Nitrification gene ratio and free ammonia explain nitrite and nitrous oxide production in urea-amended soils

Abstract The atmospheric concentration of nitrous oxide (N 2 O), a potent greenhouse gas and ozone-depleting chemical, continues to increase, due largely to the application of nitrogen (N) fertilizers. While nitrite (NO 2 − ) is a central regulator of N 2 O production in soil, NO 2 − and N 2 O responses to fertilizer addition rates cannot be readily predicted. Our objective was to determine if quantification of multiple chemical variables and structural genes associated with ammonia (NH 3 )- (AOB, encoded by amo A) and NO 2 − -oxidizing bacteria (NOB, encoded by nxr A and nxr B) could explain the contrasting responses of eight agricultural soils to five rates of urea addition in aerobic microcosms. Significant differences in NO 2 − accumulation and N 2 O production by soil type could not be explained by initial soil properties. Biologically-coherent statistical models, however, accounted for 70–89% of the total variance in NO 2 − and N 2 O. Free NH 3 concentration accounted for 50–85% of the variance in NO 2 − which, in turn, explained 62–82% of the variance in N 2 O. By itself, the time-integrated nxr A: amo A gene ratio explained 78 and 79% of the variance in cumulative NO 2 − and N 2 O, respectively. In all soils, nxr A abundances declined above critical urea addition rates, indicating a consistent pattern of suppression of Nitrobacter -associated NOB due to NH 3 toxicity. In contrast, Nitrospira -associated nxr B abundances exhibited a broader range of responses, and showed that long-term management practices (e.g., tillage) can induce a shift in dominant NOB populations which subsequently impacts NO 2 − accumulation and N 2 O production. These results highlight the challenges of predicting NO 2 − and N 2 O responses based solely on static soil properties, and suggest that models that account for dynamic processes following N addition are ultimately needed. The relationships found here provide a basis for incorporating the relevant biological and chemical processes into N cycling and N 2 O emissions models.