1
|
Kałużna M, Fischer‐Le Saux M, Pothier JF, Jacques M, Obradović A, Tavares F, Stefani E. Xanthomonas arboricola pv. juglandis and pv. corylina: Brothers or distant relatives? Genetic clues, epidemiology, and insights for disease management. MOLECULAR PLANT PATHOLOGY 2021; 22:1481-1499. [PMID: 34156749 PMCID: PMC8578823 DOI: 10.1111/mpp.13073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/06/2021] [Accepted: 04/23/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND The species Xanthomonas arboricola comprises up to nine pathovars, two of which affect nut crops: pv. juglandis, the causal agent of walnut bacterial blight, brown apical necrosis, and the vertical oozing canker of Persian (English) walnut; and pv. corylina, the causal agent of the bacterial blight of hazelnut. Both pathovars share a complex population structure, represented by different clusters and several clades. Here we describe our current understanding of symptomatology, population dynamics, epidemiology, and disease control. TAXONOMIC STATUS Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Lysobacterales (earlier synonym of Xanthomonadales); Family Lysobacteraceae (earlier synonym of Xanthomonadaceae); Genus Xanthomonas; Species X. arboricola; Pathovars: pv. juglandis and pv. corylina. HOST RANGE AND SYMPTOMS The host range of each pathovar is not limited to a single species, but each infects mainly one plant species: Juglans regia (X. arboricola pv. juglandis) and Corylus avellana (X. arboricola. pv. corylina). Walnut bacterial blight is characterized by lesions on leaves and fruits, and cankers on twigs, branches, and trunks; brown apical necrosis symptoms consist of apical necrosis originating at the stigmatic end of the fruit. A peculiar symptom, the vertical oozing canker developing along the trunk, is elicited by a particular genetic lineage of the bacterium. Symptoms of hazelnut bacterial blight are visible on leaves and fruits as necrotic lesions, and on woody parts as cankers. A remarkable difference is that affected walnuts drop abundantly, whereas hazelnuts with symptoms do not. DISTRIBUTION Bacterial blight of walnut has a worldwide distribution, wherever Persian (English) walnut is cultivated; the bacterial blight of hazelnut has a more limited distribution, although disease outbreaks are currently more frequently reported. X. arboricola pv. juglandis is regulated almost nowhere, whereas X. arboricola pv. corylina is regulated in most European and Mediterranean Plant Protection Organization (EPPO) countries. EPIDEMIOLOGY AND CONTROL For both pathogens infected nursery material is the main pathway for their introduction and spread into newly cultivated areas; additionally, infected nursery material is the source of primary inoculum. X. arboricola pv. juglandis is also disseminated through pollen. Disease control is achieved through the phytosanitary certification of nursery material (hazelnut), although approved certification schemes are not currently available. Once the disease is present in walnut/hazelnut groves, copper compounds are widely used, mostly in association with dithiocarbamates; where allowed, antibiotics (preferably kasugamycin) are sprayed. The emergence of strains highly resistant to copper currently represents the major threat for effective management of the bacterial blight of walnut. USEFUL WEBSITES: https://gd.eppo.int/taxon/XANTJU, https://gd.eppo.int/taxon/XANTCY, https://www.euroxanth.eu, http://www.xanthomonas.org.
Collapse
Affiliation(s)
- Monika Kałużna
- The National Institute of Horticultural ResearchSkierniewicePoland
| | | | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research GroupInstitute for Natural Resource SciencesZurich University of Applied SciencesWädenswilSwitzerland
| | | | | | - Fernando Tavares
- Centro de Investigação em Biodiversidade e Recursos GenéticosLaboratório Associado (CIBIO‐InBIO)Universidade do PortoPortugal
- Faculdade de CiênciasDepartamento de BiologiaUniversidade do PortoPortoPortugal
| | - Emilio Stefani
- Department of Life SciencesUniversity of Modena and Reggio EmiliaReggio EmiliaItaly
| |
Collapse
|
2
|
Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
Collapse
Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| |
Collapse
|
3
|
Vancheva T, Bogatzevska N, Moncheva P, Mitrev S, Vernière C, Koebnik R. Molecular Epidemiology of Xanthomonas euvesicatoria Strains from the Balkan Peninsula Revealed by a New Multiple-Locus Variable-Number Tandem-Repeat Analysis Scheme. Microorganisms 2021; 9:microorganisms9030536. [PMID: 33807692 PMCID: PMC8002079 DOI: 10.3390/microorganisms9030536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial spot of pepper and tomato is caused by at least three species of Xanthomonas, among them two pathovars of Xanthomonas euvesicatoria, which are responsible for significant yield losses on all continents. In order to trace back the spread of bacterial spot pathogens within and among countries, we developed the first multilocus variable number of tandem repeat analyses (MLVA) scheme for pepper- and tomato-pathogenic strains of X. euvesicatoria. In this work, we assessed the repeat numbers by DNA sequencing of 16 tandem repeat loci and applied this new tool to analyse a representative set of 88 X. euvesicatoria pepper strains from Bulgaria and North Macedonia. The MLVA-16 scheme resulted in a Hunter–Gaston Discriminatory Index (HGDI) score of 0.944 and allowed to resolve 36 MLVA haplotypes (MTs), thus demonstrating its suitability for high-resolution molecular typing. Strains from the different regions of Bulgaria and North Macedonia were found to be widespread in genetically distant clonal complexes or singletons. Sequence types of the variable number of tandem repeats (VNTR) amplicons revealed cases of size homoplasy and suggested the coexistence of different populations and different introduction events. The large geographical distribution of MTs and the existence of epidemiologically closely related strains in different regions and countries suggest long dispersal of strains on pepper in this area.
Collapse
Affiliation(s)
- Taca Vancheva
- IPME, Univ Montpellier, Cirad, IRD, Montpellier, France;
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria;
| | - Nevena Bogatzevska
- Institute of Soil Science, Agrotechnologies and Plant Protection ‘Nikola Pushkarov’, Sofia, Bulgaria;
| | - Penka Moncheva
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria;
| | - Sasa Mitrev
- Department for Plant and Environment Protection, Faculty of Agriculture, Goce Delchev University, Štip, North Macedonia;
| | - Christian Vernière
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Insitut Agro, IRD, Montpellier, France;
| | - Ralf Koebnik
- IPME, Univ Montpellier, Cirad, IRD, Montpellier, France;
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Insitut Agro, IRD, Montpellier, France;
- Correspondence: ; Tel.: +33-467-416-228
| |
Collapse
|
4
|
Martins L, Fernandes C, Albuquerque P, Tavares F. Assessment of Xanthomonas arboricola pv. juglandis Bacterial Load in Infected Walnut Fruits by Quantitative PCR. PLANT DISEASE 2019; 103:2577-2586. [PMID: 31347945 DOI: 10.1094/pdis-12-18-2253-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonas arboricola pv. juglandis is the etiologic agent of important walnut (Juglans regia L.) diseases, causing severe fruit drop and high economic losses in walnut production regions. Rapid diagnostics and knowledge of bacterial virulence fitness are key to hinder disease progression and apply timely phytosanitary measures. This work describes an X. arboricola pv. juglandis-specific real-time quantitative PCR (qPCR) using X. arboricola pv. juglandis-specific DNA markers to quantify the bacterial load in infected walnut plant tissues. Method validation was achieved using calibration curves obtained with serial dilutions of X. arboricola pv. juglandis chromosomal DNA and standard curves obtained from walnut samples spiked with X. arboricola pv. juglandis cells. High correlations (R2 > 0.990 and > 0.995) and low limits of detection (35 chromosomes/qPCR reaction and 2.7 CFU/qPCR reaction) were obtained for both markers considering the calibration and standard curves, respectively. Assessment of qPCR repeatability, reproducibility, and specificity allowed us to demonstrate the reliability and consistency of the method. Furthermore, in planta quantification of X. arboricola pv. juglandis bacterial load using infected walnut fruit samples showed a higher detection resolution compared with standard PCR detection. By allowing quantification of virulence fitness of distinct X. arboricola pv. juglandis strains in planta, the proposed qPCR method may contribute to assertive risk assessment of walnut diseases caused by X. arboricola pv. juglandis and ultimately help to improve phytosanitary practices.
Collapse
Affiliation(s)
- Leonor Martins
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
| | - Camila Fernandes
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, Oeiras, Portugal
| | - Pedro Albuquerque
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
| | - Fernando Tavares
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
| |
Collapse
|
5
|
Rache L, Blondin L, Flores C, Trujillo C, Szurek B, Restrepo S, Koebnik R, Bernal A, Vernière C. An Optimized Microsatellite Scheme for Assessing Populations of Xanthomonas phaseoli pv. manihotis. PHYTOPATHOLOGY 2019; 109:859-869. [PMID: 30908143 DOI: 10.1094/phyto-06-18-0210-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Diverse molecular markers have been used to analyze the genetic diversity of plant pathogens. Compared with traditional fingerprinting methods, multiple loci variable number of tandem repeat analyses (MLVAs) have gained importance recently due to their reproducibility, high discriminatory power, ease of performance, low cost, and throughput potential. These characteristics are desirable for continuous pathogen monitoring, especially for pathogens with relatively low genetic diversity, and for disease epidemiology studies. Genetic diversity studies of Xanthomonas phaseoli pv. manihotis, which is the causal agent of cassava bacterial blight, have shown variability and changes in the bacterial population over time. Thus, an easy and fast method needs to be developed to type populations of this pathogen in different countries of the world, especially on small scales. In this study, we developed an MLVA scheme to analyze X. phaseoli pv. manihotis variability on a local scale. The MLVA-15 scheme comprises 15 variable number of tandem repeat loci grouped into four multiplex polymerase chain reaction pools. We showed that the MLVA-15 scheme had slightly higher discriminatory ability at the locality level when compared with amplified fragment length polymorphisms. The MLVA-15 scheme allowed for an accurate determination of the number of genotypes in the sample and showed reproducibility and portability. Additionally, this scheme could be used to analyze numerous strains in a reasonable timeframe. The MLVA-15 scheme was highly specific to X. phaseoli but up to eight tandem repeat loci could be amplified from other Xanthomonas spp. Finally, we assessed the utility of the scheme for analyses of X. phaseoli pv. manihotis genetic variability in the Colombian Caribbean region. MLVA-15 distinguished 88.9% of the haplotypes in our sample. Strains originating from the same field and isolated at the same time could be discriminated. In this study, the advantages of the MLVA-15 scheme targeting 6- or 7-bp repeats were demonstrated. Moreover, this scheme was a fast method that was appropriate for routine monitoring of X. phaseoli pv. manihotis populations on a local scale and, thus, was useful for addressing epidemiological questions.
Collapse
Affiliation(s)
- Leidy Rache
- 1 Laboratorio de Interacciones Moleculares de Microorganismos Agrícolas (LIMMA), Universidad de los Andes, Bogotá D.C., Colombia
- 2 Laboratorio de Micología y Fitopatología (LAMFU), Universidad de los Andes, Bogotá D.C., Colombia
| | | | - Carolina Flores
- 4 IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Cesar Trujillo
- 1 Laboratorio de Interacciones Moleculares de Microorganismos Agrícolas (LIMMA), Universidad de los Andes, Bogotá D.C., Colombia
- 2 Laboratorio de Micología y Fitopatología (LAMFU), Universidad de los Andes, Bogotá D.C., Colombia
- 5 Affiliated until 2015
| | - Boris Szurek
- 4 IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Silvia Restrepo
- 2 Laboratorio de Micología y Fitopatología (LAMFU), Universidad de los Andes, Bogotá D.C., Colombia
| | - Ralf Koebnik
- 4 IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Adriana Bernal
- 1 Laboratorio de Interacciones Moleculares de Microorganismos Agrícolas (LIMMA), Universidad de los Andes, Bogotá D.C., Colombia
- 2 Laboratorio de Micología y Fitopatología (LAMFU), Universidad de los Andes, Bogotá D.C., Colombia
| | - Christian Vernière
- 6 Cirad, UMR BGPI, F-34398 Montpellier, France; and
- 7 BGPI, Université de Montpellier, Cirad, INRA, Montpellier SupAgro, Montpellier, France
| |
Collapse
|
6
|
Ferreira MASV, Bonneau S, Briand M, Cesbron S, Portier P, Darrasse A, Gama MAS, Barbosa MAG, Mariano RDLR, Souza EB, Jacques MA. Xanthomonas citri pv. viticola Affecting Grapevine in Brazil: Emergence of a Successful Monomorphic Pathogen. FRONTIERS IN PLANT SCIENCE 2019; 10:489. [PMID: 31057588 PMCID: PMC6482255 DOI: 10.3389/fpls.2019.00489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
The pathovar viticola of Xanthomonas citri causes bacterial canker of grapevine. This disease was first recorded in India in 1972, and later in Brazil in 1998, where its distribution is currently restricted to the northeastern region. A multilocus sequence analysis (MLSA) based on seven housekeeping genes and a multilocus variable number of tandem repeat analysis (MLVA) with eight loci were performed in order to assess the genetic relatedness among strains from India and Brazil. Strains isolated in India from three related pathovars affecting Vitaceae species and pathogenic strains isolated from Amaranthus sp. found in bacterial canker-infected vineyards in Brazil were also included. MLSA revealed lack of diversity in all seven genes and grouped grapevine and Amaranthus strains in a monophyletic group in X. citri. The VNTR (variable number of tandem repeat) typing scheme conducted on 107 strains detected 101 haplotypes. The total number of alleles per locus ranged from 5 to 12. A minimum spanning tree (MST) showed that Brazilian strains were clearly separated from Indian strains, which showed unique alleles at three loci. The two strains isolated from symptomatic Amaranthus sp. presented unique alleles at two loci. STRUCTURE analyses revealed three groups congruent with MST and a fourth group with strains from India and Brazil. Admixture among populations were observed in all groups. MST, STRUCTURE and e-BURST analyses showed that the strains collected in 1998 belong to two distinct groups, with predicted founder genotypes from two different vineyards in the same region. This suggest that one introduction of grape planting materials contaminated with genetically distinct strains took place, which was followed by pathogen adaptation. Genome sequencing of one Brazilian strain confirmed typical attributes of pathogenic xanthomonads and allowed the design of a complementary VNTR typing scheme dedicated to X. citri pv. viticola that will allow further epidemiological survey of this genetically monomorphic pathovar.
Collapse
Affiliation(s)
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Sophie Cesbron
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Perrine Portier
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Armelle Darrasse
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Marco A. S. Gama
- Laboratório de Fitobacteriologia, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | | | - Rosa de L. R. Mariano
- Laboratório de Fitobacteriologia, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Elineide B. Souza
- Laboratório de Fitobacteriologia, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| |
Collapse
|
7
|
Garita‐Cambronero J, Palacio‐Bielsa A, Cubero J. Xanthomonas arboricola pv. pruni, causal agent of bacterial spot of stone fruits and almond: its genomic and phenotypic characteristics in the X. arboricola species context. MOLECULAR PLANT PATHOLOGY 2018; 19:2053-2065. [PMID: 29575564 PMCID: PMC6638108 DOI: 10.1111/mpp.12679] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/13/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Xanthomonas arboricola pv. pruni (Xap) causes bacterial spot of stone fruits and almond, an important disease that may reduce the yield and vigour of the trees, as well as the marketability of affected fruits. Xap lies within the Xanthomonas genus, which has been intensively studied because of its strain specialization and host range complexity. Here, we summarize the recent advances in our understanding of the complexities of Xap, including studies of the molecular features that result after comparative phenotypic and genomic analyses, in order to obtain a clearer overview of the bacterial behaviour and infection mechanism in the context of the X. arboricola species. TAXONOMIC STATUS Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species X. arboricola; Pathovar pruni. HOST RANGE AND SYMPTOMS Xap infects most Prunus species, including apricot, peach, nectarine, plum and almond, and occasionally cherry. Symptoms are found on leaves, fruits, twigs and branches or trunks. In severe infections, defoliation and fruit dropping may occur. DISTRIBUTION Bacterial spot of stone fruits and almond is worldwide in distribution, with Xap being isolated in Africa, North and South America, Asia, Europe and Oceania. It is a common disease in geographical areas in which stone fruits and almonds are grown. Xap is listed as a quarantine organism in several areas of the world. GENOME The genomes of six isolates from Xap have been publicly released. The genome consists of a single chromosome of around 5 000 000 bp with 65 mol% GC content and an extrachromosomal plasmid element of around 41 000 bp with 62 mol% GC content. Genomic comparative studies in X. arboricola have allowed the identification of putative virulence components associated with the infection process of bacterial spot of stone fruits and almond. DISEASE CONTROL Management of bacterial spot of stone fruits and almond is based on an integrated approach that comprises essential measures to avoid Xap introduction in a production zone, as well as the use of tolerant or resistant plant material and chemical treatments, mainly based on copper compounds. Management programmes also include the use of appropriate cultivation practices when the disease is already established. Finally, for the effective control of the disease, appropriate detection and characterization methods are needed for use in symptomatic or asymptomatic samples as a first approach for pathogen exclusion. USEFUL WEBSITES: https://gd.eppo.int/taxon/XANTPR; http://www.cost.eu/COST_Actions/ca/CA16107; http://www.xanthomonas.org.
Collapse
Affiliation(s)
- Jerson Garita‐Cambronero
- Departamento de Protección VegetalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Madrid 28040Spain
- Centro de Investigación de Biocombustibles y Bioproductos, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Villarejo de Órbigo 24358LeónSpain
| | - Ana Palacio‐Bielsa
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón‐IA2 ‐ (CITA ‐ Universidad de Zaragoza)Zaragoza 50059Spain
| | - Jaime Cubero
- Departamento de Protección VegetalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Madrid 28040Spain
| |
Collapse
|
8
|
High-Quality Draft Genome Sequences of Five Xanthomonas arboricola pv. fragariae Isolates. GENOME ANNOUNCEMENTS 2018; 6:6/7/e01585-17. [PMID: 29449402 PMCID: PMC5814503 DOI: 10.1128/genomea.01585-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Xanthomonas arboricola pv. fragariae was described in 2001 as the causal agent of strawberry bacterial leaf blight. We report here the first draft whole-genome sequences of five X. arboricola pv. fragariae isolates from Italy and France.
Collapse
|
9
|
López-Soriano P, Boyer K, Cesbron S, Morente MC, Peñalver J, Palacio-Bielsa A, Vernière C, López MM, Pruvost O. Multilocus Variable Number of Tandem Repeat Analysis Reveals Multiple Introductions in Spain of Xanthomonas arboricola pv. pruni, the Causal Agent of Bacterial Spot Disease of Stone Fruits and Almond. PLoS One 2016; 11:e0163729. [PMID: 27669415 PMCID: PMC5036818 DOI: 10.1371/journal.pone.0163729] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/13/2016] [Indexed: 12/05/2022] Open
Abstract
Xanthomonas arboricola pv. pruni is the causal agent of the bacterial spot disease of stone fruits, almond and some ornamental Prunus species. In Spain it was first detected in 2002 and since then, several outbreaks have occurred in different regions affecting mainly Japanese plum, peach and almond, both in commercial orchards and nurseries. As the origin of the introduction(s) was unknown, we have assessed the genetic diversity of 239 X. arboricola pv. pruni strains collected from 11 Spanish provinces from 2002 to 2013 and 25 reference strains from international collections. We have developed an optimized multilocus variable number of tandem repeat analysis (MLVA) scheme targeting 18 microsatellites and five minisatellites. A high discriminatory power was achieved since almost 50% of the Spanish strains were distinguishable, confirming the usefulness of this genotyping technique at small spatio-temporal scales. Spanish strains grouped in 18 genetic clusters (conservatively delineated so that each cluster contained haplotype networks linked by up to quadruple-locus variations). Furthermore, pairwise comparisons among populations from different provinces showed a strong genetic differentiation. Our results suggest multiple introductions of this pathogen in Spain and redistribution through contaminated nursery propagative plant material.
Collapse
Affiliation(s)
| | - Karine Boyer
- UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - Sophie Cesbron
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | | | - Javier Peñalver
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Ana Palacio-Bielsa
- Centro de Investigación y Tecnología Agroalimentaria de Aragón. Instituto Agroalimentario de Aragón, IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Christian Vernière
- UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
- UMR Biologie et Génétique des Interactions Plante-Parasite, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - María M. López
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
- * E-mail:
| | - Olivier Pruvost
- UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| |
Collapse
|
10
|
Cunty A, Cesbron S, Poliakoff F, Jacques MA, Manceau C. Origin of the Outbreak in France of Pseudomonas syringae pv. actinidiae Biovar 3, the Causal Agent of Bacterial Canker of Kiwifruit, Revealed by a Multilocus Variable-Number Tandem-Repeat Analysis. Appl Environ Microbiol 2015; 81:6773-89. [PMID: 26209667 PMCID: PMC4561677 DOI: 10.1128/aem.01688-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 07/13/2015] [Indexed: 11/20/2022] Open
Abstract
The first outbreaks of bacterial canker of kiwifruit caused by Pseudomonas syringae pv. actinidiae biovar 3 were detected in France in 2010. P. syringae pv. actinidiae causes leaf spots, dieback, and canker that sometimes lead to the death of the vine. P. syringae pv. actinidifoliorum, which is pathogenic on kiwi as well, causes only leaf spots. In order to conduct an epidemiological study to track the spread of the epidemics of these two pathogens in France, we developed a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA). MLVA was conducted on 340 strains of P. syringae pv. actinidiae biovar 3 isolated in Chile, China, France, Italy, and New Zealand and on 39 strains of P. syringae pv. actinidifoliorum isolated in Australia, France, and New Zealand. Eleven polymorphic VNTR loci were identified in the genomes of P. syringae pv. actinidiae biovar 3 ICMP 18744 and of P. syringae pv. actinidifoliorum ICMP 18807. MLVA enabled the structuring of P. syringae pv. actinidiae biovar 3 and P. syringae pv. actinidifoliorum strains in 55 and 16 haplotypes, respectively. MLVA and discriminant analysis of principal components revealed that strains isolated in Chile, China, and New Zealand are genetically distinct from P. syringae pv. actinidiae strains isolated in France and in Italy, which appear to be closely related at the genetic level. In contrast, no structuring was observed for P. syringae pv. actinidifoliorum. We developed an MLVA scheme to explore the diversity within P. syringae pv. actinidiae biovar 3 and to trace the dispersal routes of epidemic P. syringae pv. actinidiae biovar 3 in Europe. We suggest using this MLVA scheme to trace the dispersal routes of P. syringae pv. actinidiae at a global level.
Collapse
Affiliation(s)
- A Cunty
- UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Institut National de la Recherche Agronomique, Beaucouzé, France Laboratoire de la Santé des Végétaux, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Angers, France
| | - S Cesbron
- UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Institut National de la Recherche Agronomique, Beaucouzé, France
| | - F Poliakoff
- Laboratoire de la Santé des Végétaux, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Angers, France
| | - M-A Jacques
- UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Institut National de la Recherche Agronomique, Beaucouzé, France
| | - C Manceau
- Laboratoire de la Santé des Végétaux, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Angers, France
| |
Collapse
|
11
|
Essakhi S, Cesbron S, Fischer-Le Saux M, Bonneau S, Jacques MA, Manceau C. Phylogenetic and Variable-Number Tandem-Repeat Analyses Identify Nonpathogenic Xanthomonas arboricola Lineages Lacking the Canonical Type III Secretion System. Appl Environ Microbiol 2015; 81:5395-410. [PMID: 26048944 PMCID: PMC4510168 DOI: 10.1128/aem.00835-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/21/2015] [Indexed: 01/13/2023] Open
Abstract
Xanthomonas arboricola is conventionally known as a taxon of plant-pathogenic bacteria that includes seven pathovars. This study showed that X. arboricola also encompasses nonpathogenic bacteria that cause no apparent disease symptoms on their hosts. The aim of this study was to assess the X. arboricola population structure associated with walnut, including nonpathogenic strains, in order to gain a better understanding of the role of nonpathogenic xanthomonads in walnut microbiota. A multilocus sequence analysis (MLSA) was performed on a collection of 100 X. arboricola strains, including 27 nonpathogenic strains isolated from walnut. Nonpathogenic strains grouped outside clusters defined by pathovars and formed separate genetic lineages. A multilocus variable-number tandem-repeat analysis (MLVA) conducted on a collection of X. arboricola strains isolated from walnut showed that nonpathogenic strains clustered separately from clonal complexes containing Xanthomonas arboricola pv. juglandis strains. Some nonpathogenic strains of X. arboricola did not contain the canonical type III secretion system (T3SS) and harbored only one to three type III effector (T3E) genes. In the nonpathogenic strains CFBP 7640 and CFBP 7653, neither T3SS genes nor any of the analyzed T3E genes were detected. This finding raises a question about the origin of nonpathogenic strains and the evolution of plant pathogenicity in X. arboricola. T3E genes that were not detected in any nonpathogenic isolates studied represent excellent candidates to be those responsible for pathogenicity in X. arboricola.
Collapse
Affiliation(s)
- Salwa Essakhi
- INRA, UMR 1345, Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Sophie Cesbron
- INRA, UMR 1345, Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | | | - Sophie Bonneau
- INRA, UMR 1345, Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Marie-Agnès Jacques
- INRA, UMR 1345, Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Charles Manceau
- INRA, UMR 1345, Institut de Recherche en Horticulture et Semences, Beaucouzé, France Anses, Laboratoire de la Santé des Végétaux, Unité Expertise-Risques Biologiques, Angers, France
| |
Collapse
|
12
|
Fischer-Le Saux M, Bonneau S, Essakhi S, Manceau C, Jacques MA. Aggressive Emerging Pathovars of Xanthomonas arboricola Represent Widespread Epidemic Clones Distinct from Poorly Pathogenic Strains, as Revealed by Multilocus Sequence Typing. Appl Environ Microbiol 2015; 81:4651-68. [PMID: 25934623 PMCID: PMC4551192 DOI: 10.1128/aem.00050-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/25/2015] [Indexed: 12/11/2022] Open
Abstract
Deep and comprehensive knowledge of the genetic structure of pathogenic species is the cornerstone on which the design of precise molecular diagnostic tools is built. Xanthomonas arboricola is divided into pathovars, some of which are classified as quarantine organisms in many countries and are responsible for diseases on nut and stone fruit trees that have emerged worldwide. Recent taxonomic studies of the genus Xanthomonas showed that strains isolated from other hosts should be classified in X. arboricola, extending the host range of the species. To investigate the genetic structure of X. arboricola and the genetic relationships between highly pathogenic strains and strains apparently not relevant to plant health, we conducted multilocus sequence analyses on a collection of strains representative of the known diversity of the species. Most of the pathovars were clustered in separate monophyletic groups. The pathovars pruni, corylina, and juglandis, responsible for pandemics in specific hosts, were highly phylogenetically related and clustered in three distinct clonal complexes. In contrast, strains with no or uncertain pathogenicity were represented by numerous unrelated singletons scattered in the phylogenic tree. Depending on the pathovar, intra- and interspecies recombination played contrasting roles in generating nucleotide polymorphism. This work provides a population genetics framework for molecular epidemiological surveys of emerging plant pathogens within X. arboricola. Based on our results, we propose to reclassify three former pathovars of Xanthomonas campestris as X. arboricola pv. arracaciae comb. nov., X. arboricola pv. guizotiae comb. nov., and X. arboricola pv. zantedeschiae comb. nov. An emended description of X. arboricola Vauterin et al. 1995 is provided.
Collapse
Affiliation(s)
- Marion Fischer-Le Saux
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Sophie Bonneau
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Salwa Essakhi
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Charles Manceau
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Marie-Agnès Jacques
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| |
Collapse
|
13
|
Draft Genome Sequences of Two Xanthomonas euvesicatoria Strains from the Balkan Peninsula. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01528-14. [PMID: 25657284 PMCID: PMC4319600 DOI: 10.1128/genomea.01528-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We report the draft genome sequences of two Xanthomonas euvesicatoria strains from the Balkan Peninsula, which were isolated from symptomatic pepper plants. The availability of these genome sequences will facilitate the development of modern genotyping assays for X. euvesicatoria strains and to define targets for resistance breeding.
Collapse
|