Highly compartmentalized microbiomes in blueberry microhabitats

Background and Aims. Blueberries are considered a superfood because of their rich content of vitamins, antioxidants, and fiber, supporting multiple health benefits. Plants host complex microbiomes that play crucial roles in resistance to pathogens, productivity, and stress tolerance. Despite its importance, a comprehensive characterization of microbiota across all major compartments of cultivated blueberry (Vaccinium corymbosum) has not been performed yet. Methods. Using high throughput sequencing of marker genes, we provide the first integrative survey of fungal and bacterial communities associated with three distinct plant compartments: rhizosphere, leaf surface, and fruit surface, and of the associated bulk soil. Results. We found strong niche differentiation, with pronounced shifts in richness, diversity, and taxonomic composition between belowground and aboveground compartments. Alpha diversity peaked in bulk soils and declined progressively toward aboveground tissues. We further detected minimal overlap across compartments, with only 9 fungal and 12 bacterial shared ASVs. These findings challenge the soil-origin hypothesis for aboveground microbiota. Conclusions. Blueberry plants harbor highly compartmentalized microbial communities shaped by selective environmental and physiological filtering. Our findings provide a baseline for future development of targeted, compartment-specific bioinoculants to enhance beneficial organisms supporting blueberry cultivation.