First Report of ‘<i>Candidatus</i> Pectobacterium maceratum’ Causing Soft Rot of Potato in Poland

Waleron, Małgorzata; Misztak, Agnieszka; Jońca, Joanna; Furmaniak, Magda; Waleron, Krzysztof

doi:10.1094/pdis-10-18-1849-pdn

Cited by 10 publications

(5 citation statements)

References 4 publications

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“…From an initial set of 17 housekeeping genes commonly used for multilocus sequence analysis (MLSA) [ 16 , 37 – 39 ], we selected five genes that were present in single copy in all genomes and showed the highest genetic diversity: acnA , dnaX , gyrA , gyrB and mtlD (Additional file 1 : Table S4). The commonly used marker gene gapA [ 40 ] was not included since each of our selected genes had a 3-to-9-fold higher number of SNPs.…”

Section: Resultsmentioning

confidence: 99%

The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool

Jonkheer

Brankovics²,

Houwers³

et al. 2021

BMC Genomics

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Background Bacterial plant pathogens of the Pectobacterium genus are responsible for a wide spectrum of diseases in plants, including important crops such as potato, tomato, lettuce, and banana. Investigation of the genetic diversity underlying virulence and host specificity can be performed at genome level by using a comprehensive comparative approach called pangenomics. A pangenomic approach, using newly developed functionalities in PanTools, was applied to analyze the complex phylogeny of the Pectobacterium genus. We specifically used the pangenome to investigate genetic differences between virulent and avirulent strains of P. brasiliense, a potato blackleg causing species dominantly present in Western Europe. Results Here we generated a multilevel pangenome for Pectobacterium, comprising 197 strains across 19 species, including type strains, with a focus on P. brasiliense. The extensive phylogenetic analysis of the Pectobacterium genus showed robust distinct clades, with most detail provided by 452,388 parsimony-informative single-nucleotide polymorphisms identified in single-copy orthologs. The average Pectobacterium genome consists of 47% core genes, 1% unique genes, and 52% accessory genes. Using the pangenome, we zoomed in on differences between virulent and avirulent P. brasiliense strains and identified 86 genes associated to virulent strains. We found that the organization of genes is highly structured and linked with gene conservation, function, and transcriptional orientation. Conclusion The pangenome analysis demonstrates that evolution in Pectobacteria is a highly dynamic process, including gene acquisitions partly in clusters, genome rearrangements, and loss of genes. Pectobacterium species are typically not characterized by a set of species-specific genes, but instead present themselves using new gene combinations from the shared gene pool. A multilevel pangenomic approach, fusing DNA, protein, biological function, taxonomic group, and phenotypes, facilitates studies in a flexible taxonomic context.

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Section: Resultsmentioning

confidence: 99%

The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool

Jonkheer

Brankovics²,

Houwers³

et al. 2021

BMC Genomics

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“…It should be emphasised that, in this study, we have detected the presence of the same Pectobacterium and Dickeya species on asymptomatic vegetables and ornamental plants as those which occurred on plants with disease symptoms in the same countries from which we have analysed samples (Brasil, Egypt, Morocco, UK, USA, Israel, Finland, Norway, the Netherlands and Poland) [ 3 , 12 , 17 , 18 , 21 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 ]. In addition, the presence of virulent strains of the same species of Pectobacterium and Dickeya has been described in the rivers of Finland [ 45 ] and France [ 39 ].…”

Section: Discussionmentioning

confidence: 99%

The International Trade of Ware Vegetables and Orna-Mental Plants—An Underestimated Risk of Accelerated Spreading of Phytopathogenic Bacteria in the Era of Globalisation and Ongoing Climatic Changes

et al. 2022

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Bacteria of the genus Pectobacterium are globally occurring pathogens that infect a broad spectrum of plants. The plant cell wall degrading enzymes allow them to cause diseases like soft rot and blackleg. Worldwide trade and exchange of plant material together with the accompanying microorganisms contributed to the rapid spread and consequently the acquisition of new traits by bacteria. The 161 pectinolytic strains were isolated from symptomless vegetables and ornamental plants acquired from Polish and foreign local food markets. All strains except four Dickeya isolates were identified as belonging to the Pectobacterium genus by PCR with species-specific primers and recA gene sequencing. The newly isolated bacteria were assigned to eight species, P. versatile (50 strains), P. carotovorum (33), P. brasiliense (27), P. atrosepticum (19), P. parmentieri (12), P. polaris (11), P. parvum (3) and P. odoriferum (2). ERIC PCR and phenotypic characteristics revealed high heterogeneity among P. carotovorum, P. brasiliense and P. versatile isolates. Moreover, a subset of the newly isolated strains was characterised by high tolerance to changing environmental conditions such as salinity, pH and water availability. These bacteria can effectively macerate the tissues of various plants, including potato, chicory and orchid. Our results indicate that Pectobacterium strains isolated from internationally traded, symptomless vegetables and ornamental plants have high potential for adaptation to adverse environmental conditions and to infect various host plants. These features may contribute to the success of the genus Pectobacterium in spreading between different climatic zones and facilitate the colonisation of different ecological niches.

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“…wasabiae and Erwinia chrysanthemi [ 21 , 22 , 23 ]. On the basis of the current taxonomy, P. atrosepticum , P. brasiliense, P. parmentieri, P. versatile , P. polaris and P. carotovorum are the most prevalent Pectobacterium species responsible for soft rot and/or blackleg diseases [ 24 , 25 , 26 , 27 , 28 , 29 , 30 ]. It should be noted, however, that the ability of pectinolytic bacteria to grow as well as develop blackleg and soft rot symptoms depends on many environmental factors such as temperature and humidity, in a species-dependent way [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

European Population of Pectobacterium punjabense: Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen

et al. 2021

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Enterobacteria belonging to the Pectobacterium and Dickeya genera are responsible for soft rot and blackleg diseases occurring in many crops around the world. Since 2016, the number of described species has more than doubled. However, some new species, such as Pectobacterium punjabense, are often poorly characterized, and little is known about their genomic and phenotypic variation. Here, we explored several European culture collections and identified seven strains of P. punjabense. All were collected from potato blackleg symptoms, sometimes from a long time ago, i.e., the IFB5596 strain isolated almost 25 years ago. We showed that this species remains rare, with less than 0.24% of P. punjabense strains identified among pectinolytic bacteria present in the surveyed collections. The analysis of the genomic diversity revealed the non-clonal character of P. punjabense species. Furthermore, the strains showed aggressiveness differences. Finally, a qPCR Taqman assay was developed for rapid and specific strain characterization and for use in diagnostic programs.

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First Report of ‘Candidatus Pectobacterium maceratum’ Causing Soft Rot of Potato in Poland

Cited by 10 publications

References 4 publications

The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool

The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool

The International Trade of Ware Vegetables and Orna-Mental Plants—An Underestimated Risk of Accelerated Spreading of Phytopathogenic Bacteria in the Era of Globalisation and Ongoing Climatic Changes

European Population of Pectobacterium punjabense: Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen

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