Abstract
Abstract
Fundamental ecological concepts such as biogeography can help inform sustainable agricultural practices. Since distinct ecological patches can exist even if the areas in between are hospitable, we examined the potential of biogeography to shape microbiomes of apple fruit within and across the orchard canopy trees. In a 2‐year study of commercial orchard blocks, we found that canopy areas showed differences in bacterial and fungal composition and diversity. The most notable differences occurred between the lower and upper canopies, with higher diversity in the lower canopy and microbial taxonomic shifts across both harvest years. PICRUSt2 was used to predict metagenomes from taxonomy, providing functional predictions across canopy zones. The lower canopy had a higher abundance of predicted genomic elements related to secondary metabolite production and a lower abundance of predicted genomic elements related to biofilm formation. This suggests potential different patterns of growth and competition as a result of differing microbial dispersal to canopy areas. These results advance the view that fundamental ecological factors such as biogeography and dispersal are important for shaping fruit microbiomes at harvest and throughout storage. This knowledge has the potential to improve our understanding of microbiome establishment and persistence in agroecosystems.