Table 2.
PCR primers and probes used in this study
| Primer/probe | Target gene | Sequencea (5′−3′) | Reference | Approach |
|---|---|---|---|---|
| 27F | Bacteria 16S rRNA | AGA GTT TGA TCM TGG CTC AG | Lane (1991) | PCR-DGGE |
| 1492R | Bacteria 16S rRNA | GGT TAC CTT GTT ACG ACT T | Lane (1991) | PCR-DGGE |
| 907R | Bacteria 16S rRNA | CCG TCA ATT CMT TTG AGT TT | Muyzer et al. (1998) | PCR-DGGE |
| 63F | Bacteria 16S rRNA | CAG GCC TAA CAC ATG CAA GTC | Marchesi et al. (1998) | PCR-DGGE |
| 665R | JS1 candidate division 16S rRNA | ACC GGG AAT TCC ACY TYC CT | Webster et al. (2004) | PCR-DGGE |
| 357Fb | Bacteria 16S rRNA | CCT ACG GGA GGC AGC AG | Muyzer et al. (1993) | PCR-DGGE |
| 518R | Universal 16S rRNA | ATT ACC GCG GCT GCT GG | Muyzer et al. (1993) | PCR-DGGE |
| 109F | Archaea 16S rRNA | ACK GCT CAG TAA CAC GT | Grosskopf et al. (1998) | PCR-DGGE |
| 958R | Archaea 16S rRNA | YCC GGC GTT GAM TCC AAT T | DeLong (1992) | PCR-DGGE |
| SAFb | Archaea 16S rRNA | CCT AYG GGG CGC AGM RGG | Nicol et al. (2003) | PCR-DGGE |
| PARCH519R | Archaea 16S rRNA | TTA CCG CGG CKG CTG | Øvreas et al. (1997) | PCR-DGGE |
| EUB338 | Bacteria 16S rRNA | GCT GCC TCC CGT AGG AGT | Amann et al. (1990) | CARD-FISH |
| EUB338-II | Bacteria 16S rRNA | GCA GCC ACC CGT AGG TGT | Daims et al. (1999) | CARD-FISH |
| EUB338-III | Bacteria 16S rRNA | GCT GCC ACC CGT AGG TGT | Daims et al. (1999) | CARD-FISH |
| ARCH915 | Archaea 16S rRNA | GTG CTC CCC CGC CAA TTC CT | Stahl and Amann (1991) | CARD-FISH |
| Uni340F | Universal 16S rRNA | CCT ACG GGR BGC ASC AG | Takai and Horikoshi (2000) | TaqMan qPCR |
| Uni806R | Universal 16S rRNA | GGA CTA CNN GGG TAT CTA AT | Takai and Horikoshi (2000) | TaqMan qPCR |
| Uni516F | Universal 16S rRNA | TGY CAG CMG CCG CGG TAA HAC VNR S | Takai and Horikoshi (2000) | TaqMan qPCR |
| 331F | Bacteria 16S rRNA | TCC TAC GGG AGG CAG CAG T | Nadkarni et al. (2002) | TaqMan qPCR |
| 797R | Bacteria 16S rRNA | GGA CTA CCA GGG TAT CTA ATC CTG TT | Nadkarni et al. (2002) | TaqMan qPCR |
| Nadkarni UNI | Bacteria 16S rRNA | CGT ATT ACC GCG GCT GCT GGC AC | Nadkarni et al. (2002) | TaqMan qPCR |
| Arch349F | Archaea 16S rRNA | GYG CAS CAG KCG MGA AW | Takai and Horikoshi (2000) | TaqMan qPCR |
| Arch806R | Archaea 16S rRNA | GGA CTA CVS GGG TAT CTA AT | Takai and Horikoshi (2000) | TaqMan qPCR |
| Arch516F | Archaea 16S rRNA | TGY CAG CCG CCG CGG TAA HAC CVG C | Takai and Horikoshi (2000) | TaqMan qPCR |
| GEO494F | Geobacteraceae 16S rRNA | AGG AAG CAC CGG CTA ACT CC | Holmes et al. (2002) | SYBR Green qPCR |
| GEO825R | Geobacteraceae 16S rRNA | TAC CCG CRA CAC CTA GT | Anderson et al. (1998) | SYBR Green qPCR |
| ME1f | mcrA | GCM ATG CAR ATH GGW ATG TC | Hales et al. (1996) | SYBR Green qPCR |
| ME3r | mcrA | TGT GTG AAS CCK ACD CCA CC | Wilms et al. (2007) | SYBR Green qPCR |
| DSR1F+ | dsrA | ACS CAC TGG AAG CAC GGC GG | Kondo et al. (2004) | SYBR Green qPCR |
| DSR-R | dsrA | GTG GMR CCG TGC AKRTTG G | Kondo et al. (2004) | SYBR Green qPCR |
a.
B = G, T or C; D = G, A or T; H = A, T or C; K = G or T; M = A or C; N = G, A, T or C; R = A or G; S = G or C; V = G, A or C; W = A or T; Y = C or T.
b.
For DGGE this primer has the GC-clamp at the 5′ end, CGCCCGCCGCGCGCGGCGGGCGGGGCGGGGGCACGGGGGG (Muyzer et al., 1993).