TABLE 2.
Identification of representative cloned sequence types present in phylogenetic groups found in both the 16S rDNA and the 16S rRNA clone libraries from PCB-polluted soil
| Bacterial division | Phylogenetic group | No. of sequences/ no. of sequence types | Representative clone | Closest relative in database (EMBL accession no.) | Length (nt)a | % Identity |
|---|---|---|---|---|---|---|
| Alpha-Proteobacteria | A-1 | 6/5 | WD208 | Sphingomonas asaccharolytica IFO 10564 (Y09639) | 1,410 | 95.32 |
| A-2 | 7/4 | WD225 | Phenylobacterium immobile (Y18216) | 1,404 | 97.08 | |
| A-3 | 5/3 | WD229 | Magnetospirillum sp. strain MSM-4 (Y17390) | 1,409 | 93.75 | |
| A-4 | 4/4 | WD2103 | Azospirillum sp. strain ASP-1 (X92464) | 1,408 | 90.13 | |
| A-7 | 2/2 | WD238 | Rhodopila globiformis DSM 161 (D86513) | 1,428 | 92.58 | |
| A-8 | 10/6 | WD248 | Acidosphaera rubrifaciens HS-AP3 (D86512) | 1,414 | 94.70 | |
| A-9 | 16/9 | WD249 | Sphingomonas subartica KF1 (X94102) | 1,411 | 96.17 | |
| A-10 | 5/4 | WD252 | Sphingomonas pruni IFO 15498 (Y09637) | 1,409 | 98.58 | |
| A-11 | 4/4 | WD267 | Afipia genosp. 13 strain G8991 (U87784) | 1,411 | 95.46 | |
| A-12 | 2/1 | WD271 | Gluconacetobacter liquefaciens LMG 1382 (X75617) | 1,413 | 92.43 | |
| A-13 | 11/5 | WD275 | Bradyrhizobium sp. strain Pe4 (AF159437) | 1,410 | 99.01 | |
| A-15 | 4/4 | WD295 | Gluconacetobacter sacchari IF2-6 (AF127412) | 1,413 | 94.55 | |
| A-16 | 6/6 | WD297 | Caulobacter vibriodes ATCC 11764 (AJ227755) | 1,408 | 97.23 | |
| A-19 | 6/4 | WD2108 | Gluconacetobacter sacchari IF2-6 (AF127412) | 1,417 | 96.47 | |
| Beta-Proteobacteria | B-2 | 11/3 | WD291 | Xylophilus ampelinus ATCC 33914 (AF078758) | 1,455 | 98.14 |
| B-3 | 10/4 | WD2115 | Variovorax sp. strain WFF52 (AB003627) | 1,457 | 99.18 | |
| B-5 | 8/5 | WD2102 | Rubrivivax gelatinosus (D16213) | 1,451 | 96.35 | |
| B-13 | 6/6 | WD221 | Burkholderia sp. strain LB400 (U86373) | 739 | 97.29 | |
| B-14 | 8/8 | WD202 | Burkholderia sp. strain N3P2 (U37344) | 1,453 | 98.97 | |
| B-15 | 5/4 | WD263 | Burkholderia sp. strain NF100 (AB025790) | 1,456 | 97.25 | |
| B-16 | 5/5 | WD206 | Burkholderia sp. strain NF100 (AB025790) | 1,455 | 97.80 | |
| B-17 | 5/3 | WD237 | Burkholderia sp. strain N2P5 (U37342) | 748 | 98.80 | |
| B-18 | 38/17 | WD227 | Burkholderia sp. strain Dha-54 (AJ011508) | 1,455 | 98.28 | |
| B-19 | 3/3 | WD268 | Burkholderia sp. strain N2P5 (U37342) | 1,451 | 97.80 | |
| B-21 | 6/4 | WD2116 | Burkholderia glathei ATCC 29195 (AB021374) | 1,455 | 97.25 | |
| Gamma-Proteobacteria | G-1 | 2/1 | WD259 | Pseudomonas sp. strain PsK (AF105389) | 1,459 | 99.32 |
| G-2 | 3/2 | WD260 | Ectothiorhodospira sp. strain Bogoria Red (AF084511) | 1,462 | 87.41 | |
| G-3 | 13/4 | WD280 | Nevskia ramosa (AJ001343) | 1,450 | 96.14 | |
| G-4 | 15/10 | WD284 | Nevskia ramosa (AJ001343) | 1,450 | 96.69 | |
| G-5 | 2/2 | WD2124 | Ectothiorhodospira sp. strain Bogoria Red (AF084511) | 1,463 | 86.74 | |
| Holophaga-Acidobacterium | H-2 | 7/5 | WD207 | Acidobacterium capsulatum (D26171) | 1,424 | 95.37 |
| H-4 | 7/7 | WD247 | Clone UA1 (AF200696) | 1,422 | 96.06 | |
| H-5 | 6/4 | WD217 | Clone UA3 (AF200699) | 1,426 | 92.50 | |
| Holophaga-Acidobacterium | H-6 | 5/3 | WD228 | Clone TRB82 (AF047646) | 1,398 | 97.14 |
| H-7 | 5/3 | WD243 | Clone TRB82 (AF047646) | 1,402 | 96.36 | |
| H-10 | 4/4 | WD261 | Clone DA052 (Y07646) | 1,461 | 93.29 | |
| H-11 | 7/7 | WD277 | Clone TRB82 (AF047646) | 1,400 | 95.14 | |
| Planctomycetales | P-4 | 3/3 | WD2112 | Isosphaera sp. strain Schlesner 640 (X81959) | 1,444 | 92.45 |
| Candidate division OP10 | O-1 | 2/2 | WD294 | Clone SJA-22 (AJ009456) | 1,439 | 86.17 |
| Not affiliated (WS-I) | N-3 | 2/2 | WD2101 | Planctomycete strain 394 (AJ231192) | 1,395 | 75.41 |
a
nt, nucleotides.