Table 2. Summary data of genomic bins on the final Illumina Velvet–Columbus assembly.
| Bin | Longest PE-scaffold (kb) | PE-scaffold (#) | ARC a (s.d.) | ORFs (#) | Proteins (#) | Related organisms | AAIO b (s.d.) | 16S ID c |
|---|---|---|---|---|---|---|---|---|
| Deltaproteobacteria | ||||||||
| r9c1 | 250 | 161 | 258 (80) | 5421 | 1282 | Desulfobacter postgatei | 96 (7) F | 99* |
| Desulfobacterium autotrophicum | 60 (14) D | 89† | ||||||
| r9c7 | 60 | 294 | 17 (11) | 1390 | 23 | Geobacter bemidjiensis | 66 (18) F | 98*1 |
| Desulfuromonas michiganensis | – | 97*2 | ||||||
| Desulfuromonas acetoxidans | 59 (17) D | – | ||||||
| r9c8 | 20 | 11 | 11 (4) | 41 | 0 | Desulfomicrobium baculatum | 88 (20) F | 99* |
| Epsilonproteobacteria | ||||||||
| r9c2 | 1 910 | 2 | 109 (3) | 1998 | 67 | Sulfurovum sp. NBC37-1 | 71 (14) F | 95* |
| r9c3 | 690 | 138 | 58 (15) | 5678 | 160 | Sulfurimonas denitrificans Sulfurimonas autotrophica | 79 (13) F 69 (15) F | 96* 94† |
| Bacteroidetes d | ||||||||
| r9c4 | 530 | 498 | 27 (15) | 3936 | 52 | Cytophaga hutchinsonii | 50 (12) F | 83† |
| r9c5 | 370 | 840 | 26 (16) | 7321 | 78 | Cytophaga hutchinsonii | 50 (12) F | 83† |
| Wandonia haliotis | – | 88*1 | ||||||
| Cytophaga fermentans | – | 90*2 | ||||||
| Firmicutes | ||||||||
| r9c6 | 60 | 395 | 8 (2) | 1873 | 2 | Clostridium cellulovorans Desulfosporosinus orientis | 76 (25) F 52 (13) F | – – |
| Other | ||||||||
| r9c9-r9c12 | 20–40 | 2–162 | 17 (11) | 17–512 | 0–6 | – | – | – |
Abbreviations: ARC, average read coverage; AAIO, average amino acid identity of orthologs; D, draft reference genome; F, fully-curated reference genome; 16S ID, percent identity between 16S rRNA genes; ORFs, predicted genes; #, number.
ARC was calculated from k-mer coverage.
Using less strict criteria for determining orthologs (i.e., without a bit-score cutoff of ⩾60) made ⩽2% difference to calculated AAIs for most of the genome bins (r9c1–r9c5), but decreased AAIs by 3–6% for r9c6 and r9c8, and by 14% for r9c7.
Percent identity match between EMIRGE-reconstructed and GenBank 16S rRNA sequences.
The determined AAI of orthologs between r9c4 and r9c5 is 53%.
* denotes the nearest isolate sequence—*1 and *2 indicate where two reconstructed 16S rRNA gene sequences correlate to a single bin (r9c7), or cannot be assigned to one of the two bins (r9c4 and r9c5). † denotes matches to other organisms for comparison.