Microbial controls of nitrogen retention and N2O production in cropping systems supporting soil carbon accrual

The fate of nitrate is central for increasing nitrogen use efficiency in cropping systems. It is influenced by ammonifiers and denitrifiers, two microbial guilds that compete for nitrate and contribute to nitrogen retention and loss, respectively, with the latter in the form of dinitrogen gas and the greenhouse gas nitrous oxide (N₂O). We hypothesized that cropping systems causing higher soil carbon:nitrate favor ammonifiers and thereby lower N₂O emissions and improve crop yield. We sampled long-term field experiments comparing annual cereal, w/wo straw return, and ley rotations under four fertilization regimes replicated in three pedoclimatic zones in Sweden. Soil carbon content has decreased in the cereal rotations since the establishment of the experiments, whereas positive effects of leys on soil carbon varied depending on clay content. Nevertheless, the ley rotations displayed consistently lower nitrate levels irrespective of fertilization regime, lower N₂O production rates, and similar or higher cereal yields compared to cereal cropping. Sequencing of 16S rRNA genes showed major differences in the soil microbiome between ley and cereal rotations, with some effects of fertilization. To tease apart effects on the functional guilds, we quantified the genetic potential of ammonifying (nrfA), denitrifying (nirK, nirS) and N₂O reducing (nosZI and nosZII) microbial communities. Nitrate availability rather than carbon content explained the apparent control of carbon:nitrate on ammonifiers vs denitrifiers, with lower levels favoring the former. Altogether, our findings highlight the importance of integrating carbon and nitrogen management strategies to improve soil carbon content while also reducing N₂O emissions from cropping systems.