Table 1.
Phylogenetic profiling of OR-IFRC metagenomes with select organisms involved in geochemical cycling.
| Organisms | Pristine (FW301) | Contaminated (FW106) | ||||
|---|---|---|---|---|---|---|
| PhyProa | 16Sb | PhyProa | 16Sb | |||
| Count | %c | Count | %c | |||
| Acetogenesis | ||||||
| Clostridium carboxidivorans | 82/47/1 | – | – | 1/0/0 | – | – |
| Clostridium ljungdahlii | 70/32/0 | – | – | 17/0/0 | – | – |
| Bacterial methane oxidation | ||||||
| Methylococcus capsulatus | 260/375/22 | 76 | 1.05 | 154/173/6 | 4 | 0.04 |
| Methylomonas | –/–/– | 1 | 0.01 | –/–/– | 0 | 0 |
| Methylosinus trichosporium | –/–/– | 1 | 0.01 | –/–/– | 0 | 0 |
| Methylosphaera | –/–/– | 2 | 0.03 | –/–/– | 0 | 0 |
| Methylobacter tundripaludum | 439/474/25 | 1 | 0.01 | 189/205/6 | 0 | 0 |
| Archaeal methane | ||||||
| Oxidation/Methanogenesis | ||||||
| Methanosarcina barkeri | 196/94/0 | 0 | 0 | 3/2/0 | 0 | 0 |
| Methanohalobium evestigatum | 93/42/3 | 6 | 0.08 | 1/0/0 | 0 | 0 |
| Denitrification | ||||||
| Rhodanobacter spd | –/–/–d | 13 | 0.18 | –/–/–d | 9041 | 85.33 |
| Paracoccus denitrifwans | 117/130/11 | 0 | 0 | 17/43/1 | 0 | 0 |
| Pseudomonas stutzeri | 167/302/46 | 795 | L1.02 | 147/201/2 | 6 | 0.06 |
| Pseudomonas fluorescens | 995/7042/10181 | 337/440/17 | ||||
| Pseudomonas syringae | 552/1115/569 | 269/244/14 | ||||
| Nitrification | ||||||
| Chromobacterium violaceum | 1016/5507/1555 | 2 | 0.01 | 127/95/4 | 0 | 0 |
| Methylococcus capsulatus | 260/357/22 | 76 | 1.05 | 154/173/6 | 3 | 0.04 |
| Nitrococcus oceani | 209/252/18 | 1 | 0.01 | 134/131/3 | 0 | 0 |
| Nitrosomonas eutropha | 115/185/11 | 0 | 0 | 104/170/6 | 0 | 0 |
| Nitrospira multiformis | 355/596/25 | 13 | 0.37 | 205/176/4 | 1 | 0.01 |
| Paracoccus denitrifwans | 117/130/11 | 0 | 0 | 17/43/1 | 0 | 0 |
| Nitrobacter winogradskyi | 104/239/41 | 5 | 0.07 | 15/11/0 | 0 | 0 |
| Anammox | ||||||
| Candidatus Kuenenia stuttgartiensis | 939/599/10 | 0 | 0 | 27/22/0 | 0 | 0 |
| Nitrogen fixation | ||||||
| Anabaena variabilis | 171/102/1 | 0 | 0 | 8/1/0 | 0 | 0 |
| Azotobacter vinelandii | 243/275/46 | 0 | 0 | 176/217/3 | 0 | 0 |
| Rhodobacter capsulatus | 51/44/6 | 1 | 0.01 | 2/7/0 | 0 | 0 |
| Bradyrhizobium japonicum | 764/1443/249 | 9 | 0.11 | 55/62/12 | 2 | 0.02 |
| Afipia sp. | 142/387/46 | 1 | 0.01 | 68/92/24 | 0 | 0 |
| Rhizobium etli | 304/402/29 | 3 | 0.04 | 43/51/0 | 2 | 0.02 |
| Sinorhizobium sp. | 219/273/10 | 0 | 0 | 56/19/0 | 0 | 0 |
| Iron reduction | ||||||
| Shewanella oneidensis | 51/43/8 | 3 | 0.04 | 21/14/1 | 0 | 0 |
| Geobacter sulfurreducens | 543/506/46 | 36 | 0.28 | 31/15/0 | 0 | 0 |
| Iron oxidation | ||||||
| Acidithiobacillus ferrooxidans | 166/197/3 | 0 | 0 | 143/194/2 | 0 | 0 |
| Sulfate reduction | ||||||
| Desulfovibrio vulgaris | 261/207/3 | 0 | 0 | 8/27/0 | 0 | 0 |
| Archaeoglobus fulgidus | 109/70/0 | 0 | 0 | 13/0/0 | 0 | 0 |
| Desulfotomaculum reducens | 198/137/2 | 0 | 0 | 10/1/0 | 0 | 0 |
| Desulfosporosinus sp. | –/–/– | 2 | 0.03 | –/–/– | 0 | 0 |
| Oxidation of sulfur compounds | ||||||
| Rhodanobacter sp. | –/–/– | 13 | 0.18 | –/–/– | 9041 | 85.33 |
| Acidithiobacillus ferrooxidans | 166/197/3 | 0 | 0 | 143/194/2 | 0 | 0 |
| Thiobacillus denitrifwans | 280/527/48 | 1 | 0.01 | 155/160/12 | 0 | 0 |
| Chlorobium limicola | 82/76/5 | 0 | 0 | 6/13/0 | 0 | 0 |
| Allochromatium vinosum | 231/255/9 | 0 | 0 | 213/236/10 | 0 | 0 |
| Beggiatoa sp. | 380/285/6 | 8 | 0.11 | 96/52/1 | 0 | 0 |
| Thiothrix nivea | 193/151/3 | – | – | 193/151/3 | – | – |
| Polyphosphate accumulation | ||||||
| Rhodanobacter sp. | –/–/– | 13 | 0.18 | –/–/– | 9041 | 85.33 |
| Candidates Accumulibacter phosphatis | 872/1898/133 | 0 | 0 | 193/255/13 | 0 | 0 |
| Dissimilatory metal reduction | ||||||
| Cupriavidus metallidurans | 452/1577/710 | 69 | 0.96 | 140/304/58 | 0 | 0 |
| Ralstonia eutropha | 450/2568/3656 | 3 | 0.04 | 138/236/9 | 0 | 0 |
| Ralstonia pickettii | 389/785/149 | 3 | 0.04 | 215/272/25 | 0 | 0 |
| Ralstonia solanacearum | 516/1249/303 | 3 | 0.04 | 209/314/22 | 0 | 0 |
| Anaeromyxobacter dehalogenans | 623/603/19 | 54 | 0.75 | 58/35/0 | 0 | 0 |
| Desulfovibrio vulgaris | 261/207/3 | 0 | 0 | 8/27/0 | 0 | 0 |
| Desulfotomaculum reducens | 198/137/2 | 0 | 0 | 10/1/0 | 0 | 0 |
| Shewanella oneidensis | 51/43/8 | 3 | 0.04 | 21/14/1 | 0 | 0 |
| Geobacter sulfurreducens | 543/506/46 | 36 | 0.28 | 31/15/0 | 0 | 0 |
aNumbers derived from IMG Phylogenetic Profiling (successive 30/60/90% BlastP identity cutoff).
b16S gene amplicons sequenced by Illumina MiSeq as described in section “Materials and Methods” (genus level information only). 16S amplicons are only classified to the genus level and may not accurately reflect strain diversity in the sample. Values are not included for Clostridium species due to the taxonomic diversity and poor classification of Clostridium species.
cAbundance of amplicons is expressed as a percentage of reads assigned to a particular genus compared to all OTU’s for the particular sample (7216 for FW301, 10571 for FW106).
dWhen the IMG phylogenetic profile was constructed for these metagenomes, Rhodanobacter genomic sequences were not present in the database and thus no Rhodanobacter denitrification genes were identified despite the fact that these genes are known to be present in the metagenomes.