Research Article
Diverse Reductive Dehalogenases Are Associated with Clostridiales-Enriched Microcosms Dechlorinating 1,2-Dichloroethane
Table 1
Summary of the OTU representatives, identified in the 16S rRNA gene libraries.
| OTU | Clones | Basic Local Alignment Search Tool-GenBank | CLASSIFIER Match Tool-Ribosomal Database Project II | | | Closest described relative | Acc. | % identity | Phylogenetic group | Closest classified relative | % certaintyA |
| 1 | 3 | 0 | Geobacter thiogenes | NR_028775 | 98.96 | Deltaproteobacteria | Geobacter | 100 | 2 | 3 | 0 | Geobacter thiogenes | NR_028775 | 98.78 | Deltaproteobacteria | Geobacter | 100 | 3 | 8 | 0 | Geobacter thiogenes | NR_028775 | 99.09 | Deltaproteobacteria | Geobacter | 100 | 4 | 3 | 0 |
Unc. bacterium | AM410013 | 97.34 | Deltaproteobacteria | Geobacter | 100 | 5 | 1 | 0 | Unc. Geobacter sp. | FM204959 | 98.63 | Deltaproteobacteria | Geobacter | 100 | 6 | 1 | 0 | Unc. Geobacter sp. | EU266833 | 98.62 | Deltaproteobacteria | Geobacter | 100 | 7 | 3 | 0 | Unc. Geobacter sp. | AY752765 | 98.56 | Deltaproteobacteria | Geobacter | 100 | 8 | 1 | 0 | Unc. Geobacter sp. | AY752765 | 98.42 | Deltaproteobacteria | Geobacter | 100 | 9 | 1 | 0 | Unc. Dehalobacter sp. | HM748813 | 99.43 | Clostridia | Acetobacterium | 100 | 10 | 4 | 0 | Unc. Sulfurimonas sp. | KF851122 | 98.34 | Epsilonproteobacteria | Sulfuricurvum | 100 | 11 | 4 | 0 | Ferribacterium sp. 7A-631 | KF441656 | 99.75 | Betaproteobacteria | Ferribacterium | 93 | 12 | 1 | 0 | Unc. Gallionellaceae bacterium | EU266776 | 96.48 | Proteobacteria | Betaproteobacteria | 100 | 13 | 1 | 0 | Unc. Rhodocyclaceae bacterium | JQ279024 | 98.83 | Betaproteobacteria | Rhodocyclaceae | 98 | 14 | 1 | 0 | Unc. Rhodocyclaceae bacterium | HQ003471 | 97.64 | Betaproteobacteria | Rhodocyclaceae | 100 | 15 | 0 | 1 | Acinetobacter baumannii | KJ958271 | 99.60 | Gammaproteobacteria | Acinetobacter | 100 | 16 | 0 | 1 | Pseudomonas putida | GU396283 | 98.97 | Gammaproteobacteria | Pseudomonas | 100 | 17 | 0 | 7 | Unc. Bacteroides sp. | AB529592 | 99.44 | Bacteroidia | Parabacteroides | 99 | 18 | 0 | 1 | Unc. Bacteroidetes bacterium | FJ535139 | 98.31 | Bacteroidia | Parabacteroides | 100 | 19 | 0 | 1 | Unc. Bacteroides sp. | JQ624314 | 99.75 | Bacteroidia | Parabacteroides | 100 | 20 | 0 | 1 | Unc. Bacteroidetes bacterium | DQ676360 | 98.97 | Bacteroidia | Porphyromonadaceae | 99 | 21 | 0 | 1 | Unc. Bacteroides sp. | FM204969 | 99.88 | Bacteroidia | Parabacteroides | 99 | 22 | 0 | 1 | Unc. Acidaminobacter sp. | HM217344 | 98.61 | Clostridia | Clostridiales Incertae Sedis XII | 91 | 23 | 0 | 6 | Unc. Acidaminobacter sp. | HM217344 | 98.78 | Clostridia | Clostridiales | 100 | 24 | 0 | 5 | Unc. Acidaminobacter sp. | HM217344 | 99.46 | Clostridia | Clostridiales Incertae Sedis XII | 80 | 25 | 2 | 0 | Unc. Hydrogenophaga sp. | HM124825 | 99.67 | Betaproteobacteria | Hydrogenophaga | 100 | 26 | 3 | 0 | Hydrogenophaga taeniospiralis | AY771764 | 98.02 | Betaproteobacteria | Hydrogenophaga | 100 | 27 | 0 | 7 | Malikia spinosa | NR_040904 | 99.86 | Betaproteobacteria | Malikia | 100 | 28 | 1 | 0 | Unc. Hydrogenophaga sp. | DQ413154 | 98.70 | Betaproteobacteria | Hydrogenophaga | 100 | 29 | 1 | 0 | Unc. Elusimicrobia bacterium | GU236016 | 94.55 | Elusimicrobia | Elusimicrobium | 98 | 30 | 0 | 2 | Hydrogenophaga taeniospiralis | AY771764 | 98.75 | Betaproteobacteria | Hydrogenophaga | 95 | 31 | 8 | 0 | Hydrogenophaga taeniospiralis | AY771764 | 99.06 | Betaproteobacteria | Hydrogenophaga | 98 | 32 | 0 | 6 | Malikia spinosa | NR_040904 | 99.73 | Betaproteobacteria | Malikia | 88 | 33 | 1 | 0 | Unc. Acidovorax sp. | AM084039 | 99.04 | Betaproteobacteria | Comamonadaceae | 100 | 34 | 3 | 1 | Unc. Dechloromonas sp. | JN679130 | 98.95 | Betaproteobacteria | Rhodocyclaceae | 100 | 35 | 1 | 0 | Unc. Gallionella sp. | FJ391502 | 98.72 | Proteobacteria | Betaproteobacteria | 100 | 36 | 0 | 2 | Vogesella indigofera | NR_040800 | 99.60 | Betaproteobacteria | Vogesella | 100 | 37 | 0 | 1 | Shewanella putrefaciens | JN019028 | 99.87 | Gammaproteobacteria | Shewanella | 100 | 38 | 9 | 0 | Sulfuricurvum kujiense | CP002355 | 99.22 | Epsilonproteobacteria | Sulfuricurvum | 100 | 39 | 1 | 0 | Unc. Arcobacter sp. | JQ861849 | 97.96 | Epsilonproteobacteria | Arcobacter | 93 | 40 | 2 | 0 | Geobacter metallireducens | NR_075011 | 98.31 | Deltaproteobacteria | Geobacter | 100 | 41 | 3 | 0 | Unc. Geobacter sp. | EU266817 | 99.76 | Deltaproteobacteria | Geobacter | 100 | 42 | 2 | 0 | Unc. Geobacter sp. | EU266841 | 99.16 | Deltaproteobacteria | Geobacter | 100 | 43 | 5 | 0 | Geobacter lovleyi | NR_074979 | 99.03 | Deltaproteobacteria | Geobacter | 100 | 44 | 1 | 0 | Geobacter thiogenes | NR_028775 | 97.48 | Deltaproteobacteria | Geobacter | 100 | 45 | 1 | 1 | Unc. Firmicutes bacterium | HQ003641 | 98.70 | Clostridia | Clostridiales Incertae Sedis XII | 100 | 46 | 0 | 20 | Unc. Firmicutes bacterium | HQ003641 | 99.45 | Clostridia | Acidaminobacter | 86 | 47 | 0 | 1 | Unc. Clostridium sp. | FM204998 | 100.0 | Clostridia | Clostridium XlVa | 100 | 48 | 0 | 3 | Acetobacterium malicum | NR_026326 | 99.53 | Clostridia | Acetobacterium | 100 | 49 | 1 | 0 | Unc. bacterium | AB759668 | 95.24 | Bacteria | Firmicutes | 100 | 50 | 2 | 0 | Unc. rumen bacterium | AB615047 | 94.24 | Lentisphaerae | Victivallis | 97 | 51 | 2 | 0 | Unc. Cytophaga sp. | EU809766 | 99.35 | Lentisphaerae | Victivallis | 97 | 52 | 1 | 0 | Denitrifying bacterium | FJ802233 | 98.54 |
Ignavibacteria | Ignavibacterium | 91 | 53 | 0 | 8 | Unc. Bacteroides sp. | FJ862827 | 99.18 | Bacteroidia | Parabacteroides | 100 | 54 | 0 | 3 | Macellibacteroides fermentans | NR_117913 | 99.08 | Bacteroidia | Parabacteroides | 99 | 55 | 0 | 1 | Unc. Bacteroidetes bacterium | FJ535139 | 94.64 | Bacteroidia | Porphyromonadaceae | 88 | 56 | 0 | 1 | Unc. Bacteroidetes bacterium | DQ676360 | 99.30 | Bacteroidia | Bacteroidales | 99 | 57 | 1 | 0 | Unc. Prolixibacter sp. | JQ723616 | 97.85 | Bacteria | Bacteroidetes | 100 | 58 | 1 | 0 | Unc. Geobacter sp. | JQ086897 | 98.72 | Deltaproteobacteria | Geobacter | 100 | 59 | 1 | 0 | Geobacter lovleyi | NR_074979 | 99.37 | Deltaproteobacteria | Geobacter | 100 | 60 | 1 | 0 | Sulfuricurvum kujiense | NR_074398 | 99.29 | Epsilonproteobacteria | Sulfuricurvum | 100 |
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Confidence threshold of the RDPII CLASSIFIER Tool is 80%.
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