Comammox Nitrospira play a minor role in N2O emissions from an alkaline arable soil

Abstract

Nitrogen addition to croplands greatly increases global emissions of the potent greenhouse gas nitrous oxide (N2O). Three ammonia-oxidizing functional guilds constitute the major producers of N2O in agricultural soils, but their relative contributions are still poorly understood, especially the newly discovered and widespread complete ammonia oxidizers (comammox). To fill this knowledge gap, we used three nitrification inhibitors: acetylene, 1-octyne, and 3,4-dimethylpyrazole phosphate (DMPP), to selectively suppress the activity of different ammonia oxidizer guilds to discriminate their relative contributions to N2O production in an alkaline arable soil. The results indicated that DMPP completely inhibited the growth of comammox Nitrospira clade A and ammonia-oxidizing bacteria (AOB) but promoted ammonia-oxidizing archaea (AOA) growth, while the abundance of comammox Nitrospira clade A increased in the presence of 1-octyne at high ammonium (NH4+) concentrations. AOB dominated N2O production in soils with inorganic NH4+ amendment, followed by AOA, while comammox Nitrospira contributed to less than 3% of total N2O emissions with an N2O yield of ∼0.083% (N2O per molecule of nitrate). The abundance of comammox Nitrospira clade A was approximately two orders of magnitude lower than that of canonical ammonia-oxidizers. Phylogenetic analysis revealed that the majority of comammox Nitrospira clade A belonged to a new cluster that was separated from the known comammox bacterium. Taken together, our results clearly and strongly demonstrate that comammox Nitrospira play only a minor role in N2O emissions in a heavily fertilized alkaline arable soil.