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

Abstract This two-year longitudinal metagenomic study in Tokaj, Hungary, profiled soil, bark, and grape berry microbiomes across three cultivation regimes (abandoned, bio-organic, conventional) and two vintages (2020–2021), using 16S rRNA and shotgun metagenomics coupled with climate-integrated, spatially matched sampling.Above-average genera (aaGs) were analyzed to assess soil-bark microbial overlap. Distinct clustering was observed, with higher aaG biomass in bark. Core taxa accounted for only 23.2% of genera but contributed equally to total biomass. Bark-specific taxa were more diverse and abundant. Random forest analysis identified cultivation-specific microbial signatures, positioning the bark microbiome as a sensitive bioindicator of vineyard management intensity. Bio-organic management favored the dominance of a few high-abundance bacterial and fungal indicators (e.g., Nakamurella flavida , Lophiostoma macrostomum ), whereas abandoned sites exhibited greater evenness but lower overall biomass.In bark-berry comparisons, bark microbiota was dominated by bacteria, whereas fungal reads prevailed in berries. Species overlap was minimal. Core taxa, present in both bark and berry microbiomes, were predominantly bacterial in bark (e.g., Microlunatus antarcticus , Kineococcus rubinsiae ) and fungal in berries (e.g., Aureobasidium pullulans , Hortaea werneckii ), with habitat-specific dominance typically exceeding a tenfold biomass difference.Fungal succession during ripening reflected vintage-specific climate: high rainfall in 2020 favored moisture-adapted taxa ( Cladosporium , Acidomyces ), whereas warm, sunny 2021 promoted thermotolerant and opportunistic species ( Aspergillus puulaauensis , Cryptococcus gattii ).Pathogens dominated both habitats, particularly in abandoned vineyards. Botrytis cinerea was the most abundant pathogen, with bioprotective taxa showing inverse patterns. Plasmopara viticola dominated in 2020, while Phaeoacremonium minimum and Aspergillus fumigatus were enriched in 2021. Targeted functional metagenomics of Botrytis -associated genes showed bark enriched in aroma biosynthesis, stress response, and cell wall-degrading functions. Abandoned vineyards carried the highest virulence gene load, while bio-organic systems favored degradation traits. Veraison-to-harvest shifts were evident in quorum sensing, phytotoxin, and bioprotection genes, indicating stage-specific pathogenic potential.