TABLE 1.

Oligonucleotide probes used in this study and fraction of total cells detected in the spring sample of coastal North Sea watera

ProbeSequence (5′ → 3′)Target organismsReferenceHybridized fraction (%)c
EUB338GCT GCC TCC CGT AGG AGTDomain Bacteria291 ± 1.3
NON338ACT CCT ACG GGA GGC AGCComplementary to EUB3382<1
ALF968GGT AAG GTT CTG CGC GTTMost α-proteobacteria1726.7 ± 1.4
ROS537CAA CGC TAA CCC CCT CCRoseobacter spp. and SAR83 α-proteobacteria12a11.0 ± 0.1
BET42abGCC TTC CCA CTT CGT TTβ-Proteobacteria28a9.3 ± 3.1
OM43-162ATG CGG CAT TAG CTA ACCOM43 clade of β-proteobacteriaThis study4.0 ± 0.2
Nso190CGA TCC CCT GCT TTT CTC CAmmonia-oxidizing β-proteobacteria313.4 ± 0.2
Nso1225CGC CAT TGT ATT ACG TGT GAAmmonia-oxidizing β-proteobacteria314.0 ± 0.4
GAM42abGCC TTC CCA CAT CGT TTγ-Proteobacteria28a20.0 ± 1.4
SAR86-1245TTA GCG TCC GTC TGT ATSAR86 cluster of γ-proteobacteria55a15.2 ± 0.2
CF319aTGG TCC GTG TCT CAG TACCytophaga-Flavobacterium2829.1 ± 3.8
  • a A formamide concentration of 55% was used in the hybridization buffer for all the probes. Hybridization and washing were performed at 35 to 37°C except for probe Nso190 (hybridization at 46°C and washing at 48°C). The concentration of sodium chloride in the washing buffer was 10 mM except for probe Nso190 (20 mM).

  • b Used with an equimolar amount of unlabeled competitor oligonucleotides.

  • c Means ± standard deviations for triplicate determinations.