Xylella fastidiosa: Insights into an Emerging Plant Pathogen

Phenology, seasonal abundance and stage-structure of spittlebug (Hemiptera: Aphrophoridae) populations in olive groves in Italy

Spittlebugs (Hemiptera: Aphrophoridae) are the dominant xylem-sap feeders in the Mediterranean area and the only proven vectors of Xylella fastidiosa ST53, the causal agent of the olive dieback epidemic in Apulia, Italy. We have investigated the structured population phenology, abundance and seasonal movement between crops and wild plant species of both the nymphal and adult stages of different spittlebug species in olive groves. Field surveys were conducted during the 2016-2018 period in four olive orchards located in coastal and inland areas in the Apulia and Liguria regions in Italy. The nymphal population in the herbaceous cover was estimated using quadrat samplings. Adults were collected through sweep nets on three different vegetational components: herbaceous cover, olive canopy and wild woody plants. Philaenus spumarius was the most abundant species; its nymphs were collected from early March and reached a peak around mid-April, when the 4th instar was prevalent. Spittlebug adults were collected from late April until late autumn. P. spumarius adults were abundant on the herbaceous cover and olive trees in late spring, and they then dispersed to wild woody hosts during the summer and returned to the olive groves in autumn when searching for oviposition sites in the herbaceous cover. A relatively high abundance of P. spumarius was observed on olive trees during summer in the Liguria Region. The present work provides a large amount of data on the life cycle of spittlebugs within an olive agroecosystem that can be used to design effective control programmes against these vectors in infected areas and to assess the risk of the establishment and spread of X. fastidiosa to Xylella-free areas.

Calcium transcriptionally regulates movement, recombination and other functions of Xylella fastidiosa under constant flow inside microfluidic chambers

Xylella fastidiosa is a xylem‐limited bacterial pathogen causing devastating diseases in many economically important crops. Calcium (Ca) is a major inorganic nutrient in xylem sap that influences virulence‐related traits of this pathogen, including biofilm formation and twitching motility. This study aimed to adapt a microfluidic system, which mimics the natural habitat of X. fastidiosa, for whole transcriptome analysis under flow conditions. A microfluidic chamber with two parallel channels was used, and RNA isolated from cells grown inside the system was analysed by RNA‐Seq. Ca transcriptionally regulated the machinery of type IV pili and other genes related to pathogenicity and host adaptation. Results were compared to our previous RNA‐Seq study in biofilm cells in batch cultures (Parker et al., 2016, Environ Microbiol 18, 1620). Ca‐regulated genes in both studies belonged to similar functional categories, but the number and tendencies (up‐/downregulation) of regulated genes were different. Recombination‐related genes were upregulated by Ca, and we proved experimentally that 2 mM Ca enhances natural transformation frequency. Taken together, our results suggest that the regulatory role of Ca in X. fastidiosa acts differently during growth in flow or batch conditions, and this can correlate to the different phases of growth (planktonic and biofilm) during the infection process.

Transmission of Xylella fastidiosa Subspecies Pauca Sequence Type 53 by Different Insect Species

Diseases associated with Xylella fastidiosa have been described mostly in North and South America. However, during the last five years, widespread X. fastidiosa infections have been reported in a constrained area of the Apulia region (southern Italy), in olives trees suffering a severe disease, denoted as Olive Quick Decline Syndrome (OQDS). Because many xylem sap-feeding insects can function as vectors for the transmission of this exotic pathogen in EU, several research programs are ongoing to assess the role of candidate vectors in the spread of the infections. Initial investigations identified Philaenus spumarius (L.) as the predominant vector species in the olive orchards affected by the OQDS. Additional experiments have been carried out during 2016 and 2017 to assess the role of other species. More specifically, adults of the spittlebugs Philaenus italosignus Drosopolous and Remane, Neophilaenus campestris (Fallen) and of the planthopper Latilica tunetana (Matsumura) (Issidae) have been tested in transmission experiments to assess their ability to acquire the bacterium from infected olives and to infect different susceptible hosts (olives, almond, myrtle –leaf milkwort, periwinkle). Acquisition rates determined by testing individual insects in quantitative PCR assays, ranging from 5.6% in N. campestris to 22.2% in P. italosignus, whereas no acquisition was recorded for L. tunetana. Successful transmissions were detected in the recipient plants exposed to P. italosignus and N. campestris, whereas no trasmissions occurred with L. tunetana. The known vector Philaenus spumarius has been included in all the experiments for validation. The systematic surveys conducted in 2016 and 2017 provided further evidence on the population dynamics and seasonal abundance of the spittlebug populations in the olive groves.

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.

Proteomic and Metabolomic Analyses of Xylella fastidiosa OMV-Enriched Fractions Reveal Association with Virulence Factors and Signaling Molecules of the DSF Family

Xylella fastidiosa releases outer membrane vesicles (OMVs) known to play a role in the systemic dissemination of this pathogen. OMVs inhibit bacterial attachment to xylem wall and traffic lipases/esterases that act on the degradation of plant cell wall. Here, we extended the characterization of X. fastidiosa OMVs by identifying proteins and metabolites potentially associated with OMVs produced by Temecula1, a Pierce's disease strain, and by 9a5c and Fb7, two citrus variegated chlorosis strains. These results strengthen that one of the OMVs multiple functions is to carry determinants of virulence, such as lipases/esterases, adhesins, proteases, porins, and a pectin lyase-like protein. For the first time, we show that the two citrus variegated chlorosis strains produce X. fastidiosa diffusible signaling factor 2 (DSF2) and citrus variegated chlorosis-DSF (likewise, Temecula1) and most importantly, that these compounds of the DSF (X. fastidiosa DSF) family are associated with OMV-enriched fractions. Altogether, our findings widen the potential functions of X. fastidiosa OMVs in intercellular signaling and host-pathogen interactions.

Genomic Diversity and Recombination among Xylella fastidiosa Subspecies

Xylella fastidiosa is an economically important bacterial plant pathogen. With insights gained from 72 genomes, this study investigated differences among the three main subspecies, which have allopatric origins: X. fastidiosa subsp. fastidiosa, multiplex, and pauca The origin of recombinogenic X. fastidiosa subsp. morus and sandyi was also assessed. The evolutionary rate of the 622 genes of the species core genome was estimated at the scale of an X. fastidiosa subsp. pauca subclade (7.62 × 10-7 substitutions per site per year), which was subsequently used to estimate divergence time for the subspecies and introduction events. The study characterized genes present in the accessory genome of each of the three subspecies and investigated the core genome to detect genes potentially under positive selection. Recombination is recognized to be the major driver of diversity in X. fastidiosa, potentially facilitating shifts to novel plant hosts. The relative effect of recombination in comparison to point mutation was calculated (r/m = 2.259). Evidence of recombination was uncovered in the core genome alignment; X. fastidiosa subsp. fastidiosa in the United States was less prone to recombination, with an average of 3.22 of the 622 core genes identified as recombining regions, whereas a specific clade of X. fastidiosa subsp. multiplex was found to have on average 9.60 recombining genes, 93.2% of which originated from X. fastidiosa subsp. fastidiosa Interestingly, for X. fastidiosa subsp. morus, which was initially thought to be the outcome of genome-wide recombination between X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex, intersubspecies homologous recombination levels reached 15.30% in the core genome. Finally, there is evidence of X. fastidiosa subsp. pauca strains from citrus containing genetic elements acquired from strains infecting coffee plants as well as genetic elements from both X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex In summary, our data provide new insights into the evolution and epidemiology of this plant pathogen.IMPORTANCEXylella fastidiosa is an important vector-borne plant pathogen. We used a set of 72 genomes that constitutes the largest assembled data set for this bacterial species so far to investigate genetic relationships and the impact of recombination on phylogenetic clades and to compare genome content at the subspecies level, and we used a molecular dating approach to infer the evolutionary rate of X. fastidiosa The results demonstrate that recombination is important in shaping the genomes of X. fastidiosa and that each of the main subspecies is under different selective pressures. We hope insights from this study will improve our understanding of X. fastidiosa evolution and biology.

Update of the Scientific Opinion on the risks to plant health posed by Xylella fastidiosa in the EU territory

EFSA was asked to update the 2015 EFSA risk assessment on Xylella fastidiosa for the territory of the EU. In particular, EFSA was asked to focus on potential establishment, short- and long-range spread, the length of the asymptomatic period, the impact of X. fastidiosa and an update on risk reduction options. EFSA was asked to take into account the different subspecies and Sequence Types of X. fastidiosa. This was attempted throughout the scientific opinion but several issues with data availability meant that this could only be partially achieved. Models for risk of establishment showed most of the EU territory may be potentially suitable for X. fastidiosa although southern EU is most at risk. Differences in estimated areas of potential establishment were evident among X. fastidiosa subspecies, particularly X. fastidiosa subsp. multiplex which demonstrated areas of potential establishment further north in the EU. The model of establishment could be used to develop targeted surveys by Member States. The asymptomatic period of X. fastidiosa varied significantly for different host and pathogen subspecies combinations, for example from a median of approximately 1 month in ornamental plants and up to 10 months in olive, for pauca. This variable and long asymptomatic period is a considerable limitation to successful detection and control, particularly where surveillance is based on visual inspection. Modelling suggested that local eradication (e.g. within orchards) is possible, providing sampling intensity is sufficient for early detection and effective control measures are implemented swiftly (e.g. within 30 days). Modelling of long-range spread (e.g. regional scale) demonstrated the important role of long-range dispersal and the need to better understand this. Reducing buffer zone width in both containment and eradication scenarios increased the area infected. Intensive surveillance for early detection, and consequent plant removal, of new outbreaks is crucial for both successful eradication and containment at the regional scale, in addition to effective vector control. The assessment of impacts indicated that almond and Citrus spp. were at lower impact on yield compared to olive. Although the lowest impact was estimated for grapevine, and the highest for olive, this was based on several assumptions including that the assessment considered only Philaenus spumarius as a vector. If other xylem-feeding insects act as vectors the impact could be different. Since the Scientific Opinion published in 2015, there are still no risk reduction options that can remove the bacterium from the plant in open field conditions. Short- and long-range spread modelling showed that an early detection and rapid application of phytosanitary measures, consisting among others of plant removal and vector control, are essential to prevent further spread of the pathogen to new areas. Further data collection will allow a reduction in uncertainty and facilitate more tailored and effective control given the intraspecific diversity of X. fastidiosa and wide host range.

Distribution and Genetic Diversity of Xylella fastidiosa subsp. pauca Associated with Olive Quick Syndrome Symptoms in Southeastern Brazil

In Brazil, the host expansion of Xylella fastidiosa subsp. pauca was recently demonstrated with the report of diseased olive trees (Olea europaea), whose symptoms were associated with olive quick decline syndrome previously described in southern Italy. We employed both polymerase chain reaction-based techniques and culture medium isolation to investigate the geographic distribution of X. fastidiosa as well as the genetic signatures of 21 strains isolated from 11 olive orchards in both São Paulo and Minas Gerais States in Brazil. X. fastidiosa subsp. pauca was detected in 83% of the orchards examined in the region, and was positively diagnosed in 43.7% of all sampled plants with typical scorching symptoms. Of the 21 strains characterized with fast-evolving microsatellite (single sequence repeat [SSR]) markers, 20 different multilocus microsatellite genotypes were observed with the overall allelic diversity of H_Nei = 0.38. Principal component analysis using the SSR markers clustered all strains, except for three, in one cluster demonstrating a limited range of genetic diversity. Multilocus sequence typing analysis showed the prevalence of a sequence type (ST16) in 75% of the samples; three other novel STs (84, 85, and 86), were detected, all belonging to the X. fastidiosa subsp. pauca cluster. These results show that genetically diverse strains of X. fastidiosa subsp. pauca are widely present in olive orchards in southeastern Brazil, which is consistent with the long history of this bacterium in that region.

Understanding How an Invasive Vector Drives Pierce's Disease Epidemics: Seasonality and Vine-to-Vine Spread

For vector-borne plant pathogens, disease epidemics may be attributable to multiple mechanisms, including introduction of a novel vector whose epidemiological role differs from that of native vectors. In such cases, understanding an exotic vector's ability to drive an epidemic is central to mitigating its impact. We studied how the invasive glassy-winged sharpshooter (Homalodisca vitripennis Germar) can drive Pierce's disease outbreaks in vineyards, focusing on its potential to promote vine-to-vine (i.e., secondary) spread of Xylella fastidiosa relative to potential constraints stemming from seasonality in the pathosystem. First, we developed a general vector-borne disease model to understand the consequences for disease dynamics of (i) seasonal acquisition efficiency and (ii) seasonal host recovery from infection. Results of the modeling indicate that these two sources of seasonality could constrain disease incidence, particularly when working in concert. Next, we established a field cage experiment to determine whether H. vitripennis promotes vine-to-vine spread, and looked for evidence of seasonality in spread. Broadly, results from the experiment supported assumptions of the model; there was modest to significant increase in the frequency of pathogen spread over the first season, and those new infections that occurred later in the season were more likely to recover during winter. Ultimately, by the end of the second season, there was not evidence of significant secondary spread, likely due to a combination of seasonal constraints and low transmission efficiency by H. vitripennis. Collectively, these results suggest that, although H. vitripennis may be able to promote vine-to-vine spread in certain contexts, it may not be the key factor explaining its impact. Rather, the ability of H. vitripennis to drive epidemics is likely to be more directly related to its potential to reach higher population densities than native vectors.

The Epidemiology of Xylella fastidiosa; A Perspective on Current Knowledge and Framework to Investigate Plant Host-Vector-Pathogen Interactions

Insect-transmitted plant diseases caused by viruses, phytoplasmas, and bacteria share many features in common regardless of the causal agent. This perspective aims to show how a model framework, developed originally for plant virus diseases, can be modified for the case of diseases incited by Xylella fastidiosa. In particular, the model framework enables the specification of a simple but quite general invasion criterion defined in terms of key plant, pathogen, and vector parameters and, importantly, their interactions, which determine whether or not an incursion or isolated outbreak of a pathogen will lead to establishment, persistence, and subsequent epidemic development. Hence, this approach is applicable to the wide range of X. fastidiosa-incited diseases that have recently emerged in southern Europe, each with differing host plant, pathogen subspecies, and vector identities. Of particular importance are parameters relating to vector abundance and activity, transmission characteristics, and behavior in relation to preferences for host infection status. Some gaps in knowledge with regard to the developing situation in Europe are noted.

Money Matters: Fueling Rapid Recent Insight Into Xylella fastidiosa-An Important and Expanding Global Pathogen

Xylella fastidiosa has emerged from relative obscurity into one of the most well-studied bacterial plant pathogens. While Pierce's disease of grape caused by this pathogen has been recognized as an important disease in warmer regions of the United States for nearly 100 years, the causal pathogen, X. fastidiosa has spread throughout much of the world and now also causes serious diseases of citrus, coffee, almond, olive, and other important crop plants. Our knowledge of this pathogen has been driven by the recent substantial research support justified by the economic importance of these diseases.

Identifying Lookouts for Epidemio-Surveillance: Application to the Emergence of Xylella fastidiosa in France

Recent detections of Xylella fastidiosa in Corsica Island, France, has raised concerns on its possible spread to mainland France and the rest of the Mediterranean Basin. Early detection of infected plants is paramount to prevent the spread of the bacteria, but little is known about this pathosystem in European environments, hence standard surveillance strategies may be ineffective. We present a new methodological approach for the design of risk-based surveillance strategies, adapted to the emerging risk caused by X. fastidiosa. Our proposal is based on a combination of machine learning techniques and network analysis that aims at understanding the main abiotic drivers of the infection, produce risk maps and identify lookouts for the design of future surveillance plans. The identified drivers coincide with known results in laboratory studies about the correlation between environmental variables, such as water stress and temperature, and the presence of the bacterium in plants. Furthermore, the produced risk maps overlap nicely with detected foci of infection, while they also highlight other susceptible regions where X. fastidiosa has not been found yet. We conclude the paper presenting a list of recommended regions for a risk-based surveillance campaign based on the predicted spread and probability of early detection of the disease.

Biological Control of Pierce's Disease of Grape by an Endophytic Bacterium

Effective preventive measures and therapies are lacking for control of Pierce's disease of grape caused by the xylem-colonizing bacterium Xylella fastidiosa responsible for serious losses in grape production. In this study we explored the potential for endophytic bacteria to alter the disease process. While most endophytic bacteria found within grape did not grow or multiply when inoculated into mature grape vines, Paraburkholderia phytofirmans strain PsJN achieved population sizes as large as 10⁶ cells/g and moved 1 m or more within 4 weeks after inoculation into vines. While X. fastidiosa achieved large population sizes and moved extensively in grape when inoculated alone, few viable cells were recovered from plants in which it was co-inoculated with strain PsJN and the incidence of leaves exhibiting scorching symptoms typical of Pierce's disease was consistently greatly reduced from that in control plants. Suppression of disease symptoms occurred not only when strain PsJN was co-inoculated with the pathogen by puncturing stems in the same site in plants, but also when inoculated at the same time but at different sites in the plant. Large population sizes of strain PsJN could be established in both leaf lamina and petioles by topical application of cell suspensions in 0.2% of an organo-silicon surfactant conferring low surface tension, and such treatments were as effective as direct puncture inoculations of this biocontrol strain in reducing disease severity. While inoculation of strain PsJN into plants by either method at the same time as or even 4 weeks after that of the pathogen resulted in large reductions in disease severity, much less disease control was conferred by inoculation of PsJN 4 weeks prior to that of the pathogen. The expression of grapevine PR1 and ETR1 within 3 weeks of inoculation was substantially higher in plants inoculated with both X. fastidiosa and strain PsJN compared with that in plants inoculated only with the pathogen or strain PsJN, suggesting that this biological control agent reduces disease by priming expression of innate disease resistance pathways in plants that otherwise would have exhibited minimal responses to the pathogen. Strain PsJN thus appears highly efficacious for the control of Pierce's disease when used as an eradicant treatment that can be easily made even by spray application.

GIS Analysis of Land-Use Change in Threatened Landscapes by Xylella fastidiosa

Land-use/land-cover analysis using Geographic Information System (GIS) application can describe and quantify the transformation of the landscape, evaluating the effectiveness of municipal planning in driving urban expansion. This approach was applied in the municipality of Spongano (Salento, South Italy) in order to evaluate the spatial heterogeneity and the transformations of the land use/land cover from 1988 to 2016. This approach was also used to examine the spread of Xylella fastidiosa, which is a plant pathogen of global importance that is reshaping the Salento landscape. The land-use maps are based on the CORINE Land Cover project classification, while the topological consistency was verified through field surveys. A change detection analysis was carried out using the land-use maps of 1988 and 2016. The most extensive land-use class is olive groves (34–36%), followed by non-irrigated arable lands and shrub and/or herbaceous vegetation associations. The main transition of land involved non-irrigated arable lands, which lost 76 ha and 23 ha to shrub and olive areas, respectively. Meanwhile, the artificial surfaces class doubled its extension, which involved mainly the transition from shrub and heterogeneous agricultural areas. However, the olive groves class is threatened by the dramatic phytosanitary condition of the area, indicating a compromised agroecosystem, which is causing a de facto transition into unproductive areas. The results highlight the inconsistency between what was planned by the urban plan in the past and how the landscape of Spongano has been changed over time. This evidence suggests that it is necessary to develop a plan based on learning by doing, in order to shape and adapt the processes of territorial transformation to the unpredictability of the ecologic, social, and economic systems, as well as ensure that these processes are always focused on environmental issues.

Temporal Dynamics of the Sap Microbiome of Grapevine Under High Pierce's Disease Pressure

Grapevine is a pillar of the California state economy and agricultural identity. This study provides a comprehensive culture-independent microbiome analysis from the sap of grapevine overtime and in a context of a vascular disease. The vascular system plays a key role by transporting nutrient, water and signals throughout the plant. The negative pressure in the xylem conduits, and low oxygen and nutrient content of its sap make it a unique and underexplored microbial environment. We hypothesized that grapevine hosts in its sap, microbes that have a beneficial impact on plant health by protecting against pathogen attack and supporting key biological processes. To address this hypothesis, we chose a vineyard under high Pierce's disease (PD). PD is caused by the xylem-dwelling pathogenic bacterium Xylella fastidiosa. We selected ten grapevines within this vineyard with a range of disease phenotypes, and monitored them over 2 growing seasons. We sampled each vines at key phenological stages (bloom, veraison, and post-harvest) and used an amplicon metagenomics approach to profile the bacterial (16S -V4) and fungal (ITS) communities of the sap. We identified a core microbiome of the sap composed of seven bacterial (Streptococcus, Micrococcus, Pseudomonas, Bacteroides, Massilia, Acinetobacter and Bacillus) and five fungal (Cladosporium, Mycosphaerella, Alternaria, Aureobasidium, and Filobasidium) taxa that were present throughout the growing season. Overall, the sap microbial makeup collected from canes was more similar to the root microbial profile. Alpha diversity metrics indicated a microbial enrichment at bloom and in vines with moderate PD severity suggesting a host-driven microbial response to environmental cues. Beta diversity metrics demonstrated that disease condition and plant phenology impacted microbial community profiles. Our study identified several potential taxonomic targets with antimicrobial and plant growth promoting capabilities that inhabit the grapevine sap and that should be further tested as potential biological control or biofertilizer agents.

Novel amplification targets for rapid detection and differentiation of Xylella fastidiosa subspecies fastidiosa and multiplex in plant and insect tissues

Xylella fastidiosa is an insect-transmitted bacterial plant pathogen which causes a variety of economically important diseases worldwide. Molecular identification of X. fastidiosa is used for quarantine screening, surveillance, and research applications; many of which require subspecies level differentiation of pathogen isolates. This study describes quantitative PCR (qPCR) and isothermal amplification assays which can rapidly identify X. fastidiosa isolates belonging to the fastidiosa and multiplex subspecies. The TaqMan qPCR primers described here are used to differentiate X. fastidiosa strains by subspecies in plant and insect tissue in a single reaction, with the inclusion of a general amplification control probe to identify potential false negative samples. This TaqMan qPCR protocol can identify between 10³ and 10⁴ cfu/ml concentrations of X. fastidiosa at the subspecies level in a variety of sample types. Additionally, loop-mediated isothermal amplification (LAMP) targets were designed for faster detection of X. fastidiosa subspecies fastidiosa and multiplex, applicable to a field setting. These assays are effective for strain differentiation in artificially and naturally inoculated plant material, and in field collected insect vectors.