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Timilsina S, Kaur A, Sharma A, Ramamoorthy S, Vallad GE, Wang N, White FF, Potnis N, Goss EM, Jones JB. Xanthomonas as a Model System for Studying Pathogen Emergence and Evolution. PHYTOPATHOLOGY 2024; 114:1433-1446. [PMID: 38648116 DOI: 10.1094/phyto-03-24-0084-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In this review, we highlight studies in which whole-genome sequencing, comparative genomics, and population genomics have provided unprecedented insights into past and ongoing pathogen evolution. These include new understandings of the adaptive evolution of secretion systems and their effectors. We focus on Xanthomonas pathosystems that have seen intensive study and improved our understanding of pathogen emergence and evolution, particularly in the context of host specialization: citrus canker, bacterial blight of rice, and bacterial spot of tomato and pepper. Across pathosystems, pathogens appear to follow a pattern of bursts of evolution and diversification that impact host adaptation. There remains a need for studies on the mechanisms of host range evolution and genetic exchange among closely related but differentially host-specialized species and to start moving beyond the study of specific strain and host cultivar pairwise interactions to thinking about these pathosystems in a community context.
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Affiliation(s)
- Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Amandeep Kaur
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Anuj Sharma
- Department of Horticultural Sciences, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | | | - Gary E Vallad
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | - Nian Wang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
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Chen JR, Aguirre-Carvajal K, Xue DY, Chang HC, Arone-Maxwell L, Lin YP, Armijos-Jaramillo V, Oliva R. Exploring the genetic makeup of Xanthomonas species causing bacterial spot in Taiwan: evidence of population shift and local adaptation. Front Microbiol 2024; 15:1408885. [PMID: 38846563 PMCID: PMC11153759 DOI: 10.3389/fmicb.2024.1408885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
The introduction of plant pathogens can quickly reshape disease dynamics in island agro-ecologies, representing a continuous challenge for local crop management strategies. Xanthomonas pathogens causing tomato bacterial spot were probably introduced in Taiwan several decades ago, creating a unique opportunity to study the genetic makeup and adaptive response of this alien population. We examined the phenotypic and genotypic identity of 669 pathogen entries collected across different regions of Taiwan in the last three decades. The analysis detected a major population shift, where X. euvesicatoria and X. vesicatoria races T1 and T2 were replaced by new races of X. perforans. After its introduction, race T4 quickly became dominant in all tomato-growing areas of the island. The genomic analysis of 317 global genomes indicates that the Xanthomonas population in Taiwan has a narrow genetic background, most likely resulting from a small number of colonization events. However, despite the apparent genetic uniformity, X. perforans race T4 shows multiple phenotypic responses in tomato lines. Additionally, an in-depth analysis of effector composition suggests diversification in response to local adaptation. These include unique mutations on avrXv3 which might allow the pathogen to overcome Xv3/Rx4 resistance gene. The findings underscore the dynamic evolution of a pathogen when introduced in a semi-isolated environment and provide insights into the potential management strategies for this important disease of tomato.
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Affiliation(s)
- Jaw-Rong Chen
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | - Kevin Aguirre-Carvajal
- Research Center of Information and Communication Technologies, University of A Coruña, A Coruña, Spain
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito, Ecuador
| | - Dao-Yuan Xue
- Seed and Seedling Management Section, Taiwan Seed Improvement and Propagation Station, Ministry of Agriculture, Taichung, Taiwan
| | - Hung-Chia Chang
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | | | - Ya-Ping Lin
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | - Vinicio Armijos-Jaramillo
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito, Ecuador
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Ricardo Oliva
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
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Jibrin MO, Timilsina S, Minsavage GV, Vallad GE, Roberts PD, Goss EM, Jones JB. Bacterial Spot of Tomato and Pepper in Africa: Diversity, Emergence of T5 Race, and Management. Front Microbiol 2022; 13:835647. [PMID: 35509307 PMCID: PMC9058171 DOI: 10.3389/fmicb.2022.835647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial spot disease was first reported from South Africa by Ethel M. Doidge in 1920. In the ensuing century after the initial discovery, the pathogen has gained global attention in plant pathology research, providing insights into host-pathogen interactions, pathogen evolution, and effector discovery, such as the first discovery of transcription activation-like effectors, among many others. Four distinct genetic groups, including Xanthomonas euvesicatoria (proposed name: X. euvesicatoria pv. euvesicatoria), Xanthomonas perforans (proposed name: X. euvesicatoria pv. perforans), Xanthomonas gardneri (proposed name: Xanthomonas hortorum pv. gardneri), and Xanthomonas vesicatoria, are known to cause bacterial spot disease. Recently, a new race of a bacterial spot pathogen, race T5, which is a product of recombination between at least two Xanthomonas species, was reported in Nigeria. In this review, our focus is on the progress made on the African continent, vis-à-vis progress made in the global bacterial spot research community to provide a body of information useful for researchers in understanding the diversity, evolutionary changes, and management of the disease in Africa.
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Affiliation(s)
- Mustafa Ojonuba Jibrin
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, United States
- Department of Crop Protection, Ahmadu Bello University, Zaria, Nigeria
| | - Sujan Timilsina
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
| | - Gerald V. Minsavage
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
| | - Garry E. Vallad
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Pamela D. Roberts
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- UF/IFAS Southwest Florida Research and Education Center, Immokalee, FL, United States
| | - Erica M. Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Jeffrey B. Jones
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
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Osdaghi E, Jones JB, Sharma A, Goss EM, Abrahamian P, Newberry EA, Potnis N, Carvalho R, Choudhary M, Paret ML, Timilsina S, Vallad GE. A centenary for bacterial spot of tomato and pepper. MOLECULAR PLANT PATHOLOGY 2021; 22:1500-1519. [PMID: 34472193 PMCID: PMC8578828 DOI: 10.1111/mpp.13125] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 05/08/2023]
Abstract
DISEASE SYMPTOMS Symptoms include water-soaked areas surrounded by chlorosis turning into necrotic spots on all aerial parts of plants. On tomato fruits, small, water-soaked, or slightly raised pale-green spots with greenish-white halos are formed, ultimately becoming dark brown and slightly sunken with a scabby or wart-like surface. HOST RANGE Main and economically important hosts include different types of tomatoes and peppers. Alternative solanaceous and nonsolanaceous hosts include Datura spp., Hyoscyamus spp., Lycium spp., Nicotiana rustica, Physalis spp., Solanum spp., Amaranthus lividus, Emilia fosbergii, Euphorbia heterophylla, Nicandra physaloides, Physalis pubescens, Sida glomerata, and Solanum americanum. TAXONOMIC STATUS OF THE PATHOGEN Domain, Bacteria; phylum, Proteobacteria; class, Gammaproteobacteria; order, Xanthomonadales; family, Xanthomonadaceae; genus, Xanthomonas; species, X. euvesicatoria, X. hortorum, X. vesicatoria. SYNONYMS (NONPREFERRED SCIENTIFIC NAMES) Bacterium exitiosum, Bacterium vesicatorium, Phytomonas exitiosa, Phytomonas vesicatoria, Pseudomonas exitiosa, Pseudomonas gardneri, Pseudomonas vesicatoria, Xanthomonas axonopodis pv. vesicatoria, Xanthomonas campestris pv. vesicatoria, Xanthomonas cynarae pv. gardneri, Xanthomonas gardneri, Xanthomonas perforans. MICROBIOLOGICAL PROPERTIES Colonies are gram-negative, oxidase-negative, and catalase-positive and have oxidative metabolism. Pale-yellow domed circular colonies of 1-2 mm in diameter grow on general culture media. DISTRIBUTION The bacteria are widespread in Africa, Brazil, Canada and the USA, Australia, eastern Europe, and south-east Asia. Occurrence in western Europe is restricted. PHYTOSANITARY CATEGORIZATION A2 no. 157, EU Annex designation II/A2. EPPO CODES XANTEU, XANTGA, XANTPF, XANTVE.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Jeffrey B. Jones
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Anuj Sharma
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Erica M. Goss
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Peter Abrahamian
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
| | - Eric A. Newberry
- Department of Entomology and Plant PathologyAuburn UniversityAuburnAlabamaUSA
| | - Neha Potnis
- Department of Entomology and Plant PathologyAuburn UniversityAuburnAlabamaUSA
| | - Renato Carvalho
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Manoj Choudhary
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Mathews L. Paret
- Department of Plant PathologyNorth Florida Research and Education CenterUniversity of FloridaQuincyFloridaUSA
| | - Sujan Timilsina
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Gary E. Vallad
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
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Potnis N. Harnessing Eco-Evolutionary Dynamics of Xanthomonads on Tomato and Pepper to Tackle New Problems of an Old Disease. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:289-310. [PMID: 34030449 DOI: 10.1146/annurev-phyto-020620-101612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacterial spot is an endemic seedborne disease responsible for recurring outbreaks on tomato and pepper around the world. The disease is caused by four diverse species, Xanthomonas gardneri, Xanthomonas euvesicatoria, Xanthomonas perforans, and Xanthomonas vesicatoria. There are no commercially available disease-resistant tomato varieties, and the disease is managed by chemical/biological control options, although these have not reduced the incidence of outbreaks. The disease on peppers is managed by disease-resistant cultivars that are effective against X. euvesicatoria but not X. gardneri. A significant shift in composition and prevalence of different species and races of the pathogen has occurred over the past century. Here, I attempt to review ecological and evolutionary processes associated with the population dynamics leading to disease emergence and spread. The goal of this review is to integrate the knowledge on population genomics and molecular plant-microbe interactions for this pathosystem to tailor disease management strategies.
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Affiliation(s)
- Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama 36849, USA;
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Abrahamian P, Klein-Gordon JM, Jones JB, Vallad GE. Epidemiology, diversity, and management of bacterial spot of tomato caused by Xanthomonas perforans. Appl Microbiol Biotechnol 2021; 105:6143-6158. [PMID: 34342710 DOI: 10.1007/s00253-021-11459-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/28/2022]
Abstract
Tomato is an important crop grown worldwide. Various plant diseases cause massive losses in tomato plants due to diverse biotic agents. Bacterial spot of tomato (BST) is a worldwide disease that results in high losses in processed and fresh tomato. Xanthomonas perforans, an aerobic, single-flagellated, rod-shaped, Gram-negative plant pathogenic bacterium, is one of the leading causes of BST. Over the past three decades, X. perforans has increasingly been reported from tomato-growing regions and became a major bacterial disease. X. perforans thrives under high humidity and high temperature, which is commonplace in tropical and subtropical climates. Distinguishing symptoms of BST are necrotic lesions that can coalesce and cause a shot-hole appearance. X. perforans can occasionally cause fruit symptoms depending on disease pressure during fruit development. Short-distance movement in the field is mainly dependent on wind-driven rain, whereas long distance movement occurs through contaminated seed or plant material. X. perforans harbors a suite of effectors that increase pathogen virulence, fitness, and dissemination. BST management mainly relies on copper-based compounds; however, resistance is widespread. Alternative compounds, such as nanomaterials, are currently being evaluated and show high potential for BST management. Resistance breeding remains difficult to attain due to limited resistant germplasm. While the increased genetic diversity and gain and loss of effectors in X. perforans limits the success of single-gene resistance, the adoption of effector-specific transgenes and quantitative resistance may lead to durable host resistance. However, further research that aims to more effectively implement novel management tools is required to curb disease spread. KEY POINTS: • Xanthomonas perforans causes bacterial spot on tomato epidemics through infected seedlings and movement of plant material. • Genetic diversity plays a major role in shaping populations which is evident in loss and gain of effectors. • Management relies on copper sprays, but nanoparticles are a promising alternative to reduce copper toxicity.
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Affiliation(s)
- Peter Abrahamian
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD, 20705, USA.
| | | | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Gary E Vallad
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA.
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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.
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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
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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.
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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
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Hernández-Huerta J, Tamez-Guerra P, Gomez-Flores R, Delgado-Gardea MCE, García-Madrid MS, Robles-Hernández L, Infante-Ramirez R. Prevalence of Xanthomonas euvesicatoria (formally X. perforans) associated with bacterial spot severity in Capsicum annuum crops in South Central Chihuahua, Mexico. PeerJ 2021; 9:e10913. [PMID: 33628644 PMCID: PMC7891084 DOI: 10.7717/peerj.10913] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/17/2021] [Indexed: 12/20/2022] Open
Abstract
Background Xanthomonas spp. causes bacterial spot disease, which reduces quality and yield of pepper crops in Mexico. Identification of phytopathogen species is necessary to implement more effective control strategies. Objective The aim of this study was to isolate and identify infecting Xanthomonas species in South Central Chihuahua pepper-producing areas. Methods Diseased plants were collected from 30 cultivation lots and bacteria were isolated from damaged tissues. Potential causative agents were isolated, identified, and characterized by biochemical and molecular analysis. Pathogenicity tests from each isolate were then performed on 30-d-old pepper seedlings, exposing five leaves to 10 µL of 1 × 108 CFU/mL bacterial suspensions of each isolate, using sterile distilled water as a control. Disease severity was determined after 10 d by calculating leaf damage percentage. Furthermore, we evaluated the susceptibility of the highest bacterial spot severity-causing isolates (13 isolates) to copper sulphate (CuS), copper gluconate (CuG), copper oxychloride + oxytetracycline hydrochloride (Cu + Ox), gentamicin + oxytetracycline hydrochloride (Gen + Ox), and gentamicin sulphate (GenS). Copper-resistance genes (copLAB) were detected by PCR analysis among isolates. Results Thirty-seven foliage isolates were identified as Xanthomonas euvesicatoria (14%), which were associated with bacterial spot disease in jalapeño pepper. Tested Xanthomonas isolates were resistant to Cu-based compounds, but susceptible to Cu + Ox. All isolates were susceptible to Gen + Ox and GenS. CopLAB genes were detected in all but one strain. Conclusions X. euvesicatoria (formally X. perforans) may be considered as an emerging pathogen of bacterial spot pepper in Mexico. Among disease management strategies, alternatives to copper should be taken into consideration.
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Affiliation(s)
- Jared Hernández-Huerta
- Facultad de Ciencias Agrotecnológicas, Universidad Autónoma de Chihuahua, Campus 1, Chihuahua, Chihuahua, México
| | - Patricia Tamez-Guerra
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Ricardo Gomez-Flores
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Ma Carmen E Delgado-Gardea
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Nuevo Campus, Chihuahua, Chihuahua, México
| | - Margarita S García-Madrid
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Nuevo Campus, Chihuahua, Chihuahua, México
| | - Loreto Robles-Hernández
- Facultad de Ciencias Agrotecnológicas, Universidad Autónoma de Chihuahua, Campus 1, Chihuahua, Chihuahua, México
| | - Rocio Infante-Ramirez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Nuevo Campus, Chihuahua, Chihuahua, México
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Development of Real-Time and Colorimetric Loop Mediated Isothermal Amplification Assay for Detection of Xanthomonas gardneri. Microorganisms 2020; 8:microorganisms8091301. [PMID: 32858943 PMCID: PMC7563391 DOI: 10.3390/microorganisms8091301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 01/16/2023] Open
Abstract
Xanthomonas gardneri is one of the causal agents of bacterial spot (BS), an economically important bacterial disease of tomato and pepper. Field-deployable and portable loop-mediated isothermal amplification (LAMP)-based instruments provide rapid and sensitive detection of plant pathogens. In order to rapidly and accurately identify and differentiate X. gardneri from other BS-causing Xanthomonas spp., we optimized a new real-time monitoring LAMP-based method targeting the X. gardneri-specific hrpB gene. Specificity and sensitivity of real-time and colorimetric LAMP assays were tested on the complex of bacterial strains pathogenic to tomato and pepper and on plants infected by the pathogen. The assay detection limit was 1 pg/μL of genomic DNA with an assay duration of only 30 min. The use of portable and handheld instruments allows for fast analysis, reducing the diagnosis time, and can contribute to proper disease management and control of X. gardneri. Due to the high efficiency of this method, we suggest its use as a standard diagnostic tool during phytosanitary controls.
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Multiplex real-time PCR for the detection of Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato and pathogenic Xanthomonas species on tomato plants. PLoS One 2020; 15:e0227559. [PMID: 31910230 PMCID: PMC6946519 DOI: 10.1371/journal.pone.0227559] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/20/2019] [Indexed: 01/08/2023] Open
Abstract
A multiplex real-time PCR method based on fluorescent TaqMan® probes was developed for the simultaneous detection of the tomato pathogenic bacteria Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato and bacterial spot-causing xanthomonads. The specificity of the multiplex assay was validated on 44 bacterial strains, including 32 target pathogen strains as well as closely related species and nontarget tomato pathogenic bacteria. The designed multiplex real-time PCR showed high sensitivity when positive amplification was observed for one pg of bacterial DNA in the cases of Clavibacter michiganensis subsp. michiganensis and Pseudomonas syringae pv. tomato bacteria and 100 pg for bacterial spot-causing xanthomonads. The reliability of the developed multiplex real-time PCR assay for in planta detection was verified by recognition of the target pathogens in 18 tomato plants artificially inoculated by each of the target bacteria and tomato samples from production greenhouses.
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12
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Molecular Epidemiology of Xanthomonas perforans Outbreaks in Tomato Plants from Transplant to Field as Determined by Single-Nucleotide Polymorphism Analysis. Appl Environ Microbiol 2019; 85:AEM.01220-19. [PMID: 31253682 DOI: 10.1128/aem.01220-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/25/2019] [Indexed: 01/15/2023] Open
Abstract
Outbreaks of bacterial spot on tomato (BST) caused by Xanthomonas perforans are a major concern for sustainable crop production. BST is a common occurrence in tomato transplants grown for field production. We hypothesized that BST outbreaks in commercial fields originate from X. perforans strains inadvertently introduced from commercial transplant facilities. To test this hypothesis, we used a genome-wide single-nucleotide polymorphism (SNP) analysis to characterize X. perforans strains recovered from tomato transplant facilities and fields in commercial production areas. X. perforans strains were isolated from symptomatic transplants prior to roguing at two commercial transplant growers. Then, the same groups of transplants were tracked to commercial fields to recover X. perforans strains from diseased plants prior to harvest. Whole-genome sequencing was carried out on 84 strains isolated from transplant and field plants from Florida and South Carolina. SNPs were called using three reference strains that represented the genetic variation of the sampled strains. Field strains showing genetic similarity to transplant strains had a difference of 2 to 210 SNPs. Transplant and field strains clustered together by grower within each phylogenomic group, consistent with expectations. The range of genetic divergence among strains isolated from field plants was similar to the range obtained from strains on transplants. Using the range of genetic variation observed in transplants, we estimate that 60% to 100% of field strains were an extension of the transplant strain population. Our results stress the importance of BST management to reduce X. perforans movement from transplant to field and to minimize subsequent disease outbreaks.IMPORTANCE Current management of Xanthomonas perforans on tomato plants mainly relies on the frequent application of pesticides. However, the lack of effective pesticides and the development of strain tolerance to certain bactericides limit the ability to control outbreaks in production fields. Better knowledge of probable sources of X. perforans inoculum during tomato production is required to refine management strategies. Tomato plants are typically established in the field using transplants. This study aimed to determine if strains from field epidemics were coming from transplant facilities or resulted from local field outbreaks. The overall goal was to identify potential sources of inoculum and subsequently develop strategies to reduce carryover from transplant production to the field. Our results indicate that tomato producers should shift disease management efforts to transplant facilities to reduce disease in the field. Improved transplant health should reduce the likelihood of bacterial spot outbreaks and subsequently reduce pesticide usage in the field.
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Burlakoti RR, Hsu CF, Chen JR, Wang JF. Population Dynamics of Xanthomonads Associated with Bacterial Spot of Tomato and Pepper during 27 Years across Taiwan. PLANT DISEASE 2018; 102:1348-1356. [PMID: 30673574 DOI: 10.1094/pdis-04-17-0465-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Bacterial spot caused by Xanthomonas spp. is the second most important bacterial disease after bacterial wilt of tomato and pepper in Taiwan. To determine the species composition of the Xanthomonas population over 27 years (1989 to 2016) across the country, a large collections of strains from tomato (n = 292) and pepper (n = 198) were examined. In the 1989 to 1999 population, all strains (n = 147) from pepper and 95% strains (n = 198) from tomato were Xanthomonas euvesicatoria. The remaining 5% of strains from tomato were X. vesicatoria. In a 2000 to 2009 population from tomato (n = 36), 22% of the strains were X. perforans and the remaining 78% strains were X. euvesicatoria. In the 2010 to 2016 population, 92% of the strains (n = 50) from pepper were still X. euvesicatoria and the remaining 8% of the strains were X. perforans; however, 99% (n = 58) of the strains from tomato were X. perforans. All of the evaluated (n = 25) strains of X. euvesicatoria collected during 1990 to 2006 were tomato race T1. Four pepper races (P1, P2, P7, and P8) were identified in the X. euvesicatoria population. The strains of X. vesicatoria collected during 1989 to 1999 (n = 8) were tomato race T2 and strains of X. perforans from tomato collected during 2010 to 2016 (n = 12) were race T4 (83%) and race T3 (17%). Four strains of X. perforans from pepper were race T4. All of the strains of X. vesicatoria and X. perforans caused a hypersensitive response in all pepper differentials. Biochemical characterization of representative strains (n = 48) showed that strains of X. euvesicatoria were negative on and amylolytic test and positive on lipase and oxidative-fermentative (OF) tests. The strains of X. vesicatoria were positive on amylolytic and OF tests and were negative on the lipase test. All X. perforans strains showed positive reactions on three tests. Evaluation of the same 48 strains for the sensitivity to copper sulfate (50, 100, 200, 300, and 400 mg liter-1) revealed that the majority of X. euvesicatoria (86%) and X. perforans (94%) strains in the 2010 to 2016 population were tolerant to copper sulfate. The findings suggest that management strategies and breeding programs should consider the new X. perforans species and their new races. The increased number of copper-sulfate-tolerant strains in the 2010 to 2016 population further shows the need for alternative options to copper for managing bacterial spot of tomato and pepper.
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Affiliation(s)
| | - Chiou-Fen Hsu
- World Vegetable Center, P. O. Box 42, Shanhua, Tainan, 74199, Taiwan
| | - Jaw-Rong Chen
- World Vegetable Center, P. O. Box 42, Shanhua, Tainan, 74199, Taiwan
| | - Jaw-Fen Wang
- World Vegetable Center, P. O. Box 42, Shanhua, Tainan, 74199, Taiwan
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14
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Barak JD, Vancheva T, Lefeuvre P, Jones JB, Timilsina S, Minsavage GV, Vallad GE, Koebnik R. Whole-Genome Sequences of Xanthomonas euvesicatoria Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors. FRONTIERS IN PLANT SCIENCE 2016; 7:1805. [PMID: 28018370 PMCID: PMC5146329 DOI: 10.3389/fpls.2016.01805] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/15/2016] [Indexed: 05/11/2023]
Abstract
Multiple species of Xanthomonas cause bacterial spot of tomato (BST) and pepper. We sequenced five Xanthomonas euvesicatoria strains isolated from three continents (Africa, Asia, and South America) to provide a set of representative genomes with temporal and geographic diversity. LMG strains 667, 905, 909, and 933 were pathogenic on tomato and pepper, except LMG 918 elicited a hypersensitive reaction (HR) on tomato. Furthermore, LMG 667, 909, and 918 elicited a HR on Early Cal Wonder 30R containing Bs3. We examined pectolytic activity and starch hydrolysis, two tests which are useful in differentiating X. euvesicatoria from X. perforans, both causal agents of BST. LMG strains 905, 909, 918, and 933 were nonpectolytic while only LMG 918 was amylolytic. These results suggest that LMG 918 is atypical of X. euvesicatoria. Sequence analysis of all the publicly available X. euvesicatoria and X. perforans strains comparing seven housekeeping genes identified seven haplotypes with few polymorphisms. Whole genome comparison by average nucleotide identity (ANI) resulted in values of >99% among the LMG strains 667, 905, 909, 918, and 933 and X. euvesicatoria strains and >99.6% among the LMG strains and a subset of X. perforans strains. These results suggest that X. euvesicatoria and X. perforans should be considered a single species. ANI values between strains of X. euvesicatoria, X. perforans, X. allii, X. alfalfa subsp. citrumelonis, X. dieffenbachiae, and a recently described pathogen of rose were >97.8% suggesting these pathogens should be a single species and recognized as X. euvesicatoria. Analysis of the newly sequenced X. euvesicatoria strains revealed interesting findings among the type 3 (T3) effectors, relatively ancient stepwise erosion of some T3 effectors, additional X. euvesicatoria-specific T3 effectors among the causal agents of BST, orthologs of avrBs3 and avrBs4, and T3 effectors shared among xanthomonads pathogenic against various hosts. The results from this study supports the finding that T3 effector repertoire and host range are fundamental for the study of host-microbe interaction but of little relevance to bacterial speciation.
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Affiliation(s)
- Jeri D. Barak
- UMR Interactions – Plantes – Microorganismes – Environnement, IRD-Cirad-Université MontpellierMontpellier, France
- Department of Plant Pathology, University of WisconsinMadison, WI, USA
| | - Taca Vancheva
- UMR Interactions – Plantes – Microorganismes – Environnement, IRD-Cirad-Université MontpellierMontpellier, France
- Faculty of Biology, Sofia University St. Kliment OhridskiSofia, Bulgaria
| | - Pierre Lefeuvre
- Pôle de Protection des Plantes, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Cirad-Université de la RéunionSaint-Pierre, Ile de la Réunion, France
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of FloridaGainsville, FL, USA
| | - Sujan Timilsina
- Department of Plant Pathology, University of FloridaGainsville, FL, USA
| | | | - Gary E. Vallad
- Gulf Coast Research and Education Center, University of FloridaWimauma, FL, USA
| | - Ralf Koebnik
- UMR Interactions – Plantes – Microorganismes – Environnement, IRD-Cirad-Université MontpellierMontpellier, France
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15
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Potnis N, Timilsina S, Strayer A, Shantharaj D, Barak JD, Paret ML, Vallad GE, Jones JB. Bacterial spot of tomato and pepper: diverse Xanthomonas species with a wide variety of virulence factors posing a worldwide challenge. MOLECULAR PLANT PATHOLOGY 2015; 16:907-20. [PMID: 25649754 PMCID: PMC6638463 DOI: 10.1111/mpp.12244] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
TAXONOMIC STATUS Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species Xanthomonas euvesicatoria, Xanthomonas vesicatoria, Xanthomonas perforans and Xanthomonas gardneri. MICROBIOLOGICAL PROPERTIES Gram-negative, rod-shaped bacterium, aerobic, motile, single polar flagellum. HOST RANGE Causes bacterial spot disease on plants belonging to the Solanaceae family, primarily tomato (Solanum lycopersicum), pepper (Capsicum annuum) and chilli peppers (Capsicum frutescens). DISEASE SYMPTOMS Necrotic lesions on all above-ground plant parts. DISTRIBUTION Worldwide distribution of X. euvesicatoria and X. vesicatoria on tomato and pepper; X. perforans and X. gardneri increasingly being isolated from the USA, Canada, South America, Africa and Europe. A wide diversity within the bacterial spot disease complex, with an ability to cause disease at different temperatures, makes this pathogen group a worldwide threat to tomato and pepper production. Recent advances in genome analyses have revealed the evolution of the pathogen with a plethora of novel virulence factors. Current management strategies rely on the use of various chemical control strategies and sanitary measures to minimize pathogen spread through contaminated seed. Chemical control strategies have been a challenge because of resistance by the pathogen. Breeding programmes have been successful in developing commercial lines with hypersensitive and quantitative resistance. However, durability of resistance has been elusive. Recently, a transgenic approach has resulted in the development of tomato genotypes with significant levels of resistance and improved yield that hold promise. In this article, we discuss the current taxonomic status, distribution of the four species, knowledge of virulence factors, detection methods and strategies for disease control with possible directions for future research.
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Affiliation(s)
- Neha Potnis
- Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA
| | - Sujan Timilsina
- Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA
| | - Amanda Strayer
- Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA
| | - Deepak Shantharaj
- Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA
| | - Jeri D Barak
- Department of Plant Pathology, Russell Laboratories, University of Wisconsin, Madison, WI, 53706, USA
| | - Mathews L Paret
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA
| | - Gary E Vallad
- North Florida Research & Education Center, University of Florida, Quincy, FL, 32351-5677, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA
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16
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Wai KPP, Siddique MI, Mo HS, Yoo HJ, Byeon SE, Jegal Y, Mekuriaw AA, Kim BS. Pathotypes of Bacterial Spot Pathogen Infecting Capsicum Peppers in Korea. THE PLANT PATHOLOGY JOURNAL 2015; 31:428-32. [PMID: 26674555 PMCID: PMC4677752 DOI: 10.5423/ppj.nt.05.2015.0074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 06/05/2023]
Abstract
Sixty-seven isolates of bacterial spot pathogen (Xanthomonas spp.) collected from six provinces of Korea were tested for the identification of their pathotypes and determination of their distribution throughout Korea in an effort to genetically manage the disease. Near isogenic lines of Early Calwonder (Capsicum annuum) pepper plants carrying Bs1 , Bs2 and Bs3 , and PI235047 (C. pubescens) were used as differential hosts. Race P1 was found to be predominant, followed by race P7, and races P3 and P8 were also observed. This is the first report of races P7 and P8 in Korea. The races P7 and P8 were differentiated from the former races P1 and P3, respectively, on the basis of their ability to elicit hypersensitive reactions to PI235047.
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Affiliation(s)
- Khin Pa Pa Wai
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701,
Korea
| | | | - Hwang-Sung Mo
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701,
Korea
| | - Hee Ju Yoo
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701,
Korea
| | - Si-Eun Byeon
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701,
Korea
| | - Yoonhyuk Jegal
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701,
Korea
| | - Alebel A. Mekuriaw
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701,
Korea
| | - Byung-Soo Kim
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701,
Korea
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17
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Abbasi PA, Khabbaz SE, Weselowski B, Zhang L. Occurrence of copper-resistant strains and a shift in Xanthomonas spp. causing tomato bacterial spot in Ontario. Can J Microbiol 2015; 61:753-61. [PMID: 26308592 DOI: 10.1139/cjm-2015-0228] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Field strains of tomato bacterial spot pathogen (Xanthomonas euvesicatoria, X. vesicatoria, X. perforans, and X. gardneri) were characterized for sensitivity to copper and species composition. A total of 98 strains were isolated from symptomatic leaf and fruit samples collected from 18 tomato fields in Ontario. In greenhouse pathogenicity tests, most of the field strains caused severe (37 strains) to highly severe (23 strains) symptoms on 'Bonny Best' tomato plants, whereas 38 strains caused moderate symptoms. In MGY agar plates amended with various concentrations of copper sulfate, 11 strains were completely sensitive (no growth) and 87 strains were resistant (grew on 1.0 mmol/L or higher copper concentration). PCR analysis of the hrp gene cluster followed by restriction digestion with HaeIII and sequencing identified X. gardneri (35 strains) and X. perforans (26 strains) as predominant species and X. euvesicatoria and X. vesicatoria as less common species in Ontario tomato fields. Separation of field strains into various species was also confirmed with starch hydrolysis activity on agar medium. Moreover, 72 field strains produced shiny greenish-yellow colonies surrounded by a milky zone on xanthomonad differential (Xan-D) medium, and the colonies of 26 strains did not produce a milky zone. Thirty-four strains could not be clustered into any species and 25 of those strains were negative for the hrp gene PCR and also did not produce a milky zone around colonies on Xan-D medium. Our results suggest a widespread existence of copper-resistant strains and an increase in X. perforans strains of bacterial spot pathogen in Ontario. This information on copper resistance and species composition within bacterial spot pathogens in Ontario will be helpful for developing effective disease management strategies, making cultivar selection, and breeding new tomato cultivars.
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Affiliation(s)
- Pervaiz A Abbasi
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada.,Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Salah Eddin Khabbaz
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada.,Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Brian Weselowski
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada.,Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Liang Zhang
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada.,Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
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18
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Schwartz AR, Potnis N, Timilsina S, Wilson M, Patané J, Martins J, Minsavage GV, Dahlbeck D, Akhunova A, Almeida N, Vallad GE, Barak JD, White FF, Miller SA, Ritchie D, Goss E, Bart RS, Setubal JC, Jones JB, Staskawicz BJ. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity. Front Microbiol 2015; 6:535. [PMID: 26089818 PMCID: PMC4452888 DOI: 10.3389/fmicb.2015.00535] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 05/15/2015] [Indexed: 11/24/2022] Open
Abstract
Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type III effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. Genomes of 67 Xanthomonas euvesicatoria (Xe), Xanthomonas perforans (Xp), and Xanthomonas gardneri (Xg) strains isolated from diseased pepper and tomato fields in the southeastern and midwestern United States were sequenced in order to determine the genetic diversity in field strains. Type III effector repertoires were computationally predicted for each strain, and multiple methods of constructing phylogenies were employed to understand better the genetic relationship of strains in the collection. A division in the Xp population was detected based on core genome phylogeny, supporting a model whereby the host-range expansion of Xp field strains on pepper is due, in part, to a loss of the effector AvrBsT. Xp-host compatibility was further studied with the observation that a double deletion of AvrBsT and XopQ allows a host range expansion for Nicotiana benthamiana. Extensive sampling of field strains and an improved understanding of effector content will aid in efforts to design disease resistance strategies targeted against highly conserved core effectors.
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Affiliation(s)
- Allison R. Schwartz
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeley, CA, USA
| | - Neha Potnis
- Department of Plant Pathology, University of FloridaGainesville, FL, USA
| | - Sujan Timilsina
- Department of Plant Pathology, University of FloridaGainesville, FL, USA
| | - Mark Wilson
- Donald Danforth Plant Science CenterSt. Louis, MO, USA
| | - José Patané
- Department of Biochemistry, Institute of Chemistry, University of São PauloSão Paulo, Brazil
| | - Joaquim Martins
- Department of Biochemistry, Institute of Chemistry, University of São PauloSão Paulo, Brazil
| | | | - Douglas Dahlbeck
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeley, CA, USA
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State UniversityManhattan, KS, USA
| | - Nalvo Almeida
- School of Computing, Federal University of Mato Grosso do SulCampo Grande, Brazil
| | - Gary E. Vallad
- Gulf Coast Research and Education Center, University of FloridaWimauma, FL, USA
| | - Jeri D. Barak
- Department of Plant Pathology, University of Wisconsin, MadisonMadison, WI, USA
| | - Frank F. White
- Department of Plant Pathology, Kansas State UniversityManhattan, KS, USA
| | - Sally A. Miller
- Department of Plant Pathology, Ohio Agricultural Research and Development CenterWooster, MA, USA
| | - David Ritchie
- Department of Plant Pathology, NC State UniversityRaleigh, NC, USA
| | - Erica Goss
- Department of Plant Pathology, University of FloridaGainesville, FL, USA
| | | | - João C. Setubal
- Department of Biochemistry, Institute of Chemistry, University of São PauloSão Paulo, Brazil
- Virginia Bioinformatics Institute, Virginia TechBlacksburg, VA, USA
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of FloridaGainesville, FL, USA
| | - Brian J. Staskawicz
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeley, CA, USA
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19
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Timilsina S, Jibrin MO, Potnis N, Minsavage GV, Kebede M, Schwartz A, Bart R, Staskawicz B, Boyer C, Vallad GE, Pruvost O, Jones JB, Goss EM. Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of Xanthomonas gardneri. Appl Environ Microbiol 2015; 81:1520-9. [PMID: 25527544 PMCID: PMC4309686 DOI: 10.1128/aem.03000-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/14/2014] [Indexed: 01/29/2023] Open
Abstract
Four Xanthomonas species are known to cause bacterial spot of tomato and pepper, but the global distribution and genetic diversity of these species are not well understood. A collection of bacterial spot-causing strains from the Americas, Africa, Southeast Asia, and New Zealand were characterized for genetic diversity and phylogenetic relationships using multilocus sequence analysis of six housekeeping genes. By examining strains from different continents, we found unexpected phylogeographic patterns, including the global distribution of a single multilocus haplotype of X. gardneri, possible regional differentiation in X. vesicatoria, and high species diversity on tomato in Africa. In addition, we found evidence of multiple recombination events between X. euvesicatoria and X. perforans. Our results indicate that there have been shifts in the species composition of bacterial spot pathogen populations due to the global spread of dominant genotypes and that recombination between species has generated genetic diversity in these populations.
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Affiliation(s)
- Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
| | - Mustafa O. Jibrin
- Department of Crop Protection, Ahmadu Bello University, Zaria, Nigeria
| | - Neha Potnis
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Gerald V. Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Misrak Kebede
- Plant Pathology Department, School of Plant Science, Haramaya University, Dire Dawa, Ethiopia
| | - Allison Schwartz
- Department of Plant and Microbial Biology, University of California—Berkeley, California, USA
| | | | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California—Berkeley, California, USA
| | - Claudine Boyer
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France
| | - Gary E. Vallad
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
| | - Olivier Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Erica M. Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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20
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Scientific Opinion on the pest categorisation of Xanthomonas campestris pv. vesicatoria (Doidge) Dye. EFSA J 2014. [DOI: 10.2903/j.efsa.2014.3720] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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21
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Huang CH, Vallad GE, Adkison H, Summers C, Margenthaler E, Schneider C, Hong J, Jones JB, Ong K, Norman DJ. A Novel Xanthomonas sp. Causes Bacterial Spot of Rose (Rosa spp.). PLANT DISEASE 2013; 97:1301-1307. [PMID: 30722131 DOI: 10.1094/pdis-09-12-0851-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A bacterial spot of rose (Rosa spp.) caused by a xanthomonad was observed in Florida and Texas. Ten representative strains collected from the two states between 2004 and 2010 were used to determine the taxonomic position of this rose pathogen. Fatty acid methyl ester analysis was performed and a nearly 2-kb 16S-23S rRNA intergenic spacer along with flanking portions of the 16S and 23S rRNA genes were sequenced for selected strains, showing that they were members of the genus Xanthomonas. Multilocus sequence typing and analysis (MLST/MLSA) and pathogenicity tests were conducted to further characterize the Xanthomonas strains. The MLSA, based on six gene fragments-fusA, gapA, gltA, gyrB, lacF, and lepA-showed that the rose strains fell into Xanthomonas axonopodis subgroup 9.2 and shared the highest similarity values (98.8 to 99.7%) with X. alfalfae subsp. citrumelonis of the subgroup. However, principal coordinate analysis grouped the rose strains into a unique cluster distinct from other members of the subgroup according to virulence phenotypes on 11 plant species belonging to five plant families (Araceae, Euphorbiaceae, Rosaceae, Rutaceae, and Solanaceae). Moreover, the rose strains were aggressive on rose and Indian Hawthorn (Rhaphiolepsis indica). On the basis of the MLSA and virulence phenotypes, the pathovar epithet rosa is proposed.
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Affiliation(s)
- Cheng-Hua Huang
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Gary E Vallad
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Heather Adkison
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Carly Summers
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Elaina Margenthaler
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Christina Schneider
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Jason Hong
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - Kevin Ong
- Texas Plant Disease Diagnostic Lab, Texas A&M University, College Station 77845
| | - David J Norman
- Mid-Florida Research and Education Center, University of Florida, IFAS, Apopka 32703
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Moreira S, Rodrigues R, Oliveira H, Medeiros A, Sudré C, Gonçalves L. Phenotypic and genotypic variation among Capsicum annuum recombinant inbred lines resistant to bacterial spot. GENETICS AND MOLECULAR RESEARCH 2013; 12:1232-42. [DOI: 10.4238/2013.april.17.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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MultiLocus Sequence Analysis- and Amplified Fragment Length Polymorphism-based characterization of xanthomonads associated with bacterial spot of tomato and pepper and their relatedness to Xanthomonas species. Syst Appl Microbiol 2012; 35:183-90. [DOI: 10.1016/j.syapm.2011.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 12/07/2011] [Accepted: 12/16/2011] [Indexed: 11/21/2022]
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Potnis N, Krasileva K, Chow V, Almeida NF, Patil PB, Ryan RP, Sharlach M, Behlau F, Dow JM, Momol MT, White FF, Preston JF, Vinatzer BA, Koebnik R, Setubal JC, Norman DJ, Staskawicz BJ, Jones JB. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. BMC Genomics 2011; 12:146. [PMID: 21396108 PMCID: PMC3071791 DOI: 10.1186/1471-2164-12-146] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 03/11/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Bacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular characteristics. The genome sequence of strain 85-10, a member of one of the species, Xanthomonas euvesicatoria (Xcv) has been previously reported. To determine the relationship of the four species at the genome level and to investigate the molecular basis of their virulence and differing host ranges, draft genomic sequences of members of the other three species were determined and compared to strain 85-10. RESULTS We sequenced the genomes of X. vesicatoria (Xv) strain 1111 (ATCC 35937), X. perforans (Xp) strain 91-118 and X. gardneri (Xg) strain 101 (ATCC 19865). The genomes were compared with each other and with the previously sequenced Xcv strain 85-10. In addition, the molecular features were predicted that may be required for pathogenicity including the type III secretion apparatus, type III effectors, other secretion systems, quorum sensing systems, adhesins, extracellular polysaccharide, and lipopolysaccharide determinants. Several novel type III effectors from Xg strain 101 and Xv strain 1111 genomes were computationally identified and their translocation was validated using a reporter gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice, and a functional Ax21 sulfation system were identified in Xcv. Genes encoding proteins with functions mediated by type II and type IV secretion systems have also been compared, including enzymes involved in cell wall deconstruction, as contributors to pathogenicity. CONCLUSIONS Comparative genomic analyses revealed considerable diversity among bacterial spot pathogens, providing new insights into differences and similarities that may explain the diverse nature of these strains. Genes specific to pepper pathogens, such as the O-antigen of the lipopolysaccharide cluster, and genes unique to individual strains, such as novel type III effectors and bacteriocin genes, have been identified providing new clues for our understanding of pathogen virulence, aggressiveness, and host preference. These analyses will aid in efforts towards breeding for broad and durable resistance in economically important tomato and pepper cultivars.
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Affiliation(s)
- Neha Potnis
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Ksenia Krasileva
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Virginia Chow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Prabhu B Patil
- Institute of Microbial Technology (CSIR), Sector 39A, Chandigarh 160036, India
| | - Robert P Ryan
- BIOMERIT Research Centre, Biosciences Institute, University College Cork, Ireland
| | - Molly Sharlach
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Franklin Behlau
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
- Fundecitrus - Fundo de Defesa da Citricultura, Av. Adhemar Pereira de Barros, 201, 14807-040 Araraquara, SP. Brazil
| | - J Max Dow
- BIOMERIT Research Centre, Biosciences Institute, University College Cork, Ireland
| | - MT Momol
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Frank F White
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - James F Preston
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Boris A Vinatzer
- Department of Plant Pathology, Physiology and Weed Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Ralf Koebnik
- Laboratoire Génome et Développement des Plantes, IRD-CNRS-Université-de Perpignan, Centre IRD, 911 Av. Agropolis, BP64501, 34394 Montpellier, France
| | - João C Setubal
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - David J Norman
- Institute of Food and Agricultural Sciences, Mid-Florida Research & Education Center, University of Florida, Apopka, FL, USA
| | - Brian J Staskawicz
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
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