1887

Abstract

A novel Gram-stain-negative strain, designated ZYY5, was isolated from rice roots. Results of 16S rRNA gene analysis indicated that strain ZYY5 was a member of the genus , with a highest similarity to DSM 18068 (98.5%). The major fatty acids were summed feature 3 (C ω7 and/or C ω6), C and summed feature 8 (C ω7 and/or C ω6). Multi-locus sequence analysis using five concatenated genes (16S rRNA, , , and ) and phylogenomic analysis based on 2940 core gene sequences showed that strain ZYY5 formed a robust cluster with strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192, while separated from the other strains of . The orthologous average nucleotide identity (ANI) and digital DNA–DNAhybridization (dDDH) values among these six strains ranged from 96.8–99.9% and 73.7–99.8%, which supported that they were belonged to the same species. However, strain ZYY5 shared 58.4 of dDDH and 94.5% of ANI values with type strain DSM 18068, which were lower than the proposed species boundary cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5 contained virulence-associated genes, which is same as the phylogenetic-related strains of the genus . Based on the results of the polyphasic approaches, we propose that strain ZYY5 represents a novel species in the genus , for which the name sp. nov. (=JCM 33020 =ACCC 61554 ) is proposed. Strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192 should also be classified in the same genomospecies of same as ZYY5.

Funding
This study was supported by the:
  • Xiao-Xia Zhang , National Natural Science Foundation of China , (Award 31670005)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004265
2020-06-18
2020-09-22
Loading full text...

Full text loading...

References

  1. Samson R, Legendre JB, Christen R, Saux MF-L, 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 [CrossRef][PubMed]
    [Google Scholar]
  2. Brady CL, Cleenwerck I, Denman S, Venter SN, Rodríguez-Palenzuela P et al. Proposal to reclassify Brenneria quercina (Hildebrand and Schroth 1967) Hauben et al. 1999 into a new 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 [CrossRef][PubMed]
    [Google Scholar]
  3. 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 [CrossRef][PubMed]
    [Google Scholar]
  4. Parkinson N, DeVos P, Pirhonen M, Elphinstone J. Dickeya aquatica sp. nov., isolated from waterways. Int J Syst Evol Microbiol 2014; 64:2264–2266 [CrossRef][PubMed]
    [Google Scholar]
  5. 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 [CrossRef][PubMed]
    [Google Scholar]
  6. 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 [CrossRef][PubMed]
    [Google Scholar]
  7. 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 [CrossRef][PubMed]
    [Google Scholar]
  8. Li B, Shi Y, Ibrahim M, Liu H, Shan C et al. Genome sequence of the rice pathogen Dickeya zeae strain ZJU1202. J Bacteriol 2012; 194:4452–4453 [CrossRef][PubMed]
    [Google Scholar]
  9. Bertani I, Passos da Silva D, Abbruscato P, Piffanelli P, Venturi V. Draft genome sequence of the plant pathogen Dickeya zeae DZ2Q, isolated from rice in Italy. Genome Announc 2013; 1:e00905-00913-e00905-00913 [CrossRef][PubMed]
    [Google Scholar]
  10. 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 [CrossRef][PubMed]
    [Google Scholar]
  11. 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]
  12. Zhou J, Zhang H, Wu J, Liu Q, Xi P et al. A novel multidomain polyketide synthase is essential for zeamine production and the virulence of Dickeya zeae . Mol Plant Microbe Interact 2011; 24:1156–1164 [CrossRef][PubMed]
    [Google Scholar]
  13. Hussain MBBM, Zhang H-B, Xu J-L, Liu Q, Jiang Z et al. The acyl-homoserine lactone-type quorum-sensing system modulates cell motility and virulence of Erwinia chrysanthemi pv. zeae. J Bacteriol 2008; 190:1045 [CrossRef][PubMed]
    [Google Scholar]
  14. Sun L, Qiu F, Zhang X, Dai X, Dong X et al. Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microb Ecol 2008; 55:415–424 [CrossRef][PubMed]
    [Google Scholar]
  15. Kawai M, Matsutera E, Kanda H, Yamaguchi N, Tani K et al. 16S ribosomal DNA-based analysis of bacterial diversity in purified water used in pharmaceutical manufacturing processes by PCR and denaturing gradient gel electrophoresis. Appl Environ Microbiol 2002; 68:699–704 [CrossRef][PubMed]
    [Google Scholar]
  16. Pariona-Llanos R, de Santi Ferrara FI, Gonzales HHS, Barbosa HR. Influence of organic fertilization on the number of culturable diazotrophic endophytic bacteria isolated from sugarcane. Eur J Soil Biol 2010; 46:387–393
    [Google Scholar]
  17. Zhang X, Sun L, Qiu F, McLean RJC, Jiang R et al. Rheinheimera tangshanensis sp. nov., a rice root-associated bacterium. Int J Syst Evol Microbiol 2008; 58:2420–2424 [CrossRef][PubMed]
    [Google Scholar]
  18. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecula Rbacteriology ASM; 1994
    [Google Scholar]
  19. Cappuccino JG, Sherman N. A Laboratory Manual: International Edition Microbiology; 2010
    [Google Scholar]
  20. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  21. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [CrossRef][PubMed]
    [Google Scholar]
  22. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613 [CrossRef][PubMed]
    [Google Scholar]
  23. Glaeser SP, Kämpfer P. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 2015; 38:237–245 [CrossRef][PubMed]
    [Google Scholar]
  24. De Vos P. Multilocus Sequence Determination and Analysis Methods in Microbiology Academic Press; 2011 pp 385–407
    [Google Scholar]
  25. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. MBE 2016; 33:1870–1874
    [Google Scholar]
  26. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  27. Kimura M. The Neutral Theory of Molecular Evolution Cambridge University Press; 1983
    [Google Scholar]
  28. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  30. Schubert M, Lindgreen S, Orlando L. AdapterRemoval V2: rapid adapter trimming, identification, and read merging. BMC Res Notes 2016; 9:88 [CrossRef][PubMed]
    [Google Scholar]
  31. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from illumina MiSeq data. Bioinformatics 2015; 31:587–589 [CrossRef][PubMed]
    [Google Scholar]
  32. John BE, Bass L. Usability and software architecture. Behav Info Technol 2001; 20:329–338
    [Google Scholar]
  33. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [CrossRef][PubMed]
    [Google Scholar]
  34. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [CrossRef][PubMed]
    [Google Scholar]
  35. 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 [CrossRef][PubMed]
    [Google Scholar]
  36. SI N, Kim YO, Yoon SH, SM H, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:1–6
    [Google Scholar]
  37. Wayne L. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics (International Committee on systematic bacteriology). Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  38. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. PNAS 2009; 106:19126–19131
    [Google Scholar]
  39. Seemann T, Torsten S. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  40. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [CrossRef][PubMed]
    [Google Scholar]
  41. Liu HL, Xin BY, Zheng JS. Build a bioinformatics analysis platform and apply it to routine analysis of microbial genomics and comparative genomics, 27 January 2020, protocol (version 1) available at protocol exchange. https://doi.org/10.21203/rs.2.21224/v1 .
  42. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992; 8:275–282 [CrossRef][PubMed]
    [Google Scholar]
  43. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [CrossRef][PubMed]
    [Google Scholar]
  44. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  45. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  46. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004265
Loading
/content/journal/ijsem/10.1099/ijsem.0.004265
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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