Deciphering the functional importance of comammox vs. canonical ammonia oxidisers in nitrification and N2O emissions in acidic agricultural soils

The discovery of comammox Nitrospira has altered our perception of the nitrogen biogeochemical cycle. However, their functional importance compared to canonical ammonia oxidisers (i.e., ammonia-oxidising bacteria (AOB) and archaea (AOA)) in agricultural soils remains elusive, especially in acidic soils. Here, we assessed the functional importance of these functional guilds in nitrification and nitrous oxide (N2O) emissions in three acidic agricultural soils by using a range of nitrification inhibitors (acetylene, 3,4-dimethylpyrazole phosphate (DMPP) and different concentrations of 1-octyne) and monitored their community assemblage and population dynamics. The sensitivity of comammox Nitrospira clade A to 1-octyne varied across soils, highlighting that the inappropriate use of 1-octyne can lead to misestimation of comammox activity. AOA were key NH3 oxidisers in the three soils, while AOB also contributed significantly to nitrification in one soil. In contrast, comammox Nitrospira always played a minor role in ammonia oxidation and N2O emissions, likely due to their low abundances, restricted cellular kinetic properties and N2O production mechanisms. Together, this study demonstrates that comammox Nitrospira play a less important role in ammonia oxidation and N2O production in acidic agricultural soils than AOA and AOB, thereby providing important novel insights into the mitigation of nitrogen fertiliser loss and N2O emissions.