Pectobacterium parvum sp. nov. having a Salmonella SPI-1-like Type III secretion system and low virulence

Miia Pasanen, Malgorzata Waleron, Thomas Schott, Ilse Cleenwerk, Agnieszka Misztak, Krysztof Waleron, Leighton Pritchard, Ramadan Bakr, Yeshitila Degefu, Jan van der Wolf, Peter Vandamme, Minna Pirhonen

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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 polymor-phism 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. Further-more, 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 s0421 T (CFBP 8630 T=LMG 30828 T) is suggested as a type strain.

Original languageEnglish
Pages (from-to)2440-2448
Number of pages9
JournalInternational Journal of Systematic and Evolutionary Microbiology
Volume70
Issue number4
DOIs
Publication statusPublished - 20 Feb 2020

Keywords

  • phylogenetic analyses
  • taxonomy
  • genomics
  • pectobacterium
  • plant pathology

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  • 1 Citations
  • 1 Comment/debate
  • 1 Software

Corrigendum: Pectobacterium parvum sp. nov., having a salmonella SPI-1-like type iii secretion system and low virulence (Int J Syst Evol Microbiol, 2020, 10.1099/ijsem.0.004057)

Pasanen, M., Waleron, M., Schott, T., Cleenwerck, I., Misztak, A., Waleron, K., Pritchard, L., Bakr, R., Degefu, Y., van der Wolf, J., Vandamme, P. & Pirhonen, M., 1 Jan 2020, In : International Journal of Systematic and Evolutionary Microbiology. 70, 4, 1 p., 004111.

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pyani v0.2.8: average nucleotide identity (ANI) and related measures for whole genome comparisons

Pritchard, L., Cock, P. & Esen, Ö., 5 Mar 2019

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  • Cite this

    Pasanen, M., Waleron, M., Schott, T., Cleenwerk, I., Misztak, A., Waleron, K., Pritchard, L., Bakr, R., Degefu, Y., van der Wolf, J., Vandamme, P., & Pirhonen, M. (2020). Pectobacterium parvum sp. nov. having a Salmonella SPI-1-like Type III secretion system and low virulence. International Journal of Systematic and Evolutionary Microbiology, 70(4), 2440-2448. https://doi.org/10.1099/ijsem.0.004057