Grapevine health is influenced by microbiome composition, which is affected by region and several plant features such as cultivar, age and rootstock. Grapevine Trunk Diseases (GTDs) are caused by several wood-colonizing fungi, leading to imbalances in microbiome composition. Here, we performed next-generation sequencing of fungal and bacterial microbiomes present in trunk samples of ninety-seven symptomatic grapevines, from two cultivars (cv. Touriga Nacional and cv. Aragonez), collected in eight Portuguese wine-producing regions. The influence of wine-producing regions, grapevine genotype, rootstock, and age was analyzed. Results indicate that microbiome composition is largely influenced by region and cultivar, with more pronounced alterations in cv. Touriga Nacional. Furthermore, relationships between microbes were characterized, revealing that several genera could engage in competitive interactions with the pathogens. We postulate that environmental conditions associated to the wine-producing regions modulate trunk endosphere and microbiome composition. Plant cultivar, age and rootstock also influence the trunk microbiome assembly, leading to distinct taxa composition in the trunk, and also altered microbe relationships.

BioISI Instituto de Biosistemas e Ciências Integrativas Faculdade de Ciências Universidade de Lisboa 1749 016 Lisboa Portugal

DNA and RNA Sensing Lab Department of Genetics and Biotechnology Universidade de Trás os Montes e Alto Douro 5000 901 Vila Real Portugal

Faculty of Horticulture Mendeleum Institute of Genetics Mendel University in Brno Valticka 334 69144 Lednice Czech Republic

Instituto de Ciencias de la Vid y del Vino University of La Rioja and Government of La Rioja 26007 Logroño Spain

LEAF Linking Landscape Environment Agriculture and Food Research Center Associated Laboratory TERRA Instituto Superior de Agronomia Universidade de Lisboa Tapada da Ajuda Lisboa Portugal

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