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

Authors: MCLAUGHLIN, SHAYNE - Dalhousie University; Yurgel, Svetlana; ABBASI, PERVAIZ - Aafc Lethrdge Research Center; ALI, SHAWLAT - Aafc Lethrdge Research Center

Submitted to: Microbial Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2025
Publication Date: 11/27/2025
Citation: Mclaughlin, S.M., Yurgel, S., Abbasi, P.A., Ali, S. 2025. Changes in Environmental Conditions Differentially Affect the Bacterial Microbiome Communities in Different Apple Fruit Tissues. Microbial Biotechnology. 17:e70225. https://doi.org/10.1111/1758-2229.70225.
DOI: https://doi.org/10.1111/1758-2229.70225

Interpretive Summary: Plant tissue is home to millions of microbes, some of which can benefit plant health by warding off pathogens. As such, harnessing these microbial communities to protect against plant pathogens is a promising avenue for eco-friendly disease control. However, these microbial communities are not static, and can be influenced by outside factors, like weather, location, and organic or conventional treatment regimes. In this study, we show that these factors influence the makeup and structure of the bacterial communities of ‘Honeycrisp’ apple fruit at harvest in Maritime Canada. We show that changes in the weather between growing seasons impact the bacterial communities of core and peel tissues differently. In addition to this, we describe the positive and negative relationship networks that define the microbial communities of core and peel tissues and identify the most important microbes in these networks. This work strengthens our current understanding of apple fruit microbial communities and the factors that influence them.

Technical Abstract: The maintenance and manipulation of the beneficial plant microbiome is seen as 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. Understanding how these factors influence microbial communities will be necessary in order to unlock the microbiome for sustainable disease management. In this study, we demonstrate significant impacts of growing season, management strategy, and geographical location 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 of core and peel tissues do not respond to changes in the external environment in the same manner, underscoring the need to include multiple tissue types in future fruit microbiome research. Finally, we describe the microbial intrakingdom co-ooperation networks of apple core and peel tissues, respectively, and discuss the key microbial taxa influencing these networks.