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Diallo A, Wonni I, Sicard A, Blondin L, Gagnevin L, Vernière C, Szurek B, Hutin M. Genetic Structure and TALome Analysis Highlight a High Level of Diversity in Burkinabe Xanthomonas Oryzae pv. oryzae Populations. RICE (NEW YORK, N.Y.) 2023; 16:33. [PMID: 37523017 PMCID: PMC10390441 DOI: 10.1186/s12284-023-00648-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Bacterial Leaf Blight of rice (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat for food security in many rice growing countries including Burkina Faso, where the disease was first reported in the 1980's. In line with the intensification of rice cultivation in West-Africa, BLB incidence has been rising for the last 15 years. West-African strains of Xoo differ from their Asian counterparts as they (i) are genetically distant, (ii) belong to new races and, (iii) contain reduced repertoires of Transcription Activator Like (TAL) effector genes. In order to investigate the evolutionary dynamics of Xoo populations in Burkina Faso, 177 strains were collected from 2003 to 2018 in three regions where BLB is occurring. Multilocus VNTR Analysis (MLVA-14) targeting 10 polymorphic loci discriminated 24 haplotypes and showed that Xoo populations were structured according to their geographical localization and year of collection. Considering their major role in Xoo pathogenicity, we assessed the TAL effector repertoires of the 177 strains upon RFLP-based profiling. Surprisingly, an important diversity was revealed with up to eight different RFLP patterns. Finally, comparing neutral vs. tal effector gene diversity allowed to suggest scenarios underlying the evolutionary dynamics of Xoo populations in Burkina Faso, which is key to rationally guide the deployment of durably resistant rice varieties against BLB in the country.
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Affiliation(s)
- A Diallo
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - I Wonni
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso.
| | - A Sicard
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Blondin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Gagnevin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - C Vernière
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - B Szurek
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - M Hutin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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Bianco MI, Ponso MA, Garita-Cambronero J, Conforte VP, Galván TE, Dunger G, Morales GM, Vojnov AA, Romero AM, Cubero J, Yaryura PM. Genomic and phenotypic insight into Xanthomonas vesicatoria strains with different aggressiveness on tomato. Front Microbiol 2023; 14:1185368. [PMID: 37440880 PMCID: PMC10333488 DOI: 10.3389/fmicb.2023.1185368] [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: 03/13/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Xanthomonas vesicatoria is one of the causal agents of bacterial spot, a disease that seriously affects the production of tomato (Solanum lycopersicum) and pepper (Capsicum annum) worldwide. In Argentina, bacterial spot is found in all tomato producing areas, with X. vesicatoria being one of the main species detected in the fields. Previously, we isolated three X. vesicatoria strains BNM 208, BNM 214, and BNM 216 from tomato plants with bacterial spot, and found they differed in their ability to form biofilm and in their degree of aggressiveness. Here, the likely causes of those differences were explored through genotypic and phenotypic studies. The genomes of the three strains were sequenced and assembled, and then compared with each other and also with 12 other publicly available X. vesicatoria genomes. Phenotypic characteristics (mainly linked to biofilm formation and virulence) were studied in vitro. Our results show that the differences observed earlier between BNM 208, BNM 214, and BNM 216 may be related to the structural characteristics of the xanthan gum produced by each strain, their repertoire of type III effectors (T3Es), the presence of certain genes associated with c-di-GMP metabolism and type IV pili (T4P). These findings on the pathogenicity mechanisms of X. vesicatoria could be useful for developing bacterial spot control strategies aimed at interfering with the infection processes.
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Affiliation(s)
- María Isabel Bianco
- Instituto de Ciencia y Tecnología Dr. César Milstein – Fundación Pablo Cassará – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Investigación en Medicina y Ciencias de la Salud, Facultad de Medicina, Universidad del Salvador, Buenos Aires, Argentina
| | - María Agustina Ponso
- Instituto Multidisciplinario de Investigación y Transferencia Agroalimentario y Biotecnológica (IMITAB, UNVM-CONICET), Instituto Académico Pedagógico de Ciencias Básicas y Aplicadas, Universidad Nacional de Villa María, Villa María, Argentina
| | | | - Valeria Paola Conforte
- Instituto de Ciencia y Tecnología Dr. César Milstein – Fundación Pablo Cassará – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Investigación en Medicina y Ciencias de la Salud, Facultad de Medicina, Universidad del Salvador, Buenos Aires, Argentina
| | - Tadeo E. Galván
- Instituto de Ciencia y Tecnología Dr. César Milstein – Fundación Pablo Cassará – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Germán Dunger
- Facultad de Ciencias Agrarias, Instituto de Ciencias Agropecuarias del Litoral, CONICET, Universidad Nacional del Litoral, Esperanza, Argentina
| | - Gustavo M. Morales
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados, Universidad Nacional de Rio Cuarto – CONICET, Rio Cuarto, Argentina
| | - Adrián Alberto Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein – Fundación Pablo Cassará – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Investigación en Medicina y Ciencias de la Salud, Facultad de Medicina, Universidad del Salvador, Buenos Aires, Argentina
| | - Ana María Romero
- Cátedra de Fitopatología, Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jaime Cubero
- Laboratorio de Bacteriología, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria/Consejo Superior de Investigaciones Científicas (INIA/CSIC), Madrid, Spain
| | - Pablo Marcelo Yaryura
- Instituto Multidisciplinario de Investigación y Transferencia Agroalimentario y Biotecnológica (IMITAB, UNVM-CONICET), Instituto Académico Pedagógico de Ciencias Básicas y Aplicadas, Universidad Nacional de Villa María, Villa María, Argentina
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Kizheva Y, Urshev Z, Dimitrova M, Bogatzevska N, Moncheva P, Hristova P. Phenotypic and Genotypic Characterization of Newly Isolated Xanthomonas euvesicatoria-Specific Bacteriophages and Evaluation of Their Biocontrol Potential. PLANTS (BASEL, SWITZERLAND) 2023; 12:947. [PMID: 36840295 PMCID: PMC9968065 DOI: 10.3390/plants12040947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Bacteriophages have greatly engaged the attention of scientists worldwide due to the continuously increasing resistance of phytopathogenic bacteria to commercially used chemical pesticides. However, the knowledge regarding phages is still very insufficient and must be continuously expanded. This paper presents the results of the isolation, characterization, and evaluation of the potential of 11 phage isolates as natural predators of a severe phytopathogenic bacterium-Xanthomonas euvesicatoria. Phages were isolated from the rhizosphere of tomato plants with symptoms of bacterial spot. The plaque morphology of all isolates was determined on a X. euvesicatoria lawn via a plaque assay. Three of the isolates were attributed to the family Myoviridae based on TEM micrographs. All phages showed good long-term viability when stored at 4 °C and -20 °C. Three of the phage isolates possessed high stability at very low pH values. Fifty-five-day persistence in a soil sample without the presence of the specific host and a lack of lytic activity on beneficial rhizosphere bacteria were found for the phage isolate BsXeu269p/3. The complete genome of the same isolate was sequenced and analyzed, and, for the first time in this paper, we report a circular representation of a linear but circularly permuted phage genome among known X. euvesicatoria phage genomes.
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Affiliation(s)
- Yoana Kizheva
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University St. “Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1000 Sofia, Bulgaria
| | - Zoltan Urshev
- R&D Department, LB Bulgaricum PLC, 14 Malashevska Str., 1000 Sofia, Bulgaria
| | - Melani Dimitrova
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University St. “Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1000 Sofia, Bulgaria
| | - Nevena Bogatzevska
- Institute of Soil Science, Agrotechnologies and Plant Protection “N. Poushkarov”, Agricultural Academy, 1331 Sofia, Bulgaria
| | - Penka Moncheva
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University St. “Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1000 Sofia, Bulgaria
| | - Petya Hristova
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University St. “Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1000 Sofia, Bulgaria
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Costa J, Pothier JF, Boch J, Stefani E, Koebnik R. Integrating Science on Xanthomonas and Xylella for Integrated Plant Disease Management. Microorganisms 2022; 11:microorganisms11010006. [PMID: 36677298 PMCID: PMC9861534 DOI: 10.3390/microorganisms11010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
Present, emerging or re-emerging plant diseases due to infection by bacteria of the Lysobacteraceae (syn: Xanthomonadaceae) family are continually challenging food security and cause significant losses to the economies of European countries each year [...].
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Affiliation(s)
- Joana Costa
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, 3000-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Emilio Stefani
- Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34394 Montpellier, France
- Correspondence: ; Tel.: +33-467-416228
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Tambong JT, Xu R, Cuppels D, Chapados J, Gerdis S, Eyres J, Koziol A, Dettman J. Whole-Genome Resources and Species-Level Taxonomic Validation of 89 Plant-Pathogenic Xanthomonas Strains Isolated from Various Host Plants. PLANT DISEASE 2022; 106:1558-1565. [PMID: 35100028 DOI: 10.1094/pdis-11-21-2498-sc] [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: 06/14/2023]
Abstract
Bacterial spot disease caused by Xanthomonas spp. is a global threat to tomato and pepper plants. A recent classification of these pathogens indicated the need for a diverse dataset of whole-genome resources. We report whole-genome resources of 89 Xanthomonas strains isolated from Canada (n = 44), the United States (n = 29), Argentina (n = 4), Brazil (n = 3), Costa Rica (n = 3), New Zealand (n = 1), Australia (n = 1), Mexico (n = 1), Taiwan (n = 1), Thailand (n = 1), and unknown (n = 1). Of these strains, 48 were previously identified to species-level based on nongenome-based approaches while 41 strains were classified only at the genus level. The average coverage of the sequencing reads was 103×. The draft genome sizes ranged from 4.53 to 5.46 Mbp with a G + C content of 63.53 to 67.78% and comprised 4,233-5,178 protein-coding sequences. Using average nucleotide identity (ANI) and genome-based DNA-DNA hybridization (gDDH) values, the taxonomic classifications were validated for 38 of the 48 strains previously assigned to species level using other methods. Ten strains previously identified as Xanthomonas campestris, X. axonopodis, X. vasicola, and X. arboricola were incorrectly assigned, and new species-level delineations are proposed. Data from ANI, gDDH, and pangenome phylogeny of shared protein families were used to assign the 41 strains, previously identified only to genus level, into five distinct species: X. euvesicatoria (pv. euvesicatoria or pv. perforans), X. hortorum pv. gardneri, X. vesicatoria, X. campestris, and X. arboricola. These 89 whole-genome sequences of Xanthomonas strains, the majority (49.4%) of which are from Canada, could be useful resources in our understanding of the global population structure and evolution of these pathogens.
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Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Diane Cuppels
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada (Retired)
| | - Julie Chapados
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jackson Eyres
- BICoE, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Adam Koziol
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Jeremy Dettman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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Antibacterial Activity of Copper Nanoparticles against Xanthomonas campestris pv. vesicatoria in Tomato Plants. Int J Mol Sci 2022; 23:ijms23084080. [PMID: 35456899 PMCID: PMC9032352 DOI: 10.3390/ijms23084080] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023] Open
Abstract
Copper-based bactericides have appeared as a new tool in crop protection and offer an effective solution to combat bacterial resistance. In this work, two copper nanoparticle products that were previously synthesized and evaluated against major bacterial and fungal pathogens were tested on their ability to control the bacterial spot disease of tomato. Growth of Xanthomonas campestris pv. vesicatoria, the causal agent of the disease, was significantly suppressed by both nanoparticles, which had superior function compared to conventional commercial formulations of copper. X-ray fluorescence spectrometry measurements in tomato leaves revealed that bioavailability of copper is superior in the case of nanoparticles compared to conventional formulations and is dependent on synthesis rather than size. This is the first report correlating bioavailability of copper to nanoparticle efficacy.
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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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