TABLE 1.

Oligonucleotide probes used for FISH and microarray hybridization experiments^a

Probe name	Probe sequence (5′-3′)	Target site (positions)	Target organism(s)	Reference(s)
EUB338	GCTGCCTCCCGTAGGAGT	338-355	Most but not all Bacteria	1, 12
EUB338-II	GCAGCCACCCGTAGGTGT	338-355	Planctomycetales	12
EUB338-III	GCTGCCACCCGTAGGTGT	338-355	Verrucomicrobiales	12
Nso1225	CGCCATTGTATTACGTGTGA	1224-1243	Most but not all beta-proteobacterial AOB (30)	38
Nso190	CGATCCCCTGCTTTTCTCC	189-207	Many but not all beta-proteobacterial AOB (30)	38
Nsv443	CCGTGACCGTTTCGTTCCG	443-461	Nitrosospira cluster 1-3 (30)	38
Ncmob	TCCTCAGAGACTACGCGG	174-191	Nitrosococcus mobilis (30)	26
NEU	CCCCTCTGCTGCACTCTA	651-668	Most halophilic and halotolerant nitrosomonads (30)	71
Cte	TTCCATCCCCCTCTGCCG	659-676	Competitor probe for NEU; Comamonas spp., Acidovorax spp., Hydrogenophaga spp., Aquaspirillum spp. (30)	71
6a192	CTTTCGATCCCCTACTTTCC	192-212	Nitrosomonas oligotropha lineage	52
c6a192	CTTTCGATCCCCGACTTTCC	192-212	Competitor probe for 6a192; Nitrosomonas eutropha	52
NONEUB	ACTCCTACGGGAGGCAGC			74
NONSENSE	AGAGAGAGAGAGAGAGAG			32
CONT	AGGAAGGAAGGAAGGAAG		Control oligonucleotide	32
CONT-COMP	CTTCCTTCCTTCCTTCCT		Complementary to CONT	32

^aMore detailed information for each probe can be obtained at the oligonucleotide online resource probeBase (33). All but CONT and CONT-COMP were used for FISH. All but EUB338-II, EUB338-III, and Cte were used for microarray analysis.