TABLE 3.
Community analysis of an Aroclor 1260-dechlorinating JN culture transferred repeatedly in the presence of vancomycin
| Clone name (accession no.)e | No. of clones | Norm %a | Bergey's classification (RDP II)b
|
No. of 16S rRNA genesc | Closest match in GenBank as determined by RDP Sequence Match and BLAST tools | % Identity | |
|---|---|---|---|---|---|---|---|
| JN18Phylogenetic group | Closest classified relative (% certainty) | ||||||
| JN18 V4 B (EF059527) | 7 | 25.8-27 | Chloroflexi | Dehalococcoides (100) | 1 | Dehalococcoides sp. strains CBDB1, FL2, GT (AF230641, AF357918 | >99.9 |
| JN18 V12 B (EF059528) | AY914178) | ||||||
| JN18 V35 B (EF059529) | |||||||
| JN18 V108 B (EF059530) | |||||||
| JN18 V2 A* (DQ168642) | 54 | 49.7-50 | Betaproteobacteria | Thauera (94) | 4d | Azoarcus sp. strain LU1 (AJ007007) | 98-99 |
| JN18 V17 A3 (DQ168643) | |||||||
| JN18 V62 (DQ168641) | |||||||
| JN18 V65 E (EF059531) | 14 | 1.7-2.8 | Gammaproteobacteria | Acinetobacter (100) | 7 | Acinetobacter sp. strain LY1 (AJ007008) | 99 |
| JN18 V5 C (EF059532) | |||||||
| JN18 A13 Q (DQ168644) | 3 | 3.7-3.8 | Gammaproteobacteria | Pseudomonas (100) | 4-7 | Uncultured bacterial clone 69-7G (AY955095) | 99 |
| JN18 A17 R (DQ168645) | |||||||
| JN18 A62 G* (DQ168649) | 9 | 7.4-7.7 | Bacteroidales | Porphyromonadaceae (83, 100) | 4 | Uncultured bacterial clone PL-7B7 (AY570639); Bacteroides sp. strain Z4 (AY949860) | 99 |
| JN18 V15 G (EF059535) | |||||||
| JN18 V95 J (EF059536) | 1 | 1.8-1.9 | Deltaproteobacteria | Geobacteraceae (98) | 2 | Uncultured bacterial clone W31 (AY770971) | 96 |
| JN18 V27 I (EF059533) | 2 | 0.6-1.5 | Clostridiales | Sedimentibacter (100) | 5-12 | Sedimentibacter sp. strain C7 (AY766466) | 96 |
| JN18 V41 S (DQ168656) | 3 | 1-2.2 | Clostridiales | Lachnospiraceae (94) | 5-12 | Anaerotruncus colihominis HKU19 (DQ082932) | 94 |
| JN18 V56 P (EF059534) | 2 | 0.6-1.5 | Clostridiales | Clostridiaceae (95) | 5-12 | Clostridium sp. strain FCB90-3 (AJ229251) | 98 |
| JN18 A7 F* (DQ168648) | 1 | 3.7-3.8 | Eubacteria | Proteobacteria (38) | ? | Uncultured bacterial strain SHA-53 (AJ249111) | 99 |
a
Percentage of clones normalized for estimated rRNA copy number.
b
Each distinct operational taxonomic unit identified by RFLP analysis was phylogenetically classified according to Bergey's Manual (27) using the naïve Bayesian rRNA classifier hosted on the RDP II site (17a). This classifier is trained on all known type strain 16S rRNA gene sequences. The query sequence is assigned a taxonomic hierarchy and the calculation is repeated for 100 trials to assign an estimate of the certainty of that taxonomic assignment.
d
Azoarcus, a close relative, possesses four 16S rRNA gene copies.