Comammox Nitrospira play an active role in nitrification of agricultural soils amended with nitrogen fertilizers

The recent discovery of complete ammonia oxidizers (comatrunox Nitrospira) challenged the paradigm of the two-step nitrification mediated by two distinct groups of nitrifiers, and raised fundamental questions regarding their niche specialization and relative contribution to nitrification in agricultural soils. Previous studies suggest that comammox Nitrospira have an oligotrophic lifestyle and would outcompete canonical ammonia oxidizers (ammonia-oxidizing bacteria and ammonia-oxidizing archaea) under ammonia-limited conditions. Here, we demonstrated that comammox Nitrospira Glade A were significantly more abundant than canonical ammonia oxidizers and (CO2)-C-13-DNA-stable isotope probing revealed that comammox Nitrospira Glade A incorporated (CO2)-C-13 into their genomes in fertilized agricultural soils during the microcosm incubation. Phylogenetic analysis of the amoA gene revealed that (CO2)-C-13-labelled comammox Nitrospira Glade A belonged to the Nitrospira inopinata-related cluster and a new cluster that was distinct from the known comammox isolates. These results demonstrated the potential important role of comammox Nitrospira in autotrophic ammonia oxidation in agricultural soils amended with nitrogen fertilizers and their lifestyle may be not strictly restricted to oligotrophic habitats. There is a potential contribution of comammox Nitrospira to soil nitrification, which calls re-evaluation of the microbial nitrogen cycling processes and the subsequent impacts on agriculture and the environment.