TABLE 1.

Oligonucleotide probes used in this study

Probe namea	Label	Sequence	Target	Reference	Function
S-D-Bact-0320-a-S-40-B (B3)	Biotin (5′ labeled)	5′ CAC TGC TGC CTC CCG TAG GAG TCT GGA CCG TGT CTC AGT T 3′	16S rRNA of bacteria	45	Capture probe; Bacteria-specific original probe used (distant)
S-D-Bact-1524-a-S-17-D (DIG 1541)	Digoxigenin (3′ labeled)	5′ AAG GAG GT G ATC CAG CC 3′	16S rRNA of bacteria	45	Detector probe; Bacteria-specific original probe used (distant)
S-D-Bact-0343-b-S-17-B	Biotin (5′ labeled)	5′ CAC TGC TGC CTC CCG TA 3′	16S rRNA of bacteria	This study	Capture probe; Bacteria specific (proximate)
S-D-Bact-0320-b-S-18-D	Digoxigenin (3′ labeled)	5′ TCT GGV CCG TRT CTC AGT 3′	16S rRNA of bacteria	This study	Detector probe; Bacteria specific (proximate)
S-D-Bact-0320-b-S-18-H	No label	5′ TCT GGV CCG TRT CTC AGT 3′	16S rRNA of bacteria	This study	Helper probe; Bacteria specific (proximate)
S-D-Bact-0518-a-S-18-D	Digoxigenin (5′ labeled)	5′ GTA TTA CCG CGG CTG CTG 3′	16S rRNA of bacteria	This study	Detector probe; Bacteria specific (proximate)
S-F-bAOB-1224-a-S-20-D (Nso1225)	Digoxigenin (5′ labeled)	5′ CGC CAT TGT ATT ACG TGT GA 3′	16S rRNA of β-AOB	28	Detector probe; AOB specific
S-S-Ral-1224-a-S-20-C	No label	5′ CAC CAT TGT ATG ACG TGT GA 3′	16S rRNA of Ralstonia eutropha	This study	Competitor probe; AOB specific
S-F-bAOB-0190-a-S-19-B (CTO18f)	Biotin	5′ CǴA TCC CCT RCT TTY CTC C 3′	16S rRNA of β-AOB	25	Capture probe; AOB specific
S-D-NBact-0320-b-A-18-H (NonBact)	Digoxigenin (5′ labeled)	5′ ACT CCT ACG GGA GGC AGC 3′	None	26	Nonbacterial probe; nonspecific

^aNomenclature based on reference 2. Probe names used previously are given in parentheses. Letters at ends of probe names correspond to label: B, biotin; D, digoxigenin; H, helper (no label); C, competitor (no label). All probes were obtained from Thermo Hybaid, Germany.