Changes in microbial assembly and ecological processes following application of Aureobasidium pullulans on apple fruit surface

The apple fruit surface hosts a diverse microbiome that plays a vital role in fruit health and resistance to postharvest decay. Aureobasidium pullulans, a core member of this microbiome, has been extensively studied for its biocontrol properties, yet its ecological role in shaping microbial community dynamics remains poorly understood. This study aimed to evaluate the effect of manipulating a native Aureobasidium, to act both as a biocontrol agent and as a modulator of the epiphytic microbiome when applied at different stages of fruit development and storage. Among 28 Aureobasidium isolates recovered from ‘Golden Delicious’ apple surfaces, A69 demonstrated the most potent antagonistic activity against Penicillium expansum through volatile and diffusible metabolite production and effective suppression of lesion development in fruit. While preharvest field applications had limited effects on microbial diversity, postharvest and combined treatments significantly reshaped both fungal and bacterial communities on the apple fruit surface. Notably, A69 treatments inhibited decay incidence in stored fruit, reduced fungal diversity and enriched beneficial bacterial and yeast genera including Vishniacozyma, Cystobasidium, Buckleyzyma, Bacillus, and Frigoribacterium, many of which exhibited antagonistic activity against key postharvest pathogens. Cross-kingdom network and ecological assembly analyses revealed that A69 promoted deterministic selection within fungal communities and fostered competitive microbial interactions, resulting in a more stable and resilient microbiome. In contrast, bacterial communities remained largely governed by stochastic processes. These findings highlight the role of A69 as an effective biocontrol agent reducing decay while fostering a disease-suppressive microbiome, providing an eco-friendly microbiome-based strategy for sustainable postharvest disease control.