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

Abstract

The dynamics of Xylella fastidiosa infections in the context of the endophytic microbiome was studied in field-grown plants of the susceptible and resistant olive cultivars Kalamata and FS17. Whole metagenome shotgun sequencing (WMSS) coupled with 16S/ITS rRNA gene sequencing was carried out on the same trees at two different stages of the infections: In Spring 2017 when plants were almost symptomless and in Autumn 2018 when the trees of the susceptible cultivar clearly showed desiccations. The progression of the infections detected in both cultivars clearly unraveled that Xylella tends to occupy the whole ecological niche and suppresses the diversity of the endophytic microbiome. However, this trend was mitigated in the resistant cultivar FS17, harboring lower population sizes and therefore lower Xylella average abundance ratio over total bacteria, and a higher α-diversity. Host cultivar had a negligible effect on the community composition and no clear associations of a single taxon or microbial consortia with the resistance cultivar were found with both sequencing approaches, suggesting that the mechanisms of resistance likely reside on factors that are independent of the microbiome structure. Overall, Proteobacteria, Actinobacteria, Firmicutes, and Bacteriodetes dominated the bacterial microbiome while Ascomycota and Basidiomycota those of Fungi.

Evaluation of Established Methods for DNA Extraction and Primer Pairs Targeting 16S rRNA Gene for Bacterial Microbiota Profiling of Olive Xylem Sap

“…Although assessment and optimization of different DNA extraction protocols should be one of the most important initial steps when developing a protocol for analysis of microbial communities in a new plant niche due to its potential significant influence on the structure and diversity of the recovered community profile (Rubin et al, 2014), for all the studies assessing olive microbiota, this assessment is lacking. Thus, although several studies have described olive endophytic microorganisms either after extraction from xylem woody chips (e.g., Keykhasaber et al, 2017;Anguita-Maeso et al, 2020;Giampetruzzi et al, 2020;Vergine et al, 2020) or from xylem sap when using a pressure chamber (Fausto et al, 2018;Sofo et al, 2019;Anguita-Maeso et al, 2020), none of those studies have examined the influence of DNA extraction kits or choice of primer pairs on microbiota characterization, which might be essential to avoid possible bias on the results.…”

Phenotypic Characterization and Transformation Attempts Reveal Peculiar Traits of Xylella fastidiosa Subspecies pauca Strain De Donno

“…In conclusion, the availability of mutants of one of the most virulent strains of X. fastidiosa paves the way for new investigations, aiming to elucidate host–pathogen interactions underpinning the mechanisms of pathogenicity and the differential responses recorded upon the infection of different olive cultivars [ 4 , 88 , 89 , 90 , 91 , 92 ], necessary for the implementation of strategies to mitigate the impact of OQDS.…”

Verticillium dahliaeinoculation andin vitropropagation modify the xylem microbiome and disease reaction to Verticillium wilt in a wild olive genotype

“…In our study, 10 keystone bacterial genera could be considered the core microbiome being transmitted from generation to generation in olive, since they were detected in all samples regardless plant propagation procedure ( in vitro vs nursery) or inoculation with the pathogen; with Cutibacterium, Pseudomonas, Anoxybacillus, Staphylococcus, Methylobacterium-Methylorubrum , and Bradyrhizobium being the most abundant, in that order. These bacterial taxa have also been identified in olive xylem in other works in which olive trees of different ages, belonging to different cultivars or growing under different environments were evaluated (Müller et al 2015; Fausto et al, 2018; Sofo et al, 2019; Anguita-Maeso et al, 2020; Giampetruzzi et al, 2020) which strength the hypothesis that those genera may represent keystone olive xylem bacteria. More interestingly, some of these genera have been already reported or used as plant growth promoting bacteria (Otieno et al, 2015; Subramanian et al, 2015) or as biological control agents against V. dahliae (Berg et al, 2002, 2006).…”

“…The role of microorganisms in the biocontrol of Verticillium wilt diseases has been reported mostly on non-woody plant species such as cotton, potato, strawberry or tomato (Azad et al, 1985; Nallanchakravarthula et al, 2014; Cao et al, 2016; Wei et al, 2019; Snelders et al, 2020) with few studies focused on woody hosts including olive (Mercado-Blanco et al, 2004; Aranda et al, 2011; Gómez-Lama Cabanás et al, 2018). However, the characterization of microbial communities inhabiting xylem vessels colonized by Vd has not been studied to date, despite some work done on other tree species or other vascular pathogens (Martín et al, 2015; Pérez-Martínez et al, 2018; Giampetruzzi et al, 2020; Vergine et al, 2020). To the best of our knowledge, this present study is the first to address this knowledge gap, by determining changes in xylem bacterial communities of a resistant olive clone after challenge inoculation with D Vd .…”