TABLE 1.
PCR primers used in this study
| Target gene (fragment length in bp) | Primer set | Sequence (5′ to 3′)a | Annealing temperature (°C) | Reference |
|---|---|---|---|---|
| pmoA (531)b | A189c | GGNGACTGGGACTTCTGG | 62 to 52 touchdownd | 32 |
| A682 | GAASGCNGAGAAGAASGC | |||
| mmoX (863) | 534fe | CCGCTGTGGAAGGGCATGAA | 62 to 52 touchdownd | 25 |
| 1393re | CACTCGTAGCGCTCCGGCTC | |||
| mxaF (557) | f1003 | GCGGCACCAACTGGGGCTGGT | 55 | 42 |
| r1561 | GGGCAGCATGAAGGGCTCCC | |||
| 16S rDNA (922) and 16S rcDNA (556) | MethT1dF | CCTTCGGGMGCYGACGAGT | 56 | 57 |
| MethT1bR | GATTCYMTGSATGTCAAGG | |||
| MethT1cRf | ATCCAATCGAGTTCCCAGGTTAAGCCC |
a
N, bases A, C, T, or G; M, bases A or C; S, bases G or C; Y, bases C or T.
b
The pmoA-targeted primers also detect amoA, which encodes the α subunit of ammonia monooxygenase in autotrophic ammonia oxidizers.
c
GC-clamp for DGGE analysis: 5′-cccccccccccccgccccccgccccccgcccccgccgccc (28).
d
PCR profile according to Henckel et al. (28).
e
The primers target the nucleotide sequence positions 534 to 553 (534f) and 1374 to 1393 (1393r), according to the open reading frame of the mmoX sequence published by Cardy et al. (7). The primer 1393r targets almost the same stretch as primer r1403 of McDonald et al. (40).
f
MethT1cR was used in RT-PCR.