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Zerbo KBF, Yameogo F, Wonni I, Somda I. Analysis of the Genetic Variation and Geographic Distribution Patterns of Xanthomonas citri pv. citri Strains in Citrus Production in Burkina Faso. PHYTOPATHOLOGY 2024:PHYTO04240121R. [PMID: 38829919 DOI: 10.1094/phyto-04-24-0121-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
It is essential to have a thorough knowledge of the genetic variation among different strains of Xanthomonas citri pv. citri, which is responsible for causing citrus bacterial canker. This understanding is important for studying disease characteristics, population structure, and evolution and ultimately for developing sustainable methods of control. A total of 48 strains obtained from citrus production areas in Burkina Faso in 2012, 2020, and 2021 were subjected to Polymerase Chain reaction (PCR) tests using specific primers. The aim was to examine the distribution of type 3 effectors and determine the geographical origins of the strains. The examination of the distribution of type 3 non-transcription-activator-like effectors (TALEs) revealed a broader range of strains obtained in 2020 and 2021 than in 2012. However, all the strains possessed a shared set of three genes, specifically, XopE2, XopN, and AvrBs2. Furthermore, all examined effectors were observed in the Bobo-Dioulasso region. Regarding the characterization of TALEs, two profiles containing two to three TALEs were discovered. Profile 1, consisting of two TALEs, was found in 37 X. citri pv. citri strains, whereas Profile 2, comprising three TALEs, was detected in 11 strains. Among the three TALEs (A, B, and C) that were identified, TALEs B and C were present in all the strains. The correlation matrix indicated a positive association between the type 3 effector content of strains and the duration of their isolation. Principal component analysis revealed a limited organization of the strains under investigation. [Formula: see text] Copyright © 2024 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)
- Kevin Ben Fabrice Zerbo
- Centre National de la Recherche Scientifique et Technologique/Institut de l'Environnement et de Recherches Agricoles (INERA)/Laboratoire Mixte International/Observatoire des Agents Pathogènes, Biosécurité et Biodiversité (LMI PathoBios), 01 BP 910, Bobo-Dioulasso, Burkina Faso
- Université Nazi BONI/Clinique des Plantes, 01 BP1091, Bobo-Dioulasso, Burkina Faso
| | - Florence Yameogo
- Centre National de la Recherche Scientifique et Technologique/Institut de l'Environnement et de Recherches Agricoles (INERA)/Laboratoire Mixte International/Observatoire des Agents Pathogènes, Biosécurité et Biodiversité (LMI PathoBios), 01 BP 910, Bobo-Dioulasso, Burkina Faso
- Université Nazi BONI/Clinique des Plantes, 01 BP1091, Bobo-Dioulasso, Burkina Faso
| | - Issa Wonni
- Centre National de la Recherche Scientifique et Technologique/Institut de l'Environnement et de Recherches Agricoles (INERA)/Laboratoire Mixte International/Observatoire des Agents Pathogènes, Biosécurité et Biodiversité (LMI PathoBios), 01 BP 910, Bobo-Dioulasso, Burkina Faso
| | - Irénée Somda
- Université Nazi BONI/Clinique des Plantes, 01 BP1091, Bobo-Dioulasso, Burkina Faso
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Haghshenas I, Taghavi SM, Zarei S, Osdaghi E. Molecular-Phylogenetic Characterization of Xanthomonas hortorum pv. pelargonii Strains Causing Leaf Spot of Geraniums in Iran. PLANT DISEASE 2024:PDIS01240262RE. [PMID: 38595058 DOI: 10.1094/pdis-01-24-0262-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Bacterial blight and leaf spot of geraniums is a destructive disease of cultivated Pelargonium species around the world. During 2020 to 2021, surveys were conducted in seven geranium-growing provinces of Iran to monitor the status of bacterial blight and leaf spot disease. The disease was observed in six surveyed provinces varying in the extent of occurrence and severity. Twenty-two gram-negative pale-yellow bacterial strains resembling members of Xanthomonas were isolated from symptomatic leaves and stems. Pathogenicity and host range assays showed that the bacterial strains were pathogenic on Pelargonium grandiflorum, P. graveolens, P. peltatum, and P. zonale. All strains were positive for a PCR test using the primer pair XcpM1/XcpM2, which is specific for X. hortorum pv. pelargonii. Phylogenetic analysis using the sequences of gyrB and lepA genes showed that the 22 strains clustered in a clade among the sequences of X. hortorum pv. pelargonii strains retrieved from GenBank but were distinct from the other pathovars of X. hortorum. BOX-PCR-based fingerprinting using BOX-A1R primer revealed that the strains isolated in this study were grouped into two clusters, while no distinct correlation was observed between the host/area of isolation and BOX-PCR fingerprinting. None of the strains obtained in this study nor the reference strain of the pathogen produced bacteriocin against each other. Results obtained in this study shed light on the geographic distribution, taxonomic status, and host range of the bacterial blight and leaf spot pathogen of geraniums in Iran, paving the path for further research on disease management.
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Affiliation(s)
- Iman Haghshenas
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Sadegh Zarei
- Department of Plant Protection, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
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Monnens TQ, Roux B, Cunnac S, Charbit E, Carrère S, Lauber E, Jardinaud MF, Darrasse A, Arlat M, Szurek B, Pruvost O, Jacques MA, Gagnevin L, Koebnik R, Noël LD, Boulanger A. Comparative transcriptomics reveals a highly polymorphic Xanthomonas HrpG virulence regulon. BMC Genomics 2024; 25:777. [PMID: 39123115 PMCID: PMC11316434 DOI: 10.1186/s12864-024-10684-6] [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: 05/21/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Bacteria of the genus Xanthomonas cause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretion system (T3SS), a process regulated by the master response regulator HrpG. Although HrpG has been studied for over two decades, its regulon across diverse Xanthomonas species, particularly beyond type III secretion, remains understudied. RESULTS In this study, we conducted transcriptome sequencing to explore the HrpG regulons of 17 Xanthomonas strains, encompassing six species and nine pathovars, each exhibiting distinct host and tissue specificities. We employed constitutive expression of plasmid-borne hrpG*, which encodes a constitutively active form of HrpG, to induce the regulon. Our findings reveal substantial inter- and intra-specific diversity in the HrpG* regulons across the strains. Besides 21 genes directly involved in the biosynthesis of the T3SS, the core HrpG* regulon is limited to only five additional genes encoding the transcriptional activator HrpX, the two T3E proteins XopR and XopL, a major facility superfamily (MFS) transporter, and the phosphatase PhoC. Interestingly, genes involved in chemotaxis and genes encoding enzymes with carbohydrate-active and proteolytic activities are variably regulated by HrpG*. CONCLUSIONS The diversity in the HrpG* regulon suggests that HrpG-dependent virulence in Xanthomonas might be achieved through several distinct strain-specific strategies, potentially reflecting adaptation to diverse ecological niches. These findings enhance our understanding of the complex role of HrpG in regulating various virulence and adaptive pathways, extending beyond T3Es and the T3SS.
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Affiliation(s)
- Thomas Quiroz Monnens
- LIPME, INRAE/CNRS UMR 0441/2594, Université de Toulouse, Université Paul Sabatier Toulouse 3, UMR, Castanet-Tolosan, 31320, France
| | - Brice Roux
- LIPME, INRAE/CNRS UMR 0441/2594, Université de Toulouse, Université Paul Sabatier Toulouse 3, UMR, Castanet-Tolosan, 31320, France
| | - Sébastien Cunnac
- PHIM, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Erika Charbit
- Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, F-49000, France
| | - Sébastien Carrère
- LIPME, INRAE/CNRS UMR 0441/2594, Université de Toulouse, Université Paul Sabatier Toulouse 3, UMR, Castanet-Tolosan, 31320, France
| | - Emmanuelle Lauber
- LIPME, INRAE/CNRS UMR 0441/2594, Université de Toulouse, Université Paul Sabatier Toulouse 3, UMR, Castanet-Tolosan, 31320, France
| | - Marie-Françoise Jardinaud
- LIPME, INRAE/CNRS UMR 0441/2594, Université de Toulouse, Université Paul Sabatier Toulouse 3, UMR, Castanet-Tolosan, 31320, France
| | - Armelle Darrasse
- Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, F-49000, France
| | - Matthieu Arlat
- LIPME, INRAE/CNRS UMR 0441/2594, Université de Toulouse, Université Paul Sabatier Toulouse 3, UMR, Castanet-Tolosan, 31320, France
| | - Boris Szurek
- PHIM, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Marie-Agnès Jacques
- Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, F-49000, France
| | - Lionel Gagnevin
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, F-97410, France
- PHIM, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, F-34398, France
| | - Ralf Koebnik
- PHIM, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Laurent D Noël
- LIPME, INRAE/CNRS UMR 0441/2594, Université de Toulouse, Université Paul Sabatier Toulouse 3, UMR, Castanet-Tolosan, 31320, France.
| | - Alice Boulanger
- LIPME, INRAE/CNRS UMR 0441/2594, Université de Toulouse, Université Paul Sabatier Toulouse 3, UMR, Castanet-Tolosan, 31320, France.
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Chuang SC, Dobhal S, Pal K, Amore TD, Alvarez AM, Arif M. Xanthomonas Strains Isolated from Hosts in the Family Araceae Reveal Diverse Phylogenetic Relationships and Origins. PHYTOPATHOLOGY 2024; 114:1963-1974. [PMID: 38568984 DOI: 10.1094/phyto-08-23-0265-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The family Araceae, comprising ornamentals including Anthurium, Dieffenbachia, Philodendron, Colocasia, and Zantedeschia, is susceptible to Xanthomonas pathogens. Previous analyses have established heterogeneity in aroid strains, yet unresolved taxonomic positions and dynamics between Xanthomonas and frequently associated Stenotrophomonas in aroids necessitate in-depth genetic investigation to resolve these complex relationships. This study utilized multilocus sequence analysis of housekeeping genes atpD, dnaA, dnaK, gltA, and gyrB to investigate 59 aroid strains, selected based on hosts, time, and geographical origins. After adding sequences from additional strains from NCBI GenBank, analysis of 161 concatenated sequences indicated that all aroid strains fell within Xanthomonas and Stenotrophomonas. Thirty-six strains isolated from Anthurium grouped under X. phaseoli, with outliers including one strain each in X. arboricola and X. sacchari and two in Stenotrophomonas. Six strains from Caladium, Dieffenbachia, and Philodendron formed host-specific subgroups within X. euvesicatoria. One strain from Dieffenbachia aligned with X. campestris, whereas strains from Colocasia, Aglaonema, and Spathiphyllum clustered with X. sacchari. Apart from the zantedeschia strain described as X. arboricola pv. zantedeschiae, two colocasia, one epipremnum, and one anthurium strain joined the X. arboricola group. Overall, this study revealed significant heterogeneity among aroid strains, with anthurium strains clustering closely despite distant geographical origins. The analysis underscores the complexity of host-pathogen specificity within Xanthomonas and emphasizes the need for further taxonomic clarification through whole-genome analysis of representative strains. The findings of this research will facilitate strain selection for inclusivity and exclusivity panels in developing diagnostic assays for X. phaseoli and xanthomonads affecting aroids.
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Affiliation(s)
- Shu-Cheng Chuang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
| | - Kanak Pal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
| | - Teresita D Amore
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
| | - Anne M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
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Okoh EB, Payne M, Lan R, Riegler M, Chapman TA, Bogema DR. A Multilocus Sequence Typing Scheme for Rapid Identification of Xanthomonas citri Based on Whole-Genome Sequencing Data. PHYTOPATHOLOGY 2024; 114:1480-1489. [PMID: 38669587 DOI: 10.1094/phyto-12-23-0490-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Xanthomonas citri is a plant-pathogenic bacterium associated with a diverse range of host plant species. It has undergone substantial reclassification and currently consists of 14 different subspecies or pathovars that are responsible for a wide range of plant diseases. Whole-genome sequencing (WGS) provides a cutting-edge advantage over other diagnostic techniques in epidemiological and evolutionary studies of X. citri because it has a higher discriminatory power and is replicable across laboratories. WGS also allows for the improvement of multilocus sequence typing (MLST) schemes. In this study, we used genome sequences of Xanthomonas isolates from the NCBI RefSeq database to develop a seven-gene MLST scheme that yielded 19 sequence types (STs) that correlated with phylogenetic clades of X. citri subspecies or pathovars. Using this MLST scheme, we examined 2,911 Xanthomonas species assemblies from NCBI GenBank and identified 15 novel STs from 37 isolates that were misclassified in NCBI. In total, we identified 545 X. citri assemblies from GenBank with 95% average nucleotide identity to the X. citri type strain, and all were classified as one of the 34 STs. All MLST classifications correlated with a phylogenetic position inferred from alignments using 92 conserved genes. We observed several instances where strains from different pathovars formed closely related monophyletic clades and shared the same ST, indicating that further investigation of the validity of these pathovars is required. Our MLST scheme described here is a robust tool for rapid classification of X. citri pathovars using WGS and a powerful method for further comprehensive taxonomic revision of X. citri pathovars.
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Affiliation(s)
- Efenaide B Okoh
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Toni A Chapman
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
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McKnight DJE, Wong-Bajracharya J, Okoh EB, Snijders F, Lidbetter F, Webster J, Haughton M, Darling AE, Djordjevic SP, Bogema DR, Chapman TA. Xanthomonas rydalmerensis sp. nov., a non-pathogenic member of Group 1 Xanthomonas. Int J Syst Evol Microbiol 2024; 74:006294. [PMID: 38536071 PMCID: PMC10995728 DOI: 10.1099/ijsem.0.006294] [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: 11/06/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024] Open
Abstract
Five bacterial isolates were isolated from Fragaria × ananassa in 1976 in Rydalmere, Australia, during routine biosecurity surveillance. Initially, the results of biochemical characterisation indicated that these isolates represented members of the genus Xanthomonas. To determine their species, further analysis was conducted using both phenotypic and genotypic approaches. Phenotypic analysis involved using MALDI-TOF MS and BIOLOG GEN III microplates, which confirmed that the isolates represented members of the genus Xanthomonas but did not allow them to be classified with respect to species. Genome relatedness indices and the results of extensive phylogenetic analysis confirmed that the isolates were members of the genus Xanthomonas and represented a novel species. On the basis the minimal presence of virulence-associated factors typically found in genomes of members of the genus Xanthomonas, we suggest that these isolates are non-pathogenic. This conclusion was supported by the results of a pathogenicity assay. On the basis of these findings, we propose the name Xanthomonas rydalmerensis, with DAR 34855T = ICMP 24941 as the type strain.
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Affiliation(s)
- Daniel J. E. McKnight
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
| | - Johanna Wong-Bajracharya
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Efenaide B. Okoh
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- Western Sydney University, Penrith, NSW, Australia
| | - Fridtjof Snijders
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Fiona Lidbetter
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - John Webster
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Mathew Haughton
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Aaron E. Darling
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
| | | | - Daniel R. Bogema
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
| | - Toni A. Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
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Qiu Y, Wei F, Meng H, Peng M, Zhang J, He Y, Wei L, Ahmed W, Ji G. Whole-genome sequencing and comparative genome analysis of Xanthomonas fragariae YM2 causing angular leaf spot disease in strawberry. FRONTIERS IN PLANT SCIENCE 2023; 14:1267132. [PMID: 38192696 PMCID: PMC10773614 DOI: 10.3389/fpls.2023.1267132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024]
Abstract
Background Angular leaf spot disease caused by plant pathogenic bacterium Xanthomonas fragariae seriously threatens strawberry crop production globally. Methods In this study, we sequenced the whole genome of X. fragariae YM2, isolated from Yunnan Province, China. In addition, we performed a comparative genome analysis of X. fragariae YM2 with two existing strains of X. fragariae YL19 and SHQP01 isolated from Liaoning and Shanghai, respectively. Results The results of Nanopore sequencing showed that X. fragariae YM2 comprises one single chromosome with a contig size of 4,263,697 bp, one plasmid contig size of 0.39 Mb, a GC content ratio of 62.27%, and 3,958 predicted coding genes. The genome of YM2 comprises gum, hrp, rpf, and xps gene clusters and lipopolysaccharide (LPS), which are typical virulence factors in Xanthomonas species. By performing a comparative genomic analysis between X. fragariae strains YM2, YL19, and SHQP01, we found that strain YM2 is similar to YL19 and SHQP01 regarding genome size and GC contents. However, there are minor differences in the composition of major virulence factors and homologous gene clusters. Furthermore, the results of collinearity analysis demonstrated that YM2 has lower similarity and longer evolutionary distance with YL19 and SHQP01, but YL19 is more closely related to SHQP01. Conclusions The availability of this high-quality genetic resource will serve as a basic tool for investigating the biology, molecular pathogenesis, and virulence of X. fragariae YM2. In addition, unraveling the potential vulnerabilities in its genetic makeup will aid in developing more effective disease suppression control measures.
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Affiliation(s)
- Yue Qiu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Agriculture, Anshun University, Anshun, Guizhou, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Fangjun Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Han Meng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Menglin Peng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jinhao Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yilu He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lanfang Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Agricultural Foundation Experiment Teaching Center, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Waqar Ahmed
- College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, China
| | - Guanghai Ji
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
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Heiden N, Roman-Reyna V, Curland RD, Dill-Macky R, Jacobs JM. Comparative Genomics of Barley-Infecting Xanthomonas translucens Shows Overall Genetic Similarity but Globally Distributed Virulence Factor Diversity. PHYTOPATHOLOGY 2023; 113:2056-2061. [PMID: 35727947 DOI: 10.1094/phyto-04-22-0113-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Xanthomonas translucens pv. translucens (Xtt) is a global barley patho-gen and a concern for resistance breeding and regulation. Long-read whole genome sequences allow in-depth understanding of pathogen diversity. We have completed long-read PacBio sequencing of two Minnesotan Xtt strains and an in-depth analysis of available Xtt genomes. We found that average nucleotide identity (ANI)-based approaches organize Xtt strains different from the previous standard multilocus sequencing analysis approach. According to ANI, Xtt forms a separate clade from X. translucens pv. undulosa and consists of three main groups which are represented on multiple continents. Some virulence factors, such as 17 Type III-secreted effectors, are highly conserved and offer potential targets for the elicitation of broad resistance. However, there is a high degree of variation in virulence factors, meaning that germplasm should be screened for resistance with a diverse panel of Xtt.
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Affiliation(s)
- Nathaniel Heiden
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
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Hong E, Bankole IA, Zhao B, Shi G, Buck JW, Feng J, Curland RD, Baldwin T, Chapara V, Liu Z. DNA Markers, Pathogenicity Test, and Multilocus Sequence Analysis to Differentiate and Characterize Cereal-Specific Xanthomonas translucens Strains. PHYTOPATHOLOGY 2023; 113:2062-2072. [PMID: 37551962 DOI: 10.1094/phyto-10-22-0381-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Xanthomonas translucens contains a group of bacterial pathogens that are closely related and have been divided into several pathovars based on their host range. X. translucens pv. undulosa (Xtu) and X. translucens pv. translucens (Xtt) are two important pathovars that cause bacterial leaf streak disease on wheat and barley, respectively. In this study, DNA markers were developed to differentiate Xtu and Xtt and were then used to characterize a collection of X. translucens strains with diverse origins, followed by confirmation and characterization with pathogenicity tests and multilocus sequence analysis/typing (MLSA/MLST). We first developed cleaved amplified polymorphic sequence markers based on the single-nucleotide polymorphisms within a cereal pathovar-specific DNA sequence. In addition, two Xtt-specific markers, designated Xtt-XopM and Xtt-SP1, were developed from comparative genomics among the sequenced Xtt/Xtu genomes. Using the developed markers, a collection of X. translucens strains were successfully identified as Xtu or Xtt. Pathogenicity tests on wheat and barley plants and MLSA of four housekeeping genes validated the pathovar assignation of those strains. Furthermore, MLSA revealed distinct subclades within both Xtu and Xtt groups. Seven and three sequence types were identified from MLST for Xtu and Xtt strains, respectively. The establishment of efficient Xtt/Xtu differentiation methods and characterization of those strains will be useful in studying disease epidemiology and host-pathogen interactions and breeding programs when screening for sources of resistance for these two important bacterial pathogens.
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Affiliation(s)
- Eunhye Hong
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Ibukunoluwa A Bankole
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Bin Zhao
- Department of Statistics, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - James W Buck
- Department of Plant Pathology, University of Georgia, Griffin, GA 30223, U.S.A
| | - Jie Feng
- Alberta Plant Health Lab, Crop Diversification Centre North, AAFRED, Edmonton, AB, T5Y 6H3, Canada
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Thomas Baldwin
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Venkata Chapara
- Langdon Research Extension Center, ND Agricultural Experimental Station, Langdon, ND 58249, U.S.A
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
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10
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González-Tobón J, Helmann TC, Daughtrey M, Stodghill PV, Filiatrault MJ. Complete Genome Sequence Resource for Xanthomonas hortorum Isolated from Greek Oregano. PLANT DISEASE 2023; 107:3259-3263. [PMID: 37833832 DOI: 10.1094/pdis-10-22-2399-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
In spring 2019, necrotic leaf spots were detected on Greek oregano (Origanum vulgare var. hirtum) plants in a commercial greenhouse operation. An isolate was recovered from the diseased plants. Partial 16S ribosomal RNA sequencing and multilocus sequence analysis revealed that the isolate was a Xanthomonas sp. but proved insufficient to identify the species with certainty. Therefore, whole-genome sequencing using both Nanopore and Illumina technologies was performed. Here, we report the complete and annotated genome sequence of Xanthomonas hortorum strain 108, which was originally isolated from Greek oregano in Long Island, NY, U.S.A.
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Affiliation(s)
- Juliana González-Tobón
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Tyler C Helmann
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853
| | - Margery Daughtrey
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Paul V Stodghill
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853
| | - Melanie J Filiatrault
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853
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11
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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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12
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Lee MH, Hong SJ, Park DS, Ham H, Kong HG. Genomic Analysis of the Carrot Bacterial Blight Pathogen Xanthomonas hortorum pv. carotae in Korea. THE PLANT PATHOLOGY JOURNAL 2023; 39:409-416. [PMID: 37550986 PMCID: PMC10412968 DOI: 10.5423/ppj.nt.11.2022.0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 08/09/2023]
Abstract
Bacterial leaf blight of carrots caused by Xanthomonas hortorum pv. carotae (Xhc) is an important worldwide seed-borne disease. In 2012 and 2013, symptoms similar to bacterial leaf blight were found in carrot farms in Jeju Island, Korea. The phenotypic characteristics of the Korean isolation strains were similar to the type strain of Xhc. Pathogenicity showed symptoms on the 14th day after inoculation on carrot plants. Identification by genetic method was multi-position sequencing of the isolated strain JJ2001 was performed using four genes (danK, gyrB, fyuA, and rpoD). The isolated strain was confirmed to be most similar to Xhc M081. Furthermore, in order to analyze the genetic characteristics of the isolated strain, whole genome analysis was performed through the next-generation sequencing method. The draft genome size of JJ2001 is 5,443,372 bp, which contains 63.57% of G + C and has 4,547 open reading frames. Specifically, the classification of pathovar can be confirmed to be similar to that of the host lineage. Plant pathogenic factors and determinants of the majority of the secretion system are conserved in strain JJ2001. This genetic information enables detailed comparative analysis in the pathovar stage of pathogenic bacteria. Furthermore, these findings provide basic data for the distribution and diagnosis of Xanthomonas hortorum pv. carotae, a major plant pathogen that infects carrots in Korea.
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Affiliation(s)
- Mi-Hyun Lee
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875,
Korea
| | - Sung-Jun Hong
- Organic Agricultural Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875,
Korea
| | - Dong Suk Park
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875,
Korea
| | - Hyeonheui Ham
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875,
Korea
| | - Hyun Gi Kong
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875,
Korea
- Department of Plant Medicine, College of Agriculture, Life & Environment Sciences, Chungbuk National University, Cheongju 28644,
Korea
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13
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Agarwal V, Stubits R, Nassrullah Z, Dillon MM. Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks. Front Microbiol 2023; 14:1213261. [PMID: 37476668 PMCID: PMC10356107 DOI: 10.3389/fmicb.2023.1213261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era of next-generation sequencing, thousands of strains from this genus have now been sequenced as part of isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data have not been synthesized and we lack a comprehensive phylogeny for the genus, with some species designations in public databases still relying on phenotypic similarities and representative sequence typing. The extent of genetic cohesiveness among Xanthomonas strains, the distribution of virulence factors across strains, and the impact of evolutionary history on host range across the genus are also poorly understood. In this study, we present a pangenome analysis of 1,910 diverse Xanthomonas genomes, highlighting their evolutionary relationships, the distribution of virulence-associated genes across strains, and rates of horizontal gene transfer. We find a number of broadly conserved classes of virulence factors and considerable diversity in the Type 3 Secretion Systems (T3SSs) and Type 3 Secreted Effector (T3SE) repertoires of different Xanthomonas species. We also use these data to re-assign incorrectly classified strains to phylogenetically informed species designations and find evidence of both monophyletic host specificity and convergent evolution of phylogenetically distant strains to the same host. Finally, we explore the role of recombination in maintaining genetic cohesion within the Xanthomonas genus as a result of both ancestral and recent recombination events. Understanding the evolutionary history of Xanthomonas species and the relationship of key virulence factors with host-specificity provides valuable insight into the mechanisms through which Xanthomonas species shift between hosts and will enable us to develop more robust resistance strategies against these highly virulent pathogens.
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Affiliation(s)
- Viplav Agarwal
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Rachel Stubits
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Zain Nassrullah
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Marcus M. Dillon
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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14
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Whole Genome Sequences of Nine Xanthomonas Strains Responsible for Common Bacterial Blight of Bean. Microbiol Resour Announc 2023; 12:e0125922. [PMID: 36779735 PMCID: PMC10019307 DOI: 10.1128/mra.01259-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
We report the complete and circularized genome sequences of nine strains of Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans, which cause common bacterial blight of bean. These assemblies provide high-quality material for functional and evolutionary studies of these legume pathogens.
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15
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Wang LH, Chan JJ, Wang YH, Fang ZQ, Lee S, Chu CC. Bacterial Leaf Blight of Polyscias guilfoylei Caused by a Novel Pathovar of Xanthomonas euvesicatoria. PLANT DISEASE 2023; 107:298-305. [PMID: 35787010 DOI: 10.1094/pdis-03-22-0602-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polyscias guilfoylei is a popular ornamental belonging to the Araliaceae family. The present study identified and characterized bacterial strains causing leaf lesions on P. guilfoylei in a nursery in Taiwan. Strains Pgu1 to Pgu5 were isolated from infected leaf tissues and Koch's postulates were fulfilled. Observation of Pgu1 under a transmission electron microscope revealed that its cells were single flagellated and rod shaped. Sequencing of Pgu1 to Pgu5's 16S ribosomal DNA showed that they belong to the genus Xanthomonas. The biochemical and physiological traits of these bacteria were determined, and many of them also resemble those of other xanthomonads. However, the strains were unable to produce yellow pigments typically found in most members of the Xanthomonas genus, even when grown on yeast dextrose calcium carbonate (YDC) agar. Physiological assays and phylogenetic analyses based on multiple loci showed that the isolates were closely associated with members of the species Xanthomonas euvesicatoria and phylogenetically distant from X. hortorum pv. hederae, the currently only known xanthomonad capable of inducing diseases on Polyscias spp. Artificial inoculation into different host plants revealed that a representative strain, Pgu1, is specialized to P. guilfoylei and perhaps other members of the Araliaceae family. Based on the results from the phylogenetic and phenotypic analyses, the present work concludes that these strains belong to a novel pathovar of X. euvesicatoria. The pathovar epithet polysciadis is proposed.
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Affiliation(s)
- Liang-Hsuan Wang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Jiun-Jie Chan
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Yi-Hsin Wang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Zi-Qing Fang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Shin Lee
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Chia-Ching Chu
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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16
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Campigli S, Rizzo D. First Report of Xanthomonas hydrangeae Causing Leaf Spot on Oakleaf Hydrangea ( Hydrangea quercifolia) in Tuscany (Italy). PLANT DISEASE 2023; 107:2514. [PMID: 36724025 DOI: 10.1094/pdis-11-22-2607-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Hydrangeas (Hydrangea L.) are popular ornamental plants used in urban landscapes and gardens worldwide for the beauty of their large flowers. In June 2022, dark brown/purple and irregular water-soaked spots coalescing into large areas of necrosis were observed on the leaves of potted Hydrangea quercifolia Bartr. plants growing in two ornamentals nurseries in Pistoia, Tuscany, Italy. Isolations, using two symptomatic plants/nursery, were performed by excising small portions of leaf tissue from the margin of the lesions, and macerating them in 100 μl of sterile distilled water (SDW). After 15 min of incubation, a loopful of the resulting suspension was streaked on yeast extract-dextrose-CaCO3 agar (YDCA) amended with 60 mg L-1 cycloheximide. Mucoid, convex and yellow colonies appeared on YDCA after incubation at 28°C for 48h. After colony purification on yeast extract-nutrient-agar (YNA), two isolates from each nursery were subject to amplification and sequence analysis of the 16S rRNA using universal primers FD1/RD1, for genus identification (Vauterin et al. 2000; Weisburg et al. 1991). All 16S rRNA sequences (OP441051) were identical and BLASTn searches indicated that the isolates belong to the genus Xanthomonas [99.9% nucleotide identity with X. hydrangeae strain LMG 31885 (LR990741.1) and 99.8% with strain LMG 31884T (NR_181958.1)]. For classification at species level, fragments of the housekeeping genes gyrB, rpoD, dnaK, and fyuA, were amplified according to Young et al. (2008). Both strands were sequenced and the consensus sequences aligned using MUSCLE as implemented in MEGA X (Kumar et al. 2018). Homologous sequences were once again identical between the isolates. A neighbor joining phylogenetic analysis of the concatenated fragments, was carried out, using the Tuscan isolate HyQ-Tu1, the type/pathotype strains of the seven pathovars of X.hortorum, proposed by Morinière et al. (2020), the four X.hydrangeae strains characterized by Dia et al. (2021) and the type strain of X.populi as the outgroup. The analysis indicated that HyQ-Tu1 isolate clusters within the X. hydrangeae branch of the recently described X. hortorum - X. hydrangeae species complex (Morinière et al. 2020; Dia et al. 2021; 2022). In agreement with this result, isolates tested positive to the LAMP assay specific for members of the complex's clade C (X. hydrangeae) (Dia et al. 2022). Based on molecular evidence, the isolates were identified as X. hydrangeae (Dia et al. 2021; Oren and Garrity, 2022). Three healthy H. quercifolia potted plants were inoculated by rubbing a 10 µl droplet of a bacterial suspension of X. hydrangeae HyQ-Tu1 adjusted to an OD600 of 0.3 (approx. 108 CFU/ml) in SDW on the adaxial surface of two leaves per plant. Two control leaves/plant were inoculated with SDW. Each inoculated leaf was enclosed for 24h in a polyethylene bag and all plants were maintained in a greenhouse at 28°C. Nine days post inoculation (DPI), leaf spots similar to those observed on naturally infected plants started to become evident on the bacteria-inoculated leaves while control leaves remained asymptomatic throughout the trial (21 DPI). Koch's postulates were fulfilled by re-isolating the bacterium from the symptomatic tissues, obtaining a positive amplification with the clade C-specific LAMP assay (Dia et al. 2022), and confirming that the gyrB sequence was 100% identical to that of X. hydrangeae HyQ-Tu1. Housekeeping gene sequences were submitted to GenBank (OP456006-9). Members of the X. hortorum - X. hydrangeae species complex have been reported to affect H. quercifolia in the USA (Uddin et al. 1996) and H. quercifolia and H. arborescens L. in Belgium (Cottyn et al. 2021). To the best of our knowledge, this is the first documentation of X. hydrangeae causing disease on H. quercifolia in Italy. Further work is required to verify the presence of the bacterium in other European countries and to assess the economic impact that it causes within and outside nurseries.
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Affiliation(s)
- Sara Campigli
- DAGRI, Piazzale delle Cascine 28Firenze, Italy, 50144
- Università degli Studi, Firenze, DAGRI, Piazzale delle Cascine 28, Italy;
| | - Domenico Rizzo
- Regione Toscana, Laboratorio Servizio Fitosanitario Regionale, Pescia, Pistoia, Italy;
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17
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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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18
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Dia NC, Morinière L, Cottyn B, Bernal E, Jacobs J, Koebnik R, Osdaghi E, Potnis N, Pothier J. Xanthomonas hortorum - beyond gardens: Current taxonomy, genomics, and virulence repertoires. MOLECULAR PLANT PATHOLOGY 2022; 23:597-621. [PMID: 35068051 PMCID: PMC8995068 DOI: 10.1111/mpp.13185] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 05/02/2023]
Abstract
TAXONOMY Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Lysobacterales (earlier synonym of Xanthomonadales); Family Lysobacteraceae (earlier synonym of Xanthomonadaceae); Genus Xanthomonas; Species X. hortorum; Pathovars: pv. carotae, pv. vitians, pv. hederae, pv. pelargonii, pv. taraxaci, pv. cynarae, and pv. gardneri. HOST RANGE Xanthomonas hortorum affects agricultural crops, and horticultural and wild plants. Tomato, carrot, artichoke, lettuce, pelargonium, ivy, and dandelion were originally described as the main natural hosts of the seven separate pathovars. Artificial inoculation experiments also revealed other hosts. The natural and experimental host ranges are expected to be broader than initially assumed. Additionally, several strains, yet to be assigned to a pathovar within X. hortorum, cause diseases on several other plant species such as peony, sweet wormwood, lavender, and oak-leaf hydrangea. EPIDEMIOLOGY AND CONTROL X. hortorum pathovars are mainly disseminated by infected seeds (e.g., X. hortorum pvs carotae and vitians) or cuttings (e.g., X. hortorum pv. pelargonii) and can be further dispersed by wind and rain, or mechanically transferred during planting and cultivation. Global trade of plants, seeds, and other propagating material constitutes a major pathway for their introduction and spread into new geographical areas. The propagules of some pathovars (e.g., X. horturum pv. pelargonii) are spread by insect vectors, while those of others can survive in crop residues and soils, and overwinter until the following growing season (e.g., X. hortorum pvs vitians and carotae). Control measures against X. hortorum pathovars are varied and include exclusion strategies (i.e., by using certification programmes and quarantine regulations) to multiple agricultural practices such as the application of phytosanitary products. Copper-based compounds against X. hortorum are used, but the emergence of copper-tolerant strains represents a major threat for their effective management. With the current lack of efficient chemical or biological disease management strategies, host resistance appears promising, but is not without challenges. The intrastrain genetic variability within the same pathovar poses a challenge for breeding cultivars with durable resistance. USEFUL WEBSITES https://gd.eppo.int/taxon/XANTGA, https://gd.eppo.int/taxon/XANTCR, https://gd.eppo.int/taxon/XANTPE, https://www.euroxanth.eu, http://www.xanthomonas.org, http://www.xanthomonas.org/dokuwiki.
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Affiliation(s)
- Nay C. Dia
- Environmental Genomics and Systems Biology Research GroupInstitute for Natural Resource SciencesZurich University of Applied SciencesWädenswilSwitzerland
- Molecular Plant BreedingInstitute of Agricultural SciencesETH ZurichZurichSwitzerland
| | - Lucas Morinière
- University of LyonUniversité Claude Bernard Lyon 1CNRSINRAEUMR Ecologie MicrobienneVilleurbanneFrance
| | - Bart Cottyn
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and FoodMerelbekeBelgium
| | - Eduardo Bernal
- Department of Plant PathologyThe Ohio State UniversityColumbusOhioUSA
| | - Jonathan M. Jacobs
- Department of Plant PathologyThe Ohio State UniversityColumbusOhioUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOhioUSA
| | - Ralf Koebnik
- Plant Health Institute of MontpellierUniversity of Montpellier, CIRAD, INRAe, Institut Agro, IRDMontpellierFrance
| | - Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Neha Potnis
- Department of Entomology and Plant PathologyAuburn UniversityAlabamaUSA
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research GroupInstitute for Natural Resource SciencesZurich University of Applied SciencesWädenswilSwitzerland
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19
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Liyanapathiranage P, Wagner N, Avram O, Pupko T, Potnis N. Phylogenetic Distribution and Evolution of Type VI Secretion System in the Genus Xanthomonas. Front Microbiol 2022; 13:840308. [PMID: 35495725 PMCID: PMC9048695 DOI: 10.3389/fmicb.2022.840308] [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: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
The type VI secretion system (T6SS) present in many Gram-negative bacteria is a contact-dependent apparatus that can directly deliver secreted effectors or toxins into diverse neighboring cellular targets including both prokaryotic and eukaryotic organisms. Recent reverse genetics studies with T6 core gene loci have indicated the importance of functional T6SS toward overall competitive fitness in various pathogenic Xanthomonas spp. To understand the contribution of T6SS toward ecology and evolution of Xanthomonas spp., we explored the distribution of the three distinguishable T6SS clusters, i3*, i3***, and i4, in approximately 1,740 Xanthomonas genomes, along with their conservation, genetic organization, and their evolutionary patterns in this genus. Screening genomes for core genes of each T6 cluster indicated that 40% of the sequenced strains possess two T6 clusters, with combinations of i3*** and i3* or i3*** and i4. A few strains of Xanthomonas citri, Xanthomonas phaseoli, and Xanthomonas cissicola were the exception, possessing a unique combination of i3* and i4. The findings also indicated clade-specific distribution of T6SS clusters. Phylogenetic analysis demonstrated that T6SS clusters i3* and i3*** were probably acquired by the ancestor of the genus Xanthomonas, followed by gain or loss of individual clusters upon diversification into subsequent clades. T6 i4 cluster has been acquired in recent independent events by group 2 xanthomonads followed by its spread via horizontal dissemination across distinct clades across groups 1 and 2 xanthomonads. We also noted reshuffling of the entire core T6 loci, as well as T6SS spike complex components, hcp and vgrG, among different species. Our findings indicate that gain or loss events of specific T6SS clusters across Xanthomonas phylogeny have not been random.
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Affiliation(s)
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Oren Avram
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
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20
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Clavijo F, Curland RD, Croce V, Lapaz MI, Dill-Macky R, Pereyra S, Siri MI. Genetic and Phenotypic Characterization of Xanthomonas Species Pathogenic in Wheat in Uruguay. PHYTOPATHOLOGY 2022; 112:511-520. [PMID: 34384244 DOI: 10.1094/phyto-06-21-0231-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial diseases affecting wheat production in Uruguay are an issue of growing concern yet remain largely uninvestigated in the region. Surveys of 61 wheat fields carried out from 2017 to 2019 yielded a regional collection of 63 strains identified by 16S rRNA gene analysis as Xanthomonas spp. A real-time PCR protocol with species-specific primers previously reported allowed the identification of 44 strains as X. translucens, the causal agent of bacterial leaf streak (BLS) in wheat and other cereal crops. Multilocus sequence analysis of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD) revealed that these strains were most closely related to X. translucens pv. undulosa, the pathovar that is most commonly associated with BLS of wheat. Multilocus sequence typing was applied to examine the genetic diversity of X. translucens strains. Strains were assigned to four different sequence types, three of which were previously reported globally. Additionally, 17 Xanthomonas strains not belonging to X. translucens were obtained from diseased wheat leaves. Phylogenetic analysis showed that these strains are closely related to X. prunicola and clustered together with previously uncharacterized Xanthomonas strains isolated from wheat in Minnesota. In planta pathogenicity assays carried out on a BLS-susceptible wheat cultivar showed that X. translucens pv. undulosa strains caused brown necrosis symptoms typical of BLS, whereas non-translucens Xanthomonas sp. strains elicited an atypical symptom of dry necrosis. These findings suggest that local wheat fields are affected by X. translucens pv. undulosa and by a new wheat pathogen within the Xanthomonas genus.
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Affiliation(s)
- Felipe Clavijo
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Udelar, 11800, Montevideo, Uruguay
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Valentina Croce
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Udelar, 11800, Montevideo, Uruguay
| | - María I Lapaz
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Udelar, 11800, Montevideo, Uruguay
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Silvia Pereyra
- Instituto Nacional de Investigación Agropecuaria, La Estanzuela, 70006, Colonia, Uruguay
| | - María I Siri
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Udelar, 11800, Montevideo, Uruguay
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21
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Phenotypic and Molecular-Phylogenetic Analyses Reveal Distinct Features of Crown Gall-Associated Xanthomonas Strains. Microbiol Spectr 2022; 10:e0057721. [PMID: 35107322 PMCID: PMC8809331 DOI: 10.1128/spectrum.00577-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In summer 2019, widespread occurrence of crown gall disease caused by Agrobacterium spp. was observed on commercially grown ornamental plants in southern Iran. Beside agrobacteria, pale yellow-pigmented Gram-negative strains resembling the members of Xanthomonas were also associated with crown gall tissues on weeping fig (Ficus benjamina) and Amaranthus sp. plants. The purpose of the present study was to characterize the crown gall-associated Xanthomonas strains using plant inoculation assays, molecular-phylogenetic analyses, and comparative genomics approaches. Pathogenicity tests showed that the Xanthomonas strains did not induce disease symptoms on their host of isolation. However, the strains induced hypersensitive reaction on tobacco, geranium, melon, squash, and tomato leaves via leaf infiltration. Multilocus sequence analysis suggested that the strains belong to clade IA of Xanthomonas, phylogenetically close to Xanthomonas translucens, X. theicola, and X. hyacinthi. Average nucleotide identity and digital DNA-DNA hybridization values between the whole-genome sequences of the strains isolated in this study and reference Xanthomonas strains are far below the accepted thresholds for the definition of prokaryotic species, signifying that these strains could be defined as two new species within clade IA of Xanthomonas. Comparative genomics showed that the strains isolated from crown gall tissues are genetically distinct from X. translucens, as almost all the type III secretion system genes and type III effectors are lacking in the former group. The data obtained in this study provide novel insight into the breadth of genetic diversity of crown gall-associated bacteria and pave the way for research on gall-associated Xanthomonas-plant interactions. IMPORTANCE Tumorigenic agrobacteria—members of the bacterial family Rhizobiaceae—cause crown gall and hairy root diseases on a broad range of plant species. These bacteria are responsible for economic losses in nurseries of important fruit trees and ornamental plants. The microclimate of crown gall and their accompanying microorganisms has rarely been studied for the microbial diversity and population dynamics of gall-associated bacteria. Here, we employed a series of biochemical tests, pathogenicity assays, and molecular-phylogenetic analyses, supplemented with comparative genomics, to elucidate the biological features, taxonomic position, and genomic repertories of five crown gall-associated Xanthomonas strains isolated from weeping fig and Amaranthus sp. plants in Iran. The strains investigated in this study induced hypersensitive reactions (HR) on geranium, melon, squash, tobacco, and tomato leaves, while they were nonpathogenic on their host of isolation. Phylogenetic analyses and whole-genome-sequence-based average nucleotide identity (ANI)/digital DNA-DNA hybridization (dDDH) calculations suggested that the Xanthomonas strains isolated from crown gall tissues belong to two taxonomically unique clades closely related to the clade IA species of the genus, i.e., X. translucens, X. hyacinthi, and X. theicola.
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22
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Tall H, Lachaux M, Diallo A, Wonni I, Tekete C, Verdier V, Szurek B, Hutin M. Confirmation report of Bacterial Leaf Streak disease of rice caused by Xanthomonas oryzae pv. oryzicola in Senegal. PLANT DISEASE 2022; 106:2253. [PMID: 35100031 DOI: 10.1094/pdis-11-21-2481-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Xanthomonas oryzae pv. X. oryzicola (Xoc), the causal agent of Bacterial Leaf Streak (BLS), is considered as one of the most important emerging pathogens of rice in Africa. This disease is estimated as responsible of 20 to 30% yield loss (Sileshi et Gebeyehu 2021) and has been characterized in several west African countries including Mali and Burkina Faso since 2003 and more recently in Ivory Coast (Wonni et al. 2014, Diallo et al. 2021). Presence of BLS symptoms in Senegal were reported by Trinh in 1980 but, to our knowledge, BLS occurrence has never been validated further and no strain of Xoc have ever been isolated from Senegalese rice fields. Xoc is transmitted by seeds which contribute to its spread through the rice trade (Sileshi et Gebeyehu 2021). To confirm Trinh's observations, we surveyed rice fields between 2014 and 2016 in eight different regions where rice is produced in Senegal. Typical disease symptoms characterized by yellow-brown to black translucent leaf streaks sometimes along with exudates, were detected in fields of several regions and collected. Leaf pieces were successively sanitized, rinsed in sterile water, and symptomatic fragments were ground using the Qiagen Tissue Lyser System (QIAGEN, Courtaboeuf, France). The leaf powder was diluted in 1.5 ml of sterile water and incubated for 30 minutes at room temperature. Ten μl of the suspension was streaked on semi-selective PSA medium and incubated at 28°C for 3 to 7 days. Characteristic round, convex, mucous, straw-yellow Xoc candidate colonies were purified from six individual leaf samples from three distinct sites in the northern Senegal River Valley. To confirm their identity, isolated strains were tested for pathogenicity and molecular characterization. All isolates were subjected to the multiplex PCR developed for the identification of X. oryzae pathovars (Lang et al., 2010) and revealed the same PCR profile (two amplicons of 324 and 691 base pairs) similar to that of the Xoc reference strain BLS256. Leaves of 5-week-old plants of O. sativa cv. Kitaake were infiltrated with a needleless syringe containing a bacterial suspension set at an optical density of 0.5. Upon seven days of incubation under greenhouse conditions (27 ± 1°C with a 12-hour photoperiod), all infiltrated spots (2 spots on 3 plants per isolate) developed water-soaked lesions similar to those caused by control strain BLS256, except when leaves were infiltrated with water. Symptomatic leaf tissues were ground and plated on PSA medium, resulting in colonies with typical Xanthomonas morphology that were diagnosed as Xoc by multiplex PCR typing, thus fulfilling Koch's postulate. At last, four of the isolates were subjected to gyrB sequencing upon PCR amplification using the universal primers XgyrB1F and XgyrB1R (Young et al., 2008). Analysis of 780bp partial gyrB sequences of strains S18-3-4, S23-1-12, S52-1-4 and S52-1-10 highlighted 100% identity with the gyrB sequence of strain BLS256 (Acc. No. CP003057). To our knowledge, this is the first report of BLS in Senegal which is supported by molecular characterization methods. This study validates the presence of BLS in Senegal and will serve as a basis for future efforts of rice breeding for locally adapted resistance. More studies are needed to clarify the spatial distribution and prevalence of BLS in Senegal as rice cultivation is expanding rapidly in the country.
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Affiliation(s)
- Hamidou Tall
- Institut Sénégalais de Recherches Agricoles, 206826, Kolda, Senegal;
| | - Marlene Lachaux
- Institut de Recherche pour le Développement Centre de Montpellier, 98751, PHIM, Montpellier, Occitanie, France;
| | - Amadou Diallo
- Institut de Recherche pour le Développement Centre de Montpellier, 98751, PHIM, Plant Health Institute of Montpellier Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- INERA, Institut de l'Environnement et Recherches Agricoles, Bobo Dioulasso, Burkina Faso;
| | - Issa Wonni
- INERA, Institut de l'Environnement et Recherches Agricoles, Plant Pathology, Bobo Dioulasso, Burkina Faso;
| | - Cheick Tekete
- USTTB, 225803, LaboREM-Biotech, Bamako, Bamako, Mali;
| | - Valérie Verdier
- Institut de Recherche pour le Développement Centre de Montpellier, 98751, PHIM, Montpellier, Occitanie, France;
| | - Boris Szurek
- Institut de Recherche pour le Développement Centre de Montpellier, 98751, PHIM, Montpellier, Occitanie, France;
| | - Mathilde Hutin
- Institut de Recherche pour le Développement Centre de Montpellier, 98751, PHIM, Montpellier, Occitanie, France;
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Dia NC, Van Vaerenbergh J, Van Malderghem C, Blom J, Smits THM, Cottyn B, Pothier JF. Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens. Int J Syst Evol Microbiol 2021; 71. [PMID: 34913859 DOI: 10.1099/ijsem.0.005163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper describes a novel species isolated in 2011 and 2012 from nursery-grown Hydrangea arborescens cultivars in Flanders, Belgium. After 4 days at 28 °C, the strains yielded yellow, round, convex and mucoid colonies. Pathogenicity of the strains was confirmed on its isolation host, as well as on Hydrangea quercifolia. Analysis using MALDI-TOF MS identified the Hydrangea strains as belonging to the genus Xanthomonas but excluded them from the species Xanthomonas hortorum. A phylogenetic tree based on gyrB confirmed the close relation to X. hortorum. Three fatty acids were dominant in the Hydrangea isolates: anteiso-C15 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Unlike X. hortorum pathovars, the Hydrangea strains were unable to grow in the presence of lithium chloride and could only weakly utilize d-fructose-6-PO4 and glucuronamide. Phylogenetic characterization based on multilocus sequence analysis and phylogenomic characterization revealed that the strains are close to, yet distinct from, X. hortorum. The genome sequences of the strains had average nucleotide identity values ranging from 94.35-95.19 % and in silico DNA-DNA hybridization values ranging from 55.70 to 59.40 % to genomes of the X. hortorum pathovars. A genomics-based loop-mediated isothermal amplification assay was developed which was specific to the Hydrangea strains for its early detection. A novel species, Xanthomonas hydrangeae sp. nov., is proposed with strain LMG 31884T (=CCOS 1956T) as the type strain.
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Affiliation(s)
- Nay C Dia
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.,Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Johan Van Vaerenbergh
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Cinzia Van Malderghem
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Giessen, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Bart Cottyn
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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24
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Jiang C, Tanaka M, Nishikawa S, Mino S, Romalde JL, Thompson FL, Gomez-Gil B, Sawabe T. Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach. Curr Microbiol 2021; 79:10. [PMID: 34905112 DOI: 10.1007/s00284-021-02725-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 01/05/2023]
Abstract
Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.
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Affiliation(s)
- Chunqi Jiang
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Mami Tanaka
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayo Nishikawa
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CRETUS & CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, España
| | - Fabiano L Thompson
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno Gomez-Gil
- CIAD, AC, Mazatlan Unit for Aquaculture and Environmental Management, Mazatlán, México
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
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25
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Diallo A, Zougrana S, Sawadogo M, Kone D, Silué D, Szurek B, Wonni I, Hutin M. First Report of Bacterial Leaf Streak Disease of Rice Caused by Xanthomonas oryzae pv. oryzicola in Ivory Coast. PLANT DISEASE 2021; 105:PDIS04210811PDN. [PMID: 34236215 DOI: 10.1094/pdis-04-21-0811-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- A Diallo
- INERA, Institut de l'Environnement et Recherches Agricoles, Bobo-Dioulasso, Burkina Faso
- IRD, Institut de Recherche pour le Développement UMR PHIM, Plant Health Institute of Montpellier, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- Université de Ouagadougou, Laboratoire de Génétique et Biotechnologies Végétales, Ouagadougou, Burkina Faso
| | - S Zougrana
- INERA, Institut de l'Environnement et Recherches Agricoles, Bobo-Dioulasso, Burkina Faso
| | - M Sawadogo
- Université de Ouagadougou, Laboratoire de Génétique et Biotechnologies Végétales, Ouagadougou, Burkina Faso
| | - D Kone
- Université Félix Houphouët-Boigny, UFR Biosciences, Laboratoire de Physiologie Végétale, Abidjan, Côte d'Ivoire
| | - D Silué
- AfricaRice, Plant Pathology, Bouaké, Ivory Coast
| | - B Szurek
- IRD, Institut de Recherche pour le Développement UMR PHIM, Plant Health Institute of Montpellier, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - I Wonni
- INERA, Institut de l'Environnement et Recherches Agricoles, Bobo-Dioulasso, Burkina Faso
| | - M Hutin
- IRD, Institut de Recherche pour le Développement UMR PHIM, Plant Health Institute of Montpellier, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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26
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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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27
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Osdaghi E, Jones JB, Sharma A, Goss EM, Abrahamian P, Newberry EA, Potnis N, Carvalho R, Choudhary M, Paret ML, Timilsina S, Vallad GE. A centenary for bacterial spot of tomato and pepper. MOLECULAR PLANT PATHOLOGY 2021; 22:1500-1519. [PMID: 34472193 PMCID: PMC8578828 DOI: 10.1111/mpp.13125] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 05/08/2023]
Abstract
DISEASE SYMPTOMS Symptoms include water-soaked areas surrounded by chlorosis turning into necrotic spots on all aerial parts of plants. On tomato fruits, small, water-soaked, or slightly raised pale-green spots with greenish-white halos are formed, ultimately becoming dark brown and slightly sunken with a scabby or wart-like surface. HOST RANGE Main and economically important hosts include different types of tomatoes and peppers. Alternative solanaceous and nonsolanaceous hosts include Datura spp., Hyoscyamus spp., Lycium spp., Nicotiana rustica, Physalis spp., Solanum spp., Amaranthus lividus, Emilia fosbergii, Euphorbia heterophylla, Nicandra physaloides, Physalis pubescens, Sida glomerata, and Solanum americanum. TAXONOMIC STATUS OF THE PATHOGEN Domain, Bacteria; phylum, Proteobacteria; class, Gammaproteobacteria; order, Xanthomonadales; family, Xanthomonadaceae; genus, Xanthomonas; species, X. euvesicatoria, X. hortorum, X. vesicatoria. SYNONYMS (NONPREFERRED SCIENTIFIC NAMES) Bacterium exitiosum, Bacterium vesicatorium, Phytomonas exitiosa, Phytomonas vesicatoria, Pseudomonas exitiosa, Pseudomonas gardneri, Pseudomonas vesicatoria, Xanthomonas axonopodis pv. vesicatoria, Xanthomonas campestris pv. vesicatoria, Xanthomonas cynarae pv. gardneri, Xanthomonas gardneri, Xanthomonas perforans. MICROBIOLOGICAL PROPERTIES Colonies are gram-negative, oxidase-negative, and catalase-positive and have oxidative metabolism. Pale-yellow domed circular colonies of 1-2 mm in diameter grow on general culture media. DISTRIBUTION The bacteria are widespread in Africa, Brazil, Canada and the USA, Australia, eastern Europe, and south-east Asia. Occurrence in western Europe is restricted. PHYTOSANITARY CATEGORIZATION A2 no. 157, EU Annex designation II/A2. EPPO CODES XANTEU, XANTGA, XANTPF, XANTVE.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Jeffrey B. Jones
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Anuj Sharma
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Erica M. Goss
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Peter Abrahamian
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
| | - Eric A. Newberry
- Department of Entomology and Plant PathologyAuburn UniversityAuburnAlabamaUSA
| | - Neha Potnis
- Department of Entomology and Plant PathologyAuburn UniversityAuburnAlabamaUSA
| | - Renato Carvalho
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Manoj Choudhary
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Mathews L. Paret
- Department of Plant PathologyNorth Florida Research and Education CenterUniversity of FloridaQuincyFloridaUSA
| | - Sujan Timilsina
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Gary E. Vallad
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
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28
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Fu B, Zhu J, Lee C, Wang L. Multilocus Sequence Analysis and Copper Ion Resistance Detection of 60 Xanthomonas arboricola pv. juglandis Isolates from China. PLANT DISEASE 2021; 105:3715-3719. [PMID: 33858185 DOI: 10.1094/pdis-02-21-0241-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Walnut bacterial blight caused by Xanthomonas arboricola pv. juglandis has serious repercussions for walnut production around the world. Between 2015 and 2017, disease samples were collected from six counties (Danjiangkou, Baokang, Suizhou, Shennongjia, Zigui, and Xingshan) in Hubei Province, China. Fifty-nine X. arboricola pv. juglandis isolates were identified by morphology and specific PCR primers from 206 isolates. The genetic diversity of 60 X. arboricola pv. juglandis isolates (59 from Hubei plus 1 from Beijing) was evaluated by multilocus sequence analysis, and their resistance to copper ion (Cu2+) treatment was determined. A neighbor-joining phylogenetic dendrogram was constructed based on four sequences of housekeeping genes (atpD-dnaK-glnA-gyrB). Two groups of isolates whose clustering was consistent with that of glnA were identified. The minimal inhibitory concentration of Cu2+ on representative X. arboricola pv. juglandis strain DW3F3 (the first genome sequenced X. arboricola pv. juglandis from China) was 115 μg/ml. Setting the copper-resistant threshold value to 125 μg/ml, 47 and 13 isolates were considered sensitive and resistant to Cu2+, respectively. Furthermore, five isolates showed Cu2+ resistance at 270 μg/ml. Compared with the copper resistance gene B (copB) from sensitive isolates, the copB gene in resistant isolates had a 15-bp insertion and eight scattered single-nucleotide polymorphisms. Interestingly, the clustering based on multilocus sequence analysis was distinct between X. arboricola pv. juglandis Cu2+-resistant and -sensitive isolates.
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Affiliation(s)
- Benzhong Fu
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan Hubei 432000, China
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011 U.S.A
| | - Jieqian Zhu
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan Hubei 432000, China
| | - Conard Lee
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011 U.S.A
| | - Lihua Wang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan Hubei 432000, China
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Ledman KE, Curland RD, Ishimaru CA, Dill-Macky R. Xanthomonas translucens pv. undulosa Identified on Common Weedy Grasses in Naturally Infected Wheat Fields in Minnesota. PHYTOPATHOLOGY 2021; 111:1114-1121. [PMID: 33225830 DOI: 10.1094/phyto-08-20-0337-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacterial leaf streak (BLS) of wheat, caused by Xanthomonas translucens pv. undulosa, has been a notable disease in Minnesota wheat fields over the past decade. Potential sources of the pathogen include infested seed and crop debris. Perennial weeds are also considered a possible inoculum source, but no surveys have been conducted to evaluate which X. translucens pathovars are present on weedy grasses that are common in Minnesota wheat fields. Multilocus sequence analysis (MLSA) of four housekeeping genes (rpoD, dnaK, fyuA, and gyrB) was used to identify 77 strains isolated from six weedy grass species, wheat, and barley in and around naturally infected wheat fields in Minnesota. The MLSA phylogeny identified all strains originating from weedy grass species, except smooth brome, as X. translucens pv. undulosa, whereas strains isolated from smooth brome were determined to be X. translucens pv. cerealis. In planta character states corroborated these identifications on a subset of 41 strains, as all strains from weedy grasses caused water-soaking on wheat and barley in greenhouse assays. Multilocus sequence typing was used to evaluate genetic diversity and revealed that sequence types of X. translucens pv. undulosa originating from weedy grass hosts are similar to those found on wheat. This study identifies both annual and perennial poaceous weeds common in Minnesota that harbor X. translucens pv. undulosa and expands our understanding of the diversity of the pathogen population.
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Affiliation(s)
- Kristi E Ledman
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Carol A Ishimaru
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Amancio L, Baia ADB, Souza EB, Sales Júnior R, Negreiros AMP, Balbino VQ, Gama MAS. First Report of Xanthomonas citri subsp. citri causing Citrus Canker on lime in Rio Grande do Norte, Brazil. PLANT DISEASE 2021; 105:4148. [PMID: 34152205 DOI: 10.1094/pdis-11-20-2498-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Citrus canker caused by Xanthomonas citri subsp. citri is one of the most important citrus diseases in the world (Gottwald et al. 2002), mainly for citrus-producing countries with humid sub-tropical regions such as United States, Argentina, and Brazil, where losses may be significant (Behlau et al. 2020). In the state of Rio Grande do Norte (RN), Brazil, citrus production is expanding and shows social and economic importance for small farmers, which produced approximately 297 tons of lime in this state in 2019 (IBGE 2021). In December 2019, we observed symptoms of erumpent lesions with margins surrounded by yellow haloes on leaves and fruit of the lime (Citrus aurantifolia cv. 'Galego') (about 5% incidence) in a plantation located in the municipality of Mossoró, RN (05°12'21.1"S, 37°19'16"W). Samples were collected from the lime orchard, and five bacterial strains (CCRMXC01 to CCRMXC05) showing yellow, convex, mucoid colonies were isolated in a nutrient-yeast-dextrose-agar medium (NYDA). Pathogenicity tests were performed on sweet orange (C. sinensis cv. 'Pêra') and lime (C. latifolia cv. 'Tahiti') seedlings. Four wounds per leaf (upper side) were carried out with an entomological pin and 10 µl of a bacterial suspension (108 CFU mL-1) were deposited on each wound. The negative control consisted of leaves treated with sterile distilled water (SDW). For each citrus species, we used four replicates per strain and one leaf with four wounds per replicate. Inoculated leaves developed erumpent lesions with margins surrounded by yellow haloes six days after inoculation (DAI) in both citrus species, while leaves treated with SDW remained symptomless. Nine DAI, we reisolated the pathogen and performed rep-PCR (REP, ERIC, and BOX-PCR) analyses (Gama et al. 2018) with the strains inoculated and reisolated to confirm the identity of the strains and to fulfill Koch's postulates. The strains were stored at the Culture Collection Rosa Mariano (CCRM) of the Phytobacteriology Laboratory at the Universidade Federal Rural de Pernambuco. The five strains reisolated showed the same REP, ERIC, and BOX-PCR profiles as the strains used for inoculations. The molecular identification was performed sequencing the dnaK, fyuA, gyrB, and rpoD genes (Young et al. 2008). Each fragment was sequenced in both the forward and reverse directions. Using the BLASTn tool, we observed that sequences of the dnaK (GenBank MW218913 to MW218917), fyuA (GenBank MW218918 to MW218922), and rpoD (GenBank MW218928 to MW218932) genes of the strains CCRMXC01 to CCRMXC05 showed 100% of identity with the sequences of these genes from the type strain (ICMP 24T) and of other strains of X. citri subsp. citri (ICMP 21 and ICMP 7493), while sequences of gryB (GenBank MW218923 to MW218927) of the former strains showed 100% identity with the gyrB sequence of the strains ICMP 24T and ICMP 7493 and 99,85% identity with strain ICMP 21. This short variation in the sequence of the gyrB gene also may be observed among strains of X. citri subsp. citri available in NCBI database (https://www.ncbi.nlm.nih.gov/). The phylogenetic analysis performed using Bayesian inference and the concatenated sequence of all the type or representative strains of species and pathovars of Xanthomonas available in GenBank showed that the strains CCRMXC01 to CCRMXC05 clustered together with strain ICMP 24T with 1.0 posterior probability. To our information, this is the first report of X. citri subsp. citri causing citrus canker on lime in RN state, Brazil.
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Affiliation(s)
- Lucas Amancio
- Universidade Federal Rural de Pernambuco, Agronomy, Recife, Pernambuco, Brazil;
| | - Ana Dulce Botelho Baia
- Universidade Estadual Paulista Julio de Mesquita Filho - Campus de Jaboticabal, 207340, Plant Pathology, Rua Rodrigues Ferreira, 45, Recife, Pernambuco, Brazil, 50810020
- Universidade Federal Rural de Pernambuco;
| | - Elineide B Souza
- Av. Dom Manoel de Medeiros, s/n. Dois Irmãos, Recife, PernambucoRecife, Brazil, 52171-900;
| | - Rui Sales Júnior
- Universidade Federal Rural do Semi-Arido, 74384, Ciências Agronômicas e Florestais, Avenida Francisco Mota, 572, Costa e Silva, Mossoró, Mossoro, Rio Grande do Norte, Brazil, 59625-900
- United States;
| | - Andreia Mitsa Paiva Negreiros
- UNIVERSIDADE FEDERAL RURAL DO SEMI-ÁRIDO, Ciências Agronômicas e Florestais, Av. Francisco Mota, 572, Costa e Silva, Mossoró, Rio Grande do Norte, Brazil, 59625-900
- Universidade Federal Rural do Semi-Arido, 74384, Mossoro, Brazil, 59625-900;
| | | | - Marco Aurélio Siqueira Gama
- Universidade Federal Rural de Pernambuco, Agronomy, Av. Dom Manuel de Medeiros, s/n., Recife, Pernambuco, Brazil, 52171-900;
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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: 8] [Impact Index Per Article: 2.7] [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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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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Curland RD, Hallada KR, Ledman KE, Dill-Macky R. First report of bacterial leaf streak caused by Xanthomonas translucens pv. undulosa on cultivated wild rice ( Zizania palustris) in Minnesota. PLANT DISEASE 2021; 105:2711. [PMID: 33797975 DOI: 10.1094/pdis-02-21-0407-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Known by the indigenous peoples of the Great Lakes region of North America as Manoomin, wild rice (Zizania palustris) is a native aquatic grass that is honored and central to Anishinaabe culture. Cultivated wild rice, the domesticated form of this cereal bred primarily for resistance to shattering, is grown commercially in paddies. In this study we examined four isolates (CIX303, CIX306, Xt-8, and Xt-22) of Xanthomonas translucens, the causative agent of bacterial leaf streak (BLS) on cereals and weedy grasses, in molecular and host range studies to confirm the pathovar identity of strains associated with cultivated wild rice. Two of the strains examined (CIX303 and CIX306), were isolated from cultivated wild rice in 2016 as part of a survey of the pathogen in Minnesota (Ledman 2019). Xt-8 and Xt-22 are historical strains of X. translucens isolated from symptomatic wild rice leaves collected in Minnesota in the late 1970s that were reported at the time to be X. campestris pv. cerealis (Bowden and Percich 1982). A host range assay was repeated twice in the greenhouse, where two leaves of six seedlings each of hard red spring wheat (cv. RB07), spring barley (cv. Quest), spring rye (cv. Prolific), oat (cv. Ogle), quackgrass, smooth brome grass and cultivated wild rice (cv. Itasca Cycle-12) were inoculated via leaf infiltration (Curland et al. 2020). X. translucens pv. cerealis LMG 679PT, X. translucens pv. secalis LMG 883PT, X. translucens pv. translucens LMG 876T, and X. translucens pv. undulosa LMG 892PT were included as reference strains. Host response profiles were determined for each strain by recording character states five days post inoculation. Water-soaking and necrosis were considered pathogenic reactions, whereas chlorosis was not. Three pathotype strains, LMG 679PT, LMG 876T, and LMG 892PT, caused water-soaking in cultivated wild rice, whereas LMG 883PT caused chlorosis. All four strains from cultivated wild rice produced water-soaking on wheat, barley, quackgrass, and cultivated wild rice, chlorosis or water-soaking on rye, chlorosis on oat, and a reddish water-soaking on smooth brome. The character states generated by these four isolates were identical only to the host response profile for LMG 892PT. LMG 679PT differed, causing chlorosis on wheat, no symptoms on quackgrass, and water-soaking on smooth brome. A 2645 bp concatenation of housekeeping genes (rpoD, dnaK, fyuA, gyrB) was used to perform a Bayesian analysis (GenBank accessions MW528365-MW528384) (Curland et al. 2018, Curland et al. 2020, Young et al. 2008). Subsequent phylogenies grouped all four strains from cultivated wild rice with LMG 892PT and LMG 883PT. A pairwise comparison revealed 100% identity between Xt-22 and LMG 892PT. The percentage identity of CIX303, CIX308, and Xt-8 to LMG 892PT was 99.96, 99.96, and 99.92, respectively. In contrast, when compared to LMG 679PT, the four strains from cultivated wild rice had a percent identity between 97.43 and 97.50. Based on host range studies combined with MLSA, we identified recent and historical isolates from Z. palustris as X. translucens pv. undulosa. Pathovar identity of strains causing BLS on cultivated wild rice in Minnesota is crucial when screening breeding materials for disease resistance. Furthermore, given that X. translucens pv. undulosa has been prevalent on wheat in Minnesota (Curland et al. 2018), expanding knowledge of its host range to include cultivated wild rice may inform disease management practices for both crops. References: Bowden, R., and Percich, J. 1982. Phytopath. 73:640-645. Curland, R., et al. 2018. Phytopath. 108:443-453. Curland, R., et al. 2020. Phytopath. 110:257-266. Ledman, K. 2019. M.S. Thesis, Univ. of Minnesota, St. P. Paul, USA. Young, J., et al. 2008. Syst. Appl. Microbiol. 31:366-377.
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Affiliation(s)
- Rebecca D Curland
- University of Minnesota System, 311816, Plant Pathology, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, Minnesota, United States, 55108;
| | - Kathryn R Hallada
- University of Minnesota System, 311816, Plant Pathology, St. Paul, Minnesota, United States;
| | - Kristi E Ledman
- University of Minnesota System, 311816, Plant Pathology, St. Paul, Minnesota, United States;
| | - Ruth Dill-Macky
- Univeristy of Minnesota, Plant Pathology, 495 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, Minnesota, United States, 55108;
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Vancheva T, Bogatzevska N, Moncheva P, Mitrev S, Vernière C, Koebnik R. Molecular Epidemiology of Xanthomonas euvesicatoria Strains from the Balkan Peninsula Revealed by a New Multiple-Locus Variable-Number Tandem-Repeat Analysis Scheme. Microorganisms 2021; 9:microorganisms9030536. [PMID: 33807692 PMCID: PMC8002079 DOI: 10.3390/microorganisms9030536] [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: 02/01/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial spot of pepper and tomato is caused by at least three species of Xanthomonas, among them two pathovars of Xanthomonas euvesicatoria, which are responsible for significant yield losses on all continents. In order to trace back the spread of bacterial spot pathogens within and among countries, we developed the first multilocus variable number of tandem repeat analyses (MLVA) scheme for pepper- and tomato-pathogenic strains of X. euvesicatoria. In this work, we assessed the repeat numbers by DNA sequencing of 16 tandem repeat loci and applied this new tool to analyse a representative set of 88 X. euvesicatoria pepper strains from Bulgaria and North Macedonia. The MLVA-16 scheme resulted in a Hunter–Gaston Discriminatory Index (HGDI) score of 0.944 and allowed to resolve 36 MLVA haplotypes (MTs), thus demonstrating its suitability for high-resolution molecular typing. Strains from the different regions of Bulgaria and North Macedonia were found to be widespread in genetically distant clonal complexes or singletons. Sequence types of the variable number of tandem repeats (VNTR) amplicons revealed cases of size homoplasy and suggested the coexistence of different populations and different introduction events. The large geographical distribution of MTs and the existence of epidemiologically closely related strains in different regions and countries suggest long dispersal of strains on pepper in this area.
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Affiliation(s)
- Taca Vancheva
- IPME, Univ Montpellier, Cirad, IRD, Montpellier, France;
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria;
| | - Nevena Bogatzevska
- Institute of Soil Science, Agrotechnologies and Plant Protection ‘Nikola Pushkarov’, Sofia, Bulgaria;
| | - Penka Moncheva
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria;
| | - Sasa Mitrev
- Department for Plant and Environment Protection, Faculty of Agriculture, Goce Delchev University, Štip, North Macedonia;
| | - Christian Vernière
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Insitut Agro, IRD, Montpellier, France;
| | - Ralf Koebnik
- IPME, Univ Montpellier, Cirad, IRD, Montpellier, France;
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Insitut Agro, IRD, Montpellier, France;
- Correspondence: ; Tel.: +33-467-416-228
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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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Wu HY, Lai QJ, Wu YM, Chung CL, Chung PC, Lin NC. First Report of Xanthomonas fragariae Causing Angular Leaf Spot on Strawberry ( Fragaria x ananassa) in Taiwan. PLANT DISEASE 2020; 105:1187-1187. [PMID: 33107797 DOI: 10.1094/pdis-07-20-1631-pdn] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Angular leaf spot of strawberry, considered an A2 quarantine pest by the European and Mediterranean Plant Protection Organization (EPPO 2019), is an important bacterial disease in many regions. Since 2017, symptoms similar to angular leaf spot were observed in several strawberry cultivars including 'Taoyuan No. 1' and 'Xiang-Shui'. Early symptoms were angular, water-soaked lesions on the abaxial leaf surface, and later, reddish-brown irregular spots and coalesced lesions developed on the adaxial surface. In the humid conditions, sticky bacterial ooze exuding from lesions was observed. To isolate the causal agent, leaves showing water-soaked lesions were surface sterilized, cut into small pieces and soaked in 5 ml sterile water for at least 15 min. The supernatant from the cut-up pieces was serially diluted followed by spreading on sucrose peptone agar (SPA) (Hayward 1960). After incubating at 20°C for 4-5 days, single colonies grown on SPA were transferred to a new SPA plate and cultured at 20°C until colonies appeared. The yellow, glossy and mucoid colonies, which resembled the colony morphology of Xanthomonas fragariae, were selected as candidates for further confirmation. First, bacterial DNA of four candidate isolates, B001, B003 and B005 from Miaoli County and B004 from Taoyuan City, was PCR amplified with X. fragariae-specific primers: XF9/XF12 (Roberts et al. 1996) and 245A/B and 295A/B (Pooler et al. 1996). All four isolates could be detected by XF9/XF12 primer. Furthermore, isolates B003 and B004 could be detected by both 245A/B and 295A/B primers, while B001 and B005 could be detected by 295A/B only. Next, DNA gyrase subunit B (gyrB) was PCR amplified with the primers XgyrB1F/XgyrB1R (Young et al. 2008). The gyrB sequences of these four isolates were deposited in GenBank with accession numbers MT754942 to MT754945. The gyrB phylogenetic tree was constructed based on Bayesian inference analysis and maximum likelihood analysis. The gyrB sequences of the four isolates from Taiwan clustered in the clade containing the type strain of X. fragariae ICMP5715, indicating that they belong to X. fragariae. B001 and B005 formed a sub-group separated from B003 and B004, suggesting genetic differences between these isolates. To fulfill Koch's postulates, the abaxial surface of strawberry leaves were syringe infiltrated (KJP Silva et al., 2017) or wounded inoculated (Wang et al., 2017) with bacterial suspensions (final OD600 = 1.0-2.0) prepared from colonies of B001 and B003 washed from SPA plates. Inoculated plants were enclosed in a plastic bag (> 90% RH) at 25/20°C (day/night) under a 12-h/12-h photoperiod. After 7-14 days, water-soaked lesions similar to those observed in the field were developed on all inoculated leaves. The bacteria were successfully re-isolated from lesions of inoculated leaves and confirmed by specific primers XF9/XF12, 245A/B and 295A/B. We also found that the disease commonly occurs in the strawberry fields/nurseries with sprinkler irrigation during winter or early spring, and was particularly serious in the windward side or near riverside. To our knowledge, this is the first report of X. fragariae causing angular leaf spot on strawberry in Taiwan. Currently, the disease only occurs severely in certain regions, but establishment of effective management strategies will be needed to prevent spreading of this disease and potential economic loss in the future.
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Affiliation(s)
- Hung-Yi Wu
- National Taiwan University, 33561, Department of Plant Pathology and Microbiology, Taipei, Taiwan;
| | - Qiao-Juan Lai
- Miaoli District Agricultural Research and Extension Station, 252861, Gongguan, Miaoli, Taiwan;
| | - Yi-Mei Wu
- Miaoli County Government, Miaoli, Taiwan;
| | - Chia-Lin Chung
- National Taiwan University, 33561, Plant Pathology and Microbiology, Taipei, Taiwan;
| | - Pei-Che Chung
- National Taiwan University, 33561, Plant Pathology and Microbiology, Taipei, Taiwan
- Miaoli District Agricultural Research and Extension Station, 252861, Gongguan, Miaoli, Taiwan;
| | - Nai-Chun Lin
- National Taiwan University, 33561, Agricultural Chemistry, NO.1, Sec 4, Roosevelt Road, Taipei, Taiwan, 10617;
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Mançano SMCN, Campana EH, Felix TP, Barrueto LRL, Pereira PS, Picão RC. Frequency and diversity of Stenotrophomonas spp. carrying bla KPC in recreational coastal waters. WATER RESEARCH 2020; 185:116210. [PMID: 32731079 DOI: 10.1016/j.watres.2020.116210] [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] [Received: 05/13/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Stenotrophomonas can survive in a wide range of environments and is considered an opportunistic pathogen. Because of its intrinsic resistance to beta-lactams, this genus is considered irrelevant in studies addressing the environmental spread of antimicrobial resistance genes of medical importance. Consequently, studies on environmental Stenotrophomonas carrying acquired carbapenemase-encoding genes are scarce, though not inexistent. Here, we investigated the frequency and diversity of Stenotrophomonas spp. carrying genes encoding carbapenemases of medical relevance in coastal waters with distinct pollution degrees over one year. Among 319 isolates recovered, 220 (68.9%) showed blaKPC. The frequency of blaKPC-positive Stenotrophomonas spp. was not correlated with thermotolerant counts in coastal waters evaluated. All isolates were susceptible to minocycline, levofloxacin, and trimethoprim-sulfamethoxazole. PFGE typing of 101 blaKPC-positive isolates revealed 55 pulsotypes with 5 subtypes, all of which carried the blaKPC-2 variant. Interspecies differentiation of pulsotypes' representatives revealed 55 isolates belonging to the S. maltophilia complex (91.7%) and 5 S. acidaminiphila (8.3%). The blaKPC-2 gene was more frequently harbored on transposable elements found in enterobacteria of clinical origin, especially Tn4401b. Even though beta-lactams are no therapeutic options to treat Stenotrophomonas infections, the occurrence of a highly relevant antimicrobial resistance determinant harbored on mobile genetic elements in a diverse collection of these ubiquitous microorganisms is noteworthy. Therefore, Stenotrophomonas may act as acceptor, stable reservoirs, and potential vectors of antimicrobial resistance in environmental settings, especially aquatic matrices, and should not be neglected.
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Affiliation(s)
- Stella Maria Casas Novas Mançano
- Laboratório de Investigação em Microbiologia Médica - Instituto de Microbiologia Paulo de Góes - Centro de Ciência da Saúde - Universidade Federal do Rio de Janeiro - Rio de Janeiro, Brazil
| | - Eloiza Helena Campana
- Laboratório de Investigação em Microbiologia Médica - Instituto de Microbiologia Paulo de Góes - Centro de Ciência da Saúde - Universidade Federal do Rio de Janeiro - Rio de Janeiro, Brazil; Laboratório de Microbiologia Clínica - Departamento de Ciências Farmacêuticas - Centro de Ciência da Saúde - Universidade Federal da Paraíba - João Pessoa, Brazil
| | - Thais Pessanha Felix
- Laboratório de Investigação em Microbiologia Médica - Instituto de Microbiologia Paulo de Góes - Centro de Ciência da Saúde - Universidade Federal do Rio de Janeiro - Rio de Janeiro, Brazil
| | - Lina Rachel Leite Barrueto
- Laboratório de Investigação em Microbiologia Médica - Instituto de Microbiologia Paulo de Góes - Centro de Ciência da Saúde - Universidade Federal do Rio de Janeiro - Rio de Janeiro, Brazil; Programa de Pós-Graduação em Ciência e Biotecnologia (PPBI) - Instituto de Biologia - Universidade Federal Fluminense - Niterói, Rio de Janeiro, Brazil
| | - Polyana Silva Pereira
- Laboratório de Investigação em Microbiologia Médica - Instituto de Microbiologia Paulo de Góes - Centro de Ciência da Saúde - Universidade Federal do Rio de Janeiro - Rio de Janeiro, Brazil
| | - Renata Cristina Picão
- Laboratório de Investigação em Microbiologia Médica - Instituto de Microbiologia Paulo de Góes - Centro de Ciência da Saúde - Universidade Federal do Rio de Janeiro - Rio de Janeiro, Brazil.
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Complete or High-Quality Draft Genome Sequences of Six Xanthomonas hortorum Strains Sequenced with Short- and Long-Read Technologies. Microbiol Resour Announc 2020; 9:9/41/e00828-20. [PMID: 33033126 PMCID: PMC7545280 DOI: 10.1128/mra.00828-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We report the genome sequences of six Xanthomonas hortorum species-level clade members, X. hortorum pathovars taraxaci, pelargonii, cynarae, and gardneri (complete genome sequences) and X. hortorum pathovars carotae and vitians (high-quality draft genome sequences). Both short- and long-read sequencing technologies were used.
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Li T, Mann R, Sawbridge T, Kaur J, Auer D, Spangenberg G. Novel Xanthomonas Species From the Perennial Ryegrass Seed Microbiome - Assessing the Bioprotection Activity of Non-pathogenic Relatives of Pathogens. Front Microbiol 2020; 11:1991. [PMID: 32983016 PMCID: PMC7479056 DOI: 10.3389/fmicb.2020.01991] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/28/2020] [Indexed: 11/13/2022] Open
Abstract
The productivity of the Australian dairy industry is underpinned by pasture grasses, and importantly perennial ryegrass. The performance of these pasture grasses is supported by the fungal endophyte Epichloë spp. that has bioprotection activities, however, the broader microbiome is not well characterized. In this study, we characterized a novel bioprotectant Xanthomonas species isolated from perennial ryegrass (Lolium perenne L. cv. Alto). In vitro and in planta bioassays against key fungal pathogens of grasses (Sclerotium rolfsii, Drechslera brizae and Microdochium nivale) indicated strong bioprotection activities. A complete circular chromosome of ∼5.2 Mb was generated for three strains of the novel Xanthomonas sp. Based on the 16S ribosomal RNA gene, the strains were closely related to the plant pathogen Xanthomonas translucens, however, comparative genomics of 22 closely related xanthomonad strains indicated that these strains were a novel species. The comparative genomics analysis also identified two unique gene clusters associated with the production of bioprotectant secondary metabolites including one associated with a novel nonribosomal peptide synthetase and another with a siderophore. The analysis also identified genes associated with an endophytic lifestyle (e.g., Type VI secretion system), while no genes associated with pathogenicity were identified (e.g., Type III secretion system and effectors). Overall, these results indicate that these strains represent a novel, bioactive, non-pathogenic species of the genus Xanthomonas. Strain GW was the designated type strain of this novel Xanthomonas sp.
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Affiliation(s)
- Tongda Li
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Ross Mann
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia
| | - Timothy Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Jatinder Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia
| | - Desmond Auer
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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Sakthivel K, Kumar A, Gautam RK, Manigundan K, Laha GS, Velazhahan R, Singh R, Yadav IS. Intra-regional diversity of rice bacterial blight pathogen, Xanthomonas oryzae pv. oryzae, in the Andaman Islands, India: revelation by pathotyping and multilocus sequence typing. J Appl Microbiol 2020; 130:1259-1272. [PMID: 32767623 DOI: 10.1111/jam.14813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/03/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
Abstract
AIM To investigate the genetic and pathogenic variability of Xanthomonas oryzae pv. oryzae causing bacterial blight in rice on the remote Andaman Islands, India. METHODS AND RESULTS A total of 27 yellow-pigmented bacterial isolates representing rice fields of Andaman Islands incited blight on the susceptible-rice cultivar, C14-8. Phenotypic, pathogenic traits and 16S rRNA gene sequences revealed their identity as X. oryzae pv. oryzae. Virulence profiling indicated the prevalence of seven pathotypes of X. oryzae pv. oryzae on the Islands. Pathotypes-VI and -VII were highly virulent, whereas the pathotype-I was less virulent. Multilocus sequence typing based on nucleotide sequence polymorphism in nine housekeeping genes dnaK; fyuA; gyrB (two loci): rpoD; fusA; gapA; gltA and lepA clustered 27 isolates into 17 sequence types (STs) segregated into two clonal-complexes (CC). While CC-I comprised of isolates from Andaman Island, the CC-II is a mixture of isolates representing mainland India and Andaman Island. The data revealed trans-boundary pathogen introduction and a consequent intra-regional diversification on these islands due to the deployment of different rice cultivars in different regions. CONCLUSIONS Genotyping and pathotyping of sland isolates revealed seven pathotypes distributed in two clonal complexes with strong indications for trans-boundary movement and consequent diversification of the bacterial pathogen. Highly virulent pathotypes of X. oryzae pv. oryzae that could overcome combinations of R-genes, xa13+Xa21 as well as xa5+xa13 were found prevalent in the Andaman Islands SIGNIFICANCE AND IMPACT OF THE STUDY: Genetic and virulence analysis of X. oryzae pv. oryzae in the Andaman Islands revealed introduction and host-mediated regional diversification and local adaptation of X oryzae pv. oryzae. The study calls for the need of multi-gene pyramiding for durable disease resistance and establishing stringent quarantine measures for safeguarding island agricultural practices in the future.
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Affiliation(s)
- K Sakthivel
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - A Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - R K Gautam
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - K Manigundan
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - G S Laha
- Division of Crop Protection, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - R Velazhahan
- Center for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - R Singh
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - I S Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
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Development of Real-Time and Colorimetric Loop Mediated Isothermal Amplification Assay for Detection of Xanthomonas gardneri. Microorganisms 2020; 8:microorganisms8091301. [PMID: 32858943 PMCID: PMC7563391 DOI: 10.3390/microorganisms8091301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 01/16/2023] Open
Abstract
Xanthomonas gardneri is one of the causal agents of bacterial spot (BS), an economically important bacterial disease of tomato and pepper. Field-deployable and portable loop-mediated isothermal amplification (LAMP)-based instruments provide rapid and sensitive detection of plant pathogens. In order to rapidly and accurately identify and differentiate X. gardneri from other BS-causing Xanthomonas spp., we optimized a new real-time monitoring LAMP-based method targeting the X. gardneri-specific hrpB gene. Specificity and sensitivity of real-time and colorimetric LAMP assays were tested on the complex of bacterial strains pathogenic to tomato and pepper and on plants infected by the pathogen. The assay detection limit was 1 pg/μL of genomic DNA with an assay duration of only 30 min. The use of portable and handheld instruments allows for fast analysis, reducing the diagnosis time, and can contribute to proper disease management and control of X. gardneri. Due to the high efficiency of this method, we suggest its use as a standard diagnostic tool during phytosanitary controls.
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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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Morinière L, Burlet A, Rosenthal ER, Nesme X, Portier P, Bull CT, Lavire C, Fischer-Le Saux M, Bertolla F. Clarifying the taxonomy of the causal agent of bacterial leaf spot of lettuce through a polyphasic approach reveals that Xanthomonas cynarae Trébaol et al. 2000 emend. Timilsina et al. 2019 is a later heterotypic synonym of Xanthomonas hortorum Vauterin et al. 1995. Syst Appl Microbiol 2020; 43:126087. [PMID: 32690196 DOI: 10.1016/j.syapm.2020.126087] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/21/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022]
Abstract
Assessment of the taxonomy and diversity of Xanthomonas strains causing bacterial leaf spot of lettuce (BLSL), commonly referred to as Xanthomonas campestris pv. vitians, has been a long-lasting issue which held back the global efforts made to understand this pathogen. In order to provide a sound basis essential to its study, we conducted a polyphasic approach on strains obtained through sampling campaigns or acquired from collections. Results of a multilocus sequence analysis crossed with phenotypic assays revealed that the pathotype strain does not match the description of the nomenspecies provided by Brown in 1918. However, strain LMG 938=CFBP 8686 does fit this description. Therefore, we propose that it replaces LMG 937=CFBP 2538 as pathotype strain of X. campestris pv. vitians. Then, whole-genome based phylogenies and overall genome relatedness indices calculated on taxonomically relevant strains exhibited the intermediate position of X. campestris pv. vitians between closely related species Xanthomonas hortorum and Xanthomonas cynarae. Phenotypic profiles characterized using Biolog microplates did not reveal stable diagnostic traits legitimizing their distinction. Therefore, we propose that X. cynarae Trébaol et al. 2000 emend. Timilsina et al. 2019 is a later heterotypic synonym of X. hortorum, to reclassify X. campestris pv. vitians as X. hortorum pv. vitians comb. nov. and to transfer X. cynarae pathovars in X. hortorum as X. hortorum pv. cynarae comb. nov. and X. hortorum pv. gardneri comb. nov. An emended description of X. hortorum is provided, making this extended species a promising model for the study of Xanthomonas quick adaptation to different hosts.
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Affiliation(s)
- Lucas Morinière
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
| | - Alexandre Burlet
- Station d'Expérimentation Rhône-Alpes Information Légumes, SERAIL, 69126 Brindas, France
| | - Emma R Rosenthal
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA
| | - Xavier Nesme
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
| | - Perrine Portier
- IRHS, INRAE, Agrocampus-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA
| | - Céline Lavire
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
| | - Marion Fischer-Le Saux
- IRHS, INRAE, Agrocampus-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France.
| | - Franck Bertolla
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
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Mirghasempour SA, Huang S, Studholme DJ, Brady CL. A Grain Rot of Rice in Iran Caused by a Xanthomonas Strain Closely Related to X. sacchari. PLANT DISEASE 2020; 104:1581-1583. [PMID: 32271645 DOI: 10.1094/pdis-01-20-0179-sc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Rice grain rot disease was detected for the first time in Mazandaran Province, Iran. The bacteria isolated from infected rice plants showed grains rotted and darkening. A Xanthomonas strain closely connected to X. sacchari was identified using molecular and whole genome sequencing approaches confirmed as the causal agent by fulfilling Koch's postulates.
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Affiliation(s)
- S Ali Mirghasempour
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Shiwen Huang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, Devon, EX4 4QD, U.K
| | - Carrie L Brady
- Centre for Research in Bioscience, University of the West of England, Bristol, BS16 1QY, U.K
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Lee YA, Yang PY, Huang SC. Characterization, Phylogeny, and Genome Analyses of Nonpathogenic Xanthomonas campestris Strains Isolated from Brassica Seeds. PHYTOPATHOLOGY 2020; 110:981-988. [PMID: 32167850 DOI: 10.1094/phyto-08-19-0319-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonads were detected by using the Xan-D(CCF) medium from the brassica seeds, and their pathogenicity was determined by plant inoculation tests. It was found that some seed lots were infested with Xanthomonas campestris pv. campestris, some with X. campestris pv. raphani, and some with nonpathogenic xanthomonads. The nonpathogenic xanthomonad strains were identified as X. campestris, and the multilocus sequence analysis showed that the nonpathogenic X. campestris strains were grouped together with pathogenic X. campestris, but not with nonpathogenic strains of X. arboricola. In addition, all isolated X. campestris pv. campestris and X. campestris pv. raphani strains were positive in the hrpF-PCR, but the nonpathogenic strains were negative. It was further found that nonpathogenic X. campestris strain nE1 does not contain the entire pathogenicity island (hrp gene cluster; type III secretion system) and all type III effector protein genes based on the whole genome sequence analyses. The nonpathogenic X. campestris strain nE1 could acquire the entire pathogenicity island from the endemic X. campestris pv. campestris and X. campestris pv. raphani strains by conjugation, but type III effector genes were not cotransferred. The studies showed that the nonpathogenic X. campestris strains indeed exist on the brassica seeds, but it could be differentiated by the PCR assays on the hrp and type III effector genes. Nevertheless, the nonpathogenic X. campestris strains cannot be ignored because they may be potential gene resources to increase genetic diversity in the endemic pathogenic X. campestris pv. campestris and X. campestris pv. raphani strains.
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Affiliation(s)
- Yung-An Lee
- Department of Life Science, Fu Jen Catholic University, Xin-Zhuang District, New Taipei City, Taiwan, Republic of China
| | - Pei-Yu Yang
- Department of Life Science, Fu Jen Catholic University, Xin-Zhuang District, New Taipei City, Taiwan, Republic of China
| | - Shau-Chang Huang
- Department of Life Science, Fu Jen Catholic University, Xin-Zhuang District, New Taipei City, Taiwan, Republic of China
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Kyrova E, Egorova M, Ignatov A. Species of the genus Xanthomonas infecting cereals and oilseeds in the Russian Federation and its diagnostics. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20201800017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Plant pathogenic bacteria of the genus Xanthomonas display high levels of genetic diversity and cause remarkable damage to about 400 plant species. In 2001–2008, a new group of strains of Xanthomonas arboricola has been found as pathogens on novel host plants such as wheat, rye, barley, tomato, sunflower, and brassicas in Russia. Physiological tests and multilocus sequence typing (MLST) analysis confirmed their position within the Xanthomonas arboricola species. The obtained draft genome sequence of Xanthomonas arboricola strain 3004 from barley plants, also virulent to sunflower, brassicas, and chestnut, has demonstrated an evidence for the lateral gene transfer (LGT) of the virulence genes. It can be suggested that the virE and other genes of T4SS, obtained due to LGT, may contribute to the host range extension. Thus, T4SS genes can be used as the target for group-specific PCR analysis of this emerging pathogen of cereals and oilseeds. We propose to use virB3, virB4, and virB9 genes to design a detection system.
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Sapkota S, Mergoum M, Liu Z. The translucens group of Xanthomonas translucens: Complicated and important pathogens causing bacterial leaf streak on cereals. MOLECULAR PLANT PATHOLOGY 2020; 21:291-302. [PMID: 31967397 PMCID: PMC7036361 DOI: 10.1111/mpp.12909] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/14/2019] [Accepted: 12/21/2019] [Indexed: 05/31/2023]
Abstract
UNLABELLED Xanthomonas translucens is a group of gram-negative bacteria that can cause important diseases in cereal crops and forage grasses. Different pathovars have been defined according to their host ranges, and molecular and biochemical characteristics. Pathovars have been placed into two major groups: translucens and graminis. The translucens group contains the pathovars causing bacterial leaf streak (BLS) on cereal crops such as wheat, barley, triticale, rye, and oat. In recent years, BLS has re-emerged as a major problem for many wheat- and barley-producing areas worldwide. The biology of the pathogens and the host-pathogen interactions in cereal BLS diseases were poorly understood. However, recent genome sequence data have provided an insight into the bacterial phylogeny and identification and pathogenicity/virulence. Furthermore, identification of sources of resistance to BLS and mapping of the resistance genes have been initiated. TAXONOMY Kingdom Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species X. translucens; translucens group pathovars: undulosa, translucens, cerealis, hordei, and secalis; graminis group pathovars: arrhenatheri, graminis, poae, phlei; newly established pathovar: pistaciae. HOST RANGE X. translucens mainly infects plant species in the Poaceae with the translucens group on cereal crop species and the graminis group on forage grass species. However, some strains have been isolated from, and are able to infect, ornamental asparagus and pistachio trees. Most pathovars have a narrow host range, while a few can infect a broad range of hosts. GENOME The complete genome sequence is available for two X. translucens pv. undulosa strains and one pv. translucens strain. A draft genome sequence is also available for at least one strain from each pathovar. The X. translucens pv. undulosa strain Xt4699 was the first to have its complete genome sequenced, which consists of 4,561,137 bp with total GC content approximately at 68% and 3,528 predicted genes. VIRULENCE MECHANISMS Like most xanthomonads, X. translucens utilizes a type III secretion system (T3SS) to deliver a suite of T3SS effectors (T3Es) inside plant cells. Transcription activator-like effectors, a special group of T3Es, have been identified in most of the X. translucens genomes, some of which have been implicated in virulence. Genetic factors determining host range virulence have also been identified.
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Affiliation(s)
- Suraj Sapkota
- Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaGriffin Campus, GriffinGAUSA
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaGriffin Campus, GriffinGAUSA
- Department of Crop and Soil SciencesUniversity of GeorgiaGriffin Campus, GriffinGAUSA
| | - Zhaohui Liu
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
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Curland RD, Gao L, Hirsch CD, Ishimaru CA. Localized Genetic and Phenotypic Diversity of Xanthomonas translucens Associated With Bacterial Leaf Streak on Wheat and Barley in Minnesota. PHYTOPATHOLOGY 2020; 110:257-266. [PMID: 31448998 DOI: 10.1094/phyto-04-19-0134-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial leaf streak (BLS) of wheat and barley has been a disease of increasing concern in the Upper Midwest over the past decade. In this study, intra- and interfield genetic and pathogenic diversity of bacteria causing BLS in Minnesota was evaluated. In 2015, 89 strains were isolated from 100 leaf samples collected from two wheat and two barley fields naturally infected with BLS. Virulence assays and multilocus sequence alignments of four housekeeping genes supported pathovar identifications. All wheat strains were pathogenic on wheat and barley and belonged to the same lineage as the Xanthomonas translucens pv. undulosa-type strain. All barley strains were pathogenic on barley but not on wheat. Three lineages of barley strains were detected. The frequency and number of sequence types of each pathovar varied within and between fields. A significant population variance was detected between populations of X. translucens pv. undulosa collected from different wheat fields. Population stratification of X. translucens pv. translucens was not detected. Significant differences in virulence were detected among three dominant sequence types of X. translucens pv. undulosa but not those of X. translucens pv. translucens. Field trials with wheat and barley plants inoculated with strains of known sequence type and virulence did not detect significant race structures within either pathovar. Knowledge of virulence, sequence types, and population structures of X. translucens on wheat and barley can support studies on plant-bacterial interactions and breeding for BLS disease resistance.
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Affiliation(s)
- Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Liangliang Gao
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Carol A Ishimaru
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Multiplex real-time PCR for the detection of Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato and pathogenic Xanthomonas species on tomato plants. PLoS One 2020; 15:e0227559. [PMID: 31910230 PMCID: PMC6946519 DOI: 10.1371/journal.pone.0227559] [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] [Received: 09/16/2019] [Accepted: 12/20/2019] [Indexed: 01/08/2023] Open
Abstract
A multiplex real-time PCR method based on fluorescent TaqMan® probes was developed for the simultaneous detection of the tomato pathogenic bacteria Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato and bacterial spot-causing xanthomonads. The specificity of the multiplex assay was validated on 44 bacterial strains, including 32 target pathogen strains as well as closely related species and nontarget tomato pathogenic bacteria. The designed multiplex real-time PCR showed high sensitivity when positive amplification was observed for one pg of bacterial DNA in the cases of Clavibacter michiganensis subsp. michiganensis and Pseudomonas syringae pv. tomato bacteria and 100 pg for bacterial spot-causing xanthomonads. The reliability of the developed multiplex real-time PCR assay for in planta detection was verified by recognition of the target pathogens in 18 tomato plants artificially inoculated by each of the target bacteria and tomato samples from production greenhouses.
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Abd-El-Khair H. Biological Control of Phyto-pathogenic Bacteria. COTTAGE INDUSTRY OF BIOCONTROL AGENTS AND THEIR APPLICATIONS 2020:299-336. [DOI: 10.1007/978-3-030-33161-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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