1887

Abstract

The genus Pectobacterium , which belongs to the bacterial family Enterobacteriaceae , contains numerous species that cause soft rot diseases in a wide range of plants. The species Pectobacterium carotovorum is highly heterogeneous, indicating a need for re-evaluation and a better classification of the species. PacBio was used for sequencing of two soft-rot-causing bacterial strains (NIBIO1006 and NIBIO1392), initially identified as P. carotovorum strains by fatty acid analysis and sequencing of three housekeeping genes (dnaX, icdA and mdh). Their taxonomic relationship to other Pectobacterium species was determined and the distance from any described species within the genus Pectobacterium was less than 94 % average nucleotide identity (ANI). Based on ANI, phylogenetic data and genome-to-genome distance, strains NIBIO1006, NIBIO1392 and NCPPB3395 are suggested to represent a novel species of the genus Pectobacterium , for which the name Pectobacterium polaris sp. nov. is proposed. The type strain is NIBIO1006 (=DSM 105255=NCPPB 4611).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002448
2017-10-25
2019-11-11
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/12/5222.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002448&mimeType=html&fmt=ahah

References

  1. Czajkowski R, Pérombelon MCM, van Veen JA, van der Wolf JM. Control of blackleg and tuber soft rot of potato caused by Pectobacterium and Dickeya species: a review. Plant Pathol 2011; 60: 999– 1013 [CrossRef]
    [Google Scholar]
  2. McCarter-Zorner NJ, Franc GD, Harrison MD, Michaud JE, Quinn CE et al. Soft rot Erwinia bacteria in surface and underground waters in southern Scotland and in Colorado, United States. J Appl Bacteriol 1984; 57: 95– 105 [CrossRef]
    [Google Scholar]
  3. McCarter-Zorner NJ, Harrison MD, Franc GD, Quinn CE, Sells IA et al. Soft rot Erwinia bacteria in the rhizosphere of weeds and crop plants in Colorado, United States and Scotland. J Appl Bacteriol 1985; 59: 357– 368 [CrossRef]
    [Google Scholar]
  4. Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M et al. Top 10 plant pathogenic bacteria in molecular plant pathology. Mol Plant Pathol 2012; 13: 614– 629 [CrossRef] [PubMed]
    [Google Scholar]
  5. Birch PRJ, Bryan G, Fenton B, Gilroy EM, Hein I et al. Crops that feed the world 8: Potato: are the trends of increased global production sustainable?. Food Secur 2012; 4: 477– 508 [CrossRef]
    [Google Scholar]
  6. van der Wolf JM, De Boer SH. Bacterial pathogens of potato. In Vreugdenhil D. (editor) Potato Biology and Biotechnology: Advances and Perspectives Amsterdam: Elsevier Science B.V; 2007; pp. 595– 617 [Crossref]
    [Google Scholar]
  7. Kim HS, Ma B, Perna NT, Charkowski AO. Phylogeny and virulence of naturally occurring type III secretion system-deficient Pectobacterium strains. Appl Environ Microbiol 2009; 75: 4539– 4549 [CrossRef] [PubMed]
    [Google Scholar]
  8. Waldee EL. Comparative studies of some peritrichous phytopathogenic bacteria. Iowa State Coll J Sci 1945; 19: 435– 484
    [Google Scholar]
  9. Gardan L, Gouy C, Christen R, Samson R. Elevation of three subspecies of Pectobacterium carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov. Int J Syst Evol Microbiol 2003; 53: 381– 391 [CrossRef] [PubMed]
    [Google Scholar]
  10. Khayi S, Cigna J, Chong TM, Quêtu-Laurent A, Chan KG et al. Transfer of the potato plant isolates of Pectobacterium wasabiae to Pectobacterium parmentieri sp. nov. Int J Syst Evol Microbiol 2016; 66: 5379– 5383 [CrossRef] [PubMed]
    [Google Scholar]
  11. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8: 12– 24 [CrossRef]
    [Google Scholar]
  12. Zhang Y, Fan Q, Loria R. A re-evaluation of the taxonomy of phytopathogenic genera Dickeya and Pectobacterium using whole-genome sequencing data. Syst Appl Microbiol 2016; 39: 252– 259 [CrossRef] [PubMed]
    [Google Scholar]
  13. Gallois A, Samson R, Ageron E, Grimont PAD. Erwinia carotovora subsp. odorifera subsp. nov., associated with odorous soft rot of chicory (Cichorium intybus L.). Int J Syst Bacteriol 1992; 42: 582– 588 [CrossRef]
    [Google Scholar]
  14. Nabhan S, de Boer SH, Maiss E, Wydra K. Taxonomic relatedness between Pectobacterium carotovorum subsp. carotovorum, Pectobacterium carotovorum subsp. odoriferum and Pectobacterium carotovorum subsp. brasiliense subsp. nov. J Appl Microbiol 2012; 113: 904– 913 [CrossRef] [PubMed]
    [Google Scholar]
  15. de Haan EG, Dekker-Nooren T, van den Bovenkamp GW, Speksnijder A, van der Zouwen PS et al. Pectobacterium carotovorum subsp. carotovorum can cause potato blackleg in temperate climates. Eur J Plant Pathol 2008; 122: 561– 569 [CrossRef]
    [Google Scholar]
  16. Dees MW, Lebecka R, Perminow JIS, Czajkowski R, Grupa A et al. Characterization of Dickeya and Pectobacterium strains obtained from diseased potato plants in different climatic conditions of Norway and Poland. Eur J Plant Pathol 2017; 148: 839– 851 [CrossRef]
    [Google Scholar]
  17. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S et al. Prokaryotic Genome Annotation Pipeline, the NCBI Handbook, 2nd ed. Bethesda, MD: National Center for Biotechnology Information; 2013
    [Google Scholar]
  18. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9: 75 [CrossRef] [PubMed]
    [Google Scholar]
  19. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14: 1394– 1403 [CrossRef] [PubMed]
    [Google Scholar]
  20. Treangen TJ, Ondov BD, Koren S, Phillippy AM. The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 2014; 15: 524 [CrossRef] [PubMed]
    [Google Scholar]
  21. Rodriguez-R L, Konstantinidis K. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4: e1900v1
    [Google Scholar]
  22. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106: 19126– 19131 [CrossRef] [PubMed]
    [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14: 60 [CrossRef] [PubMed]
    [Google Scholar]
  24. Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R et al. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res 2015; 43: W104– W108 [CrossRef] [PubMed]
    [Google Scholar]
  25. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011; 39: W347– W352 [CrossRef] [PubMed]
    [Google Scholar]
  26. Abby SS, Cury J, Guglielmini J, Néron B, Touchon M et al. Identification of protein secretion systems in bacterial genomes. Sci Rep 2016; 6: 23080 [CrossRef] [PubMed]
    [Google Scholar]
  27. Abby SS, Néron B, Ménager H, Touchon M, Rocha EP. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS One 2014; 9: e110726 [CrossRef] [PubMed]
    [Google Scholar]
  28. Néron B, Ménager H, Maufrais C, Joly N, Maupetit J et al. Mobyle: a new full web bioinformatics framework. Bioinformatics 2009; 25: 3005– 3011 [CrossRef] [PubMed]
    [Google Scholar]
  29. Charkowski A, Blanco C, Condemine G, Expert D, Franza T et al. The role of secretion systems and small molecules in soft-rot Enterobacteriaceae pathogenicity. Annu Rev Phytopathol 2012; 50: 425– 449 [CrossRef] [PubMed]
    [Google Scholar]
  30. Liu H, Coulthurst SJ, Pritchard L, Hedley PE, Ravensdale M et al. Quorum sensing coordinates brute force and stealth modes of infection in the plant pathogen Pectobacterium atrosepticum. PLoS Pathog 2008; 4: e1000093 [CrossRef] [PubMed]
    [Google Scholar]
  31. Schmitz RA, Klopprogge K, Grabbe R. Regulation of nitrogen fixation in Klebsiella pneumoniae and Azotobacter vinelandii: NifL, transducing two environmental signals to the nif transcriptional activator NifA. J Mol Microbiol Biotechnol 2002; 4: 235– 242 [PubMed]
    [Google Scholar]
  32. Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ et al. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc Natl Acad Sci USA 2004; 101: 11105– 11110 [CrossRef] [PubMed]
    [Google Scholar]
  33. Kondoh H, Ball CB, Adler J. Identification of a methyl-accepting chemotaxis protein for the ribose and galactose chemoreceptors of Escherichia coli. Proc Natl Acad Sci USA 1979; 76: 260– 264 [CrossRef] [PubMed]
    [Google Scholar]
  34. Lux R, Shi W. Chemotaxis-guided movements in bacteria. Crit Rev Oral Biol Med 2004; 15: 207– 220 [PubMed] [Crossref]
    [Google Scholar]
  35. Laurila J, Ahola V, Lehtinen A, Joutsjoki T, Hannukkala A et al. Characterization of Dickeya strains isolated from potato and river water samples in Finland. Eur J Plant Pathol 2008; 122: 213– 225 [CrossRef]
    [Google Scholar]
  36. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. 1990
    [Google Scholar]
  37. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011; 12: 402 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002448
Loading
/content/journal/ijsem/10.1099/ijsem.0.002448
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error