TABLE 1.
Detection of AOB and Nitrosomonas spp. in root, rhizosphere, and soil by PCR, DGGE, and FISHa
| Sample | AOB (Nitrosomonas) detected by:
|
||
|---|---|---|---|
| amoA PCRb | DGGEb | FISHc (107 cells [cm3 of roots]−1) | |
| KDML roots | +++ | (+) | 5.0 ± 0.8 (1.2 ± 0.4) |
| Mahsuri roots | +++ | (−) | 6.0 ± 1.0 (1.3 ± 0.4) |
| IR63087 roots | +++ | (+++) | 6.8 ± 1.2 (4.0 ± 0.3) |
| KDML rhizosphere | +++ | (+) | ND |
| Mahsuri rhizosphere | +++ | (−) | ND |
| IR63087 rhizosphere | +++ | (++) | ND |
| Unplanted soil | +++ | (+) | ND |
a
PCR was used to amplify the ammonium monooxygenase gene (amoA) which was subsequently resolved by DGGE. Cell densities were detected by FISH using group-specific oligonucleotide probes.
b
Symbols: +, ++, and +++, presence of amoA or (Nitrosomonas) PCR product in one, two, or three replicates, respectively; −, no product was detected in all replicates. Qualitative results from three replicates are presented.
c
Means (n = 15) of cell densities ± 95% confidence limits (all symbols and values in parentheses refer to Nitrosomonas).