The apple fruit microbiome: influence of orchard management, cultivar, storage time and storage atmosphere

Microbial spoilage in commercial apple storage facilities can lead to food loss of up to 30% during the storage period. While some of the causal pathogens such as Penicillium spp. and Botrytis spp. are well characterized, others such as Neofabraea spp. and Marssonina spp. are less known due to difficulties in culturing under laboratory conditions. Metagenomics allows the screening of apples for the abundance and dynamics of pathogens and the microbiome as a whole in a culture-independent way. Here we aimed at characterizing the total microbiome on the apple fruit after harvest and to elucidate the influence of the growing season, apple cultivar, orchard management practices, and storage atmosphere conditions on the microbiome by means of in vitro cultivation and metagenomics. The results allow for the characterization of infection levels of different pathogens at harvest and, to some extent, the prediction of post storage symptom development. Additionally, information about the community composition allows for the identification of the main factors driving the composition of the microbiome, the change in diversity during the storage period and the identification of beneficial microorganisms that may eventually be applied as biocontrol agents in the future. The diversity of the microbiome was shown to differ significantly between orchard management protocols, cultivar and growing season. The results indicate a potential use in the development of novel biocontrol approaches and the improvement of existing infection models. It will also allow to educate breeders on how the host genotype interacts with the microbial community and inform researchers on how microbial communities change over time. Therefore metagenomic characterization of the microbiome may provide a valuable tool to inform practitioners and researchers on disease risks and prevent postharvest losses in the near future.