Abstract

Understanding how organic amendments reshape soil microbial communities is crucial for sustainable agriculture and soil health management. This study investigated the long-term effects of diverse organic amendments on soil microbial network structure, stability, and functionality over a 25-year field experiment. We analyzed microbial communities from plots receiving five amendment types: farmyard manure (FYM), compost, green manure, biochar, and combined treatments, compared to mineral fertilizer and unamended controls. High-throughput sequencing of 16S rRNA and ITS genes revealed distinct microbial assemblages, with organic amendments increasing bacterial diversity by 28-45% and fungal diversity by 22-38%. Network analysis demonstrated that organic amendments enhanced network complexity, with FYM-treated soils showing 2.3-fold more connections and higher modularity (0.68 vs 0.42) than mineral fertilizer plots. Keystone taxa shifted from opportunistic r-strategists in mineral-fertilized soils to K-strategists including Planctomycetes and Glomeromycota in organically amended soils. Functional predictions indicated enhanced carbon cycling, nitrogen fixation, and disease suppression potential in amended soils. Structural equation modeling revealed that microbial network properties explained 67% of variation in soil multifunctionality. These findings demonstrate that long-term organic amendments fundamentally restructure microbial networks toward more stable, functionally diverse communities, providing mechanistic insights for designing resilient agroecosystems.