Table 1.
Nucleotide probes used for the PCR and FISH.
| Name | Sequence (5′–3′) | Specificity | References | Formamide concentration (%)a | Fluorescent dye |
|---|---|---|---|---|---|
| PCR PRIMERS | |||||
| Unibac-II-515f | GTGCCAGCAGCCGC | Most bacteria | Lieber et al., 2003 | - | - |
| Unibac-II-927r | CCCGTCAATTYMTTTGAGTT | Most bacteria | Lieber et al., 2003 | - | - |
| 799f | AACMGGATTAGATACCCKG | Most bacteria | Chelius and Triplett, 2001 | - | - |
| 1492r | ACCTTGTTACGACTT | Most bacteria | Lane, 1991 | - | - |
| BKH143Fw | TGGGGGATAGCYCGGCG | Burkholderia spp. | Schönmann et al., 2009 | - | - |
| BKH1434Rw | TGCGGTTAGRCTASCYACT | Burkholderia spp. | Schönmann et al., 2009 | - | - |
| FISH PROBES | |||||
| EUB338b | GCTGCCTCCCGTAGGAGT | Most bacteria | Amann et al., 1990 | 15 | Cy3 |
| EUB338IIb | GCAGCCACCCGTAGGTGT | Planctomycetales | Daims et al., 1999 | 15 | Cy3 |
| EUB338IIIb | GCTGCCACCCGTAGGTGT | Verrucomicrobiales | Daims et al., 1999 | 15 | Cy3 |
| Burkho | ACCCTCTGTTCCGACCAT | Burkholderia spp. | Hogardt et al., 2000 | 40 | Cy5 |
| NONEUB | ACTCCTACGGGAGGCAGC | - | Amann et al., 1990 | -c | -d |
a
The stringency conditions for hybridization at 41°C.
b
The probes were applied together in equimolar ratio.
c
The probe used for negative control at the same stringency conditions applied for positive FISH probe.
d
The probe used for negative control was labeled with the same fluorescent dye as corresponding positive FISH probe.