Full substitution of chemical fertilizer by organic manure decreases soil N2O emissions driven by ammonia oxidizers and gross nitrogen transformations

Abstract Replacing synthetic fertilizer by organic manure has been shown to reduce emissions of nitrous oxide (N2O), but the specific roles of ammonia oxidizing microorganisms and gross nitrogen (N) transformation in regulating N2O remain unclear. Here, we examined the effect of completely replacing chemical fertilizer with organic manure on N2O emissions, ammonia oxidizers, gross N transformation rates using a 13‐year field manipulation experiment. Our results showed that organic manure reduced cumulative N2O emissions by 16.3%–210.3% compared to chemical fertilizer. The abundance of ammonia oxidizing bacteria (AOB) was significantly lower in organic manure compared with chemical fertilizer during three growth stages of maize. Organic manure also significantly decreased AOB alpha diversity and changed their community structure. However, organic manure substitution increased the abundance of ammonia oxidizing archaea and the alpha diversity of comammox Nitrospira compared to chemical fertilizer. Interestingly, organic manure decreased organic N mineralization by 23.2%–32.9%, and autotrophic nitrification rate by 10.5%–45.4%, when compared with chemical fertilizer. This study also found a positive correlation between AOB abundance, organic N mineralization and gross autotrophic nitrification rate with N2O emission, and their contribution to N2O emission was supported by random forest analysis. Our study highlights the key roles of ammonia oxidizers and N transformation rates in predicting cropland N2O.