Abstract

Cover cropping represents a promising strategy for engineering soil microbiomes to enhance ecosystem services including carbon sequestration and disease suppression. This study evaluated the effects of different cover crop species and mixtures on soil microbial community composition, carbon dynamics, and pathogen suppression across 48 field sites over four years. High-throughput sequencing of 16S rRNA and ITS genes revealed that cover crops significantly altered soil microbiome structure, with diverse cover crop mixtures increasing microbial diversity by 65% compared to fallow controls. Legume cover crops (crimson clover, red clover) increased beneficial bacteria abundance by 240%, particularly nitrogen-fixing taxa and plant growth-promoting bacteria. Brassica cover crops (radish, mustard) enhanced fungal diversity by 85% and increased disease-suppressive taxa including Trichoderma (+320%) and Pseudomonas (+180%). Grass cover crops (rye, oats) promoted fungal networks that enhanced soil carbon sequestration rates from 0.8 to 2.4 t C ha⁻¹ yr⁻¹. Multi-species cover crop mixtures demonstrated synergistic effects, achieving 78% higher soil carbon accumulation and 65% greater disease suppression compared to monoculture covers. Network analysis identified keystone microbial taxa that mediated cover crop effects, with mycorrhizal fungi and biocontrol bacteria serving as critical nodes. Disease suppression bioassays showed 45-72% reduction in soilborne pathogens under cover crop systems, with Rhizoctonia solani, Fusarium species, and Pythium showing the strongest suppression. Economic analysis revealed net benefits of $185-295 ha⁻¹ yr⁻¹ from reduced pesticide applications and enhanced soil carbon services. Machine learning models predicted optimal cover crop species combinations for specific soil types and management objectives with 87% accuracy. These findings demonstrate that strategic cover cropping can effectively engineer soil microbiomes to deliver multiple ecosystem services, providing a biological foundation for sustainable agricultural intensification.