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

This 2021 BIOAg progress report documents initial sampling and laboratory analysis of apple-associated microbiota across organic and conventional orchards in Washington. A total of 360 samples were collected at flowering, immature fruit, harvest, and postharvest storage stages to assess fungal and bacterial diversity across tissues and management systems. DNA was extracted using CTAB protocols and prepared for dual-indexed sequencing of bacterial (16S rRNA V4 region) and fungal (ITS) communities using Illumina MiSeq. Bioinformatic analyses will be conducted using MOTHUR and PIPITS, with diversity metrics (Chao1, Shannon), NMDS ordination, and multivariate statistical models used to evaluate differences across environmental and management factors. The project aims to improve understanding of microbial interactions influencing postharvest decay and to identify microbiota with potential applications in spontaneous cider fermentation and probiotic or prebiotic development.