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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 11

Diversity within the complex, identification of and members, proposal of the novel species sp. nov. No Access

Abstract

The genus comprises plant pathogens that cause diseases in a large range of economically important crops and ornamentals. Strains previously assigned to the species are major pathogens attacking vital crops such as maize and rice. They are also frequently isolated from surface water. The newly described species is closely related to members, so that the limit between the two species can be difficult to define. In order to clearly distinguish the two species, globally described by the term ‘ complex’, we sequenced the genome of four new water isolates and compared them to 14 genomes available in databases. Calculation of average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values confirmed the phylogenomic classification into the two species and . It also allowed us to propose a new species, sp. nov., to characterize a clade distinct from those containing the type strain NCPPB2538. Strain S31 (CFBP 8716=LMG 32070) isolated from water in France is proposed as the type strain of the new species. Phenotypic analysis of eight publically available strains revealed traits common to the five tested members but apparently not shared by the type strain. Genomic analyses indicated that a simple distinction between the species , and can be obtained on the basis of the sequence. can be distinguished from the two other species by growth on -tartaric acid. Based on the marker, several strains previously identified as were re-assigned to the species or . This study also highlighted the broad host range diversity of these three species.

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  • Accepted:
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Keyword(s): Dickeya oryzae , Dickeya parazeae , Dickeya zeae , Pectobacteriaceae , phytopathogen and soft-rot Enterobacterales
Funding
This study was supported by the:
  • agence nationale de la recherche (Award ANR-17-CE32-0004-04)
    • Principle Award Recipient: NotApplicable
© 2021 The Authors
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2021-11-02
2024-05-02
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References

  1. Hugouvieux-Cotte-Pattat N, Condemine G, Gueguen E, Shevchik VE. Dickeya plant pathogens. eLS 2020 [View Article]
     [Google Scholar]
  2. Toth IK, Barny MA, Brurberg MB, Condemine G, Czajkowski R et al. Pectobacterium and Dickeya: Environment to disease development. Van Gijsegem F, van der Wolf JM, Toth IK. eds In Plant diseases caused by Dickeya and Pectobacterium species Springer editions; 2021 pp 39–84
     [Google Scholar]
  3. Samson R, Legendre JB, Christen R, Fischer-Le Saux M, Achouak W et al. Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. Int J Syst Evol Microbiol 2005; 55:1415–1427 [View Article] [PubMed]
     [Google Scholar]
  4. Brady CL, Cleenwerck I, Denman S, Venter SN, Rodrıguez-Palenzuela P et al. Proposal to reclassify Brenneria quercina (Hildebrand & Schroth 1967) Hauben et al. 1999 into a novel genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., descriptions of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. Iberica subsp. nov., and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiae as Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii . Int J Syst Evol Microbiol 2012; 62:1592–1602 [View Article] [PubMed]
     [Google Scholar]
  5. van der Wolf JM, Nijhuis EH, Kowalewska MJ, Saddler GS, Parkinson N et al. Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum). Int J Syst Evol Microbiol 2014; 64:768–774 [View Article] [PubMed]
     [Google Scholar]
  6. Tian Y, Zhao Y, Yuan X, Yi J, Fan J et al. Dickeya fangzhongdai sp. nov., a plant-pathogenic bacterium isolated from pear trees (Pyrus pyrifolia). Int J Syst Evol Microbiol 2016; 66:2831–2835 [View Article] [PubMed]
     [Google Scholar]
  7. Alič Š, Van Gijsegem F, Pédron J, Ravnikar M, Dreo T. Diversity within the novel Dickeya fangzhongdai sp., isolated from infected orchids, water and pears. Plant Pathol 2018; 67:1612–1620 [View Article]
     [Google Scholar]
  8. Hugouvieux-Cotte-Pattat N, Brochier-Armanet C, Flandrois J-P, Reverchon S. Dickeya poaceiphila sp. nov., a plant-pathogenic bacterium isolated from sugar cane (Saccharum officinarum). Int J Syst Evol Microbiol 2020; 70:4508–4514 [View Article]
     [Google Scholar]
  9. Parkinson N, DeVos P, Pirhonen M, Elphinstone J. Dickeya aquatica sp. nov., isolated from waterways. Int J Syst Evol Microbiol 2014; 64:2264–2266 [View Article] [PubMed]
     [Google Scholar]
  10. Hugouvieux-Cotte-Pattat N, Jacot-des-Combes C, Briolay J. Dickeya lacustris sp. nov., a water-living pectinolytic bacterium isolated from lakes in France. Int J Syst Evol Microbiol 2019; 69:721–726 [View Article] [PubMed]
     [Google Scholar]
  11. Oulghazi S, Pédron J, Cigna J, Lau YY, Moumni M et al. Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia. Int J Syst Evol Microbiol 2019; 69:2440–2444 [View Article] [PubMed]
     [Google Scholar]
  12. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  13. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article] [PubMed]
     [Google Scholar]
  14. Pédron J, Van Gijsegem F. Diversity in the bacterial Dickeya genus grouping plant pathogens and waterways isolates. OBM Genet 2019; 3:22
     [Google Scholar]
  15. Parkinson N, Stead D, Bew J, Heeney J, Tsror Lahkim L et al. Dickeya species relatedness and clade structure determined by comparison of recA sequences. Int J Syst Evol Microbiol 2009; 59:2388–2393 [View Article] [PubMed]
     [Google Scholar]
  16. Suharjo R, Sawada H, Takikawa Y. Phylogenetic study of Japanese Dickeya spp. and development of new rapid identification methods using PCR–RFLP. J Gen Plant Pathol 2014; 80:237–254 [View Article]
     [Google Scholar]
  17. Wang X, He SW, Guo HB, Han JG, Thin KK et al. Dickeya oryzae sp. nov., isolated from the roots of rice. Int J Syst Evol Microbiol 2020; 70:4171–4178 [View Article]
     [Google Scholar]
  18. Hu M, Li J, Chen R, Li W, Feng L et al. Dickeya zeae strains isolated from rice, banana and clivia rot plants show great virulence differentials. BMC Microbiol 2018; 18:136 [View Article]
     [Google Scholar]
  19. 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]
  20. Charkowski AO. The changing face of bacterial soft-rot diseases. Annu Rev Phytopathol 2018; 56:269–288 [View Article] [PubMed]
     [Google Scholar]
  21. Laurila J, Hannukkala A, Nykyri J, Pasanen M, Hélias V et al. Symptoms and yield reduction caused by Dickeya spp. strains isolated from potato and river water in Finland. Eur J Plant Pathol 2010; 126:249–262 [View Article]
     [Google Scholar]
  22. Potrykus M, Golanowska M, Sledz W, Zoledowska S, Motyka A et al. Biodiversity of Dickeya spp. isolated from potato plants and water sources in temperate climate. Plant Dis 2016; 100:408–417 [View Article]
     [Google Scholar]
  23. Helias V, Hamon P, Huchet E, Wolf JVD, Andrivon D. Two new effective semiselective crystal violet pectate media for isolation of Pectobacterium and Dickeya . Plant Pathol 2012; 61:339–345 [View Article]
     [Google Scholar]
  24. Meneley JC. Isolation of soft-rot Erwinia spp. from agricultural soils using an enrichment technique. Phytopathology 1976; 66:367–370 [View Article]
     [Google Scholar]
  25. Nassar A, Darrasse A, Lemattre M, Kotoujansky A, Dervin C et al. Characterization of Erwinia chrysanthemi by pectinolytic isozyme polymorphism and restriction fragment length polymorphism analysis of PCR-amplified fragments of pel genes. Appl Environ Microbiol 1996; 62:2228–2235 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. 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]
  28. 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]
  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. Kim C, Song S, Park C. The D-allose operon of Escherichia coli K-12. J Bacteriol 1997; 179:7631–7637 [View Article]
     [Google Scholar]
  31. Hurlbert RE, Jakoby WB. Tartaric acid metabolism. I. Subunits of L(+)-tartaric acid dehydrase. J Biol Chem 1965; 240:2772–2777 [PubMed]
     [Google Scholar]
  32. Zhou J, Cheng Y, Lv M, Liao L, Chen Y et al. The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species. BMC Genomics 2015; 16:571 [View Article]
     [Google Scholar]
  33. Hugouvieux-Cotte-Pattat N, Jacot-des-Combes C, Briolay J. Genomic characterization of a pectinolytic isolate of Serratia oryzae isolated from lake water. J Genomics 2019; 7:64–72 [View Article]
     [Google Scholar]
  34. Kano A, Hosotani K, Gomi K, Yamasaki-Koduko Y, Shirakawa C et al. D-Psicose induces upregulation of defense-related genes and resistance in rice against bacterial blight. J Plant Physiol 2011; 168:1852–1857 [View Article]
     [Google Scholar]
  35. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostic for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
     [Google Scholar]
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Diversity within the Dickeya zeae complex, identification of Dickeya zeae and Dickeya oryzae members, proposal of the novel species Dickeya parazeae sp. nov.
Int J Syst Evol Microbiol 71, 005059 (2021); https://doi.org/10.1099/ijsem.0.005059
/content/journal/ijsem/10.1099/ijsem.0.005059
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