Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe
    Taparia, T. ; Krijger, M.C. ; Haynes, Edward ; Elphinstone, J.G. ; Noble, R. ; Wolf, J.M. van der - \ 2020
    BMC Genomics 21 (2020). - ISSN 1471-2164
    Background: Bacterial blotch is a group of economically important diseases affecting the cultivation of common button mushroom, Agaricus bisporus. Despite being studied for more than a century, the identity and nomenclature of blotch-causing Pseudomonas species is still unclear. This study aims to molecularly characterize the phylogenetic and phenotypic diversity of blotch pathogens in Western Europe.
    Methods: In this study, blotched mushrooms were sampled from farms across the Netherlands, United Kingdom and Belgium. Bacteria were isolated from symptomatic cap tissue and tested in pathogenicity assays on fresh caps and in pots. Whole genome sequences of pathogenic and non-pathogenic isolates were used to establish phylogeny via multi-locus sequence alignment (MLSA), average nucleotide identity (ANI) and in-silico DNA:DNA hybridization (DDH) analyses. Results: The known pathogens “Pseudomonas gingeri”, P. tolaasii, “P. reactans” and P. costantinii were recovered from blotched mushroom caps. Seven novel pathogens were also identified, namely, P. yamanorum, P. edaphica, P. salomonii and strains that clustered with Pseudomonas sp. NC02 in one genomic species, and three nonpseudomonads, i.e. Serratia liquefaciens, S. proteamaculans and a Pantoea sp. Insights on the pathogenicity and symptom severity of these blotch pathogens were also generated.
    Conclusion: A detailed overview of genetic and regional diversity and the virulence of blotch pathogens in Western Europe, was obtained via the phylogenetic and phenotypic analyses. This information has implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management.
    Systemic colonization of potato plants resulting from potato haulm inoculation with Dickeya solani or Pectobacterium parmentieri
    Kastelein, P. ; Forch, M.G. ; Krijger, M.C. ; Zouwen, P.S. van der; Berg, W. van den; Wolf, J.M. van der - \ 2020
    Canadian Journal of Plant Pathology = Revue Canadienne de Phytopathologie (2020). - ISSN 0706-0661 - p. 1 - 15.
    blackleg - Confocal laser scanning microscopy - fluorescence microscopy - GFP-tagged strains - haulm destruction - leaf wounding - slow wilt
    In two glasshouse experiments, colonization of potato (Solanum tuberosum L.) plants by the bacterial pathogens Dickeya solani and Pectobacterium parmentieri was studied after leaf infection. Leaves, whether or not artificially wounded, were spray-inoculated with various densities of green-fluorescent protein tagged strains of the pathogens, avoiding contamination of soil during inoculation. Microscopy analysis indicated that both pathogens were able to penetrate and colonize hydathodes, stomata and wounds of inoculated leaves. Dickeya solani was detected at 42 days after inoculation in leaves, stems, stolons and occasionally in tubers, whereas P. parmentieri was restricted to leaves, stems and stolons, and could not be detected in tubers. The infection percentage was higher for plants with wounded leaves than for plants with untouched leaves, and higher at higher inoculum densities. Nevertheless, infection of leaves could also occur at low densities of D. solani (102 cfu mL−1). We further investigated the risks for translocation of the pathogens from infected haulms through soil into progeny tubers after haulm destruction. In a glasshouse experiment, populations of the pathogens increased in haulms in the first week after chemical or mechanical destruction, but decreased in the second week. For P. parmentieri, transmission occurred from destroyed haulms via soil into progeny tubers in soil, but not for D. solani.
    Genome Resource of Two Potato Strains of Ralstonia solanacearum Biovar 2 (Phylotype 4 IIB/sequevar 1) and Biovar 2T (Phylotype IIB/Sequevar 25) Isolated from lowlands in Iran
    Sedighian, Nasim ; Krijger, M.C. ; Taparia, T. ; Mohsen Taghavi, S. ; Wicker, Emmanuel ; Wolf, J.M. van der; Osdaghi, Ebrahim - \ 2020
    Molecular Plant-Microbe Interactions 33 (2020)7. - ISSN 0894-0282
    Ralstonia solanacearum the causal agent of bacterial wilt and brown rot disease is one of the major pathogens of solanaceous crops including potato around the globe. Biovar 2T (phylotype II/sequevar 25) of R. solanacearum is adapted to tropical lowlands and only reported from South America and Iran. So far, no genome resource of the biovar 2T of the pathogen was available. Here we present the near complete genome sequences of the biovar 2T strain CFBP 8697 as well as the strain CFBP 8695 belonging to biovar 2/race 3, both isolated from potato in Iran. The genomic data of biovar 2T will extend our understanding of the virulence features of R. solanacearum, and pave the way of research on biovar 2T functional and interaction genetics.
    Six Multiplex TaqManTM-qPCR Assays for Quantitative Diagnostics of Pseudomonas Species Causative of Bacterial Blotch Diseases of Mushrooms
    Taparia, T. ; Krijger, M.C. ; Hodgetts, Jennifer ; Hendriks, M.J.A. ; Elphinstone, J.G. ; Wolf, J.M. van der - \ 2020
    Frontiers in Microbiology (2020)11. - ISSN 1664-302X
    Bacterial blotch is a group of economically important diseases of the common button mushroom (Agaricus bisporus). Once the pathogens are introduced to a farm, mesophilic growing conditions (that are optimum for mushroom production) result in severe and widespread secondary infections. Efficient, timely and quantitative detection of the pathogens is hence critical for the design of localized control strategies and prediction of disease risk. This study describes the development of real-time TaqManTM assays that allow molecular diagnosis of three currently prevalent bacterial blotch pathogens: “Pseudomonas gingeri,” Pseudomonas tolaasii and (as yet uncharacterized) Pseudomonas strains (belonging to Pseudomonas salomonii and Pseudomonas edaphica). For each pathogen, assays targeting specific DNA markers on two different loci, were developed for primary detection and secondary verification. All six developed assays showed high diagnostic specificity and sensitivity when tested against a panel of 63 Pseudomonas strains and 40 other plant pathogenic bacteria. The assays demonstrated good analytical performance indicated by linearity across calibration curve (>0.95), amplification efficiency (>90%) and magnitude of amplification signal (>2.1). The limits of detection were optimized for efficient quantification in bacterial cultures, symptomatic tissue, infected casing soil and water samples from mushroom farms. Each target assay was multiplexed with two additional assays. Xanthomonas campestris was detected as an extraction control, to account for loss of DNA during sample processing. And the total Pseudomonas population was detected, to quantify the proportion of pathogenic to beneficial Pseudomonas in the soil. This ratio is speculated to be an indicator for blotch outbreaks. The multiplexed assays were successfully validated and applied by routine testing of diseased mushrooms, peat sources, casing soils, and water from commercial production units.
    Development and evaluation of two TaqMan assays for generic detection of Dickeya species
    Zijlstra, Carolien ; Haas, Lia Groenenboom De; Krijger, Marjon ; Verstappen, Els ; Warris, Sven ; Haan, Eisse de; Wolf, Jan van der - \ 2020
    European Journal of Plant Pathology 156 (2020). - ISSN 0929-1873 - p. 311 - 316.
    Accuracy - Blackleg - Diagnostics - Refused sample material - Seed potato - Sensitivity - Specificity

    Two TaqMan assays were developed for generic detection of Dickeya species in plant material. The assays enabled detection of all strains of D. chrysanthemi, D. dadantii, D. dianthicola, D. solani and D. zeae tested, but only weak reactions were found with strains of D. paradisiaca. The assays enabled detection of as low as 100 fg of target DNA in a background of potato DNA. The assays were evaluated with DNA extracted from potato tuber extracts, in which different Dickeya species can be present. Results of both assays were highly similar indicating that they can be used reliably in potato seed testing programs.

    Use of disease suppressiveness in the battle against potato blackleg.
    Wolf, Jan van der; Swart-Coipan, Elena ; Krijger, Marjon ; Kastelein, Pieter ; Nijhuis, Els ; Kurm, Viola ; Warris, Sven ; Fokkema, J. - \ 2019
    Use of disease suppressiveness in the battle against potato blackleg
    Wolf, J.M. van der; Coipan, E.C. ; Krijger, M.C. ; Kastelein, P. ; Nijhuis, E.H. ; Kurm, V. ; Warris, S. ; Fokkema, J. - \ 2019
    Use of disease suppressiveness in the battle against potato blackleg
    Wolf, J.M. van der; Coipan, E.C. ; Krijger, M.C. ; Kastelein, P. ; Nijhuis, E.H. ; Kurm, V. ; Warris, S. ; Fokkema, J. - \ 2019
    Valse meeldauw-vrij plantgoed van ui door warme luchtbehandeling : Teeltvoorschriften valse meeldauw-vrij verklaring; een alternatieve methode
    Evenhuis, A. ; Topper, C.G. ; Krijger, M.C. - \ 2019
    Wageningen : Wageningen Plant Research (Rapport Wageningen Plant Research 7340087100) - 26
    Development and evaluation of a triplex TaqMan assay and Next Generation Sequence Analysis for improved detection of Xylella in plant material
    Bonants, P.J.M. ; Griekspoor, Y. ; Houwers, I.M. ; Krijger, M.C. ; Zouwen, P.S. van der; Lee, T.A.J. van der; Wolf, J.M. van der - \ 2019
    Plant Disease 103 (2019)4. - ISSN 0191-2917 - 36 p.
    Xylella fastidiosa is a heterogenous gram-negative bacterial plant pathogen with a wide host range covering over 300 plant species. Since 2013, in Europe, the presence of the pathogen is increasing in a part of the Mediterranean area, but causes in particular severe disease problems in olive orchards in the Southern part of Italy. Various subspecies of the pathogen were also diagnosed in natural outbreaks and intercepted ornamental plants in Europe, among them Olea europaea, Coffea arabica and Nerium oleander. The host range of the pathogen can vary, depending on the subspecies and even the strain. The availability of fast and reliable diagnostic tools are indispensable in management strategies to control diseases caused by X. fastidiosa. To improve the reliability of the TaqMan assay, currently widely used in surveys, a triplex TaqMan assay was developed in which two specific and sensitive TaqMan assays, previously designed for X. fastidiosa, were combined with an internal control. The triplex assay exhibited the same diagnostic sensitivity as the simplex assays. In addition, the usefulness of a metagenomic approach using next generation sequencing (NGS) was demonstrated, in which total DNA extracted from plant material was sequenced. DNA extracts from plant material free of X. fastidiosa, from artificially inoculated hosts plants or from naturally infected plants sampled in France, Spain and Italy, or intercepted in Austria and The Netherlands, were analysed for the presence of X. fastidiosa using the metagenomic approach. In all samples, even in samples with a low infection level, but not in the pathogen-free samples, DNA reads were detected specific for X. fastidiosa. In most cases, the pathogen could be identified up to the subspecies level and for one sample even the whole genome could be assembled and the sequence type could be determined. All results of NGS analysed samples were confirmed with the triplex TaqMan PCR and LAMP.
    Towards improved methods for detection of Xylella fastidiosa in plant material using triplex TaqMan PCR and NGS analysis
    Bonants, P.J.M. ; Griekspoor, Y. ; Houwers, I.M. ; Krijger, M.C. ; Zouwen, P.S. van der; Lee, T.A.J. van der; Wolf, J.M. van der - \ 2018
    Spread of Xanthomonas fragariae in strawberry fields by machinery
    Kastelein, P. ; Evenhuis, A. ; Zouwen, P.S. van der; Krijger, M.C. ; Wolf, J.M. van der - \ 2018
    EPPO Bulletin 48 (2018)3. - ISSN 0250-8052 - p. 569 - 577.
    The spread of Xanthomonas fragariae in a strawberry field by mowing and runner cutting machinery was studied in the Netherlands during autumn. The blades of a rotary mower became heavily contaminated after trimming the leaves of symptomatic plants. Use of a contaminated mower resulted in infection of plants that were initially free of X. fragariae, even at a distance of 4 m (i.e. 10 mother plants) from the symptomatic plants. Directly after mowing,the pathogen could be detected on damaged leaves at a density of 103–105 cells g-1.Infections were established, although 3 months after mowing symptoms were still absent. There were indications that the use of the mower resulted in the spread of infected leaf material from symptomatic plants to neighbouring beds. Spread by a runner cutting machine was also studied. Again, after cutting the runners of symptomatic plants, high numbers of X. fragariae cells were recovered from debris on the discs of the machine. During cutting, the cut ends of runners of plants initially free of X. fragariae became contaminated, even ata distance of 4 m from the symptomatic plants, but only at low densities of 103 cfu g-1. Three months after stolon cutting, infections were detected in some of the cut plants.
    Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description
    Gétaz, Michael ; Krijger, M.C. ; Rezzonico, F. ; Smits, Theo ; Wolf, J.M. van der; Pothier, Joël F. - \ 2018
    Microbial Genomics 2018 (2018)4. - ISSN 2057-5858
    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.
    Risks for infection of strawberry plants with an aerosolized inoculum of Xanthomonas fragariae
    Wolf, J.M. van der; Evenhuis, A. ; Kastelein, P. ; Krijger, M.C. ; Funke, V.Z. ; Berg, W. van den; Moene, A.F. - \ 2018
    European Journal of Plant Pathology 152 (2018)3. - ISSN 0929-1873 - p. 711 - 722.
    Air sampling - Angular leaf spot - Fragaria x ananasa - Infection thresholds - Particle counters - TaqMan assay

    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.

    Spotless strawberry plants: how to keep them free from Xanthomonas?
    Wolf, J.M. van der; Kastelein, P. ; Evenhuis, A. ; Krijger, M.C. ; Moene, A.F. - \ 2018
    Mushroom Health: A systems study
    Taparia, T. ; Krijger, M.C. ; Hendriks, M.J.A. ; Coipan, E.C. ; Boer, W. de; Wolf, J.M. van der - \ 2017
    Mushroom Health: A systems study
    Taparia, T. ; Krijger, M.C. ; Hendriks, M.J.A. ; Coipan, E.C. ; Boer, W. de; Wolf, J.M. van der - \ 2017
    Suppressive soils for mushroom diseases : A microbiome study
    Taparia, T. ; Krijger, M.C. ; Coipan, E.C. ; Boer, W. de; Wolf, J.M. van der - \ 2017
    Dissemination of Xanthomonas fragariae, causative agent of angular leaf spot in strawberry planting material
    Evenhuis, A. ; Wolf, J.M. van der; Kastelein, P. ; Moene, A.F. ; Heusinkveld, B.G. ; Krijger, M.C. ; Zouwen, P.S. van der; Hendriks, M.J.A. - \ 2017
    Risks for infection of strawberry plants by air-borne inoculum of Xanthomonas fragariae
    Evenhuis, A. ; Wolf, J.M. van der; Kastelein, P. ; Heusinkveld, B.G. ; Krijger, M.C. ; Funke, Victoria ; Moene, A.F. - \ 2017
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