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Ramnarine SDBJ, Jayaraman J, Ramsubhag A. Crucifer Lesion-Associated Xanthomonas Strains Show Multi-Resistance to Heavy Metals and Antibiotics. Curr Microbiol 2024; 81:136. [PMID: 38598029 DOI: 10.1007/s00284-024-03646-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 04/11/2024]
Abstract
Copper resistance in phytopathogens is a major challenge to crop production globally and is known to be driven by excessive use of copper-based pesticides. However, recent studies have shown co-selection of multiple heavy metal and antibiotic resistance genes in bacteria exposed to heavy metal and xenobiotics, which may impact the epidemiology of plant, animal, and human diseases. In this study, multi-resistance to heavy metals and antibiotics were evaluated in local Xanthomonas campestris pv. campestris (Xcc) and co-isolated Xanthomonas melonis (Xmel) strains from infected crucifer plants in Trinidad. Resistance to cobalt, cadmium, zinc, copper, and arsenic (V) was observed in both Xanthomonas species up to 25 mM. Heavy metal resistance (HMR) genes were found on a small plasmid-derived locus with ~ 90% similarity to a Stenotrophomonas spp. chromosomal locus and a X. perforans pLH3.1 plasmid. The co-occurrence of mobile elements in these regions implies their organization on a composite transposon-like structure. HMR genes in Xcc strains showed the lowest similarity to references, and the cus and ars operons appear to be unique among Xanthomonads. Overall, the similarity of HMR genes to Stenotrophomonas sp. chromosomal genomes suggest their origin in this genus or a related organism and subsequent spread through lateral gene transfer events. Further resistome characterization revealed the presence of small multidrug resistance (SMR), multidrug resistance (MDR) efflux pumps, and bla (Xcc) genes for broad biocide resistance in both species. Concurrently, resistance to antibiotics (streptomycin, kanamycin, tetracycline, chloramphenicol, and ampicillin) up to 1000 µg/mL was confirmed.
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Affiliation(s)
- Stephen D B Jr Ramnarine
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine, Trinidad and Tobago.
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2
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Chuang SC, Dobhal S, Alvarez AM, Arif M. Three new species, Xanthomonas hawaiiensis sp. nov., Stenotrophomonas aracearum sp. nov., and Stenotrophomonas oahuensis sp. nov., isolated from the Araceae family. Front Microbiol 2024; 15:1356025. [PMID: 38655077 PMCID: PMC11035887 DOI: 10.3389/fmicb.2024.1356025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Xanthomonas and Stenotrophomonas are closely related genera in the family Lysobacteraceae. In our previous study of aroid-associated bacterial strains, most strains isolated from anthurium and other aroids were reclassified as X. phaseoli and other Xanthomonas species. However, two strains isolated from Spathiphyllum and Colocasia were phylogenetically distant from other strains in the Xanthomonas clade and two strains isolated from Anthurium clustered within the Stenotrophomonas clade. Phylogenetic trees based on 16S rRNA and nine housekeeping genes placed the former strains with the type strain of X. sacchari from sugarcane and the latter strains with the type strain of S. bentonitica from bentonite. In pairwise comparisons with type strains, the overall genomic relatedness indices required delineation of new species; digital DNA-DNA hybridization and average nucleotide identity values were lower than 70 and 95%, respectively. Hence, three new species are proposed: S. aracearum sp. nov. and S. oahuensis sp. nov. for two strains from anthurium and X. hawaiiensis sp. nov. for the strains from spathiphyllum and colocasia, respectively. The genome size of X. hawaiiensis sp. nov. is ~4.88 Mbp and higher than S. aracearum sp. nov. (4.33 Mbp) and S. oahuensis sp. nov. (4.68 Mbp). Gene content analysis revealed 425 and 576 core genes present in 40 xanthomonads and 25 stenotrophomonads, respectively. The average number of unique genes in Stenotrophomonas spp. was higher than in Xanthomonas spp., implying higher genetic diversity in Stenotrophomonas.
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Affiliation(s)
| | | | | | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI, United States
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3
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Pena MM, Bhandari R, Bowers RM, Weis K, Newberry E, Wagner N, Pupko T, Jones JB, Woyke T, Vinatzer BA, Jacques MA, Potnis N. Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas. Genome Biol Evol 2024; 16:evae074. [PMID: 38648506 PMCID: PMC11032200 DOI: 10.1093/gbe/evae074] [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] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their cooccurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We performed association analysis on a large data set of 337 Xanthomonas strains to explain how xanthomonads may have established association with the plants across the continuum of lifestyles from commensals to weak pathogens to pathogens. Presence of distinct transcriptional regulators, distinct nutrient utilization and assimilation genes, transcriptional regulators, and chemotaxis genes may explain lifestyle-specific adaptations of xanthomonads.
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Affiliation(s)
- Michelle M Pena
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
- Present address: Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kylie Weis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Eric Newberry
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel Aviv, Israel
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, USA
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Marie-Agnès Jacques
- Institut Agro, INRAE, IRHS, SFR QUASAV, University of Angers, Angers F-49000, France
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
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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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5
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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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6
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Coutinho TA, Jacques MA, Jones J. Editorial: Emergence and re-emergence of plant diseases caused by Xanthomonas species. Front Microbiol 2022; 13:1081601. [PMID: 36578575 PMCID: PMC9791255 DOI: 10.3389/fmicb.2022.1081601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Teresa A. Coutinho
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics/Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa,*Correspondence: Teresa A. Coutinho
| | - Marie-Agnes Jacques
- Institut Agro, INRAE, IRHS, SFR QUASAV, University of Angers, Angers, France
| | - Jeffrey Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
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7
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Lü P, Liu Y, Yu X, Shi CL, Liu X. The right microbe-associated molecular patterns for effective recognition by plants. Front Microbiol 2022; 13:1019069. [PMID: 36225366 PMCID: PMC9549324 DOI: 10.3389/fmicb.2022.1019069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Plants are constantly exposed to diverse microbes and thus develop a sophisticated perceive system to distinguish non-self from self and identify non-self as friends or foes. Plants can detect microbes in apoplast via recognition of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) on the cell surface to activate appropriate signaling in response to microbes. MAMPs are highly conserved but essential molecules of microbes and often buried in microbes’ complex structure. Mature MAMPs are released from microbes by invasion-induced hydrolytic enzymes in apoplast and accumulate in proximity of plasma membrane-localized PRRs to be perceived as ligands to activate downstream signaling. In response, microbes developed strategies to counteract these processing. Here, we review how the form, the concentration, and the size of mature MAMPs affect the PRR-mediated immune signaling. In particular, we describe some potential applications and explore potential open questions in the fields.
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Affiliation(s)
- Pengpeng Lü
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Yi Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Xixi Yu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | | | - Xiaokun Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
- *Correspondence: Xiaokun Liu,
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Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria. Mob DNA 2022; 13:19. [PMID: 35962419 PMCID: PMC9373382 DOI: 10.1186/s13100-022-00275-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/22/2022] [Indexed: 11/29/2022] Open
Abstract
Background ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact. Results Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants. Conclusions Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00275-1.
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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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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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Rosenthal E, Potnis N, Bull CT. Comparative Genomic Analysis of the Lettuce Bacterial Leaf Spot Pathogen, Xanthomonas hortorum pv. vitians, to Investigate Race Specificity. Front Microbiol 2022; 13:840311. [PMID: 35516433 PMCID: PMC9062649 DOI: 10.3389/fmicb.2022.840311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/09/2022] [Indexed: 01/01/2023] Open
Abstract
Bacterial leaf spot (BLS) of lettuce caused by Xanthomonas hortorum pv. vitians (Xhv) was first described over 100 years ago and remains a significant threat to lettuce cultivation today. This study investigated the genetic relatedness of the Xhv strains and the possible genetic sources of this race-specific pathogenicity. Whole genome sequences of eighteen Xhv strains representing the three races, along with eight related Xanthomonas strains, were included in the analysis. A maximum likelihood phylogeny based on concatenated whole genome SNPs confirmed previous results describing two major lineages of Xhv strains. Gene clusters encoding secretion systems, secondary metabolites, and bacteriocins were assessed to identify putative virulence factors that distinguish the Xhv races. Genome sequences were mined for effector genes, which have been shown to be involved in race specificity in other systems. Two effectors identified in this study, xopAQ and the novel variant xopAF2, were revealed as possible mediators of a gene-for-gene interaction between Xhv race 1 and 3 strains and wild lettuce Lactuca serriola ARM-09-161-10-1. Transposase sequence identified downstream of xopAF2 and prophage sequence found nearby within Xhv race 1 and 3 insertion sequences suggest that this gene may have been acquired through phage-mediated gene transfer. No other factors were identified from these analyses that distinguish the Xhv races.
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Affiliation(s)
- Emma Rosenthal
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
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Ramnarine SDBJ, Jayaraman J, Ramsubhag A. Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles. PeerJ 2022; 9:e12632. [PMID: 35036136 PMCID: PMC8734464 DOI: 10.7717/peerj.12632] [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] [Received: 07/27/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
Black-rot disease caused by the phytopathogen Xanthomonas campestris pv. campestris (Xcc) continues to have considerable impacts on the productivity of cruciferous crops in Trinidad and Tobago and the wider Caribbean region. While the widespread occurrence of resistance of Xcc against bactericidal agrochemicals can contribute to the high disease burdens, the role of virulence and pathogenicity features of local strains on disease prevalence and severity has not been investigated yet. In the present study, a comparative genomic analysis was performed on 6 pathogenic Xcc and 4 co-isolated non-pathogenic Xanthomonas melonis (Xmel) strains from diseased crucifer plants grown in fields with heavy chemical use in Trinidad. Native isolates were grouped into two known and four newly assigned ribosomal sequence types (rST). Mobile genetic elements were identified which belonged to the IS3, IS5 family, Tn3 transposon, resolvases, and tra T4SS gene clusters. Additionally, exogenous plasmid derived sequences with origins from other bacterial species were characterised. Although several instances of genomic rearrangements were observed, native Xcc and Xmel isolates shared a significant level of structural homology with reference genomes, Xcc ATCC 33913 and Xmel CFBP4644, respectively. Complete T1SS hlyDB, T2SS, T4SS vir and T5SS xadA, yapH and estA gene clusters were identified in both species. Only Xmel strains contained a complete T6SS but no T3SS. Both species contained a complex repertoire of extracellular cell wall degrading enzymes. Native Xcc strains contained 37 T3SS and effector genes but a variable and unique profile of 8 avr, 4 xop and 1 hpa genes. Interestingly, Xmel strains contained several T3SS effectors with low similarity to references including avrXccA1 (~89%), hrpG (~73%), hrpX (~90%) and xopAZ (~87%). Furthermore, only Xmel genomes contained a CRISPR-Cas I-F array, but no lipopolysaccharide wxc gene cluster. Xmel strains were confirmed to be non-pathogenic by pathogenicity assays. The results of this study will be useful to guide future research into virulence mechanisms, agrochemical resistance, pathogenomics and the potential role of the co-isolated non-pathogenic Xanthomonas strains on Xcc infections.
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Affiliation(s)
- Stephen D B Jr Ramnarine
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
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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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15
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Potnis N. Harnessing Eco-Evolutionary Dynamics of Xanthomonads on Tomato and Pepper to Tackle New Problems of an Old Disease. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:289-310. [PMID: 34030449 DOI: 10.1146/annurev-phyto-020620-101612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacterial spot is an endemic seedborne disease responsible for recurring outbreaks on tomato and pepper around the world. The disease is caused by four diverse species, Xanthomonas gardneri, Xanthomonas euvesicatoria, Xanthomonas perforans, and Xanthomonas vesicatoria. There are no commercially available disease-resistant tomato varieties, and the disease is managed by chemical/biological control options, although these have not reduced the incidence of outbreaks. The disease on peppers is managed by disease-resistant cultivars that are effective against X. euvesicatoria but not X. gardneri. A significant shift in composition and prevalence of different species and races of the pathogen has occurred over the past century. Here, I attempt to review ecological and evolutionary processes associated with the population dynamics leading to disease emergence and spread. The goal of this review is to integrate the knowledge on population genomics and molecular plant-microbe interactions for this pathosystem to tailor disease management strategies.
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Affiliation(s)
- Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama 36849, USA;
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16
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Buscaill P, van der Hoorn RAL. Defeated by the nines: nine extracellular strategies to avoid microbe-associated molecular patterns recognition in plants. THE PLANT CELL 2021; 33:2116-2130. [PMID: 33871653 PMCID: PMC8364246 DOI: 10.1093/plcell/koab109] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/07/2021] [Indexed: 05/13/2023]
Abstract
Recognition of microbe-associated molecular patterns (MAMPs) by cell-surface receptors is pivotal in host-microbe interactions. Both pathogens and symbionts establish plant-microbe interactions using fascinating intricate extracellular strategies to avoid recognition. Here we distinguish nine different extracellular strategies to avoid recognition by the host, acting at three different levels. To avoid the accumulation of MAMP precursors (Level 1), microbes take advantage of polymorphisms in both MAMP proteins and glycans, or downregulate MAMP production. To reduce hydrolytic MAMP release (Level 2), microbes shield MAMP precursors with proteins or glycans and inhibit or degrade host-derived hydrolases. And to prevent MAMP perception directly (Level 3), microbes degrade or sequester MAMPs before they are perceived. We discuss examples of these nine strategies and envisage three additional extracellular strategies to avoid MAMP perception in plants.
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Affiliation(s)
- Pierre Buscaill
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, UK
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17
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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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18
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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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19
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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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Abstract
Population genomics is transforming our understanding of pathogen biology and evolution, and contributing to the prevention and management of disease in diverse crops. We provide an overview of key methods in bacterial population genomics and describe recent work focusing on three topics of critical importance to plant pathology: (i) resolving pathogen origins and transmission pathways during outbreak events, (ii) identifying the genetic basis of host specificity and virulence, and (iii) understanding how pathogens evolve in response to changing agricultural practices.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Christina Straub
- Institute of Environmental Science and Research, Health and Environment, Auckland, New Zealand
- Genomics Aotearoa, New Zealand
| | - Elena Colombi
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, Western Australia, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
| | - Honour C McCann
- New Zealand Institute for Advanced Study, Massey University, Albany, New Zealand
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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21
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Secrete or perish: The role of secretion systems in Xanthomonas biology. Comput Struct Biotechnol J 2020; 19:279-302. [PMID: 33425257 PMCID: PMC7777525 DOI: 10.1016/j.csbj.2020.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 12/22/2022] Open
Abstract
Bacteria of the Xanthomonas genus are mainly phytopathogens of a large variety of crops of economic importance worldwide. Xanthomonas spp. rely on an arsenal of protein effectors, toxins and adhesins to adapt to the environment, compete with other microorganisms and colonize plant hosts, often causing disease. These protein effectors are mainly delivered to their targets by the action of bacterial secretion systems, dedicated multiprotein complexes that translocate proteins to the extracellular environment or directly into eukaryotic and prokaryotic cells. Type I to type VI secretion systems have been identified in Xanthomonas genomes. Recent studies have unravelled the diverse roles played by the distinct types of secretion systems in adaptation and virulence in xanthomonads, unveiling new aspects of their biology. In addition, genome sequence information from a wide range of Xanthomonas species and pathovars have become available recently, uncovering a heterogeneous distribution of the distinct families of secretion systems within the genus. In this review, we describe the architecture and mode of action of bacterial type I to type VI secretion systems and the distribution and functions associated with these important nanoweapons within the Xanthomonas genus.
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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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Draft Genome Sequences of Pantoea agglomerans Strains BD1274 and BD1212, Isolated from Onion Seeds, Reveal Major Differences in Pathogenicity and Functional Genes. Microbiol Resour Announc 2020; 9:9/45/e01507-19. [PMID: 33154020 PMCID: PMC7645676 DOI: 10.1128/mra.01507-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Pantoea agglomerans strains BD1274 and BD1212 were isolated from Allium cepa seeds. Strain BD1274 induced a disease symptom on a healthy onion, whereas strain BD1212 did not and remains nonpathogenic. A comparative genomic study revealed that the strains differ in their genomic compositions, particularly in the genes that confer pathogenicity. Pantoea agglomerans strains BD1274 and BD1212 were isolated from Allium cepa seeds. Strain BD1274 induced a disease symptom on a healthy onion, whereas strain BD1212 did not and remains nonpathogenic. A comparative genomic study revealed that the strains differ in their genomic compositions, particularly in the genes that confer pathogenicity.
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24
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H. D. Sagawa C, de A. B. Assis R, Zaini PA, Wilmarth PA, Phinney BS, Moreira LM, Dandekar AM. Proteome Analysis of Walnut Bacterial Blight Disease. Int J Mol Sci 2020; 21:E7453. [PMID: 33050347 PMCID: PMC7593943 DOI: 10.3390/ijms21207453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/21/2022] Open
Abstract
The interaction between the plant host, walnut (Juglans regia; Jr), and a deadly pathogen (Xanthomonas arboricola pv. juglandis 417; Xaj) can lead to walnut bacterial blight (WB), which depletes walnut productivity by degrading the nut quality. Here, we dissect this pathosystem using tandem mass tag quantitative proteomics. Walnut hull tissues inoculated with Xaj were compared to mock-inoculated tissues, and 3972 proteins were identified, of which 3296 are from Jr and 676 from Xaj. Proteins with differential abundance include oxidoreductases, proteases, and enzymes involved in energy metabolism and amino acid interconversion pathways. Defense responses and plant hormone biosynthesis were also increased. Xaj proteins detected in infected tissues demonstrate its ability to adapt to the host microenvironment, limiting iron availability, coping with copper toxicity, and maintaining energy and intermediary metabolism. Secreted proteases and extracellular secretion apparatus such as type IV pilus for twitching motility and type III secretion effectors indicate putative factors recognized by the host. Taken together, these results suggest intense degradation processes, oxidative stress, and general arrest of the biosynthetic metabolism in infected nuts. Our results provide insights into molecular mechanisms and highlight potential molecular tools for early detection and disease control strategies.
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Affiliation(s)
- Cíntia H. D. Sagawa
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
| | - Renata de A. B. Assis
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil;
| | - Paulo A. Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Davis, CA 95616, USA;
| | - Leandro M. Moreira
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil;
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
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25
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An SQ, Potnis N, Dow M, Vorhölter FJ, He YQ, Becker A, Teper D, Li Y, Wang N, Bleris L, Tang JL. Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiol Rev 2020; 44:1-32. [PMID: 31578554 PMCID: PMC8042644 DOI: 10.1093/femsre/fuz024] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/29/2019] [Indexed: 01/15/2023] Open
Abstract
Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.
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Affiliation(s)
- Shi-Qi An
- National Biofilms Innovation Centre (NBIC), Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn AL36849, USA
| | - Max Dow
- School of Microbiology, Food Science & Technology Building, University College Cork, Cork T12 K8AF, Ireland
| | | | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, Marburg 35032, Germany
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Yi Li
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX75080, USA
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
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26
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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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27
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Perez-Quintero AL, Ortiz-Castro M, Lang JM, Rieux A, Wu G, Liu S, Chapman TA, Chang C, Ziegle J, Peng Z, White FF, Plazas MC, Leach JE, Broders K. Genomic Acquisitions in Emerging Populations of Xanthomonas vasicola pv. vasculorum Infecting Corn in the United States and Argentina. PHYTOPATHOLOGY 2020; 110:1161-1173. [PMID: 32040377 DOI: 10.1094/phyto-03-19-0077-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonas vasicola pv. vasculorum is an emerging bacterial plant pathogen that causes bacterial leaf streak on corn. First described in South Africa in 1949, reports of this pathogen have greatly increased in the past years in South America and in the United States. The rapid spread of this disease in North and South America may be due to more favorable environmental conditions, susceptible hosts and/or genomic changes that favored the spread. To understand whether genetic mechanisms exist behind the recent spread of X. vasicola pv. vasculorum, we used comparative genomics to identify gene acquisitions in X. vasicola pv. vasculorum genomes from the United States and Argentina. We sequenced 41 genomes of X. vasicola pv. vasculorum and the related sorghum-infecting X. vasicola pv. holcicola and performed comparative analyses against all available X. vasicola genomes. Time-measured phylogenetic analyses showed that X. vasicola pv. vasculorum strains from the United States and Argentina are closely related and arose from two introductions to North and South America. Gene content comparisons identified clusters of genes enriched in corn X. vasicola pv. vasculorum that showed evidence of horizontal transfer including one cluster corresponding to a prophage found in all X. vasicola pv. vasculorum strains from the United States and Argentina as well as in X. vasicola pv. holcicola strains. In this work, we explore the genomes of an emerging phytopathogen population as a first step toward identifying genetic changes associated with the emergence. The acquisitions identified may contain virulence determinants or other factors associated with the spread of X. vasicola pv. vasculorum in North and South America and will be the subject of future work.
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Affiliation(s)
- Alvaro L Perez-Quintero
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | - Mary Ortiz-Castro
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | - Jillian M Lang
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | | | - Guangxi Wu
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, U.S.A
| | - Toni A Chapman
- Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | | | | | - Zhao Peng
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Maria Cristina Plazas
- Laboratorio de Fitopatología y Microbiología, Universidad Católica de Córdoba, Ob. Trejo 323, Córdoba, Argentina
| | - Jan E Leach
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | - Kirk Broders
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panamá
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28
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Timilsina S, Potnis N, Newberry EA, Liyanapathiranage P, Iruegas-Bocardo F, White FF, Goss EM, Jones JB. Xanthomonas diversity, virulence and plant-pathogen interactions. Nat Rev Microbiol 2020; 18:415-427. [PMID: 32346148 DOI: 10.1038/s41579-020-0361-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 12/19/2022]
Abstract
Xanthomonas spp. encompass a wide range of plant pathogens that use numerous virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine recent insights into host-pathogen co-evolution, diversity in Xanthomonas populations and host specificity of Xanthomonas spp. that have substantially improved our fundamental understanding of pathogen biology. We emphasize the virulence factors in xanthomonads, such as type III secreted effectors including transcription activator-like effectors, type II secretion systems, diversity resulting in host specificity, evolution of emerging strains, activation of susceptibility genes and strategies of host evasion. We summarize the genomic diversity in several Xanthomonas spp. and implications for disease outbreaks, management strategies and breeding for disease resistance.
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Affiliation(s)
- Sujan Timilsina
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Neha Potnis
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Eric A Newberry
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | | | | | - Frank F White
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Erica M Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Jeffrey B Jones
- Plant Pathology Department, University of Florida, Gainesville, FL, USA.
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29
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Bansal K, Kumar S, Patil PB. Phylogenomic Insights into Diversity and Evolution of Nonpathogenic Xanthomonas Strains Associated with Citrus. mSphere 2020; 5:e00087-20. [PMID: 32295869 PMCID: PMC7160680 DOI: 10.1128/msphere.00087-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/18/2020] [Indexed: 01/24/2023] Open
Abstract
Xanthomonas species are primarily known as a group of phytopathogens infecting diverse plants. Recent molecular studies reveal the existence of potential novel species and strains of Xanthomonas following a nonpathogenic lifestyle. In the present study, we report whole-genome sequences of four nonpathogenic strains from citrus (NPXc). Taxonogenomics revealed the surprising diversity, as each of these three isolates were found to be potential novel species that together form a citrus-associated nonpathogenic Xanthomonas species complex (NPXc complex). Interestingly, this NPXc complex is related to another nonpathogenic species, Xanthomonas sontii, from rice (NPXr). On the other hand, the fourth NPXc isolate was found to be related to nonpathogenic isolates from walnut (NPXw); altogether, they form a potential taxonomic outlier of pathogenic Xanthomonas arboricola species. Furthermore, genomic investigation of well-characterized pathogenicity clusters in NPXc isolates revealed lifestyle-specific gene content dynamics. Primarily, genes essential for virulence (i.e., type 1 secretion system [T1SS], T2SS and its effectors, T3SS and its effectors, T4SS, T6SS, adhesins, and rpf gene cluster) and adaptation (i.e., gum, iron uptake and utilization, xanthomonadin, and two-component systems) were depicted by comparative genomics of a Xanthomonas community comprising diverse lifestyles. Overall, the present analysis confers that nonpathogenic isolates of diverse hosts phylogenomically converge and are evolving in parallel with their pathogenic counterparts. Hence, there is a need to understand the world of nonpathogenic isolates from diverse and economically important hosts. Genomic knowledge and resources of nonpathogenic strains will be invaluable in both basic and applied research of the genus XanthomonasIMPORTANCEXanthomonas citri is one of the top phytopathogenic bacteria and is the causal agent of citrus canker. Interestingly, Xanthomonas is also reported to be associated with healthy citrus plants. The advent of the genomic era enabled us to carry out a detailed evolutionary study of a Xanthomonas community associated with citrus and other plants. Our genome-based investigations have revealed hidden and extreme interstrain diversity of nonpathogenic Xanthomonas strains from citrus plants, warranting further large-scale studies. This indicates an unexplored world of Xanthomonas from healthy citrus plant species that may be coevolving as a species complex with the host, unlike the variant pathogenic species. The knowledge and genomic resources will be valuable in evolutionary studies exploring its hidden potential and management of pathogenic species.
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Affiliation(s)
- Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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30
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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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31
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Martins L, Fernandes C, Albuquerque P, Tavares F. Assessment of Xanthomonas arboricola pv. juglandis Bacterial Load in Infected Walnut Fruits by Quantitative PCR. PLANT DISEASE 2019; 103:2577-2586. [PMID: 31347945 DOI: 10.1094/pdis-12-18-2253-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonas arboricola pv. juglandis is the etiologic agent of important walnut (Juglans regia L.) diseases, causing severe fruit drop and high economic losses in walnut production regions. Rapid diagnostics and knowledge of bacterial virulence fitness are key to hinder disease progression and apply timely phytosanitary measures. This work describes an X. arboricola pv. juglandis-specific real-time quantitative PCR (qPCR) using X. arboricola pv. juglandis-specific DNA markers to quantify the bacterial load in infected walnut plant tissues. Method validation was achieved using calibration curves obtained with serial dilutions of X. arboricola pv. juglandis chromosomal DNA and standard curves obtained from walnut samples spiked with X. arboricola pv. juglandis cells. High correlations (R2 > 0.990 and > 0.995) and low limits of detection (35 chromosomes/qPCR reaction and 2.7 CFU/qPCR reaction) were obtained for both markers considering the calibration and standard curves, respectively. Assessment of qPCR repeatability, reproducibility, and specificity allowed us to demonstrate the reliability and consistency of the method. Furthermore, in planta quantification of X. arboricola pv. juglandis bacterial load using infected walnut fruit samples showed a higher detection resolution compared with standard PCR detection. By allowing quantification of virulence fitness of distinct X. arboricola pv. juglandis strains in planta, the proposed qPCR method may contribute to assertive risk assessment of walnut diseases caused by X. arboricola pv. juglandis and ultimately help to improve phytosanitary practices.
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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, 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, Porto, Portugal
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, Oeiras, Portugal
| | - Pedro Albuquerque
- 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, Porto, Portugal
| | - 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, Porto, Portugal
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32
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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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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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Fernandes C, Blom J, Pothier JF, Tavares F. High-Quality Draft Genome Sequence of Xanthomonas sp. Strain CPBF 424, a Walnut-Pathogenic Strain with Atypical Features. Microbiol Resour Announc 2018; 7:e00921-18. [PMID: 30533728 PMCID: PMC6256435 DOI: 10.1128/mra.00921-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/26/2018] [Indexed: 01/11/2023] Open
Abstract
We report here the draft genome sequence of Xanthomonas sp. strain CPBF 424, isolated from a diseased walnut tree. Multilocus sequence analysis showed that this walnut-pathogenic isolate is located between the nonpathogenic X. arboricola and X. prunicola clusters. These features make this strain a promising reference to disclose new genetic determinants of pathogenesis.
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Affiliation(s)
- Camila Fernandes
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Microbial Diversity and Evolution Group, Universidade do Porto, Vairão, Portugal
- Instituto Nacional de Investigação Agrária e Veterinária, Unidade Estratégica de Investigação e Serviços de Sistemas Agrários e Florestais e Sanidade Vegetal, Oeiras, Portugal
- Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for 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, Microbial Diversity and Evolution Group, Universidade do Porto, Vairão, Portugal
- Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
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Fernandes C, Blom J, Pothier JF, Tavares F. High-Quality Draft Genome Sequence of Xanthomonas arboricola pv. juglandis CPBF 1521, Isolated from Leaves of a Symptomatic Walnut Tree in Portugal without a Past of Phytosanitary Treatment. Microbiol Resour Announc 2018; 7:e00887-18. [PMID: 30533738 PMCID: PMC6256574 DOI: 10.1128/mra.00887-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/02/2018] [Indexed: 01/30/2023] Open
Abstract
Here, we report the draft genome sequence of Xanthomonas arboricola pv. juglandis CPBF 1521, isolated from symptomatic leaves of an ornamental walnut in a public site in Portugal without any record of phytosanitary treatment. This isolate may constitute a genomic reference of a wild-type strain in comparative genomics studies.
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Affiliation(s)
- Camila Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Microbial Diversity and Evolution Group, Universidade do Porto, Vairão, Portugal
- Unidade Estratégica de Investigação e Serviços de Sistemas Agrários e Florestais e Sanidade Vegetal, Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, Portugal
- Faculdade de Ciências, Departmento de Biologia, Universidade do Porto, Porto, Portugal
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for 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, Microbial Diversity and Evolution Group, Universidade do Porto, Vairão, Portugal
- Faculdade de Ciências, Departmento de Biologia, Universidade do Porto, Porto, Portugal
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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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Firrao G, Torelli E, Polano C, Ferrante P, Ferrini F, Martini M, Marcelletti S, Scortichini M, Ermacora P. Genomic Structural Variations Affecting Virulence During Clonal Expansion of Pseudomonas syringae pv. actinidiae Biovar 3 in Europe. Front Microbiol 2018; 9:656. [PMID: 29675009 PMCID: PMC5895724 DOI: 10.3389/fmicb.2018.00656] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/20/2018] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa) biovar 3 caused pandemic bacterial canker of Actinidia chinensis and Actinidia deliciosa since 2008. In Europe, the disease spread rapidly in the kiwifruit cultivation areas from a single introduction. In this study, we investigated the genomic diversity of Psa biovar 3 strains during the primary clonal expansion in Europe using single molecule real-time (SMRT), Illumina and Sanger sequencing technologies. We recorded evidences of frequent mobilization and loss of transposon Tn6212, large chromosome inversions, and ectopic integration of IS sequences (remarkably ISPsy31, ISPsy36, and ISPsy37). While no phenotype change associated with Tn6212 mobilization could be detected, strains CRAFRU 12.29 and CRAFRU 12.50 did not elicit the hypersensitivity response (HR) on tobacco and eggplant leaves and were limited in their growth in kiwifruit leaves due to insertion of ISPsy31 and ISPsy36 in the hrpS and hrpR genes, respectively, interrupting the hrp cluster. Both strains had been isolated from symptomatic plants, suggesting coexistence of variant strains with reduced virulence together with virulent strains in mixed populations. The structural differences caused by rearrangements of self-genetic elements within European and New Zealand strains were comparable in number and type to those occurring among the European strains, in contrast with the significant difference in terms of nucleotide polymorphisms. We hypothesize a relaxation, during clonal expansion, of the selection limiting the accumulation of deleterious mutations associated with genome structural variation due to transposition of mobile elements. This consideration may be relevant when evaluating strategies to be adopted for epidemics management.
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Affiliation(s)
- Giuseppe Firrao
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy.,Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy
| | - Emanuela Torelli
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Cesare Polano
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Patrizia Ferrante
- Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Research Centre for Olive, Fruit Trees and Citrus, Rome, Italy
| | - Francesca Ferrini
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Marta Martini
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Simone Marcelletti
- Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Research Centre for Olive, Fruit Trees and Citrus, Rome, Italy
| | - Marco Scortichini
- Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Research Centre for Olive, Fruit Trees and Citrus, Rome, Italy
| | - Paolo Ermacora
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
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Saijo Y, Loo EPI, Yasuda S. Pattern recognition receptors and signaling in plant-microbe interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:592-613. [PMID: 29266555 DOI: 10.1111/tpj.13808] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/09/2017] [Accepted: 12/14/2017] [Indexed: 05/20/2023]
Abstract
Plants solely rely on innate immunity of each individual cell to deal with a diversity of microbes in the environment. Extracellular recognition of microbe- and host damage-associated molecular patterns leads to the first layer of inducible defenses, termed pattern-triggered immunity (PTI). In plants, pattern recognition receptors (PRRs) described to date are all membrane-associated receptor-like kinases or receptor-like proteins, reflecting the prevalence of apoplastic colonization of plant-infecting microbes. An increasing inventory of elicitor-active patterns and PRRs indicates that a large number of them are limited to a certain range of plant groups/species, pointing to dynamic and convergent evolution of pattern recognition specificities. In addition to common molecular principles of PRR signaling, recent studies have revealed substantial diversification between PRRs in their functions and regulatory mechanisms. This serves to confer robustness and plasticity to the whole PTI system in natural infections, wherein different PRRs are simultaneously engaged and faced with microbial assaults. We review the functional significance and molecular basis of PRR-mediated pathogen recognition and disease resistance, and also an emerging role for PRRs in homeostatic association with beneficial or commensal microbes.
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Affiliation(s)
- Yusuke Saijo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Eliza Po-Iian Loo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Shigetaka Yasuda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
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The Prevalence of Helicobacter pylori Virulence Related Genes (hpa and babA2) in Iranian Patients with Gastrointestinal Disorders. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.60947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Santana MM, Gonzalez JM, Cruz C. Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis. Front Microbiol 2017; 8:1947. [PMID: 29067010 PMCID: PMC5641340 DOI: 10.3389/fmicb.2017.01947] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/22/2017] [Indexed: 01/08/2023] Open
Abstract
Many publications highlight the importance of nitric oxide (NO) in plant–bacteria interactions, either in the promotion of health and plant growth or in pathogenesis. However, the role of NO in the signaling between bacteria and plants and in the fate of their interaction, as well as the reconstruction of their interactive evolution, remains largely unknown. Despite the complexity of the evolution of life on Earth, we explore the hypothesis that denitrification and aerobic respiration were responsible for local NO accumulation, which triggered primordial antagonistic biotic interactions, namely the first phytopathogenic interactions. N-oxides, including NO, could globally accumulate via lightning synthesis in the early anoxic ocean and constitute pools for the evolution of denitrification, considered an early step of the biological nitrogen cycle. Interestingly, a common evolution may be proposed for components of denitrification and aerobic respiration pathways, namely for NO and oxygen reductases, a theory compatible with the presence of low amounts of oxygen before the great oxygenation event (GOE), which was generated by Cyanobacteria. During GOE, the increase in oxygen caused the decrease of Earth’s temperature and the consequent increase of oxygen dissolution and availability, making aerobic respiration an increasingly dominant trait of the expanding mesophilic lifestyle. Horizontal gene transfer was certainly important in the joint expansion of mesophily and aerobic respiration. First denitrification steps lead to NO formation through nitrite reductase activity, and NO may further accumulate when oxygen binds NO reductase, resulting in denitrification blockage. The consequent transient NO surplus in an oxic niche could have been a key factor for a successful outcome of an early denitrifying prokaryote able to scavenge oxygen by NO/oxygen reductase or by an independent heterotrophic aerobic respiration pathway. In fact, NO surplus could result in toxicity causing “the first disease” in oxygen-producing Cyanobacteria. We inspected in bacteria the presence of sequences similar to the NO-producing nitrite reductase nirS gene of Thermus thermophilus, an extreme thermophilic aerobe of the Thermus/Deinococcus group, which constitutes an ancient lineage related to Cyanobacteria. In silico analysis revealed the relationship between the presence of nirS genes and phytopathogenicity in Gram-negative bacteria.
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Affiliation(s)
- Margarida M Santana
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Juan M Gonzalez
- Instituto de Recursos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Cristina Cruz
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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41
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Merda D, Briand M, Bosis E, Rousseau C, Portier P, Barret M, Jacques MA, Fischer-Le Saux M. Ancestral acquisitions, gene flow and multiple evolutionary trajectories of the type three secretion system and effectors in Xanthomonas plant pathogens. Mol Ecol 2017; 26:5939-5952. [PMID: 28869687 PMCID: PMC7168496 DOI: 10.1111/mec.14343] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/03/2017] [Accepted: 08/05/2017] [Indexed: 12/13/2022]
Abstract
Deciphering the evolutionary history and transmission patterns of virulence determinants is necessary to understand the emergence of novel pathogens. The main virulence determinant of most pathogenic proteobacteria is the type three secretion system (T3SS). The Xanthomonas genus includes bacteria responsible for numerous epidemics in agroecosystems worldwide and represents a major threat to plant health. The main virulence factor of Xanthomonas is the Hrp2 family T3SS; however, this system is not conserved in all strains and it has not been previously determined whether the distribution of T3SS in this bacterial genus has resulted from losses or independent acquisitions. Based on comparative genomics of 82 genome sequences representing the diversity of the genus, we have inferred three ancestral acquisitions of the Hrp2 cluster during Xanthomonas evolution followed by subsequent losses in some commensal strains and re‐acquisition in some species. While mutation was the main force driving polymorphism at the gene level, interspecies homologous recombination of large fragments expanding through several genes shaped Hrp2 cluster polymorphism. Horizontal gene transfer of the entire Hrp2 cluster also occurred. A reduced core effectome composed of xopF1, xopM, avrBs2 and xopR was identified that may allow commensal strains overcoming plant basal immunity. In contrast, stepwise accumulation of numerous type 3 effector genes was shown in successful pathogens responsible for epidemics. Our data suggest that capacity to intimately interact with plants through T3SS would be an ancestral trait of xanthomonads. Since its acquisition, T3SS has experienced a highly dynamic evolutionary history characterized by intense gene flux between species that may reflect its role in host adaptation.
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Affiliation(s)
- Déborah Merda
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Martial Briand
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College, Karmiel, Israel
| | - Céline Rousseau
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Perrine Portier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Matthieu Barret
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
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Ruh M, Briand M, Bonneau S, Jacques MA, Chen NWG. Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors. BMC Genomics 2017; 18:670. [PMID: 28854875 PMCID: PMC5577687 DOI: 10.1186/s12864-017-4087-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/24/2017] [Indexed: 12/25/2022] Open
Abstract
Background Common bacterial blight is a devastating bacterial disease of common bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause similar symptoms on common bean, suggesting that they have acquired common genetic determinants of adaptation to common bean. Transcription Activator-Like (TAL) effectors are bacterial type III effectors that are able to induce the expression of host genes to promote infection or resistance. Their capacity to bind to a specific host DNA sequence suggests that they are potential candidates for host adaption. Results To study the diversity of tal genes from Xanthomonas strains responsible for common bacterial blight of bean, whole genome sequences of 17 strains representing the diversity of X. citri pv. fuscans and X. phaseoli pv. phaseoli were obtained by single molecule real time sequencing. Analysis of these genomes revealed the existence of four tal genes named tal23A, tal20F, tal18G and tal18H, respectively. While tal20F and tal18G were chromosomic, tal23A and tal18H were carried on plasmids and shared between phylogenetically distant strains, therefore suggesting recent horizontal transfers of these genes between X. citri pv. fuscans and X. phaseoli pv. phaseoli strains. Strikingly, tal23A was present in all strains studied, suggesting that it played an important role in adaptation to common bean. In silico predictions of TAL effectors targets in the common bean genome suggested that TAL effectors shared by X. citri pv. fuscans and X. phaseoli pv. phaseoli strains target the promoters of genes of similar functions. This could be a trace of convergent evolution among TAL effectors from different phylogenetic groups, and comforts the hypothesis that TAL effectors have been implied in the adaptation to common bean. Conclusions Altogether, our results favour a model where plasmidic TAL effectors are able to contribute to host adaptation by being horizontally transferred between distant lineages. Electronic supplementary material The online version of this article (10.1186/s12864-017-4087-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mylène Ruh
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France.
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Vicente JG, Rothwell S, Holub EB, Studholme DJ. Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida. Int J Syst Evol Microbiol 2017; 67:3645-3654. [PMID: 28840805 DOI: 10.1099/ijsem.0.002189] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe two new species of the genus Xanthomonas, represented by yellow mucoid bacterial strains isolated from diseased leaves of watercress (Nasturtium officinale) produced in Florida, USA. One strain was pathogenic on watercress, but not in other species including a range of brassicas; other strains were not pathogenic in any of the tested plants. Data from Biolog carbon source utilization tests and nucleotide sequence data from 16S and gyrB loci suggested that both pathogenic and non-pathogenic strains were related to, yet distinct from, previously described Xanthomonas species. Multilocus sequence analysis and whole genome-wide comparisons of the average nucleotide identity (ANI) of genomes of two strains from watercress showed that these are distinct and share less than 95 % ANI with all other known species; the non-pathogenic strain WHRI 8848 is close to Xanthomonascassavae (ANI of 93.72 %) whilst the pathogenic strain WHRI 8853 is close to a large clade of species that includes Xanthomonasvesicatoria (ANI ≤90.25 %). Based on these results, we propose that both strains represent new Xanthomonas species named Xanthomonas floridensis sp. nov. (type strain WHRI 8848=ATCC TSD-60=ICMP 21312=LMG 29665=NCPPB 4601) and Xanthomonas nasturtii sp. nov. (type strain WHRI 8853=ATCC TSD-61=ICMP 21313=LMG 29666=NCPPB 4600), respectively. The presence of non-pathogenic Xanthomonas strains in watercress and their interaction with pathogenic strains needs to be further investigated. Although the importance of the new pathogenic species is yet to be determined, the bacterial disease that it causes constitutes a threat to watercress production and its distribution should be monitored.
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Affiliation(s)
- Joana G Vicente
- School of Life Sciences, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
| | - Steve Rothwell
- Vitacress Ltd, Lower Link Farm, St. Mary Bourne, Andover, Hampshire SP11 6DB, UK
| | - Eric B Holub
- School of Life Sciences, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
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Hacquard S, Spaepen S, Garrido-Oter R, Schulze-Lefert P. Interplay Between Innate Immunity and the Plant Microbiota. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:565-589. [PMID: 28645232 DOI: 10.1146/annurev-phyto-080516-035623] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.
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Affiliation(s)
- Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Stijn Spaepen
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Ruben Garrido-Oter
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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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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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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Richard D, Ravigné V, Rieux A, Facon B, Boyer C, Boyer K, Grygiel P, Javegny S, Terville M, Canteros BI, Robène I, Vernière C, Chabirand A, Pruvost O, Lefeuvre P. Adaptation of genetically monomorphic bacteria: evolution of copper resistance through multiple horizontal gene transfers of complex and versatile mobile genetic elements. Mol Ecol 2017; 26:2131-2149. [PMID: 28101896 DOI: 10.1111/mec.14007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 11/28/2016] [Accepted: 12/08/2016] [Indexed: 12/17/2022]
Abstract
Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper-resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons. In order to investigate this pattern more closely, we sequenced six copper-resistant X. citri pv. citri strains from Argentina, Martinique and Réunion, together with reference copper-resistant Xanthomonas and Stenotrophomonas strains using long-read sequencing technology. Genes involved in copper resistance were found to be strain dependent with the novel identification in X. citri pv. citri of copABCD and a cus heavy metal efflux resistance-nodulation-division system. The genes providing the adaptive trait were part of a mobile genetic element similar to Tn3-like transposons and included in a conjugative plasmid. This indicates the system's great versatility. The mining of all available bacterial genomes suggested that, within the bacterial community, the spread of copper resistance associated with mobile elements and their plasmid environments was primarily restricted to the Xanthomonadaceae family.
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Affiliation(s)
- D Richard
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France.,Plant Health Laboratory, ANSES, F-97410, St Pierre, Réunion, France.,Université de la Réunion, UMR PVBMT, F-97490, St Denis, Réunion, France
| | - V Ravigné
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - A Rieux
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - B Facon
- INRA, UMR PVBMT, F-97410, St Pierre, Réunion, France.,INRA, UMR CBGP, F-34090, Montpellier, France
| | - C Boyer
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - K Boyer
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - P Grygiel
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - S Javegny
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - M Terville
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - B I Canteros
- INTA, Estación Experimental Agropecuaria Bella Vista, Bella Vista, Argentina
| | - I Robène
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - C Vernière
- CIRAD, UMR BGPI, F-34398, Montpellier, France
| | - A Chabirand
- Plant Health Laboratory, ANSES, F-97410, St Pierre, Réunion, France
| | - O Pruvost
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - P Lefeuvre
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
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48
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Noroy C, Meyer DF. Comparative Genomics of the Zoonotic Pathogen Ehrlichia chaffeensis Reveals Candidate Type IV Effectors and Putative Host Cell Targets. Front Cell Infect Microbiol 2017; 6:204. [PMID: 28180111 PMCID: PMC5263134 DOI: 10.3389/fcimb.2016.00204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 12/21/2016] [Indexed: 12/04/2022] Open
Abstract
During infection, some intracellular pathogenic bacteria use a dedicated multiprotein complex known as the type IV secretion system to deliver type IV effector (T4E) proteins inside the host cell. These T4Es allow the bacteria to evade host defenses and to subvert host cell processes to their own advantage. Ehrlichia chaffeensis is a tick-transmitted obligate intracellular pathogenic bacterium, which causes human monocytic ehrlichiosis. Using comparative whole genome analysis, we identified the relationship between eight available E. chaffeensis genomes isolated from humans and show that these genomes are highly conserved. We identified the candidate core type IV effectome of E. chaffeensis and some conserved intracellular adaptive strategies. We assigned the West Paces strain to genetic group II and predicted the repertoires of T4Es encoded by E. chaffeensis genomes, as well as some putative host cell targets. We demonstrated that predicted T4Es are preferentially distributed in gene sparse regions of the genome. In addition to the identification of the two known type IV effectors of Anaplasmataceae, we identified two novel candidates T4Es, ECHLIB_RS02720 and ECHLIB_RS04640, which are not present in all E. chaffeensis strains and could explain some variations in inter-strain virulence. We also identified another novel candidate T4E, ECHLIB_RS02720, a hypothetical protein exhibiting EPIYA, and NLS domains as well as a classical type IV secretion signal, suggesting an important role inside the host cell. Overall, our results agree with current knowledge of Ehrlichia molecular pathogenesis, and reveal novel candidate T4Es that require experimental validation. This work demonstrates that comparative effectomics enables identification of important host pathways targeted by the bacterial pathogen. Our study, which focuses on the type IV effector repertoires among several strains of E. chaffeensis species, is an original approach and provides rational putative targets for the design of alternative therapeutics against intracellular pathogens. The collection of putative effectors of E. chaffeensis described in our paper could serve as a roadmap for future studies of the function and evolution of effectors.
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Affiliation(s)
- Christophe Noroy
- CIRAD, UMR ASTREGuadeloupe, France; INRA, UMR 1309 ASTREMontpellier, France; Université des AntillesGuadeloupe, France
| | - Damien F Meyer
- CIRAD, UMR ASTREGuadeloupe, France; INRA, UMR 1309 ASTREMontpellier, France
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Draft Genome Sequence of Two Strains of Xanthomonas arboricola Isolated from Prunus persica Which Are Dissimilar to Strains That Cause Bacterial Spot Disease on Prunus spp. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00974-16. [PMID: 27609931 PMCID: PMC5017236 DOI: 10.1128/genomea.00974-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The draft genome sequences of two strains of Xanthomonas arboricola, isolated from asymptomatic peach trees in Spain, are reported here. These strains are avirulent and do not belong to the same phylogroup as X. arboricola pv. pruni, a causal agent of bacterial spot disease of stone fruits and almonds.
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Comparative Genomic and Phenotypic Characterization of Pathogenic and Non-Pathogenic Strains of Xanthomonas arboricola Reveals Insights into the Infection Process of Bacterial Spot Disease of Stone Fruits. PLoS One 2016; 11:e0161977. [PMID: 27571391 PMCID: PMC5003339 DOI: 10.1371/journal.pone.0161977] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/15/2016] [Indexed: 02/07/2023] Open
Abstract
Xanthomonas arboricola pv. pruni is the causal agent of bacterial spot disease of stone fruits, a quarantinable pathogen in several areas worldwide, including the European Union. In order to develop efficient control methods for this disease, it is necessary to improve the understanding of the key determinants associated with host restriction, colonization and the development of pathogenesis. After an initial characterization, by multilocus sequence analysis, of 15 strains of X. arboricola isolated from Prunus, one strain did not group into the pathovar pruni or into other pathovars of this species and therefore it was identified and defined as a X. arboricola pv. pruni look-a-like. This non-pathogenic strain and two typical strains of X. arboricola pv. pruni were selected for a whole genome and phenotype comparative analysis in features associated with the pathogenesis process in Xanthomonas. Comparative analysis among these bacterial strains isolated from Prunus spp. and the inclusion of 15 publicly available genome sequences from other pathogenic and non-pathogenic strains of X. arboricola revealed variations in the phenotype associated with variations in the profiles of TonB-dependent transporters, sensors of the two-component regulatory system, methyl accepting chemotaxis proteins, components of the flagella and the type IV pilus, as well as in the repertoire of cell-wall degrading enzymes and the components of the type III secretion system and related effectors. These variations provide a global overview of those mechanisms that could be associated with the development of bacterial spot disease. Additionally, it pointed out some features that might influence the host specificity and the variable virulence observed in X. arboricola.
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