Abstract: Soil organic carbon (SOC) sequestration in agroecosystems is critical for climate change mitigation, yet the microbial pathways through which plant diversity influences SOC accumulation remain poorly understood. Using a multisite paired observational survey combined with multi-omics analyses, we investigated the microbial mechanisms underlying soil carbon dynamics in tea (Camellia sinensis) plantations under woody intercropping. Compared with monoculture, intercropping increased SOC and particulate organic carbon (POC) by 33.5% and 43.3%, respectively, whereas mineral-associated organic carbon (MAOC) remained unchanged. Microbial necromass carbon—particularly fungal necromass—increased significantly, while plant-derived carbon did not differ between treatments, suggesting that the observed carbon accumulation was primarily derived from microbial transformation rather than increased plant-derived inputs. Intercropping intensified microbial nitrogen limitation, increased the relative abundance of N-cycling functional genes, and shifted fungal community composition from Ascomycota towards Basidiomycota. Random forest modeling further revealed that NO₃^- was the strongest predictor of POC variation, whereas microbial necromass carbon was the strongest predictor of MAOC variation, suggesting that N availability and microbial transformation processes differentially regulate the accumulation of distinct SOC fractions. Collectively, our findings demonstrate that microbial-derived carbon contributes more than plant-derived carbon to soil carbon accumulation under woody intercropping, and that microbial necromass plays a particularly important role in predicting the accumulation of the more persistent MAOC pool. These results highlight microbial N limitation as a potential ecological linkage between plant diversity and soil carbon persistence, and provide a trait-based framework for managing plant–microbe interactions to enhance carbon sequestration in perennial agroforestry systems.

Key words: carbon sequestration, intercropping, nitrogen limitation, soil organic carbon, tea plantation