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. 2019 Dec 31;9(1):35.
doi: 10.3390/pathogens9010035.

The Xylella fastidiosa-Resistant Olive Cultivar "Leccino" Has Stable Endophytic Microbiota during the Olive Quick Decline Syndrome (OQDS)

Marzia Vergine  1 , Joana B Meyer  2 , Massimiliano Cardinale  1 , Erika Sabella  1 , Martin Hartmann  3 , Paolo Cherubini  4   5 , Luigi De Bellis  1 , Andrea Luvisi  1
Affiliations

The Xylella fastidiosa-Resistant Olive Cultivar "Leccino" Has Stable Endophytic Microbiota during the Olive Quick Decline Syndrome (OQDS)

Marzia Vergine et al. Pathogens. .

Abstract

Xylella fastidiosa is a highly virulent pathogen that causes Olive Quick Decline Syndrome (OQDS), which is currently devastating olive plantations in the Salento region (Apulia, Southern Italy). We explored the microbiome associated with X. fastidiosa-infected (Xf-infected) and -uninfected (Xf-uninfected) olive trees in Salento, to assess the level of dysbiosis and to get first insights into the potential role of microbial endophytes in protecting the host from the disease. The resistant cultivar "Leccino" was compared to the susceptible cultivar "Cellina di Nardò", in order to identify microbial taxa and parameters potentially involved in resistance mechanisms. Metabarcoding of 16S rRNA genes and fungal ITS2 was used to characterize both total and endophytic microbiota in olive branches and leaves. "Cellina di Nardò" showed a drastic dysbiosis after X. fastidiosa infection, while "Leccino" (both infected and uninfected) maintained a similar microbiota. The genus Pseudomonas dominated all "Leccino" and Xf-uninfected "Cellina di Nardò" trees, whereas Ammoniphilus prevailed in Xf-infected "Cellina di Nardò". Diversity of microbiota in Xf-uninfected "Leccino" was higher than in Xf-uninfected "Cellina di Nardò". Several bacterial taxa specifically associated with "Leccino" showed potential interactions with X. fastidiosa. The maintenance of a healthy microbiota with higher diversity and the presence of cultivar-specific microbes might support the resistance of "Leccino" to X. fastidiosa. Such beneficial bacteria might be isolated in the future for biological treatment of the OQDS.

Keywords: Olea europaea microbiota; Xylella fastidiosa; endophytes; plant microbiome modulation.

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Conflict of interest statement

The authors declare that they have no competing interest.

Figures

Figure 1
Figure 1
Taxonomy map of the olive microbiome. The graph shows the 30 most abundant bacterial (A) and fungal (B) OTUs, named according to the best achieved identification. Samples are grouped according to the olive cultivar and then to the sample type.
Figure 2
Figure 2
Alpha-diversity metrics. Shannon–Wiener and Equitability indices for bacterial (A) and fungal (B) microbiota in olive, grouped per sample type and ordered by cultivar. Different letters indicate significantly different means (factorial ANOVA followed by Duncan’s post hoc test, p < 0.05).
Figure 3
Figure 3
Beta-diversity analysis of the microbiota associated to the olive cultivars “Leccino” and “Cellina di Nardò”. Principal Component Analysis (PCoA) plots of the Bray–Curtis distances between bacterial epiphytic + endophytic microbiota (A), bacterial endophytic microbiota (B), bacterial endophytic microbiota, with plot scaled according to the % of variance explained by the axes (C), fungal epiphytic + endophytic microbiota (D), and fungal endophytic microbiota (E). Xf = Xylella fastidiosa.
Figure 4
Figure 4
Extended error plots showing phyla (A) and genera (B) of bacterial endophytes significantly different between Xf-infected “Cellina di Nardò” and “Leccino” olive cultivars, according to White’s nonparametric test. FDR-corrected p-values (q-values) are shown. Taxa are ordered according to the effect size of the difference. Xf = Xylella fastidiosa.
Figure 5
Figure 5
Bacterial families (A) and genera (B–M) significantly different between Xf-infected and -uninfected, “Cellina di Nardò” and “Leccino” olive cultivars (endophytes only), according to Kruskal–Wallis test at FDR-corrected p < 0.05. Xf = Xylella fastidiosa. CH = Xf-uninfected “Cellina di Nardò”; LH = Xf-uninfected “Leccino”; CI = Xf-infected “Cellina di Nardò”; LI = Xf-infected “Leccino”; “+” signs indicate outliers.
Figure 6
Figure 6
Co-occurrence network of the endophytic microbiota of “Leccino” leaves infected with Xylella fastidiosa. Node shape represents kingdom (circle = bacterial OTUs, squares = fungal OTUs), while size represents the degree (number of connections) according to the legend. Nodes were colored by phylum and labeled according to the lowest identified taxonomic level. Edges (connections) are colored green (positive) or red (negative), and they represent highly significant correlations according to four similarity measures (see Section 4 for details). Asterisks indicate taxa significantly enriched in “Leccino” (see Figure 5B–J). Arrow indicates the hub OTU Planomicrobium. The network layout was generated with the edge-forced spring-embedded algorithm, except for the X. fastidiosa cluster (Xylella OTU + first degree nodes) that was drawn separately with a circular layout for easy of interpretation (the original network is provided in Figure S6).
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