Table 5.
Oligonucleotide probes used for PCR and FISH analysis.
| Probe | Positiona | Sequence (5′→3′) | Target (reference) | Formamide (%)b | NaCl (mM)c |
|---|---|---|---|---|---|
| A751Fd,e | – | CCGACGGTGAGRGRYGAA | Archaea (Baker et al., 2003) | – | – |
| UA1204Re | – | TTMGGGGCATRCIKACCT | Archaea (Baker et al., 2003) | – | – |
| EB341Fd,e | – | CCTACGGGAGGCAGCAG | Bacteria (Muyzer et al., 1993) | – | – |
| UN517Re | – | ATTACCGCGGCTGCTGG | Bacteria (Muyzer et al., 1993) | – | – |
| DSR4Rd,e | – | GTGTAGCAGTTACCGCA | dsrB Gene (Wagner et al., 1998) | – | – |
| DSRp2060Fe | – | CAACATCGT(CT)CA(CT)ACCCAGGG | dsrB Gene (Geets et al., 2006) | – | – |
| Eub338 | 338–355 | GCTGCCTCCCGTAGGAGT | Bacteria (Amann et al., 1990) | 20 | 225 |
| Arc915 | 915–934 | GTGCTCCCCCGCCAATTCCT | Archaea (Stahl and Amann, 1991) | 40 | – |
| SRB385 | 385–402 | CGGCGTCGCTGCGTCAGG | Most desulfovibrionales (Amann et al., 1992) | 35 | 80 |
| DBB660 | 660–679 | GAATTCCACTTTCCCCTCTG | Desulfobulbus (Devereux et al., 1992) | 60 | 15.6 |
| NON338 | 338–355 | ACTCCTACGGGAGGCAGC | None (Wallner et al., 1993) | – | – |
a
Position in the 16S rRNA of E. Coli (Brosius et al., 1981).
b
Formamide concentration in hybridization buffer.
c
Sodium chloride concentration in washing buffer.
d
These primers had a 40 base pair GC-clamp at the 5′ end.
e
Probes not used for FISH.