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Utami D, Meale SJ, Young AJ. Bacterial Leaf Spot Susceptibility Screening of Chili Pepper Cultivars Using qPCR Determination of Xanthomonas euvesicatoria pv. euvesicatoria Titers. PHYTOPATHOLOGY 2024; 114:681-689. [PMID: 38079287 DOI: 10.1094/phyto-12-22-0479-r] [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: 04/16/2024]
Abstract
Bacterial leaf spot is a serious disease of chili pepper (Capsicum spp.) caused by Xanthomonas euvesicatoria pv. euvesicatoria. Conventional resistance screening is time and resource intensive. It was considered that a quick and simple determination of cultivar susceptibility could be achieved through estimating bacterial titers of inoculated plants. A SYBR quantitative polymerase chain reaction (qPCR)-based assay was compared with conventional PCR, then used to detect and enumerate pathogen titers in serial dilutions and DNA extracted from infected plant leaves. The qPCR detection limit was approximately 1 CFU µl-1, 10 times more sensitive than conventional PCR. A linear correlation (R2 = 0.994) was obtained from the standard curve comparing plate-truthed serial dilutions of the pathogen with the qPCR cycle threshold. Six strains were used to inoculate cultivars Hugo and Warlock. One strain, X. euvesicatoria pv. euvesicatoria BRIP62403, was consistently the most virulent based on visual symptoms and pathogen titers in planta inferred by qPCR performed on DNA extracted from infected leaves 2 and 6 weeks postinoculation. Visual observations 6 weeks after inoculation were highly correlated (R2 = 0.8254) to pathogen titers. The qPCR method was used to categorize 20 chili pepper cultivars 2 weeks after inoculation. A high positive correlation (R2 = 0.6826) was observed between visual scoring and pathogen titers from 20 chili pepper cultivars, facilitating categorization of susceptible, intermediate, and resistant cultivars. The qPCR approach developed here facilitates susceptibility screening of chili pepper cultivars at an early stage of selection and could be readily adapted to a range of other pathosystems.
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Affiliation(s)
- Desi Utami
- School of Agriculture and Food Sustainability, Faculty of Science, The University of Queensland, Queensland, 4343, Australia
- Department of Agricultural Microbiology, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Sarah J Meale
- School of Agriculture and Food Sustainability, Faculty of Science, The University of Queensland, Queensland, 4343, Australia
| | - Anthony J Young
- School of Agriculture and Food Sustainability, Faculty of Science, The University of Queensland, Queensland, 4343, Australia
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A Pan-Global Study of Bacterial Leaf Spot of Chilli Caused by Xanthomonas spp. PLANTS 2022; 11:plants11172291. [PMID: 36079673 PMCID: PMC9460788 DOI: 10.3390/plants11172291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022]
Abstract
Bacterial Leaf Spot (BLS) is a serious bacterial disease of chilli (Capsicum spp.) caused by at least four different Xanthomonas biotypes: X. euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, X. hortorum pv. gardneri, and X. vesicatoria. Symptoms include black lesions and yellow halos on the leaves and fruits, resulting in reports of up to 66% losses due to unsalable and damaged fruits. BLS pathogens are widely distributed in tropical and subtropical regions. Xanthomonas is able to survive in seeds and crop residues for short periods, leading to the infections in subsequent crops. The pathogen can be detected using several techniques, but largely via a combination of traditional and molecular approaches. Conventional detection is based on microscopic and culture observations, while a suite of Polymerase Chain Reaction (PCR) and Loop-Mediated Isothermal Amplification (LAMP) assays are available. Management of BLS is challenging due to the broad genetic diversity of the pathogens, a lack of resilient host resistance, and poor efficacy of chemical control. Some biological control agents have been reported, including bacteriophage deployment. Incorporating stable host resistance is a critical component in ongoing integrated management for BLS. This paper reviews the current status of BLS of chilli, including its distribution, pathogen profiles, diagnostic options, disease management, and the pursuit of plant resistance.
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Das S, Dash HR, Mangwani N, Chakraborty J, Kumari S. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J Microbiol Methods 2014; 103:80-100. [PMID: 24886836 DOI: 10.1016/j.mimet.2014.05.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 12/29/2022]
Abstract
The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.
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Affiliation(s)
- Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
| | - Hirak R Dash
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Neelam Mangwani
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Supriya Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
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Cho MS, Lee JH, Her NH, Kim C, Seol YJ, Hahn JH, Baeg JH, Kim HG, Park DS. A quantitative and direct PCR assay for the subspecies-specific detection of Clavibacter michiganensis subsp. michiganensis based on a ferredoxin reductase gene. J Microbiol 2012; 50:496-501. [PMID: 22752914 DOI: 10.1007/s12275-012-1611-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
Abstract
The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis is the causal agent of canker disease in tomato. Because it is very important to control newly introduced inoculum sources from commercial materials, the specific detection of this pathogen in seeds and seedlings is essential for effective disease control. In this study, a novel and efficient assay for the detection and quantitation of C. michiganensis subsp. michiganensis in symptomless tomato and red pepper seeds was developed. A pair of polymerase chain reaction (PCR) primers (Cmm141F/R) was designed to amplify a specific 141 bp fragment on the basis of a ferredoxin reductase gene of C. michiganensis subsp. michiganensis NCPPB 382. The specificity of the primer set was evaluated using purified DNA from 16 isolates of five C. michiganensis subspecies, one other Clavibacter species, and 17 other reference bacteria. The primer set amplified a single band of expected size from the genomic DNA obtained from the C. michiganensis subsp. michiganensis strains but not from the other C. michiganensis subspecies or from other Clavibacter species. The detection limit was a single cloned copy of the ferredoxin reductase gene of C. michiganensis subsp. michiganensis. In conclusion, this quantitative direct PCR assay can be applied as a practical diagnostic method for epidemiological research and the sanitary management of seeds and seedlings with a low level or latent infection of C. michiganensis subsp. michiganensis.
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Affiliation(s)
- Min Seok Cho
- National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707, Republic of Korea
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Albuquerque P, Caridade CMR, Rodrigues AS, Marcal ARS, Cruz J, Cruz L, Santos CL, Mendes MV, Tavares F. Evolutionary and experimental assessment of novel markers for detection of Xanthomonas euvesicatoria in plant samples. PLoS One 2012; 7:e37836. [PMID: 22655073 PMCID: PMC3359998 DOI: 10.1371/journal.pone.0037836] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 04/25/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Bacterial spot-causing xanthomonads (BSX) are quarantine phytopathogenic bacteria responsible for heavy losses in tomato and pepper production. Despite the research on improved plant spraying methods and resistant cultivars, the use of healthy plant material is still considered as the most effective bacterial spot control measure. Therefore, rapid and efficient detection methods are crucial for an early detection of these phytopathogens. METHODOLOGY In this work, we selected and validated novel DNA markers for reliable detection of the BSX Xanthomonas euvesicatoria (Xeu). Xeu-specific DNA regions were selected using two online applications, CUPID and Insignia. Furthermore, to facilitate the selection of putative DNA markers, a customized C program was designed to retrieve the regions outputted by both databases. The in silico validation was further extended in order to provide an insight on the origin of these Xeu-specific regions by assessing chromosomal location, GC content, codon usage and synteny analyses. Primer-pairs were designed for amplification of those regions and the PCR validation assays showed that most primers allowed for positive amplification with different Xeu strains. The obtained amplicons were labeled and used as probes in dot blot assays, which allowed testing the probes against a collection of 12 non-BSX Xanthomonas and 23 other phytopathogenic bacteria. These assays confirmed the specificity of the selected DNA markers. Finally, we designed and tested a duplex PCR assay and an inverted dot blot platform for culture-independent detection of Xeu in infected plants. SIGNIFICANCE This study details a selection strategy able to provide a large number of Xeu-specific DNA markers. As demonstrated, the selected markers can detect Xeu in infected plants both by PCR and by hybridization-based assays coupled with automatic data analysis. Furthermore, this work is a contribution to implement more efficient DNA-based methods of bacterial diagnostics.
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Affiliation(s)
- Pedro Albuquerque
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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Albuquerque P, Caridade CMR, Marcal ARS, Cruz J, Cruz L, Santos CL, Mendes MV, Tavares F. Identification of Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans with novel markers and using a dot blot platform coupled with automatic data analysis. Appl Environ Microbiol 2011; 77:5619-28. [PMID: 21705524 PMCID: PMC3165254 DOI: 10.1128/aem.05189-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/05/2011] [Indexed: 11/20/2022] Open
Abstract
Phytosanitary regulations and the provision of plant health certificates still rely mainly on long and laborious culture-based methods of diagnosis, which are frequently inconclusive. DNA-based methods of detection can circumvent many of the limitations of currently used screening methods, allowing a fast and accurate monitoring of samples. The genus Xanthomonas includes 13 phytopathogenic quarantine organisms for which improved methods of diagnosis are needed. In this work, we propose 21 new Xanthomonas-specific molecular markers, within loci coding for Xanthomonas-specific protein domains, useful for DNA-based methods of identification of xanthomonads. The specificity of these markers was assessed by a dot blot hybridization array using 23 non-Xanthomonas species, mostly soil dwelling and/or phytopathogens for the same host plants. In addition, the validation of these markers on 15 Xanthomonas spp. suggested species-specific hybridization patterns, which allowed discrimination among the different Xanthomonas species. Having in mind that DNA-based methods of diagnosis are particularly hampered for unsequenced species, namely, Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans, for which comparative genomics tools to search for DNA signatures are not yet applicable, emphasis was given to the selection of informative markers able to identify X. fragariae, X. axonopodis pv. phaseoli, and X. fuscans subsp. fuscans strains. In order to avoid inconsistencies due to operator-dependent interpretation of dot blot data, an image-processing algorithm was developed to analyze automatically the dot blot patterns. Ultimately, the proposed markers and the dot blot platform, coupled with automatic data analyses, have the potential to foster a thorough monitoring of phytopathogenic xanthomonads.
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Affiliation(s)
- Pedro Albuquerque
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Faculdade de Ciências, Departamento de Biologia (FCUP), Edifício FC4, Via Panorâmica no. 36, Universidade do Porto, 4150-564 Porto, Portugal
| | - Cristina M. R. Caridade
- Centro de Investigação em Ciências Geo-Espaciais (CICGE), Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
- Instituto Superior de Engenharia de Coimbra (ISEC), Rua Pedro Nunes-Quinta da Nora, 3030-199 Coimbra, Portugal
| | - Andre R. S. Marcal
- Centro de Investigação em Ciências Geo-Espaciais (CICGE), Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
- Centro de Matemática da Universidade do Porto (CMUP), Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
| | - Joana Cruz
- Instituto Nacional de Recursos Biológicos (INRB), Unidade de Investigação de Protecção de Plantas, Tapada da Ajuda, 1349-018 Lisbon, Portugal
| | - Leonor Cruz
- Instituto Nacional de Recursos Biológicos (INRB), Unidade de Investigação de Protecção de Plantas, Tapada da Ajuda, 1349-018 Lisbon, Portugal
| | - Catarina L. Santos
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Marta V. Mendes
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Fernando Tavares
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Faculdade de Ciências, Departamento de Biologia (FCUP), Edifício FC4, Via Panorâmica no. 36, Universidade do Porto, 4150-564 Porto, Portugal
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Cho MS, Kang MJ, Kim CK, Seol YJ, Hahn JH, Park SC, Hwang DJ, Ahn TY, Park DH, Lim CK, Park DS. Sensitive and Specific Detection of Xanthomonas oryzae pv. oryzae by Real-Time Bio-PCR Using Pathovar-Specific Primers Based on an rhs Family Gene. PLANT DISEASE 2011; 95:589-594. [PMID: 30731951 DOI: 10.1094/pdis-06-10-0399] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The present study describes bio-polymerase chain reaction (PCR) assays to detect bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae in rice. Successful control of X. oryzae. pv. oryzae requires a specific and reliable diagnostic tool. However, other X. oryzae pathovars are detected by currently available molecular and serological methods. In this study, SYBR Green real-time and conventional PCR primer sets were designed based on an rhs family gene of X. oryzae pv. oryzae KACC10331 because these genes are structurally diverse. The specificity of the primers was evaluated using purified DNA from 11 isolates of two X. oryzae pathovars, 21 other Xanthomonas species, and 4 other reference phytopathogenic bacteria and fungi. The assay was also able to detect at least two genome equivalents of cloned amplified target DNA using purified DNA. Thus, the SYBR Green real-time PCR-based method can be used for the rapid and specific detection of X. oryzae pv. oryzae and will potentially simplify and facilitate diagnosis and monitoring of this pathogen and guide plant disease management.
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Affiliation(s)
- Min Seok Cho
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Man Jung Kang
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Chang Kug Kim
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Young-Joo Seol
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Jang Ho Hahn
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Soo Chul Park
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Duk Ju Hwang
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Tae-Young Ahn
- Department of Microbiology, Dankook University, Cheonan 330-714, Republic of Korea
| | - Duck Hwan Park
- Division of Bio-resources Technology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chun Keun Lim
- Division of Bio-resources Technology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Dong Suk Park
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
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Moretti C, Amatulli MT, Buonaurio R. PCR-based assay for the detection of Xanthomonas euvesicatoria causing pepper and tomato bacterial spot. Lett Appl Microbiol 2009; 49:466-71. [PMID: 19674291 DOI: 10.1111/j.1472-765x.2009.02690.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To develop a PCR-based assay for Xanthomonas euvesicatoria detection in culture and in planta. METHODS AND RESULTS A fragment of 1600 bp specific for X. euvesicatoria was found by repetitive extragenic palindromic sequence-PCR. Among the primers designed on the basis of the partially sequenced fragment, the primers Xeu2.4 and Xeu2.5 direct amplification of the expected product (208 bp) for all the X. euvesicatoria strains and not for other related and unrelated phytopathogenic bacteria or saprophytic bacteria isolated from pepper and tomato phyllosphere. The assay permits the detection of X. euvesicatoria in pure culture, with a limit of detection of two bacterial cells and 1 pg of DNA per PCR, and in extracts obtained from asymptomatic inoculated tomato and pepper plants. CONCLUSIONS Primers Xeu2.4 and Xeu2.5 provide a specific, sensitive and rapid assay for the detection of X. euvesicatoria in culture and in pepper and tomato plants. SIGNIFICANCE AND IMPACT OF THE STUDY Because X. euvesicatoria is a quarantine organism in the European Union, and it is subjected to stringent international phytosanitary measures, this highly sensitivity PCR-based assay is suitable for its detection in pepper and tomato plant materials to avoid the introduction and spread of the bacterium.
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Affiliation(s)
- C Moretti
- Dipartimento di Scienze Agrarie e Ambientali, University of Perugia, Perugia, Italy.
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