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

Zobrazit více v PubMed

Azevedo-Nogueira, F. et al. The road to molecular identification and detection of fungal grapevine trunk diseases. PubMed DOI PMC

Agustí-Brisach, C. & Armengol, J. Black-foot disease of grapevine: an update on taxonomy, epidemiology and management strategies.

Berlanas, C. et al. Occurrence and diversity of black-foot disease fungi in symptomless grapevine nursery stock in Spain. PubMed DOI

Gramaje, D., Úrbez-Torres, J. R. & Sosnowski, M. R. Managing grapevine trunk diseases with respect to etiology and epidemiology: Current strategies and future prospects. PubMed DOI

Raimondo, M. L., Carlucci, A., Ciccarone, C., Sadallah, A. & Lops, F. Identification and pathogenicity of lignicolous fungi associated with grapevine trunk diseases in southern Italy.

Cobos, R. et al. The grapevine microbiome to the rescue: Implications for the biocontrol of trunk diseases. PubMed DOI PMC

Del Frari, G. et al. Pruning wound protection products induce alterations in the wood mycobiome profile of grapevines. PubMed DOI PMC

Mondello, V. et al. Management of grapevine trunk diseases: Knowledge transfer, current strategies and innovative strategies adopted in Europe.

Niem, J. M., Billones-Baaijens, R., Stodart, B. & Savocchia, S. Diversity profiling of grapevine microbial endosphere and antagonistic potential of endophytic pseudomonas against grapevine trunk diseases. PubMed DOI PMC

Bekris, F. et al. Grapevine wood microbiome analysis identifies key fungal pathogens and potential interactions with the bacterial community implicated in grapevine trunk disease appearance. PubMed DOI PMC

Berlanas, C. et al. The fungal and bacterial rhizosphere microbiome associated with grapevine rootstock genotypes in mature and young vineyards. PubMed DOI PMC

Bokulich, N. A., Thorngate, J. H., Richardson, P. M. & Mills, D. A. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. PubMed DOI PMC

Carbone, M. J. et al. Drought influences fungal community dynamics in the grapevine rhizosphere and root microbiome. PubMed DOI PMC

Deyett, E. et al. Microbial landscape of the grapevine endosphere in the context of pierce’s disease. DOI

Dissanayake, A. J. et al. Direct comparison of culture-dependent and culture-independent molecular approaches reveal the diversity of fungal endophytic communities in stems of grapevine ( DOI

Elena, G., Bruez, E., Rey, P. & Luque, J. Microbiota of grapevine woody tissues with or without esca-foliar symptoms in northeast Spain.

Gramaje, D. et al. Exploring the temporal dynamics of the fungal microbiome in rootstocks, the lesser-known half of the grapevine crop. PubMed DOI PMC

Hrycan, J., Theilmann, J., Mahovlic, A., Boulé, J. & Úrbez-Torres, J. R. Health status of ready-to-plant grapevine nursery material in Canada regarding young vine decline fungi. PubMed DOI

Patanita, M. et al. Metagenomic assessment unravels fungal microbiota associated to grapevine trunk diseases. DOI

Wei, Y. et al. High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China. PubMed DOI PMC

Geiger, A., Karácsony, Z., Golen, R., Váczy, K. Z. & Geml, J. The compositional turnover of grapevine-associated plant pathogenic fungal communities is greater among intraindividual microhabitats and PubMed

Mezzasalma, V. et al. Geographical and cultivar features differentiate grape microbiota in northern Italy and Spain vineyards. PubMed DOI PMC

Vitulo, N. et al. Bark and grape microbiome of PubMed DOI PMC

Langa-Lomba, N. et al. Metagenomic study of fungal microbial communities in two PDO Somontano Vineyards (Huesca, Spain): Effects of age, plant genotype, and initial phytosanitary status on the priming and selection of their associated microorganisms. PubMed DOI PMC

Singh, P., Santoni, S., This, P. & Péros, J.-P. Genotype-environment interaction shapes the microbial assemblage in grapevine’s phyllosphere and carposphere: An NGS approach. PubMed DOI PMC

Adejoro, D. O. et al. Grapevines escaping trunk diseases in New Zealand vineyards have a distinct microbiome structure. PubMed DOI PMC

Martínez-Diz, M. D. P. et al. Soil-plant compartments affect fungal microbiome diversity and composition in grapevine. DOI

Liu, D., Chen, Q., Zhang, P., Chen, D. & Howell, K. S. The fungal microbiome is an important component of vineyard ecosystems and correlates with regional distinctiveness of wine. PubMed DOI PMC

Wardle, D. A. et al. Ecological linkages between aboveground and belowground biota. PubMed DOI

Deyett, E. & Rolshausen, P. E. Endophytic microbial assemblage in grapevine. PubMed DOI

Singh, P. et al. Assessing the impact of plant genetic diversity in shaping the microbial community structure of DOI

Reis, P., Gaspar, A., Alves, A., Fontaine, F. & Rego, C. Response of different grapevine cultivars to infection by PubMed DOI

Sofia, J., Mota, M., Gonçalves, M. T. & Rego, C. Response of four Portuguese grapevine cultivars to infection by

Dries, L. et al. Rootstocks shape their microbiome: bacterial communities in the rhizosphere of different grapevine rootstocks. PubMed DOI PMC

D’Amico, F. et al. The rootstock regulates microbiome diversity in root and rhizosphere compartments of PubMed DOI PMC

Darriaut, R. et al. Grapevine rootstock and soil microbiome interactions: Keys for a resilient viticulture. PubMed DOI PMC

Bettenfeld, P. et al. The microbiota of the grapevine holobiont: A key component of plant health. PubMed DOI PMC

Turenne, C. Y., Sanche, S. E., Hoban, D. J., Karlowsky, J. A. & Kabani, A. M. Rapid identification of fungi by using the ITS2 genetic region and an automated fluorescent capillary electrophoresis system. PubMed DOI PMC

White, T. J., Bruns, T., Lee, S. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. in

Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. PubMed DOI

Apprill, A., McNally, S., Parsons, R. & Weber, L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. DOI

Martins-Lopes, P. et al. TrunkBioCode: Metagenomic analysis of the trunk microbiome of GTD affected grapevines. BioProject (2024).

Andrews, S.

Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: Summarize analysis results for multiple tools and samples in a single report. PubMed DOI PMC

Větrovský, T., Baldrian, P. & Morais, D. SEED 2: A user-friendly platform for amplicon high-throughput sequencing data analyses. PubMed DOI PMC

Aronesty, E. Ea-Utils: Command-line tools for processing biological sequencing data. Expression analysis. (Durham: University of Minnesota. [Google Scholar], 2011).

Bengtsson-Palme, J. et al. Improved software detection and extraction of ITS1 and ITS 2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. DOI

Edgar, R. C. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. PubMed DOI

Abarenkov, K. et al. The UNITE database for molecular identification of fungi: Recent updates and future perspectives. PubMed DOI

Katoh, K., Asimenos, G. & Toh, H. Multiple alignment of DNA sequences with MAFFT. In PubMed

Lu, Y. et al. MicrobiomeAnalyst 2.0: Comprehensive statistical, functional and integrative analysis of microbiome data. PubMed DOI PMC

Shannon, P. et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. PubMed DOI PMC