Exploring endophytic microbial communities to identify potential biocontrol agents against Xylella fastidiosa strain 'De Donno'

The compelling search for a strategy to tackle Xylella fastidiosa strain ‘De Donno’ and the Olive Quick Decline Syndrome (OQDS) it causes in olive trees, led us to explore the possibility to identify potential biocontrol agents among the microbial communities naturally inhabiting xylem vessels of infected trees. To this aim, we pursued a multiapproach study, intended to provide unprecedented information on the composition and the possible role of olive endophytic microorganisms in mitigating the effects of X. fastidiosa infections. In first instance, a Whole Metagenome Shotgun Sequencing (WMSS) coupled with 16S/ITS rRNA gene sequencing was carried out on field-grown plants of the susceptible and resistant olive cvs. ‘Kalamata’ and ‘FS17’, respectively, at two different stages of the disease progress. Characterization of bacterial and fungal communities based on this approach revealed that X. fastidiosa had a prominent role in the ecological niche it occupied and significantly lowered the microbial diversity. Although this effect was less evident in cv. ‘FS17’, collectively our data indicated that host cultivar had a marginal impact on the microbiome structure, and host resistance traits could not be associated with the presence of a single microbial taxon or specific consortia. In an effort to identify potential naturally-occurring X. fastidiosa antagonists we shifted our sights to the culturable fraction of bacterial communities isolated from trees belonging to either resistant (‘Leccino’, ‘FS17’) or susceptible (‘Kalamata’) cultivars, harboring low population sizes of X. fastidiosa and showing no or mild symptoms of OQDS. Following biological and molecular characterization of yielded isolates several different species, representative of the genera Sphingomonas, Methylobacterium, Micrococcus and Curtobacterium were identified. However, when tested in antagonistic assays against X. fastidiosa, none of them proved to be effective. Interestingly, when we included in our study different Bacillus strains previously isolated from other sources, significant antagonistic effects were detected