Table 3 Primer hits to the major phylogenetic taxa found in this study using RDP probe match

Molecular technique	Primer set	Sequence (5′ to 3′)	References	RDP probe match values (%)
				Deltaproteobacteria	Geobacter	Bacteroidia
Clone libraries	^a530F/1494R	GTCCCAGCMGCCGCGG GGTTACCTTGTTACCACTT	This study, Wani et al., 2006,	0.1 0.3	0 0.2	0.1 0
	530F/1494R	GTGCCAGCMGCCGCGG GGYTACCTTGTTACCACTT	Madrid et al., 2001	97 0.3	97 0.2	97 0
	27F/1541R	AGAGTTTGATCCTGGCTCAG AAGGAGGTGATCCAGCC	Löffler et al., 2000; Arturrson and Jansson, 2003; Kiely et al., 2011b	26 3.8	28 6	24 0.3
	63/1389	CAGGCCTAACACATGCAAGTC ACGGGCGGTGTGTACAAG	Lucas et al., 2003, Witt et al., 2011	0.8 78	0.2 82	6 31
	41F/1389R	GCTCAGATTGAACGCTGGCG ACGGGCGGTGTGTACAAG	Hongoh et al., 2003; Fisher et al., 2007	6.4 78	0.2 82	0 31
DGGE	341F/534R	CCTACGGGAGGCAGCAG ATTACCGCGGCTGCTGG	Watanabe et al., 2001; Xing et al., 2006	96 86	98 98	98 98
	341F/926R	CCTACGGGAGGCAGCAG CCGTCAATTCMTTTGAGTTT	Watanabe et al., 2001; Xing et al., 2006	96 80	98 96	98 96
	968F/1401R	AACGCGAAGAACCTTAC CGGTGTGTACAAGACCC	This study, Watanabe et al., 2001; Xing et al., 2006	59 1	15 1	0.5 0.3
454 Sequencing	343F/926R	TACGGRAGGCAGCAG CCGTCAATTYYTTTRAGTTT	This study, Liu et al., 2007 Wang and Qian, 2009	96 96	98 96	98 96
	27F/342R	AGAGTTTGATCCTGGCTCAG CTGCTGCSYCCCGTAG	Kunin et al., 2010,	27 96	28 98	24 98
	1114F/1392R	GCAACGAGCGCAACCC ACGGGCGGTGTGTRC	Engelbrektson et al., 2010; Kunin et al., 2010	94 80	97 86	0.7 37
FISH	GBS207	GAAGACAGGAGGCCCGAAA	Richter et al., 2007	0.1	3	0

Abbreviations: DGGE, denaturing gradient gel electrophoresis; FISH, fluorescent in-situ hybridization, RDP, ribosomal database project.
^aThis primer sequence was incorrectly written in the reference. The correct sequence is 5′-GTGCCAGCMGCCGCGG-3′ (Madrid et al., 2001; Rossetti et al., 2003). Deltaproteobacteria, Geobacter and Bacteroidia all had 97% probe match values when the correct sequence was used. The specificity of the PCR conditions would determine whether one mismatch would allow a primer to anneal to the template. This one mismatch did not appear to bias the targeting of any particular taxa as all probe match values for the incorrect primer gave ∼0% match.

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