Table 2.
Phylogenetic identification of AHD isolates from the microcosm and their ability to utilize biphenyl (BP), dibenzo-p-dioxin (DD), and naphthalene (NP) in addition to dibenzofuran (DF) as the sole carbon and energy source
| RDP taxonomic hierarchy assignment | 16S rRNA gene comparison | No. of strains isolateda | Utilization of:b | ||||
|---|---|---|---|---|---|---|---|
|
|
|
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| Closest relative as the type strain (accession number) | Similarity (%) | BP | DD | DF | NP | ||
| Actinobacteria | |||||||
| Janibacter | J. terrae CS12T (AF176948) | 99.8 | 1 (1, 0, 0, 0) | nt | nt | + | + |
| Mycobacterium | M. moriokaense DSM 44221T (AJ429044) | 98.9–99.2 | 3 (0, 2, 1, 0) | +y | − | +y | + |
| Nocardioides | N. aromaticivorans H-1T (AB087721) | 99.9–100 | 2 (2, 0, 0, 0) | − | − | +y | + |
| Rhodococcus | R. qingshengii djl-6T (DQ090961) | 99.2–100 | 4 (4, 0, 0, 0) | +y | − | +y | + |
| Sinomonas | S. atrocyaneus DSM 20127T (X80746) | 99.6 | 2 (1, 1, 0, 0) | − | − | + | + |
| Firmicutes | |||||||
| Paenibacillus | P. naphthalenovorans PR-N1T (AF353681) | 99.1–99.2 | 9 (1, 3, 2, 3) | − | −+1 | +y | + |
| P. borealis KK19T (AJ011322) | 97.7 | 2 (0, 1, 0, 1) | − | −+1 | + | + | |
| Proteobacteria | |||||||
| Novosphingobium | N. naphtalenivorans TUT562T (AB177883) | 99.9–100 | 6 (1, 2, 2, 1) | − | − | −+2y | + |
| Rhizobium | R. selenitireducens B1T (EF440185) | 98.9–99.0 | 9 (0, 4, 2, 3) | −+2y | −+2 | −+2y | + |
| Sphingomonas | S. wittichii RW1T (AB021492) | 99.9 | 1 (1, 0. 0, 0) | nt | nt | + | + |
| Variovorax | V. paradoxus DSM 66T (AJ420329) | 99.6 | 1 (0, 1, 0, 0) | nt | nt | +y | + |
| Dokdonella | D. koreensis DS-123T (AY987368) | 95.4–95.5 | 1 (0, 0, 1, 0) | nt | nt | +y | + |
| Unidentified | H. effusa AP103T (AY363245) | 94.7–95.0 | 2 (0, 0, 2, 0) | nt | nt | +y | + |
a
Figures in parentheses show the number of strains isolated from the microcosm on days 0, 360, 460, and 570 in order.
b
Abbreviations and symbols: +, utilization positive; +y, utilization and yellow metabolite production positive; −, utilization negative, −+1, co-metabolic degradation positive with DF; −+2, co-metabolic degradation positive with naphthalene.