TABLE 4.
Distribution of the Mmp10 homologs within the genomes of Archaea
| Lineage | No. of genomes | No. of genomes encoding Mmp10 | No. of genomes with mmpX flanking mcra |
|---|---|---|---|
| Methanococcales | 19 | 19 | 19 |
| Methanopyrales | 1 | 1 | 1 |
| Methanobacteriales | 58 | 58 | 53b |
| Methanomicrobiales | 20 | 19c | 0 |
| Methanocellales | 3 | 3 | 0 |
| Methanosarcinales | 107 | 105d | 97e |
| Methanomassiliicoccales | 8 | 0 | 0 |
| NAOAf | 19 | 5g | 1h |
| Nonmethanogenic Euryarchaeota | 348i | 0 | 0 |
| “Candidatus Bathyarchaeota” | 24 | 0 | 0 |
| “Candidatus Verstraetearchaeota” | 7 | 0 | 0 |
| “Candidatus Nezhaarchaeota” | 2 | 0 | 0 |
| Other Archaea | 359 | 0 | 0 |
The mmpX position was examined by “Show neighborhood regions with the same top COG hit (via top homolog)” command at IMG/M ER.
Not linked to mcr in Methanobrevibacter smithii TS145B and ACE6, Methanobrevibacter curvatus DSM11111, and Methanobacterium sp. Maddingley. These are all draft genomes where mmpX and mcr are on different contigs. In Methanosphaera stadtmanae, mmpX flanks the mcrC-mtr operon, with mrtBDGA 16.8 kb downstream of the mcr operon.
Absent in Methanoculleus bourgensis BA1.
These homologs were present in the Euryarchaeota archaeon JGI 0000059-G05 and Euryarchaeota sp. strain AmaM. Both rRNA and mcrA, the conventional gene markers, were absent in the first archaeon. However, it encoded an McrC subunit which had 85% amino acid identity to that from Methanosaeta concilii. The second archaeon was recently named Methermicoccus shengliensis strain AmaM (61). Therefore, both archaeal species are in fact methanogens affiliated with Methanosarcinales. These homologs were absent in Methanosarcina horonobensis JCM 15518 (draft genome) and Methanosarcina mazei Tuc01.
Not linked in any of the four Methanosaeta genomes (including JGI 0000059-G05 described above), Methanosarcina mazei 1.H.A.2.8 (draft genome with mmpX and mcr on separate contigs), Methanosalsum zhilinae, Methanoflorens stordalenmirensis, and Methermicoccus shengliensis.
NAOA, anaerobic alkane-oxidizing Archaea, including anaerobic methane, ethane, propane, and butane oxidizers.
These homologs are absent in ANME-1 (GenBank accession no. FP565147), “Candidatus Polytropus marinifundus” (GenBank accession no. GCA_003935005) and other unclassified Archaeoglobi members (GenBank accession no. GCA_004347825, GCA_004347865, GCA_004347845, and GCA_002010305), “Candidatus Argoarchaeum ethanivorans” (GenBank accession no. GCA_004193545), “Candidatus Hadesarchaeota” (GenBank accession no. GCA_004347815, GCA_004347835, and GCA_004347925), “Candidatus Korarchaeota” (GenBank accession no. GCA_004347975), “Candidatus Syntrophoarchaeum butanivorans” (GenBank accession no. GCA_001766825), “Candidatus Syntrophoarchaeum caldarius” (GenBank accession no. GCA_001766815), and “Candidatus Syntrophoarchaeum” WYZ-LMO15 (GenBank accession no. GCA_003601555). These homologs are present in all five ANME-2 genomes.
Linked in one of the ANME-2 genomes.
A total of 350 genomes were originally classified as nonmethanogenic Euryarchaeota in IMG. However, two of them belonged to Methanosarcinales as described above. Therefore, they were added to their correct group.