TABLE 3.
Illumina sequencing results and observed numbers of OTUs based on reads that were affiliated with pahAc or pahE of PAH-degrading bacteria
| Primer/primer set | Sample typea | No. of high-quality reads | No. of PAH-degrading bacterial pahAc or pahE reads (over 50% identity) | Good’s coverageb | No. of observed OTUs (90% identity) |
|---|---|---|---|---|---|
| pahAc | ODS | 75,979 | 75,363 | 0.999 | 19 |
| ASE | 172,319 | 167,140 | 0.999 | 6 | |
| BAS | 60,251 | 1,194 | 1 | 11 | |
| pahE1F/pahE1R | ODS | 330,283 | 329,093 | 0.999 | 11 |
| ASE | 463,897 | 416,736 | 0.999 | 10 | |
| BAS | 12,502 | 560 | 0.999 | 7 | |
| pahE2F/pahE2R | ODS | 2,163 | 1,957 | 0.999 | 14 |
| pahE3F/pahE3R | ODS | 62,147 | 35,071 | 0.999 | 13 |
| ASE | 60,771 | 6 | 0.999 | 2 | |
| BAS | 132,388 | 77 | 0.999 | 6 |
a
ODS, contaminated-oilfield soil; ASE, phenanthrene and pyrene enrichment culture; BAS, activated sludge of Bei Xiaohe urban sewage treatment plant.
b
Calculated from the number of OTUs (at 90% identity level) represented by only one quality-controlled Illumina read (N1) and the total number of quality-controlled Illumina reads (N) as 1 – (N1/N).