Table 1.
Quantitative PCR primers developed and used in this study.
| Target OTU | Primer name | Primer sequence (5′→3′) | Tm (°C)a | qPCR standardb | Amplicon length | Amplification efficiencyc | Detection limitd | RDP hitse |
|---|---|---|---|---|---|---|---|---|
| 1 | Cyc-467f | AACCTTAGGCCCTGACGT | 57 | Phenanthrene 1 | 128 | 1.68 | 21 | 81 |
| Cyc-577r | TGTTTAACCGCCTACGCG | 83 (68) |
aEmpirically determined PCR annealing temperature.
bRepresentative clone sequence from which plasmid DNA was used to generate a standard curve. The plasmid was linearized with PstI.
cAmplification efficiency (Pfaffl, 2001) with operational taxonomic unit (OTU)-specific primers.
dDetection limit of the qPCR assay expressed as number of 16S rRNA gene copies per milliliter of culture.
eNumber of sequences returned by the Ribosomal Database Project II release 10.18 (Cole et al., 2009; excluding sequences from this study) with no mismatches to primer pairs. Value in parentheses is the total hits that the primer pair targets.