TABLE 1.

Oligonucleotide primers and probes used in this study

Enrichment step	Primer or probe name	Use	Sequence (5′ to 3′)	Target	Reference or source
First step
	NTG200F	PCR	CTC GCG TTT TCG GAG CGG	Nitrotoga 16S rRNA gene	12
	NTG840R	PCR	CTA AGG AAG TCT CCT CCC		12
	Ntspmar62F	PCR	GCC CCG GAT TCT CGT TCG	Nitrospira marina-related Nitrospira 16S rRNA gene	11
	Ntspa662R	PCR	GGA ATT CCG CGC TCC TCT		10
	Ntspa81F	PCR	TTR TAA RGC GGC GAA CGG GT	Nitrospira lineage I and II 16S rRNA genes	This study
	Ntspa662R	PCR	GGA ATT CCG CGC TCC TCT		10
	NitSSU_130F	PCR	GGG TGA GTA ACA CGT GAA TAA	Nitrospina 16S rRNA gene	60
	NitSSU_282R	PCR	TCA GGC CGG CTA AMC A		60
	Nbacter1050F	PCR	CAC CTG TGC TCC ATG CTC CG	Nitrobacter 16S rRNA gene	61
	Nbacter1433R	PCR	CGG GTT AGC GCA CCG CCT		62
	Eub341F-GC	PCR-DGGE	CGC CCG CCG CGC CCC GCG CCC GTC CCG CCG CCC CCG CCC GCC TAC GGG AGG CAG CAG	All bacterial 16S rRNA genes	52 (modified)
	Univ907R	PCR-DGGE	CCG TCA ATT CCC TTT RAG TTT		53
Second or third step
	27f	Cloning	AGA GTT TGA TCM TGG CTC AG	All bacterial 16S rRNA genes	53
	1492r	Cloning	TAC GGY TAC CTT GTT ACG ACT T		53
	nxrB169f	PCR	TAC ATG TGG TGG AAC A	Nitrospira and Nitrospina nxrB genea	63
	nxrB638r	PCR	CGG TTC TGG TCR ATC A		63
	F1norA	PCR	CAG ACC GAC GTG TGC GAA AG	Nitrobacter nxrA gene	64
	R1norA	PCR	TCY ACA AGG AAC GGA AGG TC		64
	EUB338	FISH	GCT GCC TCC CGT AGG AGT	Most bacteria	57
	EUB338 II	FISH	GCA GCC ACC CGT AGG TGT	Most Planctomycetales	65
	EUB338 III	FISH	GCT GCC ACC CGT AGG TGT	Most Verrucomicrobiales	65
	NTG840	FISH	CTA AGG AAG TCT CCT CCC	Nitrotoga	12
	Ntspa1431	FISH	TTG GCT TGG GCG ACT TCA	Nitrospira lineage I	66
	Ntspa1151	FISH	TTC TCC TGG GCA GTC TCT CC	Nitrospira lineage II	66

^aThe reverse primer has three mismatches to the nxrB gene of Nitrospina toward the 5′ end of the primer.