Crop intensity and diversity shape soil microbial functions in agroecosystems: Insights from long-term studies

Soil microorganisms are fundamental to sustaining soil health, agricultural productivity, and the resilience of agroecosystems. However, the mechanisms linking different cropping management practices with shifts in soil microbiomes and their consequent ecosystem functions remain poorly resolved. This review synthesises evidence from long-term field experiments and global analyses to examine how two key management dimensions, cropping intensity and crop diversity, shape soil microbial communities and their functional outcomes. Our synthesis reveals that these factors act as complementary but mechanistically distinct drivers of soil microbiome assembly and ecosystem resilience. Increased cropping intensity generally enhances microbial biomass and enzyme activity by increasing biologically active soil carbon and nitrogen fractions. Meanwhile, greater crop diversity through rotation, intercropping, and cover cropping consistently promotes microbial diversity and functional capacity by increasing resource heterogeneity above and belowground and strengthening plant–microbe interactions. Within diversified cropping systems, crop type plays a central role in modulating microbial communities by selectively recruiting crop-specific microbial groups that influence rhizosphere conditions through their functional activities. Collectively, these management-driven increases in microbial diversity, functional redundancy, and network connectivity can stabilise soil food webs and enhance soil resilience. However, microbial responses are strongly context-dependent and vary with climate, soil properties, management practices, and temporal scale. In particular, excessive input intensification (e.g., heavy fertilizer use) and disturbance can disrupt microbial networks and weaken functional resilience despite increasing short-term crop yields. Integrating these insights, we propose a conceptual model linking cropping intensity and crop diversity with soil microbiome assembly and functional resilience, providing a mechanistic framework for designing cropping systems that harness soil microbiomes to support sustainable agricultural production.