1887

Abstract

In this study, we describe strain DCY64 that was isolated from the rhizosphere of three-year-old Korean ginseng root. Cells were Gram-reaction negative, oxidase- and catalase-positive, strictly aerobic, capsulated, non-motile, non-sporulating and spherical to short rod-shaped. Multiplicative budding cells were produced. Vesicles covered the surface of cells. Phylogenetic analysis placed strain DCY64 within the genus with the highest similarity to VKM B-1479 (97.6 % 16S rRNA gene sequence similarity), followed by MAFF 210191 (97.5 %), G24103 (97.4) and F11 (97.0 %). The genomic DNA G+C content was 63 mol%. The presences of summed feature 8 (Cω7 and/or Cω6), C cyclo ω8 and C as major fatty acids; phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol as major polar lipids; ubiquinone Q-10 as the predominant quinone and -homospermidine as the dominant polyamine were found in strain DCY64. These chemotaxonomic results were in accordance with those of members of the genus However, the absence of C 2-OH, C 3-OH and C 2-OH from the fatty acids profile and differences in minor polar lipids and phenotypic characteristics distinguished strain DCY64 from the closest type strains. The discrimination was also supported by unique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) fingerprints, as well as DNA–DNA hybridization values ( ≤ 48 %) between strain DCY64 and related type strains. Therefore, we propose that strain DCY64 represents a novel species of the genus . The name sp. nov. is proposed, with DCY64 ( = KCTC 32173 = JCM 19895) as the type strain.

Funding
This study was supported by the:
  • Next-Generation BioGreen 21 Program
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000512
2015-11-01
2024-12-12
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/11/3913.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000512&mimeType=html&fmt=ahah

References

  1. Albert R. A., Waas N. E., Langer S., Pavlons S. C., Feldner J. L., Rosselló-Mora R., Busse H. J. ( 2010;). Labrys wisconsinensis sp. nov., a budding bacterium isolated from Lake Michigan water, and emended description of the genus Labrys . Int J Syst Evol Microbiol 60 15701576 [View Article] [PubMed].
    [Google Scholar]
  2. Barrow G. I., Feltham R. K. A. ( 1993). Cowan and Steel's Manual for the Identification of Medical Bacteria , 3rd edn.., Cambridge: Cambridge University Press; [View Article].
    [Google Scholar]
  3. Busse J., Auling G. ( 1988;). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 11 18 [View Article].
    [Google Scholar]
  4. Carvalho M. F., De Marco P., Duque A. F., Pacheco C. C., Janssen D. B., Castro P. M. L. ( 2008;). Labrys portucalensis sp. nov., a fluorobenzene-degrading bacterium isolated from an industrially contaminated sediment in northern Portugal. Int J Syst Evol Microbiol 58 692698 [View Article] [PubMed].
    [Google Scholar]
  5. Chou Y.-J., Elliott G. N., James E. K., Lin K.-Y., Chou J.-H., Sheu S.-Y., Sheu D.-S., Sprent J. I., Chen W.-M. ( 2007;). Labrys neptuniae sp. nov., isolated from root nodules of the aquatic legume Neptunia oleracea . Int J Syst Evol Microbiol 57 577581 [View Article] [PubMed].
    [Google Scholar]
  6. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989;). Fluorometric deoxyribonucleic acid–deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39 224229 [View Article].
    [Google Scholar]
  7. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368376 [View Article] [PubMed].
    [Google Scholar]
  8. Felsenstein J. ( 1985;). Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39 783791 [View Article].
    [Google Scholar]
  9. Figueras M. J., Alperi A., Guarro J., Martínez-Murcia A. J. ( 2006;). Genotyping of isolates included in the description of a novel species should be mandatory. Int J Syst Evol Microbiol 56 11831184 [View Article] [PubMed].
    [Google Scholar]
  10. Fitch W. M. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20 406416 [View Article].
    [Google Scholar]
  11. Fritz I., Strömpl C., Abraham W.-R. ( 2004;). Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the ‘Alphaproteobacteria’ and description of Angulomicrobium amanitiforme sp. nov.. Int J Syst Evol Microbiol 54 651657 [View Article] [PubMed].
    [Google Scholar]
  12. Gomori G. ( 1955;). Preparation of buffers for use in enzyme studies. . In Methods in Enzymology, pp. 138146. Edited by Colowick S. P., Kaplan N. O. New York: Academic Press; [View Article].
    [Google Scholar]
  13. Hall T. A. ( 1999;). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41 9598.
    [Google Scholar]
  14. Hiraishi A., Ueda Y., Ishihara J., Mori T. ( 1996;). Comparative lipoquinone analysis of influent sewage and activated sludge by high performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42 457469 [View Article].
    [Google Scholar]
  15. Islam M. S., Kawasaki H., Nakagawa Y., Hattori T., Seki T. ( 2007;). Labrys okinawensis sp. nov. and Labrys miyagiensis sp. nov., budding bacteria isolated from rhizosphere habitats in Japan, and emended descriptions of the genus Labrys and Labrys monachus . Int J Syst Evol Microbiol 57 552557 [View Article] [PubMed].
    [Google Scholar]
  16. Johnson M., Zaretskaya I., Raytselis Y., Merezhuk Y., McGinnis S., Madden T. L. ( 2008;). NCBI blast: a better web interface. Nucleic Acids Res 36 (Web Server), W5W9 [View Article] [PubMed].
    [Google Scholar]
  17. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H., other authors. ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62 716721 [View Article] [PubMed].
    [Google Scholar]
  18. Lane D. J. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. Chichester: Willey;.
    [Google Scholar]
  19. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A., other authors. ( 2007;). clustal w clustal_x version 2.0. Bioinformatics 23 29472948 [View Article] [PubMed].
    [Google Scholar]
  20. Mesbah M., Premachandran U., Whitman W. B. ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39 159167 [View Article].
    [Google Scholar]
  21. Miller J. A., Kalyuzhnaya M. G., Noyes E., Lara J. C., Lidstrom M. E., Chistoserdova L. ( 2005;). Labrys methylaminiphilus sp. nov., a novel facultatively methylotrophic bacterium from a freshwater lake sediment. Int J Syst Evol Microbiol 55 12471253 [View Article] [PubMed].
    [Google Scholar]
  22. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2 233241 [View Article].
    [Google Scholar]
  23. Mouwen D. J. M., Weijtens M. J. B. M., Capita R., Alonso-Calleja C., Prieto M. ( 2005;). Discrimination of enterobacterial repetitive intergenic consensus PCR types of Campylobacter coli and Campylobacter jejuni by Fourier transform infrared spectroscopy. Appl Environ Microbiol 71 43184324 [View Article] [PubMed].
    [Google Scholar]
  24. Nguyen N. L., Kim Y. J., Hoang V. A., Tran B. T., Pham H. S., Yang D. C. ( 2015;). Paracoccus panacisoli sp. nov., isolated from a forest soil cultivated with Vietnamese ginseng. Int J Syst Evol Microbiol 65 14911497 [View Article] [PubMed].
    [Google Scholar]
  25. Nokhal T. H., Schlegel H. G. ( 1983;). Taxonomic study of Paracoccus denitrificans . Int J Syst Bacteriol 33 2637 [View Article].
    [Google Scholar]
  26. Pikovskaya R. I. ( 1948;). Mobilization of phosphorus in soil in connection with vital activity of some microbial species. Microbiologia 17 362370.
    [Google Scholar]
  27. Prescott L. M., Harley J. P. ( 2001). Laboratory Exercises in Microbiology, 5th edn., New York: McGraw-Hill;.
    [Google Scholar]
  28. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406425 [PubMed].
    [Google Scholar]
  29. Sasser M. ( 1990). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;.
    [Google Scholar]
  30. Schwyn B., Neilands J. B. ( 1987;). Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160 4756 [View Article] [PubMed].
    [Google Scholar]
  31. Stephenson D. P., Moore R. J., Allison G. E. ( 2009;). Comparison and utilization of repetitive-element PCR techniques for typing Lactobacillus isolates from the chicken gastrointestinal tract. Appl Environ Microbiol 75 67646776 [View Article] [PubMed].
    [Google Scholar]
  32. Taibi G., Schiavo M. R., Gueli M. C., Calanni-Rindina P., Muratore R., Nicotra C. M. A. ( 2000;). Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B Biomed Sci Appl 745 431437 [View Article] [PubMed].
    [Google Scholar]
  33. Tamura K., Nei M. ( 1993;). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10 512526 [PubMed].
    [Google Scholar]
  34. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 27252729 [View Article] [PubMed].
    [Google Scholar]
  35. Vasilyeva L. V., Semenov A. M. ( 1984;). Labrys monahos, a new budding prosthecate bacterium with radial symmetry. Mikrobiologiya 53 8592 (In Russian).
    [Google Scholar]
  36. Vasilyeva L. V., Semenov A. M. ( 1985;). Labrys gen. nov. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 18. Int J Syst Bacteriol 35 375376 [View Article].
    [Google Scholar]
  37. Versalovic J., Koeuth T., Lupski J. R. ( 1991;). Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19 68236831 [View Article] [PubMed].
    [Google Scholar]
  38. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., other authors. ( 1987;). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37 463464 [View Article].
    [Google Scholar]
  39. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991;). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173 697703 [PubMed].
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.000512
Loading
/content/journal/ijsem/10.1099/ijsem.0.000512
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF
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