Postharvest treatments with biocontrol agents and essential oils strongly modify the fruit microbiome

Postharvest disease management is crucial for global food security and reducing fruit storage losses. Natural compounds, such as essential oils (EOs) and biocontrol agents (BCAs), present promising alternatives to synthetic pesticides. Biofumigation with slow-release EO diffusers effectively controlled grey mould on apples and brown rot on nectarines. Metabarcoding analysis revealed significant effects of tissue type, treatment, and sampling time on fruit microbiome composition, with epiphytic microbiomes showing greater richness and evenness compared to endophytic ones. Thyme EO reduced Botrytis cinerea abundance on apples but increased Penicillium spp., while basil EO reduced Monilinia spp. on nectarines but also favoured Penicillium spp. Application of BCAs impacted both epiphytic and endophytic microbiomes, with BCAs detected as epiphytes and internalized in fruit pulp. On nectarines, BCAs reduced Monilinia spp., and on apples, Aureobasidium pullulans reduced white haze occurrence without directly decreasing associated genera. On grapes, BCAs reduced Botrytis spp. but faced challenges establishing within resilient microbial communities. These findings support integrating microbial communities and BCAs for sustainable postharvest disease management.