Integrative Analyses of Pome Fruits Associated Microbiota for Decay Prevention and Health Benefits: Final Report

Report documents continued analysis of fungal and bacterial microbiota associated with Washington apples grown under organic and conventional management. A total of 360 samples were collected across flowering, immature fruit, harvest, and postharvest storage stages, with additional sampling to evaluate fungicide effects. Microbial DNA was extracted using CTAB protocols and prepared for dual-indexed Illumina sequencing targeting bacterial 16S rRNA (V4 region) and fungal ITS regions. Bioinformatic analyses will be conducted using MOTHUR and PIPITS, with operational taxonomic units and amplicon sequence variants assigned through alignment to reference databases. Statistical analyses include diversity indices (Chao1, Shannon), NMDS ordination, mixed regression modeling, and PERMANOVA to evaluate effects of management and environmental factors. Findings will inform improved postharvest decay management strategies and support exploration of spontaneous or semi-controlled fermentation and potential probiotic applications.microbiome sequencing of apples to inform decay prevention and fermentation research.