Draft Genome Sequence of Xylella fastidiosa subsp. Fastidiosa Strain IVIA5235, Isolated from Prunus avium in Mallorca Island, Spain

We report the complete annotated genome sequence of the plant-pathogenic bacterium Xylella fastidiosa subsp. fastidiosa strain IVIA5235. This strain was recovered from a cherry tree in Mallorca, Spain

Divergent abiotic spectral pathways unravel pathogen stress signals across species

Abstract: Plant pathogens pose increasing threats to global food security, causing yield losses that exceed 30% in food-deficit regions. Xylella fastidiosa (Xf) represents the major transboundary plant pest and one of the world’s most damaging pathogens in terms of socioeconomic impact. Spectral screening methods are critical to detect non-visual symptoms of early infection and prevent spread. However, the subtle pathogen-induced physiological alterations that are spectrally detectable are entangled with the dynamics of abiotic stresses. Here, using airborne spectroscopy and thermal scanning of areas covering more than one million trees of different species, infections and water stress levels, we reveal the existence of divergent pathogen- and host-specific spectral pathways that can disentangle biotic-induced symptoms. We demonstrate that uncoupling this biotic–abiotic spectral dynamics diminishes the uncertainty in the Xf detection to below 6% across different hosts. Assessing these deviating pathways against another harmful vascular pathogen that produces analogous symptoms, Verticillium dahliae, the divergent routes remained pathogen- and host-specific, revealing detection accuracies exceeding 92% across pathosystems. These urgently needed hyperspectral methods advance early detection of devastating pathogens to reduce the billions in crop losses worldwide

Detection of Xylella fastidiosa in almond orchards by synergic use of an epidemic spread model and remotely sensed plant traits

The early detection of Xylella fastidiosa (Xf) infections is critical to the management of this dangerous plan pathogen across the world. Recent studies with remote sensing (RS) sensors at different scales have shown that Xf-infected olive trees have distinct spectral features in the visible and infrared regions (VNIR). However, further work is needed to integrate remote sensing in the management of plant disease epidemics. Here, we research how the spectral changes picked up by different sets of RS plant traits (i.e., pigments, structural or leaf protein content), can help capture the spatial dynamics of Xf spread. We coupled a spatial spread model with the probability of Xf-infection predicted by a RS-driven support vector machine (RS-SVM) model. Furthermore, we analyzed which RS plant traits contribute most to the output of the prediction models. For that, in almond orchards affected by Xf (n = 1426 trees), we conducted a field campaign simultaneously with an airborne campaign to collect high-resolution thermal images and hyperspectral images in the visible-near-infrared (VNIR, 400–850 nm) and short-wave infrared regions (SWIR, 950–1700 nm). The best performing RS-SVM model (OA = 75%; kappa = 0.50) included as predictors leaf protein content, nitrogen indices (NIs), fluorescence and a thermal indicator (Tc), alongside pigments and structural parameters. Leaf protein content together with NIs contributed 28% to the explanatory power of the model, followed by chlorophyll (22%), structural parameters (LAI and LIDFa), and chlorophyll indicators of photosynthetic efficiency. Coupling the RS model with an epidemic spread model increased the accuracy (OA = 80%; kappa = 0.48). In the almond trees where the presence of Xf was assayed by qPCR (n = 318 trees), the combined RS-spread model yielded an OA of 71% and kappa = 0.33, which is higher than the RS-only model and visual inspections (both OA = 64–65% and kappa = 0.26–31). Our work demonstrates how combining spatial epidemiological models and remote sensing can lead to highly accurate predictions of plant disease spatial distribution

Pathogenicity of Xylella fastidiosa subsp. multiplex isolates from Alicante outbreak (mainland Spain) on different hosts

In the outbreak of Xylella fastidiosa in the province of Alicante (mainland Spain), all isolates characterized so far belong to subsp. multiplex and ST6, and the main host is Prunus dulcis. Two different strains (IVIA 5901 and ESVL), isolated from almond trees in two municipalities of the Demarcated Area, were used to carry out pathogenicity tests on different plant species. The Italian strain De Donno (subsp. pauca, ST53) and the Spanish strain IVIA 5770 (subsp. fastidiosa, ST1) were also included

Patogenicidad de aislados de Xylella fastidiosa subsp. multiplex del foco de Alicante en diferentes hospedadores

Xylella fastidiosa es una de las principales bacterias de cuarentena en la Unión Europea, que habita en el xilema de la planta hospedadora y el tracto digestivo de insectos que actúan como vectores. Se multiplica en los vasos conductores de numerosas especies vegetales, pudiendo llegar a obstruir el flujo de savia, lo que provoca síntomas de estrés hídrico que pueden causar la muerte de la planta. En España, las zonas con focos activos son las Islas Baleares y la Comunidad Valenciana, con diferencias en cuanto a las características genéticas de los aislados bacterianos y las especies vegetales afectadas

Two Xylella fastidiosa subsp. multiplex strains isolated from almond in Spain differ in plasmid content and virulence traits

The plant pathogenic bacterium Xylella fastidiosa (Xf) is a major threat to agriculture and the environment worldwide. Recent devastating outbreaks in Europe highlight the potential of this pathogen to cause emergent diseases. Xf subsp. multiplex ESVL and IVIA5901 strains that belong to sequence type (ST) 6 were isolated from almond orchards within the outbreak area in Alicante province (Spain). Both strains share more than 99% of the chromosomal sequences), but the ESVL strain harbours two plasmids (pXF64-Hb_ESVL and pUCLA-ESVL). Here, virulence phenotypes and genome content were compared between both strains, using three strains from USA as a reference for the phenotypic analyses. Experiments in microfluidic chambers, used as simulation of xylem vessels, showed that twitching motility was absent in the IVIA5901 strain, while the ESVL strain had reduced twitching motility. Both Spanish strains had less biofilm formation, cell aggregation and lower virulence in tobacco compared with USA reference strains. Genome analysis of the two plasmids from ESVL revealed 51 unique coding sequences (CDS) that were absent in the chromosome of IVIA5901. Comparison of the chromosomes of both strains showed some unique CDS and SNPs in each strain with potential deleterious mutations. Genomic differences found in genes previously associated with adhesion and motility might explain the differences in the phenotypic traits studied. Although additional studies are necessary to infer the potential role of Xf plasmids, our results indicate that the presence of plasmids should be considered in the study of the mechanisms of pathogenicity and adaptation in Xf to new environments.Peer reviewe

Draft Genome Resources of Two Strains (“ESVL” and “IVIA5901”) of Xylella fastidiosa Associated with Almond Leaf Scorch Disease in Alicante, Spain

An outbreak of Xylella fastidiosa subsp. multiplex sequence type ST6 was discovered in 2017 in mainland Spain affecting almond trees. Two cultured almond strains, “ESVL” and “IVIA5901,” were subjected to high throughput sequencing and the draft genomes assembled. Phylogenetic analysis conclusively indicated they belong to the subspecies multiplex, and pairwise comparisons of the chromosomal genomes showed an average nucleotide identity higher than 99%. Interestingly, the two strains differ for the presence of the plasmids pXF64-Hb_ESVL and pUCLA-ESVL detected only in the ESVL strain. The availability of these draft genomes contribute to extend the European genomic sequence dataset, a first step toward setting new research to elucidate the pathway of introduction and spread of the numerous strains of this subspecies so far detected in Europe.This work was funded by European Union’s Horizon 2020 Framework Research Programme Projects XF-ACTORS (Xylella fastidiosa Active Containment Through a Multidisciplinary-Oriented Research Strategy grant 727987) and MSCA-RISE-2016 CURE-XF (Capacity Building and Raising Awareness in Europe and in Third Countries to Cope with Xylella fastidiosa); COST Action CA16107 EuroXanth, supported by European Cooperation in Science and Technology; and Project Desarrollo de estrategias de erradicación, contención y control de en España: Diagnóstico, estructura genética y gama de huéspedes project E-RTA2017-00004-C06-02 from Programa Estatal de I+D+I Orientada a los Retos de la Sociedad of the Spanish Government. This work used the Vincent J. Coates Genomics Sequencing Laboratory at University of California, Berkeley, supported by NIH S10 OD018174 Instrumentation Grant.Peer reviewe