Role of Soil Microbiome in Suppressing Soil-Borne Pathogens
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Abstract
The soil microbiome constitutes a vast and complex community of bacteria, fungi, archaea, protists, and viruses that play pivotal roles in maintaining soil health and agricultural productivity. Among its numerous ecological functions, the suppression of soil-borne plant pathogens stands out as one of the most agriculturally significant. Soil-borne pathogens, including Fusarium, Pythium, Rhizoctonia and Phytophthora species, are responsible for enormous economic losses in global agriculture annually. The inherent capacity of certain soils to suppress these pathogens—termed disease-suppressive soils—has been linked directly to the richness, diversity, and functional activity of the resident microbial communities. This review comprehensively examines the mechanisms through which the soil microbiome suppresses soil-borne pathogens, including antibiosis, competition for nutrients and space, induced systemic resistance, mycoparasitism and volatile compound production. It further explores the ecological and agronomic factors that shape microbial community structure and suppressive capacity, including soil pH, organic matter content, crop rotation, and the application of biological control agents. Understanding the intricate interactions within the rhizosphere and bulk soil microbiome offers transformative opportunities for the development of sustainable, microbiome-mediated disease management strategies, reducing dependence on chemical fungicides while maintaining high crop yields. Despite these advances, a critical knowledge gap persists in translating mechanistic insights into consistent, field-applicable biocontrol outcomes, particularly under variable soil conditions and diverse agricultural systems. Future research should prioritize the development of predictive microbiome-based models, the standardization of synthetic community formulations, and the integration of multi-omics approaches to unlock the full suppressive potential of soil microbial ecosystems for next-generation, sustainable crop protection.
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