TABLE 1.
PCR primers used in this study
| Primera | Sequence (5′ to 3′)b | Positionc | Specificity (sequence type) | Reference or source |
|---|---|---|---|---|
| A25f | CYGGTYGATYCTGCCRG | 9-25 | Archaea | 9 |
| A341If | CCTAIGGGGIGCAICAG | 341-357 | Archaea | This studyd |
| A958r | YCCGGCGTTGAMTCCAATT | 958-976 | Archaea | 18 |
| A1063Ir | CGGCCATGCACCICCICTC | 1045-1063 | Archaea | This studye |
| A1391r | GACGGGCGGTGTGTRCA | 1375-1391 | Archaea | 3 |
| U1492r | GGTTACCTTGTTACGACTT | 1492-1510 | Universal | 9 |
| A533r | TTACCGCGGCGGCTG | 519-533 | Most archaea | This studyf |
| MS827f | TAGGTGTCGGCCACGGT | 827-843 | Methanosaeta (KuA1, KuA3) | This studyg |
| MH163f | GGGATAATTCCGGATAGAT | 163-182 | Methanomethylovorans (KuA6) | This study |
| MH441r | ATTTATACATATGGACAGCCAAC | 419-441 | Methanomethylovorans (KuA6) | This study |
| MM402f | GAGTGCCCGTAAAATCGG | 402-419 | Part of Methanomicrobiales (KuA12) | This study |
| MM837r | CGTTTCACGATTTCTCTTCG | 818-837 | Part of Methanomicrobiales (KuA10, KuA11, KuA12) | This study |
| K311f | TGAGATGGACTCTGAGACAT | 311-330 | Part of candidate division II (KuA15, KuA16) | This study |
| K463r | CAGTCAACACAATGTGCTG | 445-463 | Part of candidate division II (KuA15, KuA16) | This study |
| K780f | AGTAAACACTGCACACTAAACA | 780-811 | Part of candidate division IV (KuA22) | This study |
| T7W | TAATACGACTCACTATAGGGC | pGEM-T vector | 42 | |
| SP6W | ATTTAGGTGACACTATAGAATACTC | pGEM-T vector | 42 |
a
f, forward PCR primer; r, reverse PCR primer.
b
I, inosine.
c
Corresponding to the numbering in the sequence of the 16R rRNA gene of E. coli.
d
This primer is a modified form of S-D-Arch-0344-a-S-20 (39).
e
This primer is a modified form of 1068 Forward (1).
f
This primer is a modified form of 533F (9).
g
This primer is a modified form of MX825 (33).