TABLE 2.

Oligonucleotide probes used in this study

ProbeSpecificitySequence (5′ to 3′)Target site (rRNA, 5′ position)% FAaReference
EUBI-III Bacteria GCW GCC WCC CGT AGG WGT16S, 33855 9
HGC69a Actinobacteria TAT AGT TAC CAC CGC CGT23S, 190730 35
AcI-852acI lineage of limnic ActinobacteriabAAT GCG TTA GCT GCG TCG CA16S, 85255This study
    AcI-852-H1Helper for AcI-852AAA CCG TGG AAG GTY CSC ACA ACT AG16S, 82655This study
    AcI-852-H2Helper for AcI-852TCC CCA GGC GGG GCR CTT16S, 87255This study
AcI-1214acI lineage of limnic ActinobacteriabCAT GCG TGC AGC CCA AGA CA16S, 121455This study
AcI-840-1Subgroup of acI lineageTCG CAC AAA CCG TGG AAG16S, 84030This study
AcI-840-2Subgroup of acI lineageTCG CAG AAA CCG TGG AAG16S, 84030This study
AcI-840-3Subgroup of acI lineageTCG CAG AGA CCG TGG AAG16S, 84030This study
    AcI-840-H1Helper for AcI-840 probesCTA GYG CCC AYC GTT TAC GG16S, 81030 13
    AcI-840-H2Helper for AcI-840 probesGTT CSC ACA ACT AGY GCC CA16S, 82030 13
    AcI-840-H3Helper for AcI-840 probesGGG GCR CTT AAT GCG TTA GCT G16S, 85930 13
Bet42aβ-ProteobacteriaGCC TTC CCA CTT CGT TT23S, 103355 24
R-BT065Beta I lineage of limnic β-proteobacteriacGTT GCC CCC TCT ACC GTT16S, 6555 38
Bet2-870Beta II lineage of limnic β-proteobacteriacCCC AGG CGG CTG ACT TCA16S, 87055 8
  • a Percent formamide (FA) in hybridization buffer for hybridizations at 35°C.

  • b Proposed in reference 47.

  • c Proposed in reference 13.