TABLE 1.
Primers used in this study
| Target gene | E. coli positionsa | Primer | Sequenceb | Reference(s) |
|---|---|---|---|---|
| Bacterial 16S rRNA | 785-803 | U785F | 5′-GGATTAGATACCCTGGTAG-3′ | 2 |
| 341-357 | U341Fc | 5′-CCTACGGGAGGCAGCAG-3′ | 2, 38 | |
| 785-803 | U803R | 5′-CTACCAGGGTATCTAATCC-3′ | 2 | |
| Type I methanotroph 16S rRNA | 988-1006 | MethT1bR | 5′-GATTCYMTGSATGTCAAGG-3′ | 61 |
| Type II methanotroph 16S rRNA | 997-1017 | MethT2R | 5′-CATCTCTGRCSAYCATACCGG-3′ | 61 |
| pmoA | A189Fc,d | 5′- GGNGACTGGGACTTCTGG-3′ | 23 | |
| Mb661Rd | 5′- CCGGMGCAACGTCYTTACC-3′ | 13 |
a
The positions refer to 16S rRNA gene primer positions.
b
N = A, C, T, or G; Y = C or T; R = A or G; M = A or C; S = C or G.
c
When the primer was used for DGGE, a GC clamp was attached to the 5′ end (see text).
d
When the primer was used for DGGE, degenerate bases (N, M, and Y) were replaced by inosine (I) (26).