Co-composted biochar–manure sustains rapeseed and cereal yields across a three-year rotation by moderating microbial substrate responsiveness

Reconciling carbon sequestration with sustained crop productivity remains a central challenge in biochar-based soil management. Carbon-stabilizing practices often intensify microbial nutrient immobilization and microbe–crop competition. Whether biochar can realign microbial carbon–nitrogen accessibility to resolve this trade-off remains unclear. We conducted a three-year field experiment under a maize-wheat-rapeseed rotation to test whether a one-time co-composted biochar–manure application reshapes microbial resource accessibility and optimizes nutrient pathways regulating crop productivity. Five treatments were compared: control (CK), biochar (B), manure (M), biochar plus manure (M+B), and co-composted biochar–manure (M+AB). Soil physicochemical properties, potential microbial substrate-utilization response (hereinafter referred to as sum of C and N substrate-induced respiration: ΣIR_C and ΣIR_N), carbon and nitrogen accessibility indices (CAI and NAI), microbial abundance, enzyme activities in 0–10 cm and 10–20 cm soil layers, and cumulative crop yield were evaluated. Compared with CK, M + AB increased soil organic carbon by 17% and improved aggregate stability relative to biochar alone. M stimulated respiration and nutrient utilization, whereas B moderated microbial activity but provided limited yield benefits. In contrast, M + AB balanced ΣIR_C and ΣIR_N responses, reduced nutrient utilization in surface soil, and enhanced nitrifier abundance in deeper soil by (115%), over M+B. CAI and NAI remained tightly coupled (R² = 0.89, P < 0.001), indicating coordinated microbial regulation of resource acquisition under M + AB, whereby CAI strongly predicted crop yield (R² up to 0.95), whereas NAI showed no independent direct relationship. Crucially, by increasing SOC while suppressing excessive microbial activity, the M + AB treatment resolved the carbon–productivity trade-off and achieved the highest cumulative yield (19%) across maize-wheat-rapeseed rotations. This was supported by PLS-PM which showed manure-driven microbial substrate-utilization response in surface soil directly constrained yield, while co-composting weakened this constraint and improved nutrient accessibility, resulting in the highest cumulative crop yield. These findings demonstrate that M + AB reshapes microbial resource accessibility rather than simply supplying nutrients, enabling sustained productivity from a single application. Managing carbon accessibility and microbial substrate-utilization response regulation is therefore critical for synchronizing soil carbon sequestration with crop productivity.