Table 3.
Bacterial populations deriving carbon from naphthalene, either directly or via cross-feeding, as detected at different time points at 10 and 20°C.
| Phylogenetic affiliationsa | Closest RDP SeqMatch type strain | Similarity scoreb | Accession no. of the type strain | 10°C | 20°C | % in TCc | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Day 04 | Day 07 | Day 14 | Day 04 | Day 07 | Day 14 | |||||||||||
| GAMMAPROTEOBACTERIA | ||||||||||||||||
| Pseudomonadaceae | ||||||||||||||||
| Pseudomonas | P. veronii CIP 104663, P. brenneri CFML 97-391, P. gessardii CIP 105469, P. proteolytica CMS 64 | 1.000 | AF064460, AF074384, AJ537603, AF268968 | >99% | >99% | >99% | >99% | 94% | 97% | 94% | 85% | 91% | 83% | 64% | 66% | ND |
| Pseudomonas | P. cichorii LMG 2162 | 1.000 | Z76658 | < 0.5% | < 0.5% | < 0.5% | < 0.5% | < 0.5% | < 0.5% | 6% | 9% | 6% | 7% | 3% | 7% | ND |
| Pseudomonas | P. peli R-20805 | 0.993 | AM114534 | ND | ND | ND | < 0.5% | 2% | 1% | < 0.5% | < 0.5% | < 0.5% | 1% | 2% | 1% | ND |
| Xanthomonadaceae | ||||||||||||||||
| Stenotrophomonas | S. rhizophila e-p10 | 1.000 | AJ293463 | ND | ND | ND | ND | 2% | 1% | < 0.5% | 2% | 1% | 4% | 14% | 13% | ND |
| Pseudoxanthomonas | P. spadix IMMIB AFH-5 | 0.998 | AM418384 | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | < 0.5% | 1% | ND |
| Shewanellaceae | ||||||||||||||||
| Shewanella | Shewanella spp. | 1.000 | Multiple hits | ND | ND | ND | ND | < 0.5% | < 0.5% | ND | < 0.5% | ND | ND | < 0.5% | < 0.5% | ND |
| BETAPROTEOBACTERIA | ||||||||||||||||
| Comamonadaceae | ||||||||||||||||
| Acidovorax | A. defluvii BSB411 | 1.000 | Y18616 | ND | ND | ND | ND | < 0.5% | < 0.5% | < 0.5% | 1% | 1% | 2% | 6% | 4% | ND |
| Comamonas | C. testosteroni ATCC 11996 | 0.998 | M11224 | ND | ND | ND | ND | < 0.5% | < 0.5% | < 0.5% | 1% | < 0.5% | 1% | 5% | 3% | ND |
| Hydrogenophaga | H. atypica BSB 41.8, H. defluvii BSB 9.5 | 0.991 | AJ585992.3 | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | < 0.5% | < 0.5% | 0.05% |
| Rhodocyclaceae | ||||||||||||||||
| Georgfuchsia | Sulfuritalea hydrogenivorans DSM 22779 | 0.967 | AB552842 | ND | ND | ND | ND | ND | ND | ND | ND | < 0.5% | 1% | 2% | < 0.5% | 0.05% |
| Hydrogenophilaceae | ||||||||||||||||
| Thiobacillus | T. thioparus ATCC 8158 | 0.993 | M79426 | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | 1% | 1% | 0.2% |
| Alcaligenaceae | ||||||||||||||||
| Bordetella | B. trematum DSM 11334 | 0.998 | AJ277798 | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | < 0.5% | < 0.5% | ND |
| ALPHAPROTEOBACTERIA | ||||||||||||||||
| Caulobacteraceae | ||||||||||||||||
| Brevundimonas | B. bullata IAM 13153 | 1.000 | D12785 | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND | < 0.5% | < 0.5% | ND |
The values shown are relative abundances of reads per library.
ND, not detected.
a
Phylogenetic affiliations are based on Ribosomal Database Project (RDP) Classifier.
b
Similarity reports the percent sequence identity over all pairwise comparable positions.
c
Percent of reads in initial total community DNA.