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Aciduliprofundum

Ignisphaera aggre Desulfurococcacea Desulfurococcacea eon SCGC AB-777_

sp. Sulfolobus sp. JCM prina ldarius SUSAZ Sulfolobus solfata ldarius DSM 639 ldarius Desulfurococcacea ldarius DSM 639 C AB-777_G05 konensis

Sulfolobus islandic Sulfolobus islandic Desulfurococcales Sulfolobus islandic Sulfolobus islandic Sulfolobus islandic Sulfolobus islandic Sulfolobus islandic

odaii dula

us HVE10/4 llowstonensis rans us us us Sulfolobus sp. A20 eon AZ1 eon AZ1nus copahuensis nsis

i is

Fervidicoccus font Desulfurococcales Desulfurococcus a is Desulfurococcus a Desulfurococcus a

Desulfurococcus m gans DSM 17230 Desulfurococcus m e archaeon AG1 e archaeon AG1

Fervidicoccus font J03

Metallosphaera cu 16833 nsis ricus Thermosphaera ag e archaeon NZ3(B Sulfolobus acidoca nsis archaeon ex4484 Fervidicoccus sp. SulfolobusSulfolobus acidoca acidoca Sulfolobus acidoca Metallosphaera ha Sulfolobus sp. SCG nsis nsis us us us us us us us Metallosphaera se Tree scale: 1 Staphylothermus h Sulfurisphaera tok Staphylothermus m Metallosphaera ye Acidianus sulfidivo eon ex4572_27 Candidatus Acidia Sulfolobales archa Sulfolobus islandic Acidianus manzae Sulfolobus islandic Sulfolobus islandic Sulfolobus islandic Sulfolobales archa

Aeropyrum camini Thermogladius archaeon cal ex4484 Acidianus brierley Acidianus hospital mylolyticus is Kam940 Acidianus hospital mylolyticus mylolyticus _217_2 B24

ucosus nium thompsoni ucosus nium thompsoni PyrodictiumPyrodictium occul delan Pyrodictium delan ex4484_135 bacter tengchonge Pyrodictium occul bacter tengchonge is bacter tengchonge Hyperthermus but bacter tengchonge gregans ) Z13 ense Desulfurococcales _42 ense Desulfurococcales Ignicoccus hospitaAeropyrum pernix x4484_82 ellenicus SY1 = JCM 12091 arinus rmarchaeota archa ens Hrk 5 ens Pyrolobus fumarii derae_58

archaeon ex4484 IgnicoccusIgnicoccus islandi hospita rchaeota archaeon CandidatusCandidatus Krypto Krypto tum Thermococcus gam tum eyi Candidatus Krypto eyi rchaeota archaeon Candidatus Krypto archaeon ex4484 ylicus CandidatusCandidatus Krypto Krypto Thermococcus gua archaeon ex4484 . ECH_B lis KIN4/I K1 ThermofilumThermofilum sp. N uzon Thermococcus sp. Thermofilum uzon 0 Thermococcus eur Thermofilum Thermococcus sp. Thermofilum sp. e ngensis Thermofilum pend Thermofilum pend Candidatus Geothe Thermococcus gor ophila 4 Thermococcus nau cus Desulfurococcales lis B80novskia Thermococcus zill Candidatus Bathya ibuta Thermococcus sp. matolerans naxoniensis Thermococcus thio _217_1 . JCHS_4 ymasensis _217_2 Thermococcus cele Candidatus Bathya Thermocladium sp ythermalis EXT12c AM4 P30 Caldivirga sp. MU8 ifontis JCMdicum 11548 Thermococcus rad Caldivirga maquili rophilum V24Sta gonarius naticumiense TE7 DSM 1351 tili Vulcanisaeta therm reducens igii VulcanisaetaVulcanisaeta sp. mout E philum str. IM2 Thermococcus P6 sp. Vulcanisaeta distr reducens Thermoproteus te ex4484_31 Thermococcus bar ThermoproteusThermoproteus uz sp Thermococcus cele r 21 neum Pyrobaculum sp. W Thermococcusiotolerans sp. PyrobaculumPyrobaculumPyrobaculum calid neut islan neum Pyrobaculum arse Thermococcus pro Pyrobaculum ogun Pyrobaculum ferri 5-4 Pyrobaculum aero Thermococcus pac ThermococcusThermococcusThermococcus pep clef sicu chaeota archaeon ossii rchaeum subterra Thermococcus kod ricrescens rchaeon ex4484_1rchaeum subterra 4557 Thermococcus onn fundus Thermococcus pie Palaeococcus ferrotonophilusificus tensis li Palaeococcus paci akarensis Candidatusarchaeon PacearCandidatus HR02 Caldia ThaumarchaeotaCandidatus a Caldia urineus zophilus Thermococcus lito philus hum ThermococcusThermococcus sp. litoficus Thermococcales a bacteriumbacterium HR35 HR37 Thermococcus sp. bacterium HR19 Thermococcus sib ralis onificans Thermococcusrchaeon sp. 2319x144_46ralis m thermolithotropm atlanticum Thermococcus sib m indicum PK m sp. TC5-1 Thermococcus sp.iricus 40_45 thermarum Thermococcus bariricus er takaii Thermococcus bar ThermovibrioDesulfurobacteriuDesulfurobacteriu amm Thermococcus par EP1 Desulfurobacteriu ontis ophilus Desulfurobacteriu hypogea_64 ophilus Pseudothermotoga Pyrococcus kukulkalvinellae Thermosulfidibact Thermococcus chi bacterium HR17 Thermotoga caldif Pyrococcustonophagus sp. ST PseudothermotogaThermotoga sp. 50 Pyrococcus horiko anii . 128-5-R1-1 Pyrococcus abyssishii 04 F5 Pyrococcus sp. NA sii PyrococcusPyrococcus furiosu furiosu2 Hydrogenivirga sp s Aquifex aeolicus V r atlanticus s DSM 3638 Aquifex aeolicusAmmonifex degenr indicus Pyrococcus yayan r autotrophicus osii Thermodesulfatato as dismutans ThermodesulfatatoThermodesulfatato iodismutans hilum Methanothermus f Thermosulfurimon iodismutans ervidus Caldimicrobium thterium hydrogenip Caldimicrobium thterium geofontis Thermodesulfobac terium geofontis nse Thermodesulfobac terium hveragerdeum Thermodesulfobac terium thermophil Fervidobacterium thailandense Thermodesulfobacterium commune Thermodesulfobacterium sp. 37_54 Methanopyrus sp. KOL6 Methanopyrus kandleri

hilus ThermusThermus thermopthermophilus Thermus thermophilus Thermus thermophilus

Nitratiruptor sp. S Nitratiruptor tergaB155-2 rcus Lebetimonas natsu Caminibacter medshimae Nautilia profundiciatlanticus Caldisericum exile ola PersephonellaCaldisericum ma exile PersephonellaPersephonella sp. hyd Persephonella sp. rina rogeniphila KM09-Lau-8 IF05-L8 Hydrogenobaculum Hydrogenobaculum Sulfolobus islandicus Sulfolobus islandicus Fervidobacterium sp. Sulfolobus islandicus Fervidobacterium Sulfolobus islandicus Fervidobacterium Sulfolobus islandicus Fervidobacterium Sulfolobus islandicus Fervidobacterium Sulfolobus islandicus Fervidobacterium pennivorans Sulfolobus islandic e Dictyoglomus ther pennivorans Sulfolobus islandicricus DictyoglomusDictyoglomus turgturg islandicum SulfolobusSulfolobus islandic shibata changbaicum Sulfolobus solfata AquifexHydrogenivirga aeolicus sp sp. SC_NGM5_G05 Sulfolobus sp. A20 nodosum 16833 mophilum is HydrogenobacterHydrogenobacter idum is idum Sulfolobus sp. JCM Thermocrinis albu ransnsis Acidianus hospital Thermocrinis mine . 128-5-R1-1 Acidianus hospital i ThermocrinisThermocrinis sp. rube G eoneon AZ1AZ1 thermophilus AcidianusAcidianusnus sulfidivo manzaecopahuensis Thermodesulfovibhydrogenophilus dula Thermodesulfovib Sulfurihydrogenib Acidianus brierleyprina Sulfurihydrogenib s Sulfolobales archakonensis CandidatusSulfolobales Acidia archa Sulfurihydrogenib rvae Sulfurihydrogenib r Metallosphaerallowstonensis se Sulfurihydrogenib BS ldariusldarius rio aggregans MetallosphaeraMetallosphaera ha cu odaii rio aggregans ium sp. YO3AOP1 ldarius SUSAZ ium yellowstonens Metallosphaera ye C AB-777_L09 Sulfolobus acidoca J03 ium sp. Sulfolobus acidoca ium azorense ium subterraneum Sulfurisphaera tok Sulfolobus acidoca Nanoarchaeum eq Sulfolobus sp. SCG ) e eon SCGC AB-777_ lis _42 cus CandidatusCandidatus Nanob Nanob

Sulfolobales archa e archaeon NZ3(B uitans Kin4-M Ignicoccus hospita Methanocaldococc archaeongans DSM ex4484e archaeon 17230 AG1 Methanocaldococc Ignicoccus islandi e archaeon AG1 Methanocaldococc

sidianus stetteri Methanocaldococc sidianus stetteri ucosus MethanocaldococcMethanothermoco Desulfurococcacea mylolyticusgregansarinus MethanocaldococcMethanocaldococc mylolyticusmylolyticus Methanocaldococc Desulfurococcales ellenicus_58 derae Methanocaldococc IgnisphaeraDesulfurococcacea aggre Desulfurococcacea us infernus us villosus us villosus MethanotorrisMethanotorris form ign bus sp.ovorans MG bus bussp. sp.JCHS CIS K1 tum eyi Candidatus Korarc tum eyi CandidatusCandidatus Korarc Korarc DesulfurococcusDesulfurococcus a m nensis us bathoardescens Desulfurococcus a ylicus DesulfurococcusThermosphaera a ag us fervensccusus okinawensis vulcanius Staphylothermus m us fervens AG86 archaeonThermogladius ex4484 cal Acidilobus sp. 7A us sp. FS406-22 Staphylothermus h Archaeoglobus ful is Archaeoglobus ful us jannaschii Archaeoglobus ful Aciduliprofundum Caldisphaera sp. Archaeoglobus ful AciduliprofundumAciduliprofundum Caldisphaera sp. 6 uncultured Acidilo SY1 = JCM 12091 FerroglobusArchaeoglobus placid pro eus uncultured Acidilo ylicus DSM 5456 8 Archaeoglobus ven unculturedAcidilobus Acidilo sacchar icicus Aeropyrum pernix Pyrodictium occul is Kam940 Geoglobus ahanga Archaeoglobus sul Caldisphaera lagu Pyrodictium delan haeumhaeota cryptofilum archaeon PyrodictiumPyrodictium occul delan haeum cryptofilum Geoglobus acetivo Desulfurococcales Spirochaetes bact Candidatus Bathya Hyperthermus but on OSP_D

on BE_D Aigarchaeota arch Thermotoga sp. 44 Fervidicoccus sp. on ECH_B_3 on OSP_D on ECH_B_2 Pyrolobus fumarii gidus Fervidicoccus font gidus gidus DSM 4304 sp. MAR08-339 boonei boonei gidus DSM 4304

Thermotoga napht Aeropyrum camini ThermotogaThermotoga sp. RQ petro

Thermotoga Thermotoga sp. TB Thermotoga sp. TB Thermotoga marit Thermotoga sp. M Thermotoga sp. KO on ECH_B_SAG-C1 ThermotogaThermotoga sp. Ce ThermotogaThermotoga sp. RQ sp. SG Hyperthermus but ThermotogaThermotoga neapo neapo Dictyoglomus sp. N us fundus on ECH_B_SAG-F0 eficus faticallidus Fervidicoccus font OPF8 Thermosipho atlan ri

erium GWB1_36_1 Thermosipho afric rans rchaeota archaeon chaeota G2 archae haeota archaeon aeon NZ13_MG1

chaeota G1 archae chaeota G2 archaechaeota G1 archae chaeota G2 archae 84_232

r bescii r besciir bescii r danielii

r sp. F32

r morganii

chaeota G2 archae phila hophila c24 ima

subterraneus subterraneus 2 subterraneus L6 YP3.1.4.1 r acetigenus XY761 r naganoensis ll2 1 litana7 chaeota G2 archae r obsidiansis litana LA10

r lactoaceticus

Z13-RE01

r owensensis r kristjanssonii r saccharolyticus

ticus r kronotskyensis B24-2 Candidatus Marsar r hydrothermalis anus 3 Candidatus Korarc

Candidatus Marsar Candidatus Marsar Candidatus MarsarCandidatus Marsar

CaldicellulosiruptoCaldicellulosirupto Caldicellulosirupto

Caldicellulosirupto Caldicellulosirupto

Candidatus Marsar Caldicellulosirupto

Caldanaerobacter Caldanaerobacter

Caldanaerobacter Caldicellulosirupto Candidatus Marsar Caldicellulosirupto

Caldicellulosirupto

Caldicellulosirupto Caldicellulosirupto

Caldicellulosirupto

Caldicellulosirupto Caldicellulosirupto SI Fig. 5. Phylogenetic reconstruction of entire RG dataset using minimal trimming of sequence alignment. Trimming was performed by Noisy, removing only 17% of positions. Branch labels show species source of RG sequence, with Archaea in blue and Bacteria in red.