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Rana R, Jaiswal G, Bansal K, Patil PB. Comparative genomics reveals the emergence of copper resistance in a non-pigmented Xanthomonas pathogen of grapevine. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:716-726. [PMID: 37254648 PMCID: PMC10667641 DOI: 10.1111/1758-2229.13164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023]
Abstract
Xanthomonas citri pv. viticola (Xcv) is the causal agent of bacterial canker in grapevine. The pathogen is restricted to India, where it was first reported in the 1970s, and Brazil. In the present study, we report the first complete genome sequence of Xcv LMG965, which is a reference pathotype strain. We also report genome sequences of additional isolates from India and comparative genome-based studies of isolates from Brazil. Apart from revealing the monophyletic origin of the pathovar, we could also confirm a common frameshift mutation in a gene that is part of the Xanthomonadin pigment biosynthetic gene cluster in all the isolates. The comparative study also revealed multiple intrinsic copper resistance-related genes in Brazilian isolates, suggesting intense selection, possibly because of heavy and indiscriminate usage of copper as an antimicrobial agent in the orchards. There is also the association of a Tn3-like transposase in the vicinity of the copper resistance genes, indicating a potential for rapid diversification through horizontal gene transfer events. The findings, along with genomic resources, will allow for systematic genetic and functional studies of Xcv.
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Affiliation(s)
- Rekha Rana
- Bacterial Genomics and Evolution LaboratoryCSIR‐Institute of Microbial TechnologyChandigarhIndia
- The Academy of Scientific and Innovative ResearchGhaziabadIndia
| | - Gagandeep Jaiswal
- Bacterial Genomics and Evolution LaboratoryCSIR‐Institute of Microbial TechnologyChandigarhIndia
- The Academy of Scientific and Innovative ResearchGhaziabadIndia
| | - Kanika Bansal
- Bacterial Genomics and Evolution LaboratoryCSIR‐Institute of Microbial TechnologyChandigarhIndia
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution LaboratoryCSIR‐Institute of Microbial TechnologyChandigarhIndia
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2
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Harrison J, Hussain RMF, Greer SF, Ntoukakis V, Aspin A, Vicente JG, Grant M, Studholme DJ. Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance. Access Microbiol 2023; 5:acmi000532.v3. [PMID: 37601434 PMCID: PMC10436009 DOI: 10.1099/acmi.0.000532.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/25/2023] [Indexed: 08/22/2023] Open
Abstract
Here we report draft-quality genome sequences for pathotype strains of eight plant-pathogenic bacterial pathovars: Xanthomonas campestris pv. asclepiadis, X. campestris pv. cannae, X. campestris pv. esculenti, X. campestris pv. nigromaculans, X. campestris pv. parthenii, X. campestris pv. phormiicola, X. campestris pv. zinniae and X. dyei pv. eucalypti (= X. campestris pv. eucalypti). We also sequenced the type strain of species X. melonis and the unclassified Xanthomonas strain NCPPB 1067. These data will be useful for phylogenomic and taxonomic studies, filling some important gaps in sequence coverage of Xanthomonas phylogenetic diversity. We include representatives of previously under-sequenced pathovars and species-level clades. Furthermore, these genome sequences may be useful in elucidating the molecular basis for important phenotypes, such as biosynthesis of coronatine-related toxins and degradation of fungal toxin cercosporin.
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Affiliation(s)
| | - Rana Muhammad Fraz Hussain
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
| | - Shannon F. Greer
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
| | - Vardis Ntoukakis
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Andrew Aspin
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Joana G. Vicente
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Murray Grant
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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Lucena LP, Benko-Iseppon AM, Brenig B, Azevedo V, Aburjaile F, Souza EB, Gama MAS. Draft Genome Sequence of Seven Pigmented Strains of Xanthomonas citri pv. anacardii, the Causal Agent of Cashew Angular Spot. PHYTOPATHOLOGY 2023; 113:1360-1364. [PMID: 36703497 DOI: 10.1094/phyto-08-22-0279-a] [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: 06/18/2023]
Abstract
Cashew (Anacardium occidentale) angular leaf spot is caused by pigmented and non-pigmented strains of Xanthomonas citri pv. anacardii, which have been isolated from infected plants in Brazil. The disease symptoms can be observed in leaves, stems, and fruits. Given that infection in young fruits results in fruits unsuitable for commercialization, angular leaf spot represents a serious threat to the cashew crop in Brazil. Here, we report the genomic sequencing of seven pigmented strains of X. citri pv. anacardii, obtained from the leaves of cashew trees from São Paulo state, Brazil, in 2009. The construction of the libraries was carried out according to the manufacturer, and whole-genome sequencing was performed using the Illumina HiSeq 2500 platform. Genome size, number of coding sequences, largest contig length, and N50 ranged from 4,996,984 to 5,003,485 bp, 4,621 to 4,643 bp, 212,513 to 362,232 bp, and 113,582 to 141,003 bp, respectively. GC content and RNA numbers were 64.68% and 54, respectively, for all strains. ANIm and dDDH analyses showed values above 99.5 and 92.1% among these strains and the non-pigmented pathotype strain of X. citri pv. anacardii (IBSBF2579PT). A maximum likelihood tree built with 2,708 core genes grouped all X. citri pv. anacardii strains in the same clade, with a 100% bootstrap. These resources will contribute in a relevant way to help understand the ecological, taxonomic, evolutionary, pathogenicity, and virulence aspects of X. citri pv. anacardii, which will be useful for the study and development of techniques for managing cashew angular leaf spot.
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Affiliation(s)
- Lucas P Lucena
- Crop Protection Area, Department of Agronomy, Universidade Federal Rural de Pernambuco, 52171-900, Recife, PE, Brazil
| | - Ana M Benko-Iseppon
- Department of Genetics, Universidade Federal de Pernambuco, 50670-901, Recife, PE, Brazil
| | - Bertram Brenig
- Department of Molecular Biology of Livestock, Institute of Veterinary Medicine, Georg August University Göttingen, 37077, Göttingen, Germany
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
| | - Flávia Aburjaile
- Department of Preventive Veterinary Medicine, Veterinary School, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
| | - Elineide B Souza
- Microbiology Area, Department of Biology, Universidade Federal Rural de Pernambuco, 52171-900, Recife, PE, Brazil
| | - Marco A S Gama
- Crop Protection Area, Department of Agronomy, Universidade Federal Rural de Pernambuco, 52171-900, Recife, PE, Brazil
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Shi T, Li C, Wang G, Huang G. Multilocus Sequence Analysis and Detection of Copper Ion Resistance of Xanthomonas phaseoli pv. manihotis Causing Bacterial Blight in Cassava. Curr Issues Mol Biol 2023; 45:5389-5402. [PMID: 37504258 PMCID: PMC10378058 DOI: 10.3390/cimb45070342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Cassava (Manihot esculenta Crantz) is an important tropical tuber crop around the world. Cassava bacterial blight, caused by Xanthomonas phaseoli pv. manihotis, is a key disease that influences cassava production worldwide. Between 2008 and 2020, 50 X. phaseoli pv. manihotis strains were isolated from diseased plant samples or acquired from China, Uganda, Cambodia, Colombia, Malaysia, and Micronesia. Using multilocus sequence analysis, the genetic diversity of X. phaseoli pv. manihotis strains was evaluated. A neighbor-joining phylogenetic dendrogram was constructed based on partial sequences of five housekeeping genes (atpD-dnaK-gyrB-efp-rpoD). The strains clustered into three groups whose clusters were consistent with atpD and RpoD gene sequences. Group I contained 46 strains from China, Uganda, Cambodia, and Micronesia, and the other two groups were comprised of strains from Colombia and Malaysia, respectively. The resistance of all these strains to copper ion (Cu2+) was determined, the minimal inhibitory concentration was between 1.3 and 1.7 mM, and there was no significant difference between strains from different geographic region. During genome annotation of the X. phaseoli pv. manihotis strain CHN01, homologous gene clusters of copLAB and xmeRSA were identified. The predicted amino acid sequences of two gene clusters were highly homologous with the copper-resistant protein from Xanthomonas strains. CopLAB and xmeRSA were amplified from all these strains, suggesting that the regulation of copper resistance is associated with two distinct metabolic pathways. CopLAB and xmeRSA were highly conserved among strains from different geographic regions, possibly associated with other conserved function.
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Affiliation(s)
- Tao Shi
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Chaoping Li
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Guofen Wang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Guixiu Huang
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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Parsafar S, Beheshti Maal K, Akkafi HR, Rahimzadeh Torabi L. Isolation and identification of specific lytic bacteriophages as a biocontrol agent against Serratia odorifera PBA-IAUF-1 and Kluyvera intermedia PBA-IAUF-6 causing bacterial canker in the grape and Siberian pear. FEMS Microbiol Lett 2023; 370:fnad115. [PMID: 37930829 DOI: 10.1093/femsle/fnad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 09/11/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
Bacterial canker, a prevalent disease among fruit trees, is a significant concern. The use of phage therapy is presently seen as a dependable biological strategy to control bacterial diseases in fruits. The objective of this research was to use various biochemical and molecular techniques to determine the types of bacteria responsible for causing cankers in various fruits. Additionally, their ability to cause disease in the fruit tissues was assessed, the specific bacteriophages targeting these bacteria were isolated and identified. The bacteria were separated from different parts of the infected fruits like grapes and Siberian pears. The selection of fruit tissues showing signs of canker disease was performed, and the validation of the isolates' pathogenicity was confirmed following Koch's principles. Subsequently, in order to establish a conclusive identification of the bacterial species, molecular identification was conducted through the sequencing of a specific fragment within the 16S rRNA following amplification by PCR by using universal primers, RW01 and DG74. Isolation and titration of phages specific to fruit spoilage bacteria was done by spot and double-layer agar method, and the growth curve of the isolated bacteriophage was drawn. The phages were detected by transmission electron microscopy (TEM). The results of the study proved the presence of canker causing agents, Kluyvera intermedia PBA-IAUF-6 with the code Sh6 in the Siberian pears, and Serratia odorifera PBA-IAUF-1 with the code Rz3 in the grape fruits, which were deposited in GenBank with the accession numbers of KU878579 and KU168605, respectively. Isolation of the specific bacteriophages to the S. odorifera PBA-IAUF-1 and K. intermedia PBA-IAUF-6 bacterial strains were done from the effluent of South Isfahan wastewater treatment plant and Caspian Sea water, respectively. The titer of the specific phage to S. odorifera PBA-IAUF-1 and K. intermedia PBA-IAUF-6 was detected in the samples as 2.2 × 10-5 and 5 × 10-11 PFU/ml, respectively. An electron micrograph of a bacteriophage that targets two different bacterial strains revealed phages with a geometrically shaped head and a flexible tail, which resembled viruses from the Siphoviridae family.
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Affiliation(s)
- Somayeh Parsafar
- Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Falavarjan 84515/155, Isfahan, Iran
| | - Keivan Beheshti Maal
- Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Falavarjan 84515/155, Isfahan, Iran
| | - Hamid Reza Akkafi
- Department of Biology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Falavarjan 84515/155, Isfahan, Iran
| | - Ladan Rahimzadeh Torabi
- Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Falavarjan 84515/155, Isfahan, Iran
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Rana R, Madhavan VN, Saroha T, Bansal K, Kaur A, Sonti RV, Patel HK, Patil PB. Xanthomonas indica sp. nov., a Novel Member of Non-Pathogenic Xanthomonas Community from Healthy Rice Seeds. Curr Microbiol 2022; 79:304. [PMID: 36064810 DOI: 10.1007/s00284-022-03001-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/16/2022] [Indexed: 11/03/2022]
Abstract
Xanthomonas is a major group of pathogenic bacteria infecting staple food crops like rice. Increasingly it is being recognized that non-pathogenic Xanthomonas (NPX) are also important members of a healthy plant microbiome. However, the vast majority of the species described in this genus are of pathogenic nature, and only a few NPX species have been reported till now. Genomic and taxonogenomic analysis of NPX is needed for the management of this important group of bacteria. In this study, two yellow-pigmented bacterial isolates were obtained from healthy rice seeds in Punjab, India. The isolates designated PPL560T and PPL568 were identified as members of the genus Xanthomonas based on biochemical tests and 16S rRNA gene sequence analysis retrieved from the whole-genome sequences. Isolates formed a distinct monophyletic lineage with Xanthomonas sontii and Xanthomonas sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by the representative species of the genus Xanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridization values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560T and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. The absence of type III secretion system-related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of the genus Xanthomonas with PPL560T = MTCC 13185 = CFBP 9039 = ICMP 24394 as its type strain and PPL568 as another constituent member.
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Affiliation(s)
- Rekha Rana
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,The Academy of Scientific and Innovative Research, Ghaziabad, India
| | | | - Tanu Saroha
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,The Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Amandeep Kaur
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ramesh V Sonti
- Indian Institute of Science Education and Research, Tirupati, India
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.
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Bansal K, Kumar S, Patil PB. Phylo-Taxonogenomics Supports Revision of Taxonomic Status of 20 Xanthomonas Pathovars to Xanthomonas citri. PHYTOPATHOLOGY 2022; 112:1201-1207. [PMID: 34844415 DOI: 10.1094/phyto-08-21-0342-sc] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Based on phylo-taxonogenomics criteria, we present amended descriptions for 20 pathovars to Xanthomonas citri. Incidentally, 18 were first reported from India. Seven out of twenty are classified as X. axonopodis, 12 out of 20 as X. campestris, and one as X. cissicola. In this study, we have generated genome sequence data of four pathovars, and the genomes of the remaining 16 were used from the published data. Comprehensive genome-based phylogenomic and taxonogenomic analyses reveal that all these pathovars belong to X. citri and need to reconcile their taxonomic status. This proposal will aid in systematic studies of a major species and its constitutent members that infect economically important plants.
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Affiliation(s)
- Kanika Bansal
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Sanjeet Kumar
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Prabhu B Patil
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
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Bragard C, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Thulke H, Van der Werf W, Civera AV, Yuen J, Zappalà L, Migheli Q, Stefani E, Vloutoglou I, Czwienczek E, Maiorano A, Streissl F, Reignault PL. Pest categorisation of Xanthomonas citri pv. viticola. EFSA J 2021; 19:e06929. [PMID: 34963789 PMCID: PMC8675326 DOI: 10.2903/j.efsa.2021.6929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The EFSA Plant Health Panel performed a pest categorisation of Xanthomonas citri pv. viticola (Nayudu) Dye, a Gram-negative bacterium belonging to the Xanthomonadaceae family. The pathogen is a well-defined taxonomic unit and is the causal agent of the leaf spot and bacterial canker of Vitis vinifera. This bacterium is present in India and Brazil, where it affects table grape cultivation; the same pathogen is able to cause a disease on Azadirachta indica and on some weed species. Reports indicate that the bacterium is present in Thailand as well. The pathogen has never been reported from the EU territory and it is not included in EU Commission Implementing Regulation 2019/2072. The pathogen can be detected on its host plants using direct isolation, serological or PCR-based methods. Its identification is achieved using biochemical and nutritional assays, together with a multilocus sequence analysis based on seven housekeeping genes. The main pathway for the entry of the pathogen into the EU territory is plant propagation material. In the EU, there is large availability of host plants, with grapevine being one of the most important crops in Europe and more specifically in its Mediterranean areas. Since X. citri pv. viticola is only reported in tropical and subtropical areas (BSh and Aw climatic zones according to the Köppen-Geiger classification), there is uncertainty whether the climatic conditions in the EU territory are suitable for its establishment. Nevertheless, due to the great importance of grapevine for the EU agriculture, any disease outbreak may have a high-economic impact. Phytosanitary measures are available to prevent the introduction of the pathogen into the EU. X. citri pv. viticola satisfies the criteria that are within the remit of EFSA to assess for this species to be regarded as a potential Union quarantine pest.
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Fu B, Zhu J, Lee C, Wang L. Multilocus Sequence Analysis and Copper Ion Resistance Detection of 60 Xanthomonas arboricola pv. juglandis Isolates from China. PLANT DISEASE 2021; 105:3715-3719. [PMID: 33858185 DOI: 10.1094/pdis-02-21-0241-re] [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: 06/12/2023]
Abstract
Walnut bacterial blight caused by Xanthomonas arboricola pv. juglandis has serious repercussions for walnut production around the world. Between 2015 and 2017, disease samples were collected from six counties (Danjiangkou, Baokang, Suizhou, Shennongjia, Zigui, and Xingshan) in Hubei Province, China. Fifty-nine X. arboricola pv. juglandis isolates were identified by morphology and specific PCR primers from 206 isolates. The genetic diversity of 60 X. arboricola pv. juglandis isolates (59 from Hubei plus 1 from Beijing) was evaluated by multilocus sequence analysis, and their resistance to copper ion (Cu2+) treatment was determined. A neighbor-joining phylogenetic dendrogram was constructed based on four sequences of housekeeping genes (atpD-dnaK-glnA-gyrB). Two groups of isolates whose clustering was consistent with that of glnA were identified. The minimal inhibitory concentration of Cu2+ on representative X. arboricola pv. juglandis strain DW3F3 (the first genome sequenced X. arboricola pv. juglandis from China) was 115 μg/ml. Setting the copper-resistant threshold value to 125 μg/ml, 47 and 13 isolates were considered sensitive and resistant to Cu2+, respectively. Furthermore, five isolates showed Cu2+ resistance at 270 μg/ml. Compared with the copper resistance gene B (copB) from sensitive isolates, the copB gene in resistant isolates had a 15-bp insertion and eight scattered single-nucleotide polymorphisms. Interestingly, the clustering based on multilocus sequence analysis was distinct between X. arboricola pv. juglandis Cu2+-resistant and -sensitive isolates.
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Affiliation(s)
- Benzhong Fu
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan Hubei 432000, China
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011 U.S.A
| | - Jieqian Zhu
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan Hubei 432000, China
| | - Conard Lee
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011 U.S.A
| | - Lihua Wang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan Hubei 432000, China
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Amancio L, Baia ADB, Souza EB, Sales Júnior R, Negreiros AMP, Balbino VQ, Gama MAS. First Report of Xanthomonas citri subsp. citri causing Citrus Canker on lime in Rio Grande do Norte, Brazil. PLANT DISEASE 2021; 105:4148. [PMID: 34152205 DOI: 10.1094/pdis-11-20-2498-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Citrus canker caused by Xanthomonas citri subsp. citri is one of the most important citrus diseases in the world (Gottwald et al. 2002), mainly for citrus-producing countries with humid sub-tropical regions such as United States, Argentina, and Brazil, where losses may be significant (Behlau et al. 2020). In the state of Rio Grande do Norte (RN), Brazil, citrus production is expanding and shows social and economic importance for small farmers, which produced approximately 297 tons of lime in this state in 2019 (IBGE 2021). In December 2019, we observed symptoms of erumpent lesions with margins surrounded by yellow haloes on leaves and fruit of the lime (Citrus aurantifolia cv. 'Galego') (about 5% incidence) in a plantation located in the municipality of Mossoró, RN (05°12'21.1"S, 37°19'16"W). Samples were collected from the lime orchard, and five bacterial strains (CCRMXC01 to CCRMXC05) showing yellow, convex, mucoid colonies were isolated in a nutrient-yeast-dextrose-agar medium (NYDA). Pathogenicity tests were performed on sweet orange (C. sinensis cv. 'Pêra') and lime (C. latifolia cv. 'Tahiti') seedlings. Four wounds per leaf (upper side) were carried out with an entomological pin and 10 µl of a bacterial suspension (108 CFU mL-1) were deposited on each wound. The negative control consisted of leaves treated with sterile distilled water (SDW). For each citrus species, we used four replicates per strain and one leaf with four wounds per replicate. Inoculated leaves developed erumpent lesions with margins surrounded by yellow haloes six days after inoculation (DAI) in both citrus species, while leaves treated with SDW remained symptomless. Nine DAI, we reisolated the pathogen and performed rep-PCR (REP, ERIC, and BOX-PCR) analyses (Gama et al. 2018) with the strains inoculated and reisolated to confirm the identity of the strains and to fulfill Koch's postulates. The strains were stored at the Culture Collection Rosa Mariano (CCRM) of the Phytobacteriology Laboratory at the Universidade Federal Rural de Pernambuco. The five strains reisolated showed the same REP, ERIC, and BOX-PCR profiles as the strains used for inoculations. The molecular identification was performed sequencing the dnaK, fyuA, gyrB, and rpoD genes (Young et al. 2008). Each fragment was sequenced in both the forward and reverse directions. Using the BLASTn tool, we observed that sequences of the dnaK (GenBank MW218913 to MW218917), fyuA (GenBank MW218918 to MW218922), and rpoD (GenBank MW218928 to MW218932) genes of the strains CCRMXC01 to CCRMXC05 showed 100% of identity with the sequences of these genes from the type strain (ICMP 24T) and of other strains of X. citri subsp. citri (ICMP 21 and ICMP 7493), while sequences of gryB (GenBank MW218923 to MW218927) of the former strains showed 100% identity with the gyrB sequence of the strains ICMP 24T and ICMP 7493 and 99,85% identity with strain ICMP 21. This short variation in the sequence of the gyrB gene also may be observed among strains of X. citri subsp. citri available in NCBI database (https://www.ncbi.nlm.nih.gov/). The phylogenetic analysis performed using Bayesian inference and the concatenated sequence of all the type or representative strains of species and pathovars of Xanthomonas available in GenBank showed that the strains CCRMXC01 to CCRMXC05 clustered together with strain ICMP 24T with 1.0 posterior probability. To our information, this is the first report of X. citri subsp. citri causing citrus canker on lime in RN state, Brazil.
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Affiliation(s)
- Lucas Amancio
- Universidade Federal Rural de Pernambuco, Agronomy, Recife, Pernambuco, Brazil;
| | - Ana Dulce Botelho Baia
- Universidade Estadual Paulista Julio de Mesquita Filho - Campus de Jaboticabal, 207340, Plant Pathology, Rua Rodrigues Ferreira, 45, Recife, Pernambuco, Brazil, 50810020
- Universidade Federal Rural de Pernambuco;
| | - Elineide B Souza
- Av. Dom Manoel de Medeiros, s/n. Dois Irmãos, Recife, PernambucoRecife, Brazil, 52171-900;
| | - Rui Sales Júnior
- Universidade Federal Rural do Semi-Arido, 74384, Ciências Agronômicas e Florestais, Avenida Francisco Mota, 572, Costa e Silva, Mossoró, Mossoro, Rio Grande do Norte, Brazil, 59625-900
- United States;
| | - Andreia Mitsa Paiva Negreiros
- UNIVERSIDADE FEDERAL RURAL DO SEMI-ÁRIDO, Ciências Agronômicas e Florestais, Av. Francisco Mota, 572, Costa e Silva, Mossoró, Rio Grande do Norte, Brazil, 59625-900
- Universidade Federal Rural do Semi-Arido, 74384, Mossoro, Brazil, 59625-900;
| | | | - Marco Aurélio Siqueira Gama
- Universidade Federal Rural de Pernambuco, Agronomy, Av. Dom Manuel de Medeiros, s/n., Recife, Pernambuco, Brazil, 52171-900;
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11
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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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12
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Martins L, Fernandes C, Blom J, Dia NC, Pothier JF, Tavares F. Xanthomonas euroxanthea sp. nov., a new xanthomonad species including pathogenic and non-pathogenic strains of walnut. Int J Syst Evol Microbiol 2020; 70:6024-6031. [PMID: 32924921 PMCID: PMC8049493 DOI: 10.1099/ijsem.0.004386] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/27/2020] [Indexed: 11/18/2022] Open
Abstract
We describe a novel species isolated from walnut (Juglans regia) which comprises non-pathogenic and pathogenic strains on walnut. The isolates, obtained from a single ornamental walnut tree showing disease symptoms, grew on yeast extract-dextrose-carbonate agar as mucoid yellow colonies characteristic of Xanthomonas species. Pathogenicity assays showed that while strain CPBF 424T causes disease in walnut, strain CPBF 367 was non-pathogenic on walnut leaves. Biolog GEN III metabolic profiles disclosed some differences between strains CPBF 367 and CPBF 424T and other xanthomonads. Multilocus sequence analysis with seven housekeeping genes (fyuA, gyrB, rpoD, atpD, dnaK, efp, glnA) grouped these strains in a distinct cluster from Xanthomonas arboricola pv. juglandis and closer to Xanthomonas prunicola and Xanthomonas arboricola pv. populi. Average nucleotide identity (ANI) analysis results displayed similarity values below 93 % to X. arboricola strains. Meanwhile ANI and digital DNA-DNA hybridization similarity values were below 89 and 50 % to non-arboricola Xanthomonas strains, respectively, revealing that they do not belong to any previously described Xanthomonas species. Furthermore, the two strains show over 98 % similarity to each other. Genomic analysis shows that strain CPBF 424T harbours a complete type III secretion system and several type III effector proteins, in contrast with strain CPBF 367, shown to be non-pathogenic in plant bioassays. Taking these data altogether, we propose that strains CPBF 367 and CPBF 424T belong to a new species herein named Xanthomonas euroxanthea sp. nov., with CPBF 424T (=LMG 31037T=CCOS 1891T=NCPPB 4675T) as the type strain.
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Affiliation(s)
- Leonor Martins
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP, Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre s/n, Porto, Portugal
| | - Camila Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP, Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre s/n, Porto, Portugal
- INIAV, Instituto Nacional de Investigação Agrária e Veterinária, Av. da República, Quinta do Marquês, Oeiras, Portugal
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Nay C. Dia
- Environmental Genomics and Systems Biology, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Fernando Tavares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP, Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre s/n, Porto, Portugal
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13
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Studholme DJ, Wicker E, Abrare SM, Aspin A, Bogdanove A, Broders K, Dubrow Z, Grant M, Jones JB, Karamura G, Lang J, Leach J, Mahuku G, Nakato GV, Coutinho T, Smith J, Bull CT. Transfer of Xanthomonas campestris pv. arecae and X. campestris pv. musacearum to X. vasicola (Vauterin) as X. vasicola pv. arecae comb. nov. and X. vasicola pv. musacearum comb. nov. and Description of X. vasicola pv. vasculorum pv. nov. PHYTOPATHOLOGY 2020; 110:1153-1160. [PMID: 31922946 DOI: 10.1094/phyto-03-19-0098-le] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present an amended description of the bacterial species Xanthomonas vasicola to include the causative agent of banana Xanthomonas wilt, as well as strains that cause disease on Areca palm, Tripsacum grass, sugarcane, and maize. Genome-sequence data reveal that these strains all share more than 98% average nucleotide with each other and with the type strain. Our analyses and proposals should help to resolve the taxonomic confusion that surrounds some of these pathogens and help to prevent future use of invalid names.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
| | - Emmanuel Wicker
- IPME, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Sadik Muzemil Abrare
- Southern Agricultural Research Institute (SARI), Areka Agricultural Research Center, Areka, Ethiopia
| | | | - Adam Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Kirk Broders
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Zoe Dubrow
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Murray Grant
- School of Life Sciences, Gibbet Hill, University of Warwick, Coventry, CV4 7AL, U.K
| | - Jeffrey B Jones
- University of Florida, Plant Pathology Department, 1453 Fifield Hall, Gainesville, FL 32611, U.S.A
| | | | - Jillian Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Jan Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - George Mahuku
- International Institute of Tropical Agiculture (IITA), East Africa Hub, IITA-Tanzania, P.O. Box 34441, Dar es Salaam, Tanzania
| | - Gloria Valentine Nakato
- International Institute of Tropical Agriculture (IITA), Plot 15B, Naguru East Road, Upper Naguru, P.O. Box 7878, Kampala, Uganda
| | - Teresa Coutinho
- Department of Microbiology and Plant Pathology, Centre for Microbial Ecology and Genomics (CMEG), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X28, Pretoria 0028, South Africa
| | | | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Penn State University, University Park, PA, U.S.A
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14
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Ferreira MASV, Bonneau S, Briand M, Cesbron S, Portier P, Darrasse A, Gama MAS, Barbosa MAG, Mariano RDLR, Souza EB, Jacques MA. Xanthomonas citri pv. viticola Affecting Grapevine in Brazil: Emergence of a Successful Monomorphic Pathogen. FRONTIERS IN PLANT SCIENCE 2019; 10:489. [PMID: 31057588 PMCID: PMC6482255 DOI: 10.3389/fpls.2019.00489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
The pathovar viticola of Xanthomonas citri causes bacterial canker of grapevine. This disease was first recorded in India in 1972, and later in Brazil in 1998, where its distribution is currently restricted to the northeastern region. A multilocus sequence analysis (MLSA) based on seven housekeeping genes and a multilocus variable number of tandem repeat analysis (MLVA) with eight loci were performed in order to assess the genetic relatedness among strains from India and Brazil. Strains isolated in India from three related pathovars affecting Vitaceae species and pathogenic strains isolated from Amaranthus sp. found in bacterial canker-infected vineyards in Brazil were also included. MLSA revealed lack of diversity in all seven genes and grouped grapevine and Amaranthus strains in a monophyletic group in X. citri. The VNTR (variable number of tandem repeat) typing scheme conducted on 107 strains detected 101 haplotypes. The total number of alleles per locus ranged from 5 to 12. A minimum spanning tree (MST) showed that Brazilian strains were clearly separated from Indian strains, which showed unique alleles at three loci. The two strains isolated from symptomatic Amaranthus sp. presented unique alleles at two loci. STRUCTURE analyses revealed three groups congruent with MST and a fourth group with strains from India and Brazil. Admixture among populations were observed in all groups. MST, STRUCTURE and e-BURST analyses showed that the strains collected in 1998 belong to two distinct groups, with predicted founder genotypes from two different vineyards in the same region. This suggest that one introduction of grape planting materials contaminated with genetically distinct strains took place, which was followed by pathogen adaptation. Genome sequencing of one Brazilian strain confirmed typical attributes of pathogenic xanthomonads and allowed the design of a complementary VNTR typing scheme dedicated to X. citri pv. viticola that will allow further epidemiological survey of this genetically monomorphic pathovar.
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Affiliation(s)
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Sophie Cesbron
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Perrine Portier
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Armelle Darrasse
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Marco A. S. Gama
- Laboratório de Fitobacteriologia, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | | | - Rosa de L. R. Mariano
- Laboratório de Fitobacteriologia, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Elineide B. Souza
- Laboratório de Fitobacteriologia, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
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