Relative abundance of denitrifying and DNRA bacteria and their activity determine nitrogen retention or loss in agricultural soil

Dissimilatory nitrate reduction to ammonium (DNRA) competes with denitrification for nitrate (NO3−) and can result in conservation of nitrogen (N), whereas denitrification leads to gaseous losses in the form of nitrogen gas or the greenhouse gas nitrous oxide (N2O). Thus, promoting DNRA bacteria in agricultural soils would be tractable, but little is known about what controls them in these systems and if management or cropping regimes can affect the competition between denitrifiers and DNRA bacteria. We hypothesized that cropping systems conserving soil organic matter (SOM) and resulting in higher C/NO3− ratios would favour DNRA over denitrification, and thereby lower the N2O emissions due to shifts in the abundances of the microbial communities involved. To test this hypothesis, we compared soil of an annual cereal rotation with a ley rotation (including barley) from a long-term field experiment, each with two different N fertilizer application rates. We quantified the gross rates of denitrification and DNRA in a15N tracing experiment and quantified the abundances of the functional genes for denitrification (nirK, nirS), DNRA (nrfA) and N2O reduction (nosZI, nosZII). The annual crop rotation had changed the soil properties, whereas the ley rotation prevented depletion of SOM resulting in higher C/NO3− ratios. The abundances of both nrfA and nosZ relative to the nir genes were higher in the ley soils, which correlated with significantly higher DNRA rates and lower N2O production, compared to the annual cereal rotation. We conclude that conservation of soil N and mitigation of N2O emissions can be mediated by the soil microbiome by management of SOM.