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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:PHYTO03240084RVW. [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] [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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2
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Kałużna M, Prokić A, Obradović A, Weldon WA, Stockwell VO, Pothier JF. Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1254107. [PMID: 37780515 PMCID: PMC10535005 DOI: 10.3389/fpls.2023.1254107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023]
Abstract
Xanthomonas arboricola pv. corylina (Xac; formerly Xanthomonas campestris pv. corylina) is the causal agent of the bacterial blight of hazelnuts, a devastating disease of trees in plant nurseries and young orchards. Currently, there are no PCR assays to distinguish Xac from all other pathovars of X. arboricola. A comparative genomics approach with publicly available genomes of Xac was used to identify unique sequences, conserved across the genomes of the pathogen. We identified a 2,440 bp genomic region that was unique to Xac and designed identification and detection systems for conventional PCR, qPCR (SYBR® Green and TaqMan™), and loop-mediated isothermal amplification (LAMP). All PCR assays performed on genomic DNA isolated from eight X. arboricola pathovars and closely related bacterial species confirmed the specificity of designed primers. These new multi-platform molecular diagnostic tools may be used by plant clinics and researchers to detect and identify Xac in pure cultures and hazelnut tissues rapidly and accurately.
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Affiliation(s)
- Monika Kałużna
- The National Institute of Horticultural Research, Skierniewice, Poland
| | - Andjelka Prokić
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Aleksa Obradović
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | | | - Virginia O. Stockwell
- United States Department of Agriculture, Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, United States
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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3
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Wang X, He SW, He Q, Ju ZC, Ma YN, Wang Z, Han JC, Zhang XX. Early inoculation of an endophyte alters the assembly of bacterial communities across rice plant growth stages. Microbiol Spectr 2023; 11:e0497822. [PMID: 37655928 PMCID: PMC10580921 DOI: 10.1128/spectrum.04978-22] [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: 12/05/2022] [Accepted: 07/07/2023] [Indexed: 09/02/2023] Open
Abstract
The core endophytes of plants are regarded as promising resources in future agroecosystems. How they affect the assembly of rice-related bacterial communities after early inoculation remains unclear. Here, we examined bacterial communities across 148 samples, including bulk and rhizosphere soils, sterilized roots, stems, and seeds at the seedling, tillering, booting, and maturity stages. Tissue cultured rice seedlings were inoculated with Xathomonas sacchari JR3-14, a core endophytic bacterium of rice seeds, before transplanting. The results revealed that α-diversity indices were significantly enhanced in the root and stem endosphere at the seedling stage. β-diversity was altered at most plant developmental stages, except for the root and stem at the booting stage. Network complexity consequently increased in the root and stem across rice growth stages, other than the stem endosphere at the booting stage. Four abundant beneficial bacterial taxa, Bacillus, Azospira, Azospirillum, and Arthrobacter, were co-enriched during the early growth stage. Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis revealed a higher relative contribution of drift and other eco-evolutionary processes mainly in root compartments across all growth stages, but the opposite pattern was observed in stem compartments. IMPORTANCE Endophytic bacteria are regarded as promising environmentally friendly resources to promote plant growth and plant health. Some of microbes from the seed are able to be carried over to next generation, and contribute to the plant's ability to adapt to new environments. However, the effects of early inoculation with core microbes on the assembly of the plant microbiome are still unclear. In our study, we demonstrate that early inoculation of the rice seed core endophytic bacterium Xanthomonas sacchari could alter community diversity, enhance complexity degree of network structure at most the growth stages, and enrich beneficial bacteria at the seedling stage of rice. We further analyzed the evolutionary processes caused by the early inoculation. Our results highlight the new possibilities for research and application of sustainable agriculture by considering the contribution of seed endophytes in crop production and breeding.
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Affiliation(s)
- Xing Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan-Wen He
- Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
| | - Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Zhi-Cheng Ju
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yi-Nan Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhe Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jia-Cheng Han
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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4
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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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5
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Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria. TAXONOMY 2023. [DOI: 10.3390/taxonomy3010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The Gram-negative bacterial genus Xanthomonas includes numerous infra-specific taxa known as pathovars, which are defined primarily on host range and disease symptoms. With the advent of molecular sequence data, many pathovars have been transferred from X. campestris into other Xanthomonas species to better harmonise taxonomy and phylogeny. We performed whole-genome shotgun sequencing on pathotype strains of the following X. campestris pathovars: blepharidis, carissae, clerodendri, convolvuli, coriandri, daturae, euphorbiae, fici, heliotropii, ionidii, lawsoniae, mirabilis, obscurae, paulliniae, pennamericanum, spermacoces, uppalii, vernoniae, viegasii and zingibericola. These genomes showed more than 98% average nucleotide identity with the type-strain of X. euvesicatoria and less than 88% with the type-strain of X. campestris. We propose the transfer of these pathovars into X. euvesicatoria and present an emended species description for X. euvesicatoria.
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6
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Cardoso JLS, Souza AA, Vieira MLC. Molecular basis for host responses to Xanthomonas infection. PLANTA 2022; 256:84. [PMID: 36114308 DOI: 10.1007/s00425-022-03994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
This review highlights the most relevant and recent updated information available on the defense responses of selected hosts against Xanthomonas spp. Xanthomonas is one of the most important genera of Gram-negative phytopathogenic bacteria, severely affecting the productivity of economically important crops worldwide, colonizing either the vascular system or the mesophyll tissue of the host. Due to its rapid propagation, Xanthomonas poses an enormous challenge to farmers, because it is usually controlled using huge quantities of copper-based chemicals, adversely impacting the environment. Thus, developing new ways of preventing colonization by these bacteria has become essential. Advances in genomic and transcriptomic technologies have significantly elucidated at molecular level interactions between various crops and Xanthomonas species. Understanding how these hosts respond to the infection is crucial if we are to exploit potential approaches for improving crop breeding and cutting productivity losses. This review focuses on our current knowledge of the defense response mechanisms in agricultural crops after Xanthomonas infection. We describe the molecular basis of host-bacterium interactions over a broad spectrum with the aim of improving our fundamental understanding of which genes are involved and how they work in this interaction, providing information that can help to speed up plant breeding programs, namely using gene editing approaches.
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Affiliation(s)
- Jéssica L S Cardoso
- Genetics Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Alessandra A Souza
- Citrus Research Center "Sylvio Moreira", Agronomic Institute (IAC), Cordeirópolis, SP, 13490-000, Brazil
| | - Maria Lucia C Vieira
- Genetics Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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7
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Cuesta-Morrondo S, Redondo C, Palacio-Bielsa A, Garita-Cambronero J, Cubero J. Complete Genome Sequence Resources of Six Strains of the Most Virulent Pathovars of Xanthomonas arboricola Using Long- and Short-Read Sequencing Approaches. PHYTOPATHOLOGY 2022; 112:1808-1813. [PMID: 35522570 DOI: 10.1094/phyto-10-21-0436-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Sara Cuesta-Morrondo
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Centro Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid 28040, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Cristina Redondo
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Centro Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid 28040, Spain
| | - Ana Palacio-Bielsa
- Departamento de Sistemas Agrícolas, Forestales y Medio Ambiente, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Avda. Montañana 930, 50059, Zaragoza, Spain
| | | | - Jaime Cubero
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Centro Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid 28040, Spain
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8
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Zarei S, Taghavi SM, Rahimi T, Mafakheri H, Potnis N, Koebnik R, Fischer-Le Saux M, Pothier JF, Palacio Bielsa A, Cubero J, Portier P, Jacques MA, Osdaghi E. Taxonomic Refinement of Xanthomonas arboricola. PHYTOPATHOLOGY 2022; 112:1630-1639. [PMID: 35196068 DOI: 10.1094/phyto-12-21-0519-r] [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: 06/14/2023]
Abstract
Xanthomonas arboricola comprises a number of economically important fruit tree pathogens classified within different pathovars. Dozens of nonpathogenic and taxonomically unvalidated strains are also designated as X. arboricola, leading to a complicated taxonomic status in the species. In this study, we have evaluated the whole-genome resources of all available Xanthomonas spp. strains designated as X. arboricola in the public databases to refine the members of the species based on DNA similarity indexes and core genome-based phylogeny. Our results show that, of the nine validly described pathovars within X. arboricola, pathotype strains of seven pathovars are taxonomically genuine, belonging to the core clade of the species regardless of their pathogenicity on the host of isolation (thus the validity of pathovar status). However, strains of X. arboricola pv. guizotiae and X. arboricola pv. populi do not belong to X. arboricola because of the low DNA similarities between the type strain of the species and the pathotype strains of these two pathovars. Thus, we propose to elevate the two pathovars to the rank of a species as X. guizotiae sp. nov. with the type strain CFBP 7408T and X. populina sp. nov. with the type strain CFBP 3123T. In addition, other mislabeled strains of X. arboricola were scattered within Xanthomonas spp. that belong to previously described species or represent novel species that await formal description.
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Affiliation(s)
- Sadegh Zarei
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Touraj Rahimi
- Department of Agronomy and Plant Breeding, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Hamzeh Mafakheri
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Ana Palacio Bielsa
- Departamento de Protección Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Jaime Cubero
- Departamento de Protección Vegetal, Centro Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - Perrine Portier
- Institut Agro, Université de Angers, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, Angers, France
| | - Marie-Agnes Jacques
- Institut Agro, Université de Angers, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, Angers, France
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
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Mafakheri H, Taghavi SM, Zarei S, Portier P, Dimkić I, Koebnik R, Kuzmanović N, Osdaghi E. Xanthomonas bonasiae sp. nov. and Xanthomonas youngii sp. nov., isolated from crown gall tissues. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005418] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus
Xanthomonas
contains a set of diverse bacterial strains, most of which are known for their pathogenicity on annual crops and fruit trees causing economically important plant diseases. Recently, five
Xanthomonas
strains were isolated from
Agrobacterium
-induced crown gall tissues of amaranth (Amaranthus sp.) and weeping fig (Ficus benjamina) plants in Iran. Phenotypic characteristics (i.e. biochemical tests and pathogenicity features) and whole genome sequence-based core-genome phylogeny followed by average nucleotide identity and digital DNA–DNA hybridization calculations suggested that these gall-associated strains belong to two new species within the genus
Xanthomonas
. In this study, we provide a formal species description for these new species where Xanthomonas bonasiae sp. nov. is proposed for the strains isolated from weeping fig with FX4T (=CFBP 8703T=DSM 112530T) as type strain. The name Xanthomonas youngii sp. nov. is proposed for the strains isolated from amaranth with AmX2T (=CFBP 8902T=DSM 112529T) as type strain.
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Affiliation(s)
- Hamzeh Mafakheri
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - S. Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Sadegh Zarei
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Perrine Portier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Ivica Dimkić
- University of Belgrade - Faculty of Biology, Chair of Biochemistry and Molecular Biology, Studentski trg 16, 11158 Belgrade, Serbia
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Nemanja Kuzmanović
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants (JKI), Institute for Plant Protection in Horticulture and Forests, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
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Richard D, Roumagnac P, Pruvost O, Lefeuvre P. A network approach to decipher the dynamics of Lysobacteraceae plasmid gene sharing. Mol Ecol 2022; 32:2660-2673. [PMID: 35593155 DOI: 10.1111/mec.16536] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 11/27/2022]
Abstract
Plasmids provide an efficient vehicle for gene sharing among bacterial populations, playing a key role in bacterial evolution. Network approaches are particularly suitable to represent multipartite relationships and are useful tools to characterize plasmid-mediated gene sharing events. The Lysobacteraceae bacterial family gathers plant commensal, plant pathogenic and opportunistic human pathogens for which plasmid mediated adaptation was reported. We searched for homologues of plasmid gene sequences from this family in all the diversity of available bacterial genome sequences and built a network of plasmid gene sharing from the results. While plasmid genes are openly shared between the bacteria of the Lysobacteraceae family, taxonomy strongly defined the boundaries of these exchanges, that only barely reached other families. Most inferred plasmid gene sharing events involved a few genes only, and evidence of full plasmid transfers were restricted to taxonomically close taxon. We detected multiple plasmid-chromosome gene transfers, among which the otherwise known sharing of a heavy metal resistance transposon. In the network, bacterial lifestyles shaped sub-structures of isolates colonizing specific ecological niches and harboring specific types of resistance genes. Genes associated to pathogenicity or antibiotic and metal resistance were among those that most importantly structured the network, highlighting the imprints of human-mediated selective pressure on pathogenic populations. A massive sequencing effort on environmental Lysobacteraceae is therefore required to refine our understanding on how this reservoir fuels the emergence and the spread of genes amongst this family and its potential impact on plant, animal and human health.
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Affiliation(s)
- D Richard
- Cirad, UMR PVBMT, F-97410 St Pierre, Réunion, France.,ANSES, Plant Health Laboratory, F-97410 St Pierre, Réunion, France.,Université de La Réunion, La Réunion, France
| | - P Roumagnac
- Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - O Pruvost
- Cirad, UMR PVBMT, F-97410 St Pierre, Réunion, France
| | - P Lefeuvre
- Cirad, UMR PVBMT, F-97410 St Pierre, Réunion, France
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11
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Dia NC, Van Vaerenbergh J, Van Malderghem C, Blom J, Smits THM, Cottyn B, Pothier JF. Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens. Int J Syst Evol Microbiol 2021; 71. [PMID: 34913859 DOI: 10.1099/ijsem.0.005163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper describes a novel species isolated in 2011 and 2012 from nursery-grown Hydrangea arborescens cultivars in Flanders, Belgium. After 4 days at 28 °C, the strains yielded yellow, round, convex and mucoid colonies. Pathogenicity of the strains was confirmed on its isolation host, as well as on Hydrangea quercifolia. Analysis using MALDI-TOF MS identified the Hydrangea strains as belonging to the genus Xanthomonas but excluded them from the species Xanthomonas hortorum. A phylogenetic tree based on gyrB confirmed the close relation to X. hortorum. Three fatty acids were dominant in the Hydrangea isolates: anteiso-C15 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Unlike X. hortorum pathovars, the Hydrangea strains were unable to grow in the presence of lithium chloride and could only weakly utilize d-fructose-6-PO4 and glucuronamide. Phylogenetic characterization based on multilocus sequence analysis and phylogenomic characterization revealed that the strains are close to, yet distinct from, X. hortorum. The genome sequences of the strains had average nucleotide identity values ranging from 94.35-95.19 % and in silico DNA-DNA hybridization values ranging from 55.70 to 59.40 % to genomes of the X. hortorum pathovars. A genomics-based loop-mediated isothermal amplification assay was developed which was specific to the Hydrangea strains for its early detection. A novel species, Xanthomonas hydrangeae sp. nov., is proposed with strain LMG 31884T (=CCOS 1956T) as the type strain.
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Affiliation(s)
- Nay C Dia
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.,Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Johan Van Vaerenbergh
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Cinzia Van Malderghem
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Giessen, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Bart Cottyn
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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Kałużna M, Fischer‐Le Saux M, Pothier JF, Jacques M, Obradović A, Tavares F, Stefani E. Xanthomonas arboricola pv. juglandis and pv. corylina: Brothers or distant relatives? Genetic clues, epidemiology, and insights for disease management. MOLECULAR PLANT PATHOLOGY 2021; 22:1481-1499. [PMID: 34156749 PMCID: PMC8578823 DOI: 10.1111/mpp.13073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/06/2021] [Accepted: 04/23/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND The species Xanthomonas arboricola comprises up to nine pathovars, two of which affect nut crops: pv. juglandis, the causal agent of walnut bacterial blight, brown apical necrosis, and the vertical oozing canker of Persian (English) walnut; and pv. corylina, the causal agent of the bacterial blight of hazelnut. Both pathovars share a complex population structure, represented by different clusters and several clades. Here we describe our current understanding of symptomatology, population dynamics, epidemiology, and disease control. TAXONOMIC STATUS Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Lysobacterales (earlier synonym of Xanthomonadales); Family Lysobacteraceae (earlier synonym of Xanthomonadaceae); Genus Xanthomonas; Species X. arboricola; Pathovars: pv. juglandis and pv. corylina. HOST RANGE AND SYMPTOMS The host range of each pathovar is not limited to a single species, but each infects mainly one plant species: Juglans regia (X. arboricola pv. juglandis) and Corylus avellana (X. arboricola. pv. corylina). Walnut bacterial blight is characterized by lesions on leaves and fruits, and cankers on twigs, branches, and trunks; brown apical necrosis symptoms consist of apical necrosis originating at the stigmatic end of the fruit. A peculiar symptom, the vertical oozing canker developing along the trunk, is elicited by a particular genetic lineage of the bacterium. Symptoms of hazelnut bacterial blight are visible on leaves and fruits as necrotic lesions, and on woody parts as cankers. A remarkable difference is that affected walnuts drop abundantly, whereas hazelnuts with symptoms do not. DISTRIBUTION Bacterial blight of walnut has a worldwide distribution, wherever Persian (English) walnut is cultivated; the bacterial blight of hazelnut has a more limited distribution, although disease outbreaks are currently more frequently reported. X. arboricola pv. juglandis is regulated almost nowhere, whereas X. arboricola pv. corylina is regulated in most European and Mediterranean Plant Protection Organization (EPPO) countries. EPIDEMIOLOGY AND CONTROL For both pathogens infected nursery material is the main pathway for their introduction and spread into newly cultivated areas; additionally, infected nursery material is the source of primary inoculum. X. arboricola pv. juglandis is also disseminated through pollen. Disease control is achieved through the phytosanitary certification of nursery material (hazelnut), although approved certification schemes are not currently available. Once the disease is present in walnut/hazelnut groves, copper compounds are widely used, mostly in association with dithiocarbamates; where allowed, antibiotics (preferably kasugamycin) are sprayed. The emergence of strains highly resistant to copper currently represents the major threat for effective management of the bacterial blight of walnut. USEFUL WEBSITES: https://gd.eppo.int/taxon/XANTJU, https://gd.eppo.int/taxon/XANTCY, https://www.euroxanth.eu, http://www.xanthomonas.org.
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Affiliation(s)
- Monika Kałużna
- The National Institute of Horticultural ResearchSkierniewicePoland
| | | | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research GroupInstitute for Natural Resource SciencesZurich University of Applied SciencesWädenswilSwitzerland
| | | | | | - Fernando Tavares
- Centro de Investigação em Biodiversidade e Recursos GenéticosLaboratório Associado (CIBIO‐InBIO)Universidade do PortoPortugal
- Faculdade de CiênciasDepartamento de BiologiaUniversidade do PortoPortoPortugal
| | - Emilio Stefani
- Department of Life SciencesUniversity of Modena and Reggio EmiliaReggio EmiliaItaly
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Te Molder D, Poncheewin W, Schaap PJ, Koehorst JJ. Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains. BMC Genomics 2021; 22:848. [PMID: 34814827 PMCID: PMC8612006 DOI: 10.1186/s12864-021-08093-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype. Until now such approaches to the pathogenomics of Xanthomonas strains have been hampered by the fragmentation of information regarding pathogenicity of individual strains over many studies. Unification of this information into a single resource was therefore considered to be an essential step. RESULTS Mining of 39 papers considering both plant-associated phenotypes, allowed for a phenotypic classification of 578 Xanthomonas strains. For 65 plant-pathogenic and 53 non-pathogenic strains the corresponding genomes were available and de novo annotated for the presence of Pfam protein domains used as features to train and compare three ML classification algorithms; CART, Lasso and Random Forest. CONCLUSION The literature resource in combination with recursive feature extraction used in the ML classification algorithms provided further insights into the virulence enabling factors, but also highlighted domains linked to traits not present in pathogenic strains.
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Affiliation(s)
- Dennie Te Molder
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Wasin Poncheewin
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
- UNLOCK, Wageningen University, Wageningen, the Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands.
- UNLOCK, Wageningen University, Wageningen, the Netherlands.
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Assis RAB, Varani AM, Sagawa CHD, Patané JSL, Setubal JC, Uceda-Campos G, da Silva AM, Zaini PA, Almeida NF, Moreira LM, Dandekar AM. A comparative genomic analysis of Xanthomonas arboricola pv. juglandis strains reveal hallmarks of mobile genetic elements in the adaptation and accelerated evolution of virulence. Genomics 2021; 113:2513-2525. [PMID: 34089784 DOI: 10.1016/j.ygeno.2021.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/01/2021] [Accepted: 06/01/2021] [Indexed: 01/25/2023]
Abstract
Xanthomonas arboricola pv. juglandis (Xaj) is the most significant aboveground walnut bacterial pathogen. Disease management uses copper-based pesticides which induce pathogen resistance. We examined the genetic repertoire associated with adaptation and virulence evolution in Xaj. Comparative genomics of 32 Xaj strains reveal the possible acquisition and propagation of virulence factors via insertion sequences (IS). Fine-scale annotation revealed a Tn3 transposon (TnXaj417) encoding copper resistance genes acquired by horizontal gene transfer and associated with adaptation and tolerance to metal-based pesticides commonly used to manage pathogens in orchard ecosystems. Phylogenomic analysis reveals IS involvement in acquisition and diversification of type III effector proteins ranging from two to eight in non-pathogenic strains, 16 to 20 in pathogenic strains, besides six other putative effectors with a reduced identity degree found mostly among pathogenic strains. Yersiniabactin, xopK, xopAI, and antibiotic resistance genes are also located near ISs or inside genomic islands and structures resembling composite transposons.
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Affiliation(s)
- Renata A B Assis
- Center of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil; Department of Plant Sciences, University of California, Davis, CA, USA
| | - Alessandro M Varani
- Faculty of Agricultural and Veterinary Sciences of Jaboticabal (FCAV), Universidade Estadual Paulista (UNESP), Department of Technology, Jaboticabal, SP, Brazil
| | - Cintia H D Sagawa
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - José S L Patané
- Cell Cycle Laboratory, Butantan Institute, Sao Paulo, SP, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Guillermo Uceda-Campos
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Aline Maria da Silva
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Paulo A Zaini
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Nalvo F Almeida
- School of Computing, Federal University of Mato Grosso do Sul, Mato Grosso do Sul, MS, Brazil
| | - Leandro Marcio Moreira
- Center of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil; Department of Biological Science, Institute of Exact and Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil.
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, Davis, CA, USA.
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Fernandes C, Martins L, Teixeira M, Blom J, Pothier JF, Fonseca NA, Tavares F. Comparative Genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis Strains Isolated from a Single Walnut Host Tree. Microorganisms 2021; 9:microorganisms9030624. [PMID: 33803052 PMCID: PMC8003016 DOI: 10.3390/microorganisms9030624] [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: 02/16/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/20/2022] Open
Abstract
The recent report of distinct Xanthomonas lineages of Xanthomonas arboricola pv. juglandis and Xanthomonas euroxanthea within the same walnut tree revealed that this consortium of walnut-associated Xanthomonas includes both pathogenic and nonpathogenic strains. As the implications of this co-colonization are still poorly understood, in order to unveil niche-specific adaptations, the genomes of three X. euroxanthea strains (CPBF 367, CPBF 424T, and CPBF 426) and of an X. arboricola pv. juglandis strain (CPBF 427) isolated from a single walnut tree in Loures (Portugal) were sequenced with two different technologies, Illumina and Nanopore, to provide consistent single scaffold chromosomal sequences. General genomic features showed that CPBF 427 has a genome similar to other X. arboricola pv. juglandis strains, regarding its size, number, and content of CDSs, while X. euroxanthea strains show a reduction regarding these features comparatively to X. arboricola pv. juglandis strains. Whole genome comparisons revealed remarkable genomic differences between X. arboricola pv. juglandis and X. euroxanthea strains, which translates into different pathogenicity and virulence features, namely regarding type 3 secretion system and its effectors and other secretory systems, chemotaxis-related proteins, and extracellular enzymes. Altogether, the distinct genomic repertoire of X. euroxanthea may be particularly useful to address pathogenicity emergence and evolution in walnut-associated Xanthomonas.
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Affiliation(s)
- Camila Fernandes
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Unidade Estratégica de Investigação e Serviços de Sistemas Agrários e Florestais e Sanidade Vegetal, INIAV, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Correspondence: (C.F.); (F.T.)
| | - Leonor Martins
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Miguel Teixeira
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Giessen, Ludwigstraße 23, 35390 Giessen, Germany;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland;
| | - Nuno A. Fonseca
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
| | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (C.F.); (F.T.)
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16
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The HrpG/HrpX Regulon of Xanthomonads-An Insight to the Complexity of Regulation of Virulence Traits in Phytopathogenic Bacteria. Microorganisms 2021; 9:microorganisms9010187. [PMID: 33467109 PMCID: PMC7831014 DOI: 10.3390/microorganisms9010187] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/05/2022] Open
Abstract
Bacteria of the genus Xanthomonas cause a wide variety of economically important diseases in most crops. The virulence of the majority of Xanthomonas spp. is dependent on secretion and translocation of effectors by the type 3 secretion system (T3SS) that is controlled by two master transcriptional regulators HrpG and HrpX. Since their discovery in the 1990s, the two regulators were the focal point of many studies aiming to decipher the regulatory network that controls pathogenicity in Xanthomonas bacteria. HrpG controls the expression of HrpX, which subsequently controls the expression of T3SS apparatus genes and effectors. The HrpG/HrpX regulon is activated in planta and subjected to tight metabolic and genetic regulation. In this review, we cover the advances made in understanding the regulatory networks that control and are controlled by the HrpG/HrpX regulon and their conservation between different Xanthomonas spp.
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17
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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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18
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Kyrova EI, Dzhalilov FS, Ignatov AN. The role of epiphytic populations in pathogenesis of the genus Xanthomonas bacteria. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20202303010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Global climate warming and involvement of new regions with endemic populations of microorganisms in commercial seed production have led to an increase in the diversity of phytopathogenic bacteria that are affecting major crops, including the fruit trees. As a rule, emergence of new pathogens is associated with importation of infected seeds and planting material, cultivation of new species and varieties of plants, and expansion of agricultural trade with foreign countries. One of the leaders in diversity among phytopathogens is the genus Xanthomonas bacteria, affecting more than 400 plant species. Among the characteristic signs of xanthomonads is the high frequency of horizontal gene transfer both within the genus and between phylogenetically removed bacterial taxa – up to 25% of the genes are of this origin. In this paper, we consider another source of increasing the number of phytopathogenic species – by the epiphytic populations. These bacteria are the likely ancestral form of the phytopathogenic bacteria of the genus Xanthomonas.
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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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Méline V, Brin C, Lebreton G, Ledroit L, Sochard D, Hunault G, Boureau T, Belin E. A Computation Method Based on the Combination of Chlorophyll Fluorescence Parameters to Improve the Discrimination of Visually Similar Phenotypes Induced by Bacterial Virulence Factors. FRONTIERS IN PLANT SCIENCE 2020; 11:213. [PMID: 32174949 PMCID: PMC7055487 DOI: 10.3389/fpls.2020.00213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 02/11/2020] [Indexed: 05/24/2023]
Abstract
Phenotyping biotic stresses in plant-pathogen interactions studies is often hindered by phenotypes that can hardly be discriminated by visual assessment. Particularly, single gene mutants in virulence factors could lack visible phenotypes. Chlorophyll fluorescence (CF) imaging is a valuable tool to monitor plant-pathogen interactions. However, while numerous CF parameters can be measured, studies on plant-pathogen interactions often focus on a restricted number of parameters. It could result in limited abilities to discriminate visually similar phenotypes. In this study, we assess the ability of the combination of multiple CF parameters to improve the discrimination of such phenotypes. Such an approach could be of interest for screening and discriminating the impact of bacterial virulence factors without prior knowledge. A computation method was developed, based on the combination of multiple CF parameters, without any parameter selection. It involves histogram Bhattacharyya distance calculations and hierarchical clustering, with a normalization approach to take into account the inter-leaves and intra-phenotypes heterogeneities. To assess the efficiency of the method, two datasets were analyzed the same way. The first dataset featured single gene mutants of a Xanthomonas strain which differed only by their abilities to secrete bacterial virulence proteins. This dataset displayed expected phenotypes at 6 days post-inoculation and was used as ground truth dataset to setup the method. The efficiency of the computation method was demonstrated by the relevant discrimination of phenotypes at 3 days post-inoculation. A second dataset was composed of transient expression (agrotransformation) of Type 3 Effectors. This second dataset displayed phenotypes that cannot be discriminated by visual assessment and no prior knowledge can be made on the respective impact of each Type 3 Effectors on leaf tissues. Using the computation method resulted in clustering the leaf samples according to the Type 3 Effectors, thereby demonstrating an improvement of the discrimination of the visually similar phenotypes. The relevant discrimination of visually similar phenotypes induced by bacterial strains differing only by one virulence factor illustrated the importance of using a combination of CF parameters to monitor plant-pathogen interactions. It opens a perspective for the identification of specific signatures of biotic stresses.
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Affiliation(s)
- Valérian Méline
- Emersys, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
- ImHorPhen, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
| | - Chrystelle Brin
- Emersys, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
| | - Guillaume Lebreton
- Phenotic Platform, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
| | - Lydie Ledroit
- Phenotic Platform, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
| | - Daniel Sochard
- Phenotic Platform, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
| | - Gilles Hunault
- ImHorPhen, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
- Laboratoire HIFIH, UPRES EA 3859, SFR 4208, Université d'Angers, Angers, France
| | - Tristan Boureau
- Emersys, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
- ImHorPhen, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
- Phenotic Platform, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
| | - Etienne Belin
- ImHorPhen, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
- Phenotic Platform, SFR 4207 QUASAV, IRHS, UMR1345, Université d'Angers, Angers, France
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes, Université d'Angers, Angers, France
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21
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Garita-Cambronero J, Sena-Vélez M, Ferragud E, Sabuquillo P, Redondo C, Cubero J. Xanthomonas citri subsp. citri and Xanthomonas arboricola pv. pruni: Comparative analysis of two pathogens producing similar symptoms in different host plants. PLoS One 2019; 14:e0219797. [PMID: 31318915 PMCID: PMC6639005 DOI: 10.1371/journal.pone.0219797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/01/2019] [Indexed: 01/06/2023] Open
Abstract
Comparative studies in Xanthomonas have provided a vast amount of data that enabled to deepen in the knowledge of those factors associated with virulence and Xanthomonas plant interaction. The species of this genus present a wide range of host plants and a large number of studies have been focused to elucidate which mechanism are involved in this characteristic. In this study, comparative genomic and phenotypic analysis were performed between X. citri subsp. citri (Xcc), one of the most studied pathogens within Xanthomonas, and X. arboricola pv. pruni (Xap), a pathogen which has aroused great interest in recent time. The work was aimed to find those elements that contribute to their host divergence despite the convergence in the symptoms that each species cause on Citrus spp. and Prunus spp., respectively. This study reveals a set of genes that could be putatively associated with the adaptation of these pathogens to their hosts, being the most remarkable those involved in environmental sensing systems such as the case of the TonB-dependent transporters, the sensors of the two-component system and the methyl accepting chemotaxis proteins. Other important variants were found in processes related to the decomposition of the cell wall as could be appreciated by their dissimilar set of cell-wall degrading enzymes. Type three effectors, as one of the most important factors in delineating the host specificity in Xanthomonas, also showed a different array when comparing both species, being some of them unique to each pathogen. On the other hand, only small variations could be connected to other features such as the motility appendages and surface adhesion proteins, but these differences were accompanied by a dissimilar capacity to attach on host and non-host leaf surface. The molecular factors found in this work provide the basis to perform a more in-depth functional analyses that unveil those actual factors associated with pathogenesis and host specificity in Xcc and Xap.
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Affiliation(s)
- Jerson Garita-Cambronero
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain.,Centro de Investigación de Biocombustibles y Bioproductos, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Villarejo de Órbigo, Leon, Spain
| | - Marta Sena-Vélez
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain.,Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Elisa Ferragud
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain
| | - Pilar Sabuquillo
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain
| | - Cristina Redondo
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain
| | - Jaime Cubero
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain
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22
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Meline V, Delage W, Brin C, Li‐Marchetti C, Sochard D, Arlat M, Rousseau C, Darrasse A, Briand M, Lebreton G, Portier P, Fischer‐Le Saux M, Durand K, Jacques M, Belin E, Boureau T. Role of the acquisition of a type 3 secretion system in the emergence of novel pathogenic strains of Xanthomonas. MOLECULAR PLANT PATHOLOGY 2019; 20:33-50. [PMID: 30076773 PMCID: PMC6430459 DOI: 10.1111/mpp.12737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Cases of emergence of novel plant-pathogenic strains are regularly reported that reduce the yields of crops and trees. However, the molecular mechanisms underlying such emergence are still poorly understood. The acquisition by environmental non-pathogenic strains of novel virulence genes by horizontal gene transfer has been suggested as a driver for the emergence of novel pathogenic strains. In this study, we tested such an hypothesis by transferring a plasmid encoding the type 3 secretion system (T3SS) and four associated type 3 secreted proteins (T3SPs) to the non-pathogenic strains of Xanthomonas CFBP 7698 and CFBP 7700, which lack genes encoding T3SS and any previously known T3SPs. The resulting strains were phenotyped on Nicotiana benthamiana using chlorophyll fluorescence imaging and image analysis. Wild-type, non-pathogenic strains induced a hypersensitive response (HR)-like necrosis, whereas strains complemented with T3SS and T3SPs suppressed this response. Such suppression depends on a functional T3SS. Amongst the T3SPs encoded on the plasmid, Hpa2, Hpa1 and, to a lesser extent, XopF1 collectively participate in suppression. Monitoring of the population sizes in planta showed that the sole acquisition of a functional T3SS by non-pathogenic strains impairs growth inside leaf tissues. These results provide functional evidence that the acquisition via horizontal gene transfer of a T3SS and four T3SPs by environmental non-pathogenic strains is not sufficient to make strains pathogenic. In the absence of a canonical effector, the sole acquisition of a T3SS seems to be counter-selective, and further acquisition of type 3 effectors is probably needed to allow the emergence of novel pathogenic strains.
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Affiliation(s)
- Valérian Meline
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Wesley Delage
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Chrystelle Brin
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Camille Li‐Marchetti
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Daniel Sochard
- Platform PHENOTICIRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Matthieu Arlat
- INRAUMR 441, Laboratoire des Interactions Plantes Micro‐organismes (LIPM)F‐31326Castanet‐TolosanFrance
| | - Céline Rousseau
- Platform PHENOTICIRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Armelle Darrasse
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Martial Briand
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Guillaume Lebreton
- Platform PHENOTICIRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Perrine Portier
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
- CIRM‐CFBP French Collection for Plant‐associated BacteriaIRHSUMR 1345INRA‐ACO‐UA42 rue Georges Morel49070Beaucouzé CedexFrance
| | - Marion Fischer‐Le Saux
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
- CIRM‐CFBP French Collection for Plant‐associated BacteriaIRHSUMR 1345INRA‐ACO‐UA42 rue Georges Morel49070Beaucouzé CedexFrance
| | - Karine Durand
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Marie‐Agnès Jacques
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Etienne Belin
- Platform PHENOTICIRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS)Université d’AngersF‐49000AngersFrance
| | - Tristan Boureau
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
- Platform PHENOTICIRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
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23
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Matilla MA, Krell T. The effect of bacterial chemotaxis on host infection and pathogenicity. FEMS Microbiol Rev 2018; 42:4563582. [PMID: 29069367 DOI: 10.1093/femsre/fux052] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/19/2017] [Indexed: 12/26/2022] Open
Abstract
Chemotaxis enables microorganisms to move according to chemical gradients. Although this process requires substantial cellular energy, it also affords key physiological benefits, including enhanced access to growth substrates. Another important implication of chemotaxis is that it also plays an important role in infection and disease, as chemotaxis signalling pathways are broadly distributed across a variety of pathogenic bacteria. Furthermore, current research indicates that chemotaxis is essential for the initial stages of infection in different human, animal and plant pathogens. This review focuses on recent findings that have identified specific bacterial chemoreceptors and corresponding chemoeffectors associated with pathogenicity. Pathogenicity-related chemoeffectors are either host and niche-specific signals or intermediates of the host general metabolism. Plant pathogens were found to contain an elevated number of chemotaxis signalling genes and functional studies demonstrate that these genes are critical for their ability to enter the host. The expanding body of knowledge of the mechanisms underlying chemotaxis in pathogens provides a foundation for the development of new therapeutic strategies capable of blocking infection and preventing disease by interfering with chemotactic signalling pathways.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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24
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Garita‐Cambronero J, Palacio‐Bielsa A, Cubero J. Xanthomonas arboricola pv. pruni, causal agent of bacterial spot of stone fruits and almond: its genomic and phenotypic characteristics in the X. arboricola species context. MOLECULAR PLANT PATHOLOGY 2018; 19:2053-2065. [PMID: 29575564 PMCID: PMC6638108 DOI: 10.1111/mpp.12679] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/13/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Xanthomonas arboricola pv. pruni (Xap) causes bacterial spot of stone fruits and almond, an important disease that may reduce the yield and vigour of the trees, as well as the marketability of affected fruits. Xap lies within the Xanthomonas genus, which has been intensively studied because of its strain specialization and host range complexity. Here, we summarize the recent advances in our understanding of the complexities of Xap, including studies of the molecular features that result after comparative phenotypic and genomic analyses, in order to obtain a clearer overview of the bacterial behaviour and infection mechanism in the context of the X. arboricola species. TAXONOMIC STATUS Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species X. arboricola; Pathovar pruni. HOST RANGE AND SYMPTOMS Xap infects most Prunus species, including apricot, peach, nectarine, plum and almond, and occasionally cherry. Symptoms are found on leaves, fruits, twigs and branches or trunks. In severe infections, defoliation and fruit dropping may occur. DISTRIBUTION Bacterial spot of stone fruits and almond is worldwide in distribution, with Xap being isolated in Africa, North and South America, Asia, Europe and Oceania. It is a common disease in geographical areas in which stone fruits and almonds are grown. Xap is listed as a quarantine organism in several areas of the world. GENOME The genomes of six isolates from Xap have been publicly released. The genome consists of a single chromosome of around 5 000 000 bp with 65 mol% GC content and an extrachromosomal plasmid element of around 41 000 bp with 62 mol% GC content. Genomic comparative studies in X. arboricola have allowed the identification of putative virulence components associated with the infection process of bacterial spot of stone fruits and almond. DISEASE CONTROL Management of bacterial spot of stone fruits and almond is based on an integrated approach that comprises essential measures to avoid Xap introduction in a production zone, as well as the use of tolerant or resistant plant material and chemical treatments, mainly based on copper compounds. Management programmes also include the use of appropriate cultivation practices when the disease is already established. Finally, for the effective control of the disease, appropriate detection and characterization methods are needed for use in symptomatic or asymptomatic samples as a first approach for pathogen exclusion. USEFUL WEBSITES: https://gd.eppo.int/taxon/XANTPR; http://www.cost.eu/COST_Actions/ca/CA16107; http://www.xanthomonas.org.
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Affiliation(s)
- Jerson Garita‐Cambronero
- Departamento de Protección VegetalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Madrid 28040Spain
- Centro de Investigación de Biocombustibles y Bioproductos, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Villarejo de Órbigo 24358LeónSpain
| | - Ana Palacio‐Bielsa
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón‐IA2 ‐ (CITA ‐ Universidad de Zaragoza)Zaragoza 50059Spain
| | - Jaime Cubero
- Departamento de Protección VegetalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Madrid 28040Spain
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25
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López MM, Lopez-Soriano P, Garita-Cambronero J, Beltrán C, Taghouti G, Portier P, Cubero J, Fischer-Le Saux M, Marco-Noales E. Xanthomonas prunicola sp. nov., a novel pathogen that affects nectarine (Prunus persica var. nectarina) trees. Int J Syst Evol Microbiol 2018; 68:1857-1866. [PMID: 29741474 DOI: 10.1099/ijsem.0.002743] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Three isolates obtained from symptomatic nectarine trees (Prunus persica var. nectarina) cultivated in Murcia, Spain, which showed yellow and mucoid colonies similar to Xanthomonas arboricola pv. pruni, were negative after serological and real-time PCR analyses for this pathogen. For that reason, these isolates were characterized following a polyphasic approach that included both phenotypic and genomic methods. By sequence analysis of the 16S rRNA gene, these novel strains were identified as members of the genus Xanthomonas, and by multilocus sequence analysis (MLSA) they were clustered together in a distinct group that showed similarity values below 95 % with the rest of the species of this genus. Whole-genome comparisons of the average nucleotide identity (ANI) of genomes of the strains showed less than 91 % average nucleotide identity with all other species of the genus Xanthomonas. Additionally, phenotypic characterization based on API 20 NE, API 50 CH and BIOLOG tests differentiated the strains from the species of the genus Xanthomonas described previously. Moreover, the three strains were confirmed to be pathogenic on peach (Prunus persica), causing necrotic lesions on leaves. On the basis of these results, the novel strains represent a novel species of the genus Xanthomonas, for which the name Xanthomonas prunicola is proposed. The type strain is CFBP 8353 (=CECT 9404=IVIA 3287.1).
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Affiliation(s)
- María M López
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315 Km 10,7, 46113 Moncada, Valencia, Spain
| | - Pablo Lopez-Soriano
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315 Km 10,7, 46113 Moncada, Valencia, Spain
| | - Jerson Garita-Cambronero
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Carretera de la Coruña Km 7,5, 28040 Madrid, Spain.,Centro de Investigación de Biocombustibles y Bioproductos, Instituto Tecnológico Agrario de Castilla y León, 24358 Villarejo de Orbigo, León, Spain
| | - Carmen Beltrán
- Consejería de Agricultura y Agua. Comunidad Autónoma Región de Murcia, Calle Mayor s/n, 30150 La Alberca, Murcia, Spain
| | - Geraldine Taghouti
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, CIRM-CFBP, 42 rue Georges Morel, 49071 Beaucouzé cedex, France
| | - Perrine Portier
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, CIRM-CFBP, 42 rue Georges Morel, 49071 Beaucouzé cedex, France
| | - Jaime Cubero
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Carretera de la Coruña Km 7,5, 28040 Madrid, Spain
| | - Marion Fischer-Le Saux
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, CIRM-CFBP, 42 rue Georges Morel, 49071 Beaucouzé cedex, France
| | - Ester Marco-Noales
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315 Km 10,7, 46113 Moncada, Valencia, Spain
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26
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Garita-Cambronero J, Palacio-Bielsa A, López MM, Cubero J. Pan-Genomic Analysis Permits Differentiation of Virulent and Non-virulent Strains of Xanthomonas arboricola That Cohabit Prunus spp. and Elucidate Bacterial Virulence Factors. Front Microbiol 2017; 8:573. [PMID: 28450852 PMCID: PMC5389983 DOI: 10.3389/fmicb.2017.00573] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/20/2017] [Indexed: 01/17/2023] Open
Abstract
Xanthomonas arboricola is a plant-associated bacterial species that causes diseases on several plant hosts. One of the most virulent pathovars within this species is X. arboricola pv. pruni (Xap), the causal agent of bacterial spot disease of stone fruit trees and almond. Recently, a non-virulent Xap-look-a-like strain isolated from Prunus was characterized and its genome compared to pathogenic strains of Xap, revealing differences in the profile of virulence factors, such as the genes related to the type III secretion system (T3SS) and type III effectors (T3Es). The existence of this atypical strain arouses several questions associated with the abundance, the pathogenicity, and the evolutionary context of X. arboricola on Prunus hosts. After an initial characterization of a collection of Xanthomonas strains isolated from Prunus bacterial spot outbreaks in Spain during the past decade, six Xap-look-a-like strains, that did not clustered with the pathogenic strains of Xap according to a multi locus sequence analysis, were identified. Pathogenicity of these strains was analyzed and the genome sequences of two Xap-look-a-like strains, CITA 14 and CITA 124, non-virulent to Prunus spp., were obtained and compared to those available genomes of X. arboricola associated with this host plant. Differences were found among the genomes of the virulent and the Prunus non-virulent strains in several characters related to the pathogenesis process. Additionally, a pan-genomic analysis that included the available genomes of X. arboricola, revealed that the atypical strains associated with Prunus were related to a group of non-virulent or low virulent strains isolated from a wide host range. The repertoire of the genes related to T3SS and T3Es varied among the strains of this cluster and those strains related to the most virulent pathovars of the species, corylina, juglandis, and pruni. This variability provides information about the potential evolutionary process associated to the acquisition of pathogenicity and host specificity in X. arboricola. Finally, based in the genomic differences observed between the virulent and the non-virulent strains isolated from Prunus, a sensitive and specific real-time PCR protocol was designed to detect and identify Xap strains. This method avoids miss-identifications due to atypical strains of X. arboricola that can cohabit Prunus.
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Affiliation(s)
- Jerson Garita-Cambronero
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - Ana Palacio-Bielsa
- Unidad de Sanidad Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón, Universidad de ZaragozaZaragoza, Spain
| | - María M. López
- Departamento de Bacteriología, Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones AgrariasValencia, Spain
| | - Jaime Cubero
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
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27
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Garita-Cambronero J, Palacio-Bielsa A, López MM, Cubero J. Pan-Genomic Analysis Permits Differentiation of Virulent and Non-virulent Strains of Xanthomonas arboricola That Cohabit Prunus spp. and Elucidate Bacterial Virulence Factors. Front Microbiol 2017; 8:573. [PMID: 28450852 DOI: 10.3389/fmicb.2017.00573.ecollection2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/20/2017] [Indexed: 05/24/2023] Open
Abstract
Xanthomonas arboricola is a plant-associated bacterial species that causes diseases on several plant hosts. One of the most virulent pathovars within this species is X. arboricola pv. pruni (Xap), the causal agent of bacterial spot disease of stone fruit trees and almond. Recently, a non-virulent Xap-look-a-like strain isolated from Prunus was characterized and its genome compared to pathogenic strains of Xap, revealing differences in the profile of virulence factors, such as the genes related to the type III secretion system (T3SS) and type III effectors (T3Es). The existence of this atypical strain arouses several questions associated with the abundance, the pathogenicity, and the evolutionary context of X. arboricola on Prunus hosts. After an initial characterization of a collection of Xanthomonas strains isolated from Prunus bacterial spot outbreaks in Spain during the past decade, six Xap-look-a-like strains, that did not clustered with the pathogenic strains of Xap according to a multi locus sequence analysis, were identified. Pathogenicity of these strains was analyzed and the genome sequences of two Xap-look-a-like strains, CITA 14 and CITA 124, non-virulent to Prunus spp., were obtained and compared to those available genomes of X. arboricola associated with this host plant. Differences were found among the genomes of the virulent and the Prunus non-virulent strains in several characters related to the pathogenesis process. Additionally, a pan-genomic analysis that included the available genomes of X. arboricola, revealed that the atypical strains associated with Prunus were related to a group of non-virulent or low virulent strains isolated from a wide host range. The repertoire of the genes related to T3SS and T3Es varied among the strains of this cluster and those strains related to the most virulent pathovars of the species, corylina, juglandis, and pruni. This variability provides information about the potential evolutionary process associated to the acquisition of pathogenicity and host specificity in X. arboricola. Finally, based in the genomic differences observed between the virulent and the non-virulent strains isolated from Prunus, a sensitive and specific real-time PCR protocol was designed to detect and identify Xap strains. This method avoids miss-identifications due to atypical strains of X. arboricola that can cohabit Prunus.
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Affiliation(s)
- Jerson Garita-Cambronero
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - Ana Palacio-Bielsa
- Unidad de Sanidad Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón, Universidad de ZaragozaZaragoza, Spain
| | - María M López
- Departamento de Bacteriología, Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones AgrariasValencia, Spain
| | - Jaime Cubero
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
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