The contribution of the apple microbiome to the production chain of apple was so far largely
unknown. Here, we describe the apple fruit microbiome and influences on its composition by parameters such as storage season, storage duration, storage technology, apple variety, and plant protection
schemes. A combined culturing and metabarcoding approach revealed significant differences in the
abundance, composition, and diversity of the apple fruit microbiome. We showed that relatively few
genera contribute a large portion of the microbiome on fruit and that the fruit microbiome changes
during the storage season depending on the storage conditions. In addition, we show that the plant
protection regime has an influence on the diversity of the fruit microbiome and on the dynamics of
pathogenic fungal genera during the storage season. For the genus Neofabraea, the quantitative results
from the metabarcoding approach were validated with real-time PCR. In conclusion, we identified
key parameters determining the composition and temporal changes of the apple fruit microbiome,
and the main abiotic driving factors of microbiome diversity on apple fruit were characterized.