TABLE 1.
Phylogenetic analysis of 16S rRNA sequences of DGGE bands detected in stable enrichment cultures
| DGGE banda | Closest RDP/GenBank relativeb
|
% Similarity to closest relativec | % Sequence similarity toc:
|
||||||
|---|---|---|---|---|---|---|---|---|---|
| Phylogenetic group | Strain or species | DGGE band 1 | DGGE band 2 | DGGE band 3 | DGGE band 4 | DGGE band 5 | DGGE band 6 | ||
| 1 | β-Proteobacteria | Burkholderia sp. strain N3P2 | 99.6 | ||||||
| 2 | β-Proteobacteria | B. glathei | 99.4 | 96.7 | |||||
| 3 | β-Proteobacteria | Burkholderia sp. strains N3P2 and N2P5 | 100 | 99.6 | 97.1 | ||||
| 4 | β-Proteobacteria | B. cepacia | 98.1 | 96.3 | 94.7 | 96.7 | |||
| 5 | β-Proteobacteria | R. solanacearum | 99.2 | 92.6 | 93.4 | 93.0 | 94.7 | ||
| 6 | β-Proteobacteria | R. solanacearum | 100 | 91.8 | 93.4 | 92.2 | 93.9 | 99.2 | |
| 7 | β-Proteobacteria | M. methylotrophus | 96.3 | 88.1 | 89.8 | 88.5 | 89.8 | 88.5 | 87.7 |
| 8 | α-Proteobacteria | A. lipoferum | 98.8 | ||||||
| 9 | Gram-positive bacteria | M. gilvumd | 100 | ||||||
| 10 | Chlamydiales | Chlamydia sp. | 96.0 | ||||||
The band numbers correspond to DGGE band numbers in the figures. The GenBank accession numbers for the DGGE band nucleotide sequences are AF247476 to AF247485, respectively.
The GenBank accession numbers for the closest database relatives are as follows: Burkholderia sp. strain N3P2, U37344; Burkholderia sp. strain N2P5, U37342; B. glathei, Y17052; B. cepacia, M22518; R. solanacearum, X67035; M. methylotrophus, L15475, A. lipoferum, Z29619; M. gilvum, X55599; and Chlamydia sp. Y07556.
DGGE band sequences were compared by using E. coli 16S rRNA positions 1115 to 1367.
M. gilvum has a 16S rRNA sequence identical to that of M. chitae and M. smegmatis in the region used for DGGE analysis.