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. 2019 Sep 6;9:12871. doi: 10.1038/s41598-019-49313-8

Table 1.

Overview of relative abundances for all KEGG orthology terms/enzyme classes associated with one or more steps of methanogenesis.

KO Enzyme(s) Gene name(s) EC-Number(s) TOP3 most abundant organisms C1 C2 C3 C3 C4 C5 C6 C7 C7 C8 C9 C9 C9
Hydro Hydro Hydro Hydro Both Hydro Hydro Aceto Hydro Aceto Aceto Aceto Hydro Aceto Both Both
AcNe BoNe HyNe BP06 BP07 BP08 BP12 BP15 BP10 BP13 BP01 BP16 BP05 BP02 BP03 BP04 BP14 BP09 BP11
Aceto-clastic K00925 Acetate kinase — ackA 2.7.2.1 19, 1210, 1777 13, 19, 163 13, 19, 163 0.218 0.233 0.228 0.268 0.149 0.204 0.215 0.063 0.120 0.148 0.492 0.515 0.145 0.349 0.309 0.269
K00625 Phosphate acetylt-ransferase — pta 2.3.1.8 19, 22, 163 19, 34, 163 19, 34, 163 0.097 0.083 0.077 0.106 0.078 0.040 0.054 0.015 0.031 0.189 0.632 0.630 0.090 0.448 0.546 0.244
K01895 Acetyl-coenzyme A synthetase — ACSS 6.2.1.1 1, 9, 36 1, 9, 302 1, 9, 302 0.116 0.071 0.062 0.077 0.105 0.118 0.092 5.218 0.043 4.268 0.155 0.061 0.056 0.977 0.056 0.066
K00193 Acetyl-CoA decarbonylase/synthase complex Subunit Beta cdh 2.3.1.169 1, 19, 65 1, 19, 65 1, 19, 65 0.434 0.310 0.255 0.705 0.201 0.275 0.314 1.622 0.099 2.574 3.578 3.325 0.165 3.146 1.783 1.961
K00197 Subunit Gamma 2.1.1.245 1, 22, 65 22, 65, 163 22, 34, 163 0.824 0.861 0.788 0.829 1.219 0.437 0.951 1.673 0.229 2.344 3.862 3.516 0.537 2.890 2.049 1.690
K00194 Subunit Delta 0.414 0.475 0.434 0.409 0.528 0.223 0.440 0.794 0.100 0.889 1.091 1.083 0.332 0.892 0.491 0.526
Sum 2.103 2.032 1.846 2.394 2.279 1.296 2.064 9.385 0.621 10.413 9.809 9.130 1.325 8.702 5.234 4.755
Acetoc-lastic & Hydrogen-otrophic K00577 Tetrahydrom-ethanopterin S-methyl-transferase Subunit A mtr 2.1.1.86 1, 3, 19 3, 19, 26 3, 19, 26 0.521 0.486 0.483 0.566 0.239 0.405 0.451 0.624 0.237 0.576 0.610 0.718 0.350 0.528 0.500 0.530
K00578 Subunit B 0.002 0.003 0.003 0.004 0.007 0.004 0.002 0.003 0.001 0.006 0.021 0.019 0.000 0.014 0.011 0.013
K00579 Subunit C 0.000 0.000 0.001 0.000 0.000 0.001 0.000 0.004 0.004 0.002 0.003 0.001 0.007 0.000 0.000 0.000
K00580 Subunit D 0.063 0.053 0.046 0.084 0.024 0.052 0.067 0.040 0.032 0.023 0.005 0.013 0.068 0.016 0.018 0.027
K00581 Subunit E 0.260 0.196 0.204 0.344 0.122 0.220 0.275 0.150 0.097 0.146 0.176 0.171 0.185 0.142 0.149 0.188
K00582 Subunit F 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.001 0.000 0.000
K00583 Subunit G 0.000 0.000 0.000 0.000 0.002 0.000 0.001 0.000 0.000 0.004 0.008 0.005 0.000 0.007 0.008 0.007
K00584 Subunit H 0.246 0.245 0.260 0.394 0.229 0.222 0.233 0.633 0.199 0.713 1.209 1.470 0.299 1.086 1.002 0.841
Sum 1.093 0.984 0.996 1.392 0.624 0.905 1.029 1.455 0.570 1.471 2.034 2.397 0.909 1.792 1.688 1.606
Hydrogen-otrophic K00200 Formylmet-hanofuran dehydrogenase Subunit A fmd 1.2.7.12 3, 19, 22 3, 22, 65 3, 26, 65 0.184 0.092 0.069 0.174 0.075 0.089 0.114 0.047 0.284 0.027 0.035 0.033 0.371 0.040 0.056 0.131
K00201 Subunit B 0.289 0.308 0.280 0.338 0.077 0.250 0.250 0.095 0.444 0.107 0.137 0.150 0.444 0.142 0.166 0.246
K00202 Subunit C 0.061 0.085 0.075 0.085 0.014 0.071 0.079 0.042 0.157 0.022 0.022 0.030 0.104 0.025 0.027 0.059
K00203 Subunit D 0.053 0.062 0.060 0.073 0.035 0.065 0.056 0.002 0.077 0.003 0.010 0.008 0.071 0.021 0.022 0.047
K11261 Subunit E 0.485 0.340 0.293 0.281 0.090 0.324 0.439 0.026 0.140 0.057 0.131 0.089 0.135 0.132 0.297 0.270
K00205 Uncharacterized protein — — Unknown — — — 0.074 0.067 0.060 0.097 0.021 0.051 0.069 0.009 0.092 0.033 0.003 0.007 0.170 0.020 0.046 0.066
K00672 Formylmet-hanofuran tetrahydrome-thanopterin N-formyltransferase — ftr 2.3.1.101 1, 3, 26 3, 26, 1683 3, 26, 1683 0.129 0.169 0.159 0.136 0.030 0.108 0.096 0.048 0.318 0.035 0.021 0.023 0.132 0.034 0.050 0.070
K01499 Methenyltetra-hydromet-hanopterin cyclohydrolase — mch 3.5.4.27* 3, 22 3, 22 3, 22 0.047 0.067 0.050 0.081 0.015 0.052 0.032 0.004 0.074 0.011 0.020 0.022 0.145 0.026 0.021 0.054
K00319 Methylenetetra-hydrome-thanopterin dehydrogenase — mtd 1.5.98.1 3, 6, 26 3, 6, 26 3, 6, 26 3.147 3.450 3.783 3.019 0.911 2.968 3.261 0.716 4.184 0.780 0.225 0.461 3.794 0.811 1.296 1.427
K13942 5,10-methenyltetra-hydrometha-nopterin hydrogenase — hmd 1.12.98.2* 185 185 185 0.000 0.000 0.000 0.000 0.005 0.000 0.000 0.002 0.000 0.000 0.001 0.001 0.007 0.000 0.000 0.000
K00320 5,10-methylen-etetrahydromethan-opterin reductase — mer 1.5.98.2 3, 43, 102 3, 43, 92 3, 43, 92 5.384 5.908 6.070 7.065 2.679 5.034 5.372 1.773 7.457 1.525 0.658 1.008 7.922 1.389 2.424 3.152
Sum 9.854 10.548 10.899 11.350 3.953 9.012 9.768 2.765 13.228 2.600 1.263 1.834 13.295 2.640 4.405 5.521
Common K00399 Methyl-CoM reductase Subunit Alpha mcr 2.8.4.1 1, 3, 22 3, 19, 22 3, 26, 43 8.010 6.397 6.470 4.849 3.222 4.739 6.355 6.625 3.292 8.172 12.755 13.288 4.747 11.437 8.533 9.775
K00401 Subunit Beta 8.002 6.508 6.344 4.731 1.755 4.384 5.717 5.649 4.351 4.780 6.689 6.593 6.703 5.882 5.438 5.988
K00402 Subunit Gamma 6.186 5.383 5.367 4.618 2.532 3.885 4.731 7.039 2.708 7.129 13.444 13.935 4.923 11.247 9.987 10.420
K03388 Hetero-disulfide reductase Subunit A2 hdr 1.8.7.3 and 1.8.98.4–6 3, 20, 26 3, 20, 26 3, 26, 134 0.604 0.546 0.543 0.594 0.602 0.647 0.577 0.079 0.573 0.109 0.051 0.074 0.917 0.215 0.208 0.361
K03389 Subunit B2 0.050 0.047 0.042 0.072 0.027 0.050 0.047 0.009 0.075 0.007 0.005 0.011 0.146 0.015 0.013 0.040
K03390 Subunit C2 0.030 0.024 0.024 0.042 0.021 0.035 0.032 0.006 0.045 0.005 0.003 0.007 0.074 0.006 0.007 0.028
K08264 Subunit D 1.8.98.1 1, 19, 22 1, 19, 22 1, 19, 22 0.003 0.002 0.002 0.032 0.022 0.001 0.018 0.213 0.001 0.180 0.157 0.232 0.004 0.142 0.123 0.096
K08265 Subunit E 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.002 0.000 0.002 0.001 0.002
K14126 F420-non-reducing hydrogenase Large subunit mvh/vhu/vhc 1.8.98.5* 3, 102, 185 3, 102 3, 102 0.035 0.037 0.044 0.022 0.025 0.021 0.018 0.004 0.028 0.035 0.009 0.015 0.048 0.023 0.025 0.018
K14127 Iron-sulfur subunit 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.002 0.000 0.011 0.003 0.006 0.005 0.002 0.000 0.001
K22516 Formate dehydro-genase Subunit Alpha fdh 1.17.98.3 and 1.8.98.6 3, 6, 26 3, 6, 26 3, 6, 26 0.392 0.660 0.663 0.665 0.355 0.474 0.538 0.558 2.457 0.431 0.153 0.301 1.524 0.263 0.248 0.425
K00125 Subunit Beta 0.110 0.147 0.140 0.152 0.136 0.095 0.098 0.099 0.653 0.067 0.045 0.080 0.480 0.057 0.045 0.095
Sum 23.423 19.752 19.640 15.778 8.697 14.332 18.132 20.282 14.184 20.926 33.317 34.545 19.571 29.289 24.627 27.248
Methylo-trophic K14080 Methylco-balamin: coenyzme M methylt-ransferase — MtaA 2.1.1.146 19, 22 19, 22 — 0.000 0.000 0.000 0.000 0.001 0.000 0.001 0.000 0.000 0.006 0.019 0.022 0.000 0.016 0.021 0.016
K04480 Methanol-corrinoid protein Co-methylt-ransferase — MtaB 2.1.1.90 19, 22, 83 19, 83, 639 19, 22, 83 0.019 0.176 0.172 0.116 0.104 0.023 0.067 0.326 0.042 0.609 1.167 0.512 0.079 1.440 1.019 0.498
K14081 Methanol-corrinoid protein — MtaC MtaC 19, 22, 65 19, 22, 65 19, 22, 65 0.015 0.026 0.024 0.031 0.024 0.007 0.014 0.045 0.007 0.146 0.298 0.124 0.006 0.361 0.249 0.139
Sum 0.035 0.202 0.196 0.146 0.129 0.030 0.081 0.371 0.049 0.761 1.483 0.657 0.084 1.817 1.289 0.653

Shown are mean values for each plant. Number of columns E-G give species number (Supplementary Table S1) of the TOP3 organisms associated with each KEGG orthology term/enzyme class.