The gleyed paddy soils in subtropical China, characterized by poor structure, high reductive substances, and low fertility, pose challenges to sustainable agriculture. This study investigates the improvement effects of applying rapeseed green manure in combination with biochar or vermicompost through field experiments, aiming to provide a theoretical basis for the organic improvement of gleyed paddy soils. The experiment included four treatments: control (CK), rapeseed green manure (GM), GM + biochar (GMB), and GM + vermicompost (GMVC). Soil physicochemical properties, aggregate stability, and fungal communities were analyzed after rice harvest. GM significantly increased the total nitrogen (TN) content in the 0–10 cm soil layer and decreased the Fe²⁺ and total glomalin-related soil protein (T-GRSP) contents. GMVC further increased the pH value, available potassium (AK) content, and Shannon index in the 0–10 cm soil layer, decreased the available phosphorus (AP) content, and increased the proportion of macro-aggregates (>2000 µm) and decreased the fractal dimension (D) in the 10–20 cm soil layer. Compared with GMVC, GMB more significantly increased the soil organic carbon content and regulated the ratio of EE-GRSP/T-GRSP in the 0–10 cm soil layer. Fungal community analysis showed Ascomycota dominance. Pearson analysis showed Westerdykella enrichment significantly correlated with reduced T-GRSP. Monte Carlo tests identified pH and SOC as key factors shaping fungal communities. The GMB strategy mitigates reductive stress, enhances nutrient availability, and activates microbial functionality. These findings offer insights and frameworks for sustainable soil management in subtropical rice agroecosystems.

Nitrous oxide (N₂O) emissions in cereal-based rotations often show short-lived peaks after fertilization, but their contribution to annual budgets and their responsiveness to straw management remain poorly quantified. We combined a 13-year legacy fertilization experiment with two years of high-frequency N₂O monitoring in a rice–wheat rotation in central China to quantify post-fertilization peak windows and test how straw-return rate modulates these windows and annual emissions. Five long-term treatments were compared: an unfertilized control (CK), straw only (2M, 12 t ha⁻¹ yr⁻¹), mineral fertilizer (NPK), and NPK with 6 or 12 t ha⁻¹ yr⁻¹ straw (MNPK and 2MNPK). Under N input, wheat-season emissions dominated annual totals, with the ratio of wheat-season to annual N₂O emissions (WN/TN, where WN denotes wheat-season N₂O emissions and TN denotes annual cumulative N₂O emissions) of ~73–75% for NPK and MNPK, significantly higher than in CK and the straw-only control. Decomposition of annual fluxes showed that 56.6–65.4% of N₂O in N-applied treatments occurred within short windows after the two wheat-season fertilizations, whereas rice-season peaks were small and largely insensitive to treatment. Planned contrasts expressed as geometric mean ratios (GMRs) with 95% confidence intervals (CIs) highlighted a strong management leverage point: increasing straw from 6 to 12 t ha⁻¹ yr⁻¹ with NPK reduced annual and wheat-season N₂O by ~47% and 58%, respectively, primarily by lowering peak magnitude and shortening peak duration. Microbial analyses suggested that treatment effects on N₂O were better reflected by community compositional shifts (β-diversity) than by α-diversity, while amoA abundance showed guild-specific responses. Collectively, this study provides an event-window quantification framework that links high-frequency field measurements to a specific, actionable mitigation lever (straw-return rate) in rice–wheat systems. Together, these results identify wheat-season post-fertilization windows as the main control points for annual N₂O in rice–wheat rotations and show that pairing NPK fertilization with higher straw return can temper short-lived peaks. By explicitly pinpointing when (which windows) and how (attenuating peak magnitude and duration) mitigation is achieved, our findings offer a management-ready and transferable basis for targeted N₂O abatement in double-cropping systems.