Packing Line Processes Reshape Apple Microbiomes: Differential Effects of Chlorine and Waxing on Bacterial and Fungal Communities

Modern postharvest apple processing facilities include steps to ensure the safety and storage of fresh-market fruit. Packing lines typically include a chlorine sterilization process before fruit waxing to maximize postharvest fruit quality. We investigated the role of chlorine dump tank sanitation and waxing in shaping microbiome community assembly on apples, which is relevant for postharvest pathogen colonization and infection. We hypothesized that each step of postharvest processing would indicate further shifts in fruit microbiome composition, notable at the prechlorine and postchlorine dump tank stages, followed by the fruit-waxing step. We found that the packing line process affected bacterial composition, but there were minimal effects on fungal composition and only at specific sampling times. In addition, adding wax to fruit increased bacterial diversity, but there was no effect with chlorine sanitation. Bacterial shifts were strongest after the waxing step, with more than half of all genera increasing in relative abundance. Using PICRUSt2, we predicted metagenomic profiles and observed that taxonomic shifts corresponded with a variety of metabolic pathways increasing in abundance, including an unexpected increase in pathways associated with methanogenesis. Although PICRUSt2 predictions on their own are prone to false positives, this finding coincides with the presence of known methanogens of the class Methanobacteria in waxed samples. The results suggest that commercial packing line processes shape the apple microbiome, uncovering potentially novel functions such as methane regulation in postharvest waxed fruit, with implications for fruit preservation and quality.