The plant immune response plays a central role in maintaining a well-balanced and healthy microbiome for plant health. However, insights into how the fruit immune response and the microbiome influence post-harvest fruit health is limited. Additionally, our understanding of microbial succession patterns throughout the full season and the source of microbial communities of the apple fruit is unknown. Here, I examined epiphytic and endophytic microbiota composition over the full developmental time course of apple fruit starting at flowering. I also investigated the temporal dynamics of both these communities and the host immune response during post-harvest storage of apple fruits.My data shows that the endophytic community in ripe fruit are similar to the community at full bloom, which suggests that the endophytic community may be derived from the flower. Conversely, epiphytic communities are more dynamic over time, which could indicate that surface microbes are strongly influenced by environmental factors. However, the abundances of a specific suite of OTUs become relatively constant as the fruit matures, indicating that the epiphytic community reaches a stable level. Further, my results demonstrate a temporal dynamic shift in these communities during post-harvest storage that coincides with a steep-decline in host immune response (as monitored by MdFLS2 and MdBAK1 gene expression). We observed the emergence of putative pathogenic/spoilage microbes belonging to genera Alternaria (fungi) and Gluconobacter and Acetobacter (bacteria) at the expense of Sporobolomyces and other genera suggested to be beneficial for plant hosts. These results suggest that the fruit immune response helps to orchestrate the microbiome composition and that the collapse of the immune response results in the proliferation of spoilage microbes and fruit rot. Consistent with our hypothesis that the fruit immune response plays a role in protection against dysbiosis, I showed that induction of fruit innate immunity with the flg22 peptide delayed the onset of fungal rot in apple fruit. Future research is required to determine if this protection is associated with compositional changes of the microbiota. To further test the influence of fruit immune response on the microbial community composition, especially endophytes that may have a profound impact on postharvest fruit rot, Acibenzolar S methyl (ASM) a systemic acquired resistance inducer, was applied to trees one week before harvest. I hypothesized that ASM application, known to robustly induce defense gene expression, will lead to a shift in microbial community composition and improved shelf life. Through my work, I demonstrated that, indeed, induction of the immune response by ASM application significantly changed the microbiota composition, especially the endophytes, in post-harvest apple fruits. The findings from my PhD research hold significant implications for the development of strategies to increase fruit quality and prolong shelf life in fruits and vegetables.
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