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

DAnjou 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. SignificanceThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and improve food safety throughout the supply chain.