Table 2. Occurrence in methanogens, methanotrophs and short-chain alkane users of 38 genes previously suggested as methanogenesis markers.
| MCR | “6 marker cluster” | F430 bioS and activation | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Nbr of genomes / lineage | Avg genome completness (%) | m1_mcrA | m2_mcrB | m3_mcrG | m4_Predicted rotamase | m5_DUF2102 | m6_DUF2112 | m7_YjiL-like | m8_DUF2113 | m9_arCOG03226 | m10_atwA | m11_mcrC | m12_mcrD | m13_cfbD | m14_cfbE | ||
| Class I / II | Methanobacteriales | 24 | 99 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Methanopyrales | 2 | 100 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Methanococcales | 15 | 100 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Methanosarcinales* | 39 | 99 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0,97 | |
| Methanomicrobiales | 16 | 99 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0,94 | 1 | |
| Methanocellales | 3 | 100 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Methanoflorentaceae | 1 | 97 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| SCAO & AOM | Msar_ANME-2a | 1 | 99 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Msar_ANME-2c | 1 | 92 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Msar_ANME-2d | 2 | 98 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Methanophagales (incl. ANME-1-THS) | 2 | 79 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | |
| NM1§‡ | 2 | 91 | 1 | 1 | 1 | 1 | 1 | 0,5 | 0,5 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Msar_GoM-Arc1 (incl. GoM-Arc1-GOS)§ | 2 | 78 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | |
| Syntrophoarchaeales | 2 | 93 | 1 | 1 | 1 | 1 | 0,5 | 1 | 1 | 1 | 1 | 1 | 0,5 | 1 | 1 | 1 | |
| CH3-dep hydro | Methanomethyliales (incl. Verst-YHS)§ | 7 | 95 | 1 | 1 | 1 | 1 | 0,86 | 1 | 0,86 | 1 | 1 | 1 | 1 | 1 | 0,86 | 0,71 |
| Methanomassiliicoccales | 11 | 99 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0,91 | 0,91 | |
| Methanofastidiosa§ | 8 | 86 | 1 | 1 | 1 | 0,75 | 1 | 1 | 1 | 0,88 | 1 | 1 | 1 | 1 | 1 | 1 | |
| NM3§ | 1 | 86 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | |
| NM4§ | 1 | 86 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| Methanonatronarchaeia (incl. Mnat-ASL) | 3 | 97 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| NM2§ | 1 | 52 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | |
| Bathyarchaeota BA1/BA2 | 2 | 92 | 1 | 1 | 1 | 0,5 | 0,5 | 0,5 | 0,5 | 0,5 | 0,5 | 1 | 0,5 | 0,5 | 0 | 0 | |
| Essentiality index in M. maripaludis | 0 | 0 | 0 | 0 | 3 | 2,5 | 0,5 | 0,5 | 3,5 | 0 | 0 | 0 | 0 | 0 | |||
| MTR | |||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| m15_mtxX | m16_AIR synthase-related | m17_Zn-ribbon protein | m18_DUF2099 | m19_DUF2117 | m20_Gly-thioamidation (McrA PTM) | m21_DUF2124 | m22_DUF2098 | m23_Soluble P-type ATPase | m24_DUF2111 | m25_arCOG04853 | m26_DUF2114 | m27_mtrA | m28_mtrB | m29_mtrC | m30_mtrD | m31_mtrE | m32_arCOG04885 | m33_Arg-methyltransf. (McrA PTM) | m34_DUF1894 | m35_DUF1890 | m36_DUF2115 | m37_DUF2119 | m38_DUF2121 |
| 1 | 1 | 1 | 1 | 0,95 | 0,95 | 0,68 | 1 | 1 | 0,59 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| 1 | 1 | 1 | 0,87 | 1 | 1 | 0,73 | 1 | 0,8 | 0,93 | 1 | 1 | 0,93 | 1 | 1 | 1 | 1 | 1 | 1 | 0,87 | 0,87 | 1 | 0,47 | 1 |
| 0,97 | 1 | 1 | 1 | 0,92 | 1 | 0,87 | 1 | 1 | 0,97 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0,97 | 1 | 1 | 0,67 | 0,21 | 0,9 | 0,67 |
| 1 | 1 | 1 | 1 | 0,44 | 1 | 0,81 | 1 | 0,94 | 0,81 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0,31 |
| 1 | 1 | 1 | 1 | 0,67 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 0 |
| 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 |
| 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 |
| 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 0 | 1 | 0 |
| 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 0 | 0 | 0,5 |
| 0 | 0,5 | 0 | 1 | 1 | 1 | 1 | 0 | 0,5 | 0,5 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0,5 | 0 | 0,5 | 0,5 | 0 | 1 | 0 |
| 0 | 1 | 0 | 0,5 | 1 | 0,5 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 1 | 1 | 0 |
| 0,5 | 0,5 | 0,5 | 0,5 | 0,5 | 0,5 | 0,5 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0,5 | 1 | 1 | 1 | 0 | 0 |
| 1 | 1 | 1 | 1 | 1 | 0 | 0,5 | 0,5 | 0 | 0 | 0,5 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0,50 | 0 |
| 0,71 | 1 | 0,71 | 1 | 0,86 | 0,86 | 1 | 1 | 1 | 0,14 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1 | 1 | 1 | 0,91 | 0,27 | 1 | 0,09 | 1 | 0 | 1 | 0 | 0 | 0,09 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1 | 1 | 0,63 | 0,63 | 0,88 | 1 | 0,88 | 0 | 1 | 0 | 0,5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1 | 1 | 1 | 1 | 1 | 0,67 | 0,33 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1 | 1 | 0 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 0 | 0,5 | 0 | 1 | 0,5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 0 | 9,5 | 0,5 | 3 | 0,5 | 1 | 5,5 | 16 | 10,5 | 11,5 | 23 | 6 | 0 | 0 | 0,5 | 0 | 0 | 0 | 13 | 5 | 6 | 3 | 3 | 2 |
The numbers in the cells colored in red/green indicate the proportion of genomes of one lineage that have a given marker (all = 1, none = 0). It is possible that some of the markers are present in the missing regions of the incomplete MAGs/genomes. For gene essentiality in Methanococcus maripaludis S2: predicted essential genes (Essentiality index ≤ 2) are highlighted in yellow and predicted none essential gene (Essentiality index ≥ 5) are highlighted in grey60. “m1”, “m2”, etc means “marker 1”, “marker 2” etc; Msar, Methanosarcinales; AOM, Anaerobic Oxidation of Methane; SCAO, short-chain alkane oxidation; CH3-dep hydro, methyl-dependent hydrogenotrophic methanogenesis; MCR, methyl-coenzyme M reductase complex; MTR, N5-Methyltetrahydromethanopterin: coenzyme M methyltransferase complex; PTM, involved in post-translational modification of McrA residues; F430 prosthetic group of MCR.
Excluding ANME-2 and GoM-Arc1 genomes.
NM1 MAGs encode for a SCAO metabolism and possibly for methanogenesis or methanotrophy.
Metabolic classification relying only on genomic predictions. The numbering and ordering of the marker was chosen to reflect their occurrence in methanogens, methanotrophs and short-chain alkane oxidizers (i.e. from the most occurrent to the less occurrent) with few modifications in the order to gather markers involved in same functions or being part of same enzymatic complexes.