TABLE 1.
Probe sequences used to screen cave mat microbial populations
| Probe | Target group | Probe sequence (5′ → 3′) | Target sitea | FAb (%) | Reference |
|---|---|---|---|---|---|
| EUB338 | Eubacteria | GCT GCC TCC CGT AGG AGT | 16S (338) | 0-40 | 10 |
| EUB338-II | Planctomycetes | GCA GCC ACC CGT AGG TGT | 16S (338) | 0-40 | 10 |
| EUB338-III | Verrucomicrobia (and others) | GCT GCC ACC CGT AGG TGT | 16S (338) | 0-40 | 10 |
| NonEUB | Negative control | ACT CCT ACG GGA GGC AGC | 16S (338) | 0 | 62 |
| ALF968 | Alphaproteobacteria | GGT AAG GTT CTG CGC GTT | 16S (968) | 20 | 38 |
| BET42a | Betaproteobacteria | GCC TTC CCA CTT CGT TT | 23S (1027) | 35 | 32 |
| GAM42a | Gammaproteobacteria | GCC TTC CCA CAT CGT TT | 23S (1027) | 35 | 32 |
| HGC69a | Actinobacteria | TAT AGT TAC CAC CGC CGT | 23S (1901) | 25 | 46 |
| LGC345A | Many Firmicutes (together with two other LGC345A probes) | TGG AAG ATT CCC TAC TGC | 16S (354) | 20 | 33 |
| LGC354B | Same as LGC345A | CGG AAG ATT CCC TAC TGC | 20 | 33 | |
| LGC354C | Same as LGC345A | CGG CGT CGC TGC GTC AGG | 20 | 33 | |
| CF319a | Some members of the “Flavobacteria” | TGG TCC GTG TCT CAG TAC | 16S (319) | 35 | 31 |
| G123Tc | Thiothrix | CCT TCC GAT CTC TAT GCA | 16S (697) | 40 | 21 |
| EPS710 | “Epsilonproteobacteria”-Thiovulum groundwater subgroup | CAG TAT CAT CCC AGC AGA | 16S (710) | 30d | 64 |
| LKC59 | Epsilonproteobacterial group I from Lower Kane Cave | TCC TCT CAT CGT TCG ACT | 16S (59) | 30 | This study |
| LKC1006 | Epsilonproteobacterial group II from Lower Kane Cave | CTC CAA TGT TTC CAT CGG | 16S (1006) | 30 | This 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.