Table 1.
Sequencing, assembly, metagenome and pyrotag statistics.
| Unamended | +O2-NO3- | +O2+NO3- | -O2-NO3- | -O2+NO3- | |
|---|---|---|---|---|---|
| Number of raw metagenome reads (median read length) | 1,644,561 (415) | 1,601,297 (469) | 342,227 (435) | 206,554 (332) | 1,446,627 (457) |
| Size (base pairs) | 559,537,102 | 308,706,277 | 80,246,742 | 59,711,589 | 354,011,745 |
| DNA scaffolds | 1,515,849 | 835,955 | 193,120 | 194,103 | 925,371 |
| Number of contigs in the assembly | 9,658 | 19,257 | 8,470 | 573 | 4,087 |
| Number of bp in assembled contigs | 7,058,808 | 12,145,462 | 7,540,157 | 326,365 | 2,187,627 |
| N50 contig length, bp | 985 | 803 | 1,459 | 935 | 802 |
| Mean coverage of assembled contigs | 3.9 | 3.4 | 5.7 | 5.1 | 3.8 |
| Genes | 1,554,721 | 821,124 | 216,380 | 160,657 | 948,029 |
| Proteins | 1,547,567 | 817,673 | 215,668 | 159,899 | 943,870 |
| RNA genes | 7,154 | 3,451 | 712 | 758 | 4,159 |
| 16S rRNA genes | 488 | 211 | 22 | 59 | 273 |
| 16S rRNA genes curated (methylotroph genes) | 458 (19) | 186 (49) | 22 (7) | 50 (2) | 261 (11) |
| Raw pyrotag sequences (median read length) | 21,348 (471) | 6,457 (403) | 27,720 (479) | 16,364 (367) | 27,714 (475) |
| Pyrotag gene clusters | 1,486 | 313 | 709 | 561 | 1,386 |
| Pyrotag diversity index (Shannon–Weaver) | 4.10 | 3.84 | 2.40 | 3.94 | 4.01 |
| COG clusters | 4,494 | 4,246 | 3,639 | 3,652 | 4,313 |
| Pfam clusters | 5,788 | 5,199 | 3,822 | 3,861 | 5,157 |
| pmoB genes | 31 | 106 | 30 | 0 | 9 |
| fae genes | 62 | 157 | 38 | 3 | 13 |
| Nitrate reductase genes | 902 | 634 | 224 | 44 | 523 |