TABLE 1.
Q- (RT)-PCR primer and probe sets used in this study.
| Target (reference) | Primer/probea | Sequence (5′–3′) | Amplicon (bp) | Annealing°C |
|---|---|---|---|---|
| 16S rRNA | 1369F | CGGTGAATACGTTCYCGG | 123 | 56 |
| Suzuki et al. (2000) | 1492R | TACGGYTACCTTGTTACGACTT | ||
| TM1389F | CTTGTACACACCGCCCGTA | |||
| napA-1 | napA-1F | GTYATGGARGAAAAATTCAA | 111 | 55 |
| Smith et al. (2007) | napA-1R | GARCCGAACATGCCRAC | ||
| napA-1 TM* | AACATGACCTGGAAG | |||
| napA-2 | napA-2F | GAACCKAYGGGYTGTTATG | 76 | 55 |
| Smith et al. (2007) | napA-2R | TGCATYTCSGCCATRTT | ||
| napA-2 TM* | CTTTGGGGTTCAA | |||
| napA-3 | napA-3F | CCCAATGCTCGCCACTG | 130 | 60 |
| Smith et al. (2007) | napA-3R | CATGTTKGAGCCCCACAG | ||
| napA-3 TM* | TGGGTTGTTACGA | |||
| narG-1 | narG-1F | GACTTCCGCATGTCRAC | 69 | 60 |
| Smith et al. (2007) | narG-1R | TTYTCGTACCAGGTGGC | ||
| narG-1 TM* | TAYTCCGACATCGT | |||
| narG-2 | narG-2F | CTCGAYCTGGTGGTYGA | 89 | 55 |
| Smith et al. (2007) | narG-2R | TTYTCGTACCAGGTSGC | ||
| narG-2 TM* | AACTTCCGCATGGA | |||
| nrfA-2 | nrfA-2F | CACGACAGCAAGACTGCCG | 67 | 60 |
| Smith et al. (2007) | nrfA-2R | CCGGCACTTTCGAGCCC | ||
| nrfA-2TM* | TTGACCGTCGGCA | |||
| nirS-e | nirS-ef-F | CACCCGGAGTTCATCGTC | 172 | 60 |
| Smith et al. (2007) | nirS-efR | ACCTTGTTGGACTGGTGGG | ||
| nirS-ef TM* | TGCTGGTCAACTA | |||
| nirS-m | nirS-m-F | GGAAACCTGTTCGTCAAGAC | 162 | 60 |
| Smith et al. (2007) | nirS-mR | CSGARTCCTTGGCGACGT | ||
| nirS-m TM | TCTGGGCCGACGCGCCGATGAAC | |||
| nirS-n | nirS-n-F | AAGGAAGTCTGGATYTC | 140 | 55 |
| Smith et al. (2007) | nirS-nR | CGTTGAACTTRCCGGT | ||
| nirS-n TM* | ATCCGAAGATSA |
*TM TaqMan Minor Groove Binding; TM, TaqMan.