Metagenomic Profiling of Bacterial (16S) and Fungal (ITS) Communities on D’Anjou Pears during Long-Term Controlled Atmosphere Storage

D’Anjou pears are routinely stored for up to nine months under controlled atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears’ natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. Overall, fungal communities exhibited lower estimated Chao1 alpha diversity (mean 18.3) compared to bacterial communities (mean 166.4). No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability or being bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas and Acinetobacter . Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium , Penicillium , Botrytis , and Mucor present at different storage stages.