Nitrogen Reduction Optimizes Microbiome and Nitrate Cycling in Crabapple Soybean Agroforestry

Excessive synthetic fertilizer application drives agroecosystem degradation. Fruit tree-legume intercropping, like the crabapple-soybean system, is a sustainable intensification strategy, but its micro-scale biogeochemical responses to reduced nitrogen (N) remain unclear. Therefore, this study aimed to evaluate how targeted N reduction alters soil N distribution and microbial mechanisms by assessing N-cycling enzymes and community diversity. A two-year field experiment was conducted to evaluate four treatments: monoculture crabapple (MX), monoculture soybean (MS), conventional crabapple-soybean intercropping (IS), and intercropping with 25% N reduction (ISN). Soil properties were analyzed across key soybean growth stages. Results showed that ISN significantly strengthened the near-tree “fertility island” effect and drove a shift toward nitrate dominance. It drove a shift toward nitrate dominance; compared to MS, ISN increased nitrate nitrogen by 61.06%, 67.05%, and 84.41% at V4, R3, and R6 stages, respectively. Furthermore, ISN alleviated enzyme substrate inhibition: soil urease activity under ISN was 63–67% higher than under IS, while nitrate reductase in IS was suppressed to merely 14.3–15.5% of ISN levels. Microbiologically, ISN enriched fungal alpha diversity and key functional taxa, including Ascomycota (reaching 85.77%). Strategically reducing N input actively modulates the soil microbiome and enzyme system, shifting the N pathway to an efficient nitrate-dominant state. This synergy optimizes nitrogen utilization, offering a robust paradigm for sustainable agroforestry management.