Xylella fastidiosa: A reemerging plant pathogen that threatens crops globally

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.

Leuconostoc mesenteroides strain MS4-derived bacteriocins: A potent antimicrobial arsenal for controlling Xylella fastidiosa infection

Xylella fastidiosa subsp. pauca (Xfp) currently presents a serious threat to agriculture in Europe and in the Mediterranean, following its discovery in several countries. Addressing this bacterial plant disease with traditional agricultural practices and management strategies has proven inadequate, highlighting the urgent need for effective and environmentally safe antibacterial solutions. In this study, we explored the antibacterial activity of the lactic acid bacterium Leuconostoc mesenteroides strain MS4-derived bacteriocins against Xfp, utilizing a combination of in vitro and in planta experiments. In particular, the cell-free precipitate (CFP) derived from strain MS4 culture in MRS broth, suppressed Xfp growth on BCYE agar plate, whereas protease K-treated CFP was inactive, highlighting the presence of antimicrobial compounds of proteinaceous nature. Additionally, fluorescence and transmission electron microscopy analyses showed that the CFP exhibits a bactericidal effect on Xfp cells, characterized by membrane disruption and subsequent cellular damage. The whole-genome sequencing and bioinformatic analysis revealed that MS4 genome consists of a circular chromosome of 1860,891 bp and a circular plasmid of 37,317 bp and most importantly to encompass six bacteriocin-encoding genes, with a peptide size ranging from 45 to 59 amino acids. MALDI-TOF/TOF MS and RPLC-ESI-MS assays performed on cell-free supernatant (CFS) confirmed the secretion of four (out of 6) bacteriocins (denoted MK-45, MR-53, MW-56, and MG-58) by MS4 in MRS broth. In spot assays, these bacteriocins displayed significant lethality against Xfp, with a minimum lethal concentration between 0.2 and 0.4 mg/mL. The application of CFP on Xfp-infected Nicotiana benthamiana plants, implemented both as preventive and curative approach, successfully controlled the infection, resulting in no visible symptoms 40 days post-inoculation. The finding of MS4 as a natural source of various potent bacteriocins against Xfp, coupled with a significant production under low-cost and uncomplicated laboratory conditions, make of MS4 a cost-effective and realistic option for sustainable management of Xf-related diseases.

N-acetylcysteine absorption and its potential dual effect improve fitness and fruit yield in Xylella fastidiosa infected plants

BACKGROUND

Xylella fastidiosa is a multi-host bacterium that can be detected in hundreds of plant species including several crops. Diseases caused by X. fastidiosa are considered a threat to global food production. The primary method for managing diseases caused by X. fastidiosa involves using insecticides to control the vector. Hence, it is necessary to adopt new and sustainable disease management technologies to control not only the insect but also the bacteria and plant health. We demonstrated that N-acetylcysteine (NAC), a low-cost cysteine analogue, is a sustainable molecule that can be used in agriculture to decrease the damage caused by X. fastidiosa and improve plant health.

RESULTS

Using 15N-NAC we proved that this analogue was absorbed by the roots and transported to different parts of the plant. Inside the plant, NAC reduced the bacterial population by 60-fold and the number of xylem vessels blocked by bacterial biofilms. This reflected in a recovery of 0.28-fold of the daily sap flow compared to health plants. In addition, NAC-treated citrus variegated chlorosis (CVC) plants decreased the oxidative stress by improving the activity of detoxifying enzymes. Moreover, the use of NAC in field conditions positively contributed to the increase in fruit yield of CVC-diseased plants.

CONCLUSION

Our research not only advances the understanding of NAC absorption in plants, but also indicates its dual effect as an antimicrobial and antioxidant molecule. This, in turn, negatively affects bacterial survival while improving plant health by decreasing oxidative stress. Overall, the positive field-based evidence supports the viability of NAC as a sustainable agricultural application. © 2024 Society of Chemical Industry.

Xylella phage MATE 2: a novel bacteriophage with potent lytic activity against Xylella fastidiosa subsp. pauca

Xylella fastidiosa (Xf) is a major phytosanitary threat to global agricultural production. The complexity and difficulty of controlling Xf underscore the pressing need for novel antibacterial agents, i.e., bacteriophages, which are natural predators of bacteria. In this study, a novel lytic bacteriophage of Xf subsp. pauca, namely Xylella phage MATE 2 (MATE 2), was isolated from sewage water in southern Italy. Biological characterization showed that MATE 2 possessed a broad-spectrum of antibacterial activity against various phytobacteria within the family Xanthomonadaceae, a rapid adsorption time (10 min), and high resistance to a broad range of pH (4-10) and temperatures (4-60°C). Most importantly, MATE 2 was able to suppress the growth of Xf subsp. pauca cells in liquid culture for 7 days, demonstrating its potential as an effective antibacterial agent against Xf. The genomic and electron microscopy analyses revealed that MATE 2 is a new species tentatively belonging to the genus Carpasinavirus within the class Caudoviricetes, with an isometric capsid head of 60 ± 5 nm along with a contractile tail of 120 ± 7.5 nm. Furthermore, the high-throughput sequencing and de novo assembly generated a single contig of 63,695 nucleotides in length; representing a complete genome composed of 95 Open Reading Frames. Bioinformatics analysis performed on MATE 2 genome revealed the absence of lysogenic mediated genes, and genes encoding virulence factors, antibiotic resistance, and toxins. This study adds a new phage to the very short list of Xf-infecting lytic phages, whose in-vitro antibacterial activity has been ascertained, while its efficacy on Xf-infected olive trees in the field has yet to be determined.

Evidence of Xylella fastidiosa Infection and Associated Thermal Signatures in Southern Highbush Blueberry (Vaccinium corymbosum Interspecific Hybrids)

Xylella fastidiosa, a gram-negative bacterium vectored to plants via feeding of infected insects, causes a number of notorious plant diseases throughout the world, such as Pierce's disease (grapes), olive quick decline syndrome, and coffee leaf scorch. Detection of Xf in infected plants can be challenging because the early foliar disease symptoms are subtle and may be attributed to multiple minor physiological stresses and/or borderline nutrient deficiencies. Furthermore, Xf may reside within an infected plant for one or more growing seasons before traditional visible diagnostic disease symptoms emerge. Any method that can identify infection during the latent period or pre-diagnostic disease progress state could substantially improve the outcome of disease control interventions. Because Xf locally and gradually impairs water movement through infected plant stems and leaves over time, infected plants may not be able to effectively dissipate heat through transpiration-assisted cooling, and this heat signature may be an important pre-diagnostic disease trait. Here, we report on the association between thermal imaging, the early stages of Xf infection, and disease development in blueberry plants, and discuss the benefits and limitations of using thermal imaging to detect bacterial leaf scorch of blueberries.

Crossing the Gateless Barriers: Factors Involved in the Movement of Circulative Bacteria Within Their Insect Vectors

Plant bacterial pathogens transmitted by hemipteran vectors pose a large threat to the agricultural industry worldwide. Although virus-vector relationships have been widely investigated, a significant gap exists in our understanding of the molecular interactions between circulative bacteria and their insect vectors, mainly leafhoppers and psyllids. In this review, we will describe how these bacterial pathogens adhere, invade, and proliferate inside their insect vectors. We will also highlight the different transmission routes and molecular factors of phloem-limited bacteria that maintain an effective relationship with the insect host. Understanding the pathogen-vector relationship at the molecular level will help in the management of vector-borne bacterial diseases.

Bioecological Traits of Spittlebugs and Their Implications for the Epidemiology and Control of the Xylella fastidiosa Epidemic in Apulia (Southern Italy)

Spatial-temporal dynamics of spittlebug populations, together with transmission biology, are of major importance to outline the disease epidemiology of Xylella fastidiosa subsp. pauca in Apulian olive groves. The spread rate of X. fastidiosa is mainly influenced by (i) the pathogen colonization of the host plant; (ii) the acquisition of the pathogen by the vector from an infected plant, and its inoculation to healthy plants; (iii) the vector population dynamics and abundance at different spatial scales; and (iv) the dispersal of the vector. In this contribution we summarize the recent advances in research on insect vectors' traits-points ii, iii, and iv-focusing on those most relevant to X. fastidiosa epidemic in Apulia. Among the vectors' bioecological traits influencing the X. fastidiosa epidemic in olive trees, we emphasize the following: natural infectivity and transmission efficiency, phenological timing of both nymphal and adult stage, the role of seminatural vegetation as a vector reservoir in the agroecosystem and landscape, and preferential and directional dispersal capabilities. Despite the research on X. fastidiosa vectors carried out in Europe in the last decade, key uncertainties on insect vectors remain, hampering a thorough understanding of pathogen epidemiology and the development of effective and targeted management strategies. Our goal is to provide a structured and contextualized review of knowledge on X. fastidiosa vectors' key traits in the Apulian epidemic, highlighting information gaps and stimulating novel research pathways on X. fastidiosa pathosystems in Europe. [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.

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.

Epidemiologically-based strategies for the detection of emerging plant pathogens

Emerging pests and pathogens of plants are a major threat to natural and managed ecosystems worldwide. Whilst it is well accepted that surveillance activities are key to both the early detection of new incursions and the ability to identify pest-free areas, the performance of these activities must be evaluated to ensure they are fit for purpose. This requires consideration of the number of potential hosts inspected or tested as well as the epidemiology of the pathogen and the detection method used. In the case of plant pathogens, one particular concern is whether the visual inspection of plant hosts for signs of disease is able to detect the presence of these pathogens at low prevalences, given that it takes time for these symptoms to develop. One such pathogen is the ST53 strain of the vector-borne bacterial pathogen Xylella fastidiosa in olive hosts, which was first identified in southern Italy in 2013. Additionally, X. fastidiosa ST53 in olive has a rapid rate of spread, which could also have important implications for surveillance. In the current study, we evaluate how well visual surveillance would be expected to perform for this pathogen and investigate whether molecular testing of either tree hosts or insect vectors offer feasible alternatives. Our results identify the main constraints to each of these strategies and can be used to inform and improve both current and future surveillance activities.

Agro-active endo-therapy treated Xylella fastidiosa subsp. pauca-infected olive trees assessed by the first 1H-NMR-based metabolomic study

Xylella fastidiosa is a xylem-limited bacterium causing a range of economically important plant diseases in hundreds of crops. Over the last decade, a severe threat due to Olive Quick Decline Syndrome (OQDS), caused by Xylella fastidiosa subspecies pauca, affected the Salento olive groves (Apulia, South-East Italy). Very few phyto-therapeutics, including a Zn/Cu citric acid biocomplex foliar treatment, were evaluated to mitigate this disease. However, the traditional foliar applications result in the agro-actives reaching only partially their target. Therefore the development of novel endo-therapeutic systems was suggested. Metabolite fingerprinting is a powerful method for monitoring both, disease progression and treatment effects on the plant metabolism, allowing biomarkers detection. We performed, for the first time, short-term monitoring of metabolic pathways reprogramming for infected Ogliarola salentina and Cima di Melfi olive trees after precision intravascular biocomplex delivery using a novel injection system. Upon endo therapy, we observed specific variations in the leaf content of some metabolites. In particular, the ¹H NMR-based metabolomics approach showed, after the injection, a significant decrease of both the disease biomarker quinic acid and mannitol with simultaneous increase of polyphenols and oleuropein related compounds in the leaf’s extracts. This combined metabolomics/endo-therapeutic methodology provided useful information in the comprehension of plant physiology for future applications in OQDS control.