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. Author manuscript; available in PMC: 2016 Feb 16.
Published in final edited form as: Environ Microbiol. 2011 May 12;13(10):2623–2632. doi: 10.1111/j.1462-2920.2011.02501.x

Table 2.

Quantitative PCR primers used in this study.

Target Group Primer Name1 Primer Sequence (5’→3’) TM (°C)2 qPCR Standard3 Amplicon Length Amp. Eff.4 (Bac; Group) Detect. Limit5 RDP Hits6
Bacteria 341F CCTACGGGAGGCAGCAG 60 -- -- -- -- --
517R ATTACCGCGGCTGCTGG
Pigmentiphaga 7 PigmF CAGGCGGTTCGGAAAG 56 SBNAP45 63 1.91; 2.03 8.86 × 106 17
PigmR TGACATACTCTAGTTCGGGA
Sphingobium 8 SGBF ACGTAGGCGGCGATTT 59 SBNAP83 70 2.03; 2.03 1.44 × 107 329
SGBR CCTCTCCAAGATTCTAGCAA
Sphingobium 9 SGB.5F ACAGTACCGGGAGAATAAGCTC 56 SBANT43 158 1.98; 1.92 2.32 × 107 128
SGB.5R CAAGCAATCCAGTCTCAAAGGCTA
Variovorax VarioF AGCTGTGCTAATACCGCATAA 61 SBNAP02 279 2.05; 1.99 8.10 × 107 65
VarioR GAGACTTTTCGTTCCGTAC
Acidovorax AcidF TAACGGAGCGAAAGCTT 55 SBPHE2-37 60 1.98; 2.01 2.08 × 107 331
AcidR GTCCGCGCAAGGCCTT
Pyrene Group 2 PG2.4F CCAAGCCGACGACGGGTAG 59 SBPYR03 94 2.02; 1.99 8.17 × 107 900
PG2.4R TTCCCCACTGCTGCCTC
Sphingomonas SPH.1F CGGTACGGAATAACTCA 50 SBFLA15 202 1.98; 1.95 8.12 × 105 37
Univ338R GCTGCCTCCCGTAGGAGT
1

Bacterial primers are from Muyzer et al. (1993), SGB.5 and Pigm primers are from Jones et al. (M. D. Jones et al., submitted), Acidovorax primers are from Singleton et al. (2007), and Univ338R are from Suzuki and Giovannoni (1996). All other primers were developed in this study.

2

PCR annealing temperature.

3

Clones from which plasmid DNA was used to generate standard curves. Each plasmid was linearized with NcoI. Clone names are as in Fig. 1.

4

Amp. Eff., Amplification efficiency (Pflaff, 2001) with eubacterial (Bac) and group-specific (Group) primers.

5

Detection limit of each qPCR assay (number of 16S rRNA gene copies/ g dry soil).

6

Number 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.

7

Pigmentiphaga-related sequences were identical to those recovered from the SIP experiment anthracene (M. D. Jones et al., submitted).

8

Targets naphthalene- and phenanthrene-associated Sphingobium sequences.

9

Targets fluoranthene-associated Sphingobium sequences. The clone used for qPCR was from a highly similar sequence recovered in clone libraries from an earlier SIP experiment with anthracene (M. D. Jones et al., submitted).