Integrated Soil–Crop System Management Promotes Microbial Necromass and Soil Organic Carbon Sequestration in Black Soil Through Microbial Transformation and Aggregate Protection

Long-term intensive cultivation has degraded soil structure and reduced soil organic carbon (SOC) retention in the black soils of Northeast China. However, the processes underlying SOC accumulation under integrated soil–crop system management (ISSM) remain poorly understood. An 11-year field experiment compared farmers’ practice (FP), high-yield and high-efficiency practice (IP), super-high-yield practice (HY), and ISSM. We assessed SOC stocks, aggregate stability, organic carbon chemistry, extracellular enzyme activities, microbial carbon-use traits, microbial community composition, and microbial necromass carbon (MNC), and used partial least squares path modeling as an exploratory analysis of potential linkages. Compared with FP, ISSM increased SOC content and stock by 87.0 and 77.0%, respectively, and achieved an SOC sequestration rate of 2.8 Mg C ha−1 yr−1. ISSM also increased mean weight diameter and geometric mean diameter by 45.0 and 61.0%, increased microbial biomass carbon and carbon use efficiency by 205.2 and 100.0%, and decreased qCO2 by 71.1%. Bacterial and fungal necromass carbon increased by 100.0 and 70.0%, respectively. The relative abundance of taxa operationally classified as growth-oriented also increased under ISSM. However, MNC/SOC did not differ significantly among treatments, while SOC aromaticity and hydrophobicity declined. Path analysis suggested that microbial carbon transformation was positively associated with necromass formation, whereas aggregate stability was associated with MNC and SOC retention. These results indicate that ISSM synchronously enlarged SOC and microbial necromass pools through sustained carbon inputs, efficient microbial transformation, and aggregate-mediated physical protection rather than through increased chemical recalcitrance.