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Amy O. Charkowski - One of the best experts on this subject based on the ideXlab platform.

  • detection of Pectobacterium spp and dickeya spp in potato tubers
    Detection of Plant-Pathogenic Bacteria in Seed and other planting material, 2017
    Co-Authors: Solke H. De Boer, Amy O. Charkowski, J.m. Van Der Wolf
    Abstract:

    Bacterial soft rot in potato doliage and tubers is caused by various species in the genera Pectobacterium and Dickeya. Until recently, most potato stem rots were characterized as blackleg, a distinctive black-colored decay starting from the seed tuber; or aerial stem rot, a soft rot of aboveground stems, usally initiaded through stem wounds.

  • Biology and control of Pectobacterium in potato
    American Journal of Potato Research, 2015
    Co-Authors: Amy O. Charkowski
    Abstract:

    Pectobacterium species cause soft rot, blackleg, and stem rot in potato and a wide range of other vegetable crops and ornamental plants. Diseases caused by Pectobacterium are controlled mainly through use of healthy planting material, sanitation and copper sprays. Environmental factors, such as temperature, moisture and soil oxygen concentration, have a large effect on development of diseases caused by Pectobacterium and disease incidence can be unpredictable. The pathogen is spread by various mechanisms including water, seed, equipment and insects. Little is understood about plant resistance to soft rot bacterial pathogens and no commercial potato cultivars are resistant to soft rot, although some have tolerance and some wild potato species are resistant. Pectobacterium is a diverse genus, with multiple species capable of infecting potato. Multiple Pectobacterium species may be found in the same field and even on the same plant. Pectobacterium strains vary in aggressiveness and the virulence genes they encode but there are many commonalities across the genus. Over the past decade, genomic studies have provided new insights into Pectobacterium biology. For example, some Pectobacterium strains may elicit plant cell death to promote disease in leaves. Strains of the pathogen also produce an orange pigment and volatile compounds that increase virulence and that may act as insect kairomones. Recent work with a supervised machine learning program has identified several novel target genes likely to contribute to plant-microbe interactions, suggesting that there is still much to learn about how soft rot bacteria cause disease. Las especies de Pectobacterium causan pudriciones blandas, pierna negra y pudrición del tallo en papa y en una gran amplitud de otros cultivos hortícolas y plantas ornamentales. Las enfermedades causadas por Pectobacterium se controlan principalmente mediante el uso de material de siembra sano, prácticas sanitarias y aspersiones de cobre. Los factores ambientales tales como la temperatura, la humedad y la concentración del oxígeno en el suelo, tienen un gran efecto en el desarrollo de enfermedades causadas por Pectobacterium y la incidencia de la enfermedad puede ser impredecible. El patógeno se dispersa por varios mecanismos incluyendo agua, semilla, equipo e insectos. Se ha entendido poco sobre la resistencia de la planta a los patógenos bacterianos de pudrición blanda, y no hay variedades comerciales de papa que sean resistentes a la pudrición blanda, aunque algunas tienen tolerancia y algunas especies de papa silvestre son resistentes. El género Pectobacterium es diverso, con múltiples especies capaces de infectar a la papa. Se pueden encontrar múltiples especies de Pectrobacterium en el mismo campo y aun en la misma planta. Las cepas de Pectobacterium varían en su agresividad y en los genes de virulencia que codifican, pero hay muchas cosas en común en todo el género. En la década pasada, estudios genómicos han proporcionado nueva información de la biología de Pectobacterium . Por ejemplo, algunas variantes de este grupo de patógenos pueden inducir muerte de la célula vegetal para promover la enfermedad en hojas. Las cepas de este patógeno también inducen un pigmento color naranja y compuestos volátiles que aumentan la virulencia y que pudieran actuar como kairomonas de insectos. El trabajo reciente con una máquina supervisada con un programa de aprendizaje ha identificado varios genes nuevos como objetivos con probabilidades de contribuir en las interacciones planta-microbio, sugiriendo que aún hay mucho por aprender acerca de cómo las bacterias de pudrición suave causan enfermedad.

  • biology and control of Pectobacterium in potato
    American Journal of Potato Research, 2015
    Co-Authors: Amy O. Charkowski
    Abstract:

    Pectobacterium species cause soft rot, blackleg, and stem rot in potato and a wide range of other vegetable crops and ornamental plants. Diseases caused by Pectobacterium are controlled mainly through use of healthy planting material, sanitation and copper sprays. Environmental factors, such as temperature, moisture and soil oxygen concentration, have a large effect on development of diseases caused by Pectobacterium and disease incidence can be unpredictable. The pathogen is spread by various mechanisms including water, seed, equipment and insects. Little is understood about plant resistance to soft rot bacterial pathogens and no commercial potato cultivars are resistant to soft rot, although some have tolerance and some wild potato species are resistant. Pectobacterium is a diverse genus, with multiple species capable of infecting potato. Multiple Pectobacterium species may be found in the same field and even on the same plant. Pectobacterium strains vary in aggressiveness and the virulence genes they encode but there are many commonalities across the genus. Over the past decade, genomic studies have provided new insights into Pectobacterium biology. For example, some Pectobacterium strains may elicit plant cell death to promote disease in leaves. Strains of the pathogen also produce an orange pigment and volatile compounds that increase virulence and that may act as insect kairomones. Recent work with a supervised machine learning program has identified several novel target genes likely to contribute to plant-microbe interactions, suggesting that there is still much to learn about how soft rot bacteria cause disease.

  • the 3 hydroxy 2 butanone pathway is required for Pectobacterium carotovorum pathogenesis
    PLOS ONE, 2011
    Co-Authors: Maria Del Pilar Marquezvillavicencio, Brooke Weber, Andrews R Witherell, David K Willis, Amy O. Charkowski
    Abstract:

    Pectobacterium species are necrotrophic bacterial pathogens that cause soft rot diseases in potatoes and several other crops worldwide. Gene expression data identified Pectobacterium carotovorum subsp. carotovorum budB, which encodes the α-acetolactate synthase enzyme in the 2,3-butanediol pathway, as more highly expressed in potato tubers than potato stems. This pathway is of interest because volatiles produced by the 2,3-butanediol pathway have been shown to act as plant growth promoting molecules, insect attractants, and, in other bacterial species, affect virulence and fitness. Disruption of the 2,3-butanediol pathway reduced virulence of P. c. subsp. carotovorum WPP14 on potato tubers and impaired alkalinization of growth medium and potato tubers under anaerobic conditions. Alkalinization of the milieu via this pathway may aid in plant cell maceration since Pectobacterium pectate lyases are most active at alkaline pH.

  • soft rot disease severity is affected by potato physiology and Pectobacterium taxa
    Plant Disease, 2011
    Co-Authors: Maria Del Pilar Marquezvillavicencio, Russell L Groves, Amy O. Charkowski
    Abstract:

    Marquez-Villavicencio, M. D. P., Groves, R. L., and Charkowski, A. O. 2011. Soft rot disease severity is affected by potato physiology and Pectobacterium taxa. Plant Dis. 95:232-241. Pectobacterium species cause disease worldwide in many crop and ornamental plants, including potato. A new Pectobacterium subspecies, P. carotovorum subsp. brasiliensis was recently described in Brazil and later found in the United States, Israel, and South Africa. Its virulence traits and host range remain unknown. A comparison of three taxa commonly found on potato showed that both P. carotovorum subsp. carotovorum and subsp. brasiliensis are more aggressive in causing tuber and stem soft rot than P. atrosepticum. Also, despite bacterial growth inhibition in vitro of P. carotovorum subsp. carotovorum and P. atrosepticum strains by P. carotovorum subsp. brasiliensis, this new subspecies and P. carotovorum subsp. carotovorum are able to co-colonize in the same infected tissue. Both subspecies were motile in lesions. Pathogenesis assays showed that host ranges of all three overlap, but are not identical. The host ranges of individual strains of P. carotovorum subsp. carotovorum and subsp. brasiliensis are limited, whereas P. atrosepticum can macerate many plant species in addition to potato. There was high variability in virulence assays with potato tuber; thus physiological factors were investigated. Tuber size, maturity, and field location had significant effects on susceptibility to soft rot, with larger, more mature tubers being more susceptible. The enterobacterial plant pathogen Pectobacterium (formerly Erwinia carotovora) causes soft rot diseases in monocot and dicot host plants in at least 35% of angiosperms (28). In potato, Pectobacterium causes wilt, soft rot, and blackleg and affects plant health during field production and storage (39,40). Tuber soft rot and aerial stem rot often occur after plants are wounded, and tuber soft rot is promoted by low oxygen conditions (6,29). In contrast, blackleg is considered a tuber-borne disease, with the bacterial pathogen causing an inky black decay on the lower part of the potato stem (40). Copper sprays may be used to prevent infection of wounded plant stems and leaves, but once the plant is colonized, there is no chemical control available for this pathogen (11). Resistance genes active against Pectobacterium have been found in multiple host species, but their sequences and mechanisms remain unknown (23–25,33,43,45,50,53,57). No currently grown commercial potato variety has an effective level of resistance to soft rot, stem rot, or blackleg. Pectobacterium pathogenesis has been studied for over a century (19). To promote rot, soft rot pathogens employ a wide range of plant cell wall degrading enzymes to disrupt and metabolize plant cells (1,48). Additional virulence determinants also have been described as contributing to bacterial invasion, establishment, multiplication, and host resistance evasion. These include the flagellar system (36), putative phytotoxins (3), quorum-sensing system (26,41,44), efflux pumps (51), the type III secretion system (16,54), and plant antimicrobial resistance systems (27). Conducive environmental factors are also critical for the infection proc

Denis Faure - One of the best experts on this subject based on the ideXlab platform.

  • Species Diversity of Dickeya and Pectobacterium Causing Potato Blackleg Disease in Pakistan.
    Plant Disease, 2020
    Co-Authors: Sohaib Sarfraz, Kashif Riaz, Said Oulghazi, Shahbaz Talib Sahi, Nasir Ahmed Rajput, Muhammad Atiq, Muhammad Rizwan Tufail, A. Hameed, Denis Faure
    Abstract:

    : Potato blackleg is caused by a diverse species of pectinolytic bacteria. In Pakistan, approximately 90% of the pathogens involved belong to Pectobacterium atrosepticum. Survey (2014 to 2017), sampling, and isolation from different potato growing areas of Punjab, Pakistan depicted an overall disease incidence of approximately 15%. Thirty-six pectinolytic strains confirmed through biochemical and pathogenicity testing were characterized via gapA gene to identify them at the species level. To further validate the identification, one strain from each species SS26 (P. atrosepticum), SS28 (Pectobacterium polaris), SS70 (Dickeya dianthicola), SS90 (Pectobacterium parmentieri), SS95 (Pectobacterium punjabense), and SS96 (Pectobacterium versatile) were selected for draft genome sequencing and multilocus sequence analysis of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA, and rplB). Phylogenetic analysis revealed considerable genetic diversity in the genus Pectobacterium. In silico DNA-DNA hybridization and average nucleotide identity values of the strains selected for genome sequencing were determined with other reference Pectobacterium and Dickeya strains. Moreover, all six representative strains were also phenotypically characterized on the basis of metabolism of different carbon sources. Overall, on the basis of genotypic and phenotypic characteristics, these 36 isolates were grouped into six species: P. atrosepticum, P. versatile, P. parmentieri, P. polaris, P. punjabense, and D. dianthicola.

  • transfer of the waterfall source isolate Pectobacterium carotovorum m022 to Pectobacterium fontis sp nov a deep branching species within the genus Pectobacterium
    International Journal of Systematic and Evolutionary Microbiology, 2019
    Co-Authors: Said Oulghazi, Jérémy Cigna, Mohieddine Moumni, Kokgan Chan, Denis Faure
    Abstract:

    Pectobacterium carotovorum M022(T) has been isolated from a waterfall source in Selangor district (Malaysia). Using genomic and phenotypic tests, we re-examined the taxonomical position of this strain. Based on 14 concatenated housekeeping genes (fusA, rpoD, rpoS, acnA, purA, gyrB, recA, mdh, mtID, groEL, secY, glyA, gapA and rpIB), multi-locus sequence analysis revealed that strain M022(T) falls into a novel Glade separated from the other Pectobacterium species. The in silico DNA-DNA hybridization and average nucleotide identity values were lower than the 70 and 95% threshold values, respectively. In addition, by combining genomic and phenotypic tests, strain M022(T) may be distinguished from the other Pectobacterium isolates by its incapacity to grow on D(+)-xylose, L-rhamnose, cellobiose and lactose. Strain M022(T) (=CFBP 8629(T)=LMG 30744(T)) is proposed as the type strain of the Pectobacterium fontis sp. nov.

  • Antagonistic Potential of N-acyl-homoserine Lactone Degrading Bacillus Species for Controlling Pectobacterium Based Infections in Potato
    INTERNATIONAL JOURNAL OF AGRICULTURE & BIOLOGY, 2019
    Co-Authors: Sohaib Sarfraz, Shahbaz Talib Sahi, Sultan Habibullah Khan, Muhammad Amjad Ali, Denis Faure
    Abstract:

    Interference with quorum sensing (QS) naturally through quorum quenching is an established bio-control approach. In the present study, quorum quenching strategy was employed against Pectobacterium atrosepticum causing blackleg disease of potato. N-acyl-homoserine lactone (NAHL) degrading bacteria were isolated from potato rhizosphere using serial dilutions on different growth mediums and their ability to degrade NAHLs was evaluated using Chromobacterium violaceum (CV026) and Agrobacterium tumefaciens (NTLR-4) biosensor strains. Six rhizospheric isolates, capable of degrading NAHLs extracted from Pectobacterium atrosepticum were molecularly identified as belonging to genus, Bacillus. NAHL degradation ability of all these 6 Bacillus strains was also assessed using plate streak and thin layer chromatography assays. Resultantly, these strains remarkably degraded both short and long chain synthetic NAHLs. Furthermore, these Bacillus species also acted as potential bio-control agents when co-inoculated under quorum quenching tuber assay and have shown effective results in reducing QSregulated soft rot tuber maceration in potatoes. Overall, all six Bacillus strains showed substantial capability in controlling Pectobacterium based infections through quenching of the NAHL signals; however, Bacillus cereus SSB1 was determined as the most efficient quencher strain. This work highlights a promising strategy for the bio-control and prevention of infectious plant diseases through quenching of the QS signals.

  • Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan.
    International Journal of Systematic and Evolutionary Microbiology, 2018
    Co-Authors: Sohaib Sarfraz, Kashif Riaz, Said Oulghazi, Jérémy Cigna, Shahbaz Talib Sahi, Habibullah Khan, Denis Faure
    Abstract:

    Pectobacterium isolates SS95T, SS54 and SS56 were collected from a potato field in the Chiniot district in the plains of the Punjab province, Pakistan. Sequencing of the gapA barcode revealed that these strains belong to a novel phylogenetic group separated from P.ectobacterium wasabiae and Pectobacterium parmentieri species. Furthermore, multilocus sequence analyses of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA and rplB) clearly distinguished the type strain, SS95T, from its closest relatives, i.e. P. parmentieri RNS 08-42-1AT and P. wasabiae CFBP3304T, as well as from all the other known Pectobacterium species. In silico DNA–DNA hybridization (

  • Pectobacterium punjabense sp nov isolated from blackleg symptoms of potato plants in pakistan
    International Journal of Systematic and Evolutionary Microbiology, 2018
    Co-Authors: Sohaib Sarfraz, Kashif Riaz, Said Oulghazi, Jérémy Cigna, Shahbaz Talib Sahi, Sultan Habibullah Khan, Denis Faure
    Abstract:

    Pectobacterium isolates SS95T, SS54 and SS56 were collected from a potato field in the Chiniot district in the plains of the Punjab province, Pakistan. Sequencing of the gapA barcode revealed that these strains belong to a novel phylogenetic group separated from P.ectobacterium wasabiae and Pectobacterium parmentieri species. Furthermore, multilocus sequence analyses of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA and rplB) clearly distinguished the type strain, SS95T, from its closest relatives, i.e. P. parmentieri RNS 08-42-1AT and P. wasabiae CFBP3304T, as well as from all the other known Pectobacterium species. In silico DNA–DNA hybridization (<44.1 %) and average nucleotide identity (<90.75 %) values of strain SS95T compared with other Pectobacterium type strains supported the delineation of a new species. Genomic and phenotypic comparisons permitted the identification of additional traits that distinguished the Pakistani isolates from all other known Pectobacterium type strains. The name Pectobacterium punjabense sp. nov. is proposed for this taxon with the type strain SS95T (=CFBP 8604T=LMG 30622T).

Minna Pirhonen - One of the best experts on this subject based on the ideXlab platform.

  • Characterisation of Pectobacterium wasabiae and Pectobacterium carotovorum subsp. carotovorum isolates from diseased potato plants in Finland
    Annals of Applied Biology, 2013
    Co-Authors: Miia Pasanen, Jaana Laurila, Günter Brader, E. T. Palva, Virpi Ahola, J.m. Van Der Wolf, Asko Hannukkala, Minna Pirhonen
    Abstract:

    To identify bacteria causing soft rot and blackleg in potato in Finland, pectinolytic enterobacteria were isolated from diseased potato stems and tubers. In addition to isolates identified as Pectobacterium atrosepticum and Dickeya sp., many of the isolated strains were identified as Pectobacterium carotovorum subsp. carotovorum. Phylogenetic analysis and biochemical tests indicated that one of the isolates from potato stems resembled Pectobacterium wasabiae. Furthermore, two blackleg-causing P. carotovorum strains recently isolated in Europe clustered with P. wasabiae, suggesting that at least some of these isolates were originally misidentified. All the other Finnish P. carotovorum isolates resembled the subsp. carotovorum type strain in biochemical tests but could be clustered into two distinct groups in the phylogenetic analysis. One of the groups mainly contained strains isolated from diseased tubers, whereas the other mainly included isolates from potato stems. In contrast to the tuber isolates, the stem isolates lacked genes in Type III secretion genes, were not able to elicit a hypersensitive response in tobacco leaves and produced only small amounts of autoinducers in the stationary phase in vitro. P. wasabiae isolate was able to cause similar amount of blackleg-like symptoms as P. atrosepticum in a field experiment with vacuum-infiltrated tubers, whereas both P. atrosepticum and P. carotovorum isolates reduced emergence and delayed growth more than P. wasabiae. Our findings confirm the presence of P. wasabiae in Finland and show that the Finnish P. carotovorum subsp. carotovorum isolates can be divided into two groups with specific characteristics and possibly also different ecologies

  • role and regulation of the flp tad pilus in the virulence of Pectobacterium atrosepticum scri1043 and Pectobacterium wasabiae scc3193
    PLOS ONE, 2013
    Co-Authors: Johanna Nykyri, Laura Mattinen, Outi Niemi, Satish Adhikari, Viia Koiv, Panu Somervuo, Xin Fang, Petri Auvinen, Tapio E Palva, Minna Pirhonen
    Abstract:

    In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers.

  • genome sequence of Pectobacterium sp strain scc3193
    Journal of Bacteriology, 2012
    Co-Authors: J P Koskinen, Johanna Nykyri, Outi Niemi, Petri Auvinen, Minna Pirhonen, Pia Laine, Heidi Harjunpaa, Lars Paulin, Tapio Palva, Liisa Holm
    Abstract:

    We report the complete and annotated genome sequence of the plant-pathogenic enterobacterium Pectobacterium sp. strain SCC3193, a model strain isolated from potato in Finland. The Pectobacterium sp. SCC3193 genome consists of a 516,411-bp chromosome, with no plasmids.

  • revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae scc3193
    PLOS Pathogens, 2012
    Co-Authors: Johanna Nykyri, Outi Niemi, Liisa Holm, Patrik Koskinen, Miia Pasanen, Jussi Noksokoivisto, Martin Broberg, Ilja Plyusnin, Petri Toronen, Minna Pirhonen
    Abstract:

    Soft rot disease is economically one of the most devastating bacterial diseases affecting plants worldwide. In this study, we present novel insights into the phylogeny and virulence of the soft rot model Pectobacterium sp. SCC3193, which was isolated from a diseased potato stem in Finland in the early 1980s. Genomic approaches, including proteome and genome comparisons of all sequenced soft rot bacteria, revealed that SCC3193, previously included in the species Pectobacterium carotovorum, can now be more accurately classified as Pectobacterium wasabiae. Together with the recently revised phylogeny of a few P. carotovorum strains and an increasing number of studies on P. wasabiae, our work indicates that P. wasabiae has been unnoticed but present in potato fields worldwide. A combination of genomic approaches and in planta experiments identified features that separate SCC3193 and other P. wasabiae strains from the rest of soft rot bacteria, such as the absence of a type III secretion system that contributes to virulence of other soft rot species. Experimentally established virulence determinants include the putative transcriptional regulator SirB, two partially redundant type VI secretion systems and two horizontally acquired clusters (Vic1 and Vic2), which contain predicted virulence genes. Genome comparison also revealed other interesting traits that may be related to life in planta or other specific environmental conditions. These traits include a predicted benzoic acid/salicylic acid carboxyl methyltransferase of eukaryotic origin. The novelties found in this work indicate that soft rot bacteria have a reservoir of unknown traits that may be utilized in the poorly understood latent stage in planta. The genomic approaches and the comparison of the model strain SCC3193 to other sequenced Pectobacterium strains, including the type strain of P. wasabiae, provides a solid basis for further investigation of the virulence, distribution and phylogeny of soft rot bacteria and, potentially, other bacteria as well.

Johanna Nykyri - One of the best experts on this subject based on the ideXlab platform.

  • genome sequence of the model plant pathogen Pectobacterium carotovorum scc1
    Standards in Genomic Sciences, 2017
    Co-Authors: Outi Niemi, Johanna Nykyri, Pia Laine, Heidi Harjunpaa, Lars Paulin, Liisa Holm, Patrik Koskinen, Miia Pasanen, Ville Pennanen, Petri Auvinen
    Abstract:

    Bacteria of the genus Pectobacterium are economically important plant pathogens that cause soft rot disease on a wide variety of plant species. Here, we report the genome sequence of Pectobacterium carotovorum strain SCC1, a Finnish soft rot model strain isolated from a diseased potato tuber in the early 1980’s. The genome of strain SCC1 consists of one circular chromosome of 4,974,798 bp and one circular plasmid of 5524 bp. In total 4451 genes were predicted, of which 4349 are protein coding and 102 are RNA genes.

  • role and regulation of the flp tad pilus in the virulence of Pectobacterium atrosepticum scri1043 and Pectobacterium wasabiae scc3193
    PLOS ONE, 2013
    Co-Authors: Johanna Nykyri, Laura Mattinen, Outi Niemi, Satish Adhikari, Viia Koiv, Panu Somervuo, Xin Fang, Petri Auvinen, Tapio E Palva, Minna Pirhonen
    Abstract:

    In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers.

  • Role and regulation of the Flp/Tad pilus in the virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193.
    PLOS ONE, 2013
    Co-Authors: Johanna Nykyri, Laura Mattinen, Outi Niemi, Satish Adhikari, Viia Koiv, Panu Somervuo, Xin Fang, Petri Auvinen, E. Tapio Palva
    Abstract:

    In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers.

  • genome sequence of Pectobacterium sp strain scc3193
    Journal of Bacteriology, 2012
    Co-Authors: J P Koskinen, Johanna Nykyri, Outi Niemi, Petri Auvinen, Minna Pirhonen, Pia Laine, Heidi Harjunpaa, Lars Paulin, Tapio Palva, Liisa Holm
    Abstract:

    We report the complete and annotated genome sequence of the plant-pathogenic enterobacterium Pectobacterium sp. strain SCC3193, a model strain isolated from potato in Finland. The Pectobacterium sp. SCC3193 genome consists of a 516,411-bp chromosome, with no plasmids.

  • revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae scc3193
    PLOS Pathogens, 2012
    Co-Authors: Johanna Nykyri, Outi Niemi, Liisa Holm, Patrik Koskinen, Miia Pasanen, Jussi Noksokoivisto, Martin Broberg, Ilja Plyusnin, Petri Toronen, Minna Pirhonen
    Abstract:

    Soft rot disease is economically one of the most devastating bacterial diseases affecting plants worldwide. In this study, we present novel insights into the phylogeny and virulence of the soft rot model Pectobacterium sp. SCC3193, which was isolated from a diseased potato stem in Finland in the early 1980s. Genomic approaches, including proteome and genome comparisons of all sequenced soft rot bacteria, revealed that SCC3193, previously included in the species Pectobacterium carotovorum, can now be more accurately classified as Pectobacterium wasabiae. Together with the recently revised phylogeny of a few P. carotovorum strains and an increasing number of studies on P. wasabiae, our work indicates that P. wasabiae has been unnoticed but present in potato fields worldwide. A combination of genomic approaches and in planta experiments identified features that separate SCC3193 and other P. wasabiae strains from the rest of soft rot bacteria, such as the absence of a type III secretion system that contributes to virulence of other soft rot species. Experimentally established virulence determinants include the putative transcriptional regulator SirB, two partially redundant type VI secretion systems and two horizontally acquired clusters (Vic1 and Vic2), which contain predicted virulence genes. Genome comparison also revealed other interesting traits that may be related to life in planta or other specific environmental conditions. These traits include a predicted benzoic acid/salicylic acid carboxyl methyltransferase of eukaryotic origin. The novelties found in this work indicate that soft rot bacteria have a reservoir of unknown traits that may be utilized in the poorly understood latent stage in planta. The genomic approaches and the comparison of the model strain SCC3193 to other sequenced Pectobacterium strains, including the type strain of P. wasabiae, provides a solid basis for further investigation of the virulence, distribution and phylogeny of soft rot bacteria and, potentially, other bacteria as well.

Malgorzata Waleron - One of the best experts on this subject based on the ideXlab platform.

  • Pectobacterium parvum sp nov having a salmonella spi 1 like type iii secretion system and low virulence
    International Journal of Systematic and Evolutionary Microbiology, 2020
    Co-Authors: Miia Pasanen, Malgorzata Waleron, Agnieszka Misztak, Krzysztof Waleron, Ilse Cleenwerck, Thomas Schott, Leighton Pritchard, Ramadan Bakr
    Abstract:

    Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain.

  • Pectobacterium polonicum sp. nov. isolated from vegetable fields
    International Journal of Systematic and Evolutionary Microbiology, 2019
    Co-Authors: Malgorzata Waleron, Agnieszka Misztak, Joanna Jońca, Magda Furmaniak, Krzysztof Waleron
    Abstract:

    Gram-stain-negative, rod-shaped pectinolytic bacteria strains designated as DPMP315T, DPMP316, DPMP317 and DPMP318 isolated from groundwater sampled from a vegetable field in the North of Poland, were subjected to the polyphasic analyses. Multilocus sequence analyses based on five housekeeping genes (gyrA, recA, recN, rpoA and rpoS) revealed their distinctiveness from the other species of the genus, simultaneously indicating that the newly described species, Pectobacterium punjabense , as well as Pectobacterium parmentieri and P. wasabiae , to be the closest relatives. In silico DNA–DNA hybridization (

  • Pectobacterium zantedeschiae sp. nov. a new species of a soft rot pathogen isolated from Calla lily (Zantedeschia spp.).
    Systematic and Applied Microbiology, 2018
    Co-Authors: Malgorzata Waleron, Agnieszka Misztak, Martyna Franczuk, Bartosz Wielgomas, Joanna Jońca, Artur Mikiciński, Tatjana Popović, Krzysztof Waleron
    Abstract:

    Abstract Four Gram-negative, rod-shaped pectinolytic bacterial strains designated as 2M, 9M, DPMP599 and DPMP600 were subjected to polyphasic analyses that revealed their distinctiveness from the other Pectobacterium species. Strains 2M and 9M were isolated from Calla lily bulbs cultivated in Central Poland. DPMP599 and DPMP600 strains were isolated from Calla lily leaves from plants grown in Serbia. Phylogenetic analyses based on nine housekeeping genes (gapA, gyrA, icdA, pgi, proA, recA, recN, rpoA, and rpoS), as well as phylogeny based on the 381 most conserved universal proteins confirmed that Pectobacterium zantedeschiae strains were distantly related to the other Pectobacterium, and indicated Pectobacterium atrosepticum, Pectobacterium betavasculorum, Pectobacterium parmentieri and Pectobacterium wasabiae as the closest relatives. Moreover, the analysis revealed that Pectobacterium zantedeschiae strains are not akin to Pectobacterium aroidearum strains, which were likewise isolated from Calla lily. The genome sequencing of the strains 2M, 9M and DPMP600 and their comparison with whole genome sequences of other Pectobacterium type strains confirmed their distinctiveness and separate species status within the genus based on parameters of in silico DNA–DNA hybridization and average nucleotide identity (ANI) values. The MALDI-TOF MS proteomic profile supported the proposition of delineation of the P. zantedeschiae and additionally confirmed the individuality of the studied strains. Based on of all of these data, it is proposed that the strains 2M, 9M, DPMP599, and DPMP600 isolated from Calla lily, previously assigned as P. atrosepticum should be reclassified as Pectobacterium zantedeschiae sp. nov. with the strain 9MT (PCM2893 = DSM105717 = IFB9009) as the type strain.

  • transfer of Pectobacterium carotovorum subsp carotovorum strains isolated from potatoes grown at high altitudes to Pectobacterium peruviense sp nov
    Systematic and Applied Microbiology, 2017
    Co-Authors: Malgorzata Waleron, Agnieszka Misztak, Martyna Franczuk, Bartosz Wielgomas, Krzysztof Waleron
    Abstract:

    Abstract Seven Gram-negative, rod-shaped pectinolytic bacteria strains designated as IFB5227, IFB5228, IFB5229, IFB5230, IFB5231, IFB5232, IFB5636, isolated from potato tubers cultivated in Peru at high altitude (2400–3800 m) were subjected to polyphasic analyses that revealed their distinctiveness from the other Pectobacterium species. Phylogenetic analyses based on five housekeeping genes (gyrA, recA, recN, rpoA and rpoS) clearly showed strains separateness, simultaneously indicating Pectobacterium atrosepticum, Pectobacterium wasabiae, Pectobacterium parmentieri and Pectobacterium betavasculorum as the closest relatives. In silico DNA–DNA hybridization of strain IFB5232T with other Pectobacterium type strains revealed significant drop in DDH value below 70%, which is a prerequisite to distinguish Pectobacterium peruviense. The ANI values supported the proposition of delineation of the P. peruviense. Genetic REP-PCR fingerprint and detailed MALDI-TOF MS proteomic profile sealed the individuality of the studied strains. However, phenotypic assays do not indicate immense differences. Provided results of analyses performed for seven Peruvian strains are the basis for novel species distinction and reclassification of the strains IFB5227-5232 and IFB5636, previously classified as Pectobacterium carotovorum subsp. carotovorum. Here, we propose to establish the IFB5232 isolate as a type strain (=PCM2893T = LMG30269T = SCRI179T) with the name Pectobacterium peruviense sp. nov.

  • occurrence of Pectobacterium wasabiae in potato field samples
    European Journal of Plant Pathology, 2013
    Co-Authors: Malgorzata Waleron, Krzysztof Waleron, Ewa Lojkowska
    Abstract:

    During the growing seasons of 1996 and 1997, samples of potato stems and tubers with symptoms of blackleg and soft rot were collected in different regions in Poland. After growing to pure cultures on crystal violet pectate (CVP) medium, isolates of bacteria were identified as Pectobacterium spp. on the basis of their ability to degrade pectate and with the use of biochemical tests. About 43 % strains isolated from 122 different plant samples were identified as Pectobacterium carotovorum subsp. carotovorum, whereas the rest of the pectinolytic bacteria was identified as Pectobacterium atrosepticum. A recent screening of these isolates with recA PCR-RFLP allowed identification of 18 different RFLP groups within the tested P. c. subsp. carotovorum strains. The third largest group of the tested P. c. subsp. carotovorum strains (14 %), which were assigned to the profile 3 recA PCR-RFLP, was re-identified as Pectobacterium wasabiae (formerly Erwinia carotovora subsp. wasabiae) on the basis of recA and 16S rRNA genes sequences. About 50 % of P. wasabiae isolated from potato, in contrast to horseradish isolates of P. wasabiae, have an ability to grow at 37°C and some of them grow on media containing 5 % of NaCl. In a pathogenicity test with 11 strains of P. wasabiae these strains showed a high capacity to rot potato tubers.