Table 1.

Ribosomal RNA-targeted oligonucleotide probes used in this study.

Probe	Fluorophorea	Target organisms	Probe sequence (5′-3′)	Competitor sequence (5′-3′)b	FAc (%)	References
L-C-gProt-1027-a-A-17 (Gam42a)	Atto 490 LS, Atto 633	Gammproteobacteria	GCCTTCCCAC ATCGTTT	GCCTTCCCAC TTCGTTT	35	Manz et al., 1992
LGC354A	Atto 633, FLUOS	Firmicutes	TGGAAGATTCC CTACTGC		35	Meier et al., 1999
LGC354B	Atto 633, FLUOS	Firmicutes	CGGAAGATTC CCTACTGC		35	Meier et al., 1999
LGC354C	Atto 633, FLUOS	Firmicutes	CCGAAGATTCC CTACTGC		35	Meier et al., 1999
EUK1195	Atto 565	Eukaryotes	GGGCATCACAGACCTG		35	Giovannoni et al., 1988
S-D-Bact-0338-a-A-18 (EUB338-I)	all dyes	most Bacteria	GCTGCCTCCC GTAGGAGT		35	Amann et al., 1990
S-∗-BactP-0338-a-A-18 (EUB338-II)	all dyes	Planctomycetales	GCAGCCACCC GTAGGTGT		35	Daims et al., 1999
S-∗-BactV-0338-a-A-18 (EUB338-III)	all dyes	Verrucomicrobia	GCTGCCACCC GTAGGTGT		35	Daims et al., 1999
NONEUB	all dyes	control probe	ACTCCTACGGGA GGCAGC		35	Wallner et al., 1993
S-D-Arch-0915-a-A-20 (Arch915)	DY-681	Archaea	GTGCTCCCCCGCC AATTCCT		35	Amann et al., 1990
Ntoga221	Atto 594	genus Nitrotoga	TATCGGCCGCTC CGAAAA	CATCGGCCGCTCC GAAAG	35	Lücker et al., 2015
S-∗-Ntspa-1431-a-A-18 (Ntspa1431)	Atto 532	Nitrospira lineage I	TTGGCTTGGGCG ACTTCA		35	Maixner et al., 2006
S-G-Ntspa-662-a-A-18 (Ntspa662)	Cy3, FLUOS	genus Nitrospira	GGAATTCCGCGCT CCTCT	GGAATTCCGCTC TCCTCT	35	Daims et al., 2001
S-∗-Ntspa-712-a-A-21 (Ntspa712)	Cy3, FLUOS	phylum Nitrospirae	CGCCTTCGCCACC GGCCTTCC	CGCCTTCGCCACCG GTGTTCC	35	Daims et al., 2001
Ntspa1131	Atto 594	Nitrospira Cluster Ib	GTGCTCGGCTT GACCCGG	GTGCTCGGCATGA CCCGG	50	Gruber-Dorninger et al., 2015
Ntspa451	Atto 633	Nitsospira Cluster Ig	AGCAGTTACCTGC CCCAT		25	Gruber-Dorninger et al., 2015
Ncom1025	Atto 490LS, FLUOS	Nitrosomona communis lineage	CTCGATTCCCT TTCGGGCA		35	Juretschko, 2000
Cl6a192	DY-681, FLUOS	Nitrosomonas oligotropha lineage	CTTTCGATCCCC TACTTTCC	CTTTCGATCCCCTGC TTTCC	35	Adamczyk et al., 2003
S-F-bAOB-1224-a-A-20 (Nso1225)	FLUOS	betaproteobacterial ammonia-oxidizing bacteria	CGCCATT GTATTACGTGTGA		35	Mobarry et al., 1996
S-∗-Nsm-0651-a-A-18 (NEU)	FLUOS	most halophilic and halotolerant Nitrosomonas spp.	CCCCTCTGCT GCACTCTA	TTCCATCCCCC TCTGCCG	40	Wagner et al., 1994
CF193a	Atto 594	Flavobacteria, Bacteroidetes, Sphingobacteria	TGGTCCGTGTCTC AGTAC		35	Manz et al., 1996
S-G-Nia-224-a-A-18 Nia224	Atto 532	genus Niabella	ATACGCACACCC GTCTTC		35	This study

^aFluorophore(s) used for labeling the respective probes. ^bCompetitors were added as unlabeled oligonucleotides and in equimolar concentrations as the labeled probes. ^cFA, formamide. The formamide concentration in the hybridization buffer (v/v) is indicated.