TABLE 1.

rRNA-targeted oligonucleotide primers and fluorescent probes used in this study

Probe or primer	Positionsa	Oligonucleotide sequence	Probe or primer specificity
16S rRNA primer
341fb	341-357	5′-CCTACGGGAGGCAGCAG-3′	Eubacteria
534rb	534-518	5′-ATTACCGCGGCTGCTGG-3′	Eubacteria
8fplc	8-27	5′-AGAGTTTGATCCTGGCTCAG-3′	Eubacteria
1492rplc	1510-1492	5′-GGTTACCTTGTTACGACTT-3′	Eubacteria
WPF445fd	445-464	5′-GGGAAGAAAAACTTAAAGCT-3′	White Point VAF (≥10 μm)
WPF464rd	464-445	5′-AGCTTTAAGTTTTTCTTCCC-3′	White Point VAF (≥10 μm)
VSO656fd	656-673	5′-GTACAGTAGAGGGAAGCG-3′	Unattached, vacuolate, sulfur-oxidizing spp.e
VSO673rd	673-656	5′-CGCTTCCCTCTACTGTAC-3′	Unattached, vacuolate, sulfur-oxidizing spp.e
16s RNA probe
Eub338f	338-355	5′-GCTGCCTCCCGTAGGAGT-3′	Eubacteria
WPF464d	445-464	5′-AGCTTTAAGTTTTTCTTCCC-3′	White Point wide, attached filaments
VSO673d	656-673	5′-CGCTTCCCTCTACTGTAC-3′	Unattached, vacuolate, sulfur-oxidizing spp.e
G123Tg	697-714	5′-CCTTCCGATCTCTATGCA-3′	Thiothrix spp.
G123T-Cg	697-714	5′-CCTTCCGATCTCTACGCA-3′	Nonsense competitor to probe G123T
23S rRNA probe
GAM42ah	1027-1043	5′-GCCTTCCCACATCGTTT-3′	Gamma proteobacteria
BET42ah	1027-1043	5′-GCCTTCCCACTTCGTTT-3′	Beta proteobacteria

a Based on E. coli 16S rRNA base pair numbering.

b Primer from reference 22.

c Primer from reference 40.

d Primer or probe designed in this study.

e Designed to target Monterey Canyon, Bay of Concepcion, and Carmel Canyon Beggiatoa spp., vacuolate Thioploca spp., and Thiomargarita namibiensis (see Materials and Methods).

f Probe from reference 39.

g Probe from reference 11.

h Probe from reference 19.