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Table 1

List of 16S rRNA-targeted oligonucleotide gene probes used for qFISH

Probe	Specificity	Sequence (5′-3′)	Formamide [%]	Dye	References
EUB 338	Most of domain bacteria	GCT GCC TCC CGT AGG AGT	0–55	FITC	Zarda et al. (1991)
Amx 820	AMX: Candidatus Brocadia anammoxidans and Candidatus Kuenenia stuttgartiensis	AAA ACC CCT CTA CTT AGT GCC C	40	Cy3	Kartal et al. (2006)
Sca 1309	AMX: Candidatus Scalindua sp.	TGG AGG CGA ATT TCA GCC TCC	5	Cy3	Schmid et al. (2003)
NIT 3	NOB: Nitrobacter sp.	CCT GTG CTC CAT GCT CCG	40	Cy3	Mobarry et al. (1997)
Ntspa 662	NOB: Nitrospira sp.	GGA ATT CCG CTC TCC TCT	35	Cy3	Daims et al. (2000)
Nso 190	AOB: Betaproteobacterial ammonia-oxidizing bacteria	CGA TCC CCT GCT TTT CTC C	55	Cy3	Mobarry et al. (1997)

Probe	Specificity	Sequence (5′-3′)	Formamide [%]	Dye	References
EUB 338	Most of domain bacteria	GCT GCC TCC CGT AGG AGT	0–55	FITC	Zarda et al. (1991)
Amx 820	AMX: Candidatus Brocadia anammoxidans and Candidatus Kuenenia stuttgartiensis	AAA ACC CCT CTA CTT AGT GCC C	40	Cy3	Kartal et al. (2006)
Sca 1309	AMX: Candidatus Scalindua sp.	TGG AGG CGA ATT TCA GCC TCC	5	Cy3	Schmid et al. (2003)
NIT 3	NOB: Nitrobacter sp.	CCT GTG CTC CAT GCT CCG	40	Cy3	Mobarry et al. (1997)
Ntspa 662	NOB: Nitrospira sp.	GGA ATT CCG CTC TCC TCT	35	Cy3	Daims et al. (2000)
Nso 190	AOB: Betaproteobacterial ammonia-oxidizing bacteria	CGA TCC CCT GCT TTT CTC C	55	Cy3	Mobarry et al. (1997)