Table 6. Microbial diversity and the associated denitrification genes in the biofilm cultures from the de novo assembled transcripts.
| Affiliation | Biofilm cultures (TPM) | Denitrification genes | ||
|---|---|---|---|---|
| Ref300N-23C | 900N-30C | 0%NaCl | ||
| •Actinobacteria | ||||
| Streptomyces | 6,103 | 729 | 2,499 | – |
| •Bacteroidetes | ||||
| Sunxiuqinia | 212 | 504 | 2,639 | norB |
| Geofilum | 77 | 109 | 1,1870 | – |
| Aequorivita | 18,218 | 25,569 | 1,398 | nirK, norB;C;D;Q, nosZ;DFY |
| Winogradskyella | 8182 | 7,917 | 169 | nirK, norC, nosZ;L;D |
| Lentimicrobium | 3032 | 3,370 | 1,671 | – |
| Xanthomarina | 190 | 4,555 | 9,598 | nirK, norB;D;C;Q, nosZ;L;D |
| •Ignavibacteriales | 5,513 | 1,4206 | 171 | napC;H |
| •Tenericutes | 6,367 | 5,003 | 13,409 | – |
| •Alphaproteobacteria | ||||
| Aminobacter | 18 | 438 | 5,385 | napA |
| Aquamicrobium | 23 | 456 | 22,835 | napA |
| Hoeflea | 3,882 | 87 | 1,365 | narG;H;J;I, nosZ;R;D, nirK |
| Hyphomicrobium | 0 | 1,679 | 3,0057 | narH;I, norB;C;Q;D;E, nosZ;D;R;F |
| Mesorhizobium | 411 | 1,050 | 12,505 | napA;D;E, nirK, nosZ |
| Paracoccus | 1,427 | 1,219 | 1,204 | nirS, narC;D;Q, nosR |
| Roseovarius | 1,2367 | 16,479 | 686 | nirS, nirK, norB;C;D;Q;E, nosZ;D;R |
| Stappia | 39,926 | 30,885 | 39,745 | napABC, napADFE-nnrS, nirK, norCBQD, nosRZDF;E |
| Maritimibacter | 6,363 | 8,360 | 10,000 | narI |
| Oceanibaculum | 18,115 | 9,071 | 25,544 | narG;H;J;I |
| •Betaproteobacteria | ||||
| Azoarcus | 48 | 120 | 2,854 | napA, nosZ |
| •Deltaproteobacteria | ||||
| Bradymonas | 73 | 9,652 | 11,178 | – |
| •Gammaproteobacteria | ||||
| Marinicella | 36,554 | 125,466 | 149,24 | nirS, norB;C;Q;D |
| Marinobacter | 14,545 | 1,122 | 264 | narG;H;J;I, norB;C;Q, nirK, nirS, nosZ;F;D;R |
| Methylophaga | 64,802 | 78,566 | 80,482 | narG;H;J;I, norB;C;D;Q;E, nosD;R |
| Idiomarina | 5,147 | 1,027 | 513 | narG;H;J nirK, nirS, norB |
| Pseudomonas | 6,175 | 1,333 | 18,198 | narG;H;J;I, nirK, nirS, norB;C;D;Q, nosZ;R, |
| Wenzhouxiangella | 132 | 2,857 | 83 | – |
| • Other bacteria | 113,200 | 243,523 | 155,554 | a |
| • Archaea | 113 | 297 | 303 | |
| • Eukarya | 181 | 352 | 416 | |
| • Phages, viruses, plasmids | 99,623 | 5,740 | 217,095 | |
| • Unclassified | 281,015 | 207,759 | 157,515 | |
| • Transcripts with no genes | 248,782 | 196,062 | 148,792 | |
Notes.
Reads that did not align to the three reference genomes and plasmids were de novo assembled. These reads were then aligned to these assembled sequences. The relative transcript levels of the assembled sequences in a metatranscriptome were expressed as transcripts per million (TPM). Putative genes from the assembled sequences were annotated for function and affiliation. The TPM of the genes affiliated to specific bacterial taxa were then summed. Denitrification genes identified by annotations from respective affiliated bacterial taxa were sorted out.
a
Denitrification genes were found scattered in other bacterial taxa.