Biocontrol of plant diseases from a holobiont perspective: microbiome-mediated mechanisms and applications

Abstract

Plant disease resistance is increasingly recognized as an emergent property of the plant holobiont, shaped not only by host genotype and pathogen virulence but also by the composition and function of associated microbial communities. The plant holobiont provides a framework for understanding how microbiome assembly across compartments, including the rhizosphere, phyllosphere, endosphere, and seeds, influences plant health and disease outcomes. Current evidence shows that disease-modulating microbiomes are structured by ecological filters such as host genotype, root exudation, environmental conditions, and transmission processes. These microbial communities contribute to disease suppression through direct pathogen inhibition, microbiome-modulated immunity and induced systemic resistance, recruitment of protective microbiota, and community-level suppression in disease-suppressive soils. Translational opportunities arising from this framework include microbiome-informed disease management, synthetic communities, microbiome engineering, endophyte deployment, microbiome transplantation, and microbiome-assisted breeding. Despite this promise, practical application remains constrained by context dependence, incomplete mechanistic resolution, and limited field validation. The holobiont perspective offers a more ecologically realistic framework for developing durable and sustainable crop protection strategies. Progress in this area will depend on integrating ecological theory, multi-omics approaches, and field-based validation to translate plant holobiont research into robust disease management applications.