Table 1.
Taxa deriving carbon from naphthalene, either directly or via cross-feeding, as detected at different time points.
| Taxon (OTU)a | Closest RDP SeqMatch type strain of the OTU representative sequence | GenBank accession no. | Similarity scoreb | Mean percent of valid reads per treatmentc | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| B1 | B2 | BF1 | BF2 | W1 | W2 | WF1 | WF2 | ||||
| Alphaproteobacteria | |||||||||||
| Caulobacterales | |||||||||||
| Brevundimonas | Brevundimonas vesicularis LMG 2350 | AJ227780 | 0.996 | 0.0 | 0.0 | 1.7 | 11.7 | 1.2 | 40.7 | 0.0 | 0.0 |
| Rhizobiales | |||||||||||
| Rhizobium | Rhizobium radiobacter IAM 12048 | AB247615 | 0.990 | 0.0 | 0.0 | 0.0 | 1.1 | 0.0 | 0.9 | 0.0 | 0.0 |
| Betaproteobacteria | |||||||||||
| Rhodocyclales | |||||||||||
| Georgfuchsia | Georgfuchsia toluolica G5G6 | EF219370 | 0.930 | 1.5 | 1.7 | 0.2 | 0.0 | 0.1 | 0.0 | 0.1 | 0.0 |
| Burkholderiales | |||||||||||
| Acidovorax | Acidovorax defluvii BSB411 | Y18616 | 0.998 | 19.7 | 24.1 | 21.9 | 36.9 | 53.3 | 1.8 | 37.0 | 12.7 |
| Variovorax | Variovorax paradoxus DSM 66 | AJ420329 | 0.994 | 0.0 | 0.1 | 0.5 | 1.1 | 0.0 | 0.0 | 0.0 | 0.0 |
| Hydrogenophaga | Hydrogenophaga taeniospiralis ATCC 49743 | AF078768 | 0.994 | 1.1 | 1.6 | 5.1 | 0.6 | 0.9 | 0.0 | 1.4 | 10.1 |
| Polaromonas | Polaromonas jejuensis JS12-13 | EU030285 | 0.998 | 0.4 | 0.5 | 0.3 | 1.1 | 1.3 | 0.0 | 0.1 | 0.1 |
| Achromobacter/Bordetella | Achromobacter xylosoxidans DSM 10346 | Y14908 | 0.996 | 0.0 | 0.0 | 3.2 | 0.0 | 1.9 | 0.0 | 0.0 | 0.0 |
| unclas. Comamonadaceae | Rhodoferax antarcticus ANT.BR | GU233447 | 0.986 | 2.1 | 2.8 | 0.8 | 1.1 | 0.8 | 0.0 | 1.1 | 1.2 |
| Methylophilales | |||||||||||
| Methylophilus | Methylotenera mobilis JLW8 | DQ287786 | 0.994 | 0.5 | 0.7 | 1.0 | 0.0 | 0.1 | 0.0 | 0.1 | 0.4 |
| Gammaproteobacteria | |||||||||||
| Pseudomonadales | |||||||||||
| Pseudomonas | Pseudomonas spp. | multiple hits | 0.998 | 68.9 | 57.0 | 10.8 | 7.3 | 35.8 | 44.3 | 56.1 | 64.2 |
| Rhizobacter | Rhizobacter fulvus Gsoil 322 | AB245356 | 0.998 | 0.8 | 1.1 | 0.3 | 0.0 | 0.1 | 0.0 | 0.0 | 0.2 |
| Unclassified | Marinobacter lutaoensis T5054 | AF288157 | 0.940 | 0.5 | 0.9 | 0.0 | 0.0 | 0.5 | 0.0 | 0.1 | 0.5 |
| Deltaproteobacteria | |||||||||||
| Bdellovibrionales | |||||||||||
| Bdellovibrio | Bdellovibrio bacteriovorus HD 100 | AJ292759 | 0.977 | 2.7 | 5.7 | 0.0 | 0.6 | 0.1 | 0.0 | 0.0 | 0.6 |
| Bacteroidetes | |||||||||||
| Flavobacteriales | |||||||||||
| Elizabethkingia | Elizabethkingia miricola GTC862 | AB071953 | 0.984 | 0.0 | 0.0 | 35.8 | 27.4 | 0.0 | 0.0 | 0.0 | 0.0 |
| Sphingobacteriales | |||||||||||
| Pedobacter | Pedobacter koreensis WPCB189 | DQ092871 | 0.986 | 0.0 | 0.0 | 0.5 | 1.1 | 0.0 | 0.0 | 0.0 | 0.0 |
| Actinobacteria | |||||||||||
| Actinomycetales | |||||||||||
| Arthrobacter | Arthrobacter equi IMMIB L-1606 | FN673551 | 0.996 | 0.0 | 0.3 | 0.0 | 0.0 | 0.3 | 0.0 | 1.0 | 2.0 |
Only those taxa are shown whose mean abundance was ≥0.5% in at least two libraries. The gray colors indicate higher relative abundance of a taxon in the library. aPhylogenetic affiliations are based on Ribosomal Database Project (RDP) Classifier. bSimilarity reports the percent sequence identity over all pairwise comparable positions. cThe mean number was calculated from triplicate samples.