TABLE 1.

PCR primers used in this study

Primer set	Individual primer	Gene	Sequence (5′→3′)	Primer position	Annealing temp (°C)	Intended target	Source
	27F	rrs	AGA GTT TGA TCM TGG CTC AG	8-27a	55	Bacteria	Lane (34)
	1492R		GGT TAC CTT GTT ACG ACT T	1510-1492a
1	nirK1F	nirK	GGM ATG GTK CCS TGG CA	526-542b	56	Universal	Braker et al. (7)
	nirK5R		GCC TCG ATC AGR TTR TGG	1040-1023b
2	F1aCu	nirK	ATC ATG GTS CTG CCG CG	568-584b	50	Universal	Hallin and Lindgren (21)
	R3Cu		GCC TCG ATC AGR TTG TGG TT	1040-1021b
3	MG763-F1aCu	nirK	ATC CTG GTC GAG CCG CC	568-584b	73	Rhodanobacter	This study
	MG763-R3Cu		GCG CGG AAG ATC GAG TGG TC	1040-1021b
4	HD-nirkF1	nirK	CCA GCT CAA CCT TCT CGT TC	439-458c	55	Hyphomicrobium denitrificans	This study
	HD-nirKR1		TTG CAT GAC GTA GAA CTC GC	1040-1021c
5	nirS1F	nirS	CCT AYT GGC CGC CRC ART	763-780d	61	Universal	Braker et al. (7)
	nirS6R		CGT TGA ACT TRC CGG T	1653-1638d
6	nosZ2F	nosZ	CGC RAC GGC AAS AAG GTS MSS GT	1603-1625e	65	Universal	Henry et al. (23)
	nosZ2R		CAK RTG CAK SGC RTG GCA GAA	1869-1849e
7	Rh-nosZ-F	nosZ	CGG CTG GGG TGT CAC CAA	303-320e	63	Rhodanobacter	This study
	Rh-nosZ-R		CAT GTG CAT CGC ATG GCA GAA	1869-1849e

^aAccording to the rrs gene of Escherichia coli (E05133).

^bAccording to the nirK gene of Alcaligenes faecalis (D13155).

^cAccording to the nirK gene of Hyphomicrobium denitrificans (AB076606).

^dAccording to the nirS gene of Pseudomonas stutzeri (X56813).

^eAccording to the nosZ gene of Pseudomonas fluorescens (AF197468).