Rootstock genotype shapes vine functional traits and associated microbiomes, with predominant shifts in the phyllosphere

Main conclusion Rootstock genotype shaped grapevine physiology and associated microbial communities, with the strongest compositional shifts consistently observed in the phyllosphere across contrasting growing seasons. Abstract Rootstocks contribute to grapevine adaptation to biotic and abiotic stresses, including drought, and influence associated microbial communities relevant to nutrient dynamics and stress resilience. However, integrated analyses of rhizosphere and phyllosphere microbiomes remain limited, particularly for newly developed drought-tolerant rootstocks (M2 and M4). This study tested the hypothesis that rootstock genotype influences vine physiology and vegetative growth while shaping microbial community composition and functional potential in the rhizosphere and phyllosphere. The study was conducted from 2023 to 2024 on Vitis vinifera cv. Barbera grafted onto six rootstocks (1103 Paulsen, 140 Ruggeri, SO4, Kober 5BB, M2, and M4). Phyllosphere and rhizosphere samples were collected at grapevine flowering and veraison, together with measurements of leaf gas exchange and stem water potential (Ψ stem ). Vegetative growth was assessed at the end of each season through leaf area, node number, and pruning weight. Microbial communities were profiled through 16S rRNA gene and ITS amplicon sequencing. Across both years, despite contrasting weather conditions, rootstock genotype affected vine performance, while the strongest differences in microbial communities were observed in the phyllosphere. Notably, M2 and M4 maintained higher Ψ stem than the other rootstocks, indicating greater drought tolerance. Phyllosphere microbiome composition appeared to be shaped by rootstock-related differences in vine physiology and vegetative growth, likely through local microenvironmental changes affecting microbial assembly. Expanding integrative research linking plant physiology and microbiome ecology could clarify how rootstock-mediated traits influence grapevine-associated microbiomes and their potential contribution to microbial terroir, ultimately supporting more resilient and sustainable viticulture under climate change.