Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

Abstract

Background: Verticillium wilt of olive (VWO) is caused by the soilborne fungal pathogen Verticillium dahliae. One of the best VWO management measures is the use of tolerant/resistant olive cultivars. Knowledge on the oliveassociated microbiome and its potential relationship with tolerance to biotic constraints is almost null. The aims of this work are (1) to describe the structure, functionality, and co-occurrence interactions of the belowground (root endosphere and rhizosphere) microbial communities of two olive cultivars qualified as tolerant (Frantoio) and susceptible (Picual) to VWO, and (2) to assess whether these communities contribute to their differential disease susceptibility level. Results: Minor differences in alpha and beta diversities of root-associated microbiota were detected between olive cultivars regardless of whether they were inoculated or not with the defoliating pathotype of V. dahliae. Nevertheless, significant differences were found in taxonomic composition of non-inoculated plants' communities, "Frantoio" showing a higher abundance of beneficial genera in contrast to "Picual" that exhibited major abundance of potential deleterious genera. Upon inoculation with V. dahliae, significant changes at taxonomic level were found mostly in Picual plants. Relevant topological alterations were observed in microbial communities' co-occurrence interactions after inoculation, both at structural and functional level, and in the positive/negative edges ratio. In the root endosphere, Frantoio communities switched to highly connected and low modularized networks, while Picual communities showed a sharply different behavior. In the rhizosphere, V. dahliae only irrupted in the microbial networks of Picual plants. Conclusions: The belowground microbial communities of the two olive cultivars are very similar and pathogen introduction did not provoke significant alterations in their structure and functionality. However, notable differences were found in their networks in response to the inoculation. This phenomenon was more evident in the root endosphere communities. Thus, a correlation between modifications in the microbial networks of this microhabitat and susceptibility/tolerance to a soilborne pathogen was found. Moreover, V. dahliae irruption in the Picual microbial networks suggests a stronger impact on the belowground microbial communities of this cultivar upon inoculation. Our results suggest that changes in the co-occurrence interactions may explain, at least partially, the differential VWO susceptibility of the tested olive cultivars.

Differences in the Endophytic Microbiome of Olive Cultivars Infected by Xylella fastidiosa across Seasons

“…When the whole microbial communities are considered, in contrast with previous studies [ 56 , 57 ], no cultivar effect on bacterial and fungal endophytic assemblages was found using both sequencing approaches. However, our result is in agreement with the results of a recent microbiome investigation on the Verticillium -olive pathosystem showing similar root endosphere and rhizosphere microbial communities between susceptible and tolerant cultivars [ 37 ]. In our study, the negligible host cultivar effect on microbiome composition might be explained by the high presence/abundance of Xylella in the orchards surveyed that seems to have overshadowed the effect of host cultivar in shaping endophytic microbial communities.…”

“…The majority of studies on the olive microbiome based on cultivation-dependent or independent sequencing, independently of Xylella infections, targeted the rhizosphere compartment [ 35 , 36 , 37 , 38 ] while they are limited for endophytes of aboveground tissues. Using 16S rRNA gene amplicon sequencing, Müller et al [ 39 ] found that the bacterial endophyte communities from leaves and boughs of wild and cultivated olives were largely shaped by the plant genotype and correlated with the geographic origin.…”

Verticillium Wilt of Olive and Its Control: What Did We Learn during the Last Decade?

“…A comprehensive knowledge of the composition, structure, and functioning of the prokaryotic and fungal communities associated with olive roots will enhance our understanding of the health, development, and fitness of this tree crop. Moreover, under the holobiont conceptual framework, innovative perspectives can be foreseen in areas such as breeding for VWO resistance and the development of novel biocontrol tools [13,184]. Earlier, the olive associated microbiota was reported as an important reservoir of microorganism with potential as BCA against VWO [185].…”

“…On the other hand, it was not known either what changes, if any, the root endosphere and rhizosphere microbial communities of olive cultivars with different VWO tolerances undergo upon inoculation with V. dahliae. Therefore, the objective of a very recent study aiming to address these questions was to assess whether the belowground microbial communities of cultivars Frantoio (VWO tolerant) and Picual (VWO susceptible) contribute to their differential disease susceptibility level [184]. Comparing the microbial communities of non-inoculated plants of each cultivar, some interesting differences were observed.…”

Characterization of the belowground microbial community in a poplar-assisted bioremediation strategy for restoring a multi-contaminated soil

“…The resulting ltered and trimmed sequences were clustered into Operational Taxonomy Units (OTUs) using UPARSE [58] from the SEED2 package and applying the average neighbour algorithm with a similarity cut off of 97%. The OTUs with less than 0.005% of high-quality reads were then ltered to avoid an overestimation of the diversity [59,60].…”