Soil Microbiome Response to Reduced Nitrogen Supply in an Over-Fertilized Wheat-Maize System

Excessive nitrogen (N) fertilization harms the diversity, structure, and function of the soil microbiome. Yet, whether such adverse effects can be repaired through reducing the subsequent N fertilization rate remains not completely clear so far. Here, using a long-term N-overfertilized wheat-maize cropping field, we assessed the effect of reducing various proportions of the subsequent N fertilization rate over six years on crop productivity, soil physicochemical and biochemical properties, and microbiome. Five treatments were employed in our field experiment: the farmers’ conventional N fertilization rate (zero reduction, as a control) and the reduction in the farmers’ N rate by 20%, 40%, 60%, and 100%. The results showed that moderate N reduction (20–40%) enhanced crop productivity and soil fertility but did not affect soil enzyme activity. Soil bacterial and fungal community diversity were insensitive to N fertilization reduction, whereas their community structures changed significantly, with more prominent alteration in the fungal community. Functional prediction indicated that average relative abundance of arbuscular mycorrhizal fungi increased with N fertilization reduction but that of ectomycorrhizal fungi decreased. Moderate N reduction (20–40%) enhanced species interactions and, thus, provided a more complex cross-kingdom microbial co-occurrence network. Both bacterial and fungal community assembly were governed by stochastic processes, and this was not altered by N fertilization reduction. Overall, the response of the soil microbiome to N fertilization reduction was greatly dependent on the reduced N proportion. The findings obtained here shed light on the importance of optimal N fertilization rate in the intensively cultivated, high-input grain production system.