Towards an Omics-Guided Framework for Microbial Biological Control of Fungal and Oomycete Diseases in Cannabis sativa: Integrating Host and Pathogen Genomics and Microbiomes

Abstract

The intensification of Cannabis sativa cultivation has increased the need for effective and sustainable plant-health strategies. Pathogen control is particularly challenging because pesticide residues may compromise product safety and quality, while repeated chemical treatments can favour the emergence of fungicide-resistant populations. Microbial biological control agents (BCAs) represent a promising component of integrated disease management, although their discovery and validation remain largely empirical. This narrative review examines the current literature on the biological control of fungal and oomycete diseases of cannabis, with particular emphasis on Fusarium-associated syndromes, Golovinomyces-associated powdery mildew, grey mould caused by Botrytis cinerea and major oomycete root rots. Cannabis-specific research remains limited and heterogeneous regarding reproducible efficacy across host genotypes, pathogens, and environments; mechanisms of protection; and application-oriented assessment of biosafety, crop quality, and formulation performance. To address these gaps, available evidence is organised within a prospective multi-omics-guided framework combining host and pathogen genomic characterisation, microbiome profiling, targeted BCA isolation, strain-level genomic analysis, preliminary safety screening and comparative in planta evaluation. Transcriptomic, metabolomic, and microbiome analyses can complement these stages by identifying molecular and community-level patterns potentially related to direct antagonism, resource competition, host defence priming and microbiome-mediated protection. The relevance of these patterns to disease suppression requires functional validation, while the resulting evidence may inform the design and evaluation of synthetic microbial communities. Integrating omics across these stages could support more traceable and application-relevant BCA development by enabling mechanistic investigation while providing a structured roadmap for advancing biological control strategies against fungal and oomycete pathogens of cannabis.