Stage-specific regulation of C-degrading genes and microbial metabolism activity during cultivation and incorporation of different leguminous green manure drives SOC pool accumulation in tropical soils

High temperatures and humidity in tropical climates hinder the effective accumulation of soil organic carbon (SOC) during fallow periods. Planting and returning leguminous green manure can promote the formation and long-term stability of SOC fractions through the microbial carbon pump (MCP) mechanism. However, the mechanisms of microbial carbon (C) sequestration at the functional gene level under different green manure crops and across management stages remain poorly understood. Here, we systematically analyzed the effects of Crotalaria juncea (CJ), Crotalaria pallida (CP), and Sesbania cannabina (SC) on SOC fractions, microbial C metabolic activity, and carbohydrate-active enzyme (CAZymes) gene abundance during cultivation and incorporation stages. Results indicate that compared to the fallow control (CK), both CP and SC significantly increased SOC and microbial biomass carbon (MBC) content during the planting and incorporation stages. Notably, the SC produced a greater increase during the incorporation stage, with SOC and MBC increasing by 51.3% and 49.1%. Both the cultivation and incorporation of green manure reduced the abundance of CAZyme genes involved in the degradation of plant-derived components (e.g., cellulose and hemicellulose). However, green manure selectively enriched chitin-degrading CAZyme genes during cultivation and peptidoglycan-degrading CAZyme genes during incorporation. Partial least squares path model revealed that changes in the functional gene profile significantly affected microbial C metabolic activity and SOC pools, and were regulated by microbial community reorganization. Moreover, CP and SC exhibited superior soil amelioration efficacy due to their higher nutrient accumulation and nitrogenase activity. Overall, variations in the abundance of CAZyme genes encoding the degradation of different C sources influence microbial C metabolic activity through the MCP mechanism, thereby promoting the accumulation of SOC pools under different leguminous green manures applications. These findings provide important theoretical and practical implications for improving soil fertility and C sequestration function in tropical farmland systems.