Olive tree core microbiome: the first learning step towards the development of control strategies for Xylella fastidiosa

The core microbiome has been increasingly recognized to be central to plant health. However, the extent to which host plant may play a role in shaping its core microbiome and their implications for host susceptibility/resistance to a particular disease, remains poorly understood. Such knowledge, besides providing insight on the potential role of core microbiome in plant resistance, could additionally contribute to the identification of microbial strains that can be used as inoculant to drive the plant microbiome to a pathogen-resistant composition. Xylella fastidiosa is now recognized as one of the major threats to the olive tree culture. In this study, the xylem tissue microbiome of infected and non-infected olive tree cultivars, with contrasting susceptibilities to X. fastidiosa, was analyzed through Illumina amplicon sequencing and further compared. This analysis was performed in samples collected in spring and in autumn. Overall, the core microbiome was dominated by members of the Proteobacteria (81% of the total bacteria reads) and Ascomycota (98% of the total fungal reads). In non-infected trees, the core microbiome was found to differ between susceptible and resistant cultivars, in particular within fungal communities. Indeed, the interaction between the host cultivar and the presence of X. fastidiosa was found to shape the core fungal community in xylem vessels. Specific fungal/bacterial signatures were detected to either the presence or the absence of X. fastidiosa in the xylem vessels, suggesting an important role of these microorganisms in pathogen establishment/development.