Pre- and post-storage dynamics of apple surface microbial communities across different cultivars

Apple, the most important temperate fruit crop globally, makes a vital contribution to Sweden’s fruit industry, but it only fulfills less than 30% of the domestic demand with local produce. This study focuses on the apple microbiota, which, aside from well-studied pathogens, remains largely unexplored, especially concerning how cultivar, environmental factors, and cropping system influence its dynamics. We investigated the microbial communities on the surfaces of three commercially important apple cultivars (‘Aroma’, ‘Frida’ and ‘Santana’) from conventional orchards, and two of them (‘Aroma’ and ‘Frida’, designated as ‘Aroma-Krav’ and ‘Frida-Krav’) – from organic orchards in southern Sweden. Using an amplicon-based metagenomic approach, temporal changes were examined in the microbiota before storage (BS, after storing the fruit for one month in cold storage prior to ultra-low oxygen (ULO) storage), after storage (AS, after storing the fruit at cultivar-specific ULO storage conditions), and after shelf life (ASHL, ten days after the fruit was taken out from the ULO storage and kept under conditions simulating supermarket shelf life). Overall, 856 bacterial and 1475 fungal amplicon sequence variants (ASVs) were detected. The leading genera among the bacterial community were Sphingomonas and Pseudomonas, and among fungi, Cladosporium, Aureobasidium, and Vishniacozyma, regardless of the storage conditions applied and cultivar considered. These dominant microbes constituted the core microbiome. Different storage conditions resulted in variations in community composition. However, diversity analyses indicated no significant differences in microbial communities across different storage durations. In contrast, genotype and cultivation practice influenced the microbial community compositions of apple fruit. This comprehensive profiling of the apple microbiome in Sweden has practical implications. Understanding the microbiome composition may help growers implement measures to mitigate damage and improve economic efficiency. Additionally, this research lays the groundwork for developing synthetic microbial communities to enhance disease management in apple production. This is especially valuable for organic orchards, where the application of synthetic pesticides and fertilizers is not permitted.