Exploring the impact of altitude variability and apple genotype on the epiphytic microbiome

Studying fruit microbial communities has been instrumental in understanding how this plant-associated microbiome influences key host functionalities. However, the impact of environmental changes and host genotype on this microbiome is unclear. This research aims to analyse, using 16S rRNA and ITS amplicon sequencing, the potential effect of altitudinal conditions and genotype on the epiphytic apple microbiome. Looking for key microbial genera with potential as biocontrol or pathogenic agents and characterizing each cultivar's core microbiome. The results revealed that the microbial communities on the apple peel comprise 64 bacterial and 49 fungal genera. Fungal diversity was affected by altitude, while bacterial assemblies varied across cultivars. Within these communities, some microorganisms with potential beneficial activity were detected in the valley which showed higher abundance than mountain orchards, suggesting a localized influence of environmental conditions. The core microbiome of each cultivar revealed significant genotype-dependent microbial associations and included several beneficial microbial taxa such as <i>Aureobasidium</i> and <i>Vishniacozyma</i>. These insights further our understanding of the interactions between plant genotypes, geographical location, and fruit epiphytic communities, revealing in the process possible biocontrol candidates. This information plays an important role in the pursuit of new modern agricultural methodologies that could minimise the reliance on chemical pesticides.