Plant organ and sampling time point determine the taxonomic structure of microbial communities associated to apple plants in the orchard environment.

Plant-associated microbial communities interact with their host and are important components of the biodiversity of natural and agro-ecosystems. Scarce knowledge is available on the establishment of plant microbiota in perennial woody plants. In this work the variability in bacterial and fungal communities in aboveground organs was analysed in leaves, bark, flowers and fruits on three apple cultivars (Gala, Fuji and Golden), in order to understand changes of the microbiota community structure from orchard planting to the first year of fruit production. Our results indicate that Proteobacteria, Bacterioidetes, Actinobacteria and Firmiculites were the dominant bacterial phyla across all samples. The majority of fungal sequences were assigned to Ascomycota and Basidiomycota. The bacterial genera Pseudomonas and Sphingomonas, and the fungal genera Aureobasidium and Filobasidium, represented a major component of the aboveground microbiota. Different parts of the apple plant harboured a specific microbiota and the effect of plant organ on the bacterial and fungal taxonomic structure exceeded the influence of sampling time and plant genotype. This work highlights the specificity of the microbiota associated with aboveground apple organs, changes of the microbiota composition during the plant development from orchard planting to the first year of fruit production, and the negligible effects of apple cultivar.