Nitrogen fertilization increases the niche breadth of soil nitrogen-cycling microbes and stabilizes their co-occurrence network in a karst agroecosystem.

Microbes play a key role in mediating soil nitrogen (N) cycling in agroecosystems. However, it remains unknown how N management practices affect the taxonomic and functional structure of soil N-cycling microbes, and their community assembly and co-occurrence networks in karst agroecosystems. Here, we conducted a field experiment to examine the effects of mineral N addition (+N) and legume (Medicago sativa) intercropping (+L) on soil N-cycling functional taxa and genes in a karst forage (Broussonetia papyrifera) agroecosystem. Results showed that compared to the control and +L treatment, mineral N addition significantly increased the functional gene diversity of nitrification-related microbes and the abundance of hao gene, but slightly reduced the abundances of nifD and nifH genes related to N fixation by 33.3−56.0 %. The abundance of nifK gene was 3.7-fold higher in the +L treatment than in the control. The assembly of microbial communities involved in ammonification, assimilatory nitrate reduction (ANR) and denitrification was controlled by a homogeneous selection process. Stochastic processes played a dominant role in shaping the communities related to nitrification, dissimilatory nitrate reduction (DNR), N fixation, and N assimilation. High soil pH and total N stimulated microbial N assimilation and the related gene abundance (e.g., GDH2), but suppressed the abundances of genes involved in N fixation. Both mineral N addition and legume intercropping significantly increased the niche breadth of the whole community and the functional groups related to denitrification, ANR, DNR and N assimilation. Actinobacteria related to N assimilation dominated the co-occurrence networks across the treatments. Compared to the control, the network robustness was significantly increased in the +N and +L treatments. Our findings indicate that there are distinct responses to the two N management practices among N-cycling functional groups and highlight the importance of N fertilization in increasing the niche breadth of N-cycling microbes and stabilizing their co-occurrence network in a karst agroecosystem. [Display omitted] • Mineral nitrogen (N) addition significantly increased the functional gene diversity of nitrification-related microbes. • High soil pH and total N promoted microbial N assimilation, but suppressed the N fixation potential. • The deterministic and stochastic processes co-drove the assembly of soil N-cycling microbial communities. • N fertilization increased the niche breadth of the whole N-cycling microbial community and stabilized the co-occurrence network. [ABSTRACT FROM AUTHOR]