TABLE 1.

16S rRNA-targeted oligonucleotide probes used in this study

Probe	Sequence (5′ to 3′)	FA (%)a	Specificity	Reference
EUB338	GCTGCCTCCCGTAGGAGT	0-50	Most bacteria	2
EUB338 II	GCAGCCACCCGTAGGTGT	0-50	Planctomycetales	4
EUB338 III	GCTGCCACCCGTAGGTGT	0-50	Verrucomicrobiales	4
Amx820	AAAACCCCTCTACTTAGTGCCC	40	“Candidatus Brocadia anammoxidans,” “Candidatus Kuenenia stuttgartiensis”	33
Nmo218	CGGCCGCTCCAAAAGCAT	35	Nitrosomonas oligotropha lineage	10
NmV	TCCTCAGAGACTACGCGG	35	Nitrosococcus mobilis lineage	13
Nse1472	ACCCCAGTCATGACCCCC	50	Nitrosomonas europea, Nitrosomonas halophila, and Nitrosomonas eutropha	13
Nsv443	CCGTGACCGTTTCGTTCCG	30	Nitrosospira spp.	21
Ntspa662	GGAATTCCGCGCTCCTCT	35	Genus Nitrospira	5
Comp Ntspa662b	GGAATTCCGCTCTCCTCT		Competitor for Ntspa662	5
NIT3	CCTGTGCTCCATGCTCCG	40	Nitrobacter spp.	47
Comp NIT3c	CCTGTGCTCCAGGCTCCG		Competitor for NIT3	47

^aFA, formamide concentration in the hybridization buffer.

^bUnlabeled probe Ntspa662 was used as a competitor to enhance specificity.

^cUnlabeled probe NIT3 was used as a competitor to enhance specificity.