Table 3.
DGGE band description: designations, loading PCA values for the DGGE band sequences (Fig. 4), number of clones and levels of similarity to closest related organisms
| DGGE band | PC1 loading | PC2 loading | No. of clones | Length (bp) | Similarity (%) | Closest related organism in GenBank (accession no.)a | Phylogenetic groupb |
|---|---|---|---|---|---|---|---|
| Originating with 4-n-NP | |||||||
| A1 | 0.642 | 0.722 | 4 | 235–239 | 99 | Pseudomonas stutzeri, isolate st104 (AM905852) | Pseudomonadaceae (γ) |
| A2 | −0.602 | 0.602 | 4 | 193–197 | 98 | Pseudomonas stutzeri, isolate st104 (AM905852) | Pseudomonadaceae (γ) |
| 1 | 98 | Uncultured bacterium clone OTU_10 (EU083488) | Phyllobacteriaceae; Parvibaculum (α) | ||||
| A3 | −0.875 | 0.285 | – | 115 | 99 | Uncultured bacterium clone OTU_8 (EU083486) | Phyllobacteriaceae; Parvibaculum (α) |
| A4 | −0.361 | −0.684 | – | 116 | 99 | Uncultured bacterium clone OTU_8 (EU083486) | Phyllobacteriaceae; Parvibaculum (α) |
| Originating with 4-n-NP and phenol | |||||||
| B1 | 0.959 | 0.173 | 1 | 198 | 99 | Pseudomonas aeruginosa strain H13 (AY074894) | Pseudomonadaceae (γ) |
| 2 | 171 | 98–99 | Uncultured bacterium clone OTU_10 (EU083488) | Phyllobacteriaceae; Parvibaculum (α) | |||
| 1 | 196 | 100 | Alcaligenes sp. 22–27 (AY999035) | Alcaligenaceae (ß) | |||
| B2 | 0.642 | 0.722 | 1 | 173 | 98 | Ochrobactrum sp. HPC481 (AY074894) | Rhizobiaceae (α) |
| 1 | 198 | 98 | Pseudomonas aeruginosa strain H13 (AY074894) | Pseudomonadaceae (γ) | |||
| 3 | 173–198 | 98–100 | Uncultured bacterium clone OTU_10 (EU083488) | Phyllobacteriaceae; Parvibaculum (α) | |||
| B3 | −0.361 | −0.684 | – | 117 | 99 | Uncultured bacterium clone OTU_8 (EU083486) | Phyllobacteriaceae; Parvibaculum (α) |
| B4 | 0.572 | −0.757 | – | 114 | 99 | Uncultured bacterium clone OTU_8 (EU083486) | Phyllobacteriaceae; Parvibaculum (α) |
| B5 | −0.300 | −0.217 | – | 114 | 99 | Uncultured bacterium clone OTU_8 (EU083486) | Phyllobacteriaceae; Parvibaculum (α) |
aSequences were matched with the closest relative from the GenBank database
bSequences were matched with the closest relative from the Ribosomal Database Project (Maidak et al. 2000)
α, β and γ represent alpha, beta and gamma Proteobacteria, respectively