INVESTIGATING THE ROLE OF SOIL MICROBIOMES IN PLANT GROWTH PROMOTION AND DISEASE SUPPRESSION IN ORGANIC FARMING SYSTEMS

Abstract

Soil microbiomes in organic farming systems play pivotal roles in both plant growth promotion and disease suppression, yet their field-scale dynamics and functional contributions remain underexplored. In this study, soils from ten certified organic farms were characterized for physicochemical properties (pH 6.3–7.7; organic matter 3.8–7.0 %) and high-throughput shotgun metagenomics revealed diverse microbial communities (Shannon index 4.3–5.9; Simpson index 0.85–0.95) dominated by Proteobacteria and Acidobacteria. Greenhouse assays using native soils under Fusarium oxysporum challenge demonstrated a 25 % reduction in plant biomass and a 68 % disease incidence in low-diversity soils, whereas high-diversity soils exhibited only 30 % incidence and minimal biomass loss. Functional gene profiling identified key pathways—antibiotic biosynthesis (mean RPKM 762 ± 45), nutrient mobilization (214 ± 18), and siderophore production (455 ± 32)—as significantly enriched in disease-suppressive soils. Correlation analyses highlighted positive associations between microbial diversity and biomass (r = 0.68, p < 0.01) and identified specific gene families linked to enhanced plant vigor and pathogen inhibition. These findings demonstrate that fostering soil microbial diversity through organic management practices—such as diverse crop rotations, compost amendments, and reduced tillage—can enhance natural disease control and crop productivity. By integrating field surveys, controlled assays, and metagenomic insights, this work provides a robust framework for microbiome-based strategies in organic agriculture. Implementation of targeted amendments or inoculants informed by farm-specific metagenomes offers a pathway to reduce external inputs, improve yield stability, and strengthen the ecological sustainability of organic systems.