The bacterial pathogen Xylella fastidiosa affects the leaf ionome of plant hosts during infection

Virulence Comparison of a Comprehensive Panel of Xylella fastidiosa Pierce's Disease Isolates from California

Xylella fastidiosa, the causal agent of Pierce's disease of grapevine, has been found in all major grape-growing regions in California, U.S.A. Large collections of X. fastidiosa isolates are available from these areas, which enable comparative studies of pathogen genetic traits and virulence. Owing to the significant resource requirements for experiments with X. fastidiosa in grapevine, however, most studies use only a single isolate to evaluate disease, and it is not clear how much variability between isolates impacts disease development in experimental or natural settings. In this study, a comprehensive panel of X. fastidiosa isolates from all California grape-growing regions was tested for virulence in susceptible grapevine and in the model host plant, tobacco. Seventy-one isolates were tested, 29 in both grapevine and tobacco. The results of this study highlight the inherent variability of inoculation experiments with X. fastidiosa, including variation in disease severity in plants inoculated with a single isolate, and variability between experimental replicates. There were limited differences in virulence between isolates that were consistent across experimental replicates, or across different host plants. This suggests that choice of isolate within the X. fastidiosa subsp. fastidiosa Pierce's disease group may not make any practical difference when testing in susceptible grape varieties, and that pathogen evolution has not significantly changed virulence of Pierce's disease isolates within California. The location of isolation also did not dictate relative disease severity. This information will inform experimental design for future studies of X. fastidiosa in grapevine and provide important context for genomic research.

Calcium modulation of bacterial wilt disease on potato

Ralstonia solanacearum species complex (RSSC) is a phytopathogenic bacterial group that causes bacterial wilt in several crops, being potato (Solanum tuberosum) one of the most important hosts. The relationship between the potato plant ionome (mineral and trace elements composition) and the resistance levels to this pathogen has not been addressed until now. Mineral content of xylem sap, roots, stems and leaves of potato genotypes with different levels of resistance to bacterial wilt was assessed in this work, revealing a positive correlation between divalent calcium (Ca) cation concentrations and genotype resistance. The aim of this study was to investigate the effect of Ca on bacterial wilt resistance, and on the growth and virulence of RSSC. Ca supplementation significantly decreased the growth rate of Ralstonia pseudosolanacearum GMI1000 in minimal medium and affected several virulence traits such as biofilm formation and twitching motility. We also incorporate for the first time the use of microfluidic chambers to follow the pathogen growth and biofilm formation in conditions mimicking the plant vascular system. By using this approach, a reduction in biofilm formation was observed when both, rich and minimal media, were supplemented with Ca. Assessment of the effect of Ca amendments on bacterial wilt progress in potato genotypes revealed a significant delay in disease progress, or a complete absence of wilting symptoms in the case of partially resistant genotypes. This work contributes to the understanding of Ca effect on virulence of this important pathogen and provides new strategies for an integrated control of bacterial wilt on potato.

IMPORTANCE

Ralstonia solanacearum species complex (RSSC) includes a diverse group of bacterial strains that cause bacterial wilt. This disease is difficult to control due to pathogen aggressiveness, persistence, wide range of hosts, and wide geographic distribution in tropical, subtropical, and temperate regions. RSSC causes considerable losses depending on the pathogen strain, host, soil type, environmental conditions, and cultural practices. In potato, losses of $19 billion per year have been estimated for this pathogen worldwide. In this study, we report for the first time the mineral composition found in xylem sap and plant tissues of potato germplasm with different levels of resistance to bacterial wilt. This study underscores the crucial role of calcium (Ca) concentration in the xylem sap and stem in relation to the resistance of different genotypes. Our in vitro experiments provide evidence of Ca's inhibitory effect on the growth, biofilm formation, and twitching movement of the model RSSC strain R. pseudosolanacearum GMI1000. This study introduces a novel element, the Ca concentration, which should be included into the integrated disease control management strategies for bacterial wilt in potatoes.

Silicon modifies leaf nutriome and improves growth of oak seedlings exposed to phosphorus deficiency and Phytophthora plurivora infection

Beneficial effects of silicon (Si) on plants have primarily been studied in crop species under single stress. Moreover, nutrient acquisition-based responses to combination of biotic and abiotic stresses (a common situation in natural habitats) have rarely been reported, in particular in conjunction with soil amendments with Si. Pedunculate oak (Quercus robur L.), one of the ecologically and economically most important tree species in Europe, is facing a severe decline due to combined stresses, but also problems in assisted regeneration in nurseries. Here, we studied the effect of Si supply on the leaf nutriome, root traits and overall growth of 12-weeks-old oak seedlings exposed to abiotic stress [low phosphorus (P) supply], biotic stress (Phytophthora plurivora root infection), and their combination. The application of Si had the strongest ameliorative effect on growth, root health and root phenome under the most severe stress conditions (i.e., combination of P deficiency and P. plurivora root infection), where it differentially affected the uptake and leaf accumulation in 11 out of 13 analysed nutrients. Silicon supply tended to reverse the pattern of change of some, but not all, leaf nutrients affected by stresses: P, boron (B) and magnesium (Mg) under P deficiency, and P, B and sulphur (S) under pathogen attack, but also nickel (Ni) and molybdenum (Mo) under all three stresses. Surprisingly, Si affected some nutrients that were not changed by a particular stress itself and decreased leaf Mg levels under all the stresses. On the other hand, pathogen attack increased leaf accumulation of Si. This exploratory work presents the complexity of nutrient crosstalk under three stresses, and opens more questions about genetic networks that control plant physiological responses. Practically, we show a potential of Si application to improve P status and root health in oak seedlings, particularly in nurseries.

Two Xylella fastidiosa subsp. multiplex Strains Isolated from Almond in Spain Differ in Plasmid Content and Virulence Traits

The plant-pathogenic bacterium Xylella fastidiosa 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. X. fastidiosa subsp. multiplex ESVL and IVIA5901 strains that belong to sequence type 6 were isolated from almond orchards within the outbreak area in Alicante province (Spain). Both strains share more than 99% of the chromosomal sequences (average nucleotide identity), but the ESVL strain harbors two plasmids (pXF64-Hb_ESVL and pUCLA-ESVL). Here, virulence phenotypes and genome content were compared between both strains, using three strains from the United States as a reference for the phenotypic analyses. Experiments in microfluidic chambers, used as a simulation of xylem vessels, showed that twitching motility was absent in the IVIA5901 strain, whereas the ESVL strain had reduced twitching motility. In general, both Spanish strains had less biofilm formation, less cell aggregation, and lower virulence in tobacco compared with U.S. reference strains. Genome analysis of the two plasmids from ESVL revealed 51 unique coding sequences that were absent in the chromosome of IVIA5901. Comparison of the chromosomes of both strains showed some unique coding sequences and single-nucleotide polymorphisms 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 X. fastidiosa plasmids, our results indicate that the presence of plasmids should be considered in the study of the mechanisms of pathogenicity and adaptation in X. fastidiosa to new environments. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Zinc Oxide-Based Nanoformulation Zinkicide Mitigates the Xylem-Limited Pathogen Xylella fastidiosa in Tobacco and Southern Highbush Blueberry

The xylem-limited pathogen Xylella fastidiosa causes severe economic losses worldwide, and no effective antimicrobial disease management options are available. The goal of this study was to evaluate the efficacy of a novel ZnO-based nanoparticle formulation, Zinkicide TMN110 (ZnK), against X. fastidiosa in vitro and in planta. In vitro, minimum bactericidal concentration (MBC) of ZnK analyzed in Pierce's Disease 2 medium was estimated at approximately 60 ppm. Time-kill kinetics assay showed a 100% reduction of culturable X. fastidiosa in less than 1 h after ZnK treatment. Microfluidic chambers assays showed that ZnK also inhibits X. fastidiosa cell aggregation and growth under flow conditions. Phytotoxicity assessments in the greenhouse demonstrated that ZnK can be applied as a soil drench in 50 ml at 500 ppm/plant/week up to four times to tobacco and blueberry without causing visible damage. ZnK was also evaluated for disease control in the greenhouse using tobacco infected with X. fastidiosa subsp. fastidiosa strain TemeculaL. ZnK soil drench weekly applications at concentrations of 500 followed by 1,000 ppm (500/1,000) and 500/500/1,000 ppm (in 50 ml each), reduced X. fastidiosa populations by >2 to 3 log₁₀ units and disease severity by approximately 57 and 76%, respectively, compared with the untreated control. Similarly, when blueberry plants infected with X. fastidiosa subsp. multiplex strain AlmaEm3 were soil drenched with ZnK at concentrations 1,000/1,000 ppm and 1,000/1,000/500 ppm (in 200 ml each), the bacterial population was reduced by approximately 1 to 2 log₁₀ units, and disease severity decreased by approximately 39 and 43%, respectively. Overall, this study shows antibacterial activity of ZnK against X. fastidiosa and its effectiveness in plants to reduce disease symptoms under controlled conditions.

Nicotiana benthamiana as a model plant host for Xylella fastidiosa: Control of infections by transient expression and endotherapy with a bifunctional peptide

Transient expression of genes encoding peptides BP134 and BP178 by means of a Potato virus X (PVX) based-vector system, and treatment with synthetic peptides by endotherapy, were evaluated in the control of Xylella fastidiosa infections, in the model plant Nicotiana benthamiana. Transient production of BP178 significantly decreased disease severity compared to PVX and non-treated control (NTC) plants, without adverse effects. Plants treated with synthetic BP134 and BP178 showed consistently lower levels of disease than NTC plants. However, the coinfection with PVX-BP134 and X. fastidiosa caused detrimental effects resulting in plant death. The levels of X. fastidiosa in three zones sampled, upwards and downwards of the inoculation/treatment point, significantly decreased compared to the NTC plants, after the treatment with BP178, but not when BP178 was produced transiently. The effect of treatment and transient production of BP178 in the induction of defense-related genes was also studied. Synthetic BP178 applied by endotherapy induced the expression of ERF1, PR1a, PAL, PALII and WRKY25, while the transient expression of BP178 overexpressed the Cath, Cyc, PR4a, 9-LOX and Endochitinase B genes. Both treatments upregulated the expression of PR1, PR3, PR4 and CycT9299 genes compared to the NTC or PVX plants. It was concluded that the effect of BP178, either by endotherapy or by transient expression, on the control of the X. fastidiosa infections in N. benthamiana, was due in part to the induction of the plant defense system in addition to its bactericidal activity reported in previous studies. However, the protection observed when BP178 was transiently produced seems mainly mediated by the induction of plant defense, because the levels of X. fastidiosa were not significantly affected.

Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits

Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.

Pathogen Adaptation to the Xylem Environment

A group of aggressive pathogens have evolved to colonize the plant xylem. In this vascular tissue, where water and nutrients are transported from the roots to the rest of the plant, pathogens must be able to thrive under acropetal xylem sap flow and scarcity of nutrients while having direct contact only with predominantly dead cells. Nevertheless, a few bacteria have adapted to exclusively live in the xylem, and various pathogens may colonize other plant niches without causing symptoms unless they reach the xylem. Once established, the pathogens modulate its physicochemical conditions to enhance their growth and virulence. Adaptation to the restrictive lifestyle of the xylem leads to genome reduction in xylem-restricted bacteria, as they have a higher proportion of pseudogenes in their genome. The basis of xylem adaptation is not completely understood; therefore, a need still exists for model systems to advance the knowledge on this topic.

The Copper-Binding Protein CutC Is Involved in Copper Homeostasis and Affects Virulence in the Xylem-Limited Pathogen Xylella fastidiosa

Copper (Cu) is an essential element that can be toxic if homeostasis is disrupted. Xylella fastidiosa, a xylem-limited plant pathogenic bacterium that causes disease in many economically important crops worldwide, has been exposed to Cu stress caused by wide application of Cu-containing antimicrobials used to control other diseases. However, X. fastidiosa Cu homeostasis mechanisms are still poorly understood. The potentially Cu-related protein CutC, which is involved in Cu tolerance in Escherichia coli and humans, has not been analyzed functionally in plant pathogenic bacteria. We demonstrate that recombinantly expressed X. fastidiosa CutC binds Cu and deletion of cutC gene (PD0586) in X. fastidiosa showed increased sensitivity to Cu-shock compared with wild type (WT) strain TemeculaL. When infecting plants in the greenhouse, cutC mutant showed decreased disease incidence and severity compared with WT but adding Cu exaggerated severity. Interestingly, the inoculation of cutC mutant caused reduced symptoms in the acropetal regions of plants. We hypothesize that X. fastidiosa cutC is involved in Cu homeostasis by binding Cu in cells, leading to Cu detoxification, which is crucial to withstand Cu-shock stress. Unveiling the role of cutC gene in X. fastidiosa facilitates further understanding of Cu homeostasis in bacterial pathogens.

Visualising the ionome in resistant and susceptible plant-pathogen interactions

At the morphological and anatomical levels, the ionome, or the elemental composition of an organism, is an understudied area of plant biology. In particular, the ionomic responses of plant-pathogen interactions are scarcely described, and there are no studies on immune reactions. In this study we explored two X-ray fluorescence (XRF)-based ionome visualisation methods (benchtop- and synchrotron-based micro-XRF [µXRF]), as well as the quantitative inductively coupled plasma optical emission spectroscopy (ICP-OES) method, to investigate the changes that occur in the ionome of compatible and incompatible plant-pathogen interactions. We utilised the agronomically important and comprehensively studied interaction between potato (Solanum tuberosum) and the late blight oomycete pathogen Phytophthora infestans as an example. We used one late blight-susceptible potato cultivar and two resistant transgenic plant lines (only differing from the susceptible cultivar in one or three resistance genes) both in control and P. infestans-inoculated conditions. In the lesions from the compatible interaction, we observed rearrangements of several elements, including a decrease of the mobile macronutrient potassium (K) and an increase in iron (Fe) and manganese (Mn), compared with the tissue outside the lesion. Interestingly, we observed distinctly different distribution patterns of accumulation at the site of inoculation in the resistant lines for calcium (Ca), magnesium (Mg), Mn and silicon (Si) compared to the susceptible cultivar. The results reveal different ionomes in diseased plants compared to resistant plants. Our results demonstrate a technical advance and pave the way for deeper studies of the plant-pathogen ionome in the future.

Divergent abiotic spectral pathways unravel pathogen stress signals across species

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.

The Influence of Copper Homeostasis Genes copA and copB on Xylella fastidiosa Virulence Is Affected by Sap Copper Concentration

Xylella fastidiosa is a xylem-limited plant pathogenic bacterium that causes diseases worldwide in crops such as grape, citrus, and olive. Although copper (Cu)-containing compounds are not used for management of X. fastidiosa-caused diseases, they are widely used in X. fastidiosa hosts in vineyards and orchards. The accumulation of Cu in soils and, therefore, plant saps, could be a challenge for X. fastidiosa survival. Here, the molecular basis of Cu homeostasis was studied in relation to virulence. Although homologous Cu-related genes copA (X. fastidiosa loci PD0100) and copB (PD0101) have been characterized in other bacteria, their functions differ among bacterial species. In vitro, both copA and copB mutants were more sensitive to Cu than the wild-type (WT) strain. Interestingly, the copA mutant was more sensitive to Cu shock, while the copB mutant was more sensitive to chronic Cu treatments. In tobacco greenhouse experiments with normal watering, both mutants reduced virulence compared with WT. But when Cu was added as a drench treatment, both copA and copB mutants had increased disease severity approximately 20 and 50% compared with mutants without Cu added, respectively, which were significantly higher than the approximately 5% observed for WT under the same conditions. These results indicate that the pathogen's Cu homeostasis affects virulence and is influenced by Cu concentration in the environment. Understanding Cu homeostasis in X. fastidiosa will help discern the outcome of Cu treatments and the adaptation of this pathogen to the xylem of plants that have been exposed to high Cu concentrations because of agricultural practices.

Assessment of Ionomic, Phenolic and Flavonoid Compounds for a Sustainable Management of Xylella fastidiosa in Morocco

Morocco belongs to the countries ranked at a high-risk level for entry, establishment, and spread of Xylella fastidiosa, which has recently re-emerged as a plant pathogen of global importance causing olive quick decline syndrome (OQDS). Symptomatic infection by X. fastidiosa leads to devastating diseases and important economic losses. To prevent such losses and damages, countries without current outbreaks like Morocco need to first understand their host plant responses to X. fastidiosa. The assessment of the macro and micro-elements content (ionome) in leaves can give basic and useful information along with being a powerful tool for the sustainable management of diseases caused by this devastating pathogen. Herein, we compare the leaf ionome of four important autochthonous Moroccan olive cultivars (‘Picholine Marocaine’, ‘Haouzia’, ‘Menara’, and ‘Meslalla’), and eight Mediterranean varieties introduced in Morocco (‘Arbequina’, ‘Arbosana’, ‘Leccino’, ‘Ogliarola salentina’, ‘Cellina di Nardo’, ‘Frantoio’, ‘Leucocarpa’, and ‘Picholine de Languedoc’), to develop hypotheses related to the resistance or susceptibility of the Moroccan olive trees to X. fastidiosa infection. Leaf ionomes, mainly Ca, Cu, Fe, Mg, Mn, Na, Zn, and P, were determined using inductively coupled plasma optical emission spectroscopy (ICP-OES). These varieties were also screened for their total phenolics and flavonoids content. Data were then involved in a comparative scheme to determine the plasticity of the pathogen. Our results showed that the varieties ‘Leccino’, ’Arbosana’, ‘Arbequina’ consistently contained higher Mn, Cu, and Zn and lower Ca and Na levels compared with the higher pathogen-sensitive ‘Ogliarola salentina’ and ‘Cellina di Nardò’. Our findings suggest that ‘Arbozana’, ‘Arbiquina’, ‘Menara’, and ‘Haouzia’ may tolerate the infection by X. fastidiosa to varying degrees, provides additional support for ‘Leccino’ having resistance to X. fastidiosa, and suggests that both ‘Ogliarola salentina’ and ‘Cellina di Nardö’ are likely sensitive to X. fastidiosa infection.

Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants

Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.

Further In Vitro Assessment and Mid-Term Evaluation of Control Strategy of Xylella fastidiosa subsp. pauca in Olive Groves of Salento (Apulia, Italy)

During recent years; Xylella fastidiosa subsp. pauca (Xfp) has spread in Salento causing relevant damage to the olive groves. Measures to contain the spreading of the pathogen include the monitoring of the areas bordering the so-called "infected" zone and the tree eradication in case of positive detection. In order to provide a control strategy aimed to maintain the tree productivity in the infected areas, we further evaluated the in vitro and in planta mid-term effectiveness of a zinc-copper-citric acid biocomplex. The compound showed an in vitro bactericidal activity and inhibited the biofilm formation in representative strains of X. fastidiosa subspecies, including Xfp isolated in Apulia from olive trees. The field mid-term evaluation of the control strategy assessed by quantitative real-time PCR in 41 trees of two olive groves of the "infected" area revealed a low concentration of Xfp over the seasons upon the regular spraying of the biocomplex over 3 or 4 consecutive years. In particular, the bacterial concentration lowered in July and October with respect to March, after six consecutive treatments. The trend was not affected by the cultivar and it was similar either in the Xfp-sensitive cultivars Ogliarola salentina and Cellina di Nardò or in the Xfp-resistant Leccino. Moreover, the scoring of the number of wilted twigs over the seasons confirmed the trend. The efficacy of the treatment in the management of olive groves subjected to a high pathogen pressure is highlighted by the yielded a good oil production.

Overexpression of Citrus reticulata SAMT in Nicotiana tabacum increases MeSA volatilization and decreases Xylella fastidiosa symptoms

MAIN CONCLUSION

Nicotiana tabacum overexpressing CrSAMT from Citrus reticulata increased production of MeSA, which works as an airborne signal in neighboring wild-type plants, inducing PR1 and increasing resistance to the pathogen Xylella fastidiosa. Xylella fastidiosa is one of the major threats to plant health worldwide, affecting yield in many crops. Despite many efforts, the development of highly productive resistant varieties has been challenging. In studying host plant resistance, the S-adenosyl-L-methionine: salicylic acid carboxyl methyltransferase gene (SAMT) from Citrus reticulata, a X. fastidiosa resistant species, was upregulated in response to pathogen infection. SAMT is involved with the catalysis and production of methyl salicylate (MeSA), an airborne signal responsible for triggering systemic acquired resistance. Here we used tobacco as a model system and generated transgenic plants overexpressing C. reticulata SAMT (CrSAMT). We performed an in silico structural characterization of CrSAMT and investigated its biotechnological potential in modulating the immune system in transgenic plants. The increase of MeSA production in transgenic lines was confirmed by gas chromatography (GC-MS). The transgenic lines showed upregulation of PR1, and their incubation with neighboring wild-type plants activated PR1 expression, indicating that MeSA worked as an airborne signal. In addition, transgenic plants showed significantly fewer symptoms when challenged with X. fastidiosa. Altogether, these data suggest that CrSAMT plays a role in host defense response and can be used in biotechnology approaches to confer resistance against X. fastidiosa.

Grapevine phenolic compounds influence cell surface adhesion of Xylella fastidiosa and bind to lipopolysaccharide

Bacterial phytopathogen Xylella fastidiosa specifically colonizes the plant vascular tissue through a complex process of cell adhesion, biofilm formation, and dispersive movement. Adaptation to the chemical environment of the xylem is essential for bacterial growth and progression of infection. Grapevine xylem sap contains a range of plant secondary metabolites such as phenolics, which fluctuate in response to pathogen infection and plant physiological state. Phenolic compounds are often involved in host-pathogen interactions and influence infection dynamics through signaling activity, antimicrobial properties, and alteration of bacterial phenotypes. The effect of biologically relevant concentrations of phenolic compounds coumaric acid, gallic acid, epicatechin, and resveratrol on growth of X. fastidiosa was assessed in vitro. None of these compounds inhibited bacterial growth, but epicatechin and gallic acid reduced cell-surface adhesion. Cell-cell aggregation decreased with resveratrol treatment, but the other phenolic compounds tested had minimal effect on aggregation. Expression of attachment (xadA) and aggregation (fimA) related genes were altered by presence of the phenolic compounds, consistent with observed phenotypes. All four of the phenolic compounds bound to purified X. fastidiosa lipopolysaccharide (LPS), a major cell-surface component. Information regarding the impact of chemical environment on pathogen colonization in plants is important for understanding the infection process and factors associated with host susceptibility.

Natural Infection of Southern Highbush Blueberry (Vaccinium corymbosum Interspecific Hybrids) by Xylella fastidiosa subsp. fastidiosa

Xylella fastidiosa (Xf) is an emerging insect-vectored, xylem-limited bacterium that can cause disease on several economically important fruit and tree crops including almond, blueberry, citrus, grapevine, peach, and pecan. On blueberry, Xf causes bacterial leaf scorch (BLS), which is prevalent in the southeastern United States. This disease, previously reported to be caused by Xf subsp. multiplex (Xfm), can result in rapid plant decline and death of southern highbush (SHB) blueberry cultivars. In 2017, a survey of blueberry plantings in southern Georgia (U.S.A.) confirmed the presence of Xf-infected plants in eight of nine sites examined, and seven isolates were cultured from infected plants. Genetic characterization of these isolates through single-locus and multilocus sequence analysis revealed that three isolates from two sites belonged to Xf subsp. fastidiosa (Xff), with significant similarity to isolates from grapevine. After these three isolates were artificially inoculated onto greenhouse-grown SHB blueberries (cv. 'Rebel'), symptoms typical of BLS developed, and Xff infection was confirmed through genetic characterization and reisolation of the bacterium to fulfill Koch's postulates. Because all previously reported Xf isolates from blueberry have been characterized as Xfm, this is the first time that isolation of Xff has been reported from naturally infected blueberry plantings. The potential impact of Xff isolates on disease management in blueberry requires further exploration. Furthermore, given that isolates from both Xfm and Xff were obtained within a single naturally infected blueberry planting, blueberry in southern Georgia may provide opportunities for intersubspecific recombination between Xff and Xfm isolates.

Secondary Metabolites in Xylella fastidiosa-Plant Interaction

During their evolutionary history, plants have evolved the ability to synthesize and accumulate small molecules known as secondary metabolites. These compounds are not essential in the primary cell functions but play a significant role in the plants’ adaptation to environmental changes and in overcoming stress. Their high concentrations may contribute to the resistance of the plants to the bacterium Xylella fastidiosa, which has recently re-emerged as a plant pathogen of global importance. Although it is established in several areas globally and is considered one of the most dangerous plant pathogens, no cure has been developed due to the lack of effective bactericides and the difficulties in accessing the xylem vessels where the pathogen grows and produces cell aggregates and biofilm. This review highlights the role of secondary metabolites in the defense of the main economic hosts of X. fastidiosa and identifies how knowledge about biosynthetic pathways could improve our understanding of disease resistance. In addition, current developments in non-invasive techniques and strategies of combining molecular and physiological techniques are examined, in an attempt to identify new metabolic engineering options for plant defense.

Soil and Leaf Ionome Heterogeneity in Xylella fastidiosa Subsp. Pauca-Infected, Non-Infected and Treated Olive Groves in Apulia, Italy

Xylella fastidiosa subsp. pauca is responsible for the "olive quick decline syndrome" (OQDS) in Salento (Apulia). The main epidemiological aspects of the syndrome are related to the pathogen spread and survival in the area, and to the biology of the insect vector. The assessment of the macro and microelements content (i.e., ionome) in soil and leaves could provide basic and useful information. Indeed, knowledge of host ionomic composition and the possibility of its modification could represent a potential tool for the management of diseases caused by X. fastidiosa. Therefore, soil and leaf ionomes of naturally infected, not infected, and zinc-copper-citric acid biocomplex treated trees of different areas of Apulia and the bordering Basilicata regions were compared. We observed that soil and leaf ionomic composition of olive farms growing in the pathogen-free areas north of the Salento Barletta-Andria-Trani BAT (Apulia) and Potenza PZ (Basilicata, Apulia bordering region) provinces is significantly different from that shown by the infected olive groves of the Salento areas (LE, BR, TA provinces). In particular, a higher content of zinc and copper both in soil and leaves was found in the studied northern areas in comparison to the southern areas. This finding could partly explain the absence of OQDS in those areas. In the infected Salento areas, the leaf ionomic profile resulted as being markedly different for the biocomplex treated compared to the untreated trees. A higher zinc content in leaves characterized treated with respect to untreated trees. On the other hand, among the not-infected trees, Xylella-resistant Leccino showed higher manganese content when compared with the higher pathogen sensitive Ogliarola salentina and Cellina di Nardò. According to these results, soil and olive leaf ionome could provide basic information for the epidemiologic study and possible control of X. f. subsp. pauca in Apulia.

CRISPR/Cas9-mediated targeted mutagenesis of TAS4 and MYBA7 loci in grapevine rootstock 101-14

Pierce’s disease (PD) of grapevine (Vitis vinifera) is caused by the bacterium Xylella fastidiosa and is vectored by xylem sap-sucking insects, whereas Grapevine Red Blotch Virus (GRBV) causes Red Blotch Disease and is transmitted in the laboratory by alfalfa leafhopper Spissistilus festinus. The significance of anthocyanin accumulations in distinct tissues of grapevine by these pathogens is unknown, but vector feeding preferences and olfactory cues from host anthocyanins may be important for these disease etiologies. Phosphate, sugar, and UV light are known to regulate anthocyanin accumulation via miR828 and Trans-Acting Small-interfering locus4 (TAS4), specifically in grape by production of phased TAS4a/b/c small-interfering RNAs that are differentially expressed and target MYBA5/6/7 transcription factor transcripts for post-transcriptional slicing and antisense-mediated silencing. To generate materials that can critically test these genes’ functions in PD and GRBV disease symptoms, we produced transgenic grape plants targeting TAS4b and MYBA7 using CRISPR/Cas9 technology. We obtained five MYBA7 lines all with bi-allelic editing events and no off-targets detected at genomic loci with homology to the guide sequence. We obtained two independent edited TAS4b lines; one bi-allelic, the other heterozygous while both had fortuitous evidences of bi-allelic TAS4a off-target editing events at the paralogous locus. No visible anthocyanin accumulation phenotypes were observed in regenerated plants, possibly due to the presence of genetically redundant TAS4c and MYBA5/6 loci or absence of inductive environmental stress conditions. The editing events encompass single base insertions and di/trinucleotide deletions of Vvi-TAS4a/b and Vvi-MYBA7 at expected positions 3 nt upstream from the guideRNA proximal adjacent motifs NGG. We also identified evidences of homologous recombinations of TAS4a with TAS4b at the TAS4a off-target in one of the TAS4b lines, resulting in a chimeric locus with a bi-allelic polymorphism, supporting independent recombination events in transgenic plants associated with apparent high Cas9 activities. The lack of obvious visible pigment phenotypes in edited plants precluded pathogen challenge tests of the role of anthocyanins in host PD and GRBV resistance/tolerance mechanisms. Nonetheless, we demonstrate successful genome-editing of non-coding RNA and MYB transcription factor loci which can serve future characterizations of the functions of TAS4a/b/c and MYBA7 in developmental, physiological, and environmental biotic/abiotic stress response pathways important for value-added nutraceutical synthesis and pathogen responses of winegrape.

Differential Responses of Tobacco to the Citrus Variegated Chlorosis and Coffee Stem Atrophy Strains of Xylella fastidiosa

Xylella fastidiosa comprises a diverse group of xylem-limited, insect-transmitted bacterial pathogens. In Brazil, the citrus variegated chlorosis (CVC) and coffee stem atrophy (CSA) diseases are caused by X. fastidiosa subspecies pauca transmitted by common insect vectors. No simple protocol allowing strain discrimination exists, making epidemiological studies, which are important for devising control measures, difficult to undertake. Here, we show that both strains can easily be distinguished based on the pattern of leaf symptoms that they induce on pin prick-inoculated tobacco seedlings, namely small orange lesions and large necrotic lesions induced by the CVC and CSA strains, respectively. These differential responses allowed us to investigate whether mixed strain infections would occur in citrus or coffee trees in the field. Seedlings were individually inoculated with X. fastidiosa colonies recovered from citrus or coffee plants from various locations at three different times. No mixed infections were detected. In two experiments, the citrus and coffee strains infected only their original hosts as well as tobacco. The usefulness of this tobacco bioassay as a tool to study X. fastidiosa spread was demonstrated. It provided evidence that, over the years, the CVC and CSA pathogens have remained limited to their original hosts, despite crop proximity and the presence of sharpshooter vectors that favor transmission of the bacteria to and between both host species.

Copper Supplementation in Watering Solution Reaches the Xylem But Does Not Protect Tobacco Plants Against Xylella fastidiosa Infection

Xylella fastidiosa is a xylem-limited plant pathogenic bacterium that causes disease in many crops worldwide. Copper (Cu) is an antimicrobial agent widely used on X. fastidiosa hosts to control other diseases. Although the effects of Cu for control of foliar pathogens are well known, it is less studied on xylem-colonizing pathogens. Previous results from our group showed that low concentrations of CuSO4 increased biofilm formation, whereas high concentrations inhibited biofilm formation and growth in vitro. In this study, we conducted in planta experiments to determine the influence of Cu in X. fastidiosa infection using tobacco as a model. X. fastidiosa-infected and noninfected plants were watered with tap water or with water supplemented with 4 mM or 8 mM of CuSO4. Symptom progression was assessed, and sap and leaf ionome analysis was performed by inductively coupled plasma with optical emission spectroscopy. Cu uptake was confirmed by increased concentrations of Cu in the sap of plants treated with CuSO4-amended water. Leaf scorch symptoms in Cu-supplemented plants showed a trend toward more severe at later time points. Quantification of total and viable X. fastidiosa in planta indicated that CuSO4-amended treatments did not inhibit but slightly increased the growth of X. fastidiosa. Cu in sap was in the range of concentrations that promote X. fastidiosa biofilm formation according to our previous in vitro study. Based on these results, we proposed that the plant Cu homeostasis machinery controls the level of Cu in the xylem, preventing it from becoming elevated to a level that would lead to bacterial inhibition.

Dominant, Heritable Resistance to Stewart's Wilt in Maize Is Associated with an Enhanced Vascular Defense Response to Infection with Pantoea stewartii

Vascular wilt bacteria such as Pantoea stewartii, the causal agent of Stewart's bacterial wilt of maize (SW), are destructive pathogens that are difficult to control. These bacteria colonize the xylem, where they form biofilms that block sap flow leading to characteristic wilting symptoms. Heritable forms of SW resistance exist and are used in maize breeding programs but the underlying genes and mechanisms are mostly unknown. Here, we show that seedlings of maize inbred lines with pan1 mutations are highly resistant to SW. However, current evidence suggests that other genes introgressed along with pan1 are responsible for resistance. Genomic analyses of pan1 lines were used to identify candidate resistance genes. In-depth comparison of P. stewartii interaction with susceptible and resistant maize lines revealed an enhanced vascular defense response in pan1 lines characterized by accumulation of electron-dense materials in xylem conduits visible by electron microscopy. We propose that this vascular defense response restricts P. stewartii spread through the vasculature, reducing both systemic bacterial colonization of the xylem network and consequent wilting. Though apparently unrelated to the resistance phenotype of pan1 lines, we also demonstrate that the effector WtsE is essential for P. stewartii xylem dissemination, show evidence for a nutritional immunity response to P. stewartii that alters xylem sap composition, and present the first analysis of maize transcriptional responses to P. stewartii infection.

Ionomic Differences between Susceptible and Resistant Olive Cultivars Infected by Xylella fastidiosa in the Outbreak Area of Salento, Italy

Olive quick decline syndrome (OQDS) is a devastating disease of olive trees in the Salento region, Italy. This disease is caused by the bacterium Xylella fastidiosa, which is widespread in the outbreak area; however, the “Leccino” variety of olives has proven to be resistant with fewer symptoms and lower bacterial populations than the “Ogliarola salentina” variety. We completed an empirical study to determine the mineral and trace element contents (viz; ionome) of leaves from infected trees comparing the two varieties, to develop hypotheses related to the resistance of Leccino trees to X. fastidiosa infection. All samples from both cultivars tested were infected by X. fastidiosa, even if leaves were asymptomatic at the time of collection, due to the high disease pressure in the outbreak area and the long incubation period of this disease. Leaves were binned for the analysis by variety, field location, and infected symptomatic and infected asymptomatic status by visual inspection. The ionome of leaf samples was determined using inductively coupled plasma optical emission spectroscopy (ICP-OES) and compared with each other. These analyses showed that Leccino variety consistently contained higher manganese (Mn) levels compared with Ogliarola salentina, and these levels were higher in both infected asymptomatic and infected symptomatic leaves. Infected asymptomatic and infected symptomatic leaves within a host genotype also showed differences in the ionome, particularly a higher concentration of calcium (Ca) and Mn levels in the Leccino cultivar, and sodium (Na) in both varieties. We hypothesize that the ionome differences in the two varieties contribute to protection against disease caused by X. fastidiosa infection.

Infections of the Xylella fastidiosa subsp. pauca Strain "De Donno" in Alfalfa (Medicago sativa) Elicits an Overactive Immune Response

Diseases caused by Xylella fastidiosa are among the most destructive for several agricultural productions. A deadly disease of olive, termed olive quick decline syndrome, is one of the most recent examples of the severe impacts caused by the introduction and spread of this bacterium in new ecosystems with favorable epidemiological conditions. Deciphering the cascade of events leading to the development of severe alterations in the susceptible host plants is a priority of several research programs investigating strategies to mitigate the detrimental impacts of the infections. However, in the case of olives, the long latent period (>1 year) makes this pathosystem not amenable for such studies. We have inoculated alfalfa (Medicago sativa) with the olive-infecting strain “De Donno” isolated from a symptomatic olive in Apulia (Italy), and we demonstrated that this highly pathogenic strain causes an overactive reaction that ends up with the necrosis of the inoculated stem, a reaction that differs from the notoriously Alfalfa Dwarf disease, caused by X. fastidiosa strains isolated from grapes and almonds. RNASeq analysis showed that major plant immunity pathways are activated, in particular, several calcium transmembrane transporters and enzymes responsible for the production of reactive oxygen species (ROS). Signs of the necrotic reaction are anticipated by the upregulation of genes responsible for plant cell death and the hypersensitive reaction. Overall the whole infection process takes four months in alfalfa, which makes this pathosystem suitable for studies involving either the plant response to the infection or the role of Xylella genes in the expression of symptoms.

Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa

High rates of homologous recombination (HR) in the bacterial plant pathogen Xylella fastidiosa have been previously detected. This study aimed to determine the extent and explore the ecological significance of HR in the genomes of recombinants experimentally generated by natural transformation and wild-type isolates. Both sets of strains displayed widespread HR and similar average size of recombined fragments consisting of random events (2-10 kb) of inter- and intrasubspecific recombination. A significantly higher proportion and greater lengths (>10 kb, maximum 31.5 kb) of recombined fragments were observed in subsp. morus and in strains isolated in Europe from intercepted coffee plants shipped from the Americas. Such highly recombinant strains pose a serious risk of emergence of novel variants, as genetically distinct and formerly geographically isolated genotypes are brought in close proximity by global trade. Recently recombined regions in wild-type strains included genes involved in regulation and signaling, host colonization, nutrient acquisition, and host evasion, all fundamental traits for X. fastidiosa ecology. Identification of four recombinant loci shared between wild-type and experimentally generated recombinants suggests potential hotspots of recombination in this naturally competent pathogen. These findings provide insights into evolutionary forces possibly affecting the adaptive potential to colonize the host environments of X. fastidiosa.

Urinary ionomic analysis reveals new relationship between minerals and longevity in a Han Chinese population

Human longevity involves genetic, nutritional, environmental and many other factors playing a key role in healthy aging. Previous studies have shown that mineral metabolism and homeostasis are associated with lifespan extension. However, the majority of them have focused on a limited number of elements and ignored the complex relationship between them. In this study, we carried out a network-based approach to investigate the urinary ionome of nonagenarians and centenarians (longevity group) when compared with their biologically unrelated and younger family members (control group) from a Han Chinese population. Several differentially changed elements were identified, almost all of which showed an elevated level in the longevity group. Correlation analysis of the ionome revealed significant element-element interactions in each group. We then divided each group into distinct subgroups according to age ranges, and built the elemental correlation network for each of them. Significant elemental correlations and correlation changes involving all examined elements were identified within or between different subgroups, implying a highly dynamic and complex crosstalk among the elements during human life. Finally, more similar elemental patterns were observed between extremely old and middle-aged people. Overall, our data reveal new relationship between urinary minerals and human longevity, which may extend our understanding of the mechanism of healthy aging.

The Ionomics of Lettuce Infected by Xanthomonas campestris pv. vitians

Bacterial leaf spot (BLS) caused by Xanthomonas campestris pv. vitians (Xcv) places a major constraint on lettuce production worldwide. The most sustainable strategy known to date for controlling BLS is the use of resistant cultivars. The nutrient elemental signature (ionome) of ten lettuce cultivars with three levels of resistance was analyzed by inductively coupled plasma optical emission spectroscopy (ICP-OES) to determine which nutrient balances are linked to resistance to BLS, and to assess the effect of Xcv infection on the ionome. The elemental concentrations were preprocessed with isometric log-ratios to define nutrient balances. Using this approach, 4 out of 11 univariate nutrient balances were found to significantly influence the resistance of lettuce cultivars to BLS (P < 0.05). These significant balances were the overall nutritional status balancing all measured nutrients with their complementary in the dry mass, as well as balances [Mn | Zn,Cu], [Zn | Cu], and [S,N | P]. Moreover, the infection of lettuce cultivars mostly affected the lettuce ionome on the [N,S | P] balance, where infection tended to lean the balance toward the N,S part relatively to P. This study shows that nutrient uptake in lettuce can be affected by BLS infection and that nutrient status influences resistance to BLS infection.

Xylella fastidiosa subsp. pauca and fastidiosa Colonize Arabidopsis Systemically and Induce Anthocyanin Accumulation in Infected Leaves

The bacterium Xylella fastidiosa is a multihost pathogen that affects perennial crops such as grapevine, sweet orange, and olive tree worldwide. It is inherently difficult to study these pathosystems owing to the long-term growth habit of the host plant. Thus, the availability of model plants becomes essential to accelerate discoveries with economic impact. In this study, we uncovered evidence that the model plant Arabidopsis thaliana can be colonized by two different X. fastidiosa subspecies, pauca and fastidiosa. We observed that these bacteria are able to move away from the inoculation point as high bacterial populations were found in distant tissues. In addition, confocal laser scanning microscopy analysis of bacterial movement inside the petiole revealed the ability of the bacterium to move against the net xylem flow during the time course of colonization forming biofilm. These findings provide evidence for the capacity of X. fastidiosa to colonize Arabidopsis. Furthermore, leaves inoculated with X. fastidiosa showed a significant accumulation of anthocyanin. We propose that the X. fastidiosa subsp. pauca or fastidiosa colonization pattern and anthocyanin accumulation in the Arabidopsis ecotype Col-0 can be used as marker phenotypes to facilitate further studies aimed at improving genetic components involved in X. fastidiosa-host interaction.

Xylella fastidiosa in Olive in Apulia: Where We Stand

A dramatic outbreak of Xylella fastidiosa decimating olive was discovered in 2013 in Apulia, Southern Italy. This pathogen is a quarantine bacterium in the European Union (EU) and created unprecedented turmoil for the local economy and posed critical challenges for its management. With the new emerging threat to susceptible crops in the EU, efforts were devoted to gain basic knowledge on the pathogen biology, host, and environmental interactions (e.g., bacterial strain(s) and pathogenicity, hosts, vector(s), and fundamental drivers of its epidemics) in order to find means to control or mitigate the impacts of the infections. Field surveys, greenhouse tests, and laboratory analyses proved that a single bacterial introduction occurred in the area, with a single genotype, belonging to the subspecies pauca, associated with the epidemic. Infections caused by isolates of this genotype turned to be extremely aggressive on the local olive cultivars, causing a new disease termed olive quick decline syndrome. Due to the initial extension of the foci and the rapid spread of the infections, eradication measures (i.e., pathogen elimination from the area) were soon replaced by containment measures including intense border surveys of the contaminated area, removal of infected trees, and mandatory vector control. However, implementation of containment measures encountered serious difficulties, including public reluctance to accept control measures, poor stakeholder cooperation, misinformation from some media outlets, and lack of robust responses by some governmental authorities. This scenario delayed and limited containment efforts and allowed the bacterium to continue its rapid dissemination over more areas in the region, as shown by the continuous expansion of the official borders of the infected area. At the research level, the European Commission and regional authorities are now supporting several programs aimed to find effective methods to mitigate and contain the impact of X. fastidiosa on olives, the predominant host affected in this epidemic. Preliminary evidence of the presence of resistance in some olive cultivars represents a promising approach currently under investigation for long-term management strategies. The present review describes the current status of the epidemic and major research achievements since 2013.

Genome Editing: Targeting Susceptibility Genes for Plant Disease Resistance

Plant pathogens pose a major threat to crop productivity. Typically, phytopathogens exploit plants' susceptibility (S) genes to facilitate their proliferation. Disrupting these S genes may interfere with the compatibility between the host and the pathogens and consequently provide broad-spectrum and durable disease resistance. In the past, genetic manipulation of such S genes has been shown to confer disease resistance in various economically important crops. Recent studies have accomplished this task in a transgene-free system using new genome editing tools, including clustered regularly interspaced palindromic repeats (CRISPR). In this Opinion article, we focus on the use of genome editing to target S genes for the development of transgene-free and durable disease-resistant crop varieties.

A framework for model analysis across multiple experiment regimes: Investigating effects of zinc on Xylella fastidiosa as a case study

Mathematical models are ubiquitous in analyzing dynamical biological systems. However, it might not be possible to explicitly account for the various sources of uncertainties in the model and the data if there is limited experimental data and information about the biological processes. The presence of uncertainty introduces problems with identifiability of the parameters of the model and determining appropriate regions to explore with respect to sensitivity and estimates of parameter values. Since the model analysis is likely dependent on the numerical estimates of the parameters, parameter identifiability should be addressed beforehand to capture biologically relevant parameter space. Here, we propose a framework which uses data from different experiment regimes to identify a region in the parameter space over which subsequent mathematical analysis can be conducted. Along with building confidence in the parameter estimates, it provides us with variations in the parameters due to changes in the experimental conditions. To determine significance of these variations, we conduct global sensitivity analysis, allowing us to make testable hypothesis for effects of changes in the experimental conditions on the biological system. As a case study, we develop a model for growth dynamics and biofilm formation of a bacterial plant pathogen, and use our framework to identify possible effects of zinc on the bacterial populations in different metabolic states. The framework reveals underlying issues with parameter identifiability and identifies a suitable region in the parameter space, sensitivity analysis over which informs us about the parameters that might be affected by addition of zinc. Moreover, these parameters prove to be identifiable in this region.

Physiological and genetic characterization of calcium phosphate precipitation by Pseudomonas species

Microbial biomineralization is a widespread phenomenon. The ability to induce calcium precipitation around bacterial cells has been reported in several Pseudomonas species but has not been thoroughly tested. We assayed 14 Pseudomonas strains representing five different species for the ability to precipitate calcium. Calcium phosphate precipitated adjacent to the colonies of all the Pseudomonas strains tested and also precipitated on the surface of colonies for several of the Pseudomonas strains assayed. The precipitate was commonly precipitated as amorphous calcium phosphate, however seven of the 14 Pseudomonas strains tested precipitated amorphous apatite in agar adjacent to the colonies. Out of the seven Pseudomonas strains that precipitated amorphous apatite, six are plant pathogenic. The formation of amorphous apatite was commonly observed in the area of the agar where amorphous calcium phosphate had previously formed. A transposon mutagenesis screen in Pseudomonas syringae pv. tomato DC3000 revealed genes involved in general metabolism, lipopolysaccharide and cell wall biogenesis, and in regulation of virulence play a role in calcium precipitation. These results shed light on the common ability of Pseudomonas species to perform calcium precipitation and the underlying genetic regulation involved in biomineralization.

Previsual symptoms of Xylella fastidiosa infection revealed in spectral plant-trait alterations

Plant pathogens cause significant losses to agricultural yields and increasingly threaten food security¹, ecosystem integrity and societies in general^2-5. Xylella fastidiosa is one of the most dangerous plant bacteria worldwide, causing several diseases with profound impacts on agriculture and the environment⁶. Primarily occurring in the Americas, its recent discovery in Asia and Europe demonstrates that X. fastidiosa's geographic range has broadened considerably, positioning it as a reemerging global threat that has caused socioeconomic and cultural damage^7,8. X. fastidiosa can infect more than 350 plant species worldwide⁹, and early detection is critical for its eradication⁸. In this article, we show that changes in plant functional traits retrieved from airborne imaging spectroscopy and thermography can reveal X. fastidiosa infection in olive trees before symptoms are visible. We obtained accuracies of disease detection, confirmed by quantitative polymerase chain reaction, exceeding 80% when high-resolution fluorescence quantified by three-dimensional simulations and thermal stress indicators were coupled with photosynthetic traits sensitive to rapid pigment dynamics and degradation. Moreover, we found that the visually asymptomatic trees originally scored as affected by spectral plant-trait alterations, developed X. fastidiosa symptoms at almost double the rate of the asymptomatic trees classified as not affected by remote sensing. We demonstrate that spectral plant-trait alterations caused by X. fastidiosa infection are detectable previsually at the landscape scale, a critical requirement to help eradicate some of the most devastating plant diseases worldwide.

Ca2+-Induced Two-Component System CvsSR Regulates the Type III Secretion System and the Extracytoplasmic Function Sigma Factor AlgU in Pseudomonas syringae pv. tomato DC3000

Two-component systems (TCSs) of bacteria regulate many different aspects of the bacterial life cycle, including pathogenesis. Most TCSs remain uncharacterized, with no information about the signal(s) or regulatory targets and/or role in bacterial pathogenesis. Here, we characterized a TCS in the plant-pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 composed of the histidine kinase CvsS and the response regulator CvsR. CvsSR is necessary for virulence of P. syringae pv. tomato DC3000, since ΔcvsS and ΔcvsR strains produced fewer symptoms than the wild type (WT) and demonstrated reduced growth on multiple hosts. We discovered that expression of cvsSR is induced by Ca²⁺ concentrations found in leaf apoplastic fluid. Thus, Ca²⁺ can be added to the list of signals that promote pathogenesis of P. syringae pv. tomato DC3000 during host colonization. Through chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) and global transcriptome analysis (RNA-seq), we discerned the CvsR regulon. CvsR directly activated expression of the type III secretion system regulators, hrpR and hrpS, that regulate P. syringae pv. tomato DC3000 virulence in a type III secretion system-dependent manner. CvsR also indirectly repressed transcription of the extracytoplasmic sigma factor algU and production of alginate. Phenotypic analysis determined that CvsSR inversely regulated biofilm formation, swarming motility, and cellulose production in a Ca²⁺-dependent manner. Overall, our results show that CvsSR is a key regulatory hub critical for interaction with host plants.IMPORTANCE Pathogenic bacteria must be able to react and respond to the surrounding environment, make use of available resources, and avert or counter host immune responses. Often, these abilities rely on two-component systems (TCSs) composed of interacting proteins that modulate gene expression. We identified a TCS in the plant-pathogenic bacterium Pseudomonas syringae that responds to the presence of calcium, which is an important signal during the plant defense response. We showed that when P. syringae is grown in the presence of calcium, this TCS regulates expression of factors contributing to disease. Overall, our results provide a better understanding of how bacterial pathogens respond to plant signals and control systems necessary for eliciting disease.

The Major Outer Membrane Protein MopB Is Required for Twitching Movement and Affects Biofilm Formation and Virulence in Two Xylella fastidiosa strains

MopB is a major outer membrane protein (OMP) in Xylella fastidiosa, a bacterial plant pathogen that causes losses on many economically important crops. Based on in silico analysis, the uncharacterized MopB protein of X. fastidiosa contains a β-barrel structure with an OmpA-like domain and a predicted calcium-binding motif. Here, MopB function was studied by mutational analysis taking advantage of the natural competence of X. fastidiosa. Mutants of mopB were constructed in two different X. fastidiosa strains, the type strain Temecula and the more virulent WM1-1. Deletion of the mopB gene impaired cell-to-cell aggregation, surface attachment, and biofilm formation in both strains. Interestingly, mopB deletion completely abolished twitching motility. Electron microscopy of the bacterial cell surface revealed that mopB deletion eliminated type IV and type I pili formation, potentially caused by destabilization of the outer membrane. Both mopB mutants showed reduced virulence using tobacco (Nicotiana tabacum) as a host under greenhouse conditions. These results suggest that MopB has pleiotropic functions in biofilm formation and twitching motility and is important for virulence of X. fastidiosa.

Natural Competence Rates Are Variable Among Xylella fastidiosa Strains and Homologous Recombination Occurs In Vitro Between Subspecies fastidiosa and multiplex

Xylella fastidiosa, an etiological agent of emerging crop diseases around the world, is naturally competent for the uptake of DNA from the environment that is incorporated into its genome by homologous recombination. Homologous recombination between subspecies of X. fastidiosa was inferred by in silico studies and was hypothesized to cause disease emergence. However, no experimental data are available on the degree to which X. fastidiosa strains are capable of competence and whether recombination can be experimentally demonstrated between subspecies. Here, using X. fastidiosa strains from different subspecies, natural competence in 11 of 13 strains was confirmed with plasmids containing antibiotic markers flanked by homologous regions and, in three of five strains, with dead bacterial cells used as source of donor DNA. Recombination frequency differed among strains and was correlated to growth rate and twitching motility. Moreover, intersubspecific recombination occurred readily between strains of subsp. fastidiosa and multiplex, as demonstrated by movement of antibiotic resistance and green fluorescent protein from donor to recipient cells and confirmed by DNA sequencing of the flanking arms of recombinant strains. Results demonstrate that natural competence is widespread among X. fastidiosa strains and could have an impact in pathogen adaptation and disease development.

In vitro Determination of Extracellular Proteins from Xylella fastidiosa

The phytopathogen Xylella fastidiosa causes economic losses in important agricultural crops. Xylem vessel occlusion caused by biofilm formation is the major mechanism underlying the pathogenicity of distinct strains of X. fastidiosa. Here, we provide a detailed in vitro characterization of the extracellular proteins of X. fastidiosa. Based on the results, we performed a comparison with a strain J1a12, which cannot induce citrus variegated chlorosis symptoms when inoculated into citrus plants. We then extend this approach to analyze the extracellular proteins of X. fastidiosa in media supplemented with calcium. We verified increases in extracellular proteins concomitant with the days of growth and, consequently, biofilm development (3-30 days). Outer membrane vesicles carrying toxins were identified beginning at 10 days of growth in the 9a5c strain. In addition, a decrease in extracellular proteins in media supplemented with calcium was observed in both strains. Using mass spectrometry, 71 different proteins were identified during 30 days of X. fastidiosa biofilm development, including proteases, quorum-sensing proteins, biofilm formation proteins, hypothetical proteins, phage-related proteins, chaperones, toxins, antitoxins, and extracellular vesicle membrane components.

New insights on molecular regulation of biofilm formation in plant-associated bacteria

Biofilms are complex bacterial assemblages with a defined three-dimensional architecture, attached to solid surfaces, and surrounded by a self-produced matrix generally composed of exopolysaccharides, proteins, lipids and extracellular DNA. Biofilm formation has evolved as an adaptive strategy of bacteria to cope with harsh environmental conditions as well as to establish antagonistic or beneficial interactions with their host. Plant-associated bacteria attach and form biofilms on different tissues including leaves, stems, vasculature, seeds and roots. In this review, we examine the formation of biofilms from the plant-associated bacterial perspective and detail the recently-described mechanisms of genetic regulation used by these organisms to orchestrate biofilm formation on plant surfaces. In addition, we describe plant host signals that bacterial pathogens recognize to activate the transition from a planktonic lifestyle to multicellular behavior.

Calcium transcriptionally regulates the biofilm machinery of Xylella fastidiosa to promote continued biofilm development in batch cultures

The functions of calcium (Ca) in bacteria are less characterized than in eukaryotes, where its role has been studied extensively. The plant-pathogenic bacterium Xylella fastidiosa has several virulence features that are enhanced by increased Ca concentrations, including biofilm formation. However, the specific mechanisms driving modulation of this feature are unclear. Characterization of biofilm formation over time showed that 4 mM Ca supplementation produced denser biofilms that were still developing at 96 h, while biofilm in non-supplemented media had reached the dispersal stage by 72 h. To identify changes in global gene expression in X. fastidiosa grown in supplemental Ca, RNA-Seq of batch culture biofilm cells was conducted at three 24-h time intervals. Results indicate that a variety of genes are differentially expressed in response to Ca, including genes related to attachment, motility, exopolysaccharide synthesis, biofilm formation, peptidoglycan synthesis, regulatory functions, iron homeostasis, and phages. Collectively, results demonstrate that Ca supplementation induces a transcriptional response that promotes continued biofilm development, while biofilm cells in nonsupplemented media are driven towards dispersion of cells from the biofilm structure. These results have important implications for disease progression in planta, where xylem sap is the source of Ca and other nutrients for X. fastidiosa.

A Two-Dimensional Multiphase Model of Biofilm Formation in Microfluidic Chambers

The bacterial pathogen Xylella fastidiosa is the causal agent of many pathological conditions of economically important agricultural crops. There is no known cure for X. fastidiosa diseases, and management of the problem is based solely in controlling the population of insect vectors, which is somewhat effective. The bacterium causes disease by forming biofilms inside the vascular system of the plant, a process that is poorly understood. In microfluidic chambers, used as artificial xylem vessels, this bacterium has been observed to reproducibly cluster into a distinct, regular pattern of aggregates, spatially separated by channels of non-biofilm components. We develop a multiphase model in two dimensions, which recapitulates this spatial patterning, suggesting that bacterial growth and attachment/detachment processes are strongly influential modulators of these patterns. This indicates plausible strategies, such as the addition of metals and chelators, for mitigating the severity of diseases induced by this bacterial pathogen.

Zinc Detoxification Is Required for Full Virulence and Modification of the Host Leaf Ionome by Xylella fastidiosa

Zinc (Zn) is an essential element for all forms of life because it is a structural or catalytic cofactor of many proteins, but it can have toxic effects at high concentrations; thus, microorganisms must tightly regulate its levels. Here, we evaluated the role of Zn homeostasis proteins in the virulence of the xylem-limited bacterium Xylella fastidiosa, causal agent of Pierce's disease of grapevine, among other diseases. Two mutants of X. fastidiosa 'Temecula' affected in genes which regulate Zn homeostasis (zur) and Zn detoxification (czcD) were constructed. Both knockouts showed increased sensitivity to Zn at physiologically relevant concentrations and increased intracellular accumulation of this metal compared with the wild type. Increased Zn sensitivity was correlated with decreased growth in grapevine xylem sap, reduced twitching motility, and downregulation of exopolysaccharide biosynthetic genes. Tobacco plants inoculated with either knockout mutant showed reduced foliar symptoms and a much reduced (czcD) or absent (zur) modification of the leaf ionome (i.e., the mineral nutrient and trace element composition), as well as reduced bacterial populations. The results show that detoxification of Zn is crucial for the virulence of X. fastidiosa and verifies our previous findings that modification of the host leaf ionome correlates with bacterial virulence.

Calcium-Enhanced Twitching Motility in Xylella fastidiosa Is Linked to a Single PilY1 Homolog

The plant-pathogenic bacterium Xylella fastidiosa is restricted to the xylem vessel environment, where mineral nutrients are transported through the plant host; therefore, changes in the concentrations of these elements likely impact the growth and virulence of this bacterium. Twitching motility, dependent on type IV pili (TFP), is required for movement against the transpiration stream that results in basipetal colonization. We previously demonstrated that calcium (Ca) increases the motility of X. fastidiosa, although the mechanism was unknown. PilY1 is a TFP structural protein recently shown to bind Ca and to regulate twitching and adhesion in bacterial pathogens of humans. Sequence analysis identified three pilY1 homologs in X. fastidiosa (PD0023, PD0502, and PD1611), one of which (PD1611) contains a Ca-binding motif. Separate deletions of PD0023 and PD1611 resulted in mutants that still showed twitching motility and were not impaired in attachment or biofilm formation. However, the response of increased twitching at higher Ca concentrations was lost in the pilY1-1611 mutant. Ca does not modulate the expression of any of the X. fastidiosa PilY1 homologs, although it increases the expression of the retraction ATPase pilT during active movement. The evidence presented here suggests functional differences between the PilY1 homologs, which may provide X. fastidiosa with an adaptive advantage in environments with high Ca concentrations, such as xylem sap.

Ionome changes in Xylella fastidiosa-infected Nicotiana tabacum correlate with virulence and discriminate between subspecies of bacterial isolates

Characterization of ionomes has been used to uncover the basis of nutrient utilization and environmental adaptation of plants. Here, ionomic profiles were used to understand the phenotypic response of a plant to infection by genetically diverse isolates of Xylella fastidiosa, a gram-negative, xylem-limited bacterial plant pathogen. In this study, X. fastidiosa isolates were used to infect a common model host (Nicotiana tabacum 'SR1'), and leaf and sap concentrations of eleven elements together with plant colonization and symptoms were assessed. Multivariate statistical analysis revealed that changes in the ionome were significantly correlated with symptom severity and bacterial populations in host petioles. Moreover, plant ionome modification by infection could be used to differentiate the X. fastidiosa subspecies with which the plant was infected. This report establishes host ionome modification as a phenotypic response to infection.

Response of Xylella fastidiosa to zinc: decreased culturability, increased exopolysaccharide production, and formation of resilient biofilms under flow conditions

The bacterial plant pathogen Xylella fastidiosa produces biofilm that accumulates in the host xylem vessels, affecting disease development in various crops and bacterial acquisition by insect vectors. Biofilms are sensitive to the chemical composition of the environment, and mineral elements being transported in the xylem are of special interest for this pathosystem. Here, X. fastidiosa liquid cultures were supplemented with zinc and compared with nonamended cultures to determine the effects of Zn on growth, biofilm, and exopolysaccharide (EPS) production under batch and flow culture conditions. The results show that Zn reduces growth and biofilm production under both conditions. However, in microfluidic chambers under liquid flow and with constant bacterial supplementation (closer to conditions inside the host), a dramatic increase in biofilm aggregates was seen in the Zn-amended medium. Biofilms formed under these conditions were strongly attached to surfaces and were not removed by medium flow. This phenomenon was correlated with increased EPS production in stationary-phase cells grown under high Zn concentrations. Zn did not cause greater adhesion to surfaces by individual cells. Additionally, viability analyses suggest that X. fastidiosa may be able to enter the viable but nonculturable state in vitro, and Zn can hasten the onset of this state. Together, these findings suggest that Zn can act as a stress factor with pleiotropic effects on X. fastidiosa and indicate that, although Zn could be used as a bactericide treatment, it could trigger the undesired effect of stronger biofilm formation upon reinoculation events.

Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development?

The facility and versatility of microRNAs (miRNAs) to evolve and change likely underlies how they have become dominant constituents of eukaryotic genomes. In this opinion article I propose that trans-acting small interfering RNA gene 4 (TAS4) evolution may be important for biosynthesis of polyphenolics, arbuscular symbiosis, and bacterial pathogen etiologies. Expression-based and phylogenetic evidence shows that TAS4 targets two novel grape (Vitis vinifera L.) MYB transcription factors (VvMYBA6, VvMYBA7) that spawn phased small interfering RNAs (siRNAs) which probably function in nutraceutical bioflavonoid biosynthesis and fruit development. Characterization of the molecular mechanisms of TAS4 control of plant development and integration into biotic and abiotic stress- and nutrient-signaling regulatory networks has applicability to molecular breeding and the development of strategies for engineering healthier foods.