Table 1 Modularity of denitrification and DNRA observed in the 249 NirK containing genomes covering fifteen different phyla. Percentage complete denitrification (Nir + Nor + Nos), incomplete denitrification (-Nor, −Nos or -Nor/-Nos), DNRA (Nar + NrfA, Nap + NrfA, NrfA, Nar + NirB, Nap + NirB or only NirB), and combined occurrence of both processes (NirK + NrfA and/or NirB) are represented for each phylum separately and over all 249 NirK genomes
From: Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers
| Â | No.of genomes | No. of nirK copies per genome | % complete denitrification | % incomplete denitrification | % DNRA | % denitrification and DNRA | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|  |  | (% of phylum) | nir + nor + nos | -nor | -nos | -nor/-nos | nap + nrfA | nar + nrfA | nrfA | nap + nirB | nar + nirB | nirB | nirK + nrfAand/or nirB |
Acidobacteria | 1 | 1 (100) | 100 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Actinobacteria | 28 | 1 (100) | 0 | 0 | 50 | 50 | 3.6 | 7.1 | 17.9 | 3.6 | 39.3 | 0 | 64.3 |
Alphaproteobacteria | 82 | 1 (92.7); 2 (6.1) or 3 (1.2) | 41.5 | 1.2 | 39.0 | 18.3 | 15.7 | 0 | 0 | 65.9 | 11 | 6.1 | 78.0 |
Bacteroidetes | 21 | 1 (100) | 42.9 | 19.0 | 28.6 | 9.5 | 9.5 | 0 | 42.9 | 9.5 | 0 | 9.5 | 66.7 |
Betaproteobacteria | 39 | 1 (92.3) or 2 (7.7) | 61.5 | 0 | 30.8 | 7.7 | 2.6 | 2.6 | 0 | 61.5 | 61.5 | 5.1 | 74.4 |
Verrucomicrobia | 2 | 1 (100) | 0 | 50 | 0 | 50 | 100 | 0 | 0 | 50 | 0 | 0 | 100 |
Chloroflexi | 5 | 1 (100) | 0 | 20 | 0 | 80 | 0 | 0 | 0 | 0 | 0 | 40 | 40 |
Deltaproteobacteria | 2 | 1 (100) | 0 | 0 | 50 | 50 | 0 | 0 | 50 | 0 | 0 | 50 | 50 |
Euryarcheaota | 13 | 1 (84.6) or 2 (15.4) | 46.2 | 0 | 38.5 | 15.3 | 0 | 0 | 0 | 0 | 0 | 7.7 | 7.7 |
Firmicutes | 27 | 1 (96.3) or 2 (3.7) | 40.8 | 7.4 | 25.9 | 25.9 | 11.1 | 11.1 | 0 | 37 | 37 | 3.7 | 55.6 |
Gammaproteobacteria | 23 | 1 (100) | 19.0 | 0 | 33.3 | 47.7 | 30.4 | 4.3 | 0 | 47.8 | 17.4 | 0 | 73.9 |
Gemmatimonadetes | 1 | 1 (100) | 0 | 100 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Nitrospirae | 2 | 1 (50) or 2 (50) | 0 | 0 | 50 | 50 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Planctomycetes | 1 | 1 (100) | 0 | 0 | 0 | 100 | 100 | 100 | 0 | 100 | 100 | 0 | 100 |
Spirochaetae | 2 | 1 (100) | 50.0 | 0 | 0 | 50.0 | 0 | 0 | 0 | 50 | 0 | 50 | 100 |
Total | 249 | 5.3 | 36.0 | 4.0 | 34.8 | 25.2 | 12.1 | 3.2 | 6.1 | 42.2 | 23.7 | 6.0 | 66.7 |