Stone Fruit Tree Microbiomes in Plant Disease Management: Progress and Future Directions

The microbiome of fruit trees shapes plant health, productivity, fruit quality, and resilience to biotic and abiotic stress. Advances in sequencing, metabolomics, and computational biology are clarifying how microbial communities influence nutrient acquisition, growth, disease resistance, and postharvest quality. However, many studies are largely descriptive and focus on a narrow set of host species and well-studied compartments. Key niches remain underexplored, including flowers, dormant buds, and graft interfaces. Temporal dynamics across seasons and years are also rarely reported, limiting inference about stability, turnover, and function. Consequently, mechanistic links between microbial taxa, metabolites, and host phenotypes are poorly resolved. In this mini-review, we synthesize current knowledge of fruit tree microbiomes and highlight features that distinguish perennial systems from annual crops. We highlight stone fruits as emerging model systems that can accelerate hypothesis-driven microbiome research in woody perennials. We then discuss how recent technological and conceptual advances are reshaping the field. We propose a transition from correlative surveys to mechanistic and translational research through integrated multi-omics, machine learning, synthetic communities, and long-term field trials. We outline priorities for stone fruits to link host genotype, climatic stress, and management with microbiome composition. We examine the potential of utilizing endophytes and carposphere communities for disease management and flavor enhancement. This will facilitate microbiome-informed production systems and broaden the reservoirs of resilient microbial resources.