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Volume 71, Issue 10

sp. nov., isolated from waterways No Access

Abstract

Through this study, we established the taxonomic status of seven strains belonging to the genus (A477-S1-J17, A398-S21-F17, A535-S3-A17, A411-S4-F17, A113-S21-F16, FL63-S17 and FL60-S17) collected from four different river streams and an artificial lake in south-east France between 2016 and 2017. Ecological surveys in rivers and lakes pointed out different repartition of strains belonging to this clade compared to the closest species, . The main phenotypic difference observed between these strains and the type strain was strongly impaired growth with rhamnose as the sole carbon source. This correlates with three different forms of pseudogenization of the -rhamnose/proton symporter gene in the genomes of strains belonging to this clade. Phylogenetic analysis using gene sequences and multi locus sequence analysis of the core genome showed that these strains formed a distinct clade within the genus closely related to Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values showed a clear discontinuity between the new clade and . However, the calculated values are potentially consistent with either splitting or merging of this new clade with . In support of the split, ANI coverages were higher within this new clade than between this new clade and . The split is also consistent with the range of observed ANI or dDDH values that currently separate several accepted species within the genus . On the basis of these data,strains A477-S1-J17, A398-S21-F17, A535-S3-A17, A411-S4-F17, A113-S21-F16, FL63-S17 and FL60-S17 represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is A477-S1-J17 (=CFBP 8805=LMG 32181).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Enterobacterale , Pectobacteriaceae , Pectobacterium , plant pathogen and soft rot
Funding
This study was supported by the:
  • Centre National de la Recherche Scientifique (Award EC2COBiohefect/Ecodyn/Dril/MicrobienCARTOBACTER)
    • Principle Award Recipient: Marie-AnneBarny
  • Agence Nationale de la Recherche (Award ANR-17-CE32-0004)
    • Principle Award Recipient: Marie-AnneBarny
© 2021 The Authors
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2021-10-11
2024-05-14
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References

  1. Adeolu M, Alnajar S, Naushad SS, 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]
  2. Ma B, Hibbing ME, Kim H-S, 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]
     [Google Scholar]
  3. Pédron J, Bertrand C, Taghouti G, Portier P, Barny M-A. Pectobacterium aquaticum sp. nov., isolated from waterways. Int J Syst Evol Microbiol 2019; 69:745–751 [View Article] [PubMed]
     [Google Scholar]
  4. Portier P, Pédron J, Taghouti G, Fischer-Le Saux M, Caullireau E et al. Elevation of Pectobacterium carotovorum subsp. odoriferum to species level as Pectobacterium odoriferum sp. nov., proposal of Pectobacterium brasiliense sp. nov. and Pectobacterium actinidiae sp. nov., emended description of Pectobacterium carotovorum and description of Pectobacterium versatile sp. nov., isolated from streams and symptoms on diverse plants. Int J Syst Evol Microbiol 2019; 69:3207–3216 [View Article] [PubMed]
     [Google Scholar]
  5. 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]
  6. Gardan L, Gouy C, Richard C, 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]
  7. Alcorn SM, Orum TV, Steigerwalt AG, Foster JLM, Fogleman JC et al. Taxonomy and pathogenicity of Erwinia cacticida sp. nov. Int J Syst Bacteriol 1991; 41:197–212 [View Article] [PubMed]
     [Google Scholar]
  8. Oulghazi S, Cigna J, Lau YY, Moumni M, Chan KG et al. Transfer of the waterfall source isolate Pectobacterium carotovorum M022 to Pectobacterium fontis sp. nov., a deep-branching species within the genus Pectobacterium. Int J Syst Evol Microbiol 2019; 69:470–475 [View Article] [PubMed]
     [Google Scholar]
  9. 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 [View Article] [PubMed]
     [Google Scholar]
  10. 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]
  11. Waleron M, Misztak A, Waleron M, Jonca J, Furmaniak M et al. Pectobacterium polonicum sp. nov. isolated from vegetable fields. Int J Syst Evol Microbiol 2019; 69:1751–1759 [View Article] [PubMed]
     [Google Scholar]
  12. Sarfraz S, Riaz K, Oulghazi S, Cigna J, Sahi ST et al. Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan. Int J Syst Evol Microbiol 2018; 68:3551–3556 [View Article] [PubMed]
     [Google Scholar]
  13. Pasanen M, Waleron M, Schott T, Cleenwerck I, Misztak A et al. Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence. Int J Syst Evol Microbiol 2020; 70:2440–2448 [View Article] [PubMed]
     [Google Scholar]
  14. Waleron M, Misztak A, Waleron M, Franczuk M, Jońca J et al. Pectobacterium zantedeschiae sp. nov. a new species of a soft rot pathogen isolated from Calla lily (Zantedeschia spp.). Syst Appl Microbiol 2019; 42:275–283S0723-2020(18)30219-4 [View Article] [PubMed]
     [Google Scholar]
  15. 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; 41:85–93S0723-2020(17)30171-6 [View Article] [PubMed]
     [Google Scholar]
  16. Perombelon MCM, Kelman A. Ecology of the soft rot erwinias. Annu Rev Phytopathol 1980; 18:361–387 [View Article]
     [Google Scholar]
  17. Quinn CE, Sells IA, Graham DC. Soft rot erwinia bacteria in the atmospheric bacterial aerosol. J Appl Bacteriol 1980; 49:175–181 [View Article]
     [Google Scholar]
  18. Burr TJ. Occurrence of soft-rot Erwinia spp. in soil and plant material. Phytopathology 1977; 77:1382
     [Google Scholar]
  19. 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]
  20. Faye P, Bertrand C, Pédron J, Barny M-A. Draft genomes of “Pectobacterium peruviense” strains isolated from fresh water in France. Stand Genomic Sci 2018; 13:27 [View Article] [PubMed]
     [Google Scholar]
  21. Portier P, Pédron J, Taghouti G, Dutrieux C, Barny M-A. Updated taxonomy of Pectobacterium genus in the CIRM-CFBP bacterial collection: when newly described species reveal “old” endemic population. Microorganisms 2020; 8:1441 [View Article]
     [Google Scholar]
  22. Pédron J, Guyon L, Lecomte A, Blottière L, Chandeysson C et al. Comparison of environmental and culture-derived bacterial communities through 16S metabarcoding: a powerful tool to assess media selectivity and detect rare taxa. Microorganisms 2020; 8:1129 [View Article]
     [Google Scholar]
  23. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article] [PubMed]
     [Google Scholar]
  26. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. 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; 101:1278–1282 [View Article] [PubMed]
     [Google Scholar]
  29. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
     [Google Scholar]
  30. 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]
  31. Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 1997; 14:685–695 [View Article] [PubMed]
     [Google Scholar]
  32. 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 [View Article]
     [Google Scholar]
  33. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  34. Jiang N, Dillon FM, Silva A, Gomez-Cano L, Grotewold E. Rhamnose in plants - from biosynthesis to diverse functions. Plant Sci 2021; 302:110687S0168-9452(20)30293-4 [View Article] [PubMed]
     [Google Scholar]
  35. 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 [View Article]
     [Google Scholar]
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Pectobacterium quasiaquaticum sp. nov., isolated from waterways
Int J Syst Evol Microbiol 71, 005042 (2021); https://doi.org/10.1099/ijsem.0.005042
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