Coupling organic-fertilizer residual effects with strip intercropping in a double-cropped rotation: Integrated gains in soil quality, water–nitrogen processes, and greenhouse-gas emissions

Previous studies have often isolated the single-season effects of organic fertilizers or seasonal advantages of intercropping. However, the "residual effects" of organic amendments coupled with multiseason rotation and intercropping systems remain largely unexplored. A three-year field experiment was conducted using a double-season rotation: wheat (with 35% organic fertilizer substitution) followed by maize–soybean intercropping (three nitrogen levels). We evaluated the long-term performance of resource-use efficiency, soil quality, and crop yield, while employing functional gene analysis to decode the microbial pathways regulating greenhouse gas mitigation. The results showed that organic fertilizer legacy coupled with intercropping improved soil quality by increasing organic matter content and decreasing bulk density, thereby elevating the soil fertility index to a peak of 0.91. These physical-chemical shifts, synergized with intercropping, boosted urease and phosphatase activities by 23.1%–52.3%. This optimized soil environment enhanced the nitrogen agronomic efficiency (NAE) and recovery efficiency (NRE) of intercropped maize and soybeans. Notably, under the reduced-nitrogen treatment (N1), maize NAE and NRE increased by 60.7–68% and 39.2–46.5%. Simultaneously, the legacy of organic fertilizer reduced water consumption while boosting water use efficiency (WUE) in both wheat and the subsequent intercropped maize. Microbiologically, although intercropping increased microbial diversity (Shannon and Pielou indices), the legacy of organic fertilizers slightly reduced these indices by selecting specific functional taxa. Crucially, the combined system upregulated genes involved in transcription, fatty acid synthesis, and urease. It enriched nxrA / B and nosZ abundance, while lowering nirK and norB . These changes were associated with lower N 2 O emissions and suggest a potential microbial contribution to reduced NO 2 – retention and enhanced N 2 O reduction, thereby sustaining yield while mitigating N 2 O emissions. Overall, integration of organic fertilizer legacy and intercropping provides agronomic and soil-quality benefits and reduces N 2 O emissions, but its overall GWP benefit is partly constrained by increased CO 2 emissions.