiales

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

Class "Methanoliparia"

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Order "Methanoliparales"

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Class "Archaeoglobia"

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Phylogeny of "Archaeoglobia"[8][9][10]
"Mnemosynellales"
"Mnemosynellaceae"

"Candidatus Mnemosynella"

Archaeoglobales

Order "Mnemosynellales"

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  • Family "Mnemosynellaceae" Adam et al. 2022

Order Archaeoglobales

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Class "Syntropharchaeia"

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Phylogeny of "Syntropharchaeia"[8][9][10]
"Syntropharchaeales"
"Syntropharchaeaceae"

"Candidatus Syntropharchaeum"

"Alkanophagales"
"Alkanophagaceae"

"Candidatus Alkanophaga"

"Methanospiraraceae"

"Candidatus Methanoxibalbensis"

"Candidatus Methanospirare"

Order "Syntropharchaeales"

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

Order "Alkanophagales"

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  • Family "Methanophagaceae" Chadwick et al. 2022
  • Family ?"Veteromethanophagaceae" Vulcano et al. 2022
  • Family "Alkanophagaceae" [B39-G2]
  • Family "Methanospiraraceae" Laso-Pérez et al. 2022

Class Methanocellia

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Order Methanocellales

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Class Methanosarcinia

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Order Methanosarcinales_A

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  • Family Methermicoccaceae Cheng et al. 2007

Order Methanotrichales

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Order Methanosarcinales

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

Class "Methanonatronarchaeia"

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Order "Methanonatronarchaeales"

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Class "Hikarchaeia"

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Order "Hikarchaeales"

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

Class "Ordosarchaeia"

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Order "Ordosarchaeales"

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  • Family "Ordosarchaeaceae" Zhao et al. 2024

Class Halobacteria

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Order Halorutilales

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  • Family Halorutilaceae Durán-Viseras et al. 2023
Phylogeny of Halobacteriales[8][9][10]

Order Halobacteriales

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

See also

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References

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  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 x y z "GTDB release 09-RS220". Genome Taxonomy Database. Retrieved 10 May 2024.
  9. ^ a b c d e f g h i j k l m n o p q r s t u v w x y z "ar53_r220.sp_label". Genome Taxonomy Database. Retrieved 10 May 2024.
  10. ^ a b c d e f g h i j k l m n o p q r s t u v w x y z "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2024.
  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 Njordarchaeales"
  16. ^ a b 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.
  17. ^ LPSN: Order "Candidatus Freyrarchaeales"
  18. ^ LPSN: Family "Candidatus Sigynarchaeaceae"
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