TABLE 1.
Oligonucleotide probes used in this study
| Probe | Specificity | Sequence (5′→3′) | Positiona | FISH FA concn (%, vol/vol)b | Slot blot Td (°C)c | Reference |
|---|---|---|---|---|---|---|
| Uni1390 | Universal (all organisms) | GACGGGCGGTGTGTACAA | 1390–1407 | 44d | 51 | |
| EUB338 | Bacteria | GCTGCCTCCCGTAGGAGT | 338–355 | 10 | 54d | 1 |
| NON338 | ACTCCTACGGGAGGCAGC | 338–355 | 10 | 47 | ||
| DSR651 | Desulforhopalus spp. | CCCCCTCCAGTACTCAAG | 651–668 | 35 | 62 | 25 |
| DSS658 | Desulfosarcina spp., Desulfofaba sp., Desulfococcus spp., Desulfofrigus spp. | TCCACTTCCCTCTCCCAT | 658–685 | 60 | 58 | 25 |
| DSV698 | Desulfovibrio spp. | GTTCCTCCAGATATCTACGG | 698–717 | 35 | 58 | 25 |
| DSV214 | Desulfomicrobium spp. | CATCCTCGGACGAATGC | 214–230 | 10 | 25 | |
| DSV407 | Desulfovibrio spp. | CCGAAGGCCTTCTTCCCT | 407–424 | 50 | 25 | |
| DSV1292 | Desulfovibrio spp. | CAATCCGGACTGGGACGC | 1292–1309 | 35 | 25 | |
| DSD131 | Desulfovibrio sp. | CCCGATCGTCTGGGCAGG | 131–148 | 20 | 25 | |
| DSMA488 | Desulfarculus sp., Desulfomonile sp., Syntrophus spp. | GCCGGTGCTTCCTTTGGCGG | 488–507 | 60 | 25 | |
| Sval428 | Desulfotalea spp., Desulfofusiis sp. | CCATCTGACAGGATTTTAC | 428–446 | 25 | 52d | 37 |
| 660 | Desulfobulbus spp. | GAATTCCACTTTCCCCTCTG | 660–679 | 60 | 59d | 6 |
| 221 | Desulfobacterium spp. | TGCGCGGACTCATCTTCAAA | 221–240 | 35 | 57d | 6 |
| DSB985 | Desulfobacter spp., Desulfobacula spp. | CACAGGATGTCAAACCCAG | 985–1003 | 20 | 53 | 25 |
| DRM432 | Desulfuromonas spp., Pelobacter spp. | CTTCCCCTCTGACAGAGC | 432–449 | 40 | 62 | This study |
| DSF672 | Desulfofrigus spp., Desulfofaba sp. | CCTCTACACCTGGAATTCC | 672–690 | 45 | This study | |
| DSC193 | Desulfosarcina spp. | AGGCCACCCTTGATCCAA | 193–210 | 35 | This study | |
| DCC209 | Desulfococcus spp. | CCCAAACGGTAGCTTCCT | 209–226 | 25 | This study | |
| DSS225 | Svalbard clone group SVAL1 | TGGTACGCGGGCTCATCT | 225–242 | 40 | This study | |
| cl81-644 | Svalbard clones Sva0081 and Sva0863 | CCCATACTCAAGTCCCTT | 644–661 | 25 | This study |
a
Position in the 16S rRNA of E. coli.
b
Formamide (FA) concentration in the hybridization buffer.
c
Td, dissociation temperature.
d
Washing buffer containing 1× SSC, and 1% SDS was used.