Grapevine rootstock genotypes shape the functional composition of phyllosphere microbiome

• Grapevine rootstock selection alters rhizosphere microbial diversity. • Phosphorus cycling genes in the phyllosphere vary between rootstock genotypes. • Microbial purine metabolic genes are linked to leaf P and N contents. The impact of rootstock selection and grafting on grapevines has been extensively studied, yet the influence on microbial functions in plant-associated environments remains underexplored. This study investigates the impact of rootstock genotypes on the grapevine microbiome in both the below-ground rhizosphere and the above-ground phyllosphere using metagenomic sequencing. Rootstock genotypes significantly influence the diversity and composition of prokaryotic taxa in rhizosphere soil. Conversely, shotgun sequencing reveals that rootstock genotypes have no impact on the taxonomic composition of the phyllosphere microbiome, although the functional gene composition does vary. In total, 252 microbial genes across 31 biogeochemical pathways were identified from the metagenomic sequences of the phyllosphere microbiome. Notably, phosphorus-cycling pathways involving purine and pyruvate metabolism showed distinct compositions among grapevine rootstock genotypes. The 25 microbial genes involved in purine and pyruvate metabolism were attributed to 482 microbial genera, with four archaeal and four Firmicutes genera each harboring no fewer than 10 genes. Additionally, the read counts of purine metabolism were significantly associated with leaf nitrogen and phosphorus contents. Our findings highlight the importance of rootstock selection in shaping the microbial functional composition in the grapevine phyllosphere, underscoring potential avenues for precision viticulture strategies that leverage microbiome management.