Antonie van Leeuwenhoek

, Volume 108, Issue 3, pp 619–626 | Cite as

Paralcaligenes ginsengisoli sp. nov., isolated from ginseng cultivated soil

Original Paper


A novel bacterial strain DCY104T isolated from soil of a ginseng field in Yeoncheon County, Republic of Korea is described in this study. Cells were short rod-shaped, motile by mean of one polar flagellum, strictly aerobic, Gramreaction negative, oxidase and catalase-positive. 16S rRNA gene sequence analysis showed that strain DCY104T shared highest similarity 98.2 % to Paralcaligenes ureilyticus GR24-5T, and from 97.7 to 97.1 % with other type strains belong to the genera Candidimonas, Pusillimonas and Parapusillimonas Otherwise, phylogenetic trees analyses indicated that strain DCY104T belongs to a single group with P. ureilyticus GR24-5T that was distinct to other genera. The major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The major cellular fatty acids consisted of C16:0, cyclo-C17:0, and summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c). The predominant polyamine was putrescine. The ubiquinone was Q-8. The genomic DNA G+C content was 55.9 mol%. These data in combination with the presence of one polar flagellum and positive activity of urease confirmed the placement of strain DCY104T in the genus Paralcaligenes. DNA–DNA relatedness between strain DCY104T and P. ureilyticus KACC 13888T was 40 %. The differences in the profiles of polar lipids, fatty acids and phenotypic characteristics in combination with DNA–DNA relatedness delineated strain DCY104T and P. ureilyticus KACC 13888T. In summary, taxonomic analyses in this study demonstrated that strain DCY104T represents a novel species within the genus Paralcaligenes, for which we propose the name Paralcaligenes ginsengisoli. The type strain is DCY104T (= KCTC 42406T = JCM 30746T).


Paralcaligenes ginsengisoli Ginseng soil One polar flagellum 



This research was supported by Korea Institute of Planning & Evaluation for Technology in Food, Agriculture, Forestry & Fisheries (KIPET No: 313038-03-1-HD030).

Supplementary material

10482_2015_517_MOESM1_ESM.docx (2.2 mb)
Supplementary material 1 (DOCX 2270 kb)


  1. Bauer AW, Kirby WM, Sherris JC, Turck M (1966) Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45:493–496PubMedGoogle Scholar
  2. Busse J, Auling G (1988) Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8CrossRefGoogle Scholar
  3. 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 39:224–229CrossRefGoogle Scholar
  4. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376PubMedCrossRefGoogle Scholar
  5. Felsenstein J (1985) Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  6. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  7. Glickmann E, Dessaux Y (1995) A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol 61:793–796PubMedCentralPubMedGoogle Scholar
  8. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98Google Scholar
  9. 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 42:457–469CrossRefGoogle Scholar
  10. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 1:36 (Web Server issue):W5-9. doi: 10.1093/nar/gkn201
  11. Kim SJ, Yoo SH, Weon HY, Kim YS, Anandham R, Suh JS, Kwon SW (2011) Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field. J Microbiol 49:502–507PubMedCrossRefGoogle Scholar
  12. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721PubMedCrossRefGoogle Scholar
  13. Lane JD (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175Google Scholar
  14. Lányí B (1988) Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67CrossRefGoogle Scholar
  15. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Bacteriol 39:159–167CrossRefGoogle Scholar
  16. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241CrossRefGoogle Scholar
  17. Pikovskaya RI (1948) Mobilization of phosphorus in soil in connection with vital capacity of source microbial species. Microbiologiya 17:362–370Google Scholar
  18. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  19. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc, NewarkGoogle Scholar
  20. Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56PubMedCrossRefGoogle Scholar
  21. Taibi G, Schiavo MR, Gueli MC, Rindina PC, Muratore R, Nicotra CM (2000) Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B Biomed Sci Appl 745:431–437PubMedCrossRefGoogle Scholar
  22. 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 10:512–526PubMedGoogle Scholar
  23. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729PubMedCentralPubMedCrossRefGoogle Scholar
  24. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882PubMedCentralPubMedCrossRefGoogle Scholar
  25. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Triiper HG (1987) Report of the ad hoc committee on reconciliation of approachesto bacterial systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  26. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703PubMedCentralPubMedGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Department of Oriental Medicinal BiotechnologyKyung Hee UniversityYongin-siRepublic of Korea
  2. 2.Graduate School of Biotechnology and Ginseng Bank, College of Life SciencesKyung Hee UniversityYongin-siRepublic of Korea

Personalised recommendations