Changes in Environmental Conditions Differentially Affect the Bacterial Microbiome Communities in Different Apple Fruit Tissues

The maintenance and manipulation of the beneficial plant microbiome is a new frontier in ecofriendly disease management, particularly during post‐harvest storage. However, the fruit microbiome is highly variable and can be influenced by both biotic and abiotic factors. A comprehensive understanding of how these factors influence microbial communities is necessary in order to unlock the microbiome for sustainable disease management. In this study, we demonstrate the impacts of the growing season and management strategy on the composition and structure of the bacterial microbiome of ‘Honeycrisp’ apples at harvest from seven different orchards in the Atlantic Maritime Ecozone, over the course of two growing seasons. We show that the bacterial communities associated with core and peel tissues respond differently to changes in external environmental conditions, underscoring the need to include multiple tissue types in future fruit microbiome research. Finally, we characterize the microbial cooperation networks of apple core and peel tissues and identify key microbial taxa influencing these networks.