Table 2. FISH probes designed in this study.
| Probe full namea | Short name | Sequence 5′–3′ | Binding positionb | FA%c | Target group |
Coveraged |
|
|---|---|---|---|---|---|---|---|
| Probe (%) | Comb (%) | ||||||
| S-G-Ntoga-0122-a-A-19 | Ntoga122 | TCCGGGTACGTTCCGATAT′ | 122–140 | 40 | Genus Nitrotoga | 98.5 | 98.5 |
| cS-G-Ntoga-0122-a-A-19e | c1Ntoga122 | TCWGGGTACGTTCCGATAT | 122–140 | — | — | ||
| cS-G-Ntoga-0122-b-A-19e | c2Ntoga122 | TCYGGGTACGTTCCGATGT | 122–140 | — | — | ||
| S-F-Gall-0178-a-A-18 | FGall178 | TCCCCCTYAGGGCATATG | 178–195 | 30 | Family Gallionellaceae | 98.9 | 98.9 |
| cS-F-Gall-0178-a-A-18e | cFGall178 | TCCCCCTYAGGGCKTATG | 178–195 | — | — | ||
| S-F-Gall-0221-a-A-18 | FGall221a | TATCGGCCACTCCGAAAG | 221–238 | 30 | Family Gallionellaceae | 71.6 | 90.2 |
| cS-F-Gall-0221-a-A-18e | c1FGall221a | TATCGGCCACTCCTAAAG | 221–238 | — | — | ||
| S-F-Gall-0221-b-A-18f | FGall221b | TATCGGCCGCTCCGAAAA | 221–238 | 30 | Genus Nitrotoga | 97.9 | |
| Family Gallionellaceae | 18.6 | ||||||
| cS-F-Gall-0221-b-A-18 | cFGall221b | CATCGGCCGCTCCGAAAG | 221–238 | — | — | ||
| S-*-Gall-0438-a-A-18 | FGall438 | GTTTTCTTTCCGGCTGAA | 438–455 | 25 | Genus Nitrotoga | 89.4 | 89.4 |
| cS-*-Gall-0438-a-A-18e | c1FGall438 | GATTTCTTTCCGGCTGAA | 438–455 | Zoogloea spp. | — | ||
| cS-*-Gall-0438-b-A-18e | c2FGall438 | GTTTTCTTCCCGGCTGAA | 438–455 | Thaurea/Dechloromonas spp. | — | ||
| cS-*-Gall-0438-c-A-18e | c3FGall438 | GTTTTCTTTCCGTCTGAA | 438–455 | Azoarcus spp. | — | ||
| S-G-Ntoga-1424-a-A-18 | Ntoga1424 | CTAGCTGCTTCTGGTAGAA | 1424–1442 | 20 | Genus Nitrotoga | 82.2 | 82.2 |
| cS-G-Ntoga-1424-a-A-18e | c1Ntoga1424 | CTAACTGCTTCTGGTAGAA | 1424–1442 | Sterolibacterium/Dechlorosoma spp. | — | ||
| cS-G-Ntoga-1424-b-A-18e | c2Ntoga1424 | CTAGCTGCTTCTGGTACAA | 1424–1442 | Acidothiobacillus spp. | — | ||
Probe nomenclature according to Alm et al. (1996).
Probe binding position according to Escherichia coli 16S rRNA gene numbering.
Percent formamide (v v−1) added to the hybridization buffer for optimal hybridization conditions.
Group coverage was calculated as the fraction of organisms with a full sequence match to the respective probe relative to the number of sequences within the respective probe target group as defined by phylogenetic analyses (see main text for details). Column ‘Probe' lists the coverage of single probes, column ‘Comb.' that of probe combinations.
Competitor probes were added to the hybridization buffer as unlabeled oligonucleotides and in equimolar amounts as the labeled probes to increase hybridization specificity.
Probe can be used alone for detection of the genus Nitrotoga or in combination with probe FGall221a for detection of the family Gallionellaceae.