Omics-Driven Insights Into Soil Microbial Diversity and Phytopathogen Interactions for Sustainable Agriculture and Food Security

Abstract

Soil microbial diversity plays a pivotal role in sustainable agriculture by regulating nutrient cycling, organic matter turnover, and natural suppression of phytopathogens, thereby supporting crop productivity and ecosystem resilience. However, intensive agricultural practices and environmental stressors have led to a decline in soil biodiversity, compromising soil functionality and food security. Recent advances in omics technologies—including metagenomics, transcriptomics, proteomics, and metabolomics offer powerful tools to unravel the complexity, of soil microbial communities and their interactions with plants and pathogens. These integrated approaches provide high-resolution insights into microbial structure, functional dynamics, metabolic pathways, and the mechanisms underpinning plant–microbe–pathogen interactions. Furthermore, omics-driven understanding supports the development of sustainable strategies such as organic farming, conservation practices, and microbial bioinoculants, which restore microbial diversity, enhance nutrient use efficiency, reduce chemical inputs, and mitigate disease pressure. By linking soil health to crop nutritional quality and broader food system sustainability, this review highlights the potential of omics-guided approaches to optimize soil microbial ecosystems for resilient agriculture and global food security.