Periodic Reporting for period 1 - WildWoodMicrobes (Wild grapevines endophytic microbiome: ecology, epigenetics and application in the biological control of wood pathogens, a synthetic microbiome approach.)
Berichtszeitraum: 2023-04-01 bis 2025-09-30
Viticulture is increasingly challenged by the decline of woody perennial crops, with grapevine trunk diseases (GTDs) representing the most serious biological threat to vineyard longevity and productivity worldwide. GTDs comprise a complex of fungal pathogens that degrade grapevine wood, reduce yield and quality, and ultimately cause plant death. Despite decades of research, effective curative solutions remain unavailable, creating major economic pressure on wine-producing regions. This challenge is particularly relevant in the current political and strategic context, where European and international policies call for reduced chemical inputs and the development of sustainable, nature-based plant protection strategies.Over the past century, grapevine cultivation has relied heavily on agrochemicals and management practices such as fungicide use, grafting and clonal propagation. While these practices have supported productivity, growing evidence shows that they have profoundly altered the grapevine-associated microbiome. Such human-driven changes are believed to have disrupted naturally balanced endophytic microbial communities, potentially weakening host resilience and facilitating the recent emergence and spread of GTD-associated pathogens.Wild populations of Vitis vinifera subsp. sylvestris (VVS) offer a unique ecological reference, as they have evolved largely outside modern viticultural practices. These populations therefore host endophytic microbiomes that are minimally affected by anthropogenic pressures. Studying these systems provides a rare opportunity to identify key microbial components associated with grapevine health and to assess whether they can be reintroduced into cultivated grapevines to restore microbiome balance and improve disease tolerance.
Building on this premise, the overall objective of this project is to translate microbial diversity from wild grapevines into innovative, microbiome-based solutions for GTD management. First, the project characterizes the endophytic microbiome of wild VVS populations across multiple European regions using DNA metabarcoding and microbial isolation, establishing both ecological baselines and a curated collection of fungal and bacterial endophytes. Second, synthetic microbiome transfers are performed to evaluate whether selected endophytic consortia can successfully establish in cultivated grapevines and reshape the wood microbiome. Finally, the project pioneers a community-level approach to biological control by testing multi-species microbial consortia for their ability to enhance plant growth, survival, graft union formation, and tolerance to key GTD pathogens, particularly Phaeomoniella chlamydospora.
The expected impacts of this project are significant at both scientific and societal levels. Scientifically, it advances understanding of grapevine endophyte ecology and the role of microbial communities in woody plant health. Strategically, it contributes to the development of sustainable disease management approaches aligned with environmental policies aimed at reducing pesticide use. At scale, successful microbiome-based interventions could extend vineyard lifespan, reduce economic losses associated with GTDs, and support the long-term sustainability of viticulture in Europe and non-European wine-producing regions. In this way, the project sets the scene for a paradigm shift from pathogen-focused control toward ecosystem-based plant health management.
Building on this premise, the overall objective of this project is to translate microbial diversity from wild grapevines into innovative, microbiome-based solutions for GTD management. First, the project characterizes the endophytic microbiome of wild VVS populations across multiple European regions using DNA metabarcoding and microbial isolation, establishing both ecological baselines and a curated collection of fungal and bacterial endophytes. Second, synthetic microbiome transfers are performed to evaluate whether selected endophytic consortia can successfully establish in cultivated grapevines and reshape the wood microbiome. Finally, the project pioneers a community-level approach to biological control by testing multi-species microbial consortia for their ability to enhance plant growth, survival, graft union formation, and tolerance to key GTD pathogens, particularly Phaeomoniella chlamydospora.
The expected impacts of this project are significant at both scientific and societal levels. Scientifically, it advances understanding of grapevine endophyte ecology and the role of microbial communities in woody plant health. Strategically, it contributes to the development of sustainable disease management approaches aligned with environmental policies aimed at reducing pesticide use. At scale, successful microbiome-based interventions could extend vineyard lifespan, reduce economic losses associated with GTDs, and support the long-term sustainability of viticulture in Europe and non-European wine-producing regions. In this way, the project sets the scene for a paradigm shift from pathogen-focused control toward ecosystem-based plant health management.
The project started by investigating the natural microbial communities of wild grapevines to understand how long-term evolution outside intensive agriculture shapes grapevine–microbe interactions. During the summer of 2023, field work was conducted in Portugal, Croatia, and Italy to locate and sample spontaneous populations of Vitis vinifera subsp. sylvestris. Wood, root-associated tissues, and surrounding soil were collected with the support of local collaborators and analyzed through DNA metabarcoding, generating a detailed overview of bacterial and fungal communities associated with wild grapevines across environments.
These analyses showed that wild grapevines host microbial communities that differ markedly from those of cultivated plants, including many taxa not previously reported in grapevine wood. Although known wood pathogens were frequently detected, they were generally present at low abundance and did not cause visible disease symptoms. This pattern indicates a stable microbial equilibrium in wild grapevine wood, where potentially harmful organisms are restrained by the surrounding microbial community. These findings directly supported the project’s hypothesis that recreating such microbial balance could enhance disease tolerance in cultivated grapevines.
At the same time, wood samples from one wild population were used to isolate living fungal and bacterial endophytes. By applying multiple culture conditions, a diverse collection of nearly two hundred isolates was established and genetically identified. This curated endophyte collection provided the biological foundation for subsequent inoculation experiments.
The project then examined whether microbial communities derived from wild grapevines could establish in cultivated plants. Synthetic consortia assembled from selected fungal isolates were inoculated into young grapevines representing genetically distant varieties. In parallel, a comparative sampling of cultivated genotypes was performed to explore host–microbiome relationships. These experiments produced robust sequencing datasets capturing both microbiome variation among grapevine genotypes and the early stages of consortium colonization. While full data analysis is ongoing, the experimental phase successfully demonstrated the technical feasibility of microbiome transfer.
In the final phase, microbial consortia were tested as a community-level biological control strategy against grapevine trunk disease pathogens. Bacterial, fungal, and mixed consortia were introduced into grafted grapevine cuttings during industrial-style propagation. Treated plants showed consistent improvements in survival, graft union formation, and vegetative growth, with some consortium–variety combinations strongly reducing mortality and enhancing early development.
When challenged with trunk disease pathogens, consortia-treated grapevines developed a clear, consortium-dependent tolerance to Phaeomoniella chlamydospora, evidenced by reduced wood symptoms and lower pathogen abundance. This demonstrates that targeted modulation of the wood microbiome can directly limit pathogen establishment and disease expression.
Overall, the project successfully moved from ecological characterization to functional testing, showing that microbial communities from wild grapevines can be isolated, transferred, and exploited to improve grapevine performance and disease tolerance. The results provide a strong proof of concept for microbiome-based, community-level approaches to sustainable trunk disease management.
These analyses showed that wild grapevines host microbial communities that differ markedly from those of cultivated plants, including many taxa not previously reported in grapevine wood. Although known wood pathogens were frequently detected, they were generally present at low abundance and did not cause visible disease symptoms. This pattern indicates a stable microbial equilibrium in wild grapevine wood, where potentially harmful organisms are restrained by the surrounding microbial community. These findings directly supported the project’s hypothesis that recreating such microbial balance could enhance disease tolerance in cultivated grapevines.
At the same time, wood samples from one wild population were used to isolate living fungal and bacterial endophytes. By applying multiple culture conditions, a diverse collection of nearly two hundred isolates was established and genetically identified. This curated endophyte collection provided the biological foundation for subsequent inoculation experiments.
The project then examined whether microbial communities derived from wild grapevines could establish in cultivated plants. Synthetic consortia assembled from selected fungal isolates were inoculated into young grapevines representing genetically distant varieties. In parallel, a comparative sampling of cultivated genotypes was performed to explore host–microbiome relationships. These experiments produced robust sequencing datasets capturing both microbiome variation among grapevine genotypes and the early stages of consortium colonization. While full data analysis is ongoing, the experimental phase successfully demonstrated the technical feasibility of microbiome transfer.
In the final phase, microbial consortia were tested as a community-level biological control strategy against grapevine trunk disease pathogens. Bacterial, fungal, and mixed consortia were introduced into grafted grapevine cuttings during industrial-style propagation. Treated plants showed consistent improvements in survival, graft union formation, and vegetative growth, with some consortium–variety combinations strongly reducing mortality and enhancing early development.
When challenged with trunk disease pathogens, consortia-treated grapevines developed a clear, consortium-dependent tolerance to Phaeomoniella chlamydospora, evidenced by reduced wood symptoms and lower pathogen abundance. This demonstrates that targeted modulation of the wood microbiome can directly limit pathogen establishment and disease expression.
Overall, the project successfully moved from ecological characterization to functional testing, showing that microbial communities from wild grapevines can be isolated, transferred, and exploited to improve grapevine performance and disease tolerance. The results provide a strong proof of concept for microbiome-based, community-level approaches to sustainable trunk disease management.
The project delivered results that open new perspectives for the sustainable management of grapevine trunk diseases. A central outcome was the demonstration that wild grapevines host a distinct and stable wood microbiome that naturally limits the development of pathogenic fungi. This balanced microbial state, largely absent in cultivated grapevines, reveals the greater resilience of wild populations and provides a clear biological target for innovation in viticulture.
Building on this discovery, the project showed that key features of this disease-suppressive microbiome can be transferred to cultivated grapevines using carefully designed microbial consortia. This represents a shift away from conventional approaches based on chemical treatments or single biocontrol strains, toward a community-level strategy in which groups of beneficial microorganisms collectively stabilize the grapevine wood environment. The effectiveness of this approach under realistic propagation conditions marks a significant advance over existing disease management options.
The most immediate impacts were observed in grapevine nursery production. Consortia applied during grafting improved plant survival, strengthened graft unions, and enhanced early growth, directly increasing nursery efficiency and reducing economic losses. In addition, treated plants showed increased tolerance to a major trunk disease pathogen, highlighting the potential of early microbiome intervention to reduce disease risk later in the vineyard.
To ensure further uptake and long-term success, additional research and demonstration trials will be needed across a wider range of genotypes and growing conditions, including field validation beyond the nursery stage. Supportive regulatory and standardization frameworks for multi-species microbial products, along with access to IP protection and investment, will be essential for commercialization. Overall, the project provides a strong scientific foundation and a credible pathway toward sustainable, microbiome-based solutions aligned with policy goals to reduce chemical inputs in agriculture.
Building on this discovery, the project showed that key features of this disease-suppressive microbiome can be transferred to cultivated grapevines using carefully designed microbial consortia. This represents a shift away from conventional approaches based on chemical treatments or single biocontrol strains, toward a community-level strategy in which groups of beneficial microorganisms collectively stabilize the grapevine wood environment. The effectiveness of this approach under realistic propagation conditions marks a significant advance over existing disease management options.
The most immediate impacts were observed in grapevine nursery production. Consortia applied during grafting improved plant survival, strengthened graft unions, and enhanced early growth, directly increasing nursery efficiency and reducing economic losses. In addition, treated plants showed increased tolerance to a major trunk disease pathogen, highlighting the potential of early microbiome intervention to reduce disease risk later in the vineyard.
To ensure further uptake and long-term success, additional research and demonstration trials will be needed across a wider range of genotypes and growing conditions, including field validation beyond the nursery stage. Supportive regulatory and standardization frameworks for multi-species microbial products, along with access to IP protection and investment, will be essential for commercialization. Overall, the project provides a strong scientific foundation and a credible pathway toward sustainable, microbiome-based solutions aligned with policy goals to reduce chemical inputs in agriculture.