Ecological filtering of culturable bacterial and fungal reservoirs across a management intensity gradient in grapevine agroecosystems

Microorganisms associated with grapevines play key roles in agroecosystem functioning, yet most studies rely on cultivation-independent approaches, leaving the culturable fraction comparatively underexplored. This fraction represents an accessible microbial resource, but the ecological and methodological filters shaping it remain poorly understood, particularly when bacteria and fungi are considered together. In this study, we investigated how plant compartment, agricultural management (conventional, organic, and wild), and culture medium influence the structure of culturable microbial communities. Using culturomics, isolates were recovered from soil, bark, leaves, and grapes on both commercial and plant-based natural media. Plant organ was the main ecological filter, and its interaction with management explained a modest but significant proportion of bacterial and fungal variance (R 2 = 0.12, p < 0.002; R 2 = 0.09, p < 0.02). Fungal communities were compartmentalized, with Dothideomycetes dominating aerial organs, whereas soil supporting Eurotiomycetes, and Sordariomycetes. Bacterial communities were more heterogeneous, with Bacilli frequently co-occurring with Actinomycetia and Gammaproteobacteria, while Acidithiobacillia and Sphingobacteriia were specifically associated with soil. Wild grapevine systems showed distinct culturable profiles compared with managed vineyards, supporting the view that lower-disturbance environments may preserve more differentiated microbial reservoirs. Culture medium acted as a secondary selective filter: commercial media often recovered a broader range of microorganisms, whereas plant-based media yielded additional taxa depending on organ and management. Overall, the culturable fraction reflects combined ecological and methodological filtering and should be viewed as an accessible microbial reservoir rather than a direct in situ proxy, with potential relevance for sustainable viticulture.