TABLE 3.
Number of phylogenetic groups, clones, and cloned sequence types from PCB-polluted soil for each of the bacterial divisions observed in either the library generated from undiluted RNA, the one generated from diluted RNA, and in both types of libraries simultaneously
| Bacterial division | No. of phylogenetic groupsa observed in 16S rRNA libraries obtained with undiluted and diluted RNA
|
|||
|---|---|---|---|---|
| Total | Both rRNA libraries | Undiluted RNA only | 1:500-diluted RNA only | |
| Proteobacteria | ||||
| Alpha subdivision | 40 (97/78) | 13 (67/50) | 17 (19/18) | 10 (11/10) |
| Beta subdivision | 18 (74/57) | 10 (59/44) | 8 (15/13) | 0 |
| Gamma subdivision | 9 (33/22) | 3 (25/15) | 3 (3/3) | 3 (4/4) |
| Holophaga-Acidobacterium | 19 (48/42) | 8 (37/31) | 3 (3/3) | 8 (8/8) |
| Actinobacteria | 6 (9/8) | 1 (2/2) | 3 (3/3) | 2 (4/3) |
| Planctomycetales | 4 (7/6) | 2 (5/4) | 1 (1/1) | 1 (1/1) |
| Candidate division OP10 | 4 (6/6) | 0 | 3 (4/4) | 1 (2/2) |
| Plastids | 1 (1/1) | 0 | 0 | 1 (1/1) |
| Low G+C gram positives | 2 (2/2) | 0 | 0 | 2 (2/2) |
| Cytophagales | 1 (1/1) | 0 | 0 | 1 (1/1) |
| Not affiliated (WPS-1) | 4 (8/7) | 1 (5/4) | 0 | 3 (3/3) |
| Total | 108 (285/230) | 38 (200/150) | 38 (48/45) | 32 (37/35) |
a
Phylogenetic group: a clone group with sequence similarity higher than 97% (98% for Burkholderia and Pseudomonas-type clones). Values in parentheses indicate the number of clones/cloned sequence types.