TABLE 2.

Group-specific rRNA ologinucleotide probes and corresponding washing conditions used in this study

Target groupProbe nameaSequence (5′→3′)Td (°C)b
UniversalUNI1390GACGGGCGGTGTGACAA44
BacteriaEUB338GCTGCCTCCCGTAGGAGT54
ArchaeaARC915GTGCTCCCCCGCCAATTCCT56
EukaryotesEUK1379TACAAAGGGCAGGGAC42
Gamma/beta proteo- bacteriaBG23S42GCCTTCCCACWTCGTTT60
S oxidizers (gamma proteobacteria)GAM660TCCACTTCCCTCTAC52
Desulfosarcina groupDSS658aTCCACTTCCCTCTCCCAT58
FlavobacteriaCFB319aTGGTCCGTGTCTCAGTAC56
PlanctomycetalesPLA927CACCGCTTGTGTGAGCCC50
Gram-positive bacteriaGB1199AGGGGGCATGATG34
  • a Probe sources are from reference 45. Probe GP1199 is specific to most but not all members of the Actinobacteria and Firmicutes; probe PLA927 was designed in this study.

  • b All probes were washed at the dissociation temperature (Td) in 1× SSC buffer (0.15 M NaCl, 0.015 M trisodium citrate [pH 7.0] containing 1% sodium dodecyl sulfate, except for probes CF319a and DSS658a which were washed with 1× SSC containing 0.1% sodium dodecyl sulfate.