Table S2.

Oligonucleotide probes used for fluorescence in situ hybridization (FISH) in this study.

Probe name 1	Target	Sequence (5′–3′)	FA 2 [%]
Eub338 3	Most Bacteria	GCT GCC TCC CGT AGG AGT	0–50
Amx820	Anaerobic ammonium-oxidizing bacteria, Candidatus “Brocadia anammoxidans” and Candidatus “Kuenenia stuttgartiensis”	AAA ACC CCT CTA CTT AGT GCC C	40
Apr820	Candidatus Anammoxoglobus propionicus	AAA CCC CTC TAC CGA GTG CCC	40
Ban162	Candidatus Brocadia anammoxidans	CGG TAG CCC CAA TTG CTT	40
BS820	Candidatus Scalindua wagneri, Candidatus Scalindua sorokinii	TAA TTC CCT CTA CTT AGT GCC C	20
Bfu613	Candidatus Brocadia fulgida	GGA TGC CGT TCT TCC GTT AAG CGG	30
Sca1309	Genus Candidatus Scalindua	TGG AGG CGA ATT TCA GCC TCC	5
Scabr1114	Candidatus Scalindua brodae	CCC GCT GGT AAC TAA AAA CAA G	20
Pla46	Planctomycetales	GAC TTG CAT GCC TAA TCC	30
Nso1225	Most beta-proteobacterial AOB	CGC CAT TGT ATT ACG TGT GA	35
Nse1472	Nitrosomonas europea, N. halophila, N. eutropha, Kraftisried-Isolat Nm103	ACC CCA GTC ATG ACC CCC	50
Ntspa662 4	Genus Nitrospira	GGA ATT CCG CGC TCC TCT	35
Ntspa1151	Sublineage II of the genus Nitrospira	TTC TCC TGG GCA GTC TCT CC	35–40
Ntspa1431	Sublineage I of the genus Nitrospira	TTG GCT TGG GCG ACT TCA	35
Ntg840	Nitrotoga arctica	CTA AGG AAG TCT CCT CCC	10–20
Nit3 4	Genus Nitrobacter	CCT GTG CTC CAT GCT CCG	40
NmII	Nitrosomonas communis lineage	TTA AGA CAC GTT CCG ATG TA	35
Alf968	Alphaproteobacteria, except of Rickettsiales	GGT AAG GTT CTG CGC GTT	20
CF319a	Most Flavobacteria, some Bacteroidetes, some Sphingobacteria	TGG TCC GTG TCT CAG TAC	35
Gam42a 4	Gammaproteobacteria	GCC TTC CCA CAT CGT TT	35

¹For probe specifications, see ProbeBase (http://www.microbial-ecology.net/probebase/) [40];

²FA = Formamide;

³Used in a mix together with Eub338 II, III and IV; and

⁴Used together with an unlabeled oligonucleotide competitor as indicated in the reference.