Table 2.
Primers used in this study
| Primer type and designation | Forward primer |
Reverse primer |
No. recovered with PCRc | No. of positive PRsc | ||
|---|---|---|---|---|---|---|
| Primer | Sequence (5′–3′) | Primer | Sequence (5′–3′) | |||
| Degenerate primer mixesa | ||||||
| 1 | RYIDW | MGNTAYATHGAYTGG | GWAIYP | GGRTADATNGCCCANCC | A1 (95), A2 (54), A5 (104) | A2 (5), A5 (84) |
| 2 | RYIDW | GWSIYP | GGRTADATNSWCCANCC | None | ||
| 3 | RYIDW | GWAVYP | GGRTANACNGCCCANCC | A1 (120) | A1 (2) | |
| 4 | RYVDW | MGNTAYGTNGAYTGG | GWSIYP | A1 (21) | None | |
| 5 | RYVDW | GWVIYP | GGRTADATNACCCANCC | None | ||
| 6 | RYVDW | GWAVYP | A1 (39) | None | ||
| 7 | YRYVDW | TAYMGNTAYGTNGAYTGG | WGVYPI | ATNGGRTANACNCCCCA | None | |
| 8 | YRYADW | TAYMGNTAYGCNGAYTGG | WGVYPI | None | ||
| Specific primersb | ||||||
| JN648742 | JN648742-F | TTCTACTTAATTCTTGCTGCT | JN648742-R | GCCCAGCCAAAGATGATAATA | A1, A2, A5 | |
| JN648793 | JN648793-F | CTATCTGATCCTTTCCGCCAT | JN648793-R | ATATAGCCCAGCCGAAGGTGA | A1, A2 | |
| JN648744 | JN648744-F | CTGATTACCGTTCCGCTCCTG | JN648744-R | ATCCGATTGTGACGATCCAGC | A5 | |
a
Degenerate primer mixes used for initial amplifications. The primers were obtained from Atamna-Ismaeel et al. (2) and Sharma et al. (20).
b
Specific primers designed to amplify PR sequences from metagenomic DNA (the names shown are the PR sequences).
c
Results shown are the sites with positive findings, with the number of positive samples at each site indicated in parentheses. For the three specific primers, the full-length genes could not be amplified (see text).