TABLE 1.

Oligonucleotides used in this study

Common name	Generic name	Target(s)	Sequence (5′-3′)	Position	Reference
Primers for PCR-DGGE
PRBA341fa	S-D-Bact-0341-a-A-18	Bacteria	CCTACGGGAGGCAGCAG	341-357	34
PRUN518r	S-D-Bact-0518-a-A-18	Bacteria	ATTACCGCGGCTGCTGG	518-534	34
ARC344fa	S-D-Arch-0344-a-A-20	Archaea	ACGGGGAGCAGCAGGCGCGA	344-363	39
ARC915r	S-D-Arch-0915-a-A-20	Archaea	GTGCTCCCCCGCCAATTCCT	915-934	39
Specific primers for Desulfitobacterium
PCP1G	S-S-D.frapp-0056-(D. frappieri PCP-1)-a-S-18	D. hafniense	CGAACGGTCCAGTGTCTA	56-73	28
PCP4D	S-S-D.frapp-0580-(D. frappieri PCP-1)-a-A-20	D. hafniense	AGGTACCGTCATGTAAGTAC	599-580	28
De2	S-G-Desulfito-704-(D. frappieri PCP-1)-a-A-22	Desulfitobacteriumb	CCTAGGTTTTCACACCAGACTT	725-704	28
De1	S-G-Desulfito-322-(D. frappieri PCP-1)-a-S-20	Desulfitobacteriumb	GCTATCGTTARTRGATGGAT	322-341	28
Fluorescent probes
ARC915-Cy3	S-D-Arch-0915-a-A-20	Archaea	GTGCTCCCCCGCCAATTCCT	934-915	42
EUB338-Cy3	S-D-Bact-0338-a-A-18	Bacteria	GCTGCCTCCCGTAGGAGT	355-338	2
NONEUB338-Cy3		Negative control	ACTCCTACGGGAGGCAGC		47
PCP-1-4-Cy3	S-S-D.frapp-0327-(D. frappieri PCP-1)-a-A-19	D. hafniense, D. chlororespirans	GCGGATCCATCTACTAACG	345-327	27
PCP-1-8-Cy5	S-S-D.frapp-0576-(D. frappieri PCP-1)-a-A-19	D. hafniense	CCGTCATGTAAGTACATTA	594-576	27
Helpers for PCP-1-8-Cy5
h3	S-S-D.frapp-0555-(D. frappieri PCP-1)-a-A-21		TTTACATACTTACCGTTCGTC	575-555	27
h4	S-S-D.frapp-0595-(D. frappieri PCP-1)-a-A-18		GGGCTTCCTCCTCAGGTA	612-595	27

^aGC clamp (CGCCCGCCGCGCGCGGCGGGCGGGGCGGGGGCACGGGGGG).

^bExcept D. metallireducens, two-nucleotide difference.