Blueberry fruits support a distinctive microbiome as a function of plant genetics

Background Plants offer a multitude of niches capable of fostering the formation of specific microbial communities including a variety of microorganisms such as bacteria, archaea, and fungi, which contribute to critical aspects of plants physiology and development. In particular, the production of blueberries is critical as they are largely consumed by humans and animals worldwide. Despite this, the microbiome of blueberry fruits along with the relation with that of other aerial parts of the plant remain poorly understood. This knowledge is of utmost importance as we consume this microbiome together with blueberries. Results We conducted a field experiment to characterize the taxonomic composition of fungal and bacterial communities colonizing the leaves and the surface and pulp of fruits on a collection of 10 different varieties of cultivated blueberry over two consecutive years. We found that, independently from the sampling time, pulp of the fruit, surface and leaves harbors specific and distinct microbiomes. Moreover, the major factor determining the structure of the microbiome of blueberry fruits and leaves was plant genetics, followed by compartment. We further identified the core microbiome for each plant compartment and demonstrated that core taxa account for the dominant fraction of the microbiota of each plant. Analyzing co-occurrence networks, we highlighted the complex set of intra and inter-kingdom interactions that drive the structure of the microbiota, and found that the correlations between core fungi and bacteria are mostly negative. Conclusions We showed that blueberries have a distinct microbiome associated with genetic components of plant varieties, and that this microbiome is consistent with time. We identified a tissue-specific core microbiome, with some genera shared among different tissues, and others consistently present only in specific tissues, and identified interactions between taxa that might potentially be exploited to manipulate the plant microbiota. As trade and production of blueberries is expanding globally as product development enhances their profile in form and function, our results are important because they provide a foundation for advancing the development of targeted microbiome management strategies, with potential applications in enhancing plant health and productivity.