1887

Abstract

A Gram-reaction-negative, catalase- and oxidase-positive, aerobic, non-motile, light yellow and rod-shaped bacterium (designated Gsoil 809) isolated from soil of ginseng field, was characterized by a polyphasic approach to clarify its taxonomic position. Strain Gsoil 809 was observed to grow optimally at 30 °C and at pH 7.0 on nutrient agar medium. Strain Gsoil 809 possessed -glucosidase activity, which was responsible for its ability to transform protopanaxatriol-type ginsenoside Rg1 to ginsenoside Rh1. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Gsoil 809 belongs to the genus of the family and was most closely related to Vu-144 (98.1 % 16S rRNA gene sequence similarity). The DNA G+C content was 39.4 mol%. The DNA–DNA hybridization value between strain Gsoil 809 and . Vu-144 was 41.27±1.03 %. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant quinone was MK-7. The major fatty acids were iso-C, iso-C G, iso-C 3-OH and summed feature 3, which supported the affiliation of Gsoil 809 to the genus . Strain Gsoil 809 contained homospermidineas the major polyamine. Moreover, the physiological and biochemical test results and low DNA–DNA relatedness value allowed the phenotypic and genotypic differentiation of strain Gsoil 809 from recognized species of the genus . Therefore, strain Gsoil 809 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Gsoil 809 (=KCTC 22820=JCM 30984).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001720
2017-04-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/4/1005.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001720&mimeType=html&fmt=ahah

References

  1. Madhaiyan M, Poonguzhali S, Senthilkumar M, Pragatheswari D, Lee JS et al. Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil. Int J Syst Evol Microbiol 2015; 65:578–586 [View Article][PubMed]
    [Google Scholar]
  2. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–176
    [Google Scholar]
  3. Im WT, Liu QM, Yang JE, Kim MS, Kim SY et al. Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of a ginseng field. J Microbiol 2010; 48:262–266 [View Article][PubMed]
    [Google Scholar]
  4. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  5. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  6. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  7. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983 [CrossRef]
    [Google Scholar]
  8. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  9. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  10. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  12. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993[PubMed]
    [Google Scholar]
  13. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria Cambridge: Cambridge University Press; 1974
    [Google Scholar]
  14. Ten LN, Im WT, Kim MK, Kang MS, Lee ST. Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 2004; 56:375–382 [View Article][PubMed]
    [Google Scholar]
  15. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67 [CrossRef]
    [Google Scholar]
  16. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
    [Google Scholar]
  17. Moore DD, Dowhan D. Preparation and analysis of DNA. In Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG. et al. (editors) Current Protocols in Molecular Biology New York, NY: Wiley; 1995 pp 2–11
    [Google Scholar]
  18. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
    [Google Scholar]
  19. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  20. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  21. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. (editors) Methods in Phytobacteriology Budapest: Akademiai Kaido; 1990 pp 199–204
    [Google Scholar]
  22. Schenkel E, Berlaimont V, Dubois J, Helson-Cambier M, Hanocq M. Improved high-performance liquid chromatographic method for the determination of polyamines as their benzoylated derivatives: application to P388 cancer cells. J Chromatogr B Biomed Appl 1995; 668:189–197 [View Article]
    [Google Scholar]
  23. Siddiqi MZ, Im WT. Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2016; 66:3449–3455 [View Article][PubMed]
    [Google Scholar]
  24. Siddiqi MZ, Im WT. Niabella aquatica sp. nov., isolated from lake water. Int J Syst Evol Microbiol 2016; 66:2774–2779 [View Article][PubMed]
    [Google Scholar]
  25. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT. Compostibacter hankyongensis gen. nov., sp. nov., isolated from compost. Int J Syst Evol Microbiol 2016; 66:3681–3687 [View Article][PubMed]
    [Google Scholar]
  26. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT. Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2016; 66:4039–4045 [View Article][PubMed]
    [Google Scholar]
  27. Wang YX, Liu JH, Xiao W, Ma XL, Lai YH et al. Aliifodinibius roseus gen. nov., sp. nov., and Aliifodinibius sediminis sp. nov., two moderately halophilic bacteria isolated from salt mine samples. Int J Syst Evol Microbiol 2013; 63:2907–2913 [View Article][PubMed]
    [Google Scholar]
  28. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001720
Loading
/content/journal/ijsem/10.1099/ijsem.0.001720
Loading

Data & Media loading...

Supplements

Supplementary File 1

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