Metagenomic analysis of the epiphytic and endophytic microbiota of plum fruits at different storage temperatures

Abstract Background: Fungal decays are one of the primary causes of postharvest losses in fruit, whose onset and development are partially determined by the interactions that occur between the fruit and its resident microbiota. Harvested plums are susceptible to decay pathogens but limited research has been conducted on the microbiota of plums in storage. Therefore, in the present study the composition, diversity, and potential function of the epiphytic and endophytic microbiota of plums during storage at 25 °C and 0 °C was investigated using metagenomic sequencing. Results: Our study indicated that the diversity of the endophytic microbial community remains relatively stable in storage, while the epiphytic community undergoes a notable decline in diversity. Additionally, known pathogens, such as Lasiodiplodia, Diaporthe, Botryosphaeria, Macrophomina, Fusarium, Pseudomonas, and Pantoea, were enriched in decaying fruit, while the reported biocontrol microorganisms Pseudoalteromonas and Aureobasidium were enriched in healthy fruit stored at 25 °C. A negative association was observed between potential biocontrol species and known pathogens within the microbial community network. Notably, decay promoting Filobasidium was specifically found in decayed plums stored at 0 °C, while the beneficial microbes Novosphingobium and Bradyrhizobium were specifically found in healthy fruit. The metagenomic analysis also revealed the presence of antibiotic resistance genes (ARGs) in both endophytic and epiphytic microbial communities in plum, and were primarily associated with members of the phylum Pseudomonadota as determined by host tracking analysis. Conclusions: Findings of the study provide insight on the community dynamics that occur in the endophytic and epiphytic microbiome in plums during storage at different temperatures (25 °C and 0 °C) which can be used to develop a comprehensive strategy for the management of postharvest diseases in plum and potentially other stone fruit crops (peaches, apricots, and cherries).