Sustainable soil management practices are associated with increases in crop defense through soil microbiome changes

Abstract Soil microbiomes regulate critical ecosystem functions, yet their relationship with agronomic practices and farmer beliefs remains unclear. Through surveying 85 organic farms, we identified five practices that reshaped soil microbiomes and linked these changes to plant defense functions. Compost and organic pesticide use were associated with decreased levels of two plant defense compounds, jasmonic and salicylic acid, while targeted irrigation, grass cover crops, and no tillage were linked to increased jasmonic acid, through changes in three microbial taxa ( Fusarium chlamydosporum ; Paenibacillus senegalensis ; Microtrichales spp.) and two beta diversity metrics. Structural equation modeling suggested no tillage, pesticide, and compost use were influenced by farmers’ beliefs in the microbiome, while adoption of targeted irrigation and grass cover crops was shaped by abiotic and economic factors. Our work indicates that soil microbiomes and their ecosystem services can be managed through farming practices and highlights sustainable pest management strategies to prioritize for outreach programs.