1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 3

Pectobacterium aquaticum sp. nov., isolated from waterways Free

Abstract

This work aimed to establish the taxonomic status of six strains (A212-S19-A16, A127-S21-F16, A105-S21-F16, A104-S21-F16, A101-S19-F16 and A35-S23-M15) isolated from three different waterways in 2015 and 2016 in south-east France. Amplification and sequencing of the gapA housekeeping gene clustered these six strains together inside the genus Pectobacterium outside of already described or proposed Pectobacterium species and supspecies. Phenotypic analysis, using GENIII Biolog plates performed with strains A212-S19-A16, A105-S21-F16, A101-S19-F16 and the closely related Pectobacterium polaris (CFBP 1403), Pectobacterium carotovorum subsp. odoriferum (CFBP 1878), ‘ Pectobacterium carotovorum subsp. actinidiae’ (CFBP 7370), Pectobacterium carotovorum subsp. carotovorum (CFBP 2046), ‘ Pectobacterium carotovorum subsp. brasiliense ’ (CFBP 6617) or the most distantly related Pectobacterium aroidearum (CFBP 8168) failed to identify specific compounds metabolized by these three strains, but weak activity was specifically observed at pH 5 with these three strains. Illumina sequencing was used to sequence these six strains. Based on phylogenetic data, average nucleotide identity values and in silico DNA–DNA hybridization results, strains A212-S19-A16, A127-S21-F16, A105-S21-F16, A101-S19-F16, A35-S23-M15 and A104-S21-F16 are suggested to represent a novel species of the genus Pectobacterium , for which the name Pectobacterium aquaticum sp. nov. is proposed. The type strain is A212-S19-A16 (=CFBP 8637=NCPPB 4640).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ecology , pectobacterium and river
© 2019 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003229
2019-02-06
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/3/745.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003229&mimeType=html&fmt=ahah

References

  1. Skerman VBD, Sneath PHA, McGowan V. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [View Article]
     [Google Scholar]
  2. 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 [View Article][PubMed]
     [Google Scholar]
  3. Nabhan S, de Boer SH, Maiss E, Wydra K. Pectobacterium aroidearum sp. nov., a soft rot pathogen with preference for monocotyledonous plants. Int J Syst Evol Microbiol 2013; 63:2520–2525 [View Article][PubMed]
     [Google Scholar]
  4. 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: [View Article][PubMed]
     [Google Scholar]
  5. Dees MW, Lysøe E, Rossmann S, Perminow J, Brurberg MB. Pectobacterium polaris sp. nov., isolated from potato (Solanum tuberosum). Int J Syst Evol Microbiol 2017; 67:5222–5229 [View Article][PubMed]
     [Google Scholar]
  6. Waleron M, Misztak A, Waleron M, Franczuk M, Wielgomas B et al. Transfer of Pectobacterium carotovorum subsp. carotovorum strains isolated from potatoes grown at high altitudes to Pectobacterium peruviense sp. nov. Syst Appl Microbiol 2018; 41:85–93 [View Article][PubMed]
     [Google Scholar]
  7. 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 [View Article][PubMed]
     [Google Scholar]
  8. Hauben L, Moore ER, Vauterin L, Steenackers M, Mergaert J et al. Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst Appl Microbiol 1998; 21:384–397 [View Article][PubMed]
     [Google Scholar]
  9. Koh YJ, Kim GH, Lee YS, Sohn SH, Koh HS et al. Pectobacterium carotovorum subsp. actinidiae subsp. nov., a new bacterial pathogen causing canker-like symptoms in yellow kiwifruit, Actinidia chinensis. N Z J Crop Hortic Sci 2012
     [Google Scholar]
  10. Marquez-Villavicencio M del P, Groves RL, Charkowski AO. Soft rot disease severity is affected by potato physiology and Pectobacterium taxa. Plant Dis 2011
     [Google Scholar]
  11. Gallois A, Samson R, Ageron E, Grimont P. Erwinia carotovora subsp. odorifera subsp. nov., associated with odorous soft rot of chicory (Cichorium intybus L.). Int J Syst Bacteriol 1992
     [Google Scholar]
  12. List Editor Validation of publication of new names and new combinations previously effectively published outside the IJSB. IntJ Syst Bacteriol 1999; 49:1–3 [View Article]
     [Google Scholar]
  13. Ma B, Hibbing ME, Kim HS, Reedy RM, Yedidia I et al. Host range and molecular phylogenies of the soft rot enterobacterial genera Pectobacterium and Dickeya. Phytopathology 2007; 97:1150–1163 [View Article][PubMed]
     [Google Scholar]
  14. Goto M, Matsumoto K. Erwinia carotovora subsp. wasabiae subsp. nov. isolated from diseased rhizomes and fibrous roots of japanese horseradish (Eutrema wasabi Maxim.). Int J Syst Bacteriol 1987; 37:130–135 [View Article]
     [Google Scholar]
  15. Quinn CE, Sells IA, Graham DC. Soft rot Erwinia bacteria in the atmospheric bacterial aerosol. J Appl Bacteriol 1980
     [Google Scholar]
  16. Burr TJ. Occurrence of Soft-rot Erwinia spp. in Soil and Plant Material. Phytopathology 1977; 77:1382 [View Article]
     [Google Scholar]
  17. Jorge PE, Harrison MD. The association of Erwinia carotovora with surface water in Northeastern Colorado. I. The presence and population of the bacterium in relation to location, season and water temperature. Am Potato J 1986; 63:517–531 [View Article]
     [Google Scholar]
  18. Perombelon MCM, Kelman A. Ecology of the soft rot Erwinias. Annu Rev Phytopathol 1980; 18:361–387 [View Article]
     [Google Scholar]
  19. Hélias V, Hamon P, Huchet E, Wolf JVD, Andrivon D. Two new effective semiselective crystal violet pectate media for isolation of Pectobacterium and Dickeya: Isolating pectolytic bacteria on CVP. Plant Pathol 2012; 61:339–345
     [Google Scholar]
  20. Adeolu M, Alnajar S, Naushad S, S Gupta R. Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575–5599 [View Article][PubMed]
     [Google Scholar]
  21. Cigna J, Dewaegeneire P, Beury A, Gobert V, Faure D. A gapA PCR-sequencing assay for Identifying the Dickeya and Pectobacterium potato pathogens. Plant Dis 2017
     [Google Scholar]
  22. 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 [View Article][PubMed]
     [Google Scholar]
  23. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999; 27:4636–4641 [View Article][PubMed]
     [Google Scholar]
  24. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinform Oxf Engl 15 2016; 32:929–931 [View Article][PubMed]
     [Google Scholar]
  25. 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 [View Article][PubMed]
     [Google Scholar]
  26. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:113 [View Article][PubMed]
     [Google Scholar]
  27. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article][PubMed]
     [Google Scholar]
  28. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article][PubMed]
     [Google Scholar]
  29. Miele V, Penel S, Duret L. Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics 2011; 12:116 [View Article][PubMed]
     [Google Scholar]
  30. Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 2010; 27:221–224 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003229
Loading
Pectobacterium aquaticum sp. nov., isolated from waterways
Int J Syst Evol Microbiol 69, 745 (2019); https://doi.org/10.1099/ijsem.0.003229
/content/journal/ijsem/10.1099/ijsem.0.003229
/content/journal/ijsem/10.1099/ijsem.0.003229
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

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