Identification of Pathogenic Microflora and Evaluation of Thymol Essential Oil for Antifungal Activity and Quality Regulation in Postharvest Goji Berries

This study investigated the isolation and identification of postharvest pathogenic microflora associated with the microbial spoilage of newly developed fresh goji berry cultivar “Ningnonqi 18” and evaluated the antifungal efficacy of thymol essential oil (TEO; 80 mg mL -1 ) in controlling decay and maintaining fruit quality during storage. Notably, Alternaria alternata, Botrytis cinerea , and Cladosporium cladosporioides were identified as primary spoilage-inducing fungal pathogens, while bacterial isolates such as Staphylococcus warneri and Acinetobacter pittii were reported as non-pathogenic to goji berries. TEO exhibited potent antifungal effects, causing membrane disruption and ultrastructural damage to identified-pathogenic fungal mycelia, hyphae and spores. Meanwhile, TEO enhanced antioxidant metabolites such as total phenolic content, total flavonoid content, and ascorbic acid, increased activities of defense-related enzymes such as catalase, superoxide dismutase, ascorbate peroxidase, phenylalanine ammonialyase, 4-coumarate:CoA ligase, cinnamate 4-hydroxylase, chitinase, and β-1,3-Glucanase, and reduced reactive oxygen species such as malondialdehyde, hydrogen peroxide, and superoxide anion. Consequently, TEO-treated goji berries maintained key quality characteristics such as firmness, color, and solid-acid balance, and reduced weight loss, decay rate, and electrolyte leakage, aided by lowered respiration and ethylene production rate. These results demonstrate that Alternaria alternata, Botrytis cinerea , and Cladosporium cladosporioides are major spoilage fungi in fresh goji berry cultivar “Ningnonqi 18”. In addition, TEO functions as a sustainable alternative to synthetic fungicides, effectively preserving postharvest quality and storage performance of fresh goji berries under enhanced disease resistance, improved antioxidant levels, and delayed ripening.