1 Supplementary Information 2 3 Descriptions of proposed taxa 4 Description of Candidatus Mnemosynella biddleae (gen. nov., sp. nov.) 5 Candidatus Mnemosynella biddleae (Mne.mo.sy.nel’la. N.L. fem. dim. n. 6 Mnemosynella, little Mnemosyne, after the Greek mythology Titaness, goddess of 7 memory, and mother of the Muses; a reference to the species containing multiple 8 methanogenesis markers and “remembering” its methanogenic ancestry; bidd’le.ae. 9 N.L. gen. fem. n. biddleae, named after Jennifer Biddle, in honor of her contributions 10 to microbial ecology). 11 Description of Candidatus Mnemosynella hypogeia (gen. nov., sp. nov.) 12 Candidatus Mnemosynella hypogeia (Description as above for the genus 13 Mnemosynella. hy.po.gei’a. N.L. fem. adj. hypogeia, subterraneous, earth-born ) 14 Description of Mnemosynellaceae (fam. nov.) 15 (Mne.mo.sy.nel.la.ce’ae. N.L. fem. n. Mnemosynella, a Candidatus genus name; - 16 aceae, ending to denote a family; N.L. fem. pl. n. Mnemosynellaceae, the 17 Mnemosynella family) 18 Description of Mnemosynellales (ord. nov.) 19 (Mne.mo.sy.nel.la’les. N.L. fem. n. Mnemosynella, a Candidatus genus name; -ales, 20 ending to denote a family; N.L. fem. pl. n. Mnemosynellales, the Mnemosynella order) 21 Description of Candidatus Hecatella orcuttiae (gen. nov., sp. nov.) 22 Candidatus Hecatella orcuttiae (He.ca.tel’la. N.L. fem. dim. n. Hecatella, little Hecate, 23 after the Greek mythology goddess of witchcraft and crossroads; a reference to the 24 species’ metabolism being at the “crossroads” of methanogenesis and the Wood- 25 Ljungdahl pathway by means of its Mtr complex; or.cut’ti.ae. N.L. gen. fem. n. 26 orcuttiae, named after Beth Orcutt, in honor of her contributions to microbial ecology, 27 including studies on the Juan de Fuca Ridge). 28 Description of Hecatellaceae (fam. nov.) 29 (He.ca.tel.la.ce’ae. N.L. fem. n. Hecatella, a Candidatus genus name; -aceae, ending 30 to denote a family; N.L. fem. pl. n. Hecatellaceae, the Hecatella family) 31 Description of Hecatellales (ord. nov.) 32 (He.ca.tel.la’les. N.L. fem. n. Hecatella, a Candidatus genus name; -ales, ending to 33 denote a family; N.L. fem. pl. n. Hecatellales, the Hecatella order) 34 Description of Candidatus Geothermarchaeum rappei (gen. nov., sp. nov.) 35 Candidatus Geothermarchaeum rappei (Ge.o.therm.ar.chae’um. Gr. fem. n. gê, the 36 earth; Gr. masc. adj. thermos, hot; N.L. neut. n. archaeum, ancient one, archaeon, 37 from Gr. masc. adj. archaîos, ancient; N.L. neut. n. Geothermarchaeum, an archaeon 38 from hot earth; rap.pe’i. N.L. gen. masc. n. rappei, named after Michael Rappé, in 39 honor of his contributions to microbial ecology, including obtaining the original samples 40 from the Juan de Fuca Ridge used in this study). 41 Description of Candidatus Scotarchaeum ottlingeri (gen. nov., sp. nov.) 42 Candidatus Scotarchaeum ottlingerii (Scot.ar.chae’um. Gr. masc. n. skotos, darkness; 43 archaeum, ancient one, archaeon, from Gr. masc. adj. archaîos, ancient; N.L. neut. n. 44 Scotarchaeum, an archaeon living in darkness; ott.lin’ge.ri. N.L. gen. masc. n. 45 ottlingeri, named after Markus Ottlinger, German visual artist depicting hydrothermal 46 settings and biofilms). 47 Description of Geothermarchaeaceae (fam. nov.) 48 (Ge.o.therm.ar.chae.a.ce’ae. N.L. neut. n. Geothermarchaeum, a Candidatus genus 49 name; -aceae, ending to denote a family; N.L. fem. pl. n. Geothermarchaeaceae, the 50 Geothermarchaeum family) 51 Description of Geothermarchaeales (ord. nov.) 52 (Ge.o.therm.ar.chae.a’les. N.L. fem. n. Geothermarchaeum, a Candidatus genus 53 name; -ales, ending to denote a family; N.L. fem. pl. n. Geothermarchaeales, the 54 Geothermarchaeum order) 55 Description of Candidatus Pyrohabitans jungbluthii (gen. nov., sp. nov.) 56 Candidatus Pyrohabitans jungbluthii (Py.ro.ha’bi.tans. Gr. neut. n. pŷr, fire; L. pres. 57 part. habitans, inhabiting; N.L. masc. n. Pyrohabitans, an inhabitant of fire; 58 jung.blu’thi.i. N.L. gen. masc. n. jungbluthii, named after Sean Jungbluth, in honor of 59 his contributions to microbial ecology, including obtaining the original samples from 60 the Juan de Fuca Ridge used in this study). 61 a 62 Supplementary Methods 63 64 Detailed description of homology search methods for Eha, Ehb, Hcg 65 Since several of the proteins in the Eha, Ehb, and Hcg sets were either DUFs or part 66 of the lists from Gao & Gupta1, we could compare the single gene distributions and 67 phylogenies to determine potential issues in the homology searches for the more 68 problematic (poorly annotated, fast evolving etc.) proteins in each complex or pathway. 69 HMM searches often produced >1000 hits for most subunits and thus a lot of 70 computational power, time, and manual work would be required to isolate our 71 homologs of interest. For that reason, we instead searched for homologs using 72 DIAMOND blastp with two seeds on the taxonomic extremes of each complex or 73 pathway. For Eha they were Methanothermobacter marburgensis 74 (Methanobacteriales) and Methanolacinia petrolearia (Methanomicrobiales), for Ehb 75 M. marburgensis and Ca. Methanosuratus petracarbonis (Verstraetearchaeota), and 76 for Hcg M. marburgensis and Desulfurobacterium thermolithotrophum 77 (Desulfurobacteriales). M. marburgensis was used as a reference for picking the first 78 seed using information from 2. Other known homologs from the literature in 79 Methanococcus maripaludis, Methanocaldococcus jannaschii, Methanothermobacter 80 thermoautotrophicus, Methanopyrus kandleri were used as (additional) seeds in some 81 cases. When obtaining fewer homologs than expected (i.e. entire clades missing 82 partially or entirely), the HMM profiles or DIAMOND seeds were expanded by using 83 all hits of the previous search round to create a new HMM profile or collection of seeds 84 and rerun the search. To clean up the datasets and retain our homologs of interest, 85 we first aligned the initial pool of hits with MUSCLE3. Then in Seaview4 we manually 86 inspected the alignments, constructed preliminary phylogenies with BioNJ5 (Poisson 87 or Observed distances) and/or PhyML6 (default options, no topology optimization), and 88 isolated (monophyletic) clades containing our homologs of interest. None of these 89 initial phylogenies were retained, since they were made on a trial and error basis, but 90 they can be reproduced through the datasets in the Supplementary Data. We 91 confirmed suspected gene losses by manually comparing the hits of the homology 92 searches with the synteny in each taxon. Below we list for each gene whether we used 93 the base seeds for a DIAMOND search and if it was found in this study as a DUF, or 94 in Gao & Gupta1 with the corresponding Pfam or arCOG accession for the HMM 95 profile. We also detail any deviations in the homology search methodology. 96 Eha 97 EhaA: (Gao & Gupta, 2007), PF17367, custom HMM from all the hits of the original 98 search 99 EhaB: (Gao & Gupta, 2007), arCOG04828 100 EhaC: DUF2109 101 EhaD: DUF2108 102 EhaE: DUF2107 103 EhaF: DUF2106 104 EhaG: DUF2105 105 EhaH: PF10125, found from synteny 106 EhaI: (Gao & Gupta, 2007) contained only arCOG05034. From Uniprot cross- 107 references for multiple sequences, we found HMM profiles for arCOG05034 and 108 arCOG06464 and pooled the hits together. Mnemosynellales, Persephonarchaea, and 109 M. kandleri were not found through HMM searches, so we added their sequences 110 manually from expected synteny and BLAST searches against NCBI. We pooled all 111 these sequences for recursive DIAMOND searches, using the hits from the previous 112 search as seeds. We stopped after 3 rounds of searches, since the number of hits 113 decreased afterwards. 114 EhaJ: base seeds 115 EhaK: (Gao & Gupta, 2007) contained only arCOG08277. From Uniprot cross-refs, 116 found HMM profiles for arCOG06676, arCOG08277, arCOG10247, arCOG60928, and 117 proceeded as with EhaI. Only 1 round of DIAMOND searches was necessary, as we 118 found no further hits afterwards. 119 EhaL: DUF2104, custom HMM from all the hits of the original search. 120 EhaM: DUF1959, custom HMM from all the hits of the original search. 121 EhaN: base seeds 122 EhaO: base seeds 123 EhaP & EhaQ: In M. kandleri, the gene called EhaP in Uniprot (AAM01675.1) is an 124 unrelated ferredoxin, distantly related to RnfB homologs in Firmicutes but also to its 125 own EhaR* (AAM01674.1). The real EhaP homolog in M. kandleri is called EhaQ 126 (AAM01677.1). However, when running BLASTp against NCBI non-redundant with the 127 M. marburgensis EhaQ, the first M. kandleri hit at twilight zone homology is 128 AAM01676.1 listed in Uniprot as EhbK (marked with an asterisk in Figure 3a). Using 129 M. maripaludis as the query, the first M. kandleri hit is the ferredoxin AAM01674.1. We 130 did not find either of these sequences in our local DIAMOND searches, even if they 131 could be considered as EhaQ-like. Many Methanococcales also carry an EhaQ-like 132 homolog that was not picked up in our homology searches but is part of the Eha cluster 133 (AAB98510.1 in M. jannaschii, marked with an asterisk in Figure 3a). 134 EhaP: base seeds, plus MSBL1 archaeon SCGC-AAA382A20 135 EhaQ: M. marburgensis and M. maripaludis 136 EhaR: The gene called EhaR in M. marburgensis (ADL58396.1) was annotated as a 137 ribokinase and only picked hits in Methanobacteriales. The one called EhaR in M. 138 maripaludis based on Uniprot and synteny (ABO34430.1) and its closest homolog in 139 M. kandleri (AAM01674.1) did have some hits in Methanobacteriales. These included 140 SCG85576.1 in Methanobacterium congolense, and when NCBI non-redundant was 141 queried, ADL59095.1 (MvhB) in M. marburgensis. However, the syntenic 142 polyferredoxin ADL58399.1, as well as SCG85576.1, and ADL59095.1, when used in 143 a BLASTp search in the same way, pick up AAM01674.1 as their first hit in M. kandleri. 144 The final seeds for EhaR were M. maripaludis (ABO34430.1), M. kandleri 145 (AAM01674.1), and M. marburgensis (ADL58399.1). 146 EhaS: base seeds, DIAMOND with all hits of the first search. 147 EhaT: base seeds, DIAMOND with all hits of the first search 148 Ehb 149 EhbA: base seeds 150 EhbB: arCOG04878 151 EhbC: (Gao & Gupta, 2007), arCOG04877 152 EhbD: base seeds 153 EhbE: base seeds 154 EhbF: base seeds 155 EhbG: (Gao & Gupta, 2007), arCOG05076 156 EhbH: base seeds 157 EhbI: base seeds 158 EhbJ: custom HMM profile from pooled hits of arCOG06490 and arCOG06683 159 EhbK: base seeds, plus M. maripaludis 160 EhbL: base seeds 161 EhbM: base seeds 162 EhbN: base seeds 163 EhbO: base seeds 164 EhbP: (Gao & Gupta, 2007), PF10622 165 Hcg 166 HcgA: base seeds 167 HcgB: DUF3236 168 HcgC: DUF1188 169 HcgD: absent in D. thermolithotrophum, seeds were M. marburgensis and M. kandleri 170 HcgE: (Gao & Gupta, 2007), arCOG01677 171 HcgF: UPF0254 172 HcgG: (Gao & Gupta, 2007), PF10113 173 174 Subunit omissions from Eha, Ehb, and Hcg supermatrices 175 As mentioned in the Methods section, certain subunits were omitted from the 176 supermatrices of Eha, Ehb, and Hcg. The specific reasons for each subunit are 177 summarized below. 178 EhaA: Missing in Methanomicrobiales; the phylogeny does not even recover the 179 monophyly of the other clades (Persephonarchaea and Methanopyrales inside 180 Methanobacteriales at different branches, Mnemosynellales inside Methanococcales). 181 EhaI: Issues in the homology searches. Very short gene with strange topology in its 182 phylogeny (Persephonarchaea and Methanococcales inside Methanobacteriales). 183 EhaK: Issues in the homology searches. Very short gene with strange topology in its 184 phylogeny (Methanopyrales inside Methanobacteriales, Methanococcales as grades 185 at the base of Methanomada, Persephonarchaea and Mnemosynellales as grades at 186 the base of Methanomicrobiales). 187 EhaP: Ferredoxin with very low conservation among clades and poorly aligning. Issues 188 with the annotations and homology searches (i.e. establishing orthology). 189 EhaQ: Ferredoxin with very limited distribution (Methanobacteriales, 190 Methanococcales). Issues with the annotations and homology searches (i.e. 191 establishing orthology). 192 EhaR: Limited distribution (Methanobacteriales, Methanococcales, Methanopyrales). 193 Issues with the annotations and homology searches (i.e. establishing orthology). 194 EhaS: Paralog of Ftr whose distribution does not match the other subunits7. Only part 195 of the Eha cluster in Methanobacteriales. 196 EhaT: Very limited distribution (only Methanobacteriales). 197 For EhaAIK their short length makes their omission probably inconsequential. In 198 general, we did not wish to risk the overall supermatrix signal by introducing multiple 199 poorly conserved subunits or with dubious orthology. Similar to EhaA, EhaC also has 200 a slightly problematic topology but is not as pronounced (Methanococcales and 201 Methanopyrales respectively monophyletic but inside Methanobacteriales). 202 EhbJ: Only omitted in the Methanococcales cluster supermatrices. Strange topology 203 of the single gene phylogeny (Methanofastidiosales and Theionarchaea at two 204 separate branches within Methanobacteriales). A similar monophyly issue exists in 205 EhbH (either Verstraetearchaeota or Methanococcales+Acherontia within 206 Methanobacteriales, depending on the root position, but monophyletic among 207 themselves) but it is less pronounced in our opinion, so that subunit was kept in the 208 supermatrices. 209 HcgD: Absent in Desulfurobacteriales; there was no monophyletic clade for the other 210 taxa in the preliminary phylogenies. 211 212 Supplementary Results & Discussion 213 214 Functional annotation and evolution of the methanogenesis markers 215 m4-m9: A cluster of six genes that are co-localized in many genomes and are 216 predicted to be co-transcribed in Methanolobus psychrophilus R158 but do not co- 217 purify with Mcr9. Some of them are absent from various alkane oxidizers but it is 218 impossible to determine whether this is a result of genome incompleteness or variation 219 in the processes controlled by these genes. There exist very few cases of putative 220 remnants among them, for example the hot spring Thaumarchaeota SAG E04 221 (GCA_000405745) that contains genes of the WLP10. M9 is a homolog of McrC. 222 m10: AtwA (also called McrA2) is an ATP-binding protein11 that is necessary for Mcr 223 activation9. We found that there exist two homologs that we call here canonical AtwA 224 and AtwA-like, assuming that the canonical AtwA has a wider taxonomic distribution. 225 The presence of multiple homologs (AtwA1, AtwA2) can be found in the annotations 226 of publicly available sequences but these do not correspond to the two clades we 227 recovered i.e. there are both so-called AtwA1 and AtwA2 sequences within both 228 canonical AtwA and AtwA-like. AtwA-like is absent in most Halobacterota methane 229 metabolizers. This distribution does not seem to be linked to the presence of multiple 230 Mcr homologs in Methanomada members, as the duplication of the atwA gene most 231 probably occurred at the LMA, while the aforementioned Mcr complexes arose from 232 more recent duplications (Figure 1a). The topology of AtwA-like with 233 Methanosarcinales at the base and non-monophyletic Methanomada might have been 234 affected by long branch attraction. However, the canonical AtwA side recovers the 235 monophyly of most lineages as expected from McrABG (Figure 1a) and corroborates 236 the poorly supported NONREV root at Halobacterota. This in turn supports that 237 anaerobic alkane oxidation (AAO) is a more recent invention but Mcr-like complexes 238 still require AtwA. 239 m11: McrC probably participates in Mcr activation, since it is part of a reductase 1+ 9 240 complex capable of reducing coenzyme F430 to the Ni form and corresponds to part 241 of the McrA3 component11. Other than McrC and m9, we identified a third distant 242 homolog only present in Methanobacteriales (Supplementary Data 2; Supplementary 243 Figure 8 only shows the canonical McrC). 244 m12-m14: McrD (m12) has been posited to be a chaperone delivering F430 from its 245 production after the reaction catalyzed by CfbE to Mcr12. However, we think that this 246 association might not be universal, since McrD is present in essentially all methane 247 metabolizers and alkane oxidizers, except for Methanophagales. CfbD (m13) and 248 CfbE (m14) have a different distribution, with one or both being absent in many AAO 249 and even some methanogens. CfbE is encoded by one Methanophagales MAG 250 (GCA_004212135, hot spring). These discrepancies indicate that several Archaea 251 might contain F430 biosynthesis variants or even a modified cofactor, such as the 13,14 252 methylthio modified F430 found in the Mcr in marine Methanophagales . 253 m15: MtxX is either a phosphotransacetylase or methyltransferase, part of the MtxXAH 254 operon in M. barkeri15,16. It is impossible to determine its function from its distribution 255 and phylogeny, since it does not consistently coexist with some other methanogenesis 256 or WLP subsystem but the association with Mtr is probably a rarity. 257 m16: M16 has sequence similarity to the AIR synthase but its function is unknown. 258 The M. maripaludis homolog (MMP0291) is annotated as “hydrogenase 259 expression/formation protein related” and in proximity to some hyp genes17. 260 m17: DUF1743 includes a series of homologs that contain one of the domains of TiaS, 261 the tRNAIle-agmatinylcytidine synthetase (that homolog was removed from the final 262 phylogeny shown in Supplementary Figure 14) and is very ancient among Archaea, 263 independent of methane metabolism. It is predicted to function as an ATPase18 but its 264 exact function in methane metabolism or as a remnant remains indeterminate. 265 m18-m19: No information in the literature, function cannot be predicted. 266 m20: M20 contains homologs of YcaO that functions as a glycine thioamidase for the 267 post-translation modification of an Mcr glycine (Gly465 in M. acetivorans) into 268 thioglycine19. The topology of our phylogeny is roughly in agreement with the one 269 published in19. This modification is absent in alkane oxidizers. 270 m21: Rossmann fold protein with a cysteinesulfonic acid modification (PDB ID: 2R47). 271 No further information could be determined. 272 m22: No useful information. 273 m23: Annotated as P-type ATPase or HAD hydrolase. Absent in Methanopyrales. 274 m24: No useful information. 275 m25: Sparse distribution: absent in Methanopyrales and many Halobacterota lineages 276 but widely present in Lokiarchaeota. Related to dihydrouridine synthase (PF0127). It 277 is co-localized with formylmethanofuran--tetrahydromethanopterin 278 formyltransferase/F420-dependent NADP oxidoreductase in Lokiarchaeota and F420H2 279 oxidase in Mnemosynella, thus a role in energy/hydrogenase-type reactions involving 280 F420 is possible. 281 m26: Based on its distribution, phylogeny, and synteny, m26 is associated with Mtr, 282 even including the Thorarchaeota clade of the canonical MtrA. Its distribution also 283 includes Persephonarchaea sequences (Supplementary Data 2) at twilight zone 284 homology that aligned poorly and ended up on a long branch, thus we removed them. 285 The presence of a divergent m26 in Persephonarchaea suggests that they are former 286 methane metabolizers (H2/CO2 or methanotrophs) that have already lost all traces of 287 Mtr and are currently also losing its related marker. 288 m32: UPF0285 is not found outside of Euryarchaeota. Its function cannot be deduced. 289 We recover a strong monophyly of Hydrothermarchaeota (where it is syntenic with Ftr) 290 with Methanomada. This agreement with the species tree (Figure 2a) and synteny 291 supports the case for Hydrothermarchaeota also being former H2/CO2 methanogens. 292 Absent in Methanopyrales; the M. kandleri gene annotated as UPF0285 (MK0078) is 293 a member of the unrelated DUF1464. 294 m33: MamA catalyzes the methylation of Arg285 (M. acetivorans)20,21. Its distribution 295 is limited to Methanomada and a subset of Halobacterota. Together with the 296 distribution and phylogeny of McmA22 and our phylogeny of m20, it suggests that the 297 M. acetivorans pattern of Mcr posttranslational modifications is not universal among 298 methane metabolizers and entirely absent in alkane oxidizers without hampering the 299 complex’s functionality. 300 m34: Limited to Methanomada and a subset of Halobacterota. Its function cannot be 301 deduced. 302 m35: Limited to Methanomada and a subset of Halobacterota. Its function cannot be 303 deduced. There exists one solved structure (PDB ID: 1KJN) of the M. 304 thermautotrophicus homolog that is a selenomethionine-containing homodimer. 305 m36: Sparse distribution in Methanomada and a subset of Halobacterota. Phylogeny 306 is very poorly resolved. 307 m37: Its distribution includes Persephonarchaea where it is syntenic with Fwd and Ftr. 308 The synteny could be related to Persephonarchaea being former methane 309 metabolizers (see below about Eha). We cannot infer anything about its function. 310 m38: Limited to Methanomada, Methanosarcinales, Methanobacteriales. Its function 311 cannot be deduced. 312 Based on their distributions and phylogenies, many of the 38 methanogenesis markers 313 should probably not be considered as such, instead being “demoted” to partial markers 314 like the various Eha and Ehb subunits. 315 A few markers (m15, m17, m18, m19, m21, m24, m36) have undergone interdomain 316 horizontal transfers from Archaea to Bacteria, suggesting that they might be 317 incorporated into other metabolic pathways without them necessarily being remnants 318 of methane metabolism. 319 For some markers whose function is impossible to infer (e.g. m15-m19) we can at 320 least hypothesize a lack of relationship with Mcr, due to their inconsistent presence in 321 alkane oxidizers, while they are found in Archaea and Bacteria often without the Wood- 322 Ljungdahl pathway (WLP). 323 M15, m16, and m17 each contain a strongly monophyletic Archaeoglobales cluster 324 (including Ca. Methanomixophus hydrogenotrophicum) with Ca. Methanodesulfokores 325 washburnensis (GCA_004347975, Korarchaeota) inside it. This observation 326 contributed to our inference that Mcr was vertically inherited in Methanodesulfokores 327 and other methylotrophic methanogenesis components were acquired horizontally. 328 Nonetheless, due to the existence of such transfers and the proximity of the 329 Proteoarchaeota Mcr and Mtr sequences to Halobacterota (Figure 1), we have to 330 consider the possibility that Proteoarchaeota acquired both complexes as ancient 331 transfers from within Halobacterota. We do not consider this scenario as likely a 332 scenario further, as it is not parsimonious and clashes with information from other 333 markers (particularly m26 that includes Thorarchaeota). 334 Evolution of the Hcg proteins 335 We observed that in Methanococcales the genomic location of the hcg genes is not 336 stable. hcgBC are clustered together in M. jannaschii and distant from hmd but hcgAG 337 and hmd are syntenic (Supplementary Figure 36), corroborating a previous synteny 338 analysis in M. maripaludis23. This is reflected in the evolutionary histories of the single 339 gene phylogenies and supermatrices where HcgBC and HcgAEFG give different 340 positions for Methanococcales that are further supported by the gene and site 341 concordance factors for the two supermatrices (Supplementary Data 13). For HcgBC, 342 there exists a monophyletic clade of Methanobacteriales and Methanococcales similar 343 to Hmd and Hmd-like. However, in HcgAEFG, Methanobacteriales are monophyletic 344 with Methanopyrales, similar to the archaeal species tree (Figure 2a), albeit not 345 strongly supported. Other than a lack of evolutionary pressure to maintain a tight 346 cluster, these data imply the involvement of homologous recombination events in the 347 evolution of the Hcg pathway and Hmd, barring other sources of bias in the 348 phylogenies. Assuming Hmd and HcgBC represent the correct history, then the most 349 parsimonious scenario involves an ancient lateral acquisition of HcgAEFG by 350 Methanobacteriales or by Methanococcales. The latter case assumes a subsequent 351 dissolution of the cluster in Methanococcales and the lack of resolution in the 352 HcgAEFG phylogeny not conflicting with the Methanopyrales-Desulfurobacteriales 353 monophyly in the HcgBC tree. Nevertheless, if we accept that the branching in 354 Methanomada should reflect the archaeal reference tree, it is HcgBC-Hmd that were 355 transferred horizontally to the ancestral Methanobacteriales or Methanococcales. In 356 any case, an acquisition by the Desulfurobacteriales in a hydrothermal environment is 357 a plausible assumption. Note that in all cases the Methanobacteriales clade includes 358 a recent transfer to Methanomicrobiales as previously noted for Hmd/Hmd-like7. 359 For the HcgBC supermatrix, both MAD and MinVar root the tree at the strongly 360 monophyletic group of Methanopyrales-Desulfurobacteriales (with relatively high 361 rootstrap support) while NONREV roots it at the strongly monophyletic group of 362 Methanobacteriales (with low rootstrap support). Neither root agrees with what we 363 would expect from the reference tree i.e. a basal separation of Methanococcales 364 (Supplementary Figure 36b, as displayed). Regarding the HcgAEFG supermatrix, 365 MAD and Minvar disagree in the root placement. MAD roots at Methanopyrales and 366 MinVar at Desulfurobacteriales. The rootstrap values strongly support the latter but 367 both are roughly consistent with what we have observed previously for Hmd/Hmd- 368 like7. In any case, this biosynthetic pathway does not appear to predate the ancestor 369 of Methanomada. Finally, as mentioned in the Supplementary Methods, the 370 Desulfurobacteriales do not seem to have a proper HcgD but we did not even recover 371 a proper HcgD monophyletic clade in the preliminary phylogenies either. Thus, it is 372 possible that various paralogs (perhaps with some promiscuity) catalyze the HcgD 373 reaction in different taxa. 374 Evolution of Eha 375 Our main interest in the evolution of Eha was the direction of the transfer between 376 Mnemosynellales and Persephonarchaea. With a root between Methanomada and 377 Halobacterota (Figure 3a, as displayed), the Persephonarchaea are not in their 378 expected position (Figure 2a) and have acquired Eha laterally. This scenario is 379 consistent with the high number of methanogenesis markers in Mnemosynellales and 380 the phylogenies of WLP genes from both the carbonyl and methyl branches (CdhB, 381 Mch, Mtd; Supplementary Figures 37-39, Supplementary Data 7). MAD and MinVar 382 outgroup-free rooting placed the root between Methanomicrobiales and the remaining 383 clades reversing the inferred direction of the transfer (Figure 3a, Supplementary Data 384 12). We recovered this scenario in the phylogenies of the WLP carbonyl 385 methyltransferase module genes (CdhDE) (Supplementary Figures 40, 41, 386 Supplementary Data 7); Eha could have been part of the same transfer event. This 387 inference also suggests that Persephonarchaea could be former methanogens, given 388 that they possess some markers but their position in these phylogenies is unresolved.
389 A second issue is the second (smaller) Methanobacteriales clade. It contains genomes 390 from a variety of genera and often genomes of partially undefined taxonomy 391 (Supplementary Data 10). There is no overlap of taxa between the two 392 Methanobacteriales clades, indicating that there were no gene duplications involved 393 but rather ancient homologous recombination events. As with Hcg, we cannot define 394 the original Methanobacteriales clade and by extension a putative source of the 395 transfer although following the species tree (Figure 2a), the smaller Methanopyrales- 396 affiliated clade is the original. Determining the position of the Methanopyrales 397 themselves in reference phylogenies has been long plagued by artifacts24,25 and it is 398 likely that such issues carry over to the Hcg and Eha phylogenies. The issue is 399 exemplified by the disagreements in the phylogenetic signal among subunits by proxy 400 of their sCF (Supplementary Figure 44a, Supplementary Data 13) where Node 232 401 (Methanopyrales + small Methanobacteriales) and Node 153 (Methanococcales + 402 large Methanobacteriales) have the lowest values among deeper nodes in the tree. 403 Other low sCF values for Node 151 (Mnemosynellales + Persephonarchaea) could be 404 related to divergence in their sequences and poor signal. Within Methanobacteriales, 405 we observed the absence of Eha in Methanosphaera, despite it possessing the WLP7 406 and Ehb (this study). Since Methanosphaera is a methylotrophic methanogen, it would 407 appear that at least for Methanobacteriales there exists a tight association between 408 H2/CO2 methanogenesis and Eha that does not persist as a methanogenesis remnant. 409 Judging from its absence in other methanogens (e.g. Nezhaarchaeota, 410 Verstraetearchaeota), Eha is not always indispensable for H2/CO2 methanogenesis. 411 Depending on whether the Euryarchaeota are monophyletic or not26 and the direction 412 of the Mnemosynellales-Persephonarchaea transfer, Eha became lost among other 413 Archaea either at least once (before the divergence of Acherontia) or at least twice 414 (Acherontia-Stygia, Proteoarchaeota). That is in addition to additional losses 415 throughout the Halobacterota and at the base of Diaforarchaea.
416 Although the identity and homology of ferredoxin homologs is fraught with ambiguity, 417 there seems to have been a lot of tinkering in Methanomada involving the EhaPQR 418 subunits that are MvhB-like ferredoxins. The Eha operon in many Methanobacteriales 419 includes an extra gene compared to what was characterized in Methanothermobacter 420 thermautotrophicus in 27. Beyond EhaQRST homologs in Methanomada clades, 421 additional tinkering can be traced to the origin of specific clades through subunit gains 422 and losses. EhaP, while almost certainly present at the LMA, has been lost by 423 Persephonarchaea. EhaI was similarly lost at the origin of Methanomicrobiales. EhaL 424 is absent in Methanomicrobiales, Persephonarchaea, and Mnemosynellales. Together 425 with the uncertainty of the Eha phylogeny root, it is impossible to determine whether 426 EhaL was lost by these lineages, or invented at the origin of Methanomada, and by 427 extension how ancient it is. Even more complicated is the case of EhaA that is missing 428 from Methanomicrobiales and the smaller Methanobacteriales clade. The simplest 429 scenario posits two individual loss events but the poorly resolved EhaA phylogeny 430 (Supplementary Data 10) is also compatible with a more complex history: EhaA 431 emerged at the base of Methanomada (or lost by Methanomicrobiales, 432 Persephonarchaea, and Mnemosynellales in one or more events) and then transferred 433 twice separately to Persephonarchaea and Mnemosynellales. The patchy distribution 434 of EhaAILP could mean that they are non-essential for the function of the 435 hydrogenase. Alternatively, the missing subunits in Methanomicrobiales, 436 Persephonarchaea, and Mnemosynellales might be related to lack of coupling 437 between H2/CO2 methanogenesis (with the exception of some Methanomicrobiales) 438 and Fwd through Eha. 439 Evolution of Ehb 440 As mentioned in the Results & Discussion section, the most extraordinary event in the 441 evolution of Ehb is the homologous recombination in the Methanococclaes. Even 442 though we suspected its existence from the synteny and single-gene phylogenies 443 (Supplementary Data 11), only rarely was the position of Methanococcales strongly 444 supported. To investigate the signal difference among subunits and its origin, we 445 reconstructed phylogenies for three different Ehb supermatrices: one with all subunits 446 (Figure 3b), one corresponding to the Methanococcales syntenic cluster 447 (EhbEFGHIKLMO, EhbJ was omitted due to its small size and inconsistent topology; 448 Supplementary Figure 42), and one for the Methanococcales cluster without subunits 449 that recover the monophyly of Methanomada (EhbEGHIKLM; Supplementary Figure 450 43). The Methanococcales cluster originated from a massive homologous 451 recombination event related to the Acherontia, perhaps followed by further transfers 452 or fast evolution of certain subunits that ended up determining the phylogenetic signal 453 of the supermatrices.
454 We further tested the putative homologous recombination of Ehb in Methanococcales 455 through our variant application of sCF (see Methods). In the sCF heatmap for the 456 supermatrix of all Ehb subunits (Supplementary Figure 44b), the nodes with low sCF 457 values in multiple subunits are 208 and 113. Node 208 simply reflects the uncertainty 458 in the internal branching of Acherontia, although transfer events cannot be discounted. 459 Node 113 corresponds to Methanomada; here it is subunits EhbBEGH that have lower 460 values. With the exception of EhbB, all of them are part of the Methanococcales Ehb 461 cluster. Most subunits of the cluster are also found together in the Euclidean clustering 462 of the heatmap. This situation persists for the EhbEFGHIKLMO supermatrix 463 (Supplementary Figure 43c) and only partially resolves for EhbEGHIKLM 464 (Supplementary Figure 43d) where Methanococcales group with Acherontia, as for 465 some subunits (especially EhbEG) their position remains inconsistent due to pervasive 466 differences in the signal or further recombination, as described above. We observed 467 the same behavior for gCF. For the complete Ehb supermatrix the gCF for Acherontia 468 is 81.25 and for Methanomada 31.25 demonstrating the signal clash among subunits. 469 For EhbEFGHIKLMO they drop to 77.78 and 22.22 respectively. Most of the signal for 470 a monophyletic Methanomada has almost vanished apart from EhbFMO. Finally, in 471 EhbEGHIKLM Methanococcales and Acherontia are monophyletic at 71.43 gCF.
472 The reasons for Ehb being retained by methylotrophic methanogens in the absence 473 of the WLP is not entirely clear. In the case of Methanofastidiosales and 474 Nuwarchaeales it seems like a last-ditch solution, since they lack any other 475 hydrogenases28. The Acherontia ancestor had already lost Eha despite our inference 7 476 that it was an H2/CO2 methanogen, given the presence of the WLP in Theionarchaea . 477 In the case of Verstraetearchaeota, Ehb has persisted in methylotrophic and H2/CO2 478 even though Eha had already been lost and is not found in other TACK methanogens 479 either. 480 Notes on the evolution of WLP 481 Owing to the higher number of available genomes since two recent in-depth analyses 482 of the WLP7,29, we made two noteworthy observations. In the carbonyl branch article30, 483 an additional set of carbonyl branch enzymes in Syntropharchaeales was ignored, 484 since they had been deemed to be too divergent and forming long branches in 485 preliminary phylogenies. In this study, we identified a close relative of that set in a 486 basal alkanotrophic Methanophagales31. The sequences from Syntropharchaeales 487 and Methanophagales form a monophyletic clade but their branching position is not 488 consistent among subunits. In contrast, the main Syntropharchaeales carbonyl branch 489 sequences are found consistently within Halobacterota (Supplementary Figures 37, 490 40, 41). We hypothesize a participation of this carbonyl branch version in AAO but its 491 exact function cannot be determined; it could function on propionyl-CoA or butyryl- 492 CoA. The evolution and comparative genomics of the carbonyl branch will eventually 493 need to be reexamined as more genomes become available. Concerning the H4MPT 494 branch, in the Mtd tree we found three Proteobacteria sequences forming a 495 monophyletic branch inside Thorarchaeota, a clear interdomain transfer and the first 496 such case for Mtd (Supplementary Figure 39). As the clade contained multiple (and 497 non-identical) sequences, we could discount the possibility of binning errors. These 498 Proteobacteria MAGs need to be studied in depth to determine the role of Mtd. Our 499 preliminary hypothesis is that they are part of either a hybrid H4MPT branch with Mtd 500 instead of bMtd in methylotrophy, or that Mtd is substituting one of the functions of 501 FolD in the H4F branch. Borrel et al., 2019 EggNOG accession number Gao & Gupta, 2007 m1_mcrA arCOG04857 MMP1559 m2_mcrB arCOG04860 MMP1555 m3_mcrG arCOG04858 MMP1558 m4_Predicted rotamase arCOG04900 MMP0154 m5_DUF2102 arCOG04901 MMP0337 m6_DUF2112 arCOG04903 MMP0312 m7_YjiL-like arCOG02679 MMP0608 m8_DUF2113 arCOG04904 MMP0656 m9_arCOG03226 arCOG03226 MMP0421 m10_atwA arCOG00185 MMP0620 m11_mcrC arCOG03225 MMP1557 m12_mcrD arCOG04859 MMP1556 m13_cfbD arCOG04888 MMP0428 m14_cfbE arCOG02822 MMP0173 m15_mtxX arCOG00854 MMP1346 m16_AIR-synthase-related arCOG00640 MMP1531 m17_Zn-ribbon protein arCOG01116 MMP1593 m18_DUF2099 arCOG04893 MMP1644 m19_DUF2117 arCOG03231 MMP0143 m20_Gly-thioamidase arCOG02882 MMP1056 m21_DUF2124 arCOG04847 MMP0563 m22_DUF2098 arCOG04846 MMP0001 m23_SolubleP-type ATPase arCOG01579 MMP1641 m24_DUF2111 arCOG04902 MMP0311 m25_arCOG04853 arCOG04853 MMP1704 m26_DUF2114 arCOG04866 MMP1223 m27_mtrA arCOG03221 MMP1564 m28_mtrB arCOG04867 MMP1563 m29_mtrC arCOG04868 MMP1562 m30_mtrD arCOG04869 MMP1561 m31_mtrE arCOG04870 MMP1560 m32_arCOG04885 arCOG04885 MMP0642 m33_Arg-methyltransferase arCOG00950 MMP1554 m34_DUF1894 arCOG04844 MMP0698 m35_DUF1890 arCOG04845 MMP0701 m36_DUF2115 arCOG03215 MMP0665 m37_DUF2119 arCOG04894 MMP1309 m38_DUF2121 arCOG03213 MMP0021 Supplementary Table 1. Table of all 38 (m1-m38) methanogenesis marker genes following the set and numbering in Borrel et al.28, their respective EggNOG accession numbers and Methanococcus maripaludis gene names as mentioned in 1. Markers noted in red are not included in Gao & Gupta1.
Genome Proposed Name NCBI assembly Genome Size (Mb) Completeness (%) Contamination (%) GC (%) Scaffolds (number) Longest Scaffold (bp) N50 (scaffolds) Contigs (number) Longest contig (bp) N50 (contigs) Coding density (%) Predicted genes (number) NRA7_88_Euryarchaeota_41_62 Ca. Mnemosynella biddleae GCA_002011165 1.50 96.08 0.65 41.18 11 341116 235752 11 341116 235752 91.98 1730 NRA7_48_Euryarchaeota_41_21 GCA_002011155 1.47 96.08 0.65 41.14 21 238144 187849 21 238144 187849 92.84 1711 nra7_reassver2_Euryarchaeota_45_14 Ca. Mnemosynella hypogeia GCA_014361165 1.29 93.46 1.31 44.82 38 106407 54584 41 106407 44894 93.21 1505 nra7_reassver2_Euryarchaeota_47_10 Ca. Mnemosynella sp. GCA_014361185 0.90 81.05 0.65 46.69 73 68921 19803 88 68921 17146 95.50 1106 NRA7_48_Candidatus_Bathyarchaeota_archaeon_52_381 Ca. Hecatella orcuttiae GCA_002011035 1.75 100 0.93 51.85 3 731052 535545 3 731052 535545 89.25 1881 NRA7_88_Candidatus_Bathyarchaeota_52_49 GCA_002009985 1.74 100 0.93 51.93 9 1267205 1267205 13 769127 497978 89.37 1890 NRA7_88_JdFR-13_38_55 Ca. Scotarchaeum ottlingeri GCA_002011075 1.70 93.20 0.97 37.67 7 1676113 1676113 11 691515 495125 90.26 1750 NRA7_48_JdFR-14_42_64 Ca. Geothermarchaeum rappei GCA_002011085 1.58 94.17 0.97 41.83 1 1583546 1583546 1 1583546 1583546 92.28 1613 NRA7_88_JdFR-14_42_10 GCA_002011085 1.44 93.20 1.29 42.03 204 69808 11815 243 40089 9032 92.17 1644 NRA7_88_JdFR-16_51_899 Ca. Pyrohabitans jungbluthii GCA_002010065 1.99 98.13 2.80 51.20 15 620739 394757 15 620739 394757 92.48 2246 NRA7_48_JdFR-16_51_665 GCA_002010065 1.17 51.04 1.87 51.06 82 64021 22921 82 64021 22921 92.30 1370 NRA7_48_JdFR-17_50_1185 GCA_002011115 1.62 74.22 2.88 50.46 101 89324 20372 124 89324 19456 91.32 1880 NRA7_48_JdFR-18_39_115 GCA_002011125 2.19 98.13 1.87 39.11 19 1917514 1917514 24 1201297 1201297 91.69 2424 Supplementary Table 2. Summary statistics of genomes binned in this study and their proposed names (see Descriptions of proposed taxa). Bins named NRA7_48 and NRA7_88 correspond to SRR3723048/U1362A and SRR3732688/U1362B from 32, while the “nra7_reassver2” bins originate to a co-assembly of the three Shengli metagenomes33.
taxon assembly coordinates location isolation_source metagenome_source Euryarchaeota archaeon JdFR-21 * GCA_002011165 47.76 N 127.76 W Pacific Ocean basaltic crustal fluids subsurface metagenome Archaeoglobi archaeon * GCA_014361165 38.15 N 118.5 E China: Dongying Shengli oilfield at Shandong province oil production facility metagenome Archaeoglobi archaeon * GCA_014361185 38.15 N 118.5 E China: Dongying Shengli oilfield at Shandong province oil production facility metagenome Candidatus Bathyarchaeota archaeon ex4484 218 GCA_002254975 27.0388 N 111.2456 W USA: Guaymas Basin, Gulf of California deep-sea hydrothermal vent sediments from dive 4484 marine sediment metagenome Candidatus Bathyarchaeota archaeon GCA_003661965 29.52416667 N 113.57000000 W Mexico: Guaymas Basin, Gulf of California deep-sea hydrothermal vent sediments from dive 4569_2 depth 12-15 cm marine sediment metagenome Candidatus Bathyarchaeota archaeon JdFR-11 * GCA_002011035 47.76 N 127.76 W Pacific Ocean basaltic crustal fluids subsurface metagenome Candidatus Bathyarchaeota archaeon GCA_003662515 29.52416667 N 113.57000000 W Mexico: Guaymas Basin, Gulf of California deep-sea hydrothermal vent sediments marine sediment metagenome Candidatus Bathyarchaeota archaeon GCA_003662485 29.52416667 N 113.57000000 W Mexico: Guaymas Basin, Gulf of California deep-sea hydrothermal vent sediments from dive 4571_4 depth 12-15 cm marine sediment metagenome Candidatus Bathyarchaeota archaeon GCA_003662305 29.52416667 N 113.57000000 W Mexico: Guaymas Basin, Gulf of California deep-sea hydrothermal vent sediments from dive 4569_2 depth 21-24 cm marine sediment metagenome Candidatus Bathyarchaeota archaeon B25 GCA_001593855 27.0119 N 111.4054 W Mexico: Guaymas Basin, Gulf of California marine sediment sample collected by push cores at a deep sea vent site during cruise AT15-25 on Alvin dive 4358 hydrothermal vent metagenome Candidatus Thorarchaeota archaeon GCA_004525055 44.0552806 N 28.6053 E Romania: Tekirghiol lake sediment sediment metagenome Candidatus Thorarchaeota archaeon GCA_004524305 44.0552806 N 28.6053 E Romania: Tekirghiol lake sediment sediment metagenome Candidatus Thorarchaeota archaeon GCA_003345595 41.3778 N 82.5108 W USA: Ohio, Lake Erie, Old Woman Creek freshwater wetland soil wetland metagenome Candidatus Thorarchaeota archaeon GCA_003345555 41.3778 N 82.5108 W USA: Ohio, Lake Erie, Old Woman Creek freshwater wetland soil wetland metagenome Candidatus Thorarchaeota archaeon GCA_004524445 44.0552806 N 28.6053 E Romania: Tekirghiol lake sediment sediment metagenome Candidatus Thorarchaeota archaeon GCA_003662765 29.52416667 N 113.57000000 W Mexico: Guaymas Basin, Gulf of California deep-sea hydrothermal vent sediments from dive 4571_4 depth 0-3 cm marine sediment metagenome Candidatus Thorarchaeota archaeon SMTZ1-83 GCA_001563325 34.7414 N 77.1234 W USA: White Oak River Estuary, North Carolina Sulfate-methane transisition zone estuary sediments 16-26 cm sediment metagenome Candidatus Thorarchaeota archaeon GCA_003662775 27.015 N 111.379 W Mexico: Guaymas Basin, Gulf of California deep-sea hydrothermal vent sediments from dive 4569_9 depth 0-3 cm marine sediment metagenome Candidatus Thorarchaeota archaeon GCA_004376265 26.28 N 86.81 W Atlantic Ocean deep sea sediments associated with petroleum seepage marine sediment metagenome Candidatus Thorarchaeota archaeon AB_25 GCA_001940705 56.103333 N 10.45783299 E Denmark: Aarhus Bay, Baltic Sea Marine sediment marine sediment metagenome Candidatus Thorarchaeota archaeon MP11T_1 GCA_002825515 22.4992 N 114.0276 E Hong Kong: Mai Po Nature Reserve mangrove wetland sediments sediment metagenome Candidatus Thorarchaeota archaeon SMTZ1-45 GCA_001563335 34.7414 N 77.1234 W USA: White Oak River Estuary, North Carolina Sulfate-methane transisition zone estuary sediments 16-26 cm sediment metagenome Candidatus Thorarchaeota archaeon MP9T_1 GCA_002825535 22.4979 N 114.0295 E Hong Kong: Mai Po Nature Reserve sediment (20-25 cm) from mangrove covering field sediment metagenome Candidatus Thorarchaeota archaeon GCA_003345545 41.3778 N 82.5108 W USA: Ohio, Lake Erie, Old Woman Creek freshwater wetland soil wetland metagenome Candidatus Thorarchaeota archaeon GCA_004524595 44.6085139 N 27.331375 E Romania: Amara lake sediment sediment metagenome Candidatus Thorarchaeota archaeon GCA_004525375 63.29 N 19.49 E Sweden: Bothnian Sea Bothnian Sea sediment, site NB8 marine sediment metagenome Candidatus Thorarchaeota archaeon GCA_004525645 63.29 N 19.49 E Sweden: Bothnian Sea Bothnian Sea sediment, site NB8 marine sediment metagenome Candidatus Thorarchaeota archaeon GCA_004524565 44.6085139 N 27.331375 E Romania: Amara lake sediment sediment metagenome Candidatus Thorarchaeota archaeon GCA_004524435 44.0552806 N 28.6053 E Romania: Tekirghiol lake sediment sediment metagenome
* genomes from metagenomes reassembled and rebinned in this study Supplementary Table 3. Detailed metadata (accessions, location, environment) for the Mnemosynellales, Hecatellales, and Thorarchaeota MAGs in Figure 2e. For convenience, since there are too many entries, the metadata for Mnemosynellales and Hecatellales 16S sequences are presented in Supplementary Data 5.
OFV67986.1 GCA 001766815 Uncharacterized conserved protein UCP005852 methanogenesis Candidatus Syntrophoarchaeum caldarius PHP46256.1 GCA 002254825 methanogenesis marker 3 protein Methanosarcinales archaeon ex4572 44 RZN14344.1 GCA 004212095 methanogenesis marker 3 protein Methanosarcinales archaeon RZB32871.1 GCA 004193545 hypothetical protein AEth 00217 Candidatus Argoarchaeum ethanivorans Methanoliparia KPV61785.1 GCA 001399795 hypothetical protein AOA66 1755 Candidatus Bathyarchaeota archaeon BA2 Hadesarchaea TDA30821.1 GCA 004347865 methanogenesis marker 3 protein Archaeoglobi archaeon TDA40603.1 GCA 004347975 methanogenesis marker 3 protein Candidatus Korarchaeota archaeon RLG36370.1 GCA 003661185 methanogenesis marker 3 protein Methanosarcinales archaeon GCA 003935005RSFX01000002.1 22922100222246212 229 GCA 003935005 -1 ID 12 229 partial 00 Archaeoglobi archaeon Syntrophoarchaeales RZN47588.1 GCA 004212155 methanogenesis marker 3 protein archaeon (Nuwarchaeales) Methanofastidiosales Methanomassiliicoccales Methanophagales Methanonatronarchaeia Methanobacteriales Methanococcales Verstraetearchaeota Nezhaarchaeota Methanopyrales Methanomicrobiales WP 042686103.1 GCF 000711905 methanogenesis marker 3 protein Methermicoccus shengliensis Methanoliparia Methanosarcinales Methanoflorentaceae Methanosarcinales (ANME-2) Methanosarcinales Methanocellales
Tree scale: 1 Supplementary Figure 1. ML phylogeny of methanogenesis marker m4. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanosarcinales (ANME-2) Methanosarcinales Methanoliparia Methanosarcinales Methanomicrobiales Methanoflorentaceae Methanocellales Methanobacteriales Methanonatronarchaeia GCA 000405745ASPK01000001.1 10453451451 10 GCA 000405745 1 ID 1 10 partial 00 Thaumarchaeota archaeon SCGC AB-179-E04 Nezhaarchaeota Methanococcales Methanomassiliicoccales Verstraetearchaeota RZN47583.1 GCA 004212155 methanogenesis marker 6 protein archaeon (Nuwarchaeales) Methanofastidiosales GCA 003935005RSFX01000002.1 22621898821944312 226 GCA 003935005 -1 ID 12 226 partial 00 Archaeoglobi archaeon Nezhaarchaeota Methanocellales OFV67131.1 GCA 001766815 Uncharacterized conserved protein UCP005642 methanogenesis Candidatus Syntrophoarchaeum caldarius RLG36908.1 GCA 003661185 methanogenesis marker 6 protein Methanosarcinales archaeon RLI89505.1 GCA 003663105 methanogenesis marker 6 protein Candidatus Altiarchaeales archaeon Methanophagales KPV61784.1 GCA 001399795 hypothetical protein AOA66 1754 Candidatus Bathyarchaeota archaeon BA2 Hadesarchaea TDA30822.1 GCA 004347865 methanogenesis marker 5 protein Archaeoglobi archaeon TDA40602.1 GCA 004347975 methanogenesis marker 5 protein Candidatus Korarchaeota archaeon Methanopyrales Tree scale: 0.1 Supplementary Figure 2. ML phylogeny of methanogenesis marker m5. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanocellales WP 042686355.1 GCF 000711905 methanogenesis marker 5 protein Methermicoccus shengliensis Methanoflorentaceae
Methanosarcinales
Methanosarcinales
Methanomicrobiales
Methanofastidiosales RZN65021.1 GCA 004212075 methanogenesis marker 5 protein Candidatus Methanoliparum thermophilum Verstraetearchaeota
Methanomassiliicoccales RZN47584.1 GCA 004212155 methanogenesis marker 5 protein archaeon (Nuwarchaeales) Methanobacteriales
Methanopyrales
Methanococcales
Nezhaarchaeota TDA40602.1 GCA 004347975 methanogenesis marker 5 protein Candidatus Korarchaeota archaeon TDA30822.1 GCA 004347865 methanogenesis marker 5 protein Archaeoglobi archaeon Methanonatronarchaeia KPV61783.1 GCA 001399795 hypothetical protein AOA66 1753 Candidatus Bathyarchaeota archaeon BA2 Hadesarchaeota GCA 003935005RSFX01000002.1 22521858221901612 225 GCA 003935005 -1 ID 12 225 partial 00 Archaeoglobi archaeon Nezhaarchaeota
Methanophagales
Syntrophoarchaeales
Tree scale: 1 Supplementary Figure 3. ML phylogeny of methanogenesis marker m6. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
RZN47585.1 GCA 004212155 methanogenesis marker 15 protein archaeon (Nuwarchaeales) Methanococcales Methanobacteriales Methanophagales Methanopyrales Verstraetearchaeota Nezhaarchaeota TDA30839.1 GCA 004347865 methanogenesis marker 15 protein Archaeoglobi archaeon TDA40601.1 GCA 004347975 methanogenesis marker 15 protein Candidatus Korarchaeota archaeon Nezhaarchaeota Methanofastidiosales Methanomassiliicoccales Methanonatronarchaeia GCA 005191415SUPS01000198.1 53738496737 5 GCA 005191415 -1 ID 37 5 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A KPV61782.1 GCA 001399795 BadF/BadG/BcrA/BcrD ATPase family protein Candidatus Bathyarchaeota archaeon BA2 Hadesarchaea Syntrophoarchaeales Methanophagales Methanomicrobiales Methanosarcinales RZN65022.1 GCA 004212075 methanogenesis marker 15 protein Candidatus Methanoliparum thermophilum Methanoflorentaceae Methanocellales
Tree scale: 0.1 Supplementary Figure 4. ML phylogeny of methanogenesis marker m7. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanobacteriales Methanococcales Verstraetearchaeota OFV67987.1 GCA 001766815 Uncharacterized conserved protein UCP019464 methanogenesis Candidatus Syntrophoarchaeum caldarius Methanosarcinales Nezhaarchaeota RZN47586.1 GCA 004212155 methanogenesis marker 17 protein archaeon (Nuwarchaeales) Methanopyrales Methanonatronarchaeia Methanomassiliicoccales Methanofastidiosales Methanophagales GCA 003935005RSFX01000002.1 22822035322100012 228 GCA 003935005 -1 ID 12 228 partial 00 Archaeoglobi archaeon Syntrophoarchaeales GCA 005191415SUPS01000198.1 43044373037 4 GCA 005191415 -1 ID 37 4 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A KPV61781.1 GCA 001399795 hypothetical protein AOA66 1751 Candidatus Bathyarchaeota archaeon BA2 Hadesarchaea TDA30823.1 GCA 004347865 methanogenesis marker 17 protein Archaeoglobi archaeon TDA40600.1 GCA 004347975 methanogenesis marker 17 protein Candidatus Korarchaeota archaeon Methanoliparia Methanoflorentaceae Methanoliparia Methanocellales Methanosarcinales (ANME-2) Methanosarcinales Methanomicrobiales Methanosarcinales
Tree scale: 0.1 Supplementary Figure 5. ML phylogeny of methanogenesis marker m8. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanobacteriales TDA30824.1 GCA 004347865 methanogenesis marker 7 protein Archaeoglobi archaeon TDA40599.1 GCA 004347975 methanogenesis marker 7 protein Candidatus Korarchaeota archaeon RZN47587.1 GCA 004212155 methanogenesis marker 7 protein archaeon (Nuwarchaeales) Methanonatronarchaeia Methanomassiliicoccales Methanofastidiosales Methanophagales OFV67990.1 GCA 001766815 Methyl-coenzyme M reductase protein C Candidatus Syntrophoarchaeum caldarius Methanosarcinales Methanopyrales Methanococcales Methanobacteriales Nezhaarchaeota Verstraetearchaeota GCA 003935005RSFX01000002.1 22721944622035112 227 GCA 003935005 -1 ID 12 227 partial 00 Archaeoglobi archaeon Syntrophoarchaeales GCA 005191415SUPS01000198.1 32127304737 3 GCA 005191415 -1 ID 37 3 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A Hadesarchaea KPV61780.1 GCA 001399795 Methyl-coenzyme M reductase operon protein C Candidatus Bathyarchaeota archaeon BA2 Methanoliparia Methanoliparia Methanomicrobiales Methanoflorentaceae Methanosarcinales Methanocellales
Tree scale: 0.1 Supplementary Figure 6. ML phylogeny of methanogenesis marker m9. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanosarcinales Methanobacteriales Methanococcales Methanopyrales OFV67991.1 GCA 001766815 methyl coenzyme M reductase system component A2 Candidatus Syntrophoarchaeum caldarius Methanophagales TDA29430.1 GCA 004347865 ABC transporter ATP-binding protein Archaeoglobi archaeon TDA40881.1 GCA 004347975 ABC transporter ATP-binding protein Candidatus Korarchaeota archaeon Nezhaarchaeota Verstraetearchaeota GCA 003935005RSFX01000019.1 31667336411 3 GCA 003935005 -1 ID 11 3 partial 00 Archaeoglobi archaeon RLG36227.1 GCA 003661185 ABC transporter ATP-binding protein Methanosarcinales archaeon Syntrophoarchaeales GCA 005191425SUPR01000115.1 87782953620 8 GCA 005191425 -1 ID 20 8 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB B RZN65545.1 GCA 004212075 ABC transporter ATP-binding protein Candidatus Methanoliparum thermophilum TDA32553.1 GCA 004347925 ABC transporter ATP-binding protein Hadesarchaea archaeon KPV61794.1 GCA 001399795 putative ABC transporter ATP-binding protein Candidatus Bathyarchaeota archaeon BA2 KPV65181.1 GCA 001399805 putative ABC transporter ATP-binding protein Candidatus Bathyarchaeota archaeon BA1 Methanoliparia Methanosarcinales (ANME-2) Syntrophoarchaeales Methanosarcinales Methanosarcinales Methanocellales Methanoflorentaceae Methanomicrobiales Methanococcales Methanopyrales Methanobacteriales Methanonatronarchaeia Methanomassiliicoccales Methanofastidiosales RZN50466.1 GCA 004212155 methyl coenzyme M reductase system component A2 archaeon (Nuwarchaeales) Methanophagales Verstraetearchaeota TDA40604.1 GCA 004347975 methyl coenzyme M reductase system component A2 Candidatus Korarchaeota archaeon TDA30838.1 GCA 004347865 methyl coenzyme M reductase system component A2 Archaeoglobi archaeon Nezhaarchaeota GCA 003935005RSFX01000021.1 27248792655814 27 GCA 003935005 1 ID 14 27 partial 00 Archaeoglobi archaeon Syntrophoarchaeales GCA 003935005RSFX01000019.1 13128311 1 GCA 003935005 1 ID 11 1 partial 10 Archaeoglobi archaeon OFV66399.1 GCA 001766825 ABC transporter ATP-binding protein Candidatus Syntrophoarchaeum butanivorans RLG36918.1 GCA 003661185 methyl coenzyme M reductase system component A2 Methanosarcinales archaeon Helarchaeota KPV61798.1 GCA 001399795 putative ABC transporter ATP-binding protein Candidatus Bathyarchaeota archaeon BA2 TDA31473.1 GCA 004347925 methyl coenzyme M reductase system component A2 Hadesarchaea archaeon Methanoliparia
Tree scale: 0.1 Supplementary Figure 7. ML phylogeny of methanogenesis marker m10. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
OFV67175.1 GCA 001766815 Methyl-coenzyme M reductase protein C Candidatus Syntrophoarchaeum caldarius GCA 003935005RSFX01000002.1 24023152123220112 240 GCA 003935005 1 ID 12 240 partial 00 Archaeoglobi archaeon GCA 005191415SUPS01000211.1 76057683653 7 GCA 005191415 -1 ID 53 7 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A Methanoliparia KPV61778.1 GCA 001399795 Methyl-coenzyme M reductase I operon protein C Candidatus Bathyarchaeota archaeon BA2 Hadesarchaea Verstraetearchaeota Nezhaarchaeota Methanococcales Methanobacteriales Methanofastidiosales Methanophagales Methanopyrales RZN50467.1 GCA 004212155 methyl-coenzyme M reductase I operon protein C archaeon (Nuwarchaeales) Methanomassiliicoccales (incl. Methanonatronarchaeia) Methanoliparia Methanomicrobiales Methanosarcinales TDA40884.1 GCA 004347975 methyl-coenzyme M reductase I operon protein C Candidatus Korarchaeota archaeon TDA30811.1 GCA 004347865 methyl-coenzyme M reductase I operon protein C Archaeoglobi archaeon WP 042686198.1 GCF 000711905 methyl-coenzyme M reductase I operon protein C Methermicoccus shengliensis Methanosarcinales Methanosarcinales Methanocellales Methanoflorentaceae
Tree scale: 0.1 Supplementary Figure 8. ML phylogeny of methanogenesis marker m11. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Verstraetearchaeota TDA40883.1 GCA 004347975 methyl-coenzyme M reductase operon protein D Candidatus Korarchaeota archaeon TDA30812.1 GCA 004347865 hypothetical protein DSO00 00340 Archaeoglobi archaeon Nezhaarchaeota Methanonatronarchaeia Methanomassiliicoccales Methanopyrales Methanococcales Methanococcales Methanococcales Methanobacteriales Methanocellales Methanobacteriales Methanoliparia Methanoflorentaceae Methanosarcinales Methanomicrobiales Methanofastidiosales RZN47590.1 GCA 004212155 hypothetical protein EF808 04115 archaeon (Νuwarchaeales) RLG36993.1 GCA 003661195 hypothetical protein DRN79 03895 Methanosarcinales archaeon Hadesarchaea KPV61779.1 GCA 001399795 Methyl-coenzyme M reductase I operon protein D Candidatus Bathyarchaeota archaeon BA2 Methanoliparia GCA 005191415SUPS01000211.1 86833724053 8 GCA 005191415 -1 ID 53 8 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A GCA 003935005RSFX01000019.1 21286165411 2 GCA 003935005 -1 ID 11 2 partial 00 Archaeoglobi archaeon RLG36282.1 GCA 003661185 hypothetical protein DRN91 08360 Methanosarcinales archaeon Syntrophoarchaeales
Tree scale: 1 Supplementary Figure 9. ML phylogeny of methanogenesis marker m12. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Verstraetearchaeota Methanobacteriales Methanococcales Methanopyrales RLF21693.1 GCA 003650865 Ni-sirohydrochlorin ac-diamide reductive cyclase catalytic subunit Thermoprotei archaeon TDA40893.1 GCA 004347975 Ni-sirohydrochlorin ac-diamide reductive cyclase catalytic subunit Candidatus Korarchaeota archaeon TDA30816.1 GCA 004347865 Ni-sirohydrochlorin ac-diamide reductive cyclase catalytic subunit Archaeoglobi archaeon Syntrophoarchaeales GCA 003935005RSFX01000021.1 13122431334014 13 GCA 003935005 -1 ID 14 13 partial 00 Archaeoglobi archaeon RLG37035.1 GCA 003661185 Ni-sirohydrochlorin ac-diamide reductive cyclase catalytic subunit Methanosarcinales archaeon Methanomassiliicoccales Methanofastidiosales Methanonatronarchaeia Methanoliparia Methanophagales Methanosarcinales (ANME-2) Methanoflorentaceae Methanocellales Methanosarcinales Methanosarcinales Methanomicrobiales Methanosarcinales
Tree scale: 0.1 Supplementary Figure 10. ML phylogeny of methanogenesis marker m13. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanobactreriales Methanococcales Methanobacteriales Verstraetearchaeota Methanopyrales RLG37031.1 GCA 003661185 coenzyme F430 synthase Methanosarcinales archaeon GCA 003935005RSFX01000021.1 14133211476614 14 GCA 003935005 -1 ID 14 14 partial 00 Archaeoglobi archaeon Syntrophoarchaeales Methanofastidiosales Methanomassiliicoccales WP 042684478.1 GCF 000711905 hypothetical protein Methermicoccus shengliensis Methanosarcinales OKY78437.1 GCA 001914405 UDP-N-acetylmuramyl pentapeptide synthase Candidatus Methanohalarchaeum thermophilum RZN42874.1 GCA 004212135 coenzyme F430 synthase Methanophagales archaeon ANME-1-THS Methanomicrobiales Methanoflorentaceae Methanosarcinales
Tree scale: 0.1 Supplementary Figure 11. ML phylogeny of methanogenesis marker m14. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Hydrothermarchaeota Methanobacteriales (incl. Methanococcales) OLS26945.1 GCA 001940645 hypothetical protein HeimC3 06030 Candidatus Heimdallarchaeota archaeon LC 3 OGD46249.1 GCA 001775995 hypothetical protein A3K70 02310 Candidatus Bathyarchaeota archaeon RBG 16 48 13 GCA 003157385PMJJ01000119.1 19144581519514 19 GCA 003157385 -1 ID 14 19 partial 00 Actinobacteria bacterium GCA 003154635PMDX01000271.1 526203369231 5 GCA 003154635 -1 ID 231 5 partial 00 Actinobacteria bacterium OGE05349.1 GCA 001774945 hypothetical protein A3F45 01530 Candidatus Curtissbacteria bacterium RIFCSPHIGHO2 12 FULL 41 17 GCA 005191415SUPS01000041.1 121240613254149 12 GCA 005191415 1 ID 149 12 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A Lokiarchaeota Lokiarchaeota GCA 005191425SUPR01000152.1 64991584261 6 GCA 005191425 -1 ID 61 6 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB B RZN45225.1 GCA 004212155 hypothetical protein EF808 07155 archaeon (Nuwarchaeales) Methanofastidiosales Syntrophoarchaeales RLI73022.1 GCA 003662965 methyltransferase Archaeoglobales archaeon RLI76452.1 GCA 003662995 methyltransferase Archaeoglobales archaeon GCA 002010215MTMY01000007.1 8764067648136 87 GCA 002010215 -1 ID 6 87 partial 00 Archaeoglobus sp. JdFR-37 ADC65876.1 GCA 000025505 phosphotransacetylase-like protein Ferroglobus placidus DSM 10642 GCA 004366975SETC01000008.1 84177491755 8 GCA 004366975 -1 ID 55 8 partial 00 Archaeoglobaceae archaeon AIY90075.1 GCA 000789255 phosphotransacetylase Geoglobus acetivorans TDA29425.1 GCA 004347865 phosphotransacetylase Archaeoglobi archaeon AKG91182.1 GCA 001006045 putative phosphotransacetylase Geoglobus ahangari TDA40587.1 GCA 004347975 phosphotransacetylase Candidatus Korarchaeota archaeon GCA 002011165MTMI01000005.1 14144551519216 14 GCA 002011165 1 ID 16 14 partial 00 Euryarchaeota archaeon JdFR-21 Methanoflorentaceae Methanomicrobiales GCA 003935005RSFX01000006.1 30628930529010218 306 GCA 003935005 -1 ID 18 306 partial 00 Archaeoglobi archaeon HAJ27633.1 GCA 003451635 TPA phosphotransacetylase Syntrophus sp. in Bacteria OPY02696.1 GCA 002067555 hypothetical protein A4E61 01247 Syntrophorhabdus sp. PtaB.Bin184 Methanocellales Methanomassiliicoccales Methanonatronarchaeia OKY78396.1 GCA 001914405 Methyltransferase subunit MtxX phosphotransacetylase family enzyme Candidatus Methanohalarchaeum thermophilum Bacteria Methanosarcinales Nezhaarchaeota Methanosarcinales (ANME-2) PPA79516.1 GCA 002926195 malic enzyme ANME-2 cluster archaeon HR1 Methanosarcinales Methanosarcinales Verstraetearchaeota RLE48916.1 GCA 003649085 hypothetical protein DRJ31 06250 Candidatus Verstraetearchaeota archaeon Methanopyrales
Tree scale: 0.1 Supplementary Figure 12. ML phylogeny of methanogenesis marker m15. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
KPV61764.1 GCA 001399795 thiamine monophosphate kinase Candidatus Bathyarchaeota archaeon BA2 RLI47174.1 GCA 003662715 hypothetical protein DRO69 01205 Candidatus Bathyarchaeota archaeon Hadesarchaea Verstraetearchaeota RLG91773.1 GCA 003661965 hypothetical protein DRO36 03445 Candidatus Bathyarchaeota archaeon Nezhaarchaeota GCA 002011125MTMF01000014.1 8065360663254 80 GCA 002011125 1 ID 4 80 partial 00 Candidatus Hydrothermarchaeota archaeon JdFR-18 Methanococcales Methanobacteriales Methanophagales Methanosarcinales TET91074.1 GCA 004377185 methanogenesis marker 2 protein Methanomassiliicoccales archaeon Theionarchaea RZN47421.1 GCA 004212155 methanogenesis marker 2 protein archaeon (Nuwarchaeales) Methanofastidiosales GCA 002494765DACJ01000084.1 15115411254555 15 GCA 002494765 -1 ID 55 15 partial 00 Euryarchaeota archaeon UBA186 Methanomassiliicoccales Methanopyrales GCA 002010215MTMY01000021.1 5952714537009 59 GCA 002010215 1 ID 9 59 partial 00 Archaeoglobus sp. JdFR-37 RLI80609.1 GCA 003662995 methanogenesis marker 2 protein Archaeoglobales archaeon ADC64250.1 GCA 000025505 methanogenesis marker protein 2 Ferroglobus placidus DSM 10642 AIY90922.1 GCA 000789255 methanogenesis marker protein 2 Geoglobus acetivorans GCA 004366975SETC01000009.1 26252592622756 26 GCA 004366975 1 ID 56 26 partial 00 Archaeoglobaceae archaeon AKG91904.1 GCA 001006045 Selenophosphate synthetase-like protein Geoglobus ahangari TDA30814.1 GCA 004347865 methanogenesis marker 2 protein Archaeoglobi archaeon TDA40891.1 GCA 004347975 methanogenesis marker 2 protein Candidatus Korarchaeota archaeon Methanomicrobiales Methanonatronarchaeia GCA 002011165MTMI01000001.1 6958516594907 69 GCA 002011165 1 ID 7 69 partial 00 Euryarchaeota archaeon JdFR-21 Syntrophoarchaeales Methanoliparia Methanoflorentaceae Methanocellales Methanosarcinales RMF91433.1 GCA 003695745 methanogenesis marker 2 protein Euryarchaeota archaeon RLG52547.1 GCA 003661385 methanogenesis marker 2 protein Candidatus Korarchaeota archaeon GCA 002010035MTMC01000005.1 42725373218 4 GCA 002010035 1 ID 18 4 partial 00 Methanopyri archaeon JdFR-15 Helarchaeota
Tree scale: 0.1 Supplementary Figure 13. ML phylogeny of methanogenesis marker m16. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
OLS15638 1 GCA 001940655 hypothetical protein RBG13Loki 0737 Candidatus Lokiarchaeota archaeon CR 4 Nezhaarchaeota TFG05377 1 GCA 004524455 sugar specific transcriptional regulator TrmB Candidatus Lokiarchaeota archaeon GCA 005191415SUPS01000053 1 171568616810176 17 GCA 005191415 1 ID 176 17 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A Methanomicrobiales Methanocellales Syntrophoarchaeales Methanoflorentaceae Methanomassiliicoccales TDA40588 1 GCA 004347975 tRNAIle2 2 agmatinylcytidine synthetase Candidatus Korarchaeota archaeon Archaeoglobales Methanomicrobiales OPY02695 1 GCA 002067555 hypothetical protein A4E61 01246 Syntrophorhabdus sp PtaB Bin184 HAJ27632 1 GCA 003451635 TPA tRNAIle2 2 agmatinylcytidine synthetase Syntrophus sp in Bacteria Methanocellales Methanobacteriales Methanopyrales Methanococcales Methanonatronarchaeia RMF91664 1 GCA 003695745 DUF1743 domain containing protein Euryarchaeota archaeon GCA 003230355QIDD01000184 1 1324584184 1 GCA 003230355 1 ID 184 1 partial 00 Euryarchaeota archaeon GCA 003230355QIDD01000191 1 527432955191 5 GCA 003230355 1 ID 191 5 partial 01 Euryarchaeota archaeon GBE18085 1 GCA 002923215 hypothetical protein BMS3Abin16 00676 archaeon BMS3Abin16 Verstraetearchaeota GCA 002011165MTMI01000001 1 5544624456017 55 GCA 002011165 1 ID 7 55 partial 00 Euryarchaeota archaeon JdFR 21 RLF21333 1 GCA 003650865 hypothetical protein DRJ68 03710 Thermoprotei archaeon GCA 003157385PMJJ01000017 1 27249322590063 27 GCA 003157385 1 ID 63 27 partial 00 Actinobacteria bacterium GCA 003154635PMDX01000335 1 91464015623118 9 GCA 003154635 1 ID 118 9 partial 00 Actinobacteria bacterium Nuwarchaeales OGD46465 1 GCA 001775995 hypothetical protein A3K70 02300 Candidatus Bathyarchaeota archaeon RBG 16 48 13 RLI75073 1 GCA 003662965 hypothetical protein DRO97 04205 Archaeoglobales archaeon GCA 002010215MTMY01000033 1 5348270492088 53 GCA 002010215 1 ID 8 53 partial 00 Archaeoglobus sp JdFR 37 ADC66653 1 GCA 000025505 methanogenesis marker protein 11 Ferroglobus placidus DSM 10642 AKG90813 1 GCA 001006045 methanogenesis imperfect marker protein 11 Geoglobus ahangari AIY90010 1 GCA 000789255 OB fold nucleic acid binding domain protein Geoglobus acetivorans GCA 004366975SETC01000008 1 82664566740655 82 GCA 004366975 1 ID 55 82 partial 00 Archaeoglobaceae archaeon TDA40593 1 GCA 004347975 hypothetical protein DSO07 08940 Candidatus Korarchaeota archaeon TDA26598 1 GCA 004347865 hypothetical protein DSO00 07315 partial Archaeoglobi archaeon TDA26126 1 GCA 004347865 hypothetical protein DSO00 07860 partial Archaeoglobi archaeon Methanofastidiosales GCA 003152735PMAZ01000069 1 424103399239 4 GCA 003152735 1 ID 239 4 partial 00 Candidatus Bathyarchaeota archaeon WP 119815563 1 GCF 003589585 hypothetical protein Candidatus Bathyarchaeota archaeon PIN79349 1 GCA 002762855 hypothetical protein COV16 04780 Candidatus Woesearchaeota archaeon CG10 big fil rev 8 21 14 0 10 34 8 PJA72076 1 GCA 002790845 hypothetical protein CO152 03330 bacterium CG 4 9 14 3 um filter 33 26 KKU02635 1 GCA 001001555 Methanogenesis marker protein 11 Candidatus Amesbacteria bacterium GW2011 GWC2 45 19 OGE26410 1 GCA 001777055 hypothetical protein A3C26 01625 Candidatus Daviesbacteria bacterium RIFCSPHIGHO2 02 FULL 39 12 OGE77002 1 GCA 001777455 hypothetical protein A3J19 01475 Candidatus Daviesbacteria bacterium RIFCSPLOWO2 02 FULL 41 8 GCA 002011125MTMF01000002 1 3965773666639 39 GCA 002011125 1 ID 9 39 partial 00 Candidatus Hydrothermarchaeota archaeon JdFR 18 Methanomicrobiales Methanosarcinales Methanoflorentaceae GCA 003935005RSFX01000009 1 29291233000721 29 GCA 003935005 1 ID 21 29 partial 00 Archaeoglobi archaeon Methanocellales
Tree scale: 0.1 Supplementary Figure 14. ML phylogeny of methanogenesis marker m17. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
KYK38878.1 GCA 001595795 hypothetical protein AYK18 00425 Theionarchaea archaeon DG-70 KYK36285.1 GCA 001595815 hypothetical protein AYK19 08980 Theionarchaea archaeon DG-70-1 Bacteria RLG60219.1 GCA 003661505 hypothetical protein DRN87 04490 Candidatus Geothermarchaeota archaeon RLI30717.1 GCA 003662535 hypothetical protein DRO48 02655 Candidatus Bathyarchaeota archaeon Bathyarchaeota Nezhaarchaeota Bathyarchaeota RLE89151.1 GCA 003650785 hypothetical protein DRJ49 03910 Thermoprotei archaeon RLF38200.1 GCA 003649835 hypothetical protein DRN00 04665 partial Thermoplasmata archaeon RLI11591.1 GCA 003662245 hypothetical protein DRO33 03845 Candidatus Bathyarchaeota archaeon RLG68986.1 GCA 003661625 hypothetical protein DRN93 01360 archaeon RLF10605.1 GCA 003649605 hypothetical protein DRJ69 02925 partial Thermoprotei archaeon Korarchaeota PWR73939.1PWR73938.1 GCA 003173355 hypothetical protein DK846 01880 Methanospirillum lacunae ADN36786.1 GCA 000147875 conserved hypothetical protein Methanolacinia petrolearia DSM 11571 GCA 003935005RSFX01000021.1 25228812375314 25 GCA 003935005 1 ID 14 25 partial 00 Archaeoglobi archaeon TFG04486.1 GCA 004524455 DUF2099 family protein Candidatus Lokiarchaeota archaeon GCA 005191415SUPS01000171.1 7564565147 7 GCA 005191415 -1 ID 7 7 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A Methanoliparia KPV61777.1 GCA 001399795 hypothetical protein AOA66 1747 Candidatus Bathyarchaeota archaeon BA2 Hadesarchaea Methanomassiliicoccales GCA 002496325DAJM01000016.1 4261934884 4 GCA 002496325 -1 ID 4 4 partial 00 Candidatus Methanoperedens sp. UBA453 Methanosarcinales Methanomassiliicoccales Syntrophoarchaeales Methanomicrobiales (incl.Verstraetearchaeota) Methanomassiliicoccales Methanobacteriales (incl. Methanofastidiosales) RZN47127.1 GCA 004212155 DUF2099 family protein archaeon (Nuwarchaeales) TDA29429.1 GCA 004347865 hypothetical protein DSO00 04210 Archaeoglobi archaeon TDA40880.1 GCA 004347975 hypothetical protein DSO07 07540 Candidatus Korarchaeota archaeon Methanococcales WP 042687040.1 GCF 000711905 DUF2099 family protein Methermicoccus shengliensis Methanosarcinales Methanonatronarchaeia Methanophagales OFV67119.1 GCA 001766815 methanogenesis marker protein 8 Candidatus Syntrophoarchaeum caldarius RLG36952.1 GCA 003661185 hypothetical protein DRN91 06655 Methanosarcinales archaeon RLG38830.1 GCA 003661185 hypothetical protein DRN91 01460 Methanosarcinales archaeon Methanoflorentaceae Methanosarcinales (ANME-2)
Tree scale: 0.1 Supplementary Figure 15. ML phylogeny of methanogenesis marker m18. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanobacteriales Methanoflorentaceae Methanococcales Methanophagales TDA32480.1 GCA 004347925 hypothetical protein DSO04 02155 partial Hadesarchaea archaeon KPV61774.1 GCA 001399795 hypothetical protein AOA66 1744 Candidatus Bathyarchaeota archaeon BA2 GCA 005191415SUPS01000002.1 353533536717261 35 GCA 005191415 -1 ID 261 35 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A Verstraetearchaeota Methanopyrales Methanosarcinales Methanosarcinales (ANME-2) PPA78515.1 GCA 002926195 hypothetical protein C00003105 00669 ANME-2 cluster archaeon HR1 Methanomassiliicoccales Methanosarcinales Methanosarcinales OPY49945.1 GCA 002067365 hypothetical protein A4E48 02071 Methanosaeta sp. PtaU1.Bin060 Methanomicrobiales Methanocellales Bacteria RZN45046.1 GCA 004212155 DUF2117 domain-containing protein archaeon (Nuwarchaeales) Methanofastidiosales TDA30241.1 GCA 004347865 hypothetical protein DSO00 01920 Archaeoglobi archaeon Methanoliparia RLF05186.1 GCA 003649565 hypothetical protein DRJ60 05985 Thermoprotei archaeon RLF23241.1 GCA 003650865 hypothetical protein DRJ68 00265 Thermoprotei archaeon RLI31618.1 GCA 003662565 hypothetical protein DRO51 03540 partial Candidatus Bathyarchaeota archaeon TDA30936.1 GCA 004347835 hypothetical protein DSO03 05835 partial Hadesarchaea archaeon TDA40592.1 GCA 004347975 hypothetical protein DSO07 08935 Candidatus Korarchaeota archaeon Methanonatronarchaeia TDA33581.1 GCA 004347925 hypothetical protein DSO04 00410 partial Hadesarchaea archaeon TDA38485.1 GCA 004348015 hypothetical protein DSO09 04235 Candidatus Verstraetearchaeota archaeon TDA35388.1 GCA 004347915 hypothetical protein DSO05 05400 Candidatus Nezhaarchaeota archaeon WYZ-LMO7
Tree scale: 0.1 Supplementary Figure 16. ML phylogeny of methanogenesis marker m19. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanococcales Methanobacteriales RLF21668.1 GCA 003650865 YcaO-related McrA-glycine thioamidation protein Thermoprotei archaeon TDA35300.1 GCA 004347915 YcaO-related McrA-glycine thioamidation protein partial Candidatus Nezhaarchaeota archaeon WYZ-LMO7 TDA26601.1 GCA 004347865 YcaO-related McrA-glycine thioamidation protein Archaeoglobi archaeon TDA40596.1 GCA 004347975 YcaO-related McrA-glycine thioamidation protein Candidatus Korarchaeota archaeon Methanomassiliicoccales Verstraetearchaeota RZN64848.1 GCA 004212075 YcaO-related McrA-glycine thioamidation protein Candidatus Methanoliparum thermophilum Methanomicrobiales Methanosarcinales RPJ51209.1 GCA 003820275 YcaO-related McrA-glycine thioamidation protein Euryarchaeota archaeon RZN46754.1 GCA 004212155 YcaO-related McrA-glycine thioamidation protein archaeon (Nuwarchaeales) Methanofastidiosales Methanosarcinales (ANME-2) RZN33543.1 GCA 004212135 YcaO-related McrA-glycine thioamidation protein Methanophagales archaeon ANME-1-THS Methanonatronarchaeia Methanophagales Methanomicrobiales Methanosarcinales Methanoflorentaceae Methanocellales
Tree scale: 0.1 Supplementary Figure 17. ML phylogeny of methanogenesis marker m20. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanococcales Methanosarcinales Methanobacteriales RLG37451.1 GCA 003661185 DUF2124 domain-containing protein Methanosarcinales archaeon OFV66438.1 GCA 001766825 Uncharacterized conserved protein UCP004962 Candidatus Syntrophoarchaeum butanivorans Methanoliparia Methanomassiliicoccales RZN36886.1 GCA 004212135 DUF2124 domain-containing protein Methanophagales archaeon ANME-1-THS Methanobacteriales Methanophagales Methanofastidiosales Methanocellales RZN47407.1 GCA 004212155 DUF2124 domain-containing protein archaeon (Nuwarchaeales) Methanopyrales Methanomicrobiales Methanoflorentaceae OKY78477.1 GCA 001914405 hypothetical protein BTN85 0968 Candidatus Methanohalarchaeum thermophilum Verstraetearchaeota Nezhaarchaeota Hadesarchaea GCA 003935005RSFX01000018.1 66682286871910 66 GCA 003935005 1 ID 10 66 partial 00 Archaeoglobi archaeon GCA 002495315DAEN01000070.1 33181366987 3 GCA 002495315 1 ID 87 3 partial 00 Thaumarchaeota archaeon UBA141 Bacteria
Tree scale: 0.1 Supplementary Figure 18. ML phylogeny of methanogenesis marker m21. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanosarcinales Methanococcales Methanobacteriales RZN48586.1 GCA 004212155 DUF2098 domain-containing protein archaeon (Nuwarchaeales) Methanopyrales Methanosarcinales ADI74398.1 GCA 000196655 Protein of unknown function DUF2098 Methanohalobium evestigatum Z-7303 GCA 003555325PWGQ01000101.1 17113851169919 17 GCA 003555325 1 ID 19 17 partial 00 Methanosarcinaceae archaeon Methanosarcinales Methanomassiliicoccales Methanosarcinales GCA 002501695DANZ01000110.1 74604491547 7 GCA 002501695 -1 ID 47 7 partial 00 Methanolobus sp. UBA474 Methanocellales Methanosarcinales Methanoliparia Verstraetearchaeota RLF08184.1 GCA 003649565 DUF2098 domain-containing protein Thermoprotei archaeon TDA35904.1 GCA 004347915 DUF2098 domain-containing protein Candidatus Nezhaarchaeota archaeon WYZ-LMO7 RLE48835.1 GCA 003650625 hypothetical protein DRJ18 01100 Candidatus Verstraetearchaeota archaeon RLF19295.1 GCA 003650865 DUF2098 domain-containing protein Thermoprotei archaeon Methanomicrobiales Methanosarcinales Methanosarcinales (ANME-2) Methanoflorentaceae Methanobacteriales
Tree scale: 0.1 Supplementary Figure 19. ML phylogeny of methanogenesis marker m22. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanobacteriales Methanococcales Methanophagales RZN50468.1 GCA 004212155 HAD family hydrolase archaeon (Nuwarchaeales) Methanofastidiosales Verstraetearchaeota TDQ68713.1 GCA 004363215 Cu+-exporting ATPase Methanimicrococcus blatticola WP 042687646.1 GCF 000711905 HAD-IC family P-type ATPase Methermicoccus shengliensis Methanoliparia Methanosarcinales Methanosarcinales Methanoflorentaceae Methanosarcinales (ANME-2) Methanocellales Methanosarcinales Methanomicrobiales Methanosarcinales
Tree scale: 0.1 Supplementary Figure 20. ML phylogeny of methanogenesis marker m23. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanococcales Methanopyrales Methanobacteriales Methanosarcinales Methanosarcinales (ANME-2) Methanosarcinales Methanophagales WP 052353323.1 GCF 000711905 DUF2111 domain-containing protein Methermicoccus shengliensis Methanomicrobiales GCA 003170935PMYA01000025.1 313031704121 3 GCA 003170935 1 ID 121 3 partial 00 Euryarchaeota archaeon Methanocellales TFH38679.1 GCA 004526155 DUF2111 domain-containing protein partial ANME-2 cluster archaeon GCA 002500605DLRR01000024.1 4421445371 4 GCA 002500605 1 ID 1 4 partial 00 Nitrospinaceae bacterium UBA7883 GCA 003935005RSFX01000001.1 3102903192907801 310 GCA 003935005 1 ID 1 310 partial 00 Archaeoglobi archaeon GCA 003935005RSFX01000001.1 3122914712918601 312 GCA 003935005 1 ID 1 312 partial 00 Archaeoglobi archaeon Methanosarcinales RZN47597.1 GCA 004212155 DUF2111 domain-containing protein archaeon (Nuwarchaeales) Methanomassiliicoccales
Tree scale: 0.1 Supplementary Figure 21. ML phylogeny of methanogenesis marker m24. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanococcales Methanobacteriales WP 042687262.1 GCF 000711905 methanogenesis marker 9 domain-containing protein Methermicoccus shengliensis (Methanosarcinales) TFF84037.1 GCA 004524155 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon TFG14410.1 GCA 004524725 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon TKJ20073.1 GCA 005223125 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon Loki b32 TET01925.1 GCA 004375715 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon TKJ23481.1 GCA 005222975 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon Loki b31 KKK42076.1 GCA 000986845 hypothetical protein Lokiarch 37770 Lokiarchaeum sp. GC14 75 KKK43695.1 GCA 000986845 hypothetical protein Lokiarch 24820 Lokiarchaeum sp. GC14 75 Lokiarchaeota TFG02024.1 GCA 004524385 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon TFG18967.1 GCA 004524535 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon TFF93567.1 GCA 004524325 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon TFG25850.1 GCA 004524515 hypothetical protein EU532 11230 Candidatus Lokiarchaeota archaeon TFF88048.1 GCA 004524185 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon TFF86019.1 GCA 004524635 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon TFF85242.1 GCA 004524075 methanogenesis marker 9 domain-containing protein Candidatus Lokiarchaeota archaeon TFG18661.1 GCA 004524545 hypothetical protein EU530 08585 Candidatus Lokiarchaeota archaeon OYT43351.1 GCA 002254685 methanogenesis marker 9 domain-containing protein Candidatus Aenigmarchaeota archaeon ex4484 56 (Aenigmaarchaeota) RLG38532.1 GCA 003661195 hypothetical protein DRN79 01465 Methanosarcinales archaeon (Methanosarcinales) GCA 005191425SUPR01000042.1 151771118190121 15 GCA 005191425 1 ID 121 15 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB B (Helarchaeota) RZN65025.1 GCA 004212075 hypothetical protein EF806 02995 Candidatus Methanoliparum thermophilum (Methanoliparia) GCA 005191415SUPS01000066.1 625883055206 6 GCA 005191415 -1 ID 206 6 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A (Helarchaeota) Methanofastidiosa Methanoflorentaceae Methanosarcinales GCA 003935005RSFX01000011.1 5958079591973 59 GCA 003935005 -1 ID 3 59 partial 00 Archaeoglobi archaeon (Archaeoglobales) GCA 002011165MTMI01000021.1 33270152812111 33 GCA 002011165 1 ID 11 33 partial 00 Euryarchaeota archaeon JdFR-21 TDQ68252.1 GCA 004363215 TIM-barrel protein Methanimicrococcus blatticola (Methanosarcinales) Methanomicrobiales Methanocellales
Tree scale: 0.1 Supplementary Figure 22. ML phylogeny of methanogenesis marker m25. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanococcales Methanopyrales Methanobacteriales Thorarchaeota RLE49395.1 GCA 003649085 methanogenesis marker 14 protein Candidatus Verstraetearchaeota archaeon (Verstraetearchaeota) Nezhaarchaeota Bathyarchaeota TDA29431.1 GCA 004347865 methanogenesis marker 14 protein Archaeoglobi archaeon (Archaeoglobales) Methanosarcinales Methanomicrobiales Methanocellales Methanoliparia Methanophagales GCA 002495885DAHG01000071.1 74590186033445 74 GCA 002495885 -1 ID 45 74 partial 00 Methanocellaceae archaeon UBA148 (Methanocellales) TDQ70240.1 GCA 004363215 putative methanogenesis marker protein 14 Methanimicrococcus blatticola (Methanosarcinales)
Tree scale: 0.1 Supplementary Figure 23. ML phylogeny of methanogenesis marker m26. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Hydrothermarchaeota Methanococcales Methanobacteriales Methanomicrobiales Methanosarcinales Methanosarcinales GCA 002495885DAHG01000060.1 2710167511 2 GCA 002495885 1 ID 11 2 partial 00 Methanocellaceae archaeon UBA148 Methanosarcinales Syntrophoarchaeales Methanoliparia Methanophagales GCA 002011165MTMI01000021.1 41663257111 4 GCA 002011165 -1 ID 11 4 partial 00 Euryarchaeota archaeon JdFR-21 Methanoflorentaceae Methanosarcinales Methanocellales
Tree scale: 0.1 Supplementary Figure 24. ML phylogeny of methanogenesis marker m32. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanopyrales PHP46238.1 GCA 002254825 methanogenesis marker radical SAM protein Methanosarcinales archaeon ex4572 44 Methanococcales Methanobacteriales Methanoliparia Methanosarcinales Methanomicrobiales Methanoflorentaceae
Tree scale: 0.1 Supplementary Figure 25. ML phylogeny of methanogenesis marker m33. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanobacteriales Methanopyrales Methanococcales GCA 003155735PMEE01000024.1 108182835555 10 GCA 003155735 1 ID 55 10 partial 01 Euryarchaeota archaeon Methanocellales Methanosarcinales Methanomicrobiales-Methanosarcinales(ANME-2)-Methanophagales
Methanoflorentaceae Methanosarcinales
Tree scale: 0.1 Supplementary Figure 26. ML phylogeny of methanogenesis marker m34. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanobacteriales Methanococcales Methanopyrales Methanomicrobiales Methanosarcinales Methanomicrobiales Methanosarcinales Methanosarcinales PPA78709.1 GCA 002926195 hypothetical protein C00003105 00875 ANME-2 cluster archaeon HR1 Methanoflorentaceae Methanosarcinales (ANME-2)
Tree scale: 0.1 Supplementary Figure 27. ML phylogeny of methanogenesis marker m35. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanobacteriales (incl. Bacteria and Methanoliparia) Methanococcales AEH07061.1 GCA 000179575 Protein of unknown function DUF2115 Methanothermococcus okinawensis IH1 Methanosarcinales ABE51518.1 GCA 000013725 protein of unknown function UPF0305 Methanococcoides burtonii DSM 6242 Methanosarcinales Methanosarcinales ACV62473.1 GCA 000024205 conserved hypothetical protein Desulfofarcimen acetoxidans DSM 771 GCA 002404215DHJG01000105.1 41787231198 4 GCA 002404215 1 ID 98 4 partial 00 Desulfosporosinus sp. UBA4726 AFV05303.1 GCA 000305815 UPF0305 protein Dehalobacter sp. CF Methanosarcinales PAV12017.1 GCA 002287235 hypothetical protein ASJ81 07985 Methanosarcina spelaei Methanomicrobiales, Methanobacteriales, Methanopyrales, Methanocellales
Tree scale: 0.1 Supplementary Figure 28. ML phylogeny of methanogenesis marker m36. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Persephonarchaea Methanosarcinales RLG51175.1 GCA 003661385 hypothetical protein DRN96 05970 Candidatus Korarchaeota archaeon Methanopyrales Methanosarcinales Methanococcales GCA 002496805DALO01000002.1 7820284621 7 GCA 002496805 1 ID 1 7 partial 00 Methanobacterium sp. UBA353 Methanobacteriales WP 141398935.1 GCF 002487355 DUF2119 domain-containing protein Candidatus Methanoperedens sp. BLZ2 Methanobacteriales RLF18525.1 GCA 003650865 DUF2119 domain-containing protein Thermoprotei archaeon (Nezhaarchaeota) RLI25222.1 GCA 003662455 DUF2119 domain-containing protein Candidatus Bathyarchaeota archaeon RLI28513.1 GCA 003662445 DUF2119 domain-containing protein Candidatus Bathyarchaeota archaeon RJX15580.1 GCA 003604315 DUF2119 domain-containing protein partial Candidatus Bathyarchaeota archaeon GCA 002011035MTLY01000003.1 3763257383262921 376 GCA 002011035 -1 ID 1 376 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 RLG91506.1 GCA 003661965 DUF2119 domain-containing protein Candidatus Bathyarchaeota archaeon RLI05554.1 GCA 003662145 DUF2119 domain-containing protein Candidatus Bathyarchaeota archaeon GCA 002011075MTMA01000002.1 2023988245513 20 GCA 002011075 1 ID 3 20 partial 00 Candidatus Geothermarchaeota archaeon JdFR-13 Methanosarcinales (ANME-2) Methanosarcinales Methanoliparia
Tree scale: 1 Supplementary Figure 29. ML phylogeny of methanogenesis marker m37. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanobacteriales
Methanococcales
Methanopyrales
Methanosarcinales
Methanosarcinales Methanomicrobiales (incl. Methanosarcinales)
Tree scale: 0.1 Supplementary Figure 30. ML phylogeny of methanogenesis marker m3. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
OIO22854.1 GCA 001871495 hypothetical protein AUJ65 05025 Candidatus Micrarchaeota archaeon CG1 02 51 15
GCA 002502855DAQK01000040.1 1328731 1 GCA 002502855 1 ID 31 1 partial 10 Methanobacterium sp. UBA279
OGH61666.1 GCA 001784175 tetrahydromethanopterin S-methyltransferase subunit A Candidatus Lindowbacteria bacterium RIFCSPLOWO2 12 FULL 62 27
GCA 003251955QKDV01000153.1 1134579 1 GCA 003251955 1 ID 79 1 partial 10 Methanospirillum hungatei
GCA 003141335PLLR01000046.1 1334476 1 GCA 003141335 1 ID 76 1 partial 10 Methanoregula sp.
GCA 002508495DANA01000068.1 107638797354 10 GCA 002508495 1 ID 54 10 partial 00 Methanoregula sp. UBA276
MAT66717.1 GCA 002699185GCA 003233235QILF01000088.1 tetrahydromethanopterin 24571656145 S-methyltransferase 2 GCA 003233235 subunit -1 A IDGammaproteobacteria 145 2 partial 00 Zetaproteobacteria bacterium bacterium ALP53678.1 GCA 001447805 tetrahydromethanopterin S-methyltransferase subunit A Candidatus Tenderia electrophaga HBP89241.1 GCA 003523945 TPA tetrahydromethanopterin S-methyltransferase subunit A partial Nitrospiraceae bacterium
GCA 003233235QILF01000020.1 13851154 1 GCA 003233235 -1 ID 154 1 partial 10 Zetaproteobacteria bacterium BAM06928.1 GCA 000284315 putative tetrahydromethanopterin S-methyltransferase subunit A Leptospirillum ferrooxidans C2-3 ODA43148.1 GCA 001707885 N5-methyltetrahydromethanopterincoenzyme M methyltransferase subunit DesulfosporosinusA sp. BG
GCA 003230455QIDZ01000412.1 1881212312 1 GCA 003230455 -1 ID 312 1 partial 00 Gemmatimonadetes bacterium
AAZ47017.1 GCA 000012425 Tetrahydromethanopterin S-methyltransferase subunit A Dechloromonas aromatica RCB
ODU25134.1 GCA 001725055 hypothetical protein ABS95 00905 Verrucomicrobia bacterium SCN 57-15
TCV86159.1 GCA 004343025 tetrahydromethanopterin S-methyltransferase subunit A Methylomonas methanica KLU62959.1 GCA 001029295 tetrahydromethanopterin PeptococcaceaeS-methyltransferaseA bacterium subunit CEB3
OJZ18020.1 GCA 001899775 tetrahydromethanopterin S-methyltransferase subunit A Thiobacillus sp. 65-29 GCA 003131315PKUV01000032.1 171703018217169 17 GCA 003131315 -1 ID 169 17 partial 00 Acidobacteriaceae bacterium
RJR47660.1 GCA 003599195 DUF4346 domain-containing protein Deltaproteobacteria bacterium GCA 003246435QKAH01000404.1 21591346331 2 GCA 003246435 1 ID 331 2 partial 00 Prolixibacteraceae bacterium
GCA 003232095QILR01000176.1 1517097177741 15 GCA 003232095 -1 ID 1 15 partial 01 Bacteroidetes bacterium
RTL37219.1 GCA 003963305 DUF4346 domain-containingOGR27191.1 GCA protein 001799355 Candidatus hypothetical Melainabacteria protein A2139 08590 bacteriumDesulfobacca sp. RBG 16 60 12 MAZ48973.1 GCA 002707495 tetrahydromethanopterin S-methyltransferase subunit A Halobacteriovoraceae bacterium
GCA 003233515QILV01000172.1 38952073271 3 GCA 003233515 1 ID 271 3 partial 00 Ignavibacteria bacterium
TAJ19938.1 GCA 004296805 DUF4346 domain-containing protein Dehalococcoidia bacterium VDK11152.1 GCA 900620265 conserved hypothetical protein Nitrosopumilaceae archaeon RME73711.1 GCA 003694875 DUF4346 domain-containing protein Planctomycetes bacterium OLD12692.1 GCA 001918745 hypothetical protein AUI97 06305 Crenarchaeota archaeon 13 1 40CM 3 52 17
WP 030241100.1 GCF 000719705 hypothetical protein Streptomyces sp. NRRL S-350 GBD86837.1 GCA 002898075 tetrahydromethanopterin S-methyltransferase subunitA bacterium BMS3Abin03 OLD11627.1 GCA 001918765 hypothetical protein AUI93 04255 Crenarchaeota archaeon 13 1 40CM 3 52 10 OGZ35285.1 GCA 001819555 hypothetical protein A2646 02100 Candidatus Portnoybacteria bacterium RIFCSPHIGHO2 02 FULL 39 12 ASQ98228.1 GCA 003595545 hypotheticalOLD09780.1 protein CGL27 GCA 001918735 39045 Streptomyces hypothetical protein sp. 11-1-2 AUI95 00105 Crenarchaeota archaeon 13 1 40CM 3 52 4
OLD13099.1 GCA 001918745 hypothetical protein AUI97 05110 Crenarchaeota archaeon 13 1 40CM 3 52 17 OHB02278.1 GCA 001825335 hypothetical protein A3A90 00550 Candidatus Zambryskibacteria bacterium RIFCSPLOWO2 01 FULL 35 19
OLD78459.1 GCA 001919675 hypothetical protein AUF62 02460 archaeon 13 1 20CM 52 20 PIU62390.1 GCA 002779595 hypothetical protein COS83 02540 archaeon CG07 land 8 20 14 0 80 38 8
TAK01019.1 GCA 004297395 DUF4346 domain-containingACO31863.1 GCA 000022565 protein mtrAChloroflexi family protein bacterium Acidobacterium capsulatum ATCC 51196
GCA 002505525DAVJ01000024.1 1093441078061 10 GCA 002505525 1 ID 61 10 partial 00 archaeon UBA431
ONI76182.1WP 050509719.1 GCA 001984155 GCF hypothetical000715745 hypotheticalprotein ALI144C protein 36525 Streptomyces Actinosynnema puniceus sp. ALI-1.44
RLI97995.1 GCA 003663225 hypothetical protein DRO99 01850 Candidatus Aenigmarchaeota archaeon
TFG80959.1 GCA 004525425 hypothetical protein E4H19 15205 partial Chromatiales bacterium WP 051209393.1 GCF 000423465 hypothetical protein Propionicicella superfundia WP 058042903.1 GCF 001445655 hypothetical protein Streptomyces sp. MBT76
PIN78610.1 GCA 002762855 hypothetical protein COV16 05790 Candidatus Woesearchaeota archaeon CG10 big fil rev 8 21 14 0 10 34 8
KKU02522.1 GCA 001001555 Thymidylate synthase Candidatus Amesbacteria bacterium GW2011 GWC2 45 19
OJW06296.1 GCA 001898225 hypothetical protein BGO39 26055 Chloroflexi bacterium 54-19 SDG18592.1 GCA 900102265PKP29307.1 tetrahydromethanopterin GCA 002842635 hypothetical S-methyltransferase protein CVU01 00595subunit Bacteroidetes A Chryseobacterium bacterium hungaricum HGW-Bacteroidetes-18 KHO46902.1 GCA 000806095 thymidylate synthase archaeon GW2011 AR4
PIY59819.1 GCA 002784405 hypothetical protein COY95 05055 Candidatus Woesearchaeota archaeon CG 4 10 14 0 8 um filter 47 5
ANH83119.1 GCA 001654455 hypothetical protein A8C56 20960 Niabella ginsenosidivorans TAL48374.1 GCA 004297575 DUF4346 domain-containing protein archaeon
OGC51241.1 GCA 001772665OGC82294.1 hypothetical protein GCA A2982001773455 04025 candidate hypothetical division WWE3protein bacterium A2V81 RIFCSPLOWO2 02035 Candidatus 01 FULL Abawacabacteria 39 13 bacterium RBG 16 42 10 PIV13822.1 GCA 002780595 hypothetical protein COS45 00855 Candidatus Huberiarchaeum crystalense HCU06949.1 GCA 003542655CRI67611.1 TPA GCA hypothetical 001499735 MmcEprotein fragment DIC42 05165 Thiocapsa partial sp. Holosporales KS1 bacterium PJC23322.1 GCA 002789015 hypothetical protein CO058 04120 candidate division WWE3 bacterium CG 4 9 14 0 2 um filter 35 11 PJC47544.1 GCA 002788555 hypothetical protein CO034 02115 partial Parcubacteria group bacterium CG 4 9 14 0 2 um filter 35 11 TAL57134.1 GCA 004299525 hypothetical protein EPN86 02290 Nanoarchaeota archaeon HCE54665.1 GCA 003516285 TPA hypothetical protein DER05 06510 Lutibacter sp.
PIS23461.1 GCA 002774285 hypothetical protein COT49 00100 partial candidate division WWE3 bacterium CG08 land 8 20 14 0 20 40 13 PJE69403.1 GCA 002793605 hypothetical protein COU98 02300 Candidatus Staskawiczbacteria bacterium CG10 big fil rev 8 21 14 0 10 38 10 ALI36089.1 GCA 000802205 tetrahydromethanopterin S-methyltransferase subunit A Candidatus Nitrocosmicus oleophilus RLE56455.1 GCA 003649225 hypothetical protein DRJ32 07915 partial Thermoprotei archaeon PIV45755.1 GCA 002780915GCA 001870125CP017922.1 hypothetical protein COS24 241922751232275608100585 Candidatus Nealsonbacteria 2419 GCA bacterium 001870125 CG02 land -1 8ID 20 1 14 2419 3 00 partial34 20 00 Candidatus Nitrosocosmicus exaquare
OGW03203.1 GCA 001804965 hypothetical protein A2889 05120 Nitrospinae bacterium RIFCSPLOWO2 01 FULL 39 10
OGG54286.1 GCA 001781055 hypothetical protein A3F84 06105 Candidatus Handelsmanbacteria bacterium RIFCSPLOWO2 12 FULL 64 10 RPJ31772.1 GCAVFJ15019.1 003820555 tetrahydromethanopterin GCA 900696045 Tetrahydromethanopterin S-methyltransferase subunit S-methyltransferase A Nitrosopumilales archaeonsubunit A Candidatus Nitrosocosmicus franklandus Bacteria RPJ52398.1 GCARPJ52509.1 003820275 GCA tetrahydromethanopterin 003820275 hypothetical S-methyltransferase protein EHJ95 03945 subunit Euryarchaeota A Euryarchaeota archaeon archaeon RPI85102.1 GCA 003856905 tetrahydromethanopterin S-methyltransferase subunit A Nitrosopumilales archaeon RMF28657.1 GCA 003695185GCA 002494895DADA01000078.1 tetrahydromethanopterin S-methyltransferase 106169664835 subunit 10 A GCA Thaumarchaeota 002494895 archaeon 1 ID 35 10 partial 00 Nitrososphaera sp. UBA210
GCA 002505485DAVG01000094.1 55182585944 5 GCA 002505485 -1 ID 44 5 partial 00 Methanosarcina sp. UBA5 PWU78689.1 GCA 003176995 tetrahydromethanopterin S-methyltransferase subunit A Thaumarchaeota archaeon AIC14620.1 GCARPJ26764.1 000698785 GCA putative 003820555 tetrahydromethanopterin tetrahydromethanopterin S-methyltransferase S-methyltransferase subunit A Nitrososphaera subunit A Nitrosopumilales viennensis EN76 archaeon GCA 003165235PLSV01000249.1GCA 004195335SDWK01000963.1 88503919593 8 GCA 2180872540 003165235 2 GCA-1 ID 00419533593 8 partial 100 ID Syntrophobacteraceae 540 2 partial 00 Shewanella bacterium sp. AIF83781.1 GCA 000730285 tetrahydromethanopterin S-methyltransferase subunit A Candidatus Nitrososphaera evergladensis SR1 AFU58749.1 GCA 000303155 putative tetrahydromethanopterin S-methyltransferase subunit A Candidatus Nitrososphaera gargensis Ga9.2
OLC36533.1 GCA 001917995ABK78054.1 tetrahydromethanopterin GCA 000200715GCA 002499525DAMC01000055.1 tetrahydromethanopterin S-methyltransferase subunit S-methyltransferase A 179198965682Thaumarchaeota subunit 17archaeon GCA A 002499525Cenarchaeum13 1 40CM 4 -138 symbiosum ID7 82 17 partial A 00 Nitrosopumilales archaeon UBA218 PIU52878.1 GCA 002779455OHD67920.1 hypothetical GCA 001829495 protein COS90 hypothetical 09160 proteinDeltaproteobacteria A2W19 06640 bacterium Spirochaetes CG07 bacterium land 8 20 RBG 14 0 1680 4960 2111 WP 051627662.1 GCF 000702565 MULTISPECIES DUF4346 domain-containing protein Bacillales WP 103287734.1OLE40838.1SHO43636.1 GCF GCA 002906215 001920395 GCA MULTISPECIES 900143675 tetrahydromethanopterin conserved tetrahydromethanopterin hypothetical S-methyltransferase protein S-methyltransferase Candidatus subunit A ThaumarchaeotaNitrosotalea subunit A sinensisCandidatus archaeon Nitrosocaldus 13 1 20CM 2 39 20
GCA 002381185DFOA01000011.1 2426688278602 24 GCA 002381185 -1 ID 2 24 partial 00 Firmicutes bacterium UBA3553 GCA 002494485DACA01000081.1 26182751876668 26 GCA 002494485 1 ID 68 26 partial 00 Nitrososphaerales archaeon UBA213 GCA 002396645DGYI01000037.1 78738177498952 78 GCA 002396645 1 ID 52 78 partial 00 Firmicutes bacterium UBA5010 PIV06505.1 GCA 002779905 hypothetical protein COS57 03070 Syntrophobacterales bacterium CG03 land 8 20 14 0 80 58 14 OLN30115.1 GCA 001936615 N5-methyltetrahydromethanopterincoenzyme M methyltransferase subunit A Desulfosporosinus sp. OL WPSMH72035.1 101477793.1CUR52839.1 CDI06674.1GCA GCFGCA 900177045 900167955GCA 001914355MRWN01000144.1 GCA900065925 Tetrahydromethanopterin 000723185tetrahydromethanopterin Tetrahydromethanopterin Tetrahydromethanopterin 38741341575 S-methyltransferase S-methyltransferase 3 S-methyltransferase GCA subunit23 001914355 kD subunit A 23 Candidatus kD -1 Nitrosotalea 23subunitID kD575 Nitrosotaleasubunit Candidatus3 partial sp. CS Candidatus 00 bavarica NitrosotaleaThaumarchaeota Nitrosotenuis devanaterra archaeon uzonensis BIN5 WP 042684064.1AJZ75992.1WP GCF GCA100182927.1 000685395 000955905 GCF tetrahydromethanopterin tetrahydromethanopterin 002787055 hypothetical S-methyltransferase S-methyltransferase protein Candidatus subunit subunit Nitrosotenuis A ACandidatus Candidatus aquarius Nitrosotenuis Nitrosotenuis chungbukensis cloacae
RPJ71132.1 GCA 003820255 tetrahydromethanopterin S-methyltransferase subunit A Alphaproteobacteria bacterium KRT60962.1GCA 003229255QIDA01000012.1 GCA 001443365 tetrahydromethanopterin 41523200512 4 GCA S-methyltransferase 003229255 -1 ID subunit 12 4 partial A Thaumarchaeota 00 Nitrosopumilaceae archaeon archaeon CSP1-1 PIU29323.1 GCA 002779205 tetrahydromethanopterinOHD66016.1 GCAS-methyltransferase 001829455 hypothetical subunit A protein Actinobacteria A2176 09625 bacterium Spirochaetes CG08 land bacterium 8 20 14 RBG0 20 1335 519 14 RDJ34478.1PIW33301.1 GCA 003352285 GCA tetrahydromethanopterin 002781805 tetrahydromethanopterin S-methyltransferase S-methyltransferase subunit A Crenarchaeota subunit A Nitrosopumilales archaeon archaeon CG15 BIG FIL POST REV 8 21 14 020 37 12 Bacteria GCAWP 000230485JH165432.1 067960032.1 GCF 001541925 656046080597 hypothetical 6 GCA protein 000230485 Nitrosopumilus 1 ID 597 6 sp. partial Nsub 00 uncultured marine crenarchaeote 'Gulf of Maine' KRO29291.1 GCA 001437625 tetrahydromethanopterin S-methyltransferase subunit A partial Nitrosopumilus sp. BACL13 MAG-121220-bin23 GCA 000230485JH165510.1 835871359180949 83 GCA 000230485 -1 ID 949 83 partial 00 uncultured marine crenarchaeote 'Gulf of Maine' RZD38340.1 GCA 004195415 tetrahydromethanopterin S-methyltransferase subunit A Thaumarchaeota archaeon RKX79604.1 GCA 003645645 hypothetical protein DRP87 02495 Spirochaetes bacterium PHY04136.1 GCA 002737455 tetrahydromethanopterin S-methyltransferase subunit A Thaumarchaeota archaeon TFG61343.1 GCA 004525155 tetrahydromethanopterin S-methyltransferase subunit A Spirochaetales bacterium ARS65264.1 GCA 002156965 Tetrahydromethanopterin S-methyltransferase subunit A 1 Candidatus Nitrosomarinus catalina RCL32584.1 GCA 003331425 tetrahydromethanopterin S-methyltransferase subunit A Nitrosopumilus sp. RKX73834.1 GCA 003645645 tetrahydromethanopterin S-methyltransferase subunit A partial Spirochaetes bacterium GCA 000230485AGBE01000115.1 1331175 1 GCA 000230485 1 ID 75 1 partial 10 uncultured marine crenarchaeote 'Gulf of Maine' GCA 000230485JH165307.1 332291223388210 33 GCA 000230485 -1 ID 210 33 partial 00 uncultured marine crenarchaeote 'Gulf of Maine' EGG41671.1 GCA 000204585 tetrahydromethanopterin S-methyltransferase 23 kD subunit Candidatus Nitrosarchaeum limnium SFB1 KPJ84910.1 GCA 001302885 hypothetical protein AMS17 15260 partial Spirochaetes bacterium DG 61 TAK17675.1 GCA 004297665 tetrahydromethanopterin S-methyltransferase subunit A Nitrosarchaeum sp. GBL41392.1 GCA 003569705 putative methyltransferase Mtx subunit A Nitrosarchaeum sp. ACL17842.1 GCA 000021965 Tetrahydromethanopterin S-methyltransferase subunit A domain protein Methanosphaerula palustris E1-9c EGP94588.1 GCA 000220175 Tetrahydromethanopterin S-methyltransferase 23 kD subunit Nitrosarchaeum koreense MY1 PIN96969.1 GCA 002763195 tetrahydromethanopterin S-methyltransferase subunit A Nitrosopumilus sp. CG10 big fil rev 8 21 14 0 10 33 7 GCA 004332335SISS01000008.1 18857293695 18 GCA 004332335 1 ID 5 18 partial 00 Methanoregulaceae archaeon UXB-2016 PJC47351.1 GCA 002788555 hypothetical protein CO034PJB98389.1 02795 Parcubacteria GCA 002789395 group bacteriumtetrahydromethanopterin CG 4 9 14 0 2 um S-methyltransferase filter 35 11 subunit A Nitrosopumilales archaeon CG 4 9 14 0 8 um filter 34 10 GCAOIP75376.1PIS17251.1 002434805DJKW01000009.1 GCA GCA 001873425 002774145 hypothetical hypothetical 5658827596695 protein protein 56 AUK07 COT59 PHY08391.1GCA 00243480501645 01620 Parcubacteria GCACandidatus -1 002737445 ID 5 56 Nealsonbacteria grouppartial tetrahydromethanopterin bacterium00 Patescibacteria bacterium CG2 30 36CG09group 21 S-methyltransferase landbacterium 8 20 14UBA6532 0 10 42 subunit 14 A Nitrosarchaeum sp. PKL63866.1 GCA 002839605 hypotheticalPKG32062.1 protein CVV32 GCA 11665 002835825 Methanomicrobiales hypothetical protein archaeon CW742 HGW-Methanomicrobiales-3 10100 Methanoregula sp. Bacteria Methanosarcinales GCAGCA 001510275LFEY01000014.1 001543015LFLC01000057.1 73591925966814 12910124010171660 73 GCA 129001510275 GCA 001543015 -1 ID 14 73 -1 partial ID 60 12900 Thaumarchaeota partial 00 Nitrosopumilus archaeon sp. casp-thauma3 LS AOA GCA 002010075MTMG01000019.1 2821532221227 28 GCA 002010075 1 ID 7 28 partial 00 Methanomicrobia archaeon JdFR-19 OPX64807.1 GCA 002067035 Tetrahydromethanopterin S-methyltransferase subunit A 1 Methanoregula sp. PtaB.Bin085 WP 042687807.1 GCF 000711905 tetrahydromethanopterinGCA 000484975AXWL01000003.1 S-methyltransferase subunit 7058050585263 A Methermicoccus 70 shengliensisGCA 000484975 1 ID 3 70 partial 00 Thaumarchaeota archaeon SCGC AAA282-K18 RKY01481.1 GCA 003644145 tetrahydromethanopterin S-methyltransferase subunit A Spirochaetes bacterium MethanosarcinalesBAI60750.1 GCA 000011005 putative tetrahydromethanopterin S-methyltransferase subunit A Methanocella paludicola SANAE AFC99718.1OPY29598.1 GCA 000251105 GCA 002067315Tetrahydromethanopterin Tetrahydromethanopterin S-methyltransferase S-methyltransferase subunit A Methanocella subunit A 1 conradii Methanocella HZ254 sp. PtaU1.Bin125 OFW56347.1 GCA 001768645 hypothetical protein A2Y75 03870 Actinobacteria bacterium RBG 13 55 18
RJP32791.1 GCA 003598015 tetrahydromethanopterin S-methyltransferase subunit A Actinobacteria bacterium WP 042687028.1 GCF 000711905 tetrahydromethanopterin S-methyltransferase subunit A Methermicoccus shengliensis TDA30829.1 GCA 004347865 tetrahydromethanopterin S-methyltransferase subunit A Archaeoglobi archaeon MethanosarcinalesMethanocellales GCA 003157385PMJJ01000039.1 161502115746118 16 GCA 003157385 -1 ID 118 16 partial 00 Actinobacteria bacterium GCA 002010075MTMG01000016.1 1141009271016493 114 GCA 002010075 1 ID 3 114 partial 00 Methanomicrobia archaeon JdFR-19 GCA 003247995QJYP01000205.1 316012335109 3 GCA 003247995 1 ID 109 3 partial 00 Phycisphaerales bacterium Methanomicrobiales RKY30468.1RKY30469.1OGV71316.1 GCA GCA 003644385 001803235 hypothetical hypothetical protein protein DRP74 A3K18 06995 22965 Candidatus Lentisphaerae Omnitrophica bacterium bacterium RIFOXYA12 64 32 GCA 002496325DAJM01000055.1 1239931010000523 123 GCA 002496325 -1 ID 23 123 partial 00 Candidatus Methanoperedens sp. UBA453 KYK25512.1 GCA 001595885 hypothetical proteinAYK23 03535 Euryarchaeota archaeon SG8-5 Methanobacteriales
GCA 002501765DAOG01000062.1 529723661129 5 GCA 002501765 1 ID 129 5 partial 00 Methanosaeta sp. UBA204
GCA 002499085DAKD01000030.1GCA 002499085 39479054848011 39 39 partial GCA 1 00 ID 11 Methanomassiliicoccales archaeon UBA280
GCA 002496385DAJR01000052.1 117355793933 GCA 002496385 11 1 ID 33 partial 11 00 Methanomassiliicoccales archaeon UBA147 RZN35134.1GCA GCA 002506015DAWR01000140.1 004211975 tetrahydromethanopterin 74604528787 S-methyltransferase 7 GCA 002506015 subunit A Methanosarcinales -1 ID 87 7 partial archaeon 00 Methanosarcinales archaeon UBA261Methanococcales
PXF57445.1 GCA 003194445 tetrahydromethanopterin S-methyltransferase subunit A ANME-2 cluster archaeon GCA 002503595DASC01000032.1RJS70772.1 GCA 51411209449 003601535 5 GCA tetrahydromethanopterin 002503595 -1 ID 49 5 partial 00 S-methyltransferase Methanosarcinales archaeon subunit UBA203 A ANME-2 cluster archaeon GCA 003553085PUPH01000167.1RLG28827.1 GCA 1365355003661105 1 GCA tetrahydromethanopterin 003553085 1 ID 55 1 partial 10 S-methyltransferase Thermoplasmata archaeon subunit A Methanosarcinales archaeon
SPP99664.1 GCA 900302705 Tetrahydromethanopterin S-methyltransferase subunit A domain protein Candidatus Sulfobium mesophilum GCA 003551675PUNG01000012.1 14111141169224 14 GCA 003551675 -1 ID 24 14 partial 00 Thermoplasmata archaeon TKJ45349.1 GCA 005223085 hypothetical protein CEE35 04270 Candidatus Aerophobetes bacterium Ae b3b Methanosarcinales GCA 003555395PWHU01000050.1 32308288660 3 GCA 003555395 1 ID 60 3 partial 00 Thermoplasmata archaeon Methanobacteriales TKJ47389.1 GCA 005223095 hypothetical protein CEE34 04130 Candidatus Aerophobetes bacterium Ae b3a GCA 003554965PWHR01000041.1 41413354192222 41 GCA 003554965 -1 ID 22 41 partial 00 Thermoplasmata archaeon Methanopyrales GCA 003162155PMMQ01000228.1 419872541172 4 GCA 003162155 -1 ID 172 4 partial 00 Nitrospiraceae bacterium GCA 003560595PWKY01000022.1 18171651772856 18 GCA 003560595 -1 ID 56 18 partial 00 Thermoplasmata archaeon GCA 002478145DLMI01000185.1 272845229147246 27 GCA 002478145 -1 ID 246 27 partial 00 Acidobacteria bacterium UBA7540 GCA 003559355PWLO01000038.1 141398514554102 14 GCA 003559355 -1 ID 102 14 partial 00 Thermoplasmata archaeon Methanoflorentaceae GCA 002329605DCTN01000006.1 55395034020778 55 GCA 002329605 -1 ID 78 55 partial 00 bacterium UBP3 UBA1439 RLE49399.1 GCA 003649085 tetrahydromethanopterin S-methyltransferase subunit A Candidatus Verstraetearchaeota archaeon PKO21921.1 GCA 002842085 hypothetical protein CVU38 12125 Chloroflexi bacterium HGW-Chloroflexi-1
PIU85594.1 GCA 002779785 hypotheticalOIP26554.1 proteinGCA 001872925 COS67 07055 hypothetical partial Deltaproteobacteriaprotein AUK39 04565 bacterium Dehalococcoidia CG06 land bacterium 8 20 14 CG2 3 00 30 44 46 19 19 Methanophagales ThorarchaeotaNezhaarchaeota Bathyarchaeota PIU67828.1 GCA 002779575 hypothetical proteinOGN93687.1 COS84 GCA03225 001795015 partial Armatimonadetes hypothetical protein bacterium A2Z75 00010CG07 Chloroflexiland 8 20 14bacterium 0 80 40 RBG 9 13 50 10 GCA 001315965BBBH01000300.1 2249629300 2 GCA 001315965 1 ID 300 2 partial 01 Methanoculleus chikugoensis JCM 10825
OGN91543.1 GCA 001795015 hypothetical protein A2Z75 07730 Chloroflexi bacterium RBG 13 50 10 Methanoliparia GCA 002011475MTNP01000049.1 4343240438663 43 GCA 002011475 -1 ID 3 43 partial 00 Dehalococcoides sp. JdFR-54 OIP27970.1 GCA 001873005 hypothetical protein AUK00 00755 Dehalococcoidia bacterium CG2 30 46 9 OGO02967.1 GCA 001796595 hypothetical protein A2Y91 06175 Chloroflexi bacterium RBG 13 54 8
GCA 002322525DCOU01000130.1 63510414236 6 GCA 002322525 1 ID 36 6 partial 00 Candidatus Omnitrophica bacterium UBA1562 PIZ14793.1 GCA 002785465 hypothetical protein COY52 11030 Candidatus Desantisbacteria bacterium CG 4 10 14 0 8 um filter 48 22
OGP93573.1 GCA 001797935 hypothetical proteinTDA31159.1 A2Z19 GCA 00830 004347835 Deltaproteobacteria hypothetical protein bacterium DSO03 RBG 05465 16 Hadesarchaea 54 18 archaeon GCA 003563775PWTX01000134.1 417592544187 4 GCA 003563775 1 ID 187 4 partial 00 Dehalococcoidia bacterium OGP81039.1OGP53411.1 GCA 001797905 GCA 001797745 hypothetical hypothetical protein A2Z08protein 01475A2Y65 Deltaproteobacteria 06835 Deltaproteobacteria bacterium bacterium RBG 16 RBG 54 11 13 52 11
TFG56181.1 GCA 004525545 hypothetical protein E4H30 05130 Methanomassiliicoccus sp.
RLA82146.1 GCA 003646585TET11700.1 hypothetical GCA 004376265 protein DRG31 4Fe-4S 07820 dicluster Deltaproteobacteria domain-containing bacterium protein Candidatus Thorarchaeota archaeon OFV68120.1 GCA 001766815 tetrahydromethanopterin S-methyltransferase subunit A Candidatus Syntrophoarchaeum caldarius OFV66443.1 GCA 001766825 tetrahydromethanopterin S-methyltransferase subunit A Candidatus Syntrophoarchaeum butanivorans
RLE55459.1 GCA 003649205 hypothetical protein DRJ40 08375 Thermoprotei archaeon
RLE56738.1 GCA 003649205 hypothetical protein DRJ40 04895 Thermoprotei archaeon RLE56693.1 GCA 003649205 hypothetical protein DRJ40 04630 Thermoprotei archaeon
GCA 002506985DAYS01000065.1 29631514116 2 GCA 002506985 1 ID 116 2 partial 00 Methanomassiliicoccaceae archaeon UBA248 GCA 003153895PMBU01000145.1 88730962395 8 GCA 003153895 -1 ID 95 8 partial 00 Methanomassiliicoccaceae archaeon GCA 003135935PNBI01000117.1 42946373142 4 GCA 003135935 1 ID 42 4 partial 00 Methanomassiliicoccaceae archaeon
RLF28587.1 GCA 003649715 hypothetical protein DRN05 03670 Thermoplasmata archaeon
OPX62778.1 GCA 002067045 Tetrahydromethanopterin S-methyltransferase subunit A 1 Methanomassiliicoccales archaeonRLJ02288.1 PtaB.Bin134 GCA 003663355 hypothetical protein DRP10 01770 Candidatus Aenigmarchaeota archaeon GCA 002497075DAML01000025.1 28255652633210 28 GCA 002497075 -1 ID 10 28 partial 00 Methanomassiliicoccaceae archaeon UBA472 OPY31706.1 GCA 002067865 Tetrahydromethanopterin S-methyltransferase subunit A 1 Methanomassiliicoccales archaeon PtaU1.Bin124
GCA 003557905PWNH01000134.1 41497226475 4 GCA 003557905 -1 ID 75 4 partial 00RLI99193.1 Methanomassiliicoccaceae GCA 003663295 hypothetical protein archaeon DRP06 04060 partial Candidatus Aenigmarchaeota archaeon OKY74304.1 GCA 001914235 hypothetical protein BM485 14375 Desulfobulbaceae bacterium DB1 PNX46947.1 GCA 002900535 hypothetical protein BV457 06660 Thermoplasmata archaeon M9B1D
KYK23934.1 GCA 001595945 hypothetical protein AYK25 00785 Thermoplasmatales archaeon SM1-50 KYK29410.1 GCA 001595805 hypothetical proteinKYK20153.1 AYK20 GCA 00159586505535 Thermoplasmatales hypothetical protein AYK21 archaeon 01665 Thermoplasmatales SG8-52-1 archaeon SG8-52-2
KYK30309.1 GCA 001595915 hypothetical protein AYK22 04185 Thermoplasmatales archaeon SG8-52-3 GCA 002498285DAGU01000102.1 97460823911 9 GCA 002498285 -1 ID 11 9 partial 00 Methanomassiliicoccus sp. UBA386
RLF53607.1 GCA 003651045 tetrahydromethanopterin S-methyltransferase subunit A Thermoplasmata archaeon
OIP49823.1 GCA 001873115 hypothetical protein AUK28 02775 Desulfobacterales bacterium CG2 30 60 27 OYT28094.1 GCA 002254885 hypothetical protein B6U98 05630 Thermoplasmatales archaeon ex4572 165 GCA 003560875PWJQ01000035.1 108234900416 10 GCA 003560875 1 ID 16 10 partial 00 Methanomassiliicoccaceae archaeon GCA 003555025PWHV01000018.1 25216262239612 25 GCA 003555025 1 ID 12 25 partial 00 MethanomassiliicoccaceaeDAC72956.1 GCA 003942085 TPA archaeon tetrahydromethanopterin S-methyltransferase subunit A Thermoplasmata archaeon
GCA 003557905PWNH01000132.1 118637939849 11 GCA 003557905 1 ID 49 11 partial 00 Methanomassiliicoccaceae archaeon
GCA 003557145PWPL01000061.1 12134681572086 12 GCA 003557145 -1 ID 86 12 partial 00 Candidatus Staskawiczbacteria bacterium
GCA 002506745DAYE01000087.1 19172891785877 19 GCA 002506745 -1 ID 77 19 partial 00 Euryarchaeota archaeon UBA33
GCA 002505885DAWE01000139.1 11116091217861 11 GCA 002505885 -1 ID 61 11 partial 00 Euryarchaeota archaeon UBA211
GCA 003555025PWHV01000035.1 88818828264019 88 GCA 003555025 1 ID 19 88 partial 00 Methanomassiliicoccaceae archaeon
EMR73621.1 000349645 GCA tetrahydromethanopterin S-methyltransferase subunit A Thermoplasmatales archaeon SCGC AB-539-N05
PJB21823.1 GCA 002790055 tetrahydromethanopterin S-methyltransferase subunit A Euryarchaeota archaeon CG 4 9 14 3 um filter 38 12
GCA 002502685DAQA01000029.1 25308193138517 25 GCA 002502685 1 ID 17 25 partial 00 Euryarchaeota archaeon UBA202
PYL08273.1 GCA 003219695 hypothetical protein DME33 07770 partial Verrucomicrobia bacterium
GCA 003555225PWGB01000052.1 41517286628 4 GCA 003555225 1 ID 28 4 partial 00 Candidatus Woesearchaeota archaeon
Tree scale: 1 Supplementary Figure 31. ML phylogeny of MtrA. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
GCA 002011125MTMF01000003.1 4539087400018 45 GCA 002011125 -1 ID 8 45 partial 00 Candidatus Hydrothermarchaeota archaeon JdFR-18
GCA 002327925DCVA01000048.1 1111308122105 11 GCA 002327925 -1 ID 5 11 partial 00Anaerolineales bacterium UBA2200
TES94061.1 GCA 004375715 tetrahydromethanopterin S-methyltransferase subunit H Candidatus Lokiarchaeota archaeon
WP 161955049.1 GCF 003116935 tetrahydromethanopterin S-methyltransferase subunit H Moorella sp. Hama-1
OLS14135.1 GCA 001940655 Tetrahydromethanopterin S-methyltransferase Candidatus Lokiarchaeota archaeon CR 4
TAK36950.1TAK33251.1 GCA 004297765 tetrahydromethanopterin S-methyltransferase subunit H partial Chloroflexi bacterium
OGD46203.1 GCA 001775995 hypothetical protein A3K7001995 Candidatus Bathyarchaeotaarchaeon RBG 4816 13 001775995 hypothetical protein OGD46203.1 GCA
SMB94957.1 GCA 900176005 tetrahydromethanopterin S-methyltransferase subunit H Thermanaeromonas toyohensis ToBE
GCA 003555305PWGP01000185.1 532434172150 5 GCA 003555305 1 ID 150 5 partial 00 Syntrophomonadaceae bacterium
GCA 005191415SUPS01000143.1 1186469557310 11 GCA 005191415 1 ID 310 11 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A GCA 005191425SUPR01000071.1 767007641153 7 GCA 005191425 -1 ID 153 7 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB B GCA 002426495DIQC01000098.1 66111703797 6 GCA 002426495 1 ID 97 6 partial 00 Thermacetogenium sp. UBA5472 TAK35050.1 GCA 004297765 tetrahydromethanopterin S-methyltransferase subunit H Chloroflexi bacterium
RZN69450.1 GCA 004212085 tetrahydromethanopterin S-methyltransferase subunit H Candidatus Methanolliviera hydrocarbonicum
GCA 003249435QKIX01000352.1 13398227 1 GCA 003249435 -1 ID 227 1 partial 10 Bacteroidetes bacterium
WP 084413314.1 GCF 000429345 hypothetical protein Desulfovirgula thermocuniculi RLG69109.1 GCA 003661625 hypothetical protein DRN93 01005 archaeonGCA 003935005RSFX01000003.1 23206982160915 23 GCA 003935005 1 ID 15 23 partial 00 Archaeoglobi archaeon
RLE69599.1 GCA 003650705 hypothetical protein DRJ34 00385 partial Thermoprotei archaeon GCA 002011165MTMI01000011.1 2725072259712 27 GCA 002011165 1 ID 2 27 partial 00 Euryarchaeota archaeon JdFR-21
RLE94042.1 GCA 003649445 hypothetical protein DRN04 04970 Thermoprotei archaeon
RLE87926.1 GCA 003650785 hypothetical protein DRJ49 05755 Thermoprotei archaeon
RLI20696.1 GCA 003662385 hypothetical protein DRO54 05620 Candidatus Bathyarchaeota archaeon SHF10940.1 GCA 900129135 tetrahydromethanopterin S-methyltransferaseRLF25258.1 GCA subunit 003650925 H Lactonifactorhypothetical protein longoviformis DRN15 00980 DSM Thermoprotei 17459 archaeon
GBF33663.1 GCA 002933875 N5-methyltetrahydromethanopterincoenzyme M methyltransferase subunit H Desulfocucumis palustris
TFG08386.1 GCA 004524425 hypothetical protein EU539 02465 Candidatus Lokiarchaeota archaeon
Lokiarchaeota
OYT25397.1 GCA 002254895 hypothetical protein B6V02 03820 Thermoprotei archaeon ex4572 64 GCA 002634385NSJL01000015.1 30282222912114 30 GCA 002634385 1 ID 14 30 partial 00 Nitrospira sp. HBY98674.1 GCA 003520455 TPA hypothetical protein DEP84 32795 Chloroflexi bacterium RLG69059.1 GCA 003661625 hypothetical protein DRN93 01180 archaeon RMF81116.1 GCA 003695675 hypothetical protein D6737 05950 Chloroflexi bacterium HBY93021.1 GCA 003520455 TPA tetrahydromethanopterin S-methyltransferase subunit H Chloroflexi bacterium LokiarchaeotaBacteria
GCA 002010065MTMD01000168.1 523283257145 5 GCA 002010065 1 ID 145 5 partial 00 Candidatus HydrothermarchaeotaRNC28546.1 archaeon JdFR-16 GCA 001515265 hypothetical protein GCAAWM53 005191415SUPS01000045.101380 Candidatus Dichloromethanomonas elyunquensis 161341414286159 16 GCA 005191415 -1 ID 159 16 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A WP 157677303.1 GCF 002224645 hypothetical protein Dehalobacterium formicoaceticum KUO92439.1GCA GCA001315925BBBF01000001.1 001516585 hypothetical protein11967952687041 AT710 03360 119 Thermocladium GCA 001315925 sp. 1ECH ID 1 B 119 partial 00 Thermocladium modestius JCM 10088 Bacteria GCA 005191425SUPR01000176.1 21143203088 2 GCA 005191425 1 ID 88 2 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB B
GCA 002011125MTMF01000003.1 4337057380048 43 GCA 002011125 1 ID 8 43 partial 00 Candidatus Hydrothermarchaeota archaeon JdFR-18 RMF89200.1 GCA 003695745 tetrahydromethanopterin S-methyltransferase subunit H Euryarchaeota archaeon GCA 003935005RSFX01000006.1TFF86231.1 52465339118TFF88465.1 GCA 004524165 5 GCA GCA 003935005 004524205 tetrahydromethanopterin 1 ID 18 tetrahydromethanopterin5 partial 00 Archaeoglobi S-methyltransferase archaeon S-methyltransferase Candidatus Lokiarchaeota Candidatus Lokiarchaeota archaeon archaeon GCA 004366975SETC01000012.1 5942252431934 59 GCA 004366975 1 ID 4 59 partial 00 Archaeoglobaceae archaeon GCA 002010215MTMY01000001.1 54029498512 5 GCA 002010215 1 ID 12 5 partialArchaeoglobales 00 Archaeoglobus sp. JdFR-37 RLG49404.1 GCA 003661385 hypothetical protein DRN96 09665 Candidatus Korarchaeota archaeon GCA 003935005RSFX01000006.1ADC65893.1 GCA 000025505 14135931452818 Tetrahydromethanopterin 14 GCA 003935005 S-methyltransferase1 ID 18 14 partial 00 Archaeoglobi Ferroglobus archaeon placidus DSM 10642 TET56114.1 GCA 004376645 hypothetical protein E3J51 05500 Candidatus Bathyarchaeota archaeon KPV62155.1 GCA 001399805 Tetrahydromethanopterin S-methyltransferase subunit H Candidatus Bathyarchaeota archaeon BA1
RLI20452.1 GCA 003662385 hypothetical protein DRO54 06240 Candidatus Bathyarchaeota archaeon Bathyarchaeota Methanoflorentaceae ACB06956.1 GCA 000019605 tetrahydromethanopterin S-methyltransferase MtrH subunit Candidatus Korarchaeum cryptofilum OPF8 Methanomicrobiales RDD53303.1 GCA 003344655 hypothetical protein BA066 05110 Candidatus Korarchaeota archaeon NZ13-K Bacteria AFK51118.1 GCA 000264495 tetrahydromethanopterin S-methyltransferase subunit H Thermogladius calderae 1633 RLG76048.1RLG83705.1 GCA 003661705 GCA 003661805 tetrahydromethanopterin tetrahydromethanopterin S-methyltransferase S-methyltransferase subunit H subunitThermoprotei H Thermoprotei archaeon archaeon Verstraetearchaeota Methanocellales RLG91259.1 GCA 003661915 tetrahydromethanopterin S-methyltransferase subunit H Thermoprotei archaeon ABN69524.1 GCA 000015945 Tetrahydromethanopterin S-methyltransferase MtrH subunit Staphylothermus marinus F1 ADI31522.1 GCA 000092465 Tetrahydromethanopterin S-methyltransferase Staphylothermus hellenicus DSM 12710 TDA30832.1 GCA 004347865 tetrahydromethanopterin S-methyltransferase subunitMethanosarcinales H Archaeoglobi archaeon
Bathyarchaeota Bathyarchaeota Thorarchaeota OGD53054.1 GCA 001775955 tetrahydromethanopterin S-methyltransferase subunit H Candidatus Bathyarchaeota archaeon RBG 13 38 9 TFG14339.1 GCA 004524445 tetrahydromethanopterin S-methyltransferase subunit H Candidatus Thorarchaeota archaeon RLE90109.1 GCA 003650785 tetrahydromethanopterin S-methyltransferase subunit H Thermoprotei archaeon Methanopyrales GCARLG91368.1 003935005RSFX01000002.1 GCA 003661965 tetrahydromethanopterin 17116599316690112 171 S-methyltransferase GCA 003935005 -1 subunit ID 12 171H Candidatus partial 00 Archaeoglobi Bathyarchaeota archaeon archaeon KXA89379.1 GCA 001548915 hypothetical protein AKJ62 03270 candidate division MSBL1 archaeon SCGC-AAA259D14 Methanobacteriales GCA 003555245PWGK01000022.1 25286022951648 25 GCA 003555245 -1 ID 48 25 partial 00 candidate division MSBL1 archaeon RLG52994.1 GCA 003661365 tetrahydromethanopterin S-methyltransferase subunit H Candidatus Korarchaeota archaeon Methanococcales GCA 003935005RSFX01000002.1AUX08117.1GCA 002010285MTNC01000005.1 GCA 88864328730712 002952775 tetrahydromethanopterin 88 GCA 0039350054648717496223 1 ID S-methyltransferase 12 46 88 GCA partial 002010285 00 Archaeoglobi subunit 1 ID H3 archaeon 46Halalkaliarchaeum partial 00 Archaeoglobus desulfuricum sp. JdFR-41
Nezhaarchaeota RLF24753.1 GCA 003650925 tetrahydromethanopterinAOW80914.1 GCA 001767315 S-methyltransferase tetrahydromethanopterin subunit H Thermoprotei S-methyltransferase archaeon subunit H Halodesulfurarchaeum formicicum PSP85940.1 GCA 003021105 tetrahydromethanopterin S-methyltransferase subunit H Halobacteriales archaeon QS 1 68 17 Bathyarchaeota WP 042685937.1ADM27238.1 GCF 000711905 GCA tetrahydromethanopterin 000145985 Tetrahydromethanopterin S-methyltransferase S-methyltransferase subunit H Methermicoccus Ignisphaera shengliensis aggregans DSM 17230 Methanosarcinales OYT51307.1 GCA 002255025 tetrahydromethanopterinRAO78711.1 S-methyltransferase GCA 003264935 subunit tetrahydromethanopterin H Candidatus Bathyarchaeota archaeon S-methyltransferase ex4484 135 subunit H Methanothermobacter tenebrarum RLI07487.1RLI46135.1 GCA GCA 003662185 003662715AAB91219.1 tetrahydromethanopterin tetrahydromethanopterin GCA 000008665 S-methyltransferase S-methyltransferase N5-methyltetrahydromethanopterincoenzyme subunit subunit H partial H Candidatus Candidatus Bathyarchaeota Bathyarchaeota archaeon M methyltransferase mtr {Methanobacterium thermoautotro Archaeoglobus fulgidus DSM 4304 PWR73786.1 GCA 003173355RLG80500.1 tetrahydromethanopterin GCA 003661825 S-methyltransferase tetrahydromethanopterin subunit HS-methyltransferase Methanospirillum lacunae subunit H partial Thermoprotei archaeon RLE67638.1 GCA 003650735 tetrahydromethanopterin S-methyltransferase subunit H Thermoprotei archaeon Methanophagales RLG39594.1 GCA 003661265 tetrahydromethanopterinGCA S-methyltransferase 002502735DAQC01000001.1 subunit H partial Candidatus Korarchaeota 1191350351359078 archaeon 119 GCA 002502735 -1 ID 8 119 partial 00 Methanoregula sp. UBA64 Thorarchaeota RLG50518.1 GCA 003661365 tetrahydromethanopterinABS55561.1 S-methyltransferase GCA 000017625 subunit H TetrahydromethanopterinCandidatus Korarchaeota archaeon S-methyltransferase MtrH subunit Methanoregula boonei 6A8 RLI07380.1KYH39065.1 GCA GCA003662205 001593875ADN37299.1 tetrahydromethanopterin tetrahydromethanopterin GCA 000147875 S-methyltransferase S-methyltransferaseTetrahydromethanopterin subunit H subunit partial HCandidatus CandidatusS-methyltransferase Bathyarchaeota Bathyarchaeota archaeon Methanolacinia archaeon B23 petrolearia DSM 11571 WP 048149267.1EHQ35521.1 GCF GCA 000784355 000243255 tetrahydromethanopterin Tetrahydromethanopterin S-methyltransferase S-methyltransferase subunit H MtrH Methanolacinia subunit Methanoplanus paynteri limicola DSM 2279 TEU09181.1 GCA 004377395 tetrahydromethanopterin S-methyltransferase subunit H Candidatus Bathyarchaeota archaeon Bacteria GCA 002011035MTLY01000008.1 6452024529232 64 GCA 002011035 -1 ID 2 64 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11
TET64612.1 GCA 004376975 tetrahydromethanopterinOLS17408.1 GCA S-methyltransferase 001940665 subunit Tetrahydromethanopterin H Candidatus Bathyarchaeota archaeon S-methyltransferase subunit H Candidatus Odinarchaeota archaeon LCB 4 GBC75608.1 GCA 002898815 hypothetical protein HRbin06 00927 archaeon HR06 Methanomassiliicoccales RLE49396.1 GCA 003649085 tetrahydromethanopterin S-methyltransferase subunit H Candidatus Verstraetearchaeota archaeon
Thorarchaeota
Bathyarchaeota
RLE57920.1 GCA RLE57920.1003649205tetrahydromethanopterin GCA S-methyltransferase subunit Thermoprotei H archaeon TFH19397.1 GCA 004525915 tetrahydromethanopterin S-methyltransferase subunit H Candidatus Bathyarchaeota archaeon
Bathyarchaeota
Lokiarchaeota
KYK30310.1 GCA 001595915 hypothetical protein AYK22 04190 Thermoplasmatales archaeon SG8-52-3
RLF53608.1 GCA 003651045 hypothetical protein DRN24 00450 Thermoplasmata archaeon KYK20152.1KYK29409.1 GCA 001595865 GCA 001595805hypothetical hypothetical protein AYK21 protein 01660 AYK20 Thermoplasmatales 05530 Thermoplasmatales archaeon archaeonSG8-52-2 SG8-52-1 PNX46948.1 GCA 002900535 hypothetical protein BV457 06665 Thermoplasmata archaeon M9B1D
DAC72957.1 GCA 003942085 TPA hypothetical protein DSN98 02630 Thermoplasmata archaeon
RLF28588.1 GCA 003649715 hypothetical protein DRN05 03675 Thermoplasmata archaeon
KYK23935.1 GCA 001595945 hypothetical protein AYK25 00790 Thermoplasmatales archaeon SM1-50
GCA 002506745DAYE01000087.1 18163861728877 18 GCA 002506745 -1 ID 77 18 partial 00 Euryarchaeota archaeon UBA33
OYT28093.1 GCA 002254885 hypothetical protein B6U98 05625 Thermoplasmatales archaeon ex4572 165 KYK25513.1 GCA 001595885 hypothetical protein AYK23 03540 Euryarchaeota archaeon SG8-5
PJB21824.1 GCA 002790055 hypothetical protein CO114 03320 partial Euryarchaeota archaeon CG 4 9 14 3 um filter 38 12 GCA 003555395PWHU01000050.1 42886380360 4 GCA 003555395 1 ID 60 4 partial 00 Thermoplasmata archaeon EMR73622.1 GCA 000349645 tetrahydromethanopterin S-methyltransferase subunit H Thermoplasmatales archaeon SCGC AB-539-N05
GCA 002502685DAQA01000029.1 26313873228317 26 GCA 002502685 1 ID 17 26 partial 00 Euryarchaeota archaeon UBA202 GCA 003554965PWHR01000041.1 40404214133522 40 GCA 003554965 -1 ID 22 40 partial 00 Thermoplasmata archaeon
GCA 003551675PUNG01000012.1 13101971111424 13 GCA 003551675 -1 ID 24 13 partial 00 Thermoplasmata archaeon
GCA 003553085PUPH01000167.1 2654156255 2 GCA 003553085 1 ID 55 2 partial 00 Thermoplasmata archaeon
GCA 000402775AQSC01000045.1 21155751640545 21 GCA 000402775 1 ID 45 21 partial 00 Euryarchaeota archaeon SCGC AAA252-I15 GCA 003559355PWLO01000038.1 131307013984102 13 GCA 003559355 -1 ID 102 13 partial 00 Thermoplasmata archaeon
RLI45129.1 GCA 003662715 tetrahydromethanopterin S-methyltransferase subunit H Candidatus Bathyarchaeota archaeon
GCA 003560595PWKY01000022.1 17162561716456 17 GCA 003560595 -1 ID 56 17 partial 00 Thermoplasmata archaeon
GCA 002011215MTML01000098.1 9104291131325 9 GCA 002011215 1 ID 25 9 partial 00 Archaeoglobus sp. JdFR-24
GCA 002496385DAJR01000052.1 127936886533 12 GCA 002496385 1 ID 33 12 partial 00 Methanomassiliicoccales archaeon UBA147
GCA 002499085DAKD01000030.1 40484774940611 40 GCA 002499085 1 ID 11 40 partial 00 Methanomassiliicoccales archaeon UBA280
TDA36701.1 GCA 004347915 tetrahydromethanopterin S-methyltransferase subunit H Candidatus Nezhaarchaeota archaeon WYZ-LMO7
Tree scale: 1 Supplementary Figure 32. ML phylogeny of MtrH. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
60 70 80 90 100 50 60 70 80 90 100 Mean ANI (%) Mean AAI (%)
NRA7_88_Euryarchaeota_41_62 63.83 GCA_002494725_Geoglobus_sp_UBA235 64.23 GCA_000194625_Archaeoglobus_veneficus_SNP6 66.94 65.31 GCA_000025285_Archaeoglobus_profundus_DSM_5631 61.16 58.41 a. GCA_002507545_Archaeoglobus_sp_UBA230 68.09 64.97 68.33 GCA_002010285_Archaeoglobus_sp_JdFR−41 60.73 59.61 61.14 GCA_002010285_Archaeoglobus_sp_JdFR−41 67.84 64.99 68.21 70.01 b. GCA_003662985_Archaeoglobales_archaeon 59.38 58.69 58.72 60.44 GCA_003978865_Archaeoglobus_sp 66.26 64.01 69.38 67.82 67.36 GCA_002010215_Archaeoglobus_sp_JdFR−37 63.8 63.49 61.11 62.85 62.05 GCA_000008665_Archaeoglobus_fulgidus_DSM_4304 68.27 65.45 69.39 74.16 69.45 67.6 GCA_003662995_Archaeoglobales_archaeon 61.15 59.99 62.4 63.96 63.46 64.18 nra7_reassver2_Euryarchaeota_47_10 64.23 74.13 65.22 64.96 64.7 63.25 65.67 GCA_001006045_Geoglobus_ahangari 65.51 74.11 60.06 61.16 59.49 63.83 60.9 GCA_001006045_Geoglobus_ahangari 67.08 64.63 69.18 68.54 67.29 67.2 70.17 65.26 GCA_002010195_Archaeoglobus_sp_JdFR−32 59.82 58.58 59.65 60.12 69.34 61.39 62.34 59.85 GCA_000385565_Archaeoglobus_sulfaticallidus_PM70−1 66.81 65.18 68.95 68.81 68.07 68.05 69.24 65.01 68.95 GCA_004347825_Archaeoglobi_archaeon 59.55 57.55 59.9 63.99 57.99 59.81 60.57 58.49 58.11 GCA_002010195_Archaeoglobus_sp_JdFR−32 65.94 64.97 67.35 67.66 67.14 66.99 67.74 64.29 67.38 70.69 GCA_003663025_Archaeoglobales_archaeon 59.98 57.81 74.84 60.21 57.45 60.41 60.59 59.26 58.93 59.34 GCA_004347865_Archaeoglobi_archaeon 89.39 63.48 66.89 67.95 67.2 65.53 68.31 63.9 67.02 66.64 65.97 GCA_003978865_Archaeoglobus_sp 59.28 58.1 60.58 59.21 58.28 60.27 60.85 59.34 58.6 57.57 58.75 GCA_000789255_Geoglobus_acetivorans 66.08 64.6 68.17 68.03 67.3 67.44 68.84 64.83 73.52 68.05 66.96 66.38 GCA_003663055_Archaeoglobales_archaeon 62.28 60.25 63.74 62.68 61.21 65.06 65.15 61.95 61.99 60.22 62.29 64.44 GCA_002010305_Archaeoglobi_archaeon_JdFR−42 64.06 64.81 64.41 64.48 64.53 64.28 64.25 63.95 63.7 65.1 64.87 63.26 64.47 nra7_reassver2_Euryarchaeota_47_10 52.38 51.03 51.78 51.54 50.45 51.85 52.11 52.05 50.88 51.33 51.71 51.09 52.01 100 GCA_003662985_Archaeoglobales_archaeon 66.23 64.11 67.68 67.41 67.33 66.72 67.74 63.91 67.51 70 69.69 66.17 67.27 64.27 GCA_004347865_Archaeoglobi_archaeon 59.45 57.83 59.82 63.97 57.72 60.05 60.69 58.87 57.99 86.87 59.06 57.94 60.49 51.05 GCA_002494725_Geoglobus_sp_UBA235 66.41 64.88 67.81 67.93 67.79 66.62 68.14 64.89 72.77 68 67.6 66.67 71.94 64.68 67.64 GCA_000385565_Archaeoglobus_sulfaticallidus_PM70−1 60.24 59.48 60.09 61.46 68.29 62.34 63.71 61.09 68.93 59.08 59.07 59.24 62.75 51.44 58.85 GCA_003662995_Archaeoglobales_archaeon 66.64 65.06 68.6 68.91 68.2 67.65 68.69 65.14 67.29 68.94 68.18 66.36 67.34 65.29 68.95 67.54 GCA_002010305_Archaeoglobi_archaeon_JdFR−42 54.65 53.69 53.86 53.43 53.75 55.39 54.62 53.87 53.54 52.44 53.33 53.42 55.87 51.19 52.7 54.17 66.54 66.51 69.1 68.26 68.15 66.94 68.77 64.79 68.86 68.33 67.56 66.84 68.3 65.39 67.7 69.29 68.13 GCA_002010215_Archaeoglobus_sp_JdFR−37 GCA_002011235_Archaeoglobus_sp_JdFR−27 60.64 59.48 59.98 61.5 85.07 62.9 63.87 60.58 69.77 58.78 59.16 59.01 62.73 51.13 59.12 69.38 55.29 66.39 65.24 67.84 71.1 67.94 67.05 67.75 64.69 67.12 70.25 70.31 66.15 67.1 66.31 81.04 67.68 68.46 68.14 GCA_002011235_Archaeoglobus_sp_JdFR−27 GCA_002507545_Archaeoglobus_sp_UBA230 61.28 59.63 61.25 69.04 60.54 62.17 63.66 61.25 60.32 64.91 60.57 59.53 62.98 52.11 65.16 61.89 54.13 63.23 66.34 65.69 68.36 68.7 68.2 67.3 67.67 64.77 67.24 71.89 71.69 66.07 67.61 66.2 70.97 67.68 68.32 68.73 71.7 GCA_002494625_Archaeoglobus_sp_UBA234 GCA_002011215_Archaeoglobus_sp_JdFR−24 59.77 59.24 60.01 61.04 69.39 63.16 63.93 60.5 69.5 58.23 58.8 58.93 63.24 51.11 58.54 68.67 54.32 69.86 60.78 64.56 74.17 64.73 65.49 64.89 64.04 67.58 83.83 65.07 65.33 64.46 63.84 64.76 63.53 64.37 65.7 64.89 64.96 64.74 65.32 nra7_reassver2_Euryarchaeota_45_14 NRA7_88_Euryarchaeota_41_62 52.71 51.58 51.78 51.59 50.61 52.49 52.1 52.3 51.74 51.33 51.36 51.17 51.68 76.69 50.73 51.73 51.72 51.67 52.17 51.49 66.46 65.76 68.37 68.12 67.8 67.47 67.4 64.47 67.14 71.08 72.91 66.17 67.24 65.44 69.43 67.44 69.04 68.51 70.24 71.01 64.8 GCA_002011215_Archaeoglobus_sp_JdFR−24 GCA_000789255_Geoglobus_acetivorans 64.41 71.89 59.73 60.14 59.22 62.97 60.43 75.13 58.67 58.79 58.75 58.32 61.2 51.77 58.69 60.26 53.85 59.81 60.37 59.69 51.99 66.87 64.72 68.63 68.56 67.84 67.54 69.23 64.53 69.5 67.96 67.43 66.75 68.63 64.94 67.2 68.7 67.99 68.57 67.55 67.19 65.19 66.85 GCA_000025505_Ferroglobus_placidus_DSM_10642 nra7_reassver2_Euryarchaeota_45_14 52.54 51.45 51.57 51.55 50.28 51.36 51.65 52.05 51.01 51.15 51.79 50.87 51.76 87.44 50.92 51.52 51.53 51.38 52.42 51.05 75.84 51.73 66.87 63.85 75.75 68.35 67.65 68.75 68.83 64.2 67.59 68.22 67.54 66.77 67.49 64.79 67.68 67.82 69.34 68.32 67.84 67.7 65.07 67.74 68.44 GCA_003663055_Archaeoglobales_archaeon GCA_002010045_Archaeoglobus_sp_JdFR−22 58.5 57.62 59.58 60.05 59.94 61.63 62.74 58.02 60.02 57.86 58.39 59.23 64.68 50.42 58.14 60.47 53.56 60.9 59.63 61.46 50.65 57.96 50.45 67.27 64.69 68.63 68.53 67.74 68.23 68.71 64.41 67.88 68.35 66.89 66.64 67.66 64.67 66.94 66.97 68.82 67.57 67.21 67.36 64.18 67.6 68.65 68.78 GCA_000025285_Archaeoglobus_profundus_DSM_5631 GCA_000008665_Archaeoglobus_fulgidus_DSM_4304 62.12 60.01 61.76 68.06 60.37 62.43 63.75 61.96 60.52 64.65 60.67 59.96 63.2 52.54 65.1 62.03 54.32 61.62 76.93 60.83 53.01 61.12 53.94 59.57 67.04 64.41 67.61 67.59 67.32 66.75 67.95 64.67 67.4 66.81 66.57 66.85 66.52 63.66 66.02 67.57 68.46 66.68 66.71 66.62 63.86 66.53 67.54 68.17 73.48 GCA_003663025_Archaeoglobales_archaeon GCA_000194625_Archaeoglobus_veneficus_SNP6 61.82 59.68 63.14 62.66 61.38 64.82 65.12 61.89 61.69 60.38 61.91 64.8 79.07 52.37 60.71 63.04 55.39 62.62 62.38 63.49 52.27 60.73 52.36 64.91 62.93 65.57 64.28 67.06 67 67.17 67.34 66.41 64.29 65.93 66.56 66.71 65.48 66.34 64.28 67.06 66.88 68.01 66.97 66.96 67.68 64.67 67.82 66.19 67.76 66.28 66.15 GCA_002010045_Archaeoglobus_sp_JdFR−22 GCA_002494625_Archaeoglobus_sp_UBA234 59.82 59.22 59.67 60.34 71.66 62.83 62.71 60.16 73.76 58.21 58.41 58.76 62.58 51.31 58.39 70.24 54.12 72.58 60.88 69.86 52.31 59.62 51.43 60.47 61.08 62.26
NRA7_88_Euryarchaeota_41_62 NRA7_88_Euryarchaeota_41_62 GCA_003978865_Archaeoglobus_sp nra7_reassver2_Euryarchaeota_47_10GCA_001006045_Geoglobus_ahangari nra7_reassver2_Euryarchaeota_45_14 GCA_003978865_Archaeoglobus_sp GCA_001006045_Geoglobus_ahangari nra7_reassver2_Euryarchaeota_47_10 nra7_reassver2_Euryarchaeota_45_14 GCA_004347825_Archaeoglobi_archaeon GCA_004347865_Archaeoglobi_archaeonGCA_000789255_Geoglobus_acetivoransGCA_002494725_Geoglobus_sp_UBA235 GCA_002494725_Geoglobus_sp_UBA235 GCA_004347825_Archaeoglobi_archaeon GCA_004347865_Archaeoglobi_archaeon GCA_000789255_Geoglobus_acetivorans GCA_002507545_Archaeoglobus_sp_UBA230GCA_002010285_Archaeoglobus_sp_JdFR.41 GCA_002010195_Archaeoglobus_sp_JdFR.32GCA_003662985_Archaeoglobales_archaeonGCA_003662995_Archaeoglobales_archaeonGCA_002010215_Archaeoglobus_sp_JdFR.37GCA_002011235_Archaeoglobus_sp_JdFR.27GCA_002494625_Archaeoglobus_sp_UBA234GCA_002011215_Archaeoglobus_sp_JdFR.24GCA_003663055_Archaeoglobales_archaeonGCA_003663025_Archaeoglobales_archaeon GCA_002010285_Archaeoglobus_sp_JdFR.41GCA_003662985_Archaeoglobales_archaeonGCA_002010215_Archaeoglobus_sp_JdFR.37GCA_003662995_Archaeoglobales_archaeonGCA_002010195_Archaeoglobus_sp_JdFR.32GCA_003663025_Archaeoglobales_archaeonGCA_003663055_Archaeoglobales_archaeonGCA_002011235_Archaeoglobus_sp_JdFR.27GCA_002507545_Archaeoglobus_sp_UBA230GCA_002011215_Archaeoglobus_sp_JdFR.24GCA_002010045_Archaeoglobus_sp_JdFR.22 GCA_000194625_Archaeoglobus_veneficus_SNP6 GCA_002010305_Archaeoglobi_archaeon_JdFR.42 GCA_000025505_Ferroglobus_placidus_DSM_10642 GCA_002010305_Archaeoglobi_archaeon_JdFR.42 GCA_000194625_Archaeoglobus_veneficus_SNP6 GCA_000008665_Archaeoglobus_fulgidus_DSM_4304 GCA_000025505_Ferroglobus_placidus_DSM_10642 GCA_000385565_Archaeoglobus_sulfaticallidus_PM70.1 GCA_000025285_Archaeoglobus_profundus_DSM_5631 GCA_000008665_Archaeoglobus_fulgidus_DSM_4304 GCA_000025285_Archaeoglobus_profundus_DSM_5631 GCA_000385565_Archaeoglobus_sulfaticallidus_PM70.1
50 60 70 80 90 100 40 50 60 70 80 90 100 Mean ANI (%) Mean AAI (%)
GCA_002255025_Candidatus_Bathyarchaeota_archaeon_ex4484_135 61.27 GCA_003662715_Candidatus_Bathyarchaeota_archaeon 48.38 GCA_005888695_Candidatus_Bathyarchaeota_archaeon 62.61 61.52 GCA_003662535_Candidatus_Bathyarchaeota_archaeon 46.42 54.56 GCA_003096255_Candidatus_Bathyarchaeota_archaeon 64.97 62.06 60.84 GCA_005888695_Candidatus_Bathyarchaeota_archaeon 62.61 48.54 47.53 GCA_001775965_Candidatus_Bathyarchaeota_archaeon_RBG_13_60_20 44.34 46.95 47.78 44.61 GCA_002010925_Candidatus_Bathyarchaeota_archaeon_JdFR−04 65.49 62.5 61.99 65.59 GCA_007050885_Candidatus_Bathyarchaeota_archaeon 49.36 49.73 47.27 49.55 45.28 GCA_003601695_Candidatus_Bathyarchaeota_archaeon 63.58 62.6 60.93 63.43 63.98 GCA_005888735_Candidatus_Bathyarchaeota_archaeon 65.25 48.85 47.85 65.51 45.22 49.13 GCA_005881615_Candidatus_Bathyarchaeota_archaeon 62.54 62.59 67.85 62.75 62.08 61.02 GCA_003151735_Candidatus_Bathyarchaeota_archaeon 47.45 55.47 50.77 47.27 47.07 50.07 46.96 GCA_007050895_Candidatus_Bathyarchaeota_archaeon 68.8 64.11 61.38 65.71 64.95 63.25 61.66 GCA_005883695_Candidatus_Bathyarchaeota_archaeon 67.52 49 47.91 63.24 44.75 49.5 66.1 47.42 c. GCA_001593855_Candidatus_Bathyarchaeota_archaeon_B25 61.02 63.08 61.73 61.9 62.46 62.6 61.09 60.77 GCA_003164295_Candidatus_Bathyarchaeota_archaeon 47.26 55.23 50.71 47.63 46.37 49.67 47.25 74.88 47.65 GCA_003601725_Candidatus_Bathyarchaeota_archaeon 63.67 63 61.54 63.94 65.25 73.2 62.73 63.42 63.32 d. GCA_005888755_Candidatus_Bathyarchaeota_archaeon 67.68 48.84 47.71 64.82 44.96 49.48 66.29 47.57 85.71 47.44 67.65 62.97 61.55 65.78 67.97 64.82 62.21 68.76 61.8 65.23 GCA_003601605_Candidatus_Bathyarchaeota_archaeon GCA_003661975_Candidatus_Bathyarchaeota_archaeon 46.91 56.07 53.84 47.66 47.33 49.09 48.08 53.09 47.7 53.09 47.66 65.05 63.71 62.7 69.67 66.71 64.33 61.66 65.24 62.74 65.19 67.28 GCA_001399795_Candidatus_Bathyarchaeota_archaeon_BA2 GCA_001593855_Candidatus_Bathyarchaeota_archaeon_B25 47.18 49.96 50.3 47.83 46.13 47.56 47.32 48.02 47.58 47.74 47.52 50.89 62.86 61.96 67.7 62.86 62.21 62.43 80.6 61.98 59.91 62.18 61.87 62.09 GCA_005888745_Candidatus_Bathyarchaeota_archaeon GCA_001918745_Crenarchaeota_archaeon_13_1_40CM_3_52_17 67.53 48.79 47.73 64.34 45.01 49.55 66.04 47.55 85 47.02 84.73 47.37 47.09 GCA_001919285_archaeon_13_1_40CM_2_52_13 62.54 61.56 66.9 60.96 60.66 61.07 70.18 61.37 62.14 62.33 61.93 63.14 69.54 GCA_001593875_Candidatus_Bathyarchaeota_archaeon_B23 46.31 50.74 51.43 47.27 56.61 46.45 47.38 47.69 46.48 47.61 47.06 51.43 48.12 47.44 GCA_002254975_Candidatus_Bathyarchaeota_archaeon_ex4484_218 62.44 59.73 61.08 62.21 62.01 62.7 61.58 63.77 64.16 62.22 63 62.36 60.8 61.68 GCA_003601775_Candidatus_Bathyarchaeota_archaeon 46.46 52.06 52.4 47.08 54.66 47.67 47.19 49.22 47.38 48.75 47.11 52.87 49.71 47.14 61.66 GCA_003151735_Candidatus_Bathyarchaeota_archaeon 75.34 61.63 62.28 64.7 65.02 63.75 62.81 69.1 61.17 63.57 67.29 64.83 63.01 63.52 63.27 GCA_005882895_Candidatus_Bathyarchaeota_archaeon 67.87 48.55 46.85 64.32 44.67 49.81 66.15 47.53 90.43 47.65 85.99 47.52 47.13 85.05 47.09 46.98 GCA_005883695_Candidatus_Bathyarchaeota_archaeon 62.36 62.29 67.39 62.54 62.37 61.93 82.05 61.58 62.06 61.7 61.79 62.47 81.99 69.19 59.58 62.65 GCA_004376295_Candidatus_Bathyarchaeota_archaeon 46.85 65.44 54.64 47.69 47.75 49.2 48.31 56.01 47.58 55.51 47.57 56.35 50.3 47.75 50.32 52.2 47.75 GCA_005888755_Candidatus_Bathyarchaeota_archaeon 62.33 61.2 68.98 62.49 60.97 61.29 86.8 61.69 61.25 62.1 61.83 61.57 80.68 69.1 63.38 62.49 82.15 GCA_001774245_Candidatus_Bathyarchaeota_archaeon_RBG_13_52_12 44.23 47 47.1 44.74 59.15 45.77 44.95 47.62 44.97 47.26 44.71 47.78 45.94 44.64 56.02 54.14 44.43 47.91 GCA_003662205_Candidatus_Bathyarchaeota_archaeon 62.33 65.06 61.96 62.04 61.71 63.2 62.11 63.43 61.28 62.35 61.13 62.23 62.2 62.44 −1 62.24 62.16 61.24 GCA_003601875_Candidatus_Bathyarchaeota_archaeon 48.46 62.16 56.17 49.5 49.11 50.6 49.11 60.67 49.25 60.35 49.64 57.83 51.75 49.16 51.6 53.68 49.45 62.03 49.76 GCA_003662325_Candidatus_Bathyarchaeota_archaeon 66.57 62.92 62.24 65.48 67.35 65.33 61.76 68.15 61.94 65.2 72.19 67.31 61.4 62.24 63.79 66.88 62.33 61.9 61.88 GCA_003661945_Candidatus_Bathyarchaeota_archaeon 48.56 60.97 56.59 49.25 48.76 49.69 49.12 57.74 48.86 57.37 48.78 57.03 51.67 48.89 50.93 52.89 48.65 62.1 48.41 66.01 GCA_003141855_Candidatus_Bathyarchaeota_archaeon 75.1 61.52 62.31 65.18 64.92 62.23 61.68 69.41 61.03 63.61 67.58 65.42 62.3 61.88 62.11 81.81 61.39 62 62.06 66.44 GCA_002010975_Candidatus_Bathyarchaeota_archaeon_JdFR−07 47.46 61.48 53.7 48.27 47.61 49.65 47.85 61.21 48.07 61.48 48.23 55.7 49.32 48.33 50.62 51.75 48.13 61.14 47.55 69.22 64.13 GCA_001768965_archaeon_RBG_16_50_20 62.55 61.87 64.91 61.86 62.66 60.47 64.92 62.15 61.01 62.24 61.39 61.75 64.26 63.08 60.84 62.15 63.68 63.96 62 62.13 61.78 GCA_004376385_Candidatus_Bathyarchaeota_archaeon 46.16 62.47 53.05 47.22 47.59 50.97 46.97 56.04 46.9 55.54 46.94 54.57 49.52 46.53 49.65 51.19 46.71 63.18 48.15 59.01 58.16 58.26 GCA_001774245_Candidatus_Bathyarchaeota_archaeon_RBG_13_52_12 61.77 62.65 60.22 61.46 60.27 60.86 60.75 63.36 61.34 60.4 60.33 61.67 60.42 59.67 −1 62.37 59.92 59.65 68.36 61.21 62.09 60.72 GCA_003661965_Candidatus_Bathyarchaeota_archaeon 47.98 51.16 51.04 48.23 46.58 49.16 48.15 49.22 48.13 49.32 48.01 51.57 57.76 48.02 49.57 50.18 47.8 51.12 46.06 53.45 52.65 51.55 49.79 GCA_003165195_Candidatus_Bathyarchaeota_archaeon 75.57 61.68 61.54 64.39 64.83 62.81 62.06 68.34 61.72 62.6 67.03 64.81 61.62 63.49 61.54 73.79 62.41 61.66 62.16 66.74 73.7 61.47 61.89 GCA_003662325_Candidatus_Bathyarchaeota_archaeon 48.17 62.08 55.6 48.33 47.41 50.26 48.94 61.59 49.08 61.88 48.81 57.78 50.95 48.85 51.03 52.76 48.34 62.16 48.09 76.34 65.38 70.27 58.86 52.36 GCA_001775955_Candidatus_Bathyarchaeota_archaeon_RBG_13_38_9 62.85 59.6 62.02 63.12 61.84 61.89 61.91 63.87 62.29 61.89 63.25 61.64 61.27 62.54 63.08 62.47 61.96 62.4 62.48 62.18 62.66 62.85 63.61 62.38 GCA_002507245_Candidatus_Bathyarchaeota_archaeon_UBA233 47.8 61.18 55.4 48.94 47.34 49.6 48.58 57.82 48.87 57.7 48.82 56.32 50.85 48.64 50.32 51.88 48.49 61.5 47.47 64.53 76.35 64.17 58.64 52 65.11 GCA_002726865_Candidatus_Bathyarchaeota_archaeon 61.25 61.65 60.77 61.93 61.19 61.15 60.99 61.68 59.81 61.91 61.89 62.44 60.78 62.15 61.76 61.91 60.58 60.89 68.43 61.42 62.05 61.69 64.39 62.14 61.02 GCA_001399795_Candidatus_Bathyarchaeota_archaeon_BA2 48.06 68.16 55.4 48.8 48.83 51.75 48.42 57.35 48.23 57.37 48.46 57.91 50.92 48.46 51.04 52.63 48.16 69.42 48.43 63.4 62.56 61.48 68.08 52.29 63.5 62.68 GCA_005888675_Candidatus_Bathyarchaeota_archaeon 61.2 61.88 94.93 62.62 62.49 60.94 67.15 61.94 60.91 61.97 61.99 60.97 67.06 67.15 61 61.53 66.68 67.08 61.88 63.25 61.36 64.3 60.81 61.46 62.19 60.74 GCA_013329615_Candidatus_Bathyarchaeota_archaeon 44.11 47.16 47.21 44.77 59.96 45.88 45.04 46.94 44.82 46.48 44.73 46.69 45.86 44.94 56.39 53.99 44.84 47.54 77.43 49.53 48.59 47.54 48.07 46.33 48.45 47.7 48.44 GCA_001399805_Candidatus_Bathyarchaeota_archaeon_BA1 63.84 63.28 62.2 66.42 66.21 64.02 62.19 64.27 61.9 65.24 66.15 72.67 63 62.65 62.19 63.8 61.52 62.34 63.53 66.61 64.03 62.63 61.93 63.02 62.37 60.94 61.81 GCA_004376975_Candidatus_Bathyarchaeota_archaeon 47.52 59.79 54.86 48.44 47.74 50.01 48.35 60.19 48.01 60.13 48.27 55.74 49.25 47.71 50.01 51.55 48.09 67.18 48.28 69.57 63.52 68.71 58.57 50.98 71.79 63 62.45 47.6 GCA_001593865_Candidatus_Bathyarchaeota_archaeon_B24 46.16 49.29 49.77 47.02 46.45 47.06 47.28 47.33 46.96 47.27 46.94 52 50.05 47.01 48.94 49.75 46.81 48.98 46.32 50.99 50.54 48.92 48.55 50.27 50.3 49.42 49.7 45.4 48.84 GCA_001593935_Candidatus_Bathyarchaeota_archaeon_B26−2 62.57 65.09 62.32 64.49 64.42 66.45 62.21 64.19 63.95 67.6 64.92 66.63 61.94 62.49 60.22 63.71 62.25 62.21 65.27 65.23 63.07 61.54 63.28 63.21 60.25 61.9 62.88 66.24 GCA_003601725_Candidatus_Bathyarchaeota_archaeon 47.58 58.1 53.92 48.07 47.87 49.33 48.36 53.81 48.19 53.77 48.12 73.29 50.64 48.06 51.18 52 48.24 57.11 47.82 58.14 57.41 56.83 55.67 52.09 57.43 57.18 59.19 47.11 55.61 50.9 GCA_002507245_Candidatus_Bathyarchaeota_archaeon_UBA233 65.68 62.58 62.32 65.17 76.95 64.48 62.28 65.7 63.37 64.67 68.04 66.41 61.79 62.16 64.41 65.37 61.95 61.84 61.35 67.46 65.32 62.35 61.23 65.69 62.08 60.6 62.23 66.12 64.56 GCA_007050895_Candidatus_Bathyarchaeota_archaeon 46.82 57.29 51.49 47.36 47.12 51.88 47.6 66.77 47.58 66.13 47.39 53.61 48 46.83 49.46 49.96 47.06 58.36 47.2 63.02 59.35 64.2 58.04 49.44 64.53 59.47 58.32 47.29 62.98 47.57 54.32 GCA_001273385_miscellaneous_Crenarchaeota_group−6_archaeon_AD8−1 67.55 58.42 60.82 64.93 65.34 63.31 61.24 68.09 60.99 63.52 67.3 65.12 62.15 59.86 63.57 66.87 59.99 58.77 65.25 66.03 66.76 61.38 60.48 66.84 62.13 60.76 61.23 63.64 62.15 65.33 GCA_003601605_Candidatus_Bathyarchaeota_archaeon 48.48 63.63 55.43 49.27 48.58 51.21 48.73 62.22 49.33 61.95 49.24 56.62 50.38 48.91 50.91 52.38 48.85 62.08 48.54 70.93 65.36 80.81 59.01 52.32 73.06 64.87 63.24 48.63 69.74 50.01 57.63 65.37 GCA_003601875_Candidatus_Bathyarchaeota_archaeon 67.13 61.91 62.52 65.71 67.87 65.01 62.89 67.46 62.61 65.31 71.73 66.91 61.3 63.52 65.15 66.88 61.84 63.36 60.75 73.99 66.81 62.14 60.96 66.66 62.31 61.45 61.98 65.76 65.12 68.22 67.51 GCA_001775955_Candidatus_Bathyarchaeota_archaeon_RBG_13_38_9 48.94 49.38 48.05 49.08 45.29 90.56 48.8 48.27 49.52 48.3 48.78 48.81 47.66 48.79 46.79 47.96 49.53 49.25 46.44 50.4 49.27 49.73 48.85 49.54 50.12 48.97 50.19 46.01 49.12 46.84 49.11 48.27 50.29 64.74 61.53 61.2 65.66 65.67 63.45 61.06 64.15 61.54 64.19 65.8 66.63 61.89 61.27 62.3 64.26 61.43 60.89 61.49 65.87 64.11 61.94 60.78 64.24 61.7 61.8 60.48 65.91 64.5 65.79 64.18 65.89 GCA_004376645_Candidatus_Bathyarchaeota_archaeon GCA_001593845_Candidatus_Bathyarchaeota_archaeon_B63 48.43 57.76 52.62 48.23 48.11 49.21 48.39 53.18 48.2 53.17 48.38 71.68 49.79 48.18 51.09 52.63 48.31 57.03 47.59 58.3 57.4 57.78 54.88 51.81 57.81 57.12 58.17 47.24 55.49 50.9 76.28 54.27 57.44 49.37 60.71 65.5 62.48 61.89 61.03 62.67 62.39 62.9 62.68 62.3 61.39 61.74 61.03 62.94 60.05 61.74 63.24 62.15 73.09 62.23 61.64 61.29 65.53 61.36 60.34 65.48 62.58 63.32 65.92 61.17 66 60.43 61.94 GCA_001593875_Candidatus_Bathyarchaeota_archaeon_B23 GCA_001273385_miscellaneous_Crenarchaeota_group−6_archaeon_AD8−1 46.17 54.92 49.54 46.56 45.8 49.99 46.66 61.69 46.35 61.49 46.65 53.21 47.36 46.35 48.1 48.82 46.59 55.5 46.69 60.15 56.53 60.54 55.16 49.56 60.17 56.82 55.88 46.63 58.75 47.46 53.44 64.69 60.63 48.73 52.88 66.7 62.79 61.6 65.41 67.68 65 60.99 68.44 61.13 64.57 72.42 67.29 60.97 62.08 62.61 66.34 61.86 61.26 61.9 99.05 66.48 62.18 61.15 66.13 62.15 60.15 61.97 66.1 65.34 67.42 65.62 74.46 65.57 61.16 GCA_003601785_Candidatus_Bathyarchaeota_archaeon GCA_005884195_Candidatus_Bathyarchaeota_archaeon 67.62 48.92 47.55 64.1 44.94 49.84 66.34 47.64 84.82 47.61 92.5 47.88 47.46 84.42 46.98 47.38 85.71 47.75 44.84 49.66 48.92 48.27 47.01 48.29 48.59 48.7 48.54 44.76 48.03 46.72 48.36 47 49.12 49.22 48.23 46.68 72.91 61.75 62.71 64.55 64.76 62.37 61.57 68.98 61.7 63.36 67.53 64.63 61.46 62.41 61.16 73.52 61.81 61.79 61.77 66.46 74.88 62.06 61.78 71.83 62.71 61.49 62.25 63.51 63.2 65.05 66.28 66.47 64.03 61.87 66.5 GCA_003589585_Candidatus_Bathyarchaeota_archaeon GCA_003096255_Candidatus_Bathyarchaeota_archaeon 46.5 60.95 52.18 46.77 47.9 51.53 47.3 55.37 46.76 55.15 46.53 53.94 49.36 46.5 48.07 51.12 46.62 61.17 48.08 58.19 58.01 58.11 78.54 49.83 58.3 58.11 66.3 47.87 57.99 48.15 55.22 58.1 58.09 49.44 54.76 55.69 46.93 62.83 61.38 67.2 62.07 62.42 60.91 84.98 60.65 61.1 62.17 61.4 61.58 80.57 69.04 60.22 61.95 82.28 85.17 62.59 61.73 62.25 63.45 61.02 60.89 62.17 61.18 66.74 61.56 63.53 62.14 59.64 61.73 60.91 62.37 61.84 61.58 GCA_001918765_Crenarchaeota_archaeon_13_1_40CM_3_52_10 GCA_002010925_Candidatus_Bathyarchaeota_archaeon_JdFR−04 47.88 59.86 56.36 48.33 48.46 49.38 48.5 56.79 49.06 57.13 48.69 56.06 49.96 49.22 50.4 53.08 48.42 61.35 48.05 65.68 75.46 63.61 58.74 51.88 65.94 80.69 63.14 47.91 63.04 49.99 57.32 59.45 65.09 49.27 56.73 57.04 48.69 58.11 GCA_002010975_Candidatus_Bathyarchaeota_archaeon_JdFR−07 67.69 62.65 62.55 65.54 67.88 64.47 62.15 67.4 61.77 64.74 79.41 66.19 62.45 62.94 64.55 66.91 61.22 61.7 61.3 70.49 66.74 61.7 60.21 66.29 62.01 62.25 62.65 65.95 64.76 68.35 67.03 70.66 66.11 60.7 70.44 66.44 62.69 GCA_001918765_Crenarchaeota_archaeon_13_1_40CM_3_52_10 67.53 48.64 47.92 63.69 44.73 49.86 66.32 47.16 85.77 47.13 88.33 47.32 47.02 84.85 47.37 47.5 86.1 47.68 44.74 49.52 49.16 48.45 47.04 48.18 48.75 49.05 48.84 44.87 48.23 46.6 48.08 47.07 49.47 49.23 47.87 46.65 87.83 46.42 49.16 GCA_003662715_Candidatus_Bathyarchaeota_archaeon 64.64 63.17 61.04 68.11 66.61 65.35 61.58 64.97 62.77 65.82 72.52 71.9 61.61 61.91 62.71 65.23 61.16 61.41 61.63 67.39 64.19 61.15 60.85 64.29 62.66 60.69 61.67 71.34 65.95 67.45 64.8 67 67.14 61.21 67.99 64.33 61.38 68.35 GCA_005888675_Candidatus_Bathyarchaeota_archaeon 63.2 48.25 47.6 94.5 45.63 50.04 64.39 47.75 63.99 48.01 64.09 48.31 47.82 64.46 47.41 47.2 64.29 48.35 45.05 50.63 49.66 48.74 47.84 48.93 48.82 49.46 48.84 45.17 48.67 47.39 48.91 47.71 49.51 49.81 48.42 47.63 63.99 47.4 49.42 63.7 GCA_013330975_Candidatus_Bathyarchaeota_archaeon 67.79 61.73 62.93 64.94 65.3 62.67 61.8 68.55 61.57 63.18 67.83 65.33 62.75 61.18 62.11 68.09 62.85 61.24 62.08 67.15 68.27 62.26 60.91 67.74 62.89 60.84 60.62 64.73 63.83 65.49 66.99 65.96 64.84 60.73 66.46 68.1 62.46 66.89 65.31 GCA_001593925_Candidatus_Bathyarchaeota_archaeon_B26−1 47.88 58.69 54.48 48.59 48.45 48.99 48.39 54 48.35 54.01 48.24 62.03 51.32 48.45 52.43 53.71 48.46 59.03 48.47 58.7 58.63 58.24 56.89 52.47 58.14 57.7 60.77 48.04 56.28 52.43 63.22 54.92 58.76 48.97 62.24 53.51 48.37 56.29 57.98 48.54 48.82 GCA_004376295_Candidatus_Bathyarchaeota_archaeon 65.1 62.57 63.77 67.87 66.44 63.94 62.66 65.34 62.75 65.06 67.36 73.19 62.69 62.46 62.73 65.05 62.17 62.27 61.73 66.76 64.59 62.08 61.01 64.44 61.73 61.52 62.53 71.27 65.09 66.76 65.1 66.3 67.45 62.17 67.14 64.38 61.61 66.97 72.64 64.4 GCA_003662515_Candidatus_Bathyarchaeota_archaeon 48.06 50.12 51.3 48.22 46.94 48.22 48.28 48.65 48.15 48.33 48.18 50.24 70.35 48.25 49.59 50.72 48.22 49.79 46.84 52.4 51.2 49.4 49.26 58.46 50.7 50.6 50.3 46.85 49.23 50.28 51.03 48.07 50.83 48.03 50.85 47.24 48.26 49.08 49.9 48.24 48.96 51.32 GCA_001918745_Crenarchaeota_archaeon_13_1_40CM_3_52_17 61.91 61.32 68.14 61.21 62.03 61.25 80.47 61.28 61.39 61.99 61.65 61.65 84.85 68.92 60.42 62.07 81.78 80.56 62.91 62.8 62.51 63.93 59.82 61.35 61.43 60.88 67.49 61.92 62.46 61.92 60.17 61.88 62 61.86 62.14 61.13 80.47 60.91 61.08 62.49 62.48 GCA_005888635_Candidatus_Bathyarchaeota_archaeon 87.52 49.18 47.41 63.46 45.02 49.18 65.5 47.7 69.03 47.49 68.23 47.66 47.55 68.02 47.09 47.27 68.22 47.61 44.83 49.34 48.83 48.37 47.05 48.14 48.79 48.8 48.8 44.91 48.2 46.89 48.27 47.32 49.18 48.92 48.65 46.58 68.24 46.95 48.93 67.91 63.94 48.6 48.2 GCA_005883085_Candidatus_Bathyarchaeota_archaeon 61.51 62.7 68.28 61.53 61.27 60.38 80.6 60.77 60.9 61.55 61.97 62.12 85.49 68.99 60.51 62.59 82.68 81.15 61.9 62.38 62.01 64.09 61.27 62.21 61.47 61.37 67.12 61.77 61.57 61.46 59.23 61.74 61.29 63.15 61.05 62.03 80.89 61.79 61.05 61.26 61.36 84.43 GCA_001399805_Candidatus_Bathyarchaeota_archaeon_BA1 47.83 65.32 55.98 48.55 47.33 49.48 48.32 55.32 48.42 55.09 48.52 56 50.44 48.22 49.4 51.71 48.13 66.31 47.18 61.85 61.59 60.17 60.82 51.01 62.02 60.94 67.94 47.35 60.8 48.93 57.39 57.35 61.98 48.9 57.03 54.34 48.29 59.21 60.3 48.68 49.32 58.83 50.01 48.38 GCA_002779555_Candidatus_Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9 66.83 62.18 62.31 65.24 66.73 63.53 62.51 68.19 62.95 64.31 71 66.56 62.12 61.34 60.66 67 63.14 61.96 63.08 70.57 67.33 60.91 61.56 66.72 62.8 61.73 61.6 66.05 64.86 66.67 65.25 68.69 65.47 61.85 70.57 67.2 62.37 69.44 66.43 67.37 66.82 62.08 61.44 GCA_002779555_Candidatus_Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9 47.47 59.56 54.09 48.32 47.62 50.59 48.56 62.55 48.38 61.77 48.26 55.29 49.57 47.99 50.06 51.4 48.07 61.25 47.9 67.46 63.12 68.24 58.41 51.14 69.25 62.45 61.92 47.89 68.3 48.88 55.7 64.73 71.23 49.28 55.83 59.56 48.15 57.56 62.53 48.38 49.34 56.54 49.69 48.49 60.27 NRA7_48_Candidatus_Bathyarchaeota_archaeon_52_381 62.17 62.55 62.79 62.54 62.69 61.08 62 62.39 65.62 62.66 62.51 63.16 64.08 60.86 64.74 62.46 61.93 62.25 63.72 62.06 61.9 62.11 62.6 61.72 61.74 61.51 62.54 64.76 63.86 62.51 59.92 61.86 63.27 64.83 61.76 62.6 61.74 62.38 63.18 62.23 63.97 61.44 61.98 62.18 GCA_003165195_Candidatus_Bathyarchaeota_archaeon 47.44 54.86 50.15 47.3 46.46 49.59 46.91 72.39 47.16 75.9 47.42 52.42 48.11 47.2 47.71 48.95 46.97 55.12 46.59 59.75 57.05 61.32 54.84 48.93 61.01 57.4 56.45 46.44 59.43 46.99 53.4 65.71 61.27 48.2 53.43 60.95 47.17 54.62 57.03 46.72 47.69 53.57 48.24 47.51 54.42 61.9 GCA_003662485_Candidatus_Bathyarchaeota_archaeon 61.41 62.94 62.99 62.08 61.32 61.79 61.94 60.73 75.97 62.12 62.71 62.3 61.51 62.28 65.37 61.34 62.39 62.61 62.55 63.06 60.66 61.82 61.87 60.98 61.13 61.39 62.86 62.69 64.37 62.29 60.4 62.48 61.86 64 62.02 60.95 62.07 62.3 62.65 61.07 62.07 61.91 61.54 62.17 66.09 GCA_005881695_Candidatus_Bathyarchaeota_archaeon 67.9 48.44 47.28 64.52 44.19 49.39 65.92 47.32 90.11 47.32 85.62 46.93 47.02 85.27 46.64 46.98 90.56 47.12 44.35 49.02 48.68 47.93 45.94 47.84 48.11 48.32 48.06 44.44 47.64 46.4 47.82 46.49 48.92 48.61 47.92 46.27 85.67 46.64 48.03 86.23 64.21 48.38 47.65 68.4 47.94 47.45 46.85 GCA_005881695_Candidatus_Bathyarchaeota_archaeon 61.05 62.24 69.04 62.12 60.73 60.89 81.98 61.06 60.81 62.31 61.73 61.63 82.43 69.79 60.66 61.89 88.76 82.3 62.37 62.11 61.23 63.97 59.96 62.39 61.1 60.19 68.03 62.39 62.04 62.28 59.99 63.23 61.46 62.66 61.99 60.25 82.22 62.4 61.74 61.28 61.55 82.16 83.03 61.91 61.48 61.74 GCA_003589585_Candidatus_Bathyarchaeota_archaeon 46.41 55.92 51.23 47.22 47.26 49.81 47.3 72.88 47.23 71.87 47.61 53.56 49.05 47.07 48.32 49.42 47.19 56.96 47.18 62.23 58.34 62.48 56.03 50.07 63.79 58.47 58.14 47.26 60.95 48 54.76 67.78 64.23 48.07 54.03 62.48 47.61 55.85 58.43 47.58 47.91 54.71 48.82 47.71 56.73 63.4 70.41 47.18 GCA_003662535_Candidatus_Bathyarchaeota_archaeon 62.88 66.4 61.74 62.82 63.22 62.72 61.98 61.36 62.87 63.08 63.92 63.41 62.09 60.46 60.56 61.39 61.29 61.99 64.32 63.47 61.72 63.25 61.12 62.46 62.64 61.69 61.41 63.81 64.64 63.76 60.31 63.01 63.44 63.46 63.82 61.75 61.36 62.43 62.94 62.33 63.75 62.15 60.91 63.6 62.5 62.91 61.75 GCA_002254975_Candidatus_Bathyarchaeota_archaeon_ex4484_218 47.02 52.01 49.51 47.5 45.81 48.18 47.75 47.56 47.31 48.13 47.38 50.58 56.47 47.14 48.63 48.47 46.62 50.4 45.63 52.28 52.19 51.07 49.53 72.61 50.89 51.49 51.54 45.95 50.5 49.34 50.54 48.78 51.21 48.77 49.36 47.59 47.59 49.31 51.48 46.88 48 51.17 58.07 47.09 50.86 50.57 47.79 46.83 48.27 GCA_003096235_Candidatus_Bathyarchaeota_archaeon 64.8 61.18 61.18 77.28 65.04 62.86 61.36 66.21 61.94 63.59 65.7 69.29 61.81 61.82 61.7 65.04 60.82 61.64 61.13 65.42 65.33 61.21 60.3 64.33 62.54 60.77 62.91 65.75 64.24 65.55 65.14 65.55 65.48 59.98 65.77 64.01 61.35 65.57 67.96 64.16 67.8 61.25 61.31 64.23 61.44 61.11 61.66 62.08 GCA_002255025_Candidatus_Bathyarchaeota_archaeon_ex4484_135 47.73 52.1 57.72 47.69 47.27 46.58 48.02 48.84 47.59 48.05 47.74 52.38 49.39 47.54 51.12 51.26 47.42 52.38 46.38 54.46 53.71 51.87 50.25 49.55 53.37 53.04 52.77 47.04 51.98 49.72 51.72 49.85 53.36 47.11 51.73 49.23 47.69 49.64 53.17 47.62 47.88 53.36 49.56 47.9 52.44 51.78 48.56 47.15 49.36 48.66 GCA_003661965_Candidatus_Bathyarchaeota_archaeon 62.37 60.95 61.75 62.38 62.76 63.17 60.22 62.05 65.14 62.64 63.43 62.6 61.02 60.82 75.78 62.27 61.54 60.83 59.47 63.61 61.96 61.84 61.55 62.28 62.81 61.32 61.06 62.76 62.31 63.64 63.42 64.7 62.33 61.6 63.06 61.54 59.71 63.54 63.8 61.3 62.82 60.37 59.67 62.26 64.89 65.46 60.71 61.24 62.21 GCA_005888745_Candidatus_Bathyarchaeota_archaeon 67.8 48.67 47.22 63.98 44.62 49.47 66.31 47.29 84.64 47.15 84.52 47.54 46.94 87.8 46.71 47.2 84.84 47.68 44.63 49.54 48.53 48.32 46.85 47.74 48.66 48.93 48.55 44.41 48.21 46.73 48.13 47.46 49.43 48.84 48.47 46.66 84.3 47.18 48.79 84.3 63.8 48.35 48.22 68.92 48.15 48.15 46.92 85.35 47.32 47.3 47.43 GCA_003662305_Candidatus_Bathyarchaeota_archaeon 61.75 63.04 61.36 61.24 62.56 61.76 62.46 60.84 90.59 63.43 62.94 62.31 61.43 61.3 64.69 60.98 61.83 61.43 61.61 62.75 60.88 62.52 60.56 61.62 61.57 59.54 62.41 62.03 63.38 62.31 60.56 61.76 62.9 63.89 61.75 61.4 63.02 61.76 63.07 60.88 63.11 62.09 61.98 62.38 65.6 76.55 61.41 61.64 61.09 65.34 GCA_005882955_Candidatus_Bathyarchaeota_archaeon 87.88 49.92 47.99 63.26 45.4 49.78 65.85 48.41 69.08 47.94 68.59 48.06 48.19 67.94 47.36 48.06 68.72 48.41 45.94 49.75 49.96 48.53 47.41 49.05 49.31 49.06 49.25 45.02 48.7 47.19 48.91 47.33 49.9 49.11 48.73 47.36 68.45 48.18 48.9 68.17 63.9 48.89 48.97 92.48 48.75 48.67 48.5 68.29 48.26 47.6 47.78 69.04 GCA_005888635_Candidatus_Bathyarchaeota_archaeon 62.91 61.72 67.82 61.86 62.08 60.04 70.65 61.06 62.08 61.84 62.23 63.81 70.75 85.46 59.47 65.13 69.94 69.72 61.89 60.34 62.54 64.29 61.91 62.54 62.97 62.65 67.6 63.02 62.33 61.78 60.37 61.72 62.01 63.02 61.23 62.82 68.77 62.49 60.62 61.4 63.1 69.39 69.81 62.15 63.01 62.14 70.14 61.13 62.04 60.7 61.76 GCA_001775995_Candidatus_Bathyarchaeota_archaeon_RBG_16_48_13 47.01 50.95 48.8 47.62 46.52 48.71 47.87 50.57 48.01 49.75 48.34 50.34 49.4 47.95 48.58 49.48 48.3 51.62 47.06 51.8 51.76 50.8 51.29 50.12 50.92 50.92 51.53 47.12 50.99 48.18 50.77 50.54 51.81 49.04 49.8 50.08 48 50.53 50.87 48.67 47.84 50.92 50.39 48.07 51.2 50.43 49.56 48.21 50.45 50.03 48.31 47.63 48.32 GCA_003601695_Candidatus_Bathyarchaeota_archaeon 46.25 56.35 53.23 47.81 47.31 48.78 47.21 52.87 47.23 52.2 47.71 71.28 49.79 47.33 50.45 51.77 47.49 55.64 47.8 57.25 56.43 55.27 54.05 50.85 57.07 55.91 57.28 46.85 54.7 50.77 73.65 53.1 56.62 48.29 70.8 52.86 47.32 53.83 56.5 46.89 47.84 61.04 49.67 47.43 56.16 54.22 51.8 47.25 52.68 49.48 50.95 47.27 47.58 49.53 GCA_005883075_Candidatus_Bathyarchaeota_archaeon 62.63 62.35 67.81 62.61 62.35 60.77 80.91 61.77 61.81 61.95 62.43 62.79 85.72 68.79 59.82 63.61 82.8 81.13 62.33 62.38 62.28 63.59 60.25 62.27 61.96 61.75 67.33 61.95 61.82 62.11 60.67 61.57 61.22 62.04 61.06 61.72 81.22 62.57 61.68 62.7 63.38 84.83 91.76 62.54 63.41 61.49 83.37 61.53 61.05 60.15 61.24 69.7 GCA_001915065_archaeon_13_2_20CM_2_53_6 74.72 48.84 47.28 62.79 44.89 49.47 65.3 46.9 67.27 46.84 67.3 47.81 46.92 67.5 46.33 47.33 67.69 47.84 45.14 48.74 49.22 48.34 46.85 48.19 48.82 48.78 48.48 45.04 47.91 46.58 48.57 46.74 48.79 49.28 48.22 46.26 67.19 46.88 48.27 67.46 63.01 48.36 48.04 75.74 48.85 48.24 46.79 67.86 46.99 46.85 47.43 67.78 75.61 47.91 47.18 GCA_003133625_Candidatus_Bathyarchaeota_archaeon 77.25 61.98 62.64 65.3 65.68 63.56 62.3 70.45 61.91 63.59 68.53 66.04 62.81 62.01 62.69 76.18 63.21 61.93 61.87 67.49 78.23 62.3 62.73 74.81 63.21 62.59 61.71 64.66 63.39 65.92 67.54 67.35 64.67 61.1 67.66 75.52 62.1 67.92 65.32 69.31 65.83 62.1 61.2 68.08 63.01 61.47 61.84 62.62 65.19 63.16 61.7 63.12 63.1 GCA_002490245_Candidatus_Bathyarchaeota_archaeon_B24−2 47.12 56.71 53.16 47.67 47.91 48.89 48.31 53.15 48.82 52.96 48.17 57.92 50.51 48.36 50.94 52.95 47.96 56.04 48.12 57.67 57.14 56.35 55.13 52.25 58.31 56.32 57.69 47.8 55.44 50.97 57.01 53.8 57.66 48.82 57.37 52.77 48.25 54.87 56.27 48.14 48.22 57.95 50.79 47.84 56.36 54.96 52.92 47.6 53.88 50.34 52.5 47.99 48.3 50.33 56.5 47.89 GCA_001273335_miscellaneous_Crenarchaeota_group−1_archaeon_SG8−32−3 68.73 61.77 61.87 65.54 65.5 62.99 61.45 79.57 61.57 64.06 68.38 65.32 59.66 60.75 61.84 69.29 60.27 60.92 62.12 67.99 70.05 60.9 60.89 68.19 61.61 61.21 60.9 64.19 63.85 65.37 67.47 67.61 64.38 60.37 68.42 69.6 60.87 67.4 65.25 68.03 64.87 60.7 61.18 67.91 61.44 60.97 62.19 61.51 65.63 61.04 60.9 60.77 61.06 71.06 GCA_002726865_Candidatus_Bathyarchaeota_archaeon 44.47 48.5 47.72 44.78 57.04 45.78 44.94 47.02 44.39 46.42 44.41 47.77 45.82 44.5 57.14 55.07 44.22 47.58 55.62 48.69 48.55 48.64 48.03 46.5 47.88 47.8 48.86 55.83 47.98 46.03 48.16 47.53 48.19 45.7 48.49 46.94 44.38 48.02 47.73 44.38 45.14 48.82 45.97 44.53 46.93 48.17 46.59 44.41 47.26 45.9 47.13 44.4 45.4 46.18 47.55 44.38 47.27 GCA_005888735_Candidatus_Bathyarchaeota_archaeon 61.43 61.1 72.22 62.8 61.98 60.92 68.61 61.78 61.21 62.03 61.77 61.86 68.7 67.89 63.2 62.69 68.2 68.78 62.14 61.26 61.82 64.44 60.14 61.53 63.35 61.05 68.36 62.63 61.82 62.32 60.12 61.28 60.91 62.81 60.92 62.63 67.8 61.37 61.42 62.66 62.3 67.88 68.67 61.07 62.72 62.26 68.63 61.33 61.67 61.32 62.44 68.32 68.42 61.91 60.95 GCA_003662645_Candidatus_Bathyarchaeota_archaeon 48.95 58.66 55.46 48.76 48.64 49.42 48.93 53.78 47.86 54.02 48.26 63.39 50.97 48.5 52.67 53.14 48.53 59.03 48.37 59.39 58.28 56.96 56.71 52.15 59.25 57.89 60.62 47.9 56.7 52.83 62.45 54.89 59.04 49.44 62.5 53.69 48.43 56.14 58.9 48.32 48.92 66.86 51.31 48.89 59.36 56.66 53.4 47.95 55.02 50.58 53.64 48.6 49.75 50.63 62.28 48.76 58.89 48.79 62.98 61.84 67.6 62.86 62.27 61.96 70.46 62.96 61.66 61.42 62.75 62.79 70.58 85.63 60.45 64.15 69.65 69.58 62.27 62.52 62.38 64.8 61.18 62.36 63.42 62.2 67.55 61.93 62.78 62.35 61.07 61.63 62.07 62.36 61.63 62.26 69.28 62.07 62.63 63.57 62.55 69.5 69.42 62.55 64.41 61.75 69.82 61.59 61.49 60.3 61.75 91.56 69.47 64.35 62.64 68.2 GCA_005882955_Candidatus_Bathyarchaeota_archaeon GCA_001273335_miscellaneous_Crenarchaeota_group−1_archaeon_SG8−32−3 49.32 57.64 50.85 48.28 47.07 53.99 48.53 67.6 48.42 67.36 48.63 54.08 49.92 47.97 48.66 49.88 49.01 58.06 47.09 62.02 59.22 63.68 57.11 51.04 65.04 59.44 59.38 47.43 62.47 48.8 55.62 79.75 65.37 48.5 55.12 64.39 48.44 56.3 59.37 48.1 48.6 55.41 48.87 49.08 57.27 63.76 66.39 48.5 68.54 49.81 50.06 48.33 48.98 49.82 54.18 48.59 54.12 47.04 55.6 64.8 61.52 68.05 62.97 63.54 61.72 69.71 60.83 61.82 62.39 62.22 62.11 70.14 73.03 61.48 63.54 69.13 69.68 62.88 62.36 62.63 64.43 60.6 61.04 62.49 61.69 67.75 63.64 62.37 62.91 60.7 62.06 62 62.58 61.21 62.08 69.1 63.59 60.39 61.99 62.46 69.02 70.46 62.24 63.79 62.76 69.74 61.72 62.29 61.34 62.05 73.63 69.88 62.78 61.21 68.81 73.19 GCA_005882905_Candidatus_Bathyarchaeota_archaeon GCA_003662205_Candidatus_Bathyarchaeota_archaeon 46.56 51.48 50.66 46.49 60.87 47.37 46.97 48.46 46.85 48.29 46.59 50.81 48.41 46.41 65.92 62.4 46.41 50.76 60.32 51.82 51.55 50.94 50.58 48.43 51.13 50.29 51.18 60.25 50.3 48.59 50.99 49.67 51.37 47.17 52.02 48.46 46.84 50.37 51.04 46.54 46.94 52.28 48.1 46.83 50.14 50.72 47.76 46.23 48.5 47.31 50.1 46.65 47.24 48.51 50.36 46.74 51.08 61.83 51.52 49.53 66.56 61.99 61.83 65.71 67.03 64.47 60.95 67.72 62.52 64.66 71.73 66.98 61.53 61.76 63.01 66.02 60.46 62.74 61.46 72.57 66.24 62 62.09 65.73 61.96 60.87 61.77 66.1 64.53 67.44 66.29 71.38 66.32 61.05 72.71 66.44 61.75 70.52 67.76 66.49 75.42 62.25 60.8 70.68 62.31 61.75 61.51 62.64 65.84 63.56 62.06 61.69 62.01 67.08 67.18 61.21 61.71 61.02 GCA_004376975_Candidatus_Bathyarchaeota_archaeon GCA_001593935_Candidatus_Bathyarchaeota_archaeon_B26−2 47.53 58.41 54.7 47.94 48.05 49.34 48.35 54.21 48.49 54.1 48.41 61.2 51.05 48.5 51.79 53.42 48.14 59.26 48.15 58.26 58.42 58.11 57.03 52.25 58.4 57.91 60.35 47.78 56.98 52.03 63.28 54.7 58.65 49.38 63.22 53.83 48.23 56.32 58.37 48.07 48.64 82.24 51.36 48.72 59.03 56.85 53.68 47.95 54.66 50.74 53.19 48.27 48.88 51.24 61.07 47.7 57.41 48.51 67.74 56.16 51.74 63.7 65.41 62.05 64.25 64.42 66.71 62.46 64.21 64.01 67.55 64.69 65.99 61.75 61.81 62.78 63.57 62.22 61.75 65.25 64.77 63.46 61.67 62.76 62.76 61.96 61.84 62.53 65.65 80.97 64.75 62.26 65.08 64.09 65.06 65.2 63.38 61.97 65.25 65.47 63.15 65.01 62.3 61.3 64.71 63.28 63.72 61.81 64.71 64.05 62.42 63.64 62.12 61.97 64.32 63.11 61.88 62.42 61.83 64.17 GCA_001593925_Candidatus_Bathyarchaeota_archaeon_B26−1 GCA_001776015_Candidatus_Bathyarchaeota_archaeon_RBG_16_57_9 44.57 47.23 47.49 44.78 97.95 45.49 45.32 47.03 45.39 46.63 45.33 47.56 46.78 45.15 55.88 54.45 45.12 47.63 59.95 48.89 48.62 48.19 48.05 46.37 48.34 47.76 48.73 60.15 47.28 46 47.85 47.91 48.55 45.38 48.03 46.24 45.19 48.22 48.29 45.32 45.76 48.77 46.65 45.4 47.32 48.5 46.49 45.27 47.51 46.25 47.05 45.21 45.7 47.02 47.17 45.03 48.03 57.23 48.29 47.73 60.8 48.08 62.59 64.68 61.53 63.48 64.49 70.2 62.11 63.07 63.19 73.59 63.29 65.01 62.52 62.48 58.87 62.62 62.84 62.74 65.34 65.05 63.1 61.41 61.54 62.96 63.25 61.58 62.86 65.57 68.62 64.05 62.11 63.7 63.4 64.83 64.49 63.03 62.1 64.89 64.66 62.96 64.55 62.19 62 64.68 63.81 63.15 61.44 64.17 62.86 62 63.45 62.4 61.98 62.56 62.96 62.8 62.09 61.81 63 68.64 GCA_001593845_Candidatus_Bathyarchaeota_archaeon_B63 GCA_003133625_Candidatus_Bathyarchaeota_archaeon 47.62 56.66 51.3 47.51 47.01 50.49 47.4 76.85 47.81 77.18 47.92 53.57 48.81 47.81 48.46 50.14 48.02 57.21 47.55 63.05 58.95 62.95 56.72 49.76 64.04 58.57 58.81 47.03 62.16 47.98 54.75 69.01 64.17 48.89 54.44 63.09 48.01 56.33 58.31 47.65 48.04 54.92 48.94 48 56.86 64.43 74.43 47.5 75.93 48.52 48.89 47.53 48.51 50.82 52.84 47.64 54.15 47.33 54.95 70.43 48.84 55.39 46.66 GCA_005884605_Candidatus_Bathyarchaeota_archaeon 62.57 62.42 67.87 60.66 60.54 62.34 80.86 61.09 60.08 63.45 61.88 62.53 85.86 71.61 60.51 63.36 83.2 81.54 61.06 61.14 61.79 63.75 59.91 62.52 61.75 61.17 67.24 62.48 62.24 62.54 59.74 62.94 61.86 62.54 61.33 61.83 80.79 62.63 61.26 60.98 61.4 85.23 87.94 62.45 61.59 62.14 83.18 61.41 60.77 60.33 61.97 72.66 88.2 61.45 60.75 68.55 72.07 70.32 62.46 61.94 61.58 GCA_003601785_Candidatus_Bathyarchaeota_archaeon 48.23 61.74 55.44 49.24 47.79 50.58 48.78 61.36 48.75 61.66 48.72 57.84 50.85 48.69 52.05 52.93 48.55 62.43 48.69 76.75 65.84 71.03 58.6 52.49 98.44 65.34 63.18 48.62 71.63 50.68 57.43 64.11 73.07 50.41 58.14 60.23 48.6 58.47 65.99 49.06 49.09 58.28 50.91 48.73 62 69.38 61.16 48.29 63.88 51.51 53.42 48.59 49.24 51.41 57.02 49.28 58.35 48.06 58.87 64.63 51.82 58.32 48.18 63.64 GCA_005882895_Candidatus_Bathyarchaeota_archaeon 62.91 61.92 68.45 62 61.35 62.78 82.43 60.98 60.72 61.73 61.51 61.85 82.1 69.71 61.02 63.58 88.81 82.71 62.18 62.04 61.64 64.16 60.51 62.01 61.92 61.39 68.03 62.98 62.18 61.63 60.49 63.18 61.71 61.25 61.84 61.26 82.36 61.86 61.54 61.65 61.94 82.07 83.17 62.15 62.06 61.97 89.28 61.67 61.69 60.97 62.48 69.83 83.57 63.28 61.47 68.25 69.87 69.57 60.66 62.05 63.88 83.23 GCA_005883075_Candidatus_Bathyarchaeota_archaeon 67.9 49.1 48.12 64.9 45.07 50.09 66.48 47.29 85.57 47.44 85.34 47.4 47.19 87.87 46.71 47.07 86.62 47.7 45 50 48.96 48.66 47.06 48.05 48.56 48.51 48.43 45 47.89 47.17 48.14 47.07 48.99 49.25 48.19 46.61 85 46.93 48.83 85.59 64.42 48.75 48.51 68.49 48.2 48.39 47.11 86.56 47.26 47.29 47.76 88.13 68.32 48.35 47.41 68.2 48.01 44.7 48.5 47.99 47.03 48.43 45.42 47.89 48.65 GCA_003152955_Candidatus_Bathyarchaeota_archaeon 62.7 62.06 64.84 61.39 62.31 60.41 64.22 61.67 61.07 61.07 62.26 61.21 64.11 64.64 61.07 62.72 64.77 63.7 61 61.81 61.53 72.24 60.82 61.89 62.81 60.04 63.73 61.61 62.15 61.97 61.05 61.96 61.09 61.59 61.68 61.88 63.79 62.12 60.69 62.26 61.85 63.57 64.46 61.4 61.75 62.15 63.63 60.73 61.02 60.47 61.66 63.38 63.17 62.95 60.84 63.6 64.23 63.82 61.23 61.6 61.02 63.23 63.67 GCA_013330975_Candidatus_Bathyarchaeota_archaeon 48.13 56.54 51.34 48.31 47.44 49.81 48.23 65.46 47.91 64.81 48.1 53.91 49.41 48.09 48.64 49.81 48.21 56.94 47.08 61.62 58.46 62.64 56.14 50.28 62.49 58.04 57.16 46.81 61.2 48.15 54.84 66.92 63.69 48.49 55.21 61.94 47.97 55.89 58.07 47.99 49 55.96 49.22 48.53 56.31 62.9 64.06 47.84 65.83 48.9 50.23 48.26 48.52 50.23 53.02 47.83 53.89 46.66 55.3 66.02 49.68 55.97 47.83 66.98 62.79 48.55 GCA_005884195_Candidatus_Bathyarchaeota_archaeon 61.82 60.77 67.54 61.38 61.96 60.92 86.64 61.16 62.29 62.05 62.03 61.74 80.37 69.07 60.46 62.65 81.93 91.62 62.46 61.22 61.68 63.9 61.16 61.63 61.67 60.75 67.3 61.54 62.41 61.75 59.2 62.07 61.22 62.17 60.58 61.37 84.99 60.83 60.92 60.93 61.17 80.23 80.66 61.34 61.6 61.84 82.23 60.64 60.86 60.15 62.27 69.78 80.88 61.81 60.61 68.82 69.47 69.56 60.61 62.14 62.33 81.2 82.27 63.93 GCA_003662485_Candidatus_Bathyarchaeota_archaeon 47.27 50.36 51.44 47.92 46.65 48.11 48.1 48.31 48.93 48.02 48.31 50.87 78.44 48.01 49.48 50.76 48.17 50.23 46.34 51.96 51.42 49.78 49.85 57.9 51.26 50.65 51.25 46.41 49.8 50.32 50.99 48.09 50.72 48.17 50.95 47.95 48.36 49.2 50.8 48.21 48.71 51.76 71.4 47.76 50.37 49.79 48.39 48.06 48.85 56.49 50.4 47.81 47.92 50.05 50.65 47.48 51.55 46.32 51.52 50.09 49.08 51.52 47.1 48.9 51.2 47.91 49.01 GCA_003601775_Candidatus_Bathyarchaeota_archaeon 64.25 64.95 62.62 62.82 62.97 63.3 61.75 64.48 62.34 64.2 62.15 64.31 63.97 62.04 −1 63.23 62.57 62.48 71.87 62.81 62.27 61.87 65.29 61.58 61.73 65.3 62.47 64.88 66.03 63.44 59.3 61.49 62.64 70.32 63.04 62.04 61.87 62.48 63.41 62.69 64.06 61.97 62.13 63.24 64.27 62.67 62.11 64.14 61.79 61.18 63.16 63.63 63.74 62.43 62.25 62.6 62.89 64.23 62.72 65.52 65.44 62.89 63.02 62.11 62.91 GCA_005883085_Candidatus_Bathyarchaeota_archaeon 67.35 47.61 47.59 64.23 44.32 49.78 65.81 46.98 85.02 46.54 84.64 47.18 46.86 86.98 46.43 46.78 85.83 47.2 43.67 49.72 48.65 48.11 46.85 47.98 47.8 48.28 48.25 44.45 47.54 46.72 47.65 46.82 48.62 49.02 47.42 45.98 84.29 46.57 48.5 84.76 64.27 47.74 47.88 68.22 48.35 48.28 46.18 85.75 47.27 46.84 47 87.48 68.16 48.01 46.77 67.93 47.68 44.16 48.31 48.16 46.35 47.89 44.97 46.83 48.04 92.36 47.21 47.86 GCA_007050885_Candidatus_Bathyarchaeota_archaeon 64.27 60.36 62.86 66.59 61.53 61.38 62 70.01 60.76 62.59 64.1 64.41 61.95 62.47 63.68 65.43 62.27 63.55 63.41 62.5 65.14 63.17 65.18 64.24 91.83 61.41 62.79 61.51 60.68 63.63 63.98 64.34 62.23 61.25 62.21 63.78 61.69 62.66 64.28 63.79 63.03 61.99 61.77 64.03 62.03 61.65 62.46 61.57 65.25 62.79 61 62.04 62.19 65.48 71.01 62.21 62.89 62.58 62.9 61.37 62.17 62.22 63.09 62.84 62.35 61.94 GCA_001768965_archaeon_RBG_16_50_20 51.86 48.84 46.89 52.06 45.03 50.17 51.96 47.65 52.3 47.61 52.06 48.5 47.72 52.05 46.24 47.19 51.76 48.18 45.75 50 49.53 48.59 48.07 48.5 49.06 48.82 48.61 45.72 48.73 46.65 49.14 47.35 49.23 49.9 49.1 47.03 52.35 48.3 48.56 51.62 52.12 48.98 48.15 52.31 49.1 48.77 47.72 52.01 47.77 48.64 48.36 51.65 51.91 48.18 48.33 52.06 48.17 44.61 49.44 47.56 46.8 49.26 45.09 48.24 48.77 52.12 48.4 47.8 51.53 GCA_003662515_Candidatus_Bathyarchaeota_archaeon 60.89 62.41 61.63 62.46 63.85 61.68 60.96 60.69 71.42 62.83 63.27 62.86 62.16 63.07 64.24 61.94 61.99 61.23 62.79 62.26 62.29 62.93 61.47 61.63 61.66 60.49 61.73 62.02 63.63 63.5 60.06 63.28 62.12 63.02 62.37 62 62.35 63.47 63.08 60.68 62.36 61.69 61.93 63.03 65.77 72.22 61.72 62.65 60.89 65.3 71.81 62.54 61.86 62.72 60.63 62.43 62.87 62.38 61.51 63.99 62.75 61.37 61.9 63.01 61.66 62.88 61.23 GCA_003141855_Candidatus_Bathyarchaeota_archaeon 47.15 55.71 50.9 47.43 46.72 49.79 47.44 82.26 47.35 75.66 47.21 53.47 48.44 47.24 47.78 49.24 47.28 56.14 47.31 61.06 58.14 61.85 56.31 49.29 62.46 57.83 57.68 46.75 60.72 47.57 54 67.85 63.18 48.39 53.45 62.38 47.34 55.63 57.48 47.36 47.77 54.27 48.34 47.26 55.78 63.02 73.37 47.35 75.06 48.08 48.92 47.45 48.18 50.04 52.42 46.66 53.6 46.82 53.85 68.75 48.51 54.48 46.84 79.39 62.14 47.28 65.8 48.01 46.98 48 GCA_001915065_archaeon_13_2_20CM_2_53_6 60.99 61.37 67.41 60.76 60.41 62.02 70.2 60.48 61.74 61.11 61.86 61.6 69.57 73.24 58.38 61.65 69.52 69.51 61.98 61.32 61.52 63.23 60.52 61.57 60.96 61.27 67.64 61.88 62.72 61.26 59.53 62.27 61.51 63.27 61.24 60.37 69.03 61.55 60.69 62.91 60.9 69.21 70.36 61.32 61.9 62.1 70.11 61.9 60.15 61.41 62.44 73.77 69.74 61.33 59.81 68.45 73.53 91.98 61.97 61.81 62.68 70.76 70.13 63.77 69.57 63.01 61.53 61.95 GCA_003152955_Candidatus_Bathyarchaeota_archaeon 51.05 48.91 47.37 51.72 44.67 49.25 51.28 48.22 51.44 47.84 51.44 48.68 47.04 50.79 46.86 47.3 51.02 48.31 44.84 49.1 49.23 47.88 47.13 48.6 48.35 48.65 48.9 44.44 48.17 46.84 49.07 47.62 49.7 49.2 48.56 47.34 51.63 47.48 48.28 51.06 51.55 48.98 47.67 51.48 49.02 48.89 47.33 50.86 47.9 47.49 47.23 51.01 51.91 48.39 47.77 51.31 48.25 44.94 48.77 48.31 47.06 48.71 44.99 48.79 48.89 51.37 48.37 47.95 51 72.37 47.49 GCA_003661975_Candidatus_Bathyarchaeota_archaeon 63.2 63.65 60.99 63.03 64.39 71.55 61.39 63.6 62.27 72.43 64.97 64.94 61.47 60.67 62.36 63.08 61.23 61.24 62.24 65.86 62.57 60.91 60.51 62.52 62.26 61.28 61.74 64.53 66.77 64.01 63.47 66.16 63.65 62.19 65.05 63.11 61.08 65.22 64.97 63.19 64.3 62.07 61.94 63.77 61.82 63.16 61.62 63 63.89 63.65 62.66 62.32 61.78 63.35 62.82 61.53 62.23 61.95 64 67.04 71.71 61.55 61.75 60.66 62.5 64.85 62.38 63.52 61.7 NRA7_48_Candidatus_Bathyarchaeota_archaeon_52_381 47.21 51.08 49.86 47.93 46.4 48.23 48.07 48.64 47.2 48.35 47.29 50.37 58.74 47.26 49.37 50.43 47.33 50.08 46.13 51.91 51.55 50.44 50.39 58.79 50.77 50.91 51.26 46.11 50.02 49.43 50.69 49.13 50.39 48.43 50.82 48.36 47.26 50.11 50.73 47.22 48.5 51.81 58.63 47.97 50.83 50.05 48.32 47.04 49.05 58.82 48.87 46.95 48 50.12 49.72 47.59 51.07 46.38 51.02 49.89 48.62 51.6 46.55 49.12 51.45 47.26 49.68 58.58 47.57 48.19 48.78 47.84 GCA_004376385_Candidatus_Bathyarchaeota_archaeon 64.64 62.26 61.73 78.2 65.76 63.52 61.75 65.82 62.05 65.07 65.99 71.47 61.69 62.67 61.88 64.86 62.01 62.42 62.51 65.81 65.01 61.22 60.88 64.52 61.89 61.74 62.48 67.3 64.78 65.7 64.9 65.63 66.24 62.16 65.82 64.44 61.79 65.62 68.93 64.63 69.53 62.37 61.86 65.41 62.11 62.02 61.69 63.02 80.91 62.35 62.67 62.24 61.97 65.57 64.68 62.17 62.52 62.31 66.28 64.98 64.24 61.28 62.12 61.7 61.65 62.28 66.46 62.09 62.38 64.36 GCA_003096235_Candidatus_Bathyarchaeota_archaeon 46.4 60.6 52.47 46.79 47.72 50.85 46.9 55.53 46.57 55.37 46.81 53.69 48.79 46.68 48.37 50.08 46.87 60.86 47.52 58.05 56.47 57.4 81.25 49.63 57.36 57.17 65.97 48 58 47.65 55.25 57.59 57.68 48.61 54.36 54.92 47.02 76.67 57.07 46.56 47.43 55.97 48.9 47.02 59.45 57.01 54.82 46.35 55.93 48.95 49.51 46.49 47.36 50.21 53.47 46.54 53.86 47.59 55.51 56.74 49.98 56 47.99 56.15 57.5 46.9 56.02 48.78 46.8 47.55 55.91 46.72 49.55 GCA_001775995_Candidatus_Bathyarchaeota_archaeon_RBG_16_48_13 63.67 61.08 64.22 63.53 61.49 62.08 61.91 63.04 61.12 61.73 61.68 62.61 64.82 61.33 62.05 65.04 61.76 61.71 63.24 62.3 63.66 63.83 63.01 63.57 61.46 62.83 62.37 64.43 63.08 62.06 62.39 62.62 63.38 63.4 61.94 63.25 62.31 62.76 62.88 63.53 63.59 61.85 61.9 63.9 63.7 62.65 61.93 61.64 62.07 62.12 63.15 62.99 63.36 65.5 61.68 62.03 63.73 64.35 62.51 62.91 63.02 61.62 62.42 60.74 61.47 63.89 62.46 61.62 62.43 61.78 62.34 GCA_003601835_Candidatus_Bathyarchaeota_archaeon 46.81 57.71 53.3 47.69 48.42 49.56 48.01 54.01 47.15 53.86 47.49 65.72 49.64 47.68 51.1 52.33 47.52 57.89 47.82 57.76 57.54 57.06 56.11 51.53 57.75 57.24 59.12 47.31 56.31 50.65 69.37 55.01 57.53 49.15 68 53.43 47.43 55.15 56.99 47.46 47.6 62.99 49.66 47.26 58.03 55.96 53.34 47.29 54.32 49.88 51.76 47.68 47.5 49.68 65.07 47.38 56.9 48.4 62.88 54.9 51.04 63.78 48.22 54.91 57.64 47.72 54.68 49.93 47.51 49.04 53.81 48.07 50.32 55.55 GCA_001776015_Candidatus_Bathyarchaeota_archaeon_RBG_16_57_9 60.69 63.25 61.06 61.71 61.54 62.38 61.11 62.24 61.23 62.2 61.36 60.9 61.54 62.35 −1 61.27 62.21 61.15 70.57 61.59 61.15 63.25 69.54 61.69 62.17 66.29 63.76 62.85 63.33 62.74 −1 64.35 61.41 68.42 61.57 62.33 61.41 61.3 61.8 62.33 60.73 60.87 61.67 62.12 62.67 62.49 61.16 61.61 61.42 59.57 61.17 62.05 61.25 62.29 61.97 61.85 61.01 62.51 61.1 63.23 64.15 61.65 61.63 60.89 60.64 67.45 60.97 61.48 61.94 62.57 61.97 62.48 GCA_005881615_Candidatus_Bathyarchaeota_archaeon 68.69 49.09 47.27 64.31 44.15 49.78 66.15 47.71 85.03 47.44 89.06 47.29 47.52 84.23 46.9 47.23 85.22 47.71 44.12 49.34 48.85 48.19 46.66 47.82 48.78 48.8 48.34 44.28 48.08 46.76 47.89 47.13 49.19 49.19 48.01 46.44 88.78 46.62 48.96 87.78 63.91 48.23 48.49 68.68 48.46 48.16 47.28 85.37 47.7 47.94 47.24 83.61 69.03 47.86 47.04 67.48 47.93 44.38 47.98 48.51 46.5 48.13 45.12 47.76 49.03 84.4 47.99 48.04 83.76 52.01 47.38 51.16 47.16 46.59 47.05 GCA_001593865_Candidatus_Bathyarchaeota_archaeon_B24 61.96 63.28 62.99 61.47 61.96 64.39 62.1 62.1 62.28 63.53 63.66 62.8 63.6 62.66 61.49 62 62.14 62.13 63.67 62.42 61.4 61.9 61.62 61.09 62.82 62.18 62.34 62.98 65.38 62.66 59.4 62.72 61.71 63.67 62.32 61.49 62.4 62.11 63.06 62.59 63.2 62.57 61.07 62.64 63.78 63.02 62.36 64.32 61.15 62.67 62.5 63.97 63 63.18 60.26 62.87 64.91 63.39 60.91 65.32 64.61 61.3 62.51 61.35 61.39 64.86 62.2 63.21 60.92 64.91 62.4 64.99 62.38 GCA_002495485_Candidatus_Bathyarchaeota_archaeon_UBA185 72.02 48.01 46.3 61.71 44.09 48.41 63.25 46.38 66 46.65 65.75 46.92 46.98 65.56 45.87 46 65.54 46.76 43.42 48.05 48.15 47.1 46.2 47.34 47.83 47.07 47.41 43.61 46.45 45.82 46.81 45.67 47.36 48.26 46.47 45.78 65.22 46.33 47.63 65.16 62.23 47.72 47.05 72.57 47.6 47.75 46.81 65.66 46.91 46.44 46.64 65.55 72.97 46.76 46.81 76.47 46.69 43.67 47.89 47.32 45.48 47.22 44.58 47.38 47.83 65.82 46.84 47.13 64.85 51.54 46.3 51.23 46.86 46 46.52 65.87 GCA_001775965_Candidatus_Bathyarchaeota_archaeon_RBG_13_60_20 59.65 63.2 59.28 61.21 60.62 61.2 61.2 61.58 60.08 60.74 59.46 61.32 60.65 60.2 58.1 60.19 60.96 61 70.33 60.4 60.26 59.63 68.04 60.13 56.93 65.74 59.99 61.72 62.67 59.53 56.45 59.56 59.69 67.96 61.02 60.82 59.44 60.66 61.14 60.2 60.91 60.05 61.56 61.17 62.29 61.48 59.88 63.48 60.64 60.6 60.63 60.34 60.12 60.92 60.81 61.53 60.14 60.93 58.9 62.96 62.99 60.06 60.49 59.38 60.38 66.58 62.77 60.36 60.83 60.89 60.72 61.27 99.5 61.28 GCA_004376645_Candidatus_Bathyarchaeota_archaeon 47.03 60.05 52.78 48.02 47.33 49.1 47.68 55.79 47.72 55.37 47.98 55.24 49.11 47.58 49.51 51.02 47.63 62.14 47.47 59.82 59.63 60.02 58.97 50.04 59.71 59.11 60.51 46.84 60.21 48.46 55.59 56.77 60.33 48.8 55.46 55.26 47.9 57.81 59.24 47.95 48.59 56.19 49.51 47.85 59.13 58.56 55.24 47.43 56.26 49.69 51.23 48.09 48.03 50.41 54.26 47.58 54.92 47.59 56.53 56.49 49.91 56.01 47.2 56.68 59.9 48.03 55.73 49.23 47.76 48.33 56.16 47.89 49.63 57.35 55.95 47.73 46.6 GCA_003661945_Candidatus_Bathyarchaeota_archaeon 65.43 64 63.36 65.5 73.23 64.11 62.71 65.75 63.05 64.58 68.82 66.58 61.92 62.36 62.99 65.14 62.07 62.73 62.74 67.82 65.38 62.37 63.38 65.04 62.72 61.61 62.45 66.05 65.59 73.4 64.37 67.92 65.73 62.7 68.16 65.59 62.06 67.26 66.72 66.03 66.37 61.65 62.17 67.01 63.02 61.92 62.36 64.16 65.3 63.48 62.82 62.67 62 66.17 65.66 62.73 62.97 61.99 67.24 65.08 64.3 62.86 62.88 61.66 61.87 62.98 62.59 63.56 61.88 64.69 65.42 62.37 61.45 62.83 61.32 GCA_005884605_Candidatus_Bathyarchaeota_archaeon 68.73 48.58 47.76 63.55 44.26 50.19 65.98 47.15 85.47 47.17 84.99 47.42 47.5 87.72 47.45 46.99 85.4 47.85 44.21 49.56 48.72 48.04 46.88 48.03 48.43 48.88 48.64 44.87 47.43 46.91 47.85 47.17 49.29 49.62 48.04 46.38 84.56 47.14 48.67 84.69 64.05 47.91 48.73 69.77 48.54 48.36 47.32 85.72 47.58 46.9 47.33 87.44 69.83 48.44 46.86 68.6 48.14 44.46 48.07 48.3 46.68 48.42 45.23 47.36 48.38 90.07 48.13 48.28 89.15 52.13 47.56 50.93 47.08 46.43 47.18 84 66.09 47.9 GCA_005882905_Candidatus_Bathyarchaeota_archaeon 74.62 49.38 47.56 63.5 45.22 49.58 65.95 47.67 66.89 47.41 67.4 48.75 47.44 67.37 47.16 47.48 67.45 48.1 45.8 49.46 49.14 49.01 46.99 47.96 48.88 49.08 48.51 45.86 48 46.89 48.96 47.8 49.12 49.27 48.59 47.04 67.46 47.55 48.32 67.46 63.46 48.65 48.47 75.28 48.15 48.28 47.29 67.74 47.77 46.97 47.37 68.05 74.8 48.04 47.73 91.98 48.02 44.62 49.43 47.7 46.9 48.07 45.51 48.26 49.44 68.03 48.16 47.82 67.98 51.91 47.45 51.67 47.72 46.6 47.22 67.68 76.1 48.21 68.28 GCA_002490245_Candidatus_Bathyarchaeota_archaeon_B24−2 62.79 63.9 61.87 63.25 64.74 64.71 62.24 62.74 62.7 65.87 64.71 64.73 61.85 62.31 62.02 63.11 61.94 62.41 63.59 65.38 63 61.63 61.92 63.08 61.28 60.92 61.98 64.71 66.29 64.21 61.99 65.17 63.7 63.37 64.85 62.44 62.31 64.77 65.49 63.36 64.38 62.53 62.26 64.23 62.78 62.82 61.85 63.83 63.39 63.38 62.84 61.36 62.25 62.96 64.06 62.17 61.67 61.81 64.46 66.03 66.03 62.94 62.18 61.33 62.23 64.29 61.71 62.85 61.47 65.94 63.89 62.59 62.06 64.94 61.85 64.94 GCA_003662305_Candidatus_Bathyarchaeota_archaeon 48.15 50.16 50.55 48.44 46.61 47.35 48.46 48.03 48.76 47.56 48.47 50.24 92.41 48.06 49.07 50.36 48.46 50.41 46.19 51.79 51.51 49.52 49.65 57.66 51.21 50.6 50.75 46.49 49.54 50.03 50.7 48.32 50.45 47.55 50.26 47.5 48.27 49.29 50.13 48.37 48.85 51.81 69.99 48.13 50.75 49.96 47.72 48.09 48.38 57.03 49.66 48.15 49.19 49.74 50.14 47.9 50.96 46.3 51.31 49.98 49.03 51.46 46.69 48.73 51.42 48.58 48.66 78.34 48.74 47.8 48.12 48 59.02 48.91 49.65 48.39 47.91 49.32 48.47 48.13 GCA_013329615_Candidatus_Bathyarchaeota_archaeon 60.34 62.67 60.86 61.65 60.62 61.22 61.05 60.78 61.05 60.63 60.7 61.81 61.74 60.9 −1 60.49 60.94 60.73 69.16 61.2 61.44 62.08 76.56 60.01 64.73 64.83 60.99 61.07 61.98 59.36 −1 59.1 60.84 67.23 61.12 61.31 61.12 58.66 60.37 60.39 60.99 61.34 61.14 61.83 61.09 60.76 60.95 62.6 59.47 57.88 60.69 61.57 60.68 61.22 60.74 61.82 60.57 60.25 60.22 62.07 62.18 61.28 61.11 59.79 60.85 66.13 62.52 61.27 60.7 60.39 61.14 62 68.85 62.28 68.2 60.74 62.15 GCA_003662645_Candidatus_Bathyarchaeota_archaeon 62.81 64.79 61.39 63.17 64.54 67.06 62 62.81 62.78 67.04 64.72 65.6 62.64 64.22 61.97 62.7 62.18 62.25 64.37 65.48 63.14 62.23 62.42 62.92 61.81 62.74 62.28 66.08 70.2 64.09 62.04 65.45 63.93 64.45 65.07 62.86 61.97 64.06 65.31 63.13 64.65 62.49 62.07 65.07 63.43 63.72 62.28 65.07 63.47 62.26 63.41 62.86 62.62 63.52 62.95 62.94 62.49 62.68 64.32 70.49 69.2 61.05 63.17 61.66 62.53 66.33 61.62 63.39 62.29 68.05 64.12 62.95 63.84 65.97 61.61 64.72 66.4 61.72 GCA_002495485_Candidatus_Bathyarchaeota_archaeon_UBA185 62.79 61.76 66.6 61.44 61.54 60.06 68.38 60.12 60.56 62.38 61.47 62.07 68.15 70.9 61.01 61.96 68 68.37 63.05 61.42 61.15 64.32 59.37 62.45 61.88 61.32 66.62 61.33 61.55 60.28 60.54 62.34 60.78 63.24 61.27 60.98 68.29 61.22 61.22 61.62 61.65 67.92 68.13 62.26 61.56 61.9 68.17 62.08 61.79 60.17 60.9 70.95 68.1 61.09 60.61 67.31 71.06 74.01 61.56 61.26 61.22 68.35 68.2 64.07 67.73 62.51 61.62 61.99 73.88 61.56 62.12 61.67 61.82 61.29 60.19 62.42 61.19 60.3 62.36 GCA_003601835_Candidatus_Bathyarchaeota_archaeon 64.24 62.56 62.65 64.54 64.63 67.52 61.4 63.77 62.51 69.22 65.1 65.11 60.98 61.54 62.18 63.85 61.46 60.84 63 65.34 63.76 62.18 60.6 63.91 60.85 61.84 61.23 65.1 67.12 64.86 63.66 65.18 64.18 63.6 65.29 63.34 61.49 65.14 65.87 63.4 65.31 62.06 60.86 64.76 62.88 62.48 61.27 63.29 64.7 62.82 62.5 60.56 60.71 63.71 63.32 61.3 61.51 62.33 64.43 66.63 68.05 62.03 61.83 61.56 61.88 64.07 61.68 62.18 61.55 67.42 65 61.71 62.22 62.48 59.98 65.39 64.67 60.49 66.55 61.81
GCA_001768965_archaeon_RBG_16_50_20
GCA_001915065_archaeon_13_2_20CM_2_53_6 GCA_001919285_archaeon_13_1_40CM_2_52_13
GCA_003662715_Candidatus_Bathyarchaeota_archaeonGCA_003662535_Candidatus_Bathyarchaeota_archaeonGCA_007050885_Candidatus_Bathyarchaeota_archaeonGCA_003151735_Candidatus_Bathyarchaeota_archaeonGCA_005883695_Candidatus_Bathyarchaeota_archaeonGCA_003164295_Candidatus_Bathyarchaeota_archaeonGCA_005888755_Candidatus_Bathyarchaeota_archaeonGCA_003661975_Candidatus_Bathyarchaeota_archaeonGCA_005882895_Candidatus_Bathyarchaeota_archaeonGCA_004376295_Candidatus_Bathyarchaeota_archaeonGCA_003601875_Candidatus_Bathyarchaeota_archaeonGCA_003661945_Candidatus_Bathyarchaeota_archaeonGCA_004376385_Candidatus_Bathyarchaeota_archaeonGCA_003661965_Candidatus_Bathyarchaeota_archaeonGCA_003662325_Candidatus_Bathyarchaeota_archaeonGCA_013329615_Candidatus_Bathyarchaeota_archaeonGCA_004376975_Candidatus_Bathyarchaeota_archaeonGCA_003601725_Candidatus_Bathyarchaeota_archaeonGCA_007050895_Candidatus_Bathyarchaeota_archaeonGCA_003601605_Candidatus_Bathyarchaeota_archaeonGCA_005884195_Candidatus_Bathyarchaeota_archaeonGCA_003096255_Candidatus_Bathyarchaeota_archaeonGCA_005888675_Candidatus_Bathyarchaeota_archaeonGCA_005888635_Candidatus_Bathyarchaeota_archaeonGCA_003165195_Candidatus_Bathyarchaeota_archaeonGCA_005881695_Candidatus_Bathyarchaeota_archaeonGCA_003589585_Candidatus_Bathyarchaeota_archaeonGCA_005888745_Candidatus_Bathyarchaeota_archaeonGCA_005882955_Candidatus_Bathyarchaeota_archaeonGCA_002726865_Candidatus_Bathyarchaeota_archaeonGCA_003662205_Candidatus_Bathyarchaeota_archaeonGCA_003133625_Candidatus_Bathyarchaeota_archaeonGCA_003601785_Candidatus_Bathyarchaeota_archaeonGCA_005883075_Candidatus_Bathyarchaeota_archaeonGCA_013330975_Candidatus_Bathyarchaeota_archaeonGCA_003662485_Candidatus_Bathyarchaeota_archaeonGCA_005883085_Candidatus_Bathyarchaeota_archaeonGCA_003152955_Candidatus_Bathyarchaeota_archaeonGCA_003096235_Candidatus_Bathyarchaeota_archaeonGCA_003601835_Candidatus_Bathyarchaeota_archaeonGCA_004376645_Candidatus_Bathyarchaeota_archaeonGCA_005882905_Candidatus_Bathyarchaeota_archaeon GCA_001768965_archaeon_RBG_16_50_20 GCA_005888695_Candidatus_Bathyarchaeota_archaeonGCA_005888735_Candidatus_Bathyarchaeota_archaeon GCA_003601775_Candidatus_Bathyarchaeota_archaeon GCA_003662515_Candidatus_Bathyarchaeota_archaeon GCA_003601695_Candidatus_Bathyarchaeota_archaeonGCA_003662645_Candidatus_Bathyarchaeota_archaeon GCA_003141855_Candidatus_Bathyarchaeota_archaeonNRA7_48_Candidatus_Bathyarchaeota_archaeon_52_381GCA_005881615_Candidatus_Bathyarchaeota_archaeonGCA_005884605_Candidatus_Bathyarchaeota_archaeon GCA_001915065_archaeon_13_2_20CM_2_53_6 GCA_001593855_Candidatus_Bathyarchaeota_archaeon_B25GCA_001593875_Candidatus_Bathyarchaeota_archaeon_B23 GCA_001399795_Candidatus_Bathyarchaeota_archaeon_BA2GCA_001593865_Candidatus_Bathyarchaeota_archaeon_B24GCA_001593845_Candidatus_Bathyarchaeota_archaeon_B63 GCA_001399805_Candidatus_Bathyarchaeota_archaeon_BA1 GCA_001919285_archaeon_13_1_40CM_2_52_13 GCA_001593925_Candidatus_Bathyarchaeota_archaeon_B26.1 GCA_002490245_Candidatus_Bathyarchaeota_archaeon_B24.2GCA_001593935_Candidatus_Bathyarchaeota_archaeon_B26.2 GCA_001918745_Crenarchaeota_archaeon_13_1_40CM_3_52_17GCA_002010975_Candidatus_Bathyarchaeota_archaeon_JdFR.07GCA_002507245_Candidatus_Bathyarchaeota_archaeon_UBA233 GCA_002010925_Candidatus_Bathyarchaeota_archaeon_JdFR.04GCA_001918765_Crenarchaeota_archaeon_13_1_40CM_3_52_10 GCA_002495485_Candidatus_Bathyarchaeota_archaeon_UBA185 GCA_003164295_Candidatus_Bathyarchaeota_archaeonGCA_005888695_Candidatus_Bathyarchaeota_archaeonGCA_003096255_Candidatus_Bathyarchaeota_archaeonGCA_003601605_Candidatus_Bathyarchaeota_archaeonGCA_005888745_Candidatus_Bathyarchaeota_archaeonGCA_003662325_Candidatus_Bathyarchaeota_archaeonGCA_003141855_Candidatus_Bathyarchaeota_archaeonGCA_005888675_Candidatus_Bathyarchaeota_archaeonGCA_003601875_Candidatus_Bathyarchaeota_archaeonGCA_004376645_Candidatus_Bathyarchaeota_archaeonGCA_013330975_Candidatus_Bathyarchaeota_archaeonGCA_004376295_Candidatus_Bathyarchaeota_archaeonGCA_005883085_Candidatus_Bathyarchaeota_archaeonGCA_005881695_Candidatus_Bathyarchaeota_archaeonGCA_003096235_Candidatus_Bathyarchaeota_archaeonGCA_003661965_Candidatus_Bathyarchaeota_archaeonGCA_003662305_Candidatus_Bathyarchaeota_archaeonGCA_005888635_Candidatus_Bathyarchaeota_archaeonGCA_005883075_Candidatus_Bathyarchaeota_archaeonGCA_003133625_Candidatus_Bathyarchaeota_archaeonGCA_005882955_Candidatus_Bathyarchaeota_archaeonGCA_004376975_Candidatus_Bathyarchaeota_archaeonGCA_005884605_Candidatus_Bathyarchaeota_archaeon GCA_013329615_Candidatus_Bathyarchaeota_archaeon GCA_003601695_Candidatus_Bathyarchaeota_archaeonGCA_005881615_Candidatus_Bathyarchaeota_archaeonGCA_007050895_Candidatus_Bathyarchaeota_archaeonGCA_003601725_Candidatus_Bathyarchaeota_archaeonGCA_003151735_Candidatus_Bathyarchaeota_archaeonGCA_005883695_Candidatus_Bathyarchaeota_archaeonGCA_005888755_Candidatus_Bathyarchaeota_archaeonGCA_003662205_Candidatus_Bathyarchaeota_archaeonGCA_003165195_Candidatus_Bathyarchaeota_archaeonGCA_002726865_Candidatus_Bathyarchaeota_archaeon GCA_003601785_Candidatus_Bathyarchaeota_archaeonGCA_003589585_Candidatus_Bathyarchaeota_archaeonGCA_003662715_Candidatus_Bathyarchaeota_archaeonNRA7_48_Candidatus_Bathyarchaeota_archaeon_52_381GCA_003662485_Candidatus_Bathyarchaeota_archaeonGCA_003662535_Candidatus_Bathyarchaeota_archaeonGCA_005888735_Candidatus_Bathyarchaeota_archaeonGCA_005882905_Candidatus_Bathyarchaeota_archaeonGCA_005882895_Candidatus_Bathyarchaeota_archaeonGCA_003152955_Candidatus_Bathyarchaeota_archaeonGCA_005884195_Candidatus_Bathyarchaeota_archaeonGCA_003601775_Candidatus_Bathyarchaeota_archaeonGCA_007050885_Candidatus_Bathyarchaeota_archaeonGCA_003662515_Candidatus_Bathyarchaeota_archaeonGCA_003661975_Candidatus_Bathyarchaeota_archaeonGCA_004376385_Candidatus_Bathyarchaeota_archaeonGCA_003661945_Candidatus_Bathyarchaeota_archaeonGCA_003662645_Candidatus_Bathyarchaeota_archaeon GCA_002254975_Candidatus_Bathyarchaeota_archaeon_ex4484_218GCA_002255025_Candidatus_Bathyarchaeota_archaeon_ex4484_135 GCA_001775955_Candidatus_Bathyarchaeota_archaeon_RBG_13_38_9 GCA_001776015_Candidatus_Bathyarchaeota_archaeon_RBG_16_57_9 GCA_001775965_Candidatus_Bathyarchaeota_archaeon_RBG_13_60_20 GCA_001774245_Candidatus_Bathyarchaeota_archaeon_RBG_13_52_12 GCA_001775995_Candidatus_Bathyarchaeota_archaeon_RBG_16_48_13 GCA_001593855_Candidatus_Bathyarchaeota_archaeon_B25GCA_001399795_Candidatus_Bathyarchaeota_archaeon_BA2 GCA_001399805_Candidatus_Bathyarchaeota_archaeon_BA1GCA_001593875_Candidatus_Bathyarchaeota_archaeon_B23 GCA_001593845_Candidatus_Bathyarchaeota_archaeon_B63 GCA_001593865_Candidatus_Bathyarchaeota_archaeon_B24 GCA_001273385_miscellaneous_Crenarchaeota_group.6_archaeon_AD8.1 GCA_001593935_Candidatus_Bathyarchaeota_archaeon_B26.2 GCA_001593925_Candidatus_Bathyarchaeota_archaeon_B26.1 GCA_002490245_Candidatus_Bathyarchaeota_archaeon_B24.2 GCA_001273335_miscellaneous_Crenarchaeota_group.1_archaeon_SG8.32.3 GCA_002010925_Candidatus_Bathyarchaeota_archaeon_JdFR.04 GCA_002507245_Candidatus_Bathyarchaeota_archaeon_UBA233GCA_001918765_Crenarchaeota_archaeon_13_1_40CM_3_52_10GCA_002010975_Candidatus_Bathyarchaeota_archaeon_JdFR.07GCA_001918745_Crenarchaeota_archaeon_13_1_40CM_3_52_17 GCA_002495485_Candidatus_Bathyarchaeota_archaeon_UBA185 GCA_002255025_Candidatus_Bathyarchaeota_archaeon_ex4484_135 GCA_002254975_Candidatus_Bathyarchaeota_archaeon_ex4484_218 GCA_001775955_Candidatus_Bathyarchaeota_archaeon_RBG_13_38_9 GCA_001776015_Candidatus_Bathyarchaeota_archaeon_RBG_16_57_9 GCA_001774245_Candidatus_Bathyarchaeota_archaeon_RBG_13_52_12GCA_001273385_miscellaneous_Crenarchaeota_group.6_archaeon_AD8.1 GCA_001775995_Candidatus_Bathyarchaeota_archaeon_RBG_16_48_13GCA_001775965_Candidatus_Bathyarchaeota_archaeon_RBG_13_60_20 GCA_001273335_miscellaneous_Crenarchaeota_group.1_archaeon_SG8.32.3 GCA_002779555_Candidatus_Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9
GCA_002779555_Candidatus_Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9 Supplementary Figure 33. Heatmap graphs of (a) mean pairwise ANI (%), (b) mean pairwise AAI (%) of Archaeoglobi GTDB representative genomes with the Mnemosynellales from this study (Ca. M. biddleae substituting JdFR-21), (c) mean pairwise ANI (%), and (d) mean pairwise AAI (%) of Bathyarchaeia GTDB representative genomes with Ca. H. orcuttiae substituting JdFR-11.
a. b.
GCA 002010305 02190 GCA 001775995 00677 KU015010||oil field GQ927606|tropical western Pacific Ocean China|marine sediment KU002086||oil field JQ327887|western Pacific|marine sediment JQ989712|Taiwan KP-9|subseafloor sediment KU030614|| GQ927688|tropical western Pacific Ocean China|marine sediment KU995269||oil field GQ927584|tropical western Pacific Ocean China|marine sediment KU025948||oil field GQ410906|tropical western Pacific Ocean China|marine sediment KM370791|Guaymas Basin|hydrothermal sediment GQ927614|tropical western Pacific Ocean China|marine sediment MTMI01000003|Juan de Fuca Ridge|basaltic crustal fluids GQ927596|tropical western Pacific Ocean China|marine sediment MTMI01000021|Juan de Fuca Ridge|basaltic crustal fluids GQ994330|West Pacific Ocean China|deep-sea sediments MTMH01000020|Juan de Fuca Ridge|basaltic crustal fluids JQ989677|Taiwan KP-9|subseafloor sediment KU009906||oil field GQ410805|tropical western Pacific Ocean China|marine sediment KU598626||oil field AB177007|Pacific Ocean Peru Margin|subseafloor sediment EU369867|Cariaco Basin Venezuela| KU598609||oil field EU369825|Cariaco Basin Venezuela| KU995296||oil field EU369868|Cariaco Basin Venezuela| KU995278||oil field EU369822|Cariaco Basin Venezuela| FJ941455|oil-water separation site Netherlands|water from an oil-water separation plant and produced water EU369833|Cariaco Basin Venezuela| FJ941453|oil-water separation site Netherlands|water from an oil-water separation plant and produced water EU369838|Cariaco Basin Venezuela| HM041908|Niiboli oilfield Japan|produced fluid from Niiboli oilfield HM244046|Honghu lake China|upper sediment KU995098||oil field AB644796|Shimokita Peninsula Japan|subseafloor sediments KU921176||oil field KC003524|USA New Jersey|marine sediment KU017464|| EU369869|Cariaco Basin Venezuela| GQ410893|tropical western Pacific Ocean China|marine sediment KU004567||oil field KC003804|USA New Jersey|marine sediment KU017875||oil field GQ927599|tropical western Pacific Ocean China|marine sediment KU027654||oil field FJ902719 KU018644||oil field JQ258743|India Ratnagiri Arabian Sea coast|tropical marine sediment around 20m water depth KU014549||oil field HM244065|Honghu lake China|upper sediment KU003974||oil field HM244235|Honghu lake|lower sediment KU008456||oil field HM187563|Hanford Site USA|saturated zone KU010806|| DQ190083|Snake River Plain Aquifer USA| KJ881625|Atlantis II Deep Red Sea |upper convective layer EU573156|North Sea Ekofisk oil field|oil field AB329777|Southern Mariana Trough|hydrothermal deposits KU003613||oil field JX196217|Hetao Basin inner Mongolia|groundwater samples KU014490||oil field HM244187|Honghu lake|lower sediment KU013215|| HM244190|Honghu lake China|lower sediment KU014969|| EU369840|Cariaco Basin Venezuela| KU007978|| EU369851|Cariaco Basin Venezuela| KU024767||oil field KJ881610|Atlantis II Deep Red Sea |upper convective layer KU007875||oil field AB213070|Southern Mariana Trough|crustal fluids KU006330||oil field HQ611193|China sea |marine sediments AB213100|Southern Mariana Trough|crustal fluids FJ446507|USA North Slope AK|oil processing facility primary separator JQ257976|India Karwar Arabian Sea coast|tropical marine sediment around 20m water depth KU001459||oil field AB329759|Southern Mariana Trough|hydrothermal deposits KU012703||oil field KP210129|Tengchong National Geothermal Park China|thermal soil KU010924||oil field GQ927663|tropical western Pacific Ocean China|marine sediment KU014130||oil field JX000679|Guaymas Basin Mexico|hydrothermal seep KU025897||oil field EU369913|Cariaco Basin Venezuela| KU029948||oil field GU824556|Cariaco Basin Caribbean Sea|anoxic water column sample KU019752||oil field EU369911|Cariaco Basin Venezuela| MTLX01000005|Juan de Fuca Ridge Pacific Ocean|basaltic crustal fluids KU029360||oil field KP090994|Guaymas Basin Mexico|hydrothermal seep KU024193|| JX507247|Guaymas Basin Mexico|hydrothermal seep KU027586|| AY555817|Bor Khlueng Thailand|hot spring KU023614||oil field AB213101|Southern Mariana Trough|crustal fluids KU001827|| JX507256|Guaymas Basin Mexico|hydrothermal seep KU598650|| FN666140|Tunisia|hot spring water KU598655||oil field AB213075|Southern Mariana Trough|crustal fluids KU598637||oil field LT575977|Bulgaria Velingrad Vlasa spring | KU023735||oil field KU004229|| KU019777|| KU010101||oil field KU021316||oil field KU011205||oil field
Tree scale: 0.1 Tree scale: 0.1 Supplementary Figure 34. ML phylogenies of the 16S genes in (a) Mnemosynellales and (b) Hecatellales. Each leaf contains the sequence accession, pipe separated with its sampling locality, and environment, depending on their availability in each sequence’s metadata in SILVA. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
a.
b. c.
d. Supplementary Figure 35. Graphical representation of synteny for genes (a) MK0750, (b) MK0854, (c) MK0927, and (d) MK1513 in the genomes of Methanopyrus kandleri, Methanothermobacter marburgensis str. Marburg, and Methanobrevibacter smithii.
0/0/0.04 a. Methanococcales
hcgF 0.29/0/0.07 Methanopyrales
0.15/0.01/0.18
hcgF 0.03/0/0.12 Methanobacteriales
hcgBhcgChcgF hmd hcgA hcgE hcgG 0.47/0.99/0.22 Desulfurobacteriales
Tree scale: 0.1
0.05/0/0.05 Methanococcales b. 0/0/0.03 Methanopyrales 0.71/0.7/0.03
0.16/0.2/0.04 Desulfurobacteriales
Methanobacteriales 0.08/0.1/0
0/0/0.14 Methanomicrobiales
0/0/0.01 GCA 000015765 Methanocorpusculum labreanum Z
Tree scale: 0.1 Supplementary Figure 36. ML phylogenies of (a) HcgAEFG (938 aa positions) along with the genomic organization of the clusters in a representative genome for each major clade, (b) HcgBC (366 aa positions). Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80), red circles correspond to the MAD root, green to MinVar, light blue to NONREV. Branch values correspond to rootstrap supports for MAD, MinVar, and NONREV respectively. For HcgAEFG, the NONREV root is within a collapsed clade. Genomes used to compare clusters were the same as Figure 3, with additionally Desulfurobacterium thermolithotrophum DSM 11699 (GCA_000191045; Desulfurobacteriales).
Archaeoglobales Archaeoglobales GCA_002011165MTMI01000018.1_1651393181398391_165 GCA_002011165 -1 ID 1_165 partial 00 Euryarchaeota archaeon JdFR-21 Methanosarcinales
Methanoliparia Methanosarcinales Methanophagales
Syntropharchaeales Methanosarcinales Methanococcales
Theionarchaea
Hydrothermarchaeota
Lokiarchaeota GCA 002011035MTLY01000007.1 6355748562904 63 GCA 002011035 1 ID 4 63 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 OHE55938.1 GCA 001830115 CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon Thaumarchaeota archaeon RBG 16 49 8 Helarchaeota
TDA37020.1 GCA 004347915 CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon Candidatus Nezhaarchaeota archaeon WYZ-LMO7 Verstraetearchaeota Methanosarcinales (ANME-2)
Methanobacteriales (incl. Methanococcales) RLG35121.1 GCA 003661125 CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon Methanosarcinales archaeon RLF45582.1 GCA 003651025 CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon Thermoplasmata archaeon Bathyarchaeota (incl. Nezhaarchaeota)
Syntropharchaeales Persephonarchaea
Thorarchaeota
Methanomicrobiales
Methanomicrobiales Methanopyrales Bathyarchaeota
RLG87401.1 GCA 003661905 hypothetical protein DRO15 04980 Thermoprotei archaeon RLG79990.1 GCA 003661825 hypothetical protein DRO13 04810 Thermoprotei archaeon RLE84654.1 GCA 003649425 CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon Thermoprotei archaeon RLE71902.1 GCA 003649255 CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon Thermoprotei archaeon RLI17227.1 GCA 003662385 CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon Candidatus Bathyarchaeota archaeon PCN50420.1 GCA 002412205 hypothetical protein B6U99 04460 Candidatus Geothermarchaeota archaeon ex4572 27 GCA 002011075MTMA01000002.1 2272236212241663 227 GCA 002011075 1 ID 3 227 partial 00 Candidatus Geothermarchaeota archaeon JdFR-13 Korarchaeota
OGD54507.1 GCA 001775955 CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon Candidatus Bathyarchaeota archaeon RBG 13 38 9 Bathyarchaeota (incl. Crenarchaeota)
Bathyarchaeota (incl. Hadesarchaea and Crenarchaeota)
Bathyarchaeota (incl. Korarchaeota) Bathyarchaeota (incl. Thaumarchaeota)
Bathyarchaeota
Bathyarchaeota
Bathyarchaeota
Methanomicrobiales (incl. Methanocellales)
Tree scale: 1 Supplementary Figure 37. ML phylogeny of CdhB. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Methanonatronarchaeia Methanoliparia Methanomicrobiales GCA 002011165MTMI01000003.1 10989126900583 109 GCA 002011165 1 ID 3 109 partial 00 Euryarchaeota archaeon JdFR-21 GCA 003935005RSFX01000008.1 26222832922927920 262 GCA 003935005 1 ID 20 262 partial 00 Archaeoglobi archaeon Methanosarcinales Methanomicrobiales Methanocellales Archaeoglobales
Methanoflorentaceae
Archaeoglobales Methanocellales Hydrothermarchaeota Methanopyrales Methanococcales Methanobacteriales KUO43151.1 GCA 001515215 hypothetical protein APU95 01240 Hadesarchaea archaeon YNP N21 OGD46213.1 GCA 001775995 methenyltetrahydromethanopterin cyclohydrolase Candidatus Bathyarchaeota archaeon RBG 16 48 13 OYT49943.1 GCA 002255065 hypothetical protein B6U73 04770 Desulfurococcales archaeon ex4484 204 KUO43161.1 GCA 001515215 hypothetical protein APU95 01290 Hadesarchaea archaeon YNP N21 OGD45963.1 GCA 001775995 methenyltetrahydromethanopterin cyclohydrolase Candidatus Bathyarchaeota archaeon RBG 16 48 13 KUO43278.1 GCA 001515215 hypothetical protein APU95 03210 Hadesarchaea archaeon YNP N21 OGD46622.1 GCA 001775995 hypothetical protein A3K70 03725 Candidatus Bathyarchaeota archaeon RBG 16 48 13 OYT51115.1 GCA 002255065 hypothetical protein B6U73 02625 partial Desulfurococcales archaeon ex4484 204 RLG54823.1 GCA 003661365 hypothetical protein DRO00 00070 Candidatus Korarchaeota archaeon Halobacteria RLG13430.1 GCA 003660905 hypothetical protein DRN66 04185 Candidatus Nanohaloarchaeota archaeon Methanomicrobiales Heimdallarchaeota Bathyarchaeota Altarchaeota Thorarchaeota Lokiarchaeota GCA 005191415SUPS01000044.1 151453115502156 15 GCA 005191415 1 ID 156 15 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A GCA 005191425SUPR01000054.1 685369516134 6 GCA 005191425 1 ID 134 6 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB B Lokiarchaeota Methanosarcinales Methanosarcinales Methanosarcinales Methanophagales RLG37401.1 GCA 003661185 methenyltetrahydromethanopterin cyclohydrolase Methanosarcinales archaeon Syntropharchaeales RQW77919.1 GCA 003857025 methenyltetrahydromethanopterin cyclohydrolase Methanothrix sp. RLF30402.1 GCA 003650975 methenyltetrahydromethanopterin cyclohydrolase Thermoplasmata archaeon GCA 002494765DACJ01000029.1 32416333371 3 GCA 002494765 -1 ID 71 3 partial 00 Euryarchaeota archaeon UBA186 Theionarchaea Hadesarchaea Persephonarchaea TKJ27026.1 GCA 005222995 methenyltetrahydromethanopterin cyclohydrolase Hadesarchaea archaeon B3 Hades KUO40742.1 GCA 001515195 methenyltetrahydromethanopterin cyclohydrolase Hadesarchaea archaeon DG-33-1 GCA 002495885DAHG01000020.1 12102461119948 12 GCA 002495885 1 ID 48 12 partial 00 Methanocellaceae archaeon UBA148 TFG21188.1 GCA 004524545 methenyltetrahydromethanopterin cyclohydrolase Candidatus Lokiarchaeota archaeon OLS17270.1 GCA 001940665 Methenyltetrahydromethanopterin cyclohydrolase Candidatus Odinarchaeota archaeon LCB 4 RLE48512.1 GCA 003649085 hypothetical protein DRJ31 07115 Candidatus Verstraetearchaeota archaeon Crenarchaeota Crenarchaeota Verstraetearchaeota RLE49770.1 GCA 003649085 methenyltetrahydromethanopterin cyclohydrolase partial Candidatus Verstraetearchaeota archaeon RLE56105.1 GCA 003649205 methenyltetrahydromethanopterin cyclohydrolase Thermoprotei archaeon Crenarchaeota
RLG40813.1 GCA 003661245 hypothetical protein DRN78 05060 Candidatus Korarchaeota archaeon Geothermarchaeota Bathyarchaeota Heimdallarchaeota GBC75164.1 GCA 002898815 Methenyltetrahydromethanopterin cyclohydrolase archaeon HR06 GCA 002507085DAYW01000032.1 2468147813 2 GCA 002507085 1 ID 13 2 partial 00 archaeon UBA168 Bathyarchaeota RLG51332.1 GCA 003661385 methenyltetrahydromethanopterin cyclohydrolase Candidatus Korarchaeota archaeon Bathyarchaeota (incl. Crenarchaeota) Bathyarchaeota RLI48947.1 GCA 003662745 methenyltetrahydromethanopterin cyclohydrolase Candidatus Bathyarchaeota archaeon Bathyarchaeota Bathyarchaeota (incl. Crenarchaeota) Nezhaarchaeota (incl. Geothermarchaeota) Korarchaeota
Tree scale: 1 Supplementary Figure 38. ML phylogeny of Mch. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Bathyarchaeota Hydrothermarchaeota Methanococcales Methanopyrales Methanobacteriales Lokiarchaeota Methanonatronarchaeia Heimdallarchaeota Archaeoglobales OLS17858.1 GCA 001940665 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Odinarchaeota archaeon LCB 4 (Odinarchaeota) TFF93278.1 GCA 004524285 methylenetetrahydromethanopterin dehydrogenase partial Candidatus Thorarchaeota archaeon RLI50417.1 GCA 003662765 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon TFF94602.1 GCA 004524285 methylenetetrahydromethanopterin dehydrogenase partial Candidatus Thorarchaeota archaeon TFG09409.1 GCA 004524435 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon TFG32492.1 GCA 004524595 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon TFG34302.1 GCA 004524595 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon RLI53487.1 GCA 003662775 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon TFG26307.1 GCA 004524565 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon GCA 002825535PJES01000266.1 772188081111 7 GCA 002825535 1 ID 111 7 partial 00 Candidatus Thorarchaeota archaeon MP9T 1 TFG14325.1 GCA 004524445 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon TFG95689.1TFG98855.1 GCA 004525575 methylenetetrahydromethanopterin dehydrogenase partial Candidatus Thorarchaeota archaeon Thorarchaeota TFH09584.1 GCA 004525645 methylenetetrahydromethanopterin dehydrogenase partial Candidatus Thorarchaeota archaeon GCA 002390245DGOX01000025.1 36345183538428 36 GCA 002390245 1 ID 28 36 partial 00 Proteobacteria bacterium UBA4455 GCA 001464935LNEL01000044.1 19222862315244 19 GCA 001464935 1 ID 44 19 partial 00 Gammaproteobacteria bacterium Ga0077536 Gammaproteobacteria TDJ70165.1 GCA 004357665 F420-dependent methylenetetrahydromethanopterin dehydrogenase Proteobacteria bacterium KXH76349.1 GCA 001563325 methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon SMTZ1-83 OLS30285.1 GCA 001940705 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon AB 25 TET09861.1 GCA 004376265 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon KXH71901.1 GCA 001563335 methylenetetrahydromethanopterin dehydrogenase Candidatus Thorarchaeota archaeon SMTZ1-45 GCA 002825515PJET01000111.1 25336803454661 25 GCA 002825515 1 ID 61 25 partial 00 Candidatus Thorarchaeota archaeon MP11T 1 Nezhaarchaeota PCN50633.1 GCA 002412205 methylenetetrahydromethanopterin dehydrogenase Candidatus Geothermarchaeota archaeon ex4572 27 (Geothermarchaeota RLF12517.1 GCA 003649615 F420-dependent methylenetetrahydromethanopterin dehydrogenase Thermoprotei archaeon RLI05364.1 GCA 003662145 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Bathyarchaeota archaeon RLI32908.1 GCA 003662565 hypothetical protein DRO51 00680 Candidatus Bathyarchaeota archaeon RJX16599.1 GCA 003604315 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Bathyarchaeota archaeon RLG91217.1 GCA 003661965 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Bathyarchaeota archaeon RLE71229.1 GCA 003649255 methylenetetrahydromethanopterin dehydrogenase partial Thermoprotei archaeon RLE51320.1 GCA 003649105 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Verstraetearchaeota archaeon RLF23754.1 GCA 003650925 F420-dependent methylenetetrahydromethanopterin dehydrogenase Thermoprotei archaeon 91.2/0.976/44 82.3/0.857/84 Bathyarchaeota 100/1/100
99.8/1/100 Korarchaeota GCA 002010885MTLO01000002.1 28010153 2 GCA 002010885 -1 ID 3 2 partial 00 Candidatus Bathyarchaeota archaeon JdFR-01 TFF89073.1 GCA 004524205 methylenetetrahydromethanopterin dehydrogenase partial Candidatus Lokiarchaeota archaeon GCA 005191415SUPS01000240.1 74848568488 7 GCA 005191415 -1 ID 88 7 partial 00 Candidatus Helarchaeota ASGARD archaeon Hel GB A RLI08739.1 GCA 003662215 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Bathyarchaeota archaeon RLE67926.1 GCA 003650735 F420-dependent methylenetetrahydromethanopterin dehydrogenase Thermoprotei archaeon RLI89986.1 GCA 003663105 hypothetical protein DRO65 03610 partial Candidatus Altiarchaeales archaeon TDA32661.1 GCA 004347835 F420-dependent methylenetetrahydromethanopterin dehydrogenase Hadesarchaea archaeon TDA29776.1 GCA 004347925 F420-dependent methylenetetrahydromethanopterin dehydrogenase Hadesarchaea archaeon Persephonarchaea (MSBL-1) KUO39546.1 GCA 001515185 methylenetetrahydromethanopterin dehydrogenase Hadesarchaea archaeon DG-33 TKJ27028.1 GCA 005222995 methylenetetrahydromethanopterin dehydrogenase Hadesarchaea archaeon B3 Hades PCN51095.1 GCA 002412205 methylenetetrahydromethanopterin dehydrogenase Candidatus Geothermarchaeota archaeon ex4572 27 GCA 002011075MTMA01000002.1 2082046232054653 208 GCA 002011075 -1 ID 3 208 partial 00 Candidatus Geothermarchaeota archaeon JdFR-13 OYT51119.1 GCA 002254985 methylenetetrahydromethanopterin dehydrogenase Desulfurococcales archaeon ex4484 217 2 RLG70822.1 GCA 003661705 F420-dependent methylenetetrahydromethanopterin dehydrogenase Thermoprotei archaeon RLG74973.1 GCA 003661705 F420-dependent methylenetetrahydromethanopterin dehydrogenase Thermoprotei archaeon RLE57497.1 GCA 003649185 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Verstraetearchaeota archaeon RLI08423.1 GCA 003662185 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Bathyarchaeota archaeon KON31235.1 GCA 001273415 methylenetetrahydromethanopterin dehydrogenase miscellaneous Crenarchaeota group-15 archaeon DG-45 GCA 001577155LSCO01000129.1 53463429034 5 GCA 001577155 1 ID 34 5 partial 00 Candidatus Bathyarchaeota archaeon TCS64 OGD52156.1 GCA 001775965 methylenetetrahydromethanopterin dehydrogenase Candidatus Bathyarchaeota archaeon RBG 13 60 20 RLI32315.1 GCA 003662595 methylenetetrahydromethanopterin dehydrogenase partial Candidatus Bathyarchaeota archaeon TET70900.1 GCA 004377085 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Bathyarchaeota archaeon TEU12577.1 GCA 004377395 F420-dependent methylenetetrahydromethanopterin dehydrogenase Candidatus Bathyarchaeota archaeon Thaumarchaeota Archaeoglobales Methanomicrobiales Methanoflorentaceae Methanophagales RLG38457.1 GCA 003661185 F420-dependent methylenetetrahydromethanopterin dehydrogenase Methanosarcinales archaeon OFV67750.1 GCA 001766815 N5N10-methylenetetrahydromethanopterin dehydrogenase Candidatus Syntrophoarchaeum caldarius GCA 002011165MTMI01000003.1 6056517573323 60 GCA 002011165 1 ID 3 60 partial 00 Euryarchaeota archaeon JdFR-21 GCA 002505645DAVS01000173.1 28031645141 2 GCA 002505645 1 ID 141 2 partial 00 archaeon UBA460 TET80027.1TET74445.1 GCA 004376735 methylenetetrahydromethanopterin dehydrogenase partial Candidatus Heimdallarchaeota archaeon GCA 002495885DAHG01000004.1 23211732198542 23 GCA 002495885 -1 ID 42 23 partial 00 Methanocellaceae archaeon UBA148 Methanosarcinales Methanocellales
Tree scale: 0.1 Supplementary Figure 39. ML phylogeny of Mtd. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
Syntropharchaeales Methanophagales GCA 003935005RSFX01000008.1 36374923882020 36 GCA 003935005 1 ID 20 36 partial 00 Archaeoglobi archaeon Archaeoglobales Methanoliparia Methanosarcinales Hydrothermarchaeota GCA_002011165MTMI01000018.1_1631367491379331_163 GCA_002011165 -1 ID 1_163 partial 00 Euryarchaeota archaeon JdFR-21 Persephonarchaea Methanococcales Methanobacteriales ADP77323.1 GCA 000166095 acetyl-CoA decarbonylase/synthase delta subunit Methanothermus fervidus DSM 2088 Methanococcales GCA 002011035MTLY01000005.1 3729475306747 37 GCA 002011035 -1 ID 7 37 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 OHE55939.1 GCA 001830115 CO dehydrogenase/acetyl-CoA synthase subunit delta Thaumarchaeota archaeon RBG 16 49 8 GCA 002495885DAHG01000004.1 17153511651142 17 GCA 002495885 1 ID 42 17 partial 00 Methanocellaceae archaeon UBA148 Theionarchaea RLG69915.1 GCA 003661645 acetyl-CoA synthase subunit delta partial Euryarchaeota archaeon Lokiarchaeota Helarchaeota Methanopyrales Altarchaeota GCA 000402775AQSC01000056.1 14129311410056 14 GCA 000402775 1 ID 56 14 partial 00 Euryarchaeota archaeon SCGC AAA252-I15 RLG37513.1 GCA 003661185 CO dehydrogenase/acetyl-CoA synthase subunit delta Methanosarcinales archaeon Syntropharchaeales RLG74829.1 GCA 003661705 acetyl-CoA synthase subunit delta Thermoprotei archaeon RLE57308.1 GCA 003649205 CO dehydrogenase/acetyl-CoA synthase subunit delta Thermoprotei archaeon Verstraetearchaeota TDA37022.1 GCA 004347915 acetyl-CoA synthase subunit delta Candidatus Nezhaarchaeota archaeon WYZ-LMO7 Bathyarchaeota Nezhaarchaeota (incl. Geothermarchaeota) RLI05774.1 GCA 003662185 CO dehydrogenase/acetyl-CoA synthase subunit delta partial Candidatus Bathyarchaeota archaeon Hadesarchaea Bathyarchaeota Thorarchaeota Bathyarchaeota Bathyarchaeota Methanomicrobiales (incl. Methanocellales) Bathyarchaeota RLI31060.1 GCA 003662535 CO dehydrogenase/acetyl-CoA synthase subunit delta Candidatus Bathyarchaeota archaeon RLG62632.1 GCA 003661565 CO dehydrogenase/acetyl-CoA synthase subunit delta archaeon Bathyarchaeota (incl. Crenarchaeota) RLG52509.1 GCA 003661385 CO dehydrogenase/acetyl-CoA synthase subunit delta Candidatus Korarchaeota archaeon Bathyarchaeota Bathyarchaeota RLI33440.1 GCA 003662595 CO dehydrogenase/acetyl-CoA synthase subunit delta Candidatus Bathyarchaeota archaeon RLG54192.1 GCA 003661365 CO dehydrogenase/acetyl-CoA synthase subunit delta Candidatus Korarchaeota archaeon Hadesarchaeota RLG79988.1 GCA 003661825 CO dehydrogenase/acetyl-CoA synthase subunit delta Thermoprotei archaeon OYT27097.1OYT27096.1 GCA 002254895 hypothetical protein B6V02 00490 Thermoprotei archaeon ex4572 64 RLE86404.1 GCA 003650785 CO dehydrogenase/acetyl-CoA synthase subunit delta Thermoprotei archaeon RLE71822.1 GCA 003649255 CO dehydrogenase/acetyl-CoA synthase subunit delta Thermoprotei archaeon Geothermarchaeota
Tree scale: 1 Supplementary Figure 40. ML phylogeny of CdhD. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
RLG37514.1 GCA 003661185 acetyl-CoA decarbonylase/synthase complex subunit gamma Methanosarcinales archaeon Syntropharchaeales Syntropharchaeales Methanophagales
Methanosarcinales Methanoliparia Archaeoglobales
OHE55945.1 GCA 001830115 hypothetical protein A3K61 03980 Thaumarchaeota archaeon RBG 16 49 8 GCA 002011035MTLY01000005.1 3628013294677 36 GCA 002011035 -1 ID 7 36 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 GCA 002495885DAHG01000004.1 18165191790742 18 GCA 002495885 1 ID 42 18 partial 00 Methanocellaceae archaeon UBA148 Theionarchaea Hydrothermarchaeota GCA_002011165MTMI01000018.1_1611349331362761_161 GCA_002011165 -1 ID 1_161 partial 00 Euryarchaeota archaeon JdFR-21 Persephonarchaea Altarchaeota
RLG79253.1 GCA 003661825 hypothetical protein DRO13 06250 partial Thermoprotei archaeon Methanopyrales
Methanobacteriales Methanococcales RLG69916.1 GCA 003661645 acetyl-CoA decarbonylase/synthase complex subunit gamma Euryarchaeota archaeon Lokiarchaeota Helarchaeota RLE48354.1 GCA 003649085 acetyl-CoA decarbonylase/synthase complex subunit gamma Candidatus Verstraetearchaeota archaeon RLE51289.1 GCA 003649105 acetyl-CoA decarbonylase/synthase complex subunit gamma Candidatus Verstraetearchaeota archaeon RLE57309.1 GCA 003649205 acetyl-CoA decarbonylase/synthase complex subunit gamma Thermoprotei archaeon TDA37023.1 GCA 004347915 acetyl-CoA decarbonylase/synthase complex subunit gamma Candidatus Nezhaarchaeota archaeon WYZ-LMO7 Bathyarchaeota Nezhaarchaeota (incl. Geothermarchaeota) Thorarchaeota Hadesarchaea Bathyarchaeota
RLI33439.1 GCA 003662595 acetyl-CoA decarbonylase/synthase complex subunit gamma partial Candidatus Bathyarchaeota archaeon Korarchaeota
Hadesarchaea RLE86403.1 GCA 003650785 acetyl-CoA decarbonylase/synthase complex subunit gamma partial Thermoprotei archaeon RLE71820.1 GCA 003649255 acetyl-CoA decarbonylase/synthase complex subunit gamma Thermoprotei archaeon RLG79992.1 GCA 003661825 acetyl-CoA decarbonylase/synthase complex subunit gamma partial Thermoprotei archaeon Geothermarchaeota Korarchaeota Bathyarchaeota
Bathyarchaeota (incl. Crenarchaeota) Bathyarchaeota (incl. Crenarchaeota) RLI31057.1 GCA 003662535 acetyl-CoA decarbonylase/synthase complex subunit gamma Candidatus Bathyarchaeota archaeon RLG62633.1 GCA 003661565 acetyl-CoA decarbonylase/synthase complex subunit gamma partial archaeon Bathyarchaeota Bathyarchaeota (incl. Crenarchaeota)
Bathyarchaeota Methanomicrobiales (incl. Methanocellales)
Tree scale: 0.1 Supplementary Figure 41. ML phylogeny of CdhE. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
0.02/0/0.02 Methanococcales
0/0/0.17 Methanobacteriales
0/0/0.01 GCA 004212155 archaeon (Nuwarchaeales)
Theionarchaea 0.01/0/0.01
Methanofastidiosales
0.93/0.99/0.01 Verstraetearchaeota
Tree scale: 0.1 Supplementary Figure 42. ML phylogeny of EhbEFGHIKLMO (1914 aa positions). Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80), red circle corresponds to the MAD root, green to MinVar, light blue to NONREV. Branch values correspond to rootstrap supports for MAD, MinVar, and NONREV respectively.
Methanobacteriales
0.22/0.1/0.03 Methanococcales
0/0/0.01 0.03/0.02/0.06 GCA 004212155 archaeon (Nuwarchaeales) Theionarchaea 0.25/0.05/0.03
0/0/0.13 Methanofastidiosales
0.5/0.83/0.11 Verstraetearchaeota
Tree scale: 0.1 Supplementary Figure 43. ML phylogeny of EhbEGHIKLM (1135 aa positions). Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80), red circle corresponds to the MAD root, green to MinVar. Branch values correspond to rootstrap supports for MAD, MinVar, and NONREV respectively. The NONREV root is within a collapsed clade.
20 40 60 80 100 20 40 60 80 sCF sCF
ehaF(DUF2106) ehbC* a. Methanococcales b. ehbO* 114 ehaC(DUF2109) 154 Methanococcales 113 ehbD* 153 ehaH 130 Methanobacteriales ehbA* 170 Methanobacteriales ehaG(DUF2105) GCA 004212155 archaeon (Nuwarchaeales) 152 ehbB* 208 233 ehaJ* Methanopyrales ehbH 209 Theionarchaea 232 ehbI* 207 ehaE(DUF2107) 234 Methanobacteriales ehbE* 210 Methanofastidiosales ehaO* GCA 001549095 candidate division MSBL1 archaeon SCGC-AAA259E19 ehbF* 151 GCA 002011165 Euryarchaeota archaeon JdFR-21 ehaD(DUF2108) Verstraetearchaeota ehbG 112
150 ehaM(DUF1959) Methanomicrobiales ehbM* Tree scale: 0.1 ehbJ ehaN* Tree scale: 0.1 ehbP ehaB Node208 Node113 Node114 Node207 Node130 Node210 Node112 Node209 Node234 Node233 Node232 Node152 Node153 Node151 Node150 Node170 Node154
20 40 60 80 sCF 20 40 60 80 sCF
ehbF* c. 117 Methanococcales d. ehbI*
ehbG 116 139 Methanobacteriales 133 Methanobacteriales ehbE* ehbO* GCA 004212155 archaeon (Nuwarchaeales) 118 Methanococcales 212 GCA 004212155 archaeon (Nuwarchaeales) 213 Theionarchaea 117 ehbM* 135 211 ehbH 136 Theionarchaea 134 ehbI* 214 Methanofastidiosales 137 Methanofastidiosales ehbG 115 ehbE* Verstraetearchaeota
Tree scale: 0.1 116 Verstraetearchaeota
ehbH ehbM* Tree scale: 0.1 Node116 Node212 Node211 Node133 Node213 Node115 Node117 Node214 Node135 Node117 Node118 Node139 Node134 Node136 Node116 Node137
363 Methanosarcinales
355 Syntrophoarchaeales GCA 001766825 Candidatus Syntrophoarchaeum butanivorans 362 353 GCA 003935005 Archaeoglobi archaeon
354 347 Helarchaeota
352 224 Methanosarcinales 349 Methanoliparia 225 348 GCA 004347925 Hadesarchaea archaeon 425 Methanococcales 350 40 60 80 20 40 60 80 351 Bathyarchaeota sCF sCF 312 Methanopyrales
380 Methanonatronarchaeales 241 e. 379 mtrE f. 242 Methanobacteriales 382 Methanomassiliicoccales mcrA 367 GCA 003649085 Candidatus Verstraetearchaeota archaeon mtrD 375 Methanofastidiosales 226 232 233 Nezhaarchaeota 368 GCA 004212155 archaeon (Nuwarchaeales) 228 369 mtrA 370 Methanophagales 229 Bathyarchaeota GCA 004347865 Archaeoglobi archaeon 227 mcrB 366 419 GCA 004347975 Candidatus Korarchaeota archaeon mtrC 235 Methanophagales 412 GCA 004347915 Candidatus Nezhaarchaeota archaeon WYZ-LMO7 234 413 240 Methanoliparia 414 Verstraetearchaeota mtrB GCA 004347865 Archaeoglobi archaeon 422 Methanobacteriales 411 mtrG 315 Methanosarcinales 313 421 mcrG 521 Methanococcales 389 Methanomicrobiales 480 mtrF 314 482 Methanobacteriales 385 481 386 Methanocellales 420 516 Methanococcales 383 Node363 Node370 Node375 Node685 Node413 Node419 Node687 Node516 Node349 Node521 Node616 Node422 Node348 Node380 Node351 Node482 Node539 Node369 Node411 Node355 Node352 Node368 Node684 Node537 Node421 Node379 Node367 Node538 Node540 Node420 Node347 Node366 Node480 Node353 Node382 Node414 Node362 Node412 Node354 Node350 Node481
GCA 004212075 Candidatus Methanoliparum thermophilum Node235 Node313 Node315 Node227 Node314 Node232 Node383 Node241 Node225 Node242 Node226 Node385 Node224 Node312 Node234 Node228 Node233 Node240 Node389 Node425 Node386 384 Methanoflorentaceae
540 Methanosarcinales 537 539 Tree scale: 0.1
616 Methanomicrobiales
538 685 Methanoflorentaceae 684
687 Methanocellales
Tree scale: 0.1 Supplementary Figure 44. Heatmap graphs of subunit-specific site concordance factors for the main clades in the phylogenies of (a) EhaBCDEFGHJMNO, (b) EhbABCDEFGHIJMOP, (c) EhbEFGHIMO, (d) EhbEGHIM, (e) McrABG, (f) MtrABCDEFG. Cladograms were derived from Euclidean distance clustering. Subunits noted with asterisks have known homologs in other hydrogenases (generic subunits). Some subunits are missing from the sCF analyses, as the concatenation dataset needs to, in terms of distribution, perfectly match the datasets of the single subunits. In case major clades of the supermatrix phylogenies were absent in the single subunit phylogenies, those subunits were omitted from the analysis.
● ● 5 4 ● ● a. ● ● 30 ● c. ● ● b. ● ● ● ● ● 4 ● ● ● ● ● ● 3 ● ● ● ● ● ● ● 20 3
● 2 ● ● Rate ● Rate Rate 2 ● ● ● 10 ● 1 1 ● ● ● ● ● 0 0 0 MCR_alpha MCR_beta MCR_gamma MCR_alpha MCR_beta MCR_gamma MCR_alpha MCR_beta MCR_gamma
subunit name subunit name subunit name
● ● ● 5 ● 40 4 ● ● d. ● e. f. ● 4 ● ● 30 ● ● ● ● ● ● 3 ● ● ● ● ● ● ● ● 3 ● ● ● ● 20 ● Rate Rate 2 Rate ● ● 2
10 1 1
● ● ● ● ● ● 0 0 0 MtrB MtrE MtrC MtrD MtrG MtrB MtrE MtrF. MtrA MtrC MtrD MtrG MtrF. MtrA MtrB MtrE MtrC MtrD MtrG MtrF. MtrA
subunit name subunit name subunit name
5 ● ● ● 40 ● ● 5 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● g. ● ● h. ● ● ● ● i. ● ● ● 4 ● ● ● ● ● ● ● ● ● ● ● ● 4 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 30 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 3 ● ● ● ● 3 ● ● ● ● ● ● ● ● ● ● ● ● ● ● 20 ● ● ● ● ● ● ● Rate ● ● Rate ● ● ● Rate ● 2 ● ● ● 2 ● ● ● ● ● ● ● ● ● ● 1 10 ● 1 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0 0 0 EhaB EhaM EhaL EhaT EhaR EhaD EhaC EhaS EhaA EhaE EhaG EhaQ EhaF EhaN EhaH EhaP EhaK EhaO EhaI EhaJ EhaB EhaM EhaB EhaL EhaM EhaT EhaR EhaL EhaD EhaC EhaT EhaS EhaA EhaR EhaE EhaG EhaQ EhaD EhaC EhaF EhaS EhaN EhaA EhaE EhaH EhaP EhaG EhaQ EhaK EhaF EhaO EhaN EhaI EhaJ EhaH EhaP EhaK EhaO EhaI EhaJ
subunit name subunit name subunit name
5 ● ● 5 ● 40 ● ● ● j. ● ● ● ● k. ● ● ● ● 4 ● ● ● l. ● ● ● ● 4 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 30 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 3 ● ● ● ● ● ● ● ● ● ● ● 3 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 20 ● Rate Rate 2 Rate 2
1 10 1 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0 0 0 EhbC EhbC EhbB EhbM EhbL EhbG EhbP EhbF EhbI EhbB EhbJ EhbM EhbK EhbA EhbE EhbC EhbL EhbN EhbD EhbH EhbG EhbP EhbF EhbI EhbO EhbJ EhbK EhbA EhbE EhbB EhbM EhbN EhbD EhbH EhbL EhbO EhbG EhbP EhbF EhbI EhbJ EhbK EhbA EhbE EhbN EhbD EhbH EhbO
subunit name subunit name subunit name Supplementary Figure 45. Boxplots for site-specific evolutionary rates for each subunit of (a, b, c) Mcr, (d, e, f) Mtr, (g, h, i) Eha, (j, k, l) Ehb. The plots for each complex correspond to Poisson ML, Poisson+G16 ML, Poisson+G16 empirical Bayesian respectively.
Bacteria Crenarchaeota (incl. Aigarchaeota and Persephonarchaea) KUO42472.1 GCA 001515205 methanol-5-hydroxybenzimidazolylcobamide methyltransferase Hadesarchaea archaeon YNP 45 Bacteria (incl. Methanocellales)
Methanobacteriales
RWX74113.1 GCA 004028775 Methanolcorrinoid methyltransferase Candidatus Methanosuratus subterraneum TDA40896.1 GCA 004347975 methanol--corrinoid methyltransferase Candidatus Korarchaeota archaeon
RZN48503.1 GCA 004212155 methanol--corrinoid methyltransferase archaeon (Nuwarchaeales) Methanosarcinales WP 042684251.1 GCF 000711905 methanol-5-hydroxybenzimidazolylcobamide methyltransferase Methermicoccus shengliensis Methanomassiliicoccales Methanonatronarchaeia
Persephonarchaea
Tree scale: 0.1 Supplementary Figure 46. ML phylogeny of MtaB. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80), red circle corresponds to the MAD root, green to MinVar.
Methanosarcinales WP 135612605.1 GCF 900774055 monomethylaminecorrinoid methyltransferase Methanococcoides sp. AM1 HAE43291.1 GCA 003446975 TPA hypothetical protein DCG34 10315 Clostridiales bacterium GCA 002011125MTMF01000002.1 3864396657579 38 GCA 002011125 1 ID 9 38 partial 00 Candidatus Hydrothermarchaeota archaeon JdFR-18 GCA 002011035MTLY01000008.1 1921715451729152 192 GCA 002011035 -1 ID 2 192 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 Methanosarcinales Bacteria GCA 002011035MTLY01000008.1 1671516791522932 167GCA 002011035MTLY01000008.1 1681523511530702 168 GCA 002011035 1 ID 2 167 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 Methanonatronarchaeia (incl. Persephonarchaea) Methanomassiliicoccales GCA 002010075MTMG01000003.1 4029132297379 40GCA 002010075MTMG01000003.1 4129819305179 41 GCA 002010075 1 ID 9 40 partial 00 Methanomicrobia archaeon JdFR-19 GCA 002011125MTMF01000005.1 1881664921670973 188GCA 002011125MTMF01000005.1 1891672241678713 189 GCA 002011125 1 ID 3 188 partial 00 Candidatus Hydrothermarchaeota archaeon JdFR-18 Bacteria Crenarchaeota GCA 002011035MTLY01000004.1 1213186 1 GCA 002011035 1 ID 6 1 partial 10 Candidatus Bathyarchaeota archaeon JdFR-11 GCA 002634385NSJL01000046.1 14186862009871 14 GCA 002634385 -1 ID 71 14 partial 00 Nitrospira sp. WP 089610783.1 GCF 002224645 monomethylaminecorrinoid methyltransferase Dehalobacterium formicoaceticum KON26250.1 GCA 001273375 hypothetical protein AC480 06040 miscellaneous Crenarchaeota group archaeon SMTZ1-55 KON27255.1 GCA 001273375 hypothetical protein AC480 04710 miscellaneous Crenarchaeota group archaeon SMTZ1-55 KUO40500.1 GCA 001515205 hypothetical protein APZ16 05285 Hadesarchaea archaeon YNP 45 KUO42841.1 GCA 001515215 hypothetical protein APU95 04320 Hadesarchaea archaeon YNP N21 TFH10947.1 GCA 004525685 monomethylaminecorrinoid methyltransferase Candidatus Atribacteria bacterium GCA 002348045DDYO01000313.1 3558188373 3 GCA 002348045 -1 ID 73 3 partial 00 Anaerolineales bacterium UBA2232 Bacteria (incl. Verstraetearchaeota) Bacteria (incl. Verstraetearchaeota) Bacteria Bacteria OGS43488.1 GCA 001800675 hypothetical protein A3K76 00010 Euryarchaeota archaeon RBG 13 57 23 OGS56137.1 GCA 001800815 hypothetical protein A3K60 07815 Euryarchaeota archaeon RBG 19FT COMBO 56 21 OGS41864.1 GCA 001800735 hypothetical protein A3K67 08030 Euryarchaeota archaeon RBG 16 62 10 TFG70026.1 GCA 004525325 monomethylaminecorrinoid methyltransferase Methanomassiliicoccus sp. RLI44867.1 GCA 003662715 hypothetical protein DRO69 06425 Candidatus Bathyarchaeota archaeon RLI07488.1 GCA 003662185 hypothetical protein DRO24 02935 Candidatus Bathyarchaeota archaeon RLI44864.1 GCA 003662715 hypothetical protein DRO69 06410 Candidatus Bathyarchaeota archaeon KXH70542.1 GCA 001563335 hypothetical protein AM325 15765 Candidatus Thorarchaeota archaeon SMTZ1-45 GCA 002825515PJET01000142.1 8953910918211 8 GCA 002825515 1 ID 211 8 partial 00 Candidatus Thorarchaeota archaeon MP11T 1 GCA 002011035MTLY01000003.1 8992059934291 89 GCA 002011035 -1 ID 1 89 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 GCA 002403855DHIO01000035.1 53557555714013 53 GCA 002403855 1 ID 13 53 partial 00 Acidimicrobiia bacterium UBA4744 GCA 002418265DIDS01000032.1 40453044668619 40 GCA 002418265 -1 ID 19 40 partial 00 Acidimicrobiia bacterium UBA5794 GCA 002435875DIVN01000084.1 13884101 1 GCA 002435875 -1 ID 101 1 partial 10 Anaerolineales bacterium UBA6131 GCA 002403855DHIO01000035.1 75808688227113 75 GCA 002403855 -1 ID 13 75 partial 00 Acidimicrobiia bacterium UBA4744 GCA 002407845DHPK01000029.1 2428315297033 24 GCA 002407845 1 ID 3 24 partial 00 Leptolinea sp. UBA5366 Bacteria GCA 002011035MTLY01000010.1 24237522513410 24 GCA 002011035 -1 ID 10 24 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 GCA 002011035MTLY01000010.1 25251572654510 25 GCA 002011035 -1 ID 10 25 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 GCA 002011035MTLY01000002.1 3431166325395 34 GCA 002011035 -1 ID 5 34 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 GCA 002011035MTLY01000002.1 3936320377055 39 GCA 002011035 1 ID 5 39 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 GCA 002011035MTLY01000001.1 1312743 1 GCA 002011035 -1 ID 3 1 partial 10 Candidatus Bathyarchaeota archaeon JdFR-11 GCA 002011035MTLY01000002.1 2062073362086105 206 GCA 002011035 1 ID 5 206 partial 01 Candidatus Bathyarchaeota archaeon JdFR-11 KUO43153.1 GCA 001515215 hypothetical protein APU95 01250 Hadesarchaea archaeon YNP N21 Tree scale: 0.1 PUA34233.1 GCA 003056285 hypothetical protein B9J98 01185 Aigarchaeota archaeon NZ13 MG1 Supplementary Figure 47. ML phylogeny of MtmB. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80), red circle corresponds to the MAD root, green to MinVar.
Bacteria Methanosarcinales Bacteria Bacteria Methanomassiliicoccales Methanosarcinales Methanomassiliicoccales GCA 002010075MTMG01000003.1 4331413324719 43GCA 002010075MTMG01000003.1 4432490328079 44 GCA 002010075 1 ID 9 43 partial 00 Methanomicrobia archaeon JdFR-19 GCA 002011125MTMF01000005.1 1961731181741793 196GCA 002011125MTMF01000005.1 1951727731731173 195 GCA 002011125 -1 ID 3 196 partial 00 Candidatus Hydrothermarchaeota archaeon JdFR-18 Methanonatronarchaeia GCA 002011125MTMF01000001.1 2702402082412631 270GCA 002011125MTMF01000001.1 2712412942415961 271 GCA 002011125 1 ID 1 270 partial 00 Candidatus Hydrothermarchaeota archaeon JdFR-18 Bathyarchaeota (JdFR-11)
Tree scale: 0.1 Supplementary Figure 48. ML phylogeny of MtbB. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80), red circle corresponds to the MAD root, green to MinVar.
GCA 002383325DFYJ01000020.1 11122571372350 11 GCA 002383325 1 ID 50 11 partial 00 CandidatusAminicenantes bacterium UBA4085
GCA 000402175AQSV01000063.1 22477393763 2 GCA 000402175 1 ID 63 2 partial 00 Cloacimonetes bacterium JGI 0000014-H19
GCA 000405385ASOP01000039.1GCA 67507896739 6 000405385 GCA 1 ID 39 6 partialAminicenantes 00 bacterium SCGCAAA252-K06
GCA 003141555PLMN01000004.1 2932352338181 29 GCA 003141555 -1 ID 1 29 partial 00 CandidatusAminicenantes bacterium
PKK82679.1 GCA 002838945 hypothetical protein CVT49 12430 candidate division Zixibacteria bacterium HGW-Zixibacteria-1
GCA 002010725MTOP01000021.1 785741005252 7 GCA 002010725 1 ID 52 7 partial 00 CandidatusAminicenantes bacterium JdFR-80
KPK68069.1 GCA 001303805 hypothetical protein AMJ87 12455 candidate division WOR 3 bacterium SM23 60 KPK64614.1 GCA 001303785 hypothetical protein AMJ83 02115 candidate division WOR 3 bacterium SM23 42
PWI46762.1 GCA 003144275 hypothetical protein CEE45 15145 Candidatus Heimdallarchaeota archaeon B3 Heim GCA 002010665MTON01000001.1 6667649691213 66 GCA 002010665 -1 ID 3 66 partial 00 CandidatusAminicenantes bacterium JdFR-78
RFT16103.1 GCA 003426165 hypothetical protein OP8BY 2109 Candidatus Saccharicenans subterraneum
RKY90152.1 GCA 003644835 hypothetical protein DRQ01 09645 Ignavibacteriae bacterium
OGD30339.1 GCA 001773825 hypothetical proteinA2Y56 08970 CandidatusAminicenantes bacterium RBG 13 63 10
OLS31111.1 GCA 001940755 Trimethylamine methyltransferase MttB Candidatus Heimdallarchaeota archaeon AB 125
OLS29093.1 GCA 001940725 Trimethylamine methyltransferase MttB Candidatus Heimdallarchaeota archaeon LC 2
KPK89613.1 GCA 001304035 hypothetical proteinAMJ80 09555 bacterium SM23 31
RLI71513.1 GCA 003662885 hypothetical protein DRO91 05535 Candidatus Heimdallarchaeota archaeon
TFG77902.1 GCA 004525465 hypothetical protein E4H23 08310 Chrysiogenales bacterium
TET69890.1 GCA 004377005 hypotheticalAminicenantes TET69890.1protein bacteriumE3J4407215 GCA Candidatus
RLE02572.1 GCA 003648765 hypothetical protein DRJ11 06825 CandidatusAminicenantes bacterium
RKY86883.1 GCA 003644825 hypothetical protein DRQ09 05430 candidate division KSB1 bacterium
OQX95999.1 GCA 002084535 hypothetical protein B6I21 02530 candidate division KSB1 bacterium 4572 119
GCA 002403075DHHB01000042.1 34310563252557 34 GCA 002403075 -1 ID 57 34 partial 00 bacterium UBP1 UBA4783
GCA 003369535QTKF01000019.1 13117153517298914 131 GCA 003369535 1 ID 14 131 partial 00 bacterium 0218 GCA 002825515PJET01000193.1 42139357276 4 GCA 002825515 -1 ID 76 4 partial 00 Candidatus Thorarchaeota archaeon MP11T 1 KXB04566.1 GCA 001549435 hypothetical protein AKJ50 02270 candidate division MSBL1 archaeon SCGC-AAA382A13
KPL03566.1KPJ58672.1 GCA 001304225 GCA 001302905 hypothetical hypothetical protein AMJ73 protein 06355 AMJ46 candidate 13795 Latescibacteria division Zixibacteria bacterium bacterium DG 63 SM1 73 KPK74393.1 GCA 001303995 hypothetical protein AMJ89 06460 candidate division Zixibacteria bacterium SM23 73
GCA 003369535QTKF01000066.1 53692514665 5 GCA 003369535 1 ID 65 5 partial 00 bacterium 0218 TET71878.1 GCA 004376595 hypothetical protein E3J56 06185 Candidatus Aminicenantes bacterium
KPL18293.1 GCA 001304015 hypothetical protein AMJ92 08615 candidate division Zixibacteria bacterium SM23 81 KXH72482.1 GCA 001563335 hypothetical protein AM325 09035 Candidatus Thorarchaeota archaeon SMTZ1-45
RLI23348.1 GCA 003662445 hypothetical protein DRO58 09245 Candidatus Bathyarchaeota archaeon
KXH70682.1 GCA 001563325 hypothetical protein AM324 09700 Candidatus Thorarchaeota archaeon SMTZ1-83
TFG29918.1RDE11001.1 GCA 004524565 GCA 003345595 hypothetical hypothetical protein EU528protein 08940C4K49 Candidatus 12345 Candidatus Thorarchaeota Thorarchaeota archaeon archaeon
TET08543.1 GCA 004376265 hypothetical protein E3J86 10535 Candidatus Thorarchaeota archaeon
KXB05407.1 GCA 001549435 hypothetical protein AKJ50 01020 candidate division MSBL1 archaeon SCGC-AAA382A13 EHQ87584.1 GCA 000244895 trimethylaminecorrinoid methyltransferase Desulfosporosinus youngiae DSM 17734
GCA 003553735PWFD01000018.1 191700618469105 19 GCA 003553735 -1 ID 105 19 partial 00 Syntrophomonadaceae bacterium AJB41817.1 GCA 000813245 Trimethylaminecorrinoid methyltransferase Thermofilum adornatus 1505 GCA 003564055PWSG01000065.1 87593899353 8 GCA 003564055 -1 ID 53 8 partial 01 Syntrophomonadaceae bacterium MAF85407.1 GCA 002688105 hypothetical protein CL875 02835 Dehalococcoidales bacterium KYH39063.1 GCA 001593875 hypothetical protein AYL28 001560 Candidatus Bathyarchaeota archaeon B23 GCA 002397275DHAA01000153.1 24256682711052 24 GCA 002397275 1 ID 52 24 partial 00 Thermacetogenium sp. UBA4966
OGD27877.1 GCA 001775755 hypothetical protein A2V57 01655 Candidatus Aminicenantes bacterium RBG 19FT COMBO 65 30 GCA 003554725PWHC01000117.1 427534204603 4 GCA 003554725 -1 ID 603 4 partial 00 Syntrophomonadaceae bacterium
TFG57598.1 GCA 004525195 hypothetical protein E4H35 03590 partial Candidatus Aminicenantes bacterium OGD12781.1 GCA 001775695 hypothetical protein A2Y86 00045 Candidatus Aminicenantes bacterium RBG 13 62 12
ABL78864.1 GCA 000015225 trimethylaminecorrinoid methyltransferase Thermofilum pendens Hrk 5 OQY07229.1 GCA 002084545 hypothetical protein B6I22 03530 Desulfobacteraceae bacterium 4572 123
OGD26029.1 GCA 001773925 hypothetical protein A2028 04355 Candidatus Aminicenantes bacterium RBG 19FT COMBO 59 29 RLG93461.1 GCA 003661945 hypothetical protein DRO34 00250 Candidatus Bathyarchaeota archaeon HCS49247.1 GCA 003524335 TPA hypothetical protein DIW61 13730 Candidatus Aminicenantes bacterium MBP17804.1 GCA 002725285 hypothetical protein CMQ21 02820 Gammaproteobacteria bacterium RLI08185.1 GCA 003662205 hypothetical protein DRO42 06800 Candidatus Bathyarchaeota archaeon
GCA 000493965AWNV01000011.1 43715517811 4 GCA 000493965 -1 ID 11 4 partial 00 Candidatus Aminicenans sakinawicola JGI OTU-1 GCA 003247995QJYP01000301.1 329024338177 3 GCA 003247995 -1 ID 177 3 partial 00 Phycisphaerales bacterium PLJ77490.1 GCA 002855745 hypothetical protein B7L53 06160 Thermofilum sp. NZ13 OYT52016.1 GCA 002255025 hypothetical protein B6U66 02870 Candidatus Bathyarchaeota archaeon ex4484 135 OFX38058.1 GCA 001768195 hypothetical protein A2X03 03750 Bacteroidetes bacterium GWA2 40 15 TET64609.1 GCA 004376975 hypothetical protein E3J49 03795 Candidatus Bathyarchaeota archaeon RLI39786.1 GCA 003662655 hypothetical protein DRO60 00270 Candidatus Bathyarchaeota archaeon WP 089609525.1EHQ91178.1 GCF 002224645 GCA 000244895trimethylamine--corrinoid trimethylaminecorrinoid methyltransferase methyltransferase Dehalobacterium Desulfosporosinus formicoaceticum youngiae DSM 17734 GCA 000404445ASML01000034.1 15167131815534 15 GCA 000404445 -1 ID 34 15 partial 00 BRC1 bacterium SCGC AAA257-C11
TET70034.1 GCA 004376595 hypothetical protein E3J56 08695 partial Candidatus Aminicenantes bacterium TGE31712.1 GCA 004766055 trimethylamine--corrinoid methyltransferase Desulfosporosinus sp. Sb-LF PUA31642.1 GCA 003056265 hypothetical protein B7O98 09085 Zestosphaera tikiterensis AET69589.1 GCA 000235605 trimethylaminecorrinoid methyltransferase Desulfosporosinus orientis DSM 765
OGG06706.1 GCA 001780825 hypothetical protein A3F83 07590 Candidatus Glassbacteria bacterium RIFCSPLOWO2 12 FULL 58 11
GCA 002482535DLGE01000008.1 74827078415814 74 GCA 002482535 -1 ID 14 74 partial 00 Peptococcaceae bacterium UBA7702 OYT26272.1 GCA 002254895 hypothetical protein B6V02 02065 Thermoprotei archaeon ex4572 64 TET82687.1 GCA 004377125 hypothetical protein E3J37 06860 Anaerolineales bacteriumGCA 003171295PMYF01000525.1 42371382276 4 GCA 003171295 -1 ID 76 4 partial 00 Acidobacteria bacterium
RLE07602.1 GCA 003648795 hypothetical protein DRZ78 02705 Candidatus Aerophobetes bacterium AFV12931.1HBV89207.1 GCA 000305935 GCA 003513495 trimethylamine TPA trimethylamine--corrinoid methyltransferase Thermacetogenium methyltransferase phaeum Desulfosporosinus DSM 12270 sp.
TEU11976.1 GCA 004377365 hypothetical protein E3J21 22330 Anaerolineales bacterium GCA 002478145DLMI01000122.1 319493391155 3 GCA 002478145 1 ID 155 3 partial 00 Acidobacteria bacterium UBA7540
RLC68229.1 GCA 003647955 hypothetical protein DRI48 00155 Chloroflexi bacterium GCA 003551305PUMJ01000079.1 182098322431298 18 GCA 003551305 1 ID 298 18 partial 00 Candidatus Brocadiaceae bacterium RLF08828.1 GCA 003649605GCA 000583195JARN01000259.1 hypothetical protein DRJ69 05805 25852003259 Thermoprotei archaeon2 GCA 000583195 1 ID 259 2 partial 00 Dehalococcoidia bacterium DscP2 RLC69082.1 GCA 003648005 hypothetical protein DRI52 09290 Chloroflexi bacterium
RLF25173.1 GCARLG76221.1 003650925RLE54881.1 GCA hypothetical 003661705 GCA 003649205 protein hypothetical DRN15 hypothetical 00520protein protein ThermoproteiDRO23 DRJ40 01705 09900archaeon Thermoprotei Thermoprotei archaeon archaeon EHQ90593.1 GCA 000244895 trimethylaminecorrinoid methyltransferase Desulfosporosinus youngiae DSM 17734 RLE96420.1 GCA 003649495 hypothetical protein DRJ96 06640 Thermoprotei archaeon WP 089611796.1 GCF 002224645 trimethylamine--corrinoid methyltransferase Dehalobacterium formicoaceticum KJS48276.1 GCA 000961805AET66811.1 trimethylaminecorrinoid GCA 000235605 methyltransferase trimethylaminecorrinoid Peptococcaceae methyltransferase bacterium BRH Desulfosporosinus c23 orientis DSM 765
RLE11085.1 GCA 003648865 hypothetical protein DRI96 06830 Candidatus Aerophobetes bacterium HBV89208.1 GCA 003513495 TPA trimethylamine--corrinoid methyltransferase Desulfosporosinus sp. GCA 003141795PLNO01000120.1 31527291844 3 GCA 003141795 1 ID 44 3 partial 00 Spirochaetaceae bacterium RPI47981.1 GCA 003819865 hypothetical protein EHM56 14310 Chloroflexi bacterium
GCA 002375925DFNE01000084.1 161498716414103 16 GCA 002375925 1 ID 103 16 partial 00 Firmicutes bacterium UBA3575 TFG70729.1 GCA 004525325 hypothetical protein E4H25 01215 Methanomassiliicoccus sp. RLE93914.1 GCA 003649445 hypothetical protein DRN04 05490 Thermoprotei archaeon Bacteria PWB53032.1GCA GCA 002412925DHVZ01000077.1 003105035 hypothetical protein 16617374717516286 C3F13 10455 Anaerolineales 166 GCA bacterium 002412925 1 ID 86 166 partial 00 Anaerolineales bacterium UBA5195 KPK91688.1TET80807.1 GCAPKO13974.1 GCA001303965 004377125 hypothetical GCA hypothetical 002840755 protein protein hypothetical AMJ88 E3J37 12895 10475 protein Anaerolineae Anaerolineales CVU39 bacterium16475 bacterium Chloroflexi SM23 63 bacterium HGW-Chloroflexi-10 OGO25867.1 GCA 001796835 hypothetical protein A2W33 08450 Chloroflexi bacterium RBG 16 52 11 GCA 003563035PWTA01000055.1 740135428127 7 GCA 003563035 1 ID 127 7 partial 00 Anaerolineae bacterium
GCA 003564075PWSC01000237.1 868138228414 8 GCA 003564075 1 ID 414 8 partial 00 Anaerolineae bacterium OGS43212.1 GCA 001800675OGS48280.1 hypothetical GCA 001800795 protein A3K76 hypothetical 05710 Euryarchaeota protein A3K68 archaeon 03615 RBGEuryarchaeota 13 57 23 archaeon RBG 16 68 13 GCA 003235355QJWK01001052.1 323893807980 3 GCA 003235355 1 ID 980 3 partial 00 Chloroflexi bacterium OGS56167.1 GCA 001800815OGS46894.1 hypothetical GCA 001800745protein A3K60 hypothetical 02235 Euryarchaeota protein A3K66 archaeon 01185 RBG Euryarchaeota 19FT COMBO archaeon 56 21 RBG 16 67 27 Bacteria TFG67817.1 GCAOGS62701.1 004525325 GCAhypothetical 001800825 protein hypothetical E4H25 06905 protein Methanomassiliicoccus A3K59 01010 Euryarchaeota sp. archaeon RBG 19FT COMBO 69 17
RLB13642.1 GCA 003646815 trimethylamine methyltransferase partial Deltaproteobacteria bacterium GCA 003236135QJVL01000242.1 431684580509 4 GCA 003236135 1 ID 509 4 partial 00 Anaerolineae bacterium KUO43214.1 GCA 001515215 hypothetical protein APU95 01820 Hadesarchaea archaeon YNP N21 OGS42409.1 GCA 001800735RLI39232.1 hypothetical GCA 003662715 protein A3K67hypothetical 06775 protein partial DRO69Euryarchaeota 14515 archaeon Candidatus RBG Bathyarchaeota 16 62 10 archaeon RLI45908.1 GCA 003662715 hypothetical protein DRO69 04245 Candidatus Bathyarchaeota archaeon SMC88216.1 GCA 900176365 trimethylaminecorrinoid methyltransferase Desulfobacterium vacuolatum DSM 3385 ABE53169.1 GCA 000013725 Trimethylamine methyltransferase Methanococcoides burtonii DSM 6242 GBC62257.1 GCA 003851005 trimethylamine methyltransferase Desulfonema ishimotonii GCA 002506175DAXB01000063.1 31223274977 3 GCA 002506175 1 ID 77 3 partial 00 Methanomassiliicoccaceae archaeon UBA113
RLI46042.1 GCA 003662715 hypothetical protein DRO69 03995 Candidatus Bathyarchaeota archaeon KXB05142.1 GCA 001549435 hypothetical protein AKJ50 01720 candidate division MSBL1 archaeon SCGC-AAA382A13 WP 135612607.1 GCF 900774055 hypothetical protein Methanococcoides sp. AM1 RMG98467.1 GCA 003696525 trimethylamine methyltransferase Candidatus Dadabacteria bacterium RLA86707.1 GCA 003643875 hypothetical protein DRG34 06265 Deltaproteobacteria bacterium PSP20600.1 GCA 003022085EHQ90549.1 hypothetical GCA protein 000244895 BRC61 trimethylaminecorrinoid 07020 Halobacteriales methyltransferase archaeon QH 10 Desulfosporosinus 65 19 youngiae DSM 17734
GCA 001735875DS021251.1 112725067348932 112 GCA 001735875 1 ID 32 112 partial 00 Olavius algarvensis Delta 1 endosymbiont PSP84841.1 GCA 003021105 trimethylamine--corrinoid methyltransferase Halobacteriales archaeon QS 1 68 17 Bacteria GCA 002011035MTLY01000008.1 1741583081593032 174GCA 002011035MTLY01000008.1 1751593671597922 175 GCA 002011035 1 ID 2 174 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 PSP84301.1 GCA 003021105 trimethylamine--corrinoid methyltransferase Halobacteriales archaeon QS 1 68 17 MethanomassiliicoccalesGCA 002010075MTMG01000013.1 1601252481262732 160GCA 002010075MTMG01000013.1 1591247591251482 159 GCA 002010075 -1 ID 2 160 partial 00 Methanomicrobia archaeon JdFR-19 GCA 002011125MTMF01000005.1 1761531151541133 176GCA 002011125MTMF01000005.1 1751526291530483 175 GCA 002011125 -1 ID 3 176 partial 00 Candidatus Hydrothermarchaeota archaeon JdFR-18 SHH00015.1 GCA 900129775 trimethylaminecorrinoid methyltransferase Halobaculum gomorrense ESS12699.1 GCA 000496235 Trimethylaminecorrinoid methyltransferase uncultured archaeon A07HR60 Methanosarcinales OKY77550.1 GCA 001914405 Trimethylaminecorrinoid methyltransferase MttB2 Candidatus Methanohalarchaeum thermophilum GCA 003555005PWHS01000019.1 53817481531 5GCA 003555005PWHS01000019.1 64882529231 6 GCA 003555005 1 ID 31 5 partial 00 Methanonatronarchaeia archaeon MethanomassiliicoccalesOUJ19433.1OUJ19434.1 GCA 002153915 Trimethylaminecorrinoid methyltransferase MttB2 Methanonatronarchaeum thermophilum AUX08808.1 GCA 002952775 trimethylamine-corrinoid protein Co-methyltransferase Halalkaliarchaeum desulfuricum
MBL10730.1 GCA 002721105 hypothetical protein CL402 09500 Acidiferrobacteraceae bacterium RLI39777.1 GCA 003662715 hypothetical protein DRO69 13865 partial Candidatus Bathyarchaeota archaeon TET30944.1 GCA 004376485 trimethylamine--corrinoid methyltransferase Candidatus Aerophobetes bacterium Bacteria SEM35607.1 GCA 900109985 trimethylaminecorrinoid methyltransferase Candidatus Frackibacter sp. WG12 OGS47550.1 GCA 001800745 hypothetical protein A3K66 05230 Euryarchaeota archaeon RBG 16 67 27 Bacteria OGS59936.1 GCA 001800825 hypothetical protein A3K59 08185 Euryarchaeota archaeon RBG 19FT COMBO 69 17 ADL13358.1 GCA 000144695 trimethylamine methyltransferase Acetohalobium arabaticum DSM 5501 OGS61398.1 GCA 001800825 hypothetical protein A3K59 07370 Euryarchaeota archaeon RBG 19FT COMBO 69 17 OKY78407.1 GCA 001914405 Trimethylaminecorrinoid methyltransferase MttB2 Candidatus Methanohalarchaeum thermophilum TFG69623.1 GCA 004525325 hypothetical protein E4H25 04460 Methanomassiliicoccus sp. OGS44411.1 GCA 001800675 hypothetical protein A3K76 03320 Euryarchaeota archaeon RBG 13 57 23 Bacteria OGS56900.1 GCA 001800815 hypothetical protein A3K60 01760 Euryarchaeota archaeon RBG 19FT COMBO 56 21 TFG69622.1 GCA 004525325 hypothetical protein E4H25 04455 Methanomassiliicoccus sp. OGS44412.1 GCA 001800675 hypothetical protein A3K76 03325 Euryarchaeota archaeon RBG 13 57 23 OLN31946.1 GCA 001936615 Trimethylamine methyltransferase family protein Desulfosporosinus sp. OL OGS56901.1 GCA 001800815 hypothetical protein A3K60 01765 Euryarchaeota archaeon RBG 19FT COMBO 56 21 OGS41833.1 GCA 001800735 hypothetical protein A3K67 03085 Euryarchaeota archaeon RBG 16 62 10 RLB90569.1 GCA 003647305 trimethylamine--corrinoid methyltransferase Deltaproteobacteria bacterium Bacteria TFG67438.1 GCA 004525325 hypothetical protein E4H25 07450 partial Methanomassiliicoccus sp. OGS43603.1 GCA 001800675 hypothetical protein A3K76 04015 Euryarchaeota archaeon RBG 13 57 23 HCY84316.1 GCA 003538835 TPA trimethylamine--corrinoid methyltransferase Desulfobacteraceae bacterium Bacteria OGS55226.1 GCA 001800815 hypothetical protein A3K60 04770 Euryarchaeota archaeon RBG 19FT COMBO 56 21 GCA 003236115QJVS01000223.1 11341546903 1 GCA 003236115 1 ID 903 1 partial 00 Desulfobacterales bacterium OEU77143.1 GCA 001751085 trimethylamine methyltransferase Desulfobacterales bacterium C00003060 RTZ96131.1 GCA 003973265 trimethylamine--corrinoid methyltransferase Deltaproteobacteria bacterium TDF70623.1 GCA 004353525 trimethylamine--corrinoid methyltransferase Clostridia bacterium k32
KGK81132.1 GCA 000765145 trimethylamine methyltransferase Desulfosporosinus sp. HMP52 GCA 001735875DS021246.1 16511037311185427 165 GCA 001735875 1 ID 27 165 partial 00 Olavius algarvensis Delta 1 endosymbiont KJS88155.1 GCA 000802045 trimethylamine methyltransferase Peptococcaceae bacterium BICA1-8 PWB50163.1 GCA 003105035 hypothetical protein C3F13 16985 Anaerolineales bacterium OGN99107.1 GCA 001796475 hypothetical protein A2Z71 10990 Chloroflexi bacterium RBG 13 50 21 SHF39025.1 GCA 900129135 trimethylaminecorrinoid methyltransferase Lactonifactor longoviformis DSM 17459 OGN93589.1 GCA 001796435 hypothetical protein A2Y88 12840 Chloroflexi bacterium RBG 13 48 10 RLE15127.1 GCA 003648845 hypothetical protein DRJ04 01070 Candidatus Aerophobetes bacterium RLI43593.1 GCA 003662715 hypothetical protein DRO69OGS43008.1 09095 CandidatusGCA 001800675 Bathyarchaeota hypothetical archaeon protein A3K76 01215 Euryarchaeota archaeon RBG 13 57 23 SHF22160.1 GCA 900129135 trimethylaminecorrinoid methyltransferase Lactonifactor longoviformis DSM 17459 OGS57043.1 GCA 001800815 hypothetical protein A3K60 08135 Euryarchaeota archaeon RBG 19FT COMBO 56 21 PKM81219.1 GCA 002840275 trimethylamine--corrinoid methyltransferase Firmicutes bacterium HGW-Firmicutes-14 RLI08493.1 GCA 003662185 hypothetical protein DRO24 01145OGS63394.1 Candidatus GCA Bathyarchaeota 001800825 archaeonhypothetical protein A3K59 06060 Euryarchaeota archaeon RBG 19FT COMBO 69 17 RLG91996.1 GCA 003661945 hypothetical protein DRO34 03160 Candidatus Bathyarchaeota archaeon RLC63179.1 GCA 003647945 hypothetical proteinOGS51643.1 DRI01 05690 GCA 001800715Chloroflexi bacteriumhypothetical protein A3K75 03665 Euryarchaeota archaeon RBG 13 61 15 OGS43499.1 GCA 001800675 hypothetical protein A3K76 00075 partial Euryarchaeota archaeon RBG 13 57 23
OGS57008.1 GCA 001800815 hypothetical protein A3K60 03980 EuryarchaeotaRLI39723.1 archaeon GCA 003662715 RBG 19FT hypothetical COMBO 56 protein 21 DRO69 13930 partial Candidatus Bathyarchaeota archaeon OGS56088.1 GCA 001800815 hypothetical protein A3K60 02905 Euryarchaeota archaeon RBG 19FT COMBO 56 21 OGS44009.1 GCA 001800675 hypotheticalOGS47545.1 protein GCA A3K76 001800745 00880 Euryarchaeotahypothetical protein archaeon A3K66 RBG 05205 13 57Euryarchaeota 23 archaeon RBG 16 67 27
OGS51912.1 GCA 001800715 hypothetical protein A3K75 01440 partial Euryarchaeota archaeon RBG 13 61 15 OHB42024.1 GCA 001824555 hypothetical protein A2Y13 07770 Planctomycetes bacterium GWC2 45 44 RLI45973.1 GCA 003662715 trimethylamine methyltransferaseOGS47542.1 partial Candidatus GCA 001800745 Bathyarchaeota hypothetical archaeon protein A3K66 05185 Euryarchaeota archaeon RBG 16 67 27 TFG18049.1 GCA 004524705 hypothetical protein EU533 07965 Candidatus Lokiarchaeota archaeon OGS59938.1 GCA 001800825 hypotheticalGCA 004557845SFFM01000008.1 protein A3K59 08195 Euryarchaeota 73804598186860 archaeon RBG 73 19FTGCA 004557845COMBO 69 17-1 ID 60 73 partial 00 Alphaproteobacteria bacterium TFG26416.1 GCA 004524515 hypothetical protein EU532 09855 Candidatus Lokiarchaeota archaeon OGS42463.1 GCA 001800735 hypothetical protein A3K67 04195 Euryarchaeota archaeon RBG 16 62 10 RLB42198.1 GCA 003646995 hypothetical protein DRH12 06280 Deltaproteobacteria bacterium RLI44263.1 GCA 003662745 hypothetical protein DRO61 12355 Candidatus Bathyarchaeota archaeon TFG70388.1 GCA 004525325OPX38530.1 hypothetical proteinGCA 002049905 E4H25 02285 hypothetical Methanomassiliicoccus protein B1H11 sp. 04440 partial Desulfobacteraceae bacterium 4484 190.1 OGS45114.1 GCA 001800675 hypothetical protein A3K76 05975 Euryarchaeota archaeon RBG 13 57 23 TFG12417.1 GCA 004524495 hypothetical protein EU535 06240 Candidatus Lokiarchaeota archaeon OGS56284.1 GCA 001800815 hypotheticalRLB18184.1 protein GCA A3K60 003646815 07470 Euryarchaeota hypothetical proteinarchaeon DRG82 RBG 19FT 04495 COMBO Deltaproteobacteria 56 21 bacterium TFF84072.1 GCA 004524155 hypothetical protein EU552 01735 Candidatus Lokiarchaeota archaeon Bacteria OGS55578.1OGS42974.1 GCA 001800815 GCA 001800675 hypothetical hypothetical protein protein A3K60 A3K7607710 Euryarchaeota01420 Euryarchaeota archaeon archaeon RBG 19FT RBG COMBO 13 57 23 56 21
TFF99556.1 GCA 004524365 hypothetical protein EU541 04610 Candidatus Lokiarchaeota archaeon RLI41974.1 GCA 003662715 hypothetical protein DRO69 10945 Candidatus Bathyarchaeota archaeon TFG68626.1 GCA 004525325 hypothetical protein E4H25 05670 Methanomassiliicoccus sp.
RLG51254.1 GCA 003661385 trimethylamine methyltransferase partial Candidatus Korarchaeota archaeon RLI43922.1 GCA 003662715 hypothetical protein DRO69 08565 partial Candidatus Bathyarchaeota archaeon Bacteria OGS51739.1 GCA 001800715 hypothetical protein A3K75 01075 Euryarchaeota archaeon RBG 13 61 15 TES94979.1 GCA 004375715 hypothetical protein E3J90 10640 Candidatus Lokiarchaeota archaeon RLI44222.1RLI43744.1 GCA 003662715GCA 003662715 hypothetical hypothetical protein protein DRO69 DRO69 07870 08980Candidatus Candidatus Bathyarchaeota Bathyarchaeota archaeon archaeon RLG40761.1 GCA 003661265 hypothetical protein DRO05 05565 Candidatus Korarchaeota archaeon
RLI43749.1 GCA 003662715 hypothetical protein DRO69 08950 Candidatus Bathyarchaeota archaeon GCA 002011035MTLY01000008.1 1421240561255132 142 GCA 002011035 1 ID 2 142 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11 Bacteria TFH19016.1 GCA 004525915 trimethylamine methyltransferase Candidatus Bathyarchaeota archaeon
TFF99554.1 GCA 004524365 hypothetical protein EU541 04600 Candidatus Lokiarchaeota archaeon OGN71754.1 GCA 001796335 hypothetical protein A2X25 02310 Chloroflexi bacterium GWB2 49 20 KUO42027.1 GCA 001515205 hypothetical protein APZ16 03525 Hadesarchaea archaeon YNP 45 TET13435.1 GCA 004376425 hypothetical protein E3J82 03005 partial Candidatus Thorarchaeota archaeon
TAL32222.1 GCA 004297825 hypothetical protein EPN93 16535 Spirochaetes bacterium OGN71775.1 GCA 001796335 hypothetical protein A2X25 02425 Chloroflexi bacterium GWB2 49 20 OGS46895.1 GCA 001800745 hypothetical protein A3K66 01190 Euryarchaeota archaeon RBG 16 67 27 TKJ26752.1 GCA 005222975 hypothetical protein CEE42 04020 Candidatus Lokiarchaeota archaeon Loki b31 GCA 003557365PWOO01000092.1 21823312453 2 GCA 003557365 -1 ID 53 2 partial 01 bacterium GCA 003566315PXDS01000120.1 432234719148 4 GCA 003566315 1 ID 148 4 partial 00 Candidatus Omnitrophica bacterium TFG12665.1 GCA 004524445 hypothetical protein EU537 08870 Candidatus Thorarchaeota archaeon OGS46081.1 GCA 001800745 hypothetical protein A3K66 04940 Euryarchaeota archaeon RBG 16 67 27 RLG41728.1 GCA 003661265 trimethylamine methyltransferase Candidatus Korarchaeota archaeon
TFG07999.1 GCA 004524425 hypothetical protein EU539 03530 Candidatus Lokiarchaeota archaeon OGD54884.1 GCA 001775955 hypothetical protein A3K80 01545 Candidatus Bathyarchaeota archaeon RBG 13 38 9 RPI87074.1 GCA 003820065 hypothetical protein EHM41 06275 Chloroflexi bacterium
OGS52309.1 GCA 001800715 hypothetical protein A3K75 05510 Euryarchaeota archaeon RBG 13 61 15 KXH74023.1 GCA 001563325 hypothetical protein AM324 16015 Candidatus Thorarchaeota archaeon SMTZ1-83 GBC75359.1 GCA 002898815 hypothetical protein HRbin06 00677 archaeon HR06 RDE15736.1 GCA 003345595 hypothetical protein C4K49 05765 Candidatus Thorarchaeota archaeon TFG70734.1 GCA 004525325 hypothetical protein E4H25 01240 Methanomassiliicoccus sp. OGS56102.1OGS44041.1 GCA 001800815 GCA 001800675 hypothetical hypothetical protein A3K60protein 00990 A3K76 partial 00740 Euryarchaeota Euryarchaeota archaeon archaeon RBG RBG 19FT 13 57COMBO 23 56 21 TFG70730.1 GCA 004525325 hypothetical protein E4H25 01220 Methanomassiliicoccus sp. OLS31774.1 GCA 001940705 Trimethylamine methyltransferase MttB Candidatus Thorarchaeota archaeon AB 25
RJP23744.1 GCA 003598085 hypothetical protein C4520 05695 Candidatus Abyssubacteria bacterium SURF 5 TET08784.1 GCA 004376265 hypothetical protein E3J86 09915 Candidatus Thorarchaeota archaeon GCA 003247535QJZD01000232.1 217613224237 2 GCA 003247535 1 ID 237 2 partial 00 Desulfobacterales bacterium KXH74032.1 GCA 001563335 hypothetical protein AM325 13130 partial Candidatus Thorarchaeota archaeon SMTZ1-45
GCA 002367275DFBE01000039.1 70618636330576 70 GCA 002367275 1 ID 76 70 partial 00 Dehalococcoidia bacterium UBA3088 OGS55428.1OGS45033.1 GCA 001800815OGS42537.1 GCA 001800675 hypothetical GCA 001800735 hypothetical protein hypothetical A3K60 protein 05335 A3K76protein Euryarchaeota 01695A3K67 Euryarchaeota 07650 archaeon partial Euryarchaeota archaeon RBG 19FT RBG COMBO archaeon 13 57 5623 RBG21 16 62 10 OGS41606.1 GCA 001800735 hypothetical protein A3K67 06625 Euryarchaeota archaeon RBG 16 62 10 GCA 002292015DBBD01000147.1 14127291421013 14 GCA 002292015 -1 ID 13 14 partial 00 Firmicutes bacterium UBA993 OEU67758.1 GCA 001751165 hypothetical protein BBJ57 05095 Desulfobacterales bacterium PC51MH44 KUO40682.1 GCA 001515205 hypothetical protein APZ16 02230 Hadesarchaea archaeon YNP 45 OGS44317.1 GCAOGS43007.1 001800675OQY08210.1 GCA hypothetical 001800675 GCA 002084545protein hypothetical A3K76 hypothetical 02320 protein Euryarchaeota A3K76 protein 01200 B6I22 archaeon Euryarchaeota 01180 RBG Desulfobacteraceae 13 57 archaeon 23 RBG bacterium 13 57 23 4572 123
KUO43095.1 GCA 001515215 hypothetical protein APU95 00970 Hadesarchaea archaeon YNP N21 OGS56731.1 GCA 001800815 hypothetical protein A3K60 02605 Euryarchaeota archaeon RBG 19FT COMBO 56 21 OGS52099.1 GCA 001800715 hypothetical protein A3K75 02155 Euryarchaeota archaeon RBG 13 61 15 OQY08093.1 GCA 002084545 hypothetical protein B6I22 01785 Desulfobacteraceae bacterium 4572 123 GBC75170.1 GCA 002898815 hypothetical protein HRbin06 00484 archaeon HR06
GCA 003160755QEXZ01000012.1 87664914224 8 GCA 003160755 1 ID 24 8 partial 00 Methanomicrobiales archaeon OGS59930.1 GCA 001800825 hypothetical protein A3K59 08150 Euryarchaeota archaeon RBG 19FT COMBO 69 17 RLI44305.1 GCA 003662715 hypothetical protein DRO69 07675 Candidatus Bathyarchaeota archaeon GCA 003170895PMYG01000303.1 537005163143 5 GCA 003170895 1 ID 143 5 partial 00Actinobacteria bacterium RLI14771.1 GCA 003662305 hypothetical protein DRO43 03145 Candidatus Bathyarchaeota archaeon TFH10948.1 GCA 004525685 hypothetical protein E4H08 02495 Candidatus Atribacteria bacterium KUK31230.1 GCA 001508855 Trimethylamine methyltransferase MttB Thermoanaerobacterales bacterium 50 218
RLI43750.1 GCA 003662715 hypothetical protein DRO69 08955 Candidatus Bathyarchaeota archaeon GCA 002348045DDYO01000313.1 63688514573 6 GCA 002348045 -1 ID 73 6 partial 00 Anaerolineales bacterium UBA2232TET13183.1 GCA 004376225 hypothetical protein E3J84 00385 Candidatus Aerophobetes bacterium RLE13374.1 GCA 003648865 hypothetical protein DRI96 03075 Candidatus Aerophobetes bacterium
RLE15295.1 GCA 003648865 hypothetical protein DRI96 00085 Candidatus Aerophobetes bacterium
OHD74495.1 GCA 001829505 hypothetical protein A2V99 14005 Spirochaetes bacterium RBG 16 67 19 TET12908.1 GCA 004376225 hypothetical protein E3J84 00790 Candidatus Aerophobetes bacterium
MAF85475.1 GCA 002688105 hypothetical protein CL875 03205 Dehalococcoidales bacterium RLE82478.1 GCA 003649305KUO40861.1 hypothetical GCA protein 001515205 DRJ52 hypothetical02135 Thermoprotei protein APZ16 archaeon 01465 Hadesarchaea archaeon YNP 45 RLE77721.1 GCA 003649295 hypothetical protein DRJ56 01680 partial Thermoprotei archaeon GCA 002011035MTLY01000002.1 9892356937985 98 GCA 002011035 1 ID 5 98 partial 00 Candidatus Bathyarchaeota archaeon JdFR-11
SKC70553.1 GCA 900167445 trimethylamine---corrinoid protein Co-methyltransferase Maledivibacter halophilus
GCA 002011035MTLY01000002.1 1161132551146975 116 GCA 002011035 1 ID 5 116 partial 00 CandidatusAQV00767.1 Bathyarchaeota GCA 002009335 trimethylamine archaeon JdFR-11 methyltransferase Desulfococcus multivorans
TET64220.1 GCA 004376885 trimethylamine methyltransferase Candidatus Aerophobetes bacterium
RJS85021.1 GCA 003601735 hypothetical protein CW702 01650 Candidatus Bathyarchaeota archaeon RLB93897.1 GCA 003647365 trimethylamine methyltransferase Deltaproteobacteria bacterium
TKJ45623.1 GCA 005223095 trimethylamine methyltransferase partial Candidatus Aerophobetes bacterium Ae b3a WP 024336650.1 GCF 000421285 trimethylamine methyltransferase Desulfotignum balticum
RLC05950.1 GCA 003647375 trimethylamine methyltransferase Deltaproteobacteria bacterium HAJ33938.1 GCA 003451675 TPA trimethylamine methyltransferase Candidatus Atribacteria bacterium WP 027362824.1 GCF 000420085 trimethylamine methyltransferase Desulfospira joergensenii
RKX78753.1 GCA 003645645 trimethylamine methyltransferase Spirochaetes bacterium GCA 000402295AQRW01000160.1 131235213800160 13 GCA 000402295 1 ID 160 13 partial 00 Candidatus Aerophobus profundus SCGC AAA252-L23
THB81124.1 GCA 004796375 trimethylamine methyltransferase partial Desulfobacteraceae bacterium RLE40464.1 GCA 003650565 trimethylamine methyltransferase Candidatus Acetothermia bacterium
RLI48235.1 GCA 003662765 trimethylamine methyltransferase Candidatus Thorarchaeota archaeon
GCA 003552795PUOM01000241.1 12441689295 1 GCA 003552795 -1 ID 295 1 partial 00 Halomonas sp.
GCA 000404345ASMN01000018.1 85326677418 8 GCA 000404345 1 ID 18 8 partial 00 Aerophobetes bacterium SCGC AAA255-F10
SHG15360.1 GCA 900129305 trimethylamine---corrinoid protein Co-methyltransferase Desulfacinum infernum DSM 9756
GCA 003236115QJVS01001144.1 5461260631032 5 GCA 003236115 -1 ID 1032 5 partial 00 Desulfobacterales bacterium
GCA 003558815PWOU01000014.1 12311793216 1 GCA 003558815 1 ID 216 1 partial 00 Candidatus Brocadiaceae bacterium GCA 001735875DS021316.1 50314073285897 50 GCA 001735875 -1 ID 97 50 partial 00 Olavius algarvensis Delta 1 endosymbiont
GCA 003567495PWZK01000046.1 31301277092 3 GCA 003567495 -1 ID 92 3 partial 00 Candidatus Brocadiaceae bacterium
GCA 003551785PUNP01000699.1 111437764 1 GCA 003551785 1 ID 764 1 partial 10 Candidatus Brocadiaceae bacterium GCA 002849045NCRO01000344.1 523273775273 5 GCA 002849045 -1 ID 273 5 partial 00 Candidatus Atribacteria bacterium RS-JS1
GCA 003558595PWPW01000040.1 431244560147 4 GCA 003558595 1 ID 147 4 partial 00 Candidatus Brocadiaceae bacterium GCA 003160755QEXZ01000012.1 13133101475824 13 GCA 003160755 1 ID 24 13 partial 00 Methanomicrobiales archaeon
GCA 002327445DCWA01000032.1 15617658717803833 156 GCA 002327445 1 ID 33 156 partial 00 Desulfobacteraceae bacterium UBA2174
GCA 003551325PUMK01000027.1 2367180677 2 GCA 003551325 -1 ID 77 2 partial 00 Candidatus Acetothermia bacterium
GCA 003562845PWTL01000051.1 31722316140 3 GCA 003562845 -1 ID 3 40 partial 00 Candidatus Acetothermia bacterium
GCA 003566155PXEP01000098.1 429374376163 4 GCA 003566155 -1 ID 4163 partial 00 Candidatus Acetothermia bacterium
Tree scale: 0.1 Supplementary Figure 49. ML phylogeny of MttB. Black circles indicate strongly supported branches (ultrafast bootstrap >=95, aLRT SH-like >=80).
a. b.
c. Supplementary Figure 50. Homology model of the ancestral McrA sequence (orange) with the a) Mcr-like, b) Halobacterota, c) Proteoarchaeota roots aligned with the template structure of the M. marburgensis McrA (PDB ID: 1HBU, chain D; red). The view is focused on the methyl-CoM binding cavity.
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