Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems

Pseudogenes and host specialization in the emergent bacterial plant pathogen Xylella fastidiosa

Pseudogenes are regarded as "junk" DNA, representing vestigial functions no longer needed for fitness. Accordingly, a higher number of pseudogenes in a bacterial human pathogen was previously hypothesized to be a hallmark of host specialists. In this study, we tested this hypothesis on the emergent bacterial plant pathogen Xylella fastidiosa (Xf) to link pseudogene makeup and host specificity. Xf is an ideal subject for these studies by being a xylem-limited pathogen that underwent extensive genome reduction. Using natural host range data of 151 strains and Pseudofinder analysis on Xf whole genome sequences, we observed that Xf subsp. sandyi had the highest pseudogene content, followed by subsp. morus, while subsp. pauca, fastidiosa, and multiplex had the lowest. The first two subspecies are known to have a limited host range compared to the others, aligning with the hypothesis of a greater number of pseudogenes corresponding to narrower host range. Weed isolates are presumably host specialists because they had the highest pseudogene content. Using a thorough pseudogene map across genomes and empirical pathogenicity data on blueberries, we screened for genes potentially involved in blueberry specialization. Targets were identified by selecting sequences pseudogenized (i) in strains infecting hosts different from blueberry and (ii) only in blueberry asymptomatic strains. Six sequences were identified with a potential role in blueberry infection, including one that was common between the two criteria. Here, we generated hypotheses on host range and specificity of Xf strains that need to be tested experimentally to help understand this devastating plant pathogen.IMPORTANCEXylella fastidiosa is a highly destructive plant pathogen that infects hundreds of landscape and agriculturally important plant species mainly in Europe and the Americas. Nevertheless, the host range of specific genotypes and underlying mechanisms of host specificity remain unclear. These are important aspects to determine the potential risk of infection in specific areas depending on the genetic makeup of the pathogen population and hosts present. This study offers valuable insights into the role of pseudogenization in the genomes of different X. fastidiosa strains, linking it to host specialization. Despite the limited information available for the host range of different strains of this pathogen, this research proposes a relationship between the abundance of pseudogenes and host specificity. These findings are essential for predicting potential host shifts by this pathogen, aiding in the development of strategies to prevent its spread. Additionally, the identification of candidate genes putatively important for symptom development in blueberries offers targets for prevention and control efforts.

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.

Ten Challenges to Understanding and Managing the Insect-Transmitted, Xylem-Limited Bacterial Pathogen Xylella fastidiosa

An unprecedented plant health emergency in olives has been registered over the last decade in Italy, arguably more severe than what occurred repeatedly in grapes in the United States in the last 140 years. These emergencies are epidemics caused by a stealthy pathogen, the xylem-limited, insect-transmitted bacterium Xylella fastidiosa. Although these epidemics spurred research that answered many questions about the biology and management of this pathogen, many gaps in knowledge remain. For this review, we set out to represent both the U.S. and European perspectives on the most pressing challenges that need to be addressed. These are presented in 10 sections that we hope will stimulate discussion and interdisciplinary research. We reviewed intrinsic problems that arise from the fastidious growth of X. fastidiosa, the lack of specificity for insect transmission, and the economic and social importance of perennial mature woody plant hosts. Epidemiological models and predictions of pathogen establishment and disease expansion, vital for preparedness, are based on very limited data. Most of the current knowledge has been gathered from a few pathosystems, whereas several hundred remain to be studied, probably including those that will become the center of the next epidemic. Unfortunately, aspects of a particular pathosystem are not always transferable to others. We recommend diversification of research topics of both fundamental and applied nature addressing multiple pathosystems. Increasing preparedness through knowledge acquisition is the best strategy to anticipate and manage diseases caused by this pathogen, described as "the most dangerous plant bacterium known worldwide."

Sensitivity of Xylella fastidiosa subsp. pauca Salento-1 to light at 410 nm

All over the world, from America to the Mediterranean Sea, the plant pathogen Xylella fastidiosa represents one of the most difficult challenges with many implications at ecological, agricultural, and economic levels. X. fastidiosa is a rod-shaped Gram-negative bacterium belonging to the family of Xanthomonadaceae. It grows at very low rates and infects a wide range of plants thanks to different vectors. Insects, through their stylets, suck a sap rich in nutrients and inject bacteria into xylem vessels. Since, until now, no antimicrobial treatment has been successfully applied to kill X. fastidiosa and/or prevent its diffusion, in this study, antimicrobial blue light (aBL) was explored as a potential anti-Xylella tool. Xylella fastidiosa subsp. pauca Salento-1, chosen as a model strain, showed a certain degree of sensitivity to light at 410 nm. The killing effect was light dose dependent and bacterial concentration dependent. These preliminary results support the potential of blue light in decontamination of agricultural equipment and/or plant surface; however, further investigations are needed for in vivo applications.

Xylem Embolism and Pathogens: Can the Vessel Anatomy of Woody Plants Contribute to X. fastidiosa Resistance?

The maintenance of an intact water column in the xylem lumen several meters above the ground is essential for woody plant viability. In fact, abiotic and biotic factors can lead to the formation of emboli in the xylem, interrupting sap flow and causing consequences on the health status of the plant. Anyway, the tendency of plants to develop emboli depends on the intrinsic features of the xylem, while the cyto-histological structure of the xylem plays a role in resistance to vascular pathogens, as in the case of the pathogenic bacterium Xylella fastidiosa. Analysis of the scientific literature suggests that on grapevine and olive, some xylem features can determine plant tolerance to vascular pathogens. However, the same trend was not reported in citrus, indicating that X. fastidiosa interactions with host plants differ by species. Unfortunately, studies in this area are still limited, with few explaining inter-cultivar insights. Thus, in a global context seriously threatened by X. fastidiosa, a deeper understanding of the relationship between the physical and mechanical characteristics of the xylem and resistance to stresses can be useful for selecting cultivars that may be more resistant to environmental changes, such as drought and vascular pathogens, as a way to preserve agricultural productions and ecosystems.

Natural Recombination among Type I Restriction-Modification Systems Creates Diverse Genomic Methylation Patterns among Xylella fastidiosa Strains

Xylella fastidiosa is an important bacterial plant pathogen causing high-consequence diseases in agricultural crops around the world. Although as a species X. fastidiosa can infect many host plants, there is significant variability between strains regarding virulence on specific host plant species and other traits. Natural competence and horizontal gene transfer are believed to occur frequently in X. fastidiosa and likely influence the evolution of this pathogen. However, some X. fastidiosa strains are difficult to manipulate genetically using standard transformation techniques. Several type I restriction-modification (R-M) systems are encoded in the X. fastidiosa genome, which may influence horizontal gene transfer and recombination. Type I R-M systems themselves may undergo recombination, exchanging target recognition domains (TRDs) between specificity subunits (hsdS) to generate novel alleles with new target specificities. In this study, several conserved type I R-M systems were compared across 129 X. fastidiosa genome assemblies representing all known subspecies and 32 sequence types. Forty-four unique TRDs were identified among 50 hsdS alleles, which are arrayed in 31 allele profiles that are generally conserved within a monophyletic cluster of strains. Inactivating mutations were identified in type I R-M systems of specific strains, showing heterogeneity in the complements of functional type I R-M systems across X. fastidiosa. Genomic DNA methylation patterns were characterized in 20 X. fastidiosa strains and associated with type I R-M system allele profiles. Overall, these data suggest hsdS genes recombine among Xylella strains and/or unknown donors, and the resulting TRD reassortment establishes differential epigenetic modifications across Xylella lineages. IMPORTANCE Economic impacts on agricultural production due to X. fastidiosa have been severe in the Americas, Europe, and parts of Asia. Despite a long history of research on this pathogen, certain fundamental questions regarding the biology, pathogenicity, and evolution of X. fastidiosa have still not been answered. Wide-scale whole-genome sequencing has begun to provide more insight into X. fastidiosa genetic diversity and horizontal gene transfer, but the mechanics of genomic recombination in natural settings and the extent to which this directly influences bacterial phenotypes such as plant host range are not well understood. Genome methylation is an important factor in horizontal gene transfer and bacterial recombination that has not been comprehensively studied in X. fastidiosa. This study characterizes methylation associated with type I restriction-modification systems across a wide range of X. fastidiosa strains and lays the groundwork for a better understanding of X. fastidiosa biology and evolution through epigenetics.

Integrating Science on Xanthomonas and Xylella for Integrated Plant Disease Management

Present, emerging or re-emerging plant diseases due to infection by bacteria of the Lysobacteraceae (syn: Xanthomonadaceae) family are continually challenging food security and cause significant losses to the economies of European countries each year [...].

Xylella fastidiosa in Europe: From the Introduction to the Current Status

Xylella fastidiosa is xylem-limited bacterium capable of infecting a wide range of host plants, resulting in Pierce's disease in grapevine, citrus variegated chlorosis, olive quick decline syndrome, peach phony disease, plum leaf scald, alfalfa dwarf, margin necrosis and leaf scorch affecting oleander, coffee, almond, pecan, mulberry, red maple, oak, and other types of cultivated and ornamental plants and forest trees. In the European Union, X. fastidiosa is listed as a quarantine organism. Since its first outbreak in the Apulia region of southern Italy in 2013 where it caused devastating disease on Olea europaea (called olive leaf scorch and quick decline), X. fastidiosa continued to spread and successfully established in some European countries (Corsica and PACA in France, Balearic Islands, Madrid and Comunitat Valenciana in Spain, and Porto in Portugal). The most recent data for Europe indicates that X. fastidiosa is present on 174 hosts, 25 of which were newly identified in 2021 (with further five hosts discovered in other parts of the world in the same year). From the six reported subspecies of X. fastidiosa worldwide, four have been recorded in European countries (fastidiosa, multiplex, pauca, and sandyi). Currently confirmed X. fastidiosa vector species are Philaenus spumarius, Neophilaenus campestris, and Philaenus italosignus, whereby only P. spumarius (which has been identified as the key vector in Apulia, Italy) is also present in Americas. X. fastidiosa control is currently based on pathogen-free propagation plant material, eradication, territory demarcation, and vector control, as well as use of resistant plant cultivars and bactericidal treatments.

Using Genomes and Evolutionary Analyses to Screen for Host-Specificity and Positive Selection in the Plant Pathogen Xylella fastidiosa

Xylella fastidiosa infects several economically important crops in the Americas, and it also recently emerged in Europe. Here, using a set of Xylella genomes reflective of the genus-wide diversity, we performed a pan-genome analysis based on both core and accessory genes for two purposes: (i) to test associations between genetic divergence and plant host species and (ii) to identify positively selected genes that are potentially involved in arms-race dynamics. For the former, tests yielded significant evidence for the specialization of X. fastidiosa to plant host species. This observation contributes to a growing literature suggesting that the phylogenetic history of X. fastidiosa lineages affects the host range. For the latter, our analyses uncovered evidence of positive selection across codons for 5.3% (67 of 1,257) of the core genes and 5.4% (201 of 3,691) of the accessory genes. These genes are candidates to encode interacting factors with plant and insect hosts. Most of these genes had unknown functions, but we did identify some tractable candidates, including nagZ_2, which encodes a beta-glucosidase that is important for Neisseria gonorrhoeae biofilm formation; cya, which modulates gene expression in pathogenic bacteria, and barA, a membrane associated histidine kinase that has roles in cell division, metabolism, and pili formation.

IMPORTANCEXylella fastidiosa causes devasting diseases to several critical crops. Because X. fastidiosa colonizes and infects many plant species, it is important to understand whether the genome of X. fastidiosa has genetic determinants that underlie specialization to specific host plants. We analyzed genome sequences of X. fastidiosa to investigate evolutionary relationships and to test for evidence of positive selection on specific genes. We found a significant signal between genome diversity and host plants, consistent with bacterial specialization to specific plant hosts. By screening for positive selection, we identified both core and accessory genes that may affect pathogenicity, including genes involved in biofilm formation.

The XadA Trimeric Autotransporter Adhesins in Xylella fastidiosa Differentially Contribute to Cell Aggregation, Biofilm Formation, Insect Transmission and Virulence to Plants

Surface adhesion strategies are widely employed by bacterial pathogens during establishment and systemic spread in their host. A variety of cell-surface appendages such as pili, fimbriae, and afimbrial adhesins are involved in these processes. The phytopathogen Xylella fastidiosa employs several of these structures for efficient colonization of its insect and plant hosts. Among the adhesins encoded in the X. fastidiosa genome, three afimbrial adhesins, XadA1, Hsf/XadA2, and XadA3, are predicted to be trimeric autotransporters with a C-terminal YadA-anchor membrane domain. We analyzed the individual contributions of XadA1, XadA2, and XadA3 to various cellular behaviors both in vitro and in vivo. Using isogenic X. fastidiosa mutants, we found that cell-cell aggregation and biofilm formation were severely impaired in the absence of XadA3. No significant reduction of cell-surface attachment was found with any mutant under flow conditions. Acquisition by insect vectors and transmission to grapevines were reduced in the XadA3 deletion mutant. While the XadA3 mutant was hypervirulent in grapevines, XadA1 or XadA2 deletion mutants conferred lower disease severity than the wild-type strain. This insight of the importance of these adhesive proteins and their individual contributions to different aspects of X. fastidiosa biology should guide new approaches to reduce pathogen transmission and disease development. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.