Understanding the olive microbiome of susceptible and resistant cultivars for sustainable biocontrol

Abstract: Olive quick decline syndrome (OQDS) is a devastating olive disease, which emerged few years ago in the region of Apulia (southern Italy) as a result of the bacterial infections caused by Xylella fastidiosa subsp. pauca. Bacterial infections were consistently associated with severe desiccations on the local cvs Cellina di Nardò and Ogliarola salentina, whereas mild symptoms were found in the infected trees of the cvs Leccino and FS17, indicating that these cvs may harbour traits of resistance. Investigations on the olive microbiome of OQDS-resistant and susceptible cultivars were undertaken to identify potential protecting endophytes for a sustainable strategy of biocontrol. In this study, bacterial and fungal communities of the xylem of infected trees of the cvs FS17 and Kalamata, respectively symptomless and highly symptomatic, were analysed by barcode (16 S rRNA V4 and ITS1-spanning amplicons) and whole shotgun (WSS) sequencing. Overall, the core microbiome was dominated by fungi, accounting 99.8% and 88.4% of the total reads by barcode and WSS sequencing, respectively, while Proteobacteria and Ascomycota are the most represented phyla with both techniques. This fungi/bacteria ratio was maintained in all trees of the cv FS17 while it was inverted in the susceptible cv Kalamata, in which Xylella colonised the majority of the ecological niche in the heavily infected plants. Bacteria were isolated from the sapwood of olive trees of the cv Kalamata and FS17 and plate assays were performed to evaluate the antagonistic activity of these olive endophytes against X. fastidiosa. Moreover, bacterial communities of selected trees of the cv FS17 were isolated, purified and co-inoculated with X. fastidiosa into potted olive plants of the cv Cellina di Nardò for evaluating potential effects on the evolution and progression of Xylella infections in this susceptible cultivar. Data on antagonistic activity of isolated endophytes and the progress of Xylella infections and/or symptom appearance in these microbiome–Xf co-inoculated plants will be presented