TABLE 1.
TaqMan probes designed for this study and used to quantify different methanogen groups from environmental DNA
| Probe name | Target group | Probe sequence (5′-3′)a | Positionb | Clone(s) used as standard(s) (GenBank accession no.) |
|---|---|---|---|---|
| mbac-mcrA | Methanobacteriaceae mcrA | ARGCACCKAACAMCATGGACACWGT | 1154 | M. wolfeii (AB300780), M. arboriphilus (AF 414035) |
| mrtA | Methanobacteriaceae mrtA | CCAACTCYCTCTCMATCAGRAGCG | 1433 | M. thermoauto-trophicum (NC 000916), mrtA_dig_E8 (EU980398) |
| mcp | Methanocorpusculaceae | AGCCGAAGAAACCAAGTCTGGACC | 1319 | mlas_bog39 (DQ680603) |
| msp | Methanospirillaceae | TGGTWCMACCAACTCACTCTCTGTC | 1419 | mcrA_dig_D16 (EU980421), mcrA_dig_D46 (EU980419) |
| MCR-7 | Uncultured MCR-7 group | TGSCTTGACCTTRTCCWTCTCGYTS | 1134 | mcrA_dig_E5 (EU980422), mcrA_dig_E10 (EU980423) |
| MCR-2a | Uncultured MCR-2 group | CCACTCTACTGCCGGTATCAACG | 1317 | mcrA_dig_D43 (EU980402), mcrA_dig_E16 (EU980418) |
| MCR-2b | Uncultured MCR-2 group | ATGTATCTCTGCAGCAGCCGGTACA | 1269 | mcrA_dig_DC17 (EU980412), mcrA_dig_E6 (EU980407) |
| Fen | Uncultured Fen Cluster group | AAVCACGGYGGYMTCGGMAAG | 1071 | mcrA_bog_10 (EU980434), mcrA_bog_12 (EU980424) |
| msar | Methanosarcina | TCTCTCWGGCTGGTAYCTCTCCATGTAC | 1272 | M. barkeri (Y00158), M. acetivorans (NC 003552) |
| msa | Methanosaetaceae | CCTTGGCRAATCCKCCGWACTTG | 1107 | M. concilli (AF414037) |
a
R = A or G; K = G or T; M = A or C; W = A or T; Y = C or T; S = G or C; V = A, C, or G.
b
The 5′ end of the sense strand, based on M. thermoautotrophicum mcrA delta H (U10036) numbering.