Complex Interactions Between Soil Microbiome, Plant Immune Priming, and Disease Suppression in Vegetable Cropping Systems of South East Nigeria: A Systems Biology Perspective

Soil microbiome-plant immune system interactions represent a frontier research area with transformative potential for disease-resistant vegetable production without dependence on synthetic fungicides. In the intensively cultivated vegetable systems of South East Nigeria, the mechanistic basis of natural disease suppression and plant immune priming by beneficial soil microorganisms has not been studied using systems biology approaches. This dissertation investigates the tripartite interaction network among soil microbiome composition, plant immune gene expression, and suppression of Phytophthora blight (Phytophthora capsici) in pepper production systems across Anambra, Enugu, and Imo states. Metagenomic sequencing, plant transcriptomic profiling, and targeted metabolomics were integrated using multi-omics network analysis across 40 paired disease-suppressive and disease-conducive field plots. Causal mediation analysis was applied to disentangle direct microbiome effects from indirect immune priming pathways. Results reveal that Bacillus, Streptomyces, and Trichoderma-enriched microbiomes consistently trigger systemic acquired resistance gene networks in adjacent pepper plants, mediated through volatile organic compound and MAMP signaling. The study provides the first mechanistic multi-omics evidence for microbially-induced immune priming as a driver of natural disease suppression in Nigerian vegetable systems. Keywords: soil microbiome, plant immunity, disease suppression, systems biology, South East Nigeria