Longitudinal metagenomic insights into soil, bark, and berry microbiomes under abandoned, bio-organic, and conventional cultivation in Tokaj vineyard

Abstract

Vineyard microbiomes play a crucial role in plant health, disease dynamics, and wine quality, yet their responses to cultivation practices and climate variability remain insufficiently resolved. This two-year longitudinal metagenomic study in Tokaj, Hungary, characterized soil, bark, and grape berry microbiomes under abandoned, bio-organic, and conventional management across the 2020–2021 vintages using 16 S rRNA amplicon and shotgun sequencing with climate-integrated, spatially matched sampling. Distinct community clustering was observed across habitats and management types. Above-average genera (aaGs) revealed stronger relative abundance in bark, with core taxa representing 23.2% of genera but contributing equally to overall abundance. Bark-specific taxa were more diverse and abundant, and random forest models identified cultivation-specific microbial signatures, positioning bark as a sensitive bioindicator of management intensity. Bio-organic systems favored a few dominant bacterial and fungal indicators, whereas abandoned vineyards showed greater evenness but lower relative frequencies. Bark communities were bacteria-dominated, while berries were dominated by fungi, with minimal species overlap. Vintage climate strongly influenced fungal succession: the rainy 2020 favored moisture-adaptedtaxa, whereas the warm 2021 promoted thermotolerant and opportunistic species. Pathogens were prevalent, especially in abandoned sites. Functional metagenomics indicated higher virulence gene loads in abandoned systems and enrichment of degradation and stress-related traits under bio-organic management. Overall, vineyard management and vintage climate might structure habitat-specific microbiomes, with bark emerging as a possible indicator of ecological and pathogenic shifts.