Synergistic effect of intercropping and straw incorporation on soil carbon sequestration

Intercropping has been shown to enhance soil organic carbon (SOC) sequestration, but the magnitude of this effect is often modest. Straw incorporation can increase multiple soil carbon pools, yet it remains unclear whether there are synergistic effects on SOC between these two practices, and what roles microbial and micro-food web pathways play in this process. Our study is based on a 12-year field experiment established in Zhangye City, Gansu Province, with residue management practices (straw removal vs. straw incorporation) and cropping systems (pea and maize monocultures, and pea/maize intercropping). We measured soil carbon fractions and performed amplicon and metagenomic sequencing. Intercropping modestly but consistently increased SOC and mineral-associated organic carbon concentrations by 3.7% and 4.8% compared to monoculture, while straw incorporation significantly increased them by 18.6% and 19.5% compared to straw removal. Notably, intercropping significantly increased microbial biomass carbon concentration and C-acquiring enzyme activities only under straw incorporation. Network analysis showed that intercropping, under straw incorporation, was associated with a higher proportion of potential protist-mediated interactions and more keystone taxa, which were positively correlated with SOC. Metagenomic analysis revealed that straw incorporation increased the abundance of carbon fixation modules and labile plant-derived carbon degradation genes, while intercropping with straw incorporation further enriched key carbon cycling genes linked to soil carbon pools. Overall, these findings suggest that straw incorporation amplifies the intercropping effect on soil carbon sequestration primarily by enhancing microbial-mediated carbon transformation. This study highlights the importance of integrating intercropping with appropriate residue management to promote long-term soil carbon stabilization.