‘Candidatus Korarchaeum cryptofilum OPF8’
‘Candidatus Caldiarchaeum subterraneum’ (‘Aigarchaeota’/HWCG I)
‘Candidatus Nitrososphaera gargensis’
Group I.1b
Cenarchaeum symbiosum A
‘Candidatus Nitrosopumilus salaria BD31’
‘Candidatus Nitrosoarchaeum koreensis MY1’
‘Candidatus Nitrosoarchaeum limnia SFB1’
Thermofilum pendens Hrk 5
Caldivirga maquilingensis IC-167
Vulcanisaeta moutnovskia 768-28
Vulcanisaeta distributa DSM 14429
Thermoproteus uzoniensis 768-20
Thermoproteus tenax Kra 1
Pyrobaculum islandicum DSM 4184
Pyrobaculum aerophilum str. IM2
Pyrobaculum neutrophilum V24Sta
Pyrobaculum sp. 1860
Pyrobaculum calidifontis JCM 11548
Pyrobaculum oguniense TE7
Pyrobaculum arsenaticum DSM 13514
Acidianus hospitalis W1
Metallosphaera yellowstonensis MK1
Metallosphaera cuprina Ar-4
Metallosphaera sedula DSM 5348
Sulfolobus islandicus L.S.2.15
Sulfolobus solfataricus P2
Sulfolobus tokodaii str. 7
Sulfolobus acidocaldarius DSM 639
Staphylothermus hellenicus DSM 12710
Staphylothermus marinus F1
Thermosphaera aggregans DSM 11486
Desulfurococcus mucosus DSM 2162
Desulfurococcus fermentans DSM 16532
Desulfurococcus kamchatkensis 1221n
Ignisphaera aggregans DSM 17230
Ignicoccus hospitalis KIN4 I
Acidilobus saccharovorans 345-15
Aeropyrum pernix K1
Pyrolobus fumarii 1A
Hyperthermus butylicus DSM 5456
Nanoarchaeum equitans Kin4-M
Nanoarchaeota
‘Candidatus Parvarchaeum acidiphilum’
ARMAN-4
‘Candidatus Parvarchaeum acidophilus’
ARMAN-5
Pyrococcus yayanosii CH1
Pyrococcus furiosus DSM 3638
Pyrococcus horikoshii OT3
Pyrococcus sp. NA2
Pyrococcus abyssi GE5
Thermococcus barophilus MP
Thermococcus litoralis DSM 5473
Thermococcus sibiricus MM 739
Thermococcus onnurineus NA1
Thermococcus kodakarensis KOD1
Thermococcus gammatolerans EJ3
Thermococcus sp. AM4
Methanopyrus kandleri AV19
Methanopyrales
Methanothermus fervidus DSM 2088
Methanothermobacter thermautotrophicus str. Delta H
Methanothermobacter marburgensis str. Marburg
Methanobrevibacter smithii ATCC 35061
Methanobrevibacter ruminantium M1
Methanosphaera stadtmanae DSM 3091
Methanobacterium sp. AL-21
Methanocaldococcus infernus ME
Methanocaldococcus sp. FS406-22
Methanocaldococcus jannaschii DSM 2661
Methanocaldococcus vulcanius M7
Methanocaldococcus fervens AG86
Methanotorris formicicus Mc-S-70
Methanotorris igneus Kol 5
Methanothermococcus okinawensis IH1
Methanococcus aeolicus Nankai-3
Methanococcus voltae A3
Methanococcus vannielii SB
Methanococcus maripaludis C5
‘Candidatus Micrarchaeum acidiphilum’
ARMAN-2
uncultured marine group II euryarchaeote
Group II
Aciduliprofundum boonei T469
DHEV2
Thermoplasma acidophilum DSM 1728
Thermoplasma volcanium GSS1
Ferroplasma acidarmanus fer1
Picrophilus torridus DSM 9790
Archaeoglobus veneficus SNP6
Archaeoglobus fulgidus DSM 4304
Ferroglobus placidus DSM 10642
Archaeoglobus profundus DSM 5631
Methanosarcina barkeri str. Fusaro
Methanosarcina acetivorans C2A
Methanosarcina mazei Go1
Methanohalobium evestigatum Z-7303
Methanosalsum zhilinae DSM 4017
Methanococcoides burtonii DSM 6242
Methanohalophilus mahii DSM 5219
Methanocella arvoryzae MRE50
Methanocella paludicola SANAE
Methanocella conradii HZ254
Methanosaeta concilii GP6
Methanosaeta harundinacea 6Ac
Methanosaeta thermophila PT
Methanoculleus marisnigri JR1
Methanoplanus limicola DSM 2279
Methanoplanus petrolearius DSM 11571
Methanospirillum hungatei JF-1
Methanocorpusculum labreanum Z
Methanosphaerula palustris E1-9c
Methanolinea tarda NOBI-1
Methanoregula boonei 6A8
‘Candidatus Haloredivivus sp. G17’
‘Candidatus Nanosalinarum sp. J07AB56’
‘Candidatus Nanosalina sp. J07AB43’
Haladaptatus paucihalophilus DX253
Halalkalicoccus jeotgali B3
Natronomonas pharaonis DSM 2160
Halorubrum lacusprofundi ATCC 49239
halophilic archaeon DL31
Haloquadratum walsbyi DSM 16790
Haloferax volcanii DS2
Halogeometricum borinquense DSM 11551
Halorhabdus utahensis DSM 12940
Halorhabdus tiamatea SARL4B
Halomicrobium mukohataei DSM 12286
Haloarcula marismortui ATCC 43049
Haloarcula hispanica ATCC 33960
Halobacterium salinarum R1
Natrinema pellirubrum DSM 15624
Haloterrigena turkmenica DSM 5511
Halopiger xanaduensis SH-6
Natrialba magadii ATCC 43099
Natronobacterium gregoryi SP2
0.1
Korarchaeota
Thaumarchaeota
Group I.1a
Thermoproteales
Sulfolobales
Desulfurococcales
Crenarchaeota
Thermococcales
Methanobacteriales
Methanococcales
Methanosarcinales
Methanocellales
Methanomicrobiales
Halobacteriales
Nanohaloarchaea
Archaeoglobales
Thermoplasmatales
Euryarchaeota
Methanogen class II
Methanogen class I
Fig. 6.9 Phylogeny of Archaea. Phylogeny of Archaea based on a
concatenation of ribosomal proteins present in archaea for which complete genome sequences are available. These proteins are a good
alternative to 16S rRNA because they allow inferring better resolved
(and less biased) phylogenies. They are now commonly used to infer
reference phylogenies of microorganisms
6 Taxonomy and Phylogeny of Prokaryotes
165
‘Candidatus Caldiarchaeum subterraneum’ (‘Aigarchaeota’/HWCG I)
‘Candidatus Nitrososphaera gargensis’
Group I.1b
Cenarchaeum symbiosum A
‘Candidatus Nitrosopumilus salaria BD31’
‘Candidatus Nitrosoarchaeum koreensis MY1’
‘Candidatus Nitrosoarchaeum limnia SFB1’
Thermofilum pendens Hrk 5
Caldivirga maquilingensis IC-167
Vulcanisaeta moutnovskia 768-28
Vulcanisaeta distributa DSM 14429
Thermoproteus uzoniensis 768-20
Thermoproteus tenax Kra 1
Pyrobaculum islandicum DSM 4184
Pyrobaculum aerophilum str. IM2
Pyrobaculum neutrophilum V24Sta
Pyrobaculum sp. 1860
Pyrobaculum calidifontis JCM 11548
Pyrobaculum oguniense TE7
Pyrobaculum arsenaticum DSM 13514
Acidianus hospitalis W1
Metallosphaera yellowstonensis MK1
Metallosphaera cuprina Ar-4
Metallosphaera sedula DSM 5348
Sulfolobus islandicus L.S.2.15
Sulfolobus solfataricus P2
Sulfolobus tokodaii str. 7
Sulfolobus acidocaldarius DSM 639
Staphylothermus hellenicus DSM 12710
Staphylothermus marinus F1
Thermosphaera aggregans DSM 11486
Desulfurococcus mucosus DSM 2162
Desulfurococcus fermentans DSM 16532
Desulfurococcus kamchatkensis 1221n
Ignisphaera aggregans DSM 17230
Ignicoccus hospitalis KIN4 I
Acidilobus saccharovorans 345-15
Aeropyrum pernix K1
Pyrolobus fumarii 1A
Hyperthermus butylicus DSM 5456
Nanoarchaeum equitans Kin4-M
Nanoarchaeota
‘Candidatus Parvarchaeum acidiphilum’
ARMAN-4
‘Candidatus Parvarchaeum acidophilus’
ARMAN-5
Pyrococcus yayanosii CH1
Pyrococcus furiosus DSM 3638
Pyrococcus horikoshii OT3
Pyrococcus sp. NA2
Pyrococcus abyssi GE5
Thermococcus barophilus MP
Thermococcus litoralis DSM 5473
Thermococcus sibiricus MM 739
Thermococcus onnurineus NA1
Thermococcus kodakarensis KOD1
Thermococcus gammatolerans EJ3
Thermococcus sp. AM4
Methanopyrus kandleri AV19
Methanopyrales
Methanothermus fervidus DSM 2088
Methanothermobacter thermautotrophicus str. Delta H
Methanothermobacter marburgensis str. Marburg
Methanobrevibacter smithii ATCC 35061
Methanobrevibacter ruminantium M1
Methanosphaera stadtmanae DSM 3091
Methanobacterium sp. AL-21
Methanocaldococcus infernus ME
Methanocaldococcus sp. FS406-22
Methanocaldococcus jannaschii DSM 2661
Methanocaldococcus vulcanius M7
Methanocaldococcus fervens AG86
Methanotorris formicicus Mc-S-70
Methanotorris igneus Kol 5
Methanothermococcus okinawensis IH1
Methanococcus aeolicus Nankai-3
Methanococcus voltae A3
Methanococcus vannielii SB
Methanococcus maripaludis C5
‘Candidatus Micrarchaeum acidiphilum’
ARMAN-2
uncultured marine group II euryarchaeote
Group II
Aciduliprofundum boonei T469
DHEV2
Thermoplasma acidophilum DSM 1728
Thermoplasma volcanium GSS1
Ferroplasma acidarmanus fer1
Picrophilus torridus DSM 9790
Archaeoglobus veneficus SNP6
Archaeoglobus fulgidus DSM 4304
Ferroglobus placidus DSM 10642
Archaeoglobus profundus DSM 5631
Methanosarcina barkeri str. Fusaro
Methanosarcina acetivorans C2A
Methanosarcina mazei Go1
Methanohalobium evestigatum Z-7303
Methanosalsum zhilinae DSM 4017
Methanococcoides burtonii DSM 6242
Methanohalophilus mahii DSM 5219
Methanocella arvoryzae MRE50
Methanocella paludicola SANAE
Methanocella conradii HZ254
Methanosaeta concilii GP6
Methanosaeta harundinacea 6Ac
Methanosaeta thermophila PT
Methanoculleus marisnigri JR1
Methanoplanus limicola DSM 2279
Methanoplanus petrolearius DSM 11571
Methanospirillum hungatei JF-1
Methanocorpusculum labreanum Z
Methanosphaerula palustris E1-9c
Methanolinea tarda NOBI-1
Methanoregula boonei 6A8
‘Candidatus Haloredivivus sp. G17’
‘Candidatus Nanosalinarum sp. J07AB56’
‘Candidatus Nanosalina sp. J07AB43’
Haladaptatus paucihalophilus DX253
Halalkalicoccus jeotgali B3
Natronomonas pharaonis DSM 2160
Halorubrum lacusprofundi ATCC 49239
halophilic archaeon DL31
Haloquadratum walsbyi DSM 16790
Haloferax volcanii DS2
Halogeometricum borinquense DSM 11551
Halorhabdus utahensis DSM 12940
Halorhabdus tiamatea SARL4B
Halomicrobium mukohataei DSM 12286
Haloarcula marismortui ATCC 43049
Haloarcula hispanica ATCC 33960
Halobacterium salinarum R1
Natrinema pellirubrum DSM 15624
Haloterrigena turkmenica DSM 5511
Halopiger xanaduensis SH-6
Natrialba magadii ATCC 43099
Natronobacterium gregoryi SP2
0.1
Korarchaeota
Thaumarchaeota
Group I.1a
Thermoproteales
Sulfolobales
Desulfurococcales
Crenarchaeota
Thermococcales
Methanobacteriales
Methanococcales
Methanosarcinales
Methanocellales
Methanomicrobiales
Halobacteriales
Nanohaloarchaea
Archaeoglobales
Thermoplasmatales
Euryarchaeota
Methanogen class II
Methanogen class I
Fig. 6.9 Phylogeny of Archaea. Phylogeny of Archaea based on a
concatenation of ribosomal proteins present in archaea for which complete genome sequences are available. These proteins are a good
alternative to 16S rRNA because they allow inferring better resolved
(and less biased) phylogenies. They are now commonly used to infer
reference phylogenies of microorganisms
6 Taxonomy and Phylogeny of Prokaryotes
165