Table 2.
Environmental samples analyzed in this study, PCR amplification cycles, and numbers of cloned comammox amoA sequences and OTUs retrieved from each sample.
| Sample name | ID | Habitat type | Gene amplified | Amplification cycles | Nclones | NOTUs |
|---|---|---|---|---|---|---|
| Wolfenbüttel | WB | Engineered (GWW) | Clade A amoA | 25 | 24 | 5 |
| Clade B amoA | 25 | 28c | 3 | |||
| Friedrichshof | FH | Engineered (DWTP) | Clade A amoA | 25 | 23 | 4 |
| Clade B amoA | 25 | 22d | 3 | |||
| Spiekeroog | SP | Engineered (DWTP) | Clade A amoA | 25 | 22 | 1 |
| Clade B amoA | 25 | 23 | 2 | |||
| Breeheia | BH | Engineered (DWTP) | Clade A amoA | 30 | 10 | 3 |
| Clade B amoA | 30 | 10 | 3 | |||
| Lieshout | LS | Engineered (WWTP) | Clade A amoA | 30 | 8 | 2 |
| VetMed | VM | Engineered (WWTP) | Clade A amoA | 30 | 20c | 4 |
| Ingolstadt | IS | Engineered (WWTP) | Clade A amoA | 30 | 5 | 1 |
| Recirculating aquaculture systema | RAS | Engineered | Clade A amoA | 30 | 7 | 4 |
| Clade B amoA | 30 | 8 | 3 | |||
| Vercelli rice soilb | VS | Rice paddy soil | Clade A amoA | 35 | 26 | 7 |
| Clade B amoA | 35 | 41 | 5 | |||
| Vercelli rice rhizosphere | VR | Rhizosphere | Clade A amoA | 35 | 31 | 8 |
| Clade B amoA | 35 | 29 | 6 | |||
| Klausen-Leopoldsdorf | KLD | Forest soil | Clade B amoA | 35 | 60 | 8 |
| Herrenseea | HS | Brackish lake sediment | Clade A amoA | 30 | 10 | 3 |
| River Schwarza enrichment (inoculated with river biofilm and fed with ammonium) | RS | Freshwater biofilm | Clade A amoA | 35 | 37 | 2 |
a
Unspecific PCR products were obtained with the degenerate comammox amoA clade A targeted primers.
b
Unspecific PCR products were obtained with the degenerate comammox amoA clade B targeted primers.
c
One of the obtained sequences was classified as pmoA gene by phylogenetic analysis.
d
One of the obtained sequences was classified as comammox amoA clade A gene by phylogenetic analysis.