Mining the Endophytic Microbiome and Leveraging the Pedigrees of Vitis vinifera for Integrated Management Strategies of Pierce' s Disease
Agricultural chemicals have been an invaluable tool to fertilize crops and manage diseases, but as consumer demand for sustainable and safer products continues to rise, it’s becoming imperative to find alternative management strategies that are environmentally sustainable and safe to humans. Grapevine (Vitis vinifera L.) is a staple crop to California agriculture and is valued at $6.25 billion. This perennial plant is plagued by Pierce’s Disease (PD), caused by the xylem limited bacterium, Xylella fastidiosa. Under field conditions, grapevine varieties can exhibit a spectrum of disease phenotypes and some vines appear to escape the disease (i.e., no to little symptoms). We hypothesize that the endophytic microbiome, as well as the variety of the host, may impact disease outcome. Harnessing this knowledge can lead to integrated and sustainable approaches for agriculture.
We present the first comprehensive culture-independent microbial study of an agricultural crop, including previously unexplored niches: sap and wood. Our results indicate that the majority of endophytes are derived from the rhizosphere. Disease, season, year, and biocompartment all play crucial roles in microbial assemblage. However, a core microbiome shapes the backbone of the grapevine endosphere. Our results showed that two endophytes native to California grapevines, Pseudomonas and Achromobacter negatively correlated with Xylella. We developed novel pathogen-specific qPCR primers to assess X. fastidiosa population in planta. In planta bioassays indicated that‘ Thompson Seedless’ exhibited the highest pathogen titre, disease ratings and lowest stem hydraulic conductivity; suggesting a cultivar’s pedigree and underlining xylem anatomy shape disease susceptibility. In planta, P. viridiflava and A. xylosidans showed protective qualities against X. fastidiosa. In vitro assays were conducted to elucidate potential microbe-pathogen interactions and indicated that the mechanism of protection is not through direct antagonism but possibly via alteration of plant-pathogen interaction. In conclusion, this research elucidates the endophytic grapevine microbiome and deepens our understanding of the grapevine-Xylella-microbe relationship, producing two potential biocontrols and the foundation to new management strategies for Pierce’s Disease.