TABLE 1.

Probe sequences used to screen cave mat microbial populations

ProbeTarget groupProbe sequence (5′ → 3′)Target siteaFAb (%)Reference
EUB338EubacteriaGCT GCC TCC CGT AGG AGT16S (338)0-4010
EUB338-IIPlanctomycetesGCA GCC ACC CGT AGG TGT16S (338)0-4010
EUB338-IIIVerrucomicrobia (and others)GCT GCC ACC CGT AGG TGT16S (338)0-4010
NonEUBNegative controlACT CCT ACG GGA GGC AGC16S (338)062
ALF968AlphaproteobacteriaGGT AAG GTT CTG CGC GTT16S (968)2038
BET42aBetaproteobacteriaGCC TTC CCA CTT CGT TT23S (1027)3532
GAM42aGammaproteobacteriaGCC TTC CCA CAT CGT TT23S (1027)3532
HGC69aActinobacteriaTAT AGT TAC CAC CGC CGT23S (1901)2546
LGC345AMany Firmicutes (together with two other LGC345A probes)TGG AAG ATT CCC TAC TGC16S (354)2033
LGC354BSame as LGC345ACGG AAG ATT CCC TAC TGC2033
LGC354CSame as LGC345ACGG CGT CGC TGC GTC AGG2033
CF319aSome members of the “FlavobacteriaTGG TCC GTG TCT CAG TAC16S (319)3531
G123TcThiothrixCCT TCC GAT CTC TAT GCA16S (697)4021
EPS710“Epsilonproteobacteria”-Thiovulum groundwater subgroupCAG TAT CAT CCC AGC AGA16S (710)30d64
LKC59Epsilonproteobacterial group I from Lower Kane CaveTCC TCT CAT CGT TCG ACT16S (59)30This study
LKC1006Epsilonproteobacterial group II from Lower Kane CaveCTC CAA TGT TTC CAT CGG16S (1006)30This study
  • a E. coli 16S rRNA position (6).

  • b Formamide (FA) percentage in the FISH hybridization buffer.

  • c Used in conjunction with a competitor probe, G123T-C (5′-CCTTCCGATCTCTACGCA-3′) (21).

  • d This formamide concentration differs from the one suggested in the original publication (64) because we applied a different hybridization temperature.