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Liang X, Wei F, Yang H, Fan L, Cai X, Ma Y, Shi J, Xing K, Qiu L, Li X, Lu L, Ji J, Wen Y, Feng J. Flagella-Driven Motility Is Critical to the Virulence of Xanthomonas fragariae in Strawberry. PLANT DISEASE 2023; 107:3506-3516. [PMID: 37157097 DOI: 10.1094/pdis-03-23-0409-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: 05/10/2023]
Abstract
Xanthomonas fragariae (X. fragariae) is the causal agent of angular leaf spots (ALS) in strawberry plants. Recently, a study in China isolated X. fragariae strain YL19, which was observed to cause both typical ALS symptoms and dry cavity rot in strawberry crown tissue; this was the first X. fragariae strain to have both these effects in strawberry. In this study, from 2020 to 2022, we isolated 39 X. fragariae strains from diseased strawberries in different production areas in China. Multilocus sequence typing (MLST) and phylogenetic analysis showed that X. fragariae strain YLX21 was genetically different from YL19 and other strains. Tests indicated that YLX21 and YL19 had different pathogenicities toward strawberry leaves and stem crowns. YLX21 did not cause ALS symptoms, rarely caused dry cavity rot in strawberry crown after wound inoculation, and never caused dry cavity rot after spray inoculation, but it did cause severe ALS symptoms after spray inoculation. However, YL19 caused more severe symptoms in strawberry crowns under both conditions. Moreover, YL19 had a single polar flagellum, while YLX21 had no flagellum. Motility and chemotaxis assays showed that YLX21 had weaker motility than YL19, which may explain why YLX21 tended to multiply in situ within the strawberry leaf rather than migrate to other tissues, causing more severe ALS symptoms and mild crown rot symptoms. Taken together, the new strain YLX21 helped us reveal critical factors underlying the pathogenicity of X. fragariae and the mechanism by which dry cavity rot in strawberry crowns forms.
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Affiliation(s)
- Xia Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Feng Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Hongliang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Li Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Xiaolin Cai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Yangyang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Jiancheng Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Kun Xing
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Lijuan Qiu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Xixuan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Lijuan Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Jie Ji
- Institute of Plant Protection, Fujian Academy of Agriculture Sciences, Fuzhou 350013, Fujian, China
| | - Yingqiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiayue Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
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DNA Markers for Detection and Genotyping of Xanthomonas euroxanthea. Microorganisms 2022; 10:microorganisms10061078. [PMID: 35744598 PMCID: PMC9227330 DOI: 10.3390/microorganisms10061078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 12/04/2022] Open
Abstract
Xanthomonas euroxanthea is a bacterial species encompassing both pathogenic and non-pathogenic strains and is frequently found colonizing the same host plants as X. arboricola. This presents the need to develop a detection and genotyping assay able to track these bacteria in microbial consortia with other xanthomonads. Eight X. euroxanthea-specific DNA markers (XEA1-XEA8) were selected by comparative genomics and validated in silico regarding their specificity and consistency using BLASTn, synteny analysis, CG content, codon usage (CAI/eCAI values) and genomic proximity to plasticity determinants. In silico, the selected eight DNA markers were found to be specific and conserved across the genomes of 11 X. euroxanthea strains, and in particular, five DNA markers (XEA4, XEA5, XEA6, XEA7 and XEA8) were unfailingly found in these genomes. A multiplex of PCR targeting markers XEA1 (819 bp), XEA8 (648 bp) and XEA5 (295 bp) was shown to successfully detect X. euroxanthea down to 1 ng of DNA (per PCR reaction). The topology of trees generated with the concatenated sequences of three markers (XEA5, XEA6 and XEA8) and four housekeeping genes (gyrB, rpoD, fyuA and acnB) underlined the equal discriminatory power of these features and thus the suitability of the DNA markers to discriminate X. euroxanthea lineages. Overall, this study displays a DNA-marker-based method for the detection and genotyping of X. euroxanthea strains, contributing to monitoring for its presence in X. arboricola-colonizing habitats. The present study proposes a workflow for the selection of species-specific detection markers. Prospectively, this assay could contribute to unveil alternative host species of Xanthomonas euroxanthea; and improve the control of phytopathogenic strains.
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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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Gétaz M, Puławska J, Smits TH, Pothier JF. Host-Pathogen Interactions between Xanthomonas fragariae and Its Host Fragaria × ananassa Investigated with a Dual RNA-Seq Analysis. Microorganisms 2020; 8:E1253. [PMID: 32824783 PMCID: PMC7465820 DOI: 10.3390/microorganisms8081253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 12/31/2022] Open
Abstract
Strawberry is economically important and widely grown, but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, the gene expression of both plant and bacteria in planta was analyzed at two time points, 12 and 29 days post inoculation, in order to compare the pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28,588 known genes in strawberry and 4046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis-related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most X. fragariae genes involved in host interaction, recognition, and pathogenesis were lower expressed at late-phase infection. This study gives a first insight into the interaction of X. fragariae with its host. The strawberry plant changed gene expression in order to consistently adapt its metabolism with the progression of infection.
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Affiliation(s)
- Michael Gétaz
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
| | - Joanna Puławska
- Department of Phytopathology, Research Institute of Horticulture, 96-100 Skierniewice, Poland;
| | - Theo H.M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
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Wang H, Turechek WW. Detection of Viable Xanthomonas fragariae Cells in Strawberry Using Propidium Monoazide and Long-Amplicon Quantitative PCR. PLANT DISEASE 2020; 104:1105-1112. [PMID: 32040389 DOI: 10.1094/pdis-10-19-2248-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonas fragariae causes angular leaf spot in strawberry. The pathogen's association with its host tissue is thought to be a condition for its survival. Consequently, transmission of the pathogen to field production sites occurs almost exclusively through the movement of contaminated planting stock. The aim of this study was to develop a propidium monoazide (PMA)-quantitative PCR (qPCR) protocol for specific detection of viable X. fragariae cells. The qPCR procedure was developed for two different primer pairs: one producing a long amplicon (863 bp) and the other a short amplicon (61 bp). Both pairs were tested on mixtures of viable and heat-killed bacteria cells, bacteria-spiked strawberry petiole samples, and petioles collected from symptomatic, inoculated plants. The results showed that long-amplicon PMA-qPCR enabled specific and sensitive detection of X. fragariae with a detection limit of 103 CFU/ml, and it significantly improved PMA efficiency in differentiating viable from dead bacterial cells relative to short-amplicon PMA-qPCR. Based on the delta threshold cycle (Ct) values (i.e., the difference in Ct values between PMA-treated and nontreated samples), the long-amplicon PMA-qPCR was able to suppress the detection of dead X. fragariae cells 1.9- to 3.1-fold across all petiole samples tested. The quantification results from PMA-qPCR for mixtures of viable and dead cells were highly correlated with the predicted bacterial concentrations in a linear relationship (R2 = 0.981). This assay can be useful for identifying inoculum sources in the strawberry production cycle, which may lead to improved disease management strategies.
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Affiliation(s)
- Hehe Wang
- Department of Agricultural and Environmental Sciences, Clemson University, Blackville, SC
| | - William W Turechek
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Fort Pierce, FL
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mRNA extraction of Xanthomonas fragariae in strawberry and validation of reference genes for the RT-qPCR for study of bacterial gene expression. Mol Biol Rep 2019; 46:5723-5733. [PMID: 31368022 DOI: 10.1007/s11033-019-05006-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/26/2019] [Indexed: 01/11/2023]
Abstract
This is the first study which describes a unique procedure of isolating of high-quality, intact RNA from strawberry leaves of Xanthomonas fragariae, three most suitable reference genes, crucial for the normalization of RT-qPCR data for this pathogen and accurate expression analysis of target genes. In our study, various mathematic algorithms: NormFinder geNorm, BestKeeper, the delta CT method, RefFinder were adopted for validation of most stable reference genes from nine candidate genes (ffh, glyA, gyrA, gyrB, proC, pykA, recA, rpoB, rpoD). The analyses allowing to select three most suitable pioneer reference genes, gyrB, ffh, and pykA, that we recommend for the normalization of RT-qPCR data and for the study of the expression of target genes in Xf. Moreover, their combination as references allowed for an accurate expression analysis and computation of the fold change of the flhF and iroN2 genes in Xf. These two genes are important for the success of the colonization of plant tissue and pathogenicity and sequences of primers designed to study these genes, are presented.
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Haack SE, Walse SS, Nguyen K, Adaskaveg JE. Management of Xanthomonas fragariae with Pre- and Postharvest Treatments to Overcome Trade Barriers for California Strawberries. PLANT DISEASE 2019; 103:1256-1263. [PMID: 30964420 DOI: 10.1094/pdis-08-18-1395-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Xanthomonas fragariae, the causal agent of angular leaf spot (ALS) of strawberry, is a quarantine pathogen in some export markets, causing trade restrictions and economic loss to the California fresh-market strawberry industry. Preharvest chemical management options are limited to copper, and there are no postharvest treatments available that reduce populations of the pathogen if ALS is detected at an export destination. Here, we report high preharvest efficacy for the experimental bactericide amino thiadiazole and the commercial product zinc thiadiazole, alone and in mixtures with low rates of copper or the antibiotic kasugamycin, with average disease incidence reduction of up to 92.8% compared with the control. Although effective against quarantine insect pests of strawberry, postharvest methyl bromide fumigation was ineffective against X. fragariae in diseased plant tissue at a standard commercial rate. Postharvest propylene oxide fumigation, used for decades by the California nut industries for insect and microbial disinfestation, significantly reduced X. fragariae populations in infected leaflet tissues by at least 2.5-log compared with controls at a dose of ≥142 µg/ml for 2 h at 15 to 20°C. Fumigated leaflets showed little to no phytotoxicity at effective rates, and fumigated fruit were not significantly affected in appearance or susceptibility to postharvest gray mold or Rhizopus rot following storage at 2°C for 3 days and at 15°C for an additional 5 days. Together, these new treatments offer potential strategies for establishing a systems approach with preharvest treatments significantly reducing the risk of ALS on plants and, in response to quarantine detections, a postharvest fumigation treatment that reduces viable pathogen populations in existing lesions.
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Affiliation(s)
- Stacey E Haack
- 1 Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521; and
| | - Spencer S Walse
- 2 San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture, Agricultural Research Service, Parlier, CA 93648
| | - Kevin Nguyen
- 1 Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521; and
| | - James E Adaskaveg
- 1 Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521; and
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Gétaz M, Krijger M, Rezzonico F, Smits THM, van der Wolf JM, Pothier JF. Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description. Microb Genom 2018; 4:e000189. [PMID: 29874158 PMCID: PMC6113873 DOI: 10.1099/mgen.0.000189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/11/2018] [Indexed: 11/18/2022] Open
Abstract
Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry plants. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing tools on a comprehensive strain collection representing global and temporal distribution of the pathogen. Clustered regularly interspaced short palindromic repeat regions (CRISPRs) and variable number of tandem repeats (VNTRs) were identified within the reference genome of X. fragariae LMG 25863 as a potential source of variation. Strains from our collection were whole-genome sequenced and used in order to identify variable spacers and repeats for discriminative purpose. CRISPR spacer analysis and multiple-locus VNTR analysis (MLVA) displayed a congruent population structure, in which two major groups and a total of four subgroups were revealed. The two main groups were genetically separated before the first X. fragariae isolate was described and are potentially responsible for the worldwide expansion of the bacterial disease. Three primer sets were designed for discriminating CRISPR-associated markers in order to streamline group determination of novel isolates. Overall, this study describes typing methods to discriminate strains and monitor the pathogen population structure, more especially in the view of a new outbreak of the pathogen.
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Affiliation(s)
- Michael Gétaz
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | - Marjon Krijger
- Wageningen University and Research, Wageningen, the Netherlands
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | | | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
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Wang H, McTavish C, Turechek WW. Colonization and Movement of Xanthomonas fragariae in Strawberry Tissues. PHYTOPATHOLOGY 2018; 108:681-690. [PMID: 29298111 DOI: 10.1094/phyto-10-17-0356-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Xanthomonas fragariae causes angular leaf spot of strawberry, an important disease in strawberry growing regions worldwide. To better understand how X. fragariae multiplies and moves in strawberry plants, a green fluorescent protein (GFP)-labeled strain was constructed and used to monitor the pathogen's presence in leaf, petiole, and crown tissue with fluorescence microscopy following natural and wound inoculation in three strawberry cultivars. Taqman PCR was used to quantify bacterial densities in these same tissues regardless of the presence of GFP signal. Results showed X. fragariae colonized leaf mesophyll, the top 1 cm portion of the petiole adjacent to the leaf blade, and was occasionally found colonizing xylem vessels down to the middle of the petioles. The colonization of vascular bundles and the limited systemic movement that was observed appeared to be a passive process, of which the frequency increased with wounding and direct infiltration of bacteria into leaf veins. X. fragariae was able to directly enter petioles and colonize the space under the epidermis. Systemic movement of the bacteria into crown and other uninoculated tissues was not detected visually by GFP. However, X. fragariae was occasionally detected in these tissues by qPCR, but at quantities very near the qPCR detection limit. Petiole tissue harboring bacteria introduced either by direct entry through natural openings or wounds, or by systemic movement from infected foliar tissue, likely serves as a main source of initial inoculum in field plantings.
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Affiliation(s)
- Hehe Wang
- First author: Department of Plant and Environmental Sciences, Clemson University, Blackville, SC; second author: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Physiology and Pathology of Tree Fruits Research, Wenatchee, WA; and third author: USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL
| | - Christine McTavish
- First author: Department of Plant and Environmental Sciences, Clemson University, Blackville, SC; second author: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Physiology and Pathology of Tree Fruits Research, Wenatchee, WA; and third author: USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL
| | - William W Turechek
- First author: Department of Plant and Environmental Sciences, Clemson University, Blackville, SC; second author: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Physiology and Pathology of Tree Fruits Research, Wenatchee, WA; and third author: USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL
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van der Wolf JM, Evenhuis A, Kastelein P, Krijger MC, Funke VZ, van den Berg W, Moene AF. Risks for infection of strawberry plants with an aerosolized inoculum of Xanthomonas fragariae. EUROPEAN JOURNAL OF PLANT PATHOLOGY 2018; 152:711-722. [PMID: 30930545 PMCID: PMC6404663 DOI: 10.1007/s10658-018-1513-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 06/09/2023]
Abstract
Xanthomonas fragariae is the causative agent of angular leaf spot of strawberry, a quarantine organism in plant propagation material in the European Union. Field experiments were conducted to assess the risks for infection of strawberry plants through dispersal of an aerosolized inoculum. In practice, pathogen aerosols can be formed during mowing of an infected crop or by water splashing on symptomatic plants during overhead irrigation or rain. In our experiments, aerosols were generated by spraying suspensions of X. fragariae with a density of 108 cfu ml-1 or water under pressure vertically up into the air. In strawberry plants (cv Elsanta) placed at 1.3, 5 and 10 m distance downwind from the spray boom, infections were found, as evidenced with a combination of dilution-plating and molecular techniques, but more frequently in plants wetted prior to inoculation than in plants kept dry. A logarithmic decrease in infection incidence was found with the distance to the inoculum source. Symptomatic plants were found up to 5 m distance from the inoculum source. No infected plants were found in plants placed 4 m upwind or treated with water. In glasshouse studies, it was shown that under conditions favorable for disease development, spray-inoculation of strawberry plants with estimated densities of X. fragariae as low as 2000 cfu per plant were able to cause symptoms both in cv Elsanta and cv Sonata. Results indicate that there is a considerable risk on infections of strawberry plants exposed to aerosolized inoculum.
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Affiliation(s)
- J. M. van der Wolf
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - A. Evenhuis
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - P. Kastelein
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - M. C. Krijger
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - V. Z. Funke
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - W. van den Berg
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - A. F. Moene
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
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Kuang YS, Li SH, Guo Y, Lu JH, He JR, Luo BJ, Jiang FJ, Shen H, Papasian CJ, Pang H, Xia HM, Deng HW, Qiu X. Composition of gut microbiota in infants in China and global comparison. Sci Rep 2016; 6:36666. [PMID: 27827448 PMCID: PMC5101483 DOI: 10.1038/srep36666] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/18/2016] [Indexed: 12/25/2022] Open
Abstract
Symbiotic gut microbiota is essential for human health, and its compositional changes have been associated with various complex disorders. However, systematic investigation of the acquisition and development of gut microbial communities during early infancy are relatively rare, particularly for infants from non-Western countries. In this study, we characterize the colonization and development of infant microbiota in healthy Chinese infants and compare the pattern with those from other countries. The fecal microbiota of 2-month-old infants was considerably more diverse than that of neonates, as indicated by higher relative abundances of Veillonella, Clostridium, Bacteroides, Lactobacillus, Collinsella and Prevotella, and reduction of Escherichia and Enterococcus. The fecal microbiota of vaginally delivered infants (both neonates and 2-month-old) had significant enrichment of Bacteroides, Parabacteroides and Megamonas, whereas cesarean delivered infants had enrichment of Prevotella, Streptococcus and Trabulsiella. By global comparison, we identify three different enterotypes, referred as “P-type”, “A-type ”and “F-type” which were highly abundant in Proteobacteria, Actinobacteria and Firmicutes, respectively. The three enterotypes’ compositons vary geographically. All Chinese infants in our study belong to the P-type. These findings may provide novel insights into our understanding of the establishment of infant fecal bacterial communities.
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Affiliation(s)
- Ya-Shu Kuang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, People's Republic of China
| | - Sheng-Hui Li
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, People's Republic of China
| | - Yong Guo
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, People's Republic of China
| | - Jin-Hua Lu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, People's Republic of China
| | - Jian-Rong He
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, People's Republic of China
| | - Bei-Jun Luo
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, People's Republic of China
| | - Feng-Ju Jiang
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, People's Republic of China
| | - Hui Shen
- Center of Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane School of Public Health and Tropic Medicine, New Orleans, Louisiana, USA
| | - Christopher J Papasian
- Department of Basic Medical Science, School of Medicine, University of Missouri - Kansas City, Kansas City, Missouri, USA
| | - Herbert Pang
- School of Public Health, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Hui-Min Xia
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, People's Republic of China.,Department of Neonatal Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Hong-Wen Deng
- Center of Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, Tulane School of Public Health and Tropic Medicine, New Orleans, Louisiana, USA
| | - Xiu Qiu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, People's Republic of China.,Department of Woman and Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
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12
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Wang H, Turechek WW. A Loop-Mediated Isothermal Amplification Assay and Sample Preparation Procedure for Sensitive Detection of Xanthomonas fragariae in Strawberry. PLoS One 2016; 11:e0147122. [PMID: 26766068 PMCID: PMC4713083 DOI: 10.1371/journal.pone.0147122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/29/2015] [Indexed: 11/18/2022] Open
Abstract
Xanthomonas fragariae is a bacterium that causes angular leaf spot of strawberry. Asymptomatic infection is common and contributes to the difficulties in disease management. The aim of this study was to develop a loop-mediated isothermal amplification (LAMP) assay as an efficient method for detection of asymptomatic infections of X. fragariae. In addition, a new method of sample preparation was developed that allows sampling of a larger amount of plant tissue, hence increasing the detection rate in real-life samples. The sample preparation procedure includes an overnight incubation of strawberry tissues in phosphate-buffered saline (PBS), followed by a quick sample concentration and a boiling step to extract DNA for amplification. The detection limit of the LAMP assay was approximately 2×10(3) CFU/mL for pure bacteria culture and 300 CFU/mL for bacteria spiked strawberry leaf and petiole samples. LAMP provided a 2-3 fold lower detection limit than the standard qPCR assay but was faster, and more user-friendly. The LAMP assay should serve as a rapid, sensitive and cost-effective tool for detecting asymptomatic infections of X. fragariae in strawberry nursery stock and contribute to improved disease management.
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Affiliation(s)
- Hehe Wang
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States of America
| | - William W. Turechek
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States of America
- * E-mail:
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13
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Mirmajlessi SM, Destefanis M, Gottsberger RA, Mänd M, Loit E. PCR-based specific techniques used for detecting the most important pathogens on strawberry: a systematic review. Syst Rev 2015; 4:9. [PMID: 25588564 PMCID: PMC4320524 DOI: 10.1186/2046-4053-4-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/02/2015] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Strawberry diseases are a major limiting factor that severely impact plant agronomic performance. Regarding limitations of traditional techniques for detection of pathogens, researchers have developed specific DNA-based tests as sensitive and specific techniques. The aim of this review is to provide an overview of polymerase chain reaction (PCR)-based methods used for detection or quantification of the most widespread strawberry pathogens, such as Fusarium oxysporum f.sp. fragariae, Phytophthora fragariae, Colletotrichum acutatum, Verticillium dahliae, Botrytis cinerea, Macrophomina phaseolina, and Xanthomonas fragariae. An updated and detailed list of published PCR protocols is presented and discussed, aimed at facilitating access to information that could be particularly useful for diagnostic laboratories in order to develop a rapid, cost-effective, and reliable monitoring technique. METHODS The study design was a systematic review of PCR-based techniques used for detection and quantification of strawberry pathogens. Using appropriate subject headings, AGRICOLA, AGRIS, BASE, Biological Abstracts, CAB Abstracts, Google Scholar, Scopus, Web of Knowledge, and SpringerLink databases were searched from their inception up to April 2014. Two assessors independently reviewed the titles, abstracts, and full articles of all identified citations. Selected articles were included if one of the mentioned strawberry pathogens was investigated based on PCR methods, and a summary of pre-analytical requirements for PCR was provided. RESULTS A total of 259 titles and abstracts were reviewed, of which 22 full texts met all the inclusion criteria. Our systematic review identified ten different protocols for X. fragariae, eight for P. fragariae, four for B. cinerea, six for C. acutatum, three for V. dahlia, and only one for F. oxysporum. The accuracy and sensitivity of PCR diagnostic methods is the focus of most studies included in this review. However, a large proportion of errors in laboratories occur in the pre-analytical phase of the testing process. Due to heterogeneity, results could not be meta-analyzed. CONCLUSIONS From a systematic review of the currently available published literature, effective detection assays to detect the major strawberry pathogens have been developed. These assays can function as a basis for clinical labs, regulatory personnel, and other diagnosticians to adapt or implement for detection of these six important strawberry pathogens.
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Affiliation(s)
- Seyed Mahyar Mirmajlessi
- />Department of Field Crops and Grassland Husbandry, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Marialaura Destefanis
- />Pesticides, Plant Health and Seed Testing Laboratories, Department of Agriculture, Food and the Marine, Backweston Campus, Celbridge, Co. Kildare Ireland
| | - Richard Alexander Gottsberger
- />Department for Molecular Diagnostics of Plant Diseases, Institute for Sustainable Plant Production, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Marika Mänd
- />Department of Plant Protection, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Evelin Loit
- />Department of Field Crops and Grassland Husbandry, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
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Albuquerque P, Caridade CMR, Marcal ARS, Cruz J, Cruz L, Santos CL, Mendes MV, Tavares F. Identification of Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans with novel markers and using a dot blot platform coupled with automatic data analysis. Appl Environ Microbiol 2011; 77:5619-28. [PMID: 21705524 PMCID: PMC3165254 DOI: 10.1128/aem.05189-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/05/2011] [Indexed: 11/20/2022] Open
Abstract
Phytosanitary regulations and the provision of plant health certificates still rely mainly on long and laborious culture-based methods of diagnosis, which are frequently inconclusive. DNA-based methods of detection can circumvent many of the limitations of currently used screening methods, allowing a fast and accurate monitoring of samples. The genus Xanthomonas includes 13 phytopathogenic quarantine organisms for which improved methods of diagnosis are needed. In this work, we propose 21 new Xanthomonas-specific molecular markers, within loci coding for Xanthomonas-specific protein domains, useful for DNA-based methods of identification of xanthomonads. The specificity of these markers was assessed by a dot blot hybridization array using 23 non-Xanthomonas species, mostly soil dwelling and/or phytopathogens for the same host plants. In addition, the validation of these markers on 15 Xanthomonas spp. suggested species-specific hybridization patterns, which allowed discrimination among the different Xanthomonas species. Having in mind that DNA-based methods of diagnosis are particularly hampered for unsequenced species, namely, Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans, for which comparative genomics tools to search for DNA signatures are not yet applicable, emphasis was given to the selection of informative markers able to identify X. fragariae, X. axonopodis pv. phaseoli, and X. fuscans subsp. fuscans strains. In order to avoid inconsistencies due to operator-dependent interpretation of dot blot data, an image-processing algorithm was developed to analyze automatically the dot blot patterns. Ultimately, the proposed markers and the dot blot platform, coupled with automatic data analyses, have the potential to foster a thorough monitoring of phytopathogenic xanthomonads.
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Affiliation(s)
- Pedro Albuquerque
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Faculdade de Ciências, Departamento de Biologia (FCUP), Edifício FC4, Via Panorâmica no. 36, Universidade do Porto, 4150-564 Porto, Portugal
| | - Cristina M. R. Caridade
- Centro de Investigação em Ciências Geo-Espaciais (CICGE), Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
- Instituto Superior de Engenharia de Coimbra (ISEC), Rua Pedro Nunes-Quinta da Nora, 3030-199 Coimbra, Portugal
| | - Andre R. S. Marcal
- Centro de Investigação em Ciências Geo-Espaciais (CICGE), Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
- Centro de Matemática da Universidade do Porto (CMUP), Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
| | - Joana Cruz
- Instituto Nacional de Recursos Biológicos (INRB), Unidade de Investigação de Protecção de Plantas, Tapada da Ajuda, 1349-018 Lisbon, Portugal
| | - Leonor Cruz
- Instituto Nacional de Recursos Biológicos (INRB), Unidade de Investigação de Protecção de Plantas, Tapada da Ajuda, 1349-018 Lisbon, Portugal
| | - Catarina L. Santos
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Marta V. Mendes
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Fernando Tavares
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Faculdade de Ciências, Departamento de Biologia (FCUP), Edifício FC4, Via Panorâmica no. 36, Universidade do Porto, 4150-564 Porto, Portugal
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