TABLE 1.
Oligonucleotide probes
| Probe | Specificity | Probe sequence (5′-3′) | Target sitea (rRNA positions) | % FAb | NaCl (mM)c | Reference |
|---|---|---|---|---|---|---|
| EUB338 | Bacteria | GCTGCCTCCCGTAGGAGT | 16S (338–355) | 20 | 225 | 3 |
| ALF1b | α Subclass of the class Proteobacteria, several members of the δ subclass of Proteobacteria, genus Nitrospira, most spirochetes | CGTTCGYTCTGAGCCAG | 16S (19–35) | 20 | 225 | 19 |
| BET42a | β Subclass of Proteobacteria | GCCTTCCCACTTCGTTT | 23S (1027–1043) | 35d | 80 | 19 |
| GAM42a | γ Subclass of Proteobacteria | GCCTTCCCACATCGTTT | 23S (1027–1043) | 35e | 80 | 19 |
| NSO190 | Ammonia-oxidizing β-subclass Proteobacteria | CGATCCCCTGCTTTTCTCC | 16S (190–208) | 55 | 20 | 21 |
| NSV443 | Nitrosospira spp. | CCGTGACCGTTTCGTTCCG | 16S (444–462) | 30 | 112 | 21 |
| NSM156 | Nitrosomonas spp. | TATTAGCACATCTTTCGAT | 16S (653–670) | 40 | 56 | 21 |
| NIT3 | Nitrobacter spp. | CCTGTGCTCCATGCTCCG | 16S (1035–1048) | 40f | 56 | 34 |
| NSR826 | Freshwater Nitrospira spp. | GTAACCCGCCGACACTTA | 16S (826–843) | 20 | 225 | This study |
| NSR1156 | Freshwater Nitrospira spp. | CCCGTTCTCCTGGGCAGT | 16S (1156–1173) | 30 | 112 | This study |
| NSR447 | Clones g6, o9, and o14 | GGTTTCCCGTTCCATCTT | 16S (447–464) | 30 | 112 | This study |
a
E. coli numbering (9).
b
Percentage formamide in the hybridization buffer.
c
Millimolar concentration of sodium chloride in the washing buffer.
d
Used with an equimolar amount of unlabeled competitor oligonucleotide GAM42.
e
Used with an equimolar amount of unlabeled competitor oligonucleotide BET42a.
f
Used with an equimolar amount of unlabeled competitor oligonucleotide CNIT3 (34).