Meta-analysis of grapevine microbiota: Insights into the influence of cultivars, plant parts, geography, and vineyard practices on bacterial diversity

Investigating the grapevine microbiome is crucial for developing sustainable management practices in viticulture. This meta-analysis used amplicon metagenomics to analyze bacterial sequences from the Sequence Read Archive, covering 756 grapevine accessions. The dataset includes 378 paired end sequencing runs across twelve cultivars, four sample types, six origins, and two vineyard conditions. The analysis revealed significant variations in microbial communities across different grapevine cultivars and sample types, highlighting the influence of both the cultivar and ecological niche on microbial diversity. Differential abundance analyses further identified key microbial taxa driving variations across different grapevine plant parts. Furthermore, the study identified microbial taxa that consistently thrive across diverse conditions, suggesting their potential role in grapevine health and development. These findings support the possibility of utilizing specific microbial agents for biological control and sustainable vineyard management. This meta-analysis underscores the complexity of the grapevine microbiome and its pivotal role in vineyard ecosystems, providing valuable insights for future research and the advancement of sustainable viticulture practices. • Grapevine microbiome varies by cultivar, niche, and vineyard practices. • Key microbial taxa support sustainable vineyard management. • Actinobacteria and Proteobacteria dominate grapevine niches. • Core taxa persist across conditions, highlighting their importance. • Microbial diversity enhances plant health and eco-friendly viticulture.