Table S13 | Descriptions of proposed taxa above the rank of . Taxon delineation and rank assignment are based on a concatenated protein phylogeny and relative evolutionary divergence, respectively (GTDB Release 04-R89; Parks et al., 2018). In the membership column, taxa proposed in the present study are highlighted in red. Proposed name Category Nomenclature type Etymology Membership

Halobacteriota* phyl. nov. class Halobacteria Ha.lo.bac.te.ri.o'ta. N.L. neut. n. Halobacterium a Halobacteria, Archaeoglobi, Methanocellia, corrig. Grant et al. 2002 generic name providing the stem of the name of the ‘Methanomicrobia’, Methanonatronarchaeia, emend. Gupta et al. type class; -ota ending to denote a phylum; N.L. Methanosarcinia, Candidatus 2015 neut. pl. n. Halobacteriota the phylum of the Syntropharchaeia Halobacteria class Thermoplasmatota phyl. nov. class Ther.mo.plas.ma.to’ta. N.L. neut. n. Thermoplasma Thermoplasmata, Candidatus Poseidoniia Thermoplasmata a generic name providing the stem of the name of Reysenbach 2002 the type class;; -ota ending to denote a phylum; N.L. neut. pl. n. Thermoplasmatota the phylum of the Thermoplasmata class Methanocellia class. nov. order Me.tha.no.cel’li.a. N.L. fem. n. Methanocella type Methanocellales Methanocellales genus of the type order of the class; -ia ending to Sakai et al. 2008 denote a class; N.L. neut. pl. n. Methanocellia the class of the order Methanocellales Methanosarcinia class. nov. order Me.tha.no.sar.ci’ni.a. N.L. fem. n. Methanosarcina Methanosarcinales, Methanotrichales Methanosarcinales type genus of the type order of the class; -ia ending Boone et al. 2002 to denote a class; N.L. neut. pl. n. Methanosarcinia the class of the order Methanosarcinales Methanotrichales ord. nov. genus Methanothrix Me.tha.no.tri.cha’les. N.L. fem. n. Methanothrix ‘Methanotrichaceae’ (heterotypic synonym Huser et al. 1983 type genus of the order; -ales ending to denote an Methanosaetaceae) order; N.L. fem. pl. n. Methanotrichales the Methanothrix order Thermofilales ord. nov. genus Ther.mo.fi.la’les. N.L. neut. n. Thermofilum type Zilig et al. 1983 genus of the order; -ales ending to denote an order; emend. Toshchakov N.L. fem. pl. n. Thermofilales the Thermofilum et al. 2015 order Haladaptataceae fam. nov. genus Haladaptatus Hal.a.dap.ta.ta.ce’ae. N.L. masc. n. Haladaptatus Haladaptatus Savage et al. 2007 type genus of the family; -aceae ending to denote a emend. Cui et al. family; N.L. fem. pl. n. Haladaptataceae the 2010 Haladaptatus family Ignicoccaceae fam. nov. genus Ignicoccus Ig.ni.coc.ca.ce’ae. N.L. masc. n. Ignicoccus type Ignicoccus Huber et al. 2000 genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Ignicoccaceae the Ignicoccus family 1

Ignisphaeraceae fam. nov. genus Ig.ni.spha.e.ra.ce’ae. N.L. fem. n. Ignisphaera type Ignisphaera Niederberger et al. genus of the family; -aceae ending to denote a 2006 family; N.L. fem. pl. n. Ignisphaeraceae the Ignisphaera family Methanoculleaceae fam. nov. genus Me.tha.no.cul.le.a.ce’ae. N.L. masc. n. Methanoculleus Methanoculleus Methanoculleus type genus of the family; -aceae Maestrojuán et al. ending to denote a family; N.L. fem. pl. n. 1990 Methanoculleaceae the Methanoculleus family Methanosphaerulac fam. nov. genus Me.tha.no.spha.e.ru.la.ce’ae. N.L. fem. n. Methanosphaerula eae Methanosphaerula Methanosphaerula type genus of the family; -aceae Cadillo-Quiroz et al. ending to denote a family; N.L. fem. pl. n. 2009 Methanosphaerulaceae the Methanosphaerula family Methanothermobac fam. nov. genus Me.tha.no.ther.mo.bac.te.ra.ce’ae. N.L. masc. n. Methanothermobacter teraceae Methanothermobacte Methanothermobacter type genus of the family; - r Wasserfallen et al. aceae ending to denote a family; N.L. fem. pl. n. 2000 Methanothermobacteraceae the Methanothermobacter family Thermocladiaceae fam. nov. genus Ther.mo.cla.di.a.ce’ae. N.L. neut. n. , Caldivirga, Vulcanisaeta Thermocladium Itoh Thermocladium type genus of the family; -aceae et al. 1998 ending to denote a family; N.L. fem. pl. n. Thermocladiaceae the Thermocladium family

* Note: The ANI comparison (98.88%) between the recently sequenced genome from the type strain of the , Halobacterium salinarum DSM 3754 (GCF_008124605.1), and the GTDB species representative (GCF_000006805.1) confirmed the correct species assignment in GTDB.

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Table S14 | Descriptions of proposed novel combinations at the rank of species. Taxon delineation and rank assignment are based on a concatenated protein phylogeny and relative evolutionary divergence, respectively (GTDB Release 04-R89; Parks et al., 2018).

Proposed name Basonym Nomenclature Etymology Detailed description type Haloterrigena thermotolerans PR5T = ATCC ther.mo.to’le.rans. Gr. adj. thermos The description is the same as for thermotolerans Montalvo-Rodríguez et al. 700275 = DSM hot; L. part. adj. tolerans tolerating; Haloterrigena thermotolerans given by comb. nov. 2000 (heterotypic synonym: 11552 N.L. part. adj. thermotolerans Montalvo-Rodríguez et al., 2000. Haloterrigena jeotgali Roh et tolerant of a high temperature al. 2009) Natrinema limicola Haloterrigena limicola Cui et JCM 13563T = li.mi’co.la. L. n. limus mud; L. suff. The description is the same as for comb. nov. al. 2006 CGMCC 1.5333 -cola from L. n. incola dweller; Haloterrigena limicola given by Cui et al., = AX-7 N.L. n. limicola mud-dweller 2006.

Natrinema Haloterrigena saccharevitans AB14T = AS sac.char.e.vi’tans. L. n. saccharon - The description is the same as for saccharevitans Xu et al. 2005 1.3730 = i kind of sugar; L. part. adj. evitans Haloterrigena saccharevitans given by Xu et comb. nov. CGMCC 1.3730 avoiding; N.L. part. adj. al 2005. = JCM 12889 saccharevitans sugar-avoiding Natrinema Halopiger salifodinae Zhang et CGMCC sa.li.fo.di.na’e. L. gen. n. The description is the same as for Halopiger salifodinae comb. al. 2013 1.12284T = JCM salifodinae of a saltpit, salt mine salifodinae given by Zhang et al 2013. nov. 18547 = KCY07- B2 = DSM 26231 Natronorubrum Haloterrigena daqingensis JX313T = da.qin.gen’se. N.L. neut. adj. The description is the same as for daqingense comb. Wang et al. 2010 CGMCC 1.8909 daqingense pertaining to Daqing, Haloterrigena daqingensis given by Wang et nov. = NBRC 105739 North-East China, where the type al 2010. strain was isolated

For information about the synonyms that resulted from the application of species clustering at GTDB please see Suppl. file 02 “GTDB r89 archaeal synonyms”. This file is a modification of Suppl. Table 6 in Parks et al. (https://www.biorxiv.org/content/10.1101/771964v2.abstract). Note: The authors of the strain designation of Haloterrigena thermotolerans (Natrinema thermotolerans comb. nov.) erroneously indicated strain DSM 11522 instead of DSM 11552 which resulted in the type strain of Haloterrigena thermotolerans not being considering in the decision on priority. We requested to correct the error at NCBI based on personal communication with the authors and here we correct the order of synonyms as Haloterrigena thermotolerans Montalvo-Rodríguez et al. 2000 has priority over Haloterrigena jeotgali Roh et al. 2009, which was then transferred to the genus Natrinema as Natrinema thermotolerans comb. nov.

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Table S15 | Descriptions of proposed Candidatus taxa above the rank of genus. Taxon delineation and rank assignment are based on a concatenated protein phylogeny and relative evolutionary divergence, respectively (GTDB Release 04-R89; Parks et al., 2018). In the description column, taxa proposed in the present study are highlighted in red. Proposed name Category Nomenclature type Etymology GTDB species representative (04-R89)1 Candidatus phyl.nov. class Candidatus Had.ar.chae.o'ta. N.L. neut. n. Candidatus Hadarchaeia Hadarchaeota Hadarchaeia Hadarchaeum a (Candidatus) GTDB representative of the lowest rank of the taxon is generic name providing the root of the genome designated as YNP_45 the name of the type class; -ota (GCA_001515205.2) representing Candidatus ending to denote a phylum; N.L. Hadarchaeum yellowstonense (Chuvochina et al., neut. pl. n. Hadarchaeota the 2018). phylum of the class Hadarchaeia Candidatus phyl.nov. class Candidatus Hu.ber.ar.chae.o'ta. N.L. neut. n. Candidatus Huberarchaeia Huberarchaeota corrig. Huberarchaeia Huberarchaeum a (Candidatus) GTDB representative of the lowest rank of the taxon is (in place of malformed generic name; -ota ending to denote the genome designated as Huberarchaeaota; a phylum; N.L. neut. pl. n. CG_4_9_14_0_8_um_filter_31_21 synonym: Huberarchae Huberarchaeota the phylum of the (GCA_002789275.1) representing Candidatus (Probst et al., 2018)) class Huberarchaeia Huberarchaeum crystalense (Probst et al., 2018). Based on personal communication with the first author, type material for the species has been selected as per GTDB species representative criteria. Candidatus class. order Candidatus Had.ar.chae’i.a. N.L. neut. n. Candidatus Hadarchaeales Hadarchaeia (synonym: nov. Hadarchaeales Hadarchaeum, type genus of the GTDB representative of the lowest rank of the taxon is Hadesarchaeia (Baker type order Hadarchaeales; -ia the genome designated as YNP_45 et al. 2016)) ending to denote a class; N.L. neut. (GCA_001515205.2) representing Candidatus pl. n. Hadarchaeia the class of the Hadarchaeum yellowstonense (Chuvochina et al., order Hadarchaeales 2018). Candidatus class. order Candidatus Ae.nig.mat.ar.chae’i.a. N.L. neut. n. Candidatus Aenigmatarchaeales Aenigmatarchaeia nov. Aenigmatarchaeales Aenigmatarchaeum corrig. a GTDB representative of the lowest rank of the taxon is corrig. (in place of (Candidatus) generic name; -ia the genome designated as SCGC AAA011-O16 malformed ending to denote a class; N.L. neut. (GCA_000405245.1) representing Candidatus Aenigmarchaeia) pl. n. Aenigmatarchaeia the Aenigmatarchaeum subterraneum corrig. (Rinke et al., Aenigmatarchaeum class 2013; Oren et al., 2020).

Candidatus class. order Candidatus Hu.ber.ar.cha.eia’i.a. N.L. neut. n. Candidatus Huberarchaeales Huberarchaeia nov. Huberarchaeales Huberarchaeum a (Candidatus) GTDB representative of the lowest rank of the taxon is generic name; -ia ending to denote the genome designated as a class; N.L. neut. pl. n. CG_4_9_14_0_8_um_filter_31_21 Huberarchaeia the Huberarchaeum (GCA_002789275.1) representing Candidatus class Huberarchaeum crystalense (Probst et al., 2018). Based 4

on personal communication with the first author, type material for the species has been selected as per GTDB species representative criteria. Candidatus class. order Candidatus Hy.dro.therm.ar.chae’i.a. N.L. neut. Candidatus Hydrothermarchaeales Hydrothermarchaeia nov. Hydrothermarchaeales n. Hydrothermarchaeum a GTDB representative of the lowest rank of the taxon is (Candidatus) generic name; -ia the genome designated as JdFR-18 (GCA_002011125.1) ending to denote a class; N.L. neut. representing Candidatus Hydrothermarchaeum profundi pl. n. Hydrothermarchaeia the (Chuvochina et al., 2018). Hydrothermarchaeum class Candidatus class. order Candidatus I.ain.ar.chae’i.a. N.L. neut. n. Candidatus Iainarchaeales Iainarchaeia nov. Iainarchaeales Iainarchaeum a (Candidatus) GTDB representative of the lowest rank of the taxon is generic name; -ia ending to denote the genome designated as SCGC AAA011-E11 a class; N.L. neut. pl. n. (GCA_000402355.1) representing Candidatus Iainarchaeia the Iainarchaeum Iainarchaeum andersonii (Rinke et al., 2013). class Candidatus class. order Candidatus Kor.ar.chae’i.a. N.L. neut. n. Candidatus Korarchaeales Korarchaeia nov. Korarchaeales Korarchaeum a (Candidatus) GTDB representative of the lowest rank of the taxon is generic name; -ia ending to denote the genome designated as OPF8 (GCF_000019605.1) a class; N.L. neut. pl. n. representing Candidatus Korarchaeum cryptofilum Korarchaeia the Korarchaeum (Elkins et al., 2018). class Candidatus Nanosalinia class. order Candidatus Na.no.sa.li’ni.a. N.L. fem. n. Candidatus Nanosalinales nov. Nanosalinales Nanosalina a (Candidatus) generic GTDB representative of the lowest rank of the taxon is name; -ia ending to denote a class; the genome designated as J07AB43 (GCA_000220375.1) N.L. neut. pl. n. Nanosalinia the representing Candidatus Nanosalina sp. (Narasingarao Nanosalina class et al., 2012). Candidatus ord. nov. genus Candidatus A.ci.du.li.pro.fun.da’les. N.L. neut. Candidatus Aciduliprofundaceae Aciduliprofundales Aciduliprofundum n. Aciduliprofundum (Candidatus) GTDB representative of the lowest rank of the taxon is corrig. (in place of type genus of the order; -ales the genome designated as T469 (GCF_000025665.1) malformed ending to denote an order; N.L. representing Candidatus Acidiprofundales) fem. pl. n. Aciduliprofundales the (Reysenbach et al., 2006). The proposed type is the Aciduliprofundum order GTDB species representative and has identical 16S rRNA gene sequence with one from the original study (DQ451875.1). Candidatus ord. nov. genus Candidatus Ae.nig.mat.ar.chae.a’les. N.L. neut. Candidatus Aenigmatarchaeaceae Aenigmatarchaeales Aenigmatarchaeum n. Aenigmatarchaeum corrig. GTDB representative of the lowest rank of the taxon is corrig. (in place of corrig. (Candidatus) type genus of the the genome designated as SCGC AAA011-O16 malformed order; -ales ending to denote an (GCA_000405245.1) representing Candidatus Aenigmarchaeales) order; N.L. fem. pl. n. Aenigmatarchaeum subterraneum corrig. (Rinke et al., 2013; Oren et al., 2020). 5

Aenigmatarchaeales the Aenigmatarchaeum order Candidatus ord. nov. genus Candidatus Cald.ar.chae.a’les. N.L. neut. n. Candidatus Caldarchaeaceae Caldarchaeales corrig. Caldarchaeum corrig. Caldarchaeum corrig. (Candidatus) GTDB representative of the lowest rank of the taxon is (in place of malformed type genus of the order; -ales the genome GCA_000270325.1 without alphanumeric Caldiarchaeales) ending to denote an order; N.L. designation, representing Candidatus Caldarchaeum fem. pl. n. Caldarchaeales the subterraneum corrig. (Nunoura et al., 2011; Oren et al., Caldarchaeum order 2020). Candidatus ord. nov. genus Candidatus Had.ar.chae.a’les. N.L. neut. n. Candidatus Hadarchaeaceae Hadarchaeales Hadarchaeum Hadarchaeum (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the order; -ales ending to the genome designated as YNP_45 denote an order; N.L. fem. pl. n. (GCA_001515205.2) representing Candidatus Hadarchaeales the Hadarchaeum Hadarchaeum yellowstonense (Chuvochina et al., order 2018). Candidatus ord. nov. genus Candidatus Hu.ber.ar.chae.a’les. N.L. neut. n. Candidatus Huberarchaeaceae Huberarchaeales Huberarchaeum Huberarchaeum (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the order; -ales ending to the genome designated as denote an order; N.L. fem. pl. n. CG_4_9_14_0_8_um_filter_31_21 Huberarchaeales the (GCA_002789275.1) representing Candidatus Huberarchaeum order Huberarchaeum crystalense (Probst et al., 2018). Based on personal communication with the first author, type material for the species has been selected as per GTDB species representative criteria. Candidatus ord. nov. genus Candidatus Hy.dro.therm.ar.chae.a’les. N.L. Candidatus Hydrothermarchaeaceae Hydrothermarchaeales Hydrothermarchaeum neut. n. Hydrothermarchaeum GTDB representative of the lowest rank of the taxon is (Candidatus) type genus of the the genome designated as JdFR-18 (GCA_002011125.1) order; -ales ending to denote an representing Candidatus Hydrothermarchaeum profundi order; N.L. fem. pl. n. (Chuvochina et al., 2018). Hydrothermarchaeales the Hydrothermarchaeum order Candidatus ord. nov. genus Candidatus I.ain.ar.chae.a’les. N.L. neut. n. Candidatus Iainarchaeaceae Iainarchaeales Iainarchaeum Iainarchaeum (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the order; -ales ending to the genome designated as SCGC AAA011-E11 denote an order; N.L. fem. pl. n. (GCA_000402355.1) representing Candidatus Iainarchaeales the Iainarchaeum Iainarchaeum andersonii (Rinke et al., 2013). order Candidatus ord. nov. genus Candidatus Kor.ar.chae.a’les. N.L. neut. n. Candidatus Korarchaeaceae Korarchaeales Korarchaeum Korarchaeum (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the order; -ales ending to the genome designated as OPF8 (GCF_000019605.1) denote an order; N.L. fem. pl. n. 6

Korarchaeales the Korarchaeum representing Candidatus Korarchaeum cryptofilum order (Elkins et al., 2018). Candidatus ord. nov. genus Candidatus Me.tha.no.fas.ti.di.o.sa’les. N.L. Candidatus Methanofastidiosaceae Methanofastidiosales Methanofastidiosum neut. n. Methanofastidiosum Type material of the lowest rank of the taxon has not (Candidatus) type genus of the been designated by the authors and originally named order; -ales ending to denote an species appears ambiguous as all genomes representing order; N.L. fem. pl. n. Candidatus Methanofastidiosum methylothiophilum Methanofastidiosales the corrig. (Nobu et al., 2016) are placed into separate Methanofastidiosum order species based on GTDB species clustering. As all species are placed within the same genus, we choose, with the consent of the authors (Nobu et al., 2016), the only available high quality genome as GTDB representative of the lowest rank of the taxon, which is the genome designated as Methanofastidiosum sp001587575 (GCA_001587575.1).

Candidatus ord. nov. genus Candidatus Na.no.sa.li.na’les. N.L. fem. n. Candidatus Nanosalinales Nanosalinales Nanosalina Nanosalina (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the order; -ales ending to the genome designated as J07AB43 (GCA_000220375.1) denote an order; N.L. fem. pl. n. representing Candidatus Nanosalina sp. (Narasingarao Nanosalinales the Nanosalina et al., 2012). order Candidatus ord. nov. genus Candidatus Parvarchaeales. N.L. neut. n. Candidatus Parvarchaeaceae Parvarchaeales Parvarchaeum Parvarchaeum (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the order; -ales ending to the genome designated as ARMAN-4 denote an order; N.L. fem. pl. n. (GCA_002412065.1) representing Ca. P. acidiphilum Parvarchaeales the Parvarchaeum (Baker et al., 2010). order Note that the authors did not designate the type species of the genus in the original publication. Candidatus fam. nov. genus Candidatus A.ci.du.li.pro.fund.a.ce’ae. N.L. Candidatus Aciduliprofundum Aciduliprofundaceae Aciduliprofundum neut. n. Aciduliprofundum GTDB representative of the lowest rank of the taxon is (Candidatus) type genus of the the genome designated as T469 (GCF_000025665.1) family; -aceae ending to denote a representing Candidatus Aciduliprofundum boonei family; N.L. fem. pl. n. (Reysenbach et al., 2006). The proposed type is the Aciduliprofundaceae the GTDB species representative and has identical 16S Aciduliprofundum family rRNA gene sequence with one from the original study (DQ451875.1). Candidatus fam. nov. genus Candidatus Ae.nig.mat.ar.chae.a.ce’ae. N.L. Candidatus Aenigmatarchaeum corrig. Aenigmatarchaeum neut. n. Aenigmatarchaeum corrig. GTDB representative of the lowest rank of the taxon is corrig. (Candidatus) type genus of the the genome designated as SCGC AAA011-O16 7

Aenigmatarchaeaceae family; -aceae ending to denote a (GCA_000405245.1) representing Candidatus (in place of family; N.L. fem. pl. n. Aenigmatarchaeum subterraneum corrig. (Rinke et al., Aenigmarchaeaceae) Aenigmatarchaeaceae the 2013; Oren et al., 2020). Aenigmatarchaeum family Candidatus fam. nov. genus Candidatus Cald.ar.chae.a.ce’ae. N.L. neut. n. Candidatus Caldarchaeum corrig. Caldarchaeaceae corrig. Caldarchaeum corrig. Caldarchaeum corrig. (Candidatus) GTDB representative of the lowest rank of the taxon is (in place of type genus of the family; -aceae the genome GCA_000270325.1 without alphanumeric Caldiarchaeaceae) ending to denote a family; N.L. designation, representing Candidatus Caldarchaeum fem. pl. n. Caldarchaeaceae the subterraneum corrig. (Nunoura et al., 2011; Oren et al., Caldarchaeum family 2020). Candidatus fam. nov. genus Candidatus Had.ar.chae.a.ce’ae. N.L. neut. n. Candidatus Hadarchaeum Hadarchaeaceae Hadarchaeum Hadarchaeum (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the family; -aceae ending the genome designated as YNP_45 to denote a family; N.L. fem. pl. n. (GCA_001515205.2) representing Candidatus Hadarchaeaceae the Hadarchaeum Hadarchaeum yellowstonense (Chuvochina et al., family 2018). Candidatus fam. nov. genus Candidatus Hu.ber.ar.chae.a.ce’ae. N.L. neut. Candidatus Huberarchaeum Huberarchaeaceae Huberarchaeum n. Huberarchaeum (Candidatus) GTDB representative of the lowest rank of the taxon is type genus of the family; -aceae the genome designated as ending to denote a family; N.L. CG_4_9_14_0_8_um_filter_31_21 fem. pl. n. Huberarchaeaceae the (GCA_002789275.1) representing Candidatus Huberarchaeum family Huberarchaeum crystalense (Probst et al., 2018), based on the personal communication with the authors. Candidatus fam. nov. genus Candidatus Hy.dro.therm.ar.chae.a.ce’ae. N.L. Candidatus Hydrothermarchaeum Hydrothermarchaeaceae Hydrothermarchaeum neut. n. Hydrothermarchaeum GTDB representative of the lowest rank of the taxon is (Candidatus) type genus of the the genome designated as JdFR-18 (GCA_002011125.1) family; -aceae ending to denote a representing Candidatus Hydrothermarchaeum profundi family; N.L. fem. pl. n. (Chuvochina et al., 2018). Hydrothermarchaeacea the Hydrothermarchaeum family Candidatus fam. nov. genus Candidatus I.ain.ar.chae.a.ce’ae. N.L. neut. n. Candidatus Iainarchaeum Iainarchaeaceae Iainarchaeum Iainarchaeum (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the family; -aceae ending the genome designated as SCGC AAA011-E11 to denote a family; N.L. fem. pl. n. (GCA_000402355.1) representing Candidatus Iainarchaeaceae the Iainarchaeum Iainarchaeum andersonii (Rinke et al., 2013). family Candidatus fam. nov. genus Candidatus Kor.ar.chae.a.ce’ae. N.L. neut. n. Candidatus Korarchaeum Korarchaeaceae Korarchaeum Korarchaeum (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the family; -aceae ending the genome designated as OPF8 (GCF_000019605.1) to denote a family; N.L. fem. pl. n. 8

Korarchaeaceae the Korarchaeum representing Candidatus Korarchaeum cryptofilum family (Elkins et al., 2018).

Candidatus fam. nov. genus Candidatus Me.tha.no.fas.ti.di.o.sa.ce’ae. N.L. Candidatus Methanofastidiosum Methanofastidiosaceae Methanofastidiosum neut. n. Methanofastidiosum (Candidatus) type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Methanofastidiosaceae the Methanofastidiosum family Candidatus fam. nov. genus Candidatus Me.tha.no.hal.ar.chae.a.ce’ae. N.L. Candidatus Methanohalarchaeum Methanohalarchaeaceae Methanohalarchaeum neut. n. Methanohalarchaeum GTDB representative of the lowest rank of the taxon is (Candidatus) type genus of the the genome designated as HMET1 (GCA_001914405.1) family; -aceae ending to denote a representing Candidatus Methanohalarchaeum family; N.L. fem. pl. n. thermophilum (Sorokin et al., 2017; Sorokin et al., Methanohalarchaeaceae the 2018). Methanohalarchaeum family Candidatus fam. nov. genus Candidatus Na.no.sa.li.na.ce’ae. N.L. fem. n. Candidatus Nanosalina, Candidatus Nanosalinarum Nanosalinaceae Nanosalina Nanosalina (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the family; -aceae ending the genome designated as J07AB43 (GCA_000220375.1) to denote a family; N.L. fem. pl. n. representing Candidatus Nanosalina sp. (Narasingarao Nanosalinaceae the Nanosalina et al., 2012). family Candidatus fam. nov. genus Candidatus Parv.ar.chae.a.ce’ae. N.L. neut. n. Candidatus Parvarchaeum Parvarchaeaceae Parvarchaeum Parvarchaeum (Candidatus) type GTDB representative of the lowest rank of the taxon is genus of the family; -aceae ending the genome designated as ARMAN-4 to denote a family; N.L. fem. pl. n. (GCA_002412065.1) representing Ca. P. acidiphilum Parvarchaeaceae the (Baker et al., 2010). Parvarchaeum family Note that the authors did not designate the type species of the genus in the original publication.

1 The International Committee on Systematics of Prokaryotes (ICSP) is currently reviewing the proposal to use genomic DNA sequences as type material for valid publication of archaeal and bacterial species names. Depending on ICSP’s decision, the Candidatus taxa in this table could be proposed by designating type genomes.

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Table S16 | Descriptions of proposed novel combinations of Candidatus taxa at the rank of species. Taxon delineation and rank assignment are based on a concatenated protein phylogeny and relative evolutionary divergence, respectively (GTDB Release 04-R89; Parks et al., 2018).

Proposed name Basonym Nomenclature Etymology Description type* Candidatus Nanopusillus Candidatus Nst1 ( stet’te.ri. N.L. gen. n. stetteri named The description is the same as for stetteri Nanobsidianus GCF_000387965.1) after the German microbiologist Karl Candidatus Nanobsidianus stetteri given by stetteri Stetter for his contributions to Podar et al., 2013; Castelle et al., 2015 understanding systematics and ecology** Candidatus Candidatus SPOT01 ca.ta.lin.en’sis. N.L. masc. adj. The description is the same as for Nitrosopumilus Nitrosomarinus (GCF_002156965.1) catalinensis pertaining to Catalina Candidatus Nitrosomarinus catalinensis catalinensis corrig. (in catalinensis Island corrig. given by Ahlgren et al., 2017 (Oren place of malformed corrig. et al., 2020) Candidatus Nitrosopumilus catalina) Candidatus Candidatus G22 (Assembly tyr.rell.en’se. N.L. neut. adj. tyrrellense The description is the same as for tyrrellense corrig. (in Halobonum accession: corrig. pertaining to Lake Tyrrell Candidatus Halobonum tyrrellense corrig. place of malformed tyrrellense GCF_000495475.1) given by Ugalde et al., 2013 (Oren et al., Candidatus Halobaculum corrig. 2020) tyrrellensis)

*genome designated in the original publication; ** etymology as provided in (Oren et al., 2020)

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Table S17 | GTDB Latin placeholder names. Name and rank in GTDB release 04-R89 as well as the original published name and rank are provided, followed by the reason why the rank is not proposed in this study. In some instances, original names were modified by addition of the suffix that reflect their rank based on RED/GTDB phylogeny.

GTDB name GTDB Original name and Reference Reason category category / rank Asgardarchaeota phylum Asgard Zaremba-Niedzwiedzka No type material and no designated nomenclature type (superphylum) et al., 2017 Iainarchaeota phylum Diapherotrites Rinke et al., 2013 Based on the Candidatus genus Iainarchaeum; tentative (phylum) placement, requires additional phylogenomic analyses once more genomes of this lineage become available. Altarchaeia corrig. (in place of class N/A N/A Type species/material of the genus is not sequenced yet malformed Altiarchaeia) Bathyarchaeia class Candidatus Meng et al., 2014 No type material and no designated nomenclature type Bathyarchaeota (phylum) Heimdallarchaeia class Candidatus Zaremba- Niedzwiedzka No type material and no designated nomenclature type Heimdallarchaeota et al., 2017 (phylum) Lokiarchaeia class Candidatus Spang et al., 2015 type MAG (Lokiarchaeum) does not pass quality criteria Lokiarchaeota (phylum) Candidatus Syntropharchaeia class N/A Laso-Pérez et al., 2016 Based on the Candidatus genus Syntropharchaeum corrig. corrig. (in place of malformed (Laso-Pérez et al., 2016; Oren et al., 2020); but type Syntrophoarchaeia) material and nomenclature type of the genus was not designated in the original paper Candidatus family N/A Laso-Pérez et al., 2016 Based on the Candidatus genus Syntropharchaeum corrig. Syntropharchaeaceae corrig. (Laso-Pérez et al., 2016; Oren et al., 2020); but type (in place of material and nomenclature type of the genus was not Syntrophoarchaeaceae) designated in the original paper

Gearchaeales corrig. (in place order Candidatus Kozubal et al., 2013 No type material and no designated nomenclature type of malformed Geoarchaeales) Geoarchaeota (phylum) Gearchaeaceae corrig. (in family Candidatus Kozubal et al., 2013 No type material and no designated nomenclature type place of malformed Geoarchaeota Geoarchaeaceae) (phylum)

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Marsarchaeales order Candidatus Jay et al., 2018 No type material and no designated nomenclature type Marsarchaeota (phylum) Marsarchaeaceae family Candidatus Jay et al., 2018 No type material and no designated nomenclature type Marsarchaeota (phylum) Pacearchaeales order Candidatus Castelle et al., 2015 No type material and no designated nomenclature type Pacearchaeota (phylum) Thorarchaeales order Candidatus Seitz et al., 2016 No type material and no designated nomenclature type Thorarchaeota (phylum) Thorarchaeaceae family Candidatus Seitz et al., 2016 No type material and no designated nomenclature type Thorarchaeota (phylum) Woesearchaeales family Candidatus Castelle et al., 2015 No type material and no designated nomenclature type Woesearchaeota (phylum) Ignicoccales order N/A N/A Based on the genus Ignicoccus; tentative placement, requires additional phylogenomic analyses once more genomes of this lineage become available. Halalkalicoccaceae family N/A N/A Based on the genus Halalkalicoccus, but type species of the genus is not sequenced yet Salinarchaeaceae family N/A N/A Based on the genus Salinarchaeum, but type species of the genus is not sequenced yet Methanofollaceae family N/A N/A Based on the genus Methanofollis, but type species of the genus is not sequenced yet Natronoarchaeaceae family N/A N/A Based on the genus Natronoarchaeum, but type species of the genus is not sequenced yet Pyrococcus chitonophagus Novel Thermococcus Huber et al., 1996 Does not fulfill the requirements of two strains being combina chitonophagus deposited in two independent culture collections tion (species) Natrinema mahii Novel Haloterrigena mahii Ding et al., 2017 Strain availability in at least two culture collections could combina (species) not be verified tion Natrinema hispanicum Novel Haloterrigena Romano et al., 2007. Type strain of the species has been sequenced recently combina hispanica (species) (GCF_004217335.1), and based on ANI comparison it tion represents different species with the genome included in the analyses here (GCA_900111485.1).

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Table S18 | Emended descriptions. Emended description of the family Methanonatronarchaeaceae Sorokin et al. 2018 The description remains as given by Sorokin et al. (2018) with the following modifications. The properties of the family based on its sole genus Methanonatronarchaeaum.

Emended description of the order Methanonatronarchaeales Sorokin et al. 2018 The description remains as given by Sorokin et al. (2018) with the following modifications. The order contains the families Methanonatronarchaeaceae and Candidatus Methanohalarchaeaceae. The type genus remains Methanonatronarchaeaum.

Emended description of the class Halobacteria (Cavalier-Smith 2002) Grant et al. 2002 emend. Gupta et al. 2015 The description remains as given by Gupta et al. (2015) with the following modifications. The class contains the sole order which is the type order of the class.

Emended description of the order Halobacteriales Grant and Larsen 1989 emend. Gupta et al. 2015 The description remains as given by Gupta et al. (2015) with the following modifications. The properties of the order correspond to that of the class Halobacteria and based on the following families: , Haladaptaceae, Haloarculaceae, Halococcaceae, Haloferacaceae, Natrialbaceae, and provisional families ‘Halalkalicoccaceae’, ‘Natronoarchaeacea’, ‘Salinarchaeacea’.

Emended description of the class Thermoplasmata Reysenbach 2002 The description remains as given by Reysenbach (2001) with the following modifications. The class contains the following orders: Thermoplasmatales, Methanomassiliicoccales, and Aciduliprofundales.

Emended description of the order Methanosarcinales Boone et al. 2002 The description remains as given by Boone et al. (2002) with the following modifications. The order contains the following families: Methanosarcinaceae, Methermicoccaceae, ‘Methanoperedentaceae’ corrig.

Emended description of the class Nitrososphaeria Stieglmeier et al. 2014 The description remains as given by Stieglmeier (2014) with the following modifications. The class contains the following orders: Nitrososphaerales, Candidatus Caldarchaeales corrig.

Emended description of the class * Reysenbach 2002 The description remains as given by Reysenbach (2001) with the following modifications. The class contains the following orders: , , Sulfolobales, Thermofilales and provisional orders ‘Geoarchaeales’, ‘Ignicoccales’, and ‘Marsarchaeales’

*Alternative spelling Thermoprotea has been proposed as name Thermoprotei is on the list of nomina rejicienda (Oren et al., 2015) 14

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