Different fungal and bacterial pathogen infections alter the grapevine microbiome and phenolic profiles in a localized and specific manner

Authors: Castro, Claudia; Mekdara, Nalong; Harmon, Frank; Coleman-Derr, Devin; Wallis, Christopher

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/18/2026
Publication Date: 6/16/2026
Citation: Castro, C.A., Mekdara, N., Harmon, F.G., Coleman-Derr, D.A., Wallis, C.M. 2026. Different fungal and bacterial pathogen infections alter the grapevine microbiome and phenolic profiles in a localized and specific manner. Frontiers in Plant Science. 17. Article 1838241. https://doi.org/10.3389/fpls.2026.1838241.
DOI: https://doi.org/10.3389/fpls.2026.1838241

Interpretive Summary: Crop plants, including grapevines, have microbial cells living in direct contact with them that provide many beneficial services to their host such as protection against pathogens, drought tolerance, and nutrient uptake. These microbial communities are dynamic and respond to abiotic or biotic environmental changes events such as infections by fungal and bacterial agents. In this study, we investigated the effects of five major grapevine pathogens, Diplodia seriata, Eutypa lata, Neofusicoccum parvum, Phaeoacremonium minimum, and Xylella fastidiosa, on host microbial community and phenolic compounds profiles across multiple plant tissues. Our findings highlight distinct microbial and phenolic signatures associated with each pathogen and underscore the importance of spatial context in studying plant-host microbiome-pathogen interactions. These insights contribute to a better understanding of grapevine disease ecology and may inform future strategies for monitoring and controlling pathogen spread in perennial crops like grapevines.

Technical Abstract: Plant pathogens pose a critical threat to global agriculture by significantly reducing crop productivity through the negative impact on plant physiology and associated microbial communities. Grapevines (Vitis vinifera), a high value crop worldwide, are highly susceptible to a range of bacterial and fungal vascular pathogens. In this study, we investigated the effects of five major grapevine pathogens—Diplodia seriata, Eutypa lata, Neofusicoccum parvum, Phaeoacremonium minimum, and Xylella fastidiosa—on host microbiome composition and phenolic secondary metabolite profiles across multiple plant tissues. Using 16S rRNA and ITS sequencing and HPLC analysis, we found that pathogen infection induced significant pathogen-specific alterations in both bacterial and fungal communities, predominantly at the inoculation site. Additionally, infections triggered localized changes in phenolic compounds, especially stilbenoids, consistent with host defense responses. Notably, fungal pathogens broadly disrupted bacterial communities, while X. fastidiosa had a more limited and distal effect. Our findings highlight distinct microbiome and metabolic signatures associated with each pathogen and underscore the importance of spatial context in studying plant–host microbiome–pathogen interactions. These insights contribute to a systems-level understanding of grapevine disease ecology and may inform future strategies for monitoring and controlling pathogen spread in perennial crops such as grapevines.