Blueberry plants support a distinctive microbiome as a function of plant genetics and tissue

Abstract

Background Fruits, such as blueberries, are critical for food production and ecosystem sustainability as they are largely consumed by humans and animals worldwide. The microbial communities (bacteria, archaea, and fungi) within and on the surface of these fruits play a key role in regulating food quality, alongside supporting crucial aspects of plant physiology and development. However, the specific factors shaping the microbiomes of blueberry fruits, as well as their relationship with other above-ground parts of the plant such as leaves and their stability over different years, remain poorly understood. 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 cultivars of 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. The major factor determining the structure of the microbiome of blueberry fruits and leaves was plant genetics, followed by tissue. We further identified the core microbiome for each plant tissue and demonstrated that core taxa account for the dominant fraction of the microbiota of each plant. Conclusions We showed that blueberries have a distinct microbiome associated with plant cultivar, 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. As trade and production of blueberries is expanding globally, our results provide a foundation for advancing the development of targeted microbiome management strategies, with potential applications in enhancing plant health and productivity.