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

Introduction: 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 ( Materials and methods: For grapevines infected with each of the five pathogens, a combination of 16S rRNA and Internal Transcribed Spacer (ITS) sequencing was performed alongside high-performance liquid chromatography analysis. Generated data were compared to observe if changes in host chemistry caused by infection from one of the pathogens could be associated with shifts in microbial communities both around and away from the initial infection sites. Results: 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 Discussion: Our findings highlight distinct microbiome and metabolic signatures associated with each pathogen and underscore the importance of examining different host tissues in studying plant-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.