Assembly and Function of Fruit Microbiomes and Insights into Management

The study of fruit microbiomes, defined as the microbial community in and on fruit, is a novel frontier that provides the potential for contextualizing pathogen infection and biocontrol in a more holistic and ecological approach. Differences in sample year tend to explain the greatest variation in fruit microbiome studies, with geography, preharvest management regime, and cold storage also resulting in pronounced shifts. However, effects of cultivar and fungicides can be more subtle, with some studies identifying minor or no shifts. This highlights that while agricultural management is important in shaping fruit microbiomes, environmental and spatiotemporal factors are also important to consider. Additionally, there is a need for more studies that delve deeper into the functional roles of the fruit microbiome, which require extension of ‘omics technologies such as shotgun metagenomics and metabolomics to move beyond taxonomic composition and begin to determine what important roles fruit microbial communities can play. Some studies are investigating the role of native microbiota in biocontrol and how native fruit microbiomes influence the fermentation process, and the field must build on these experiments to gain a more complete understanding of how the fruit microbiome is related to pathogen dynamics and modulation of fruit quality.