Antonie van Leeuwenhoek

, Volume 108, Issue 3, pp 711–720 | Cite as

Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng

Original Paper


The type strain DCY99T was isolated from soil collected from a ginseng field in Hwacheon, Republic of Korea. Strain DCY99T is Gram-negative, non-spore forming, motile, rod-shaped, and strictly aerobic. The bacteria grow optimally at 25–30 °C and pH 6.0–6.5. Phylogenetically, strain DCY99T is most closely related to Sphingomonas oligophenolica JCM 12082T, followed by Sphingomonas asaccharolytica KCTC 2825T, Sphingomonas mali KCTC 2826T, Sphingomonas cynarae JCM17498T, Sphingomonas pruni KCTC 2824T, and Sphingomonas glacialis DSM 22294T. The DNA–DNA relatedness between strain DCY99T and S. oligophenolica JCM 12082T was 15.6 ± 0.4 %, and the DNA G+C content of strain DCY99T was 64.4 mol%. An isoprenoid quinone was detected and identified as ubiquinone Q-10, and sym-homospermidine was identified as the major polyamine of DCY99T. The major polar lipids were identified as sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylcholine. C14:02OH, C16:0, and summed feature 8 (C18:1ω7c:/C18:1ω6c) were identified as the major fatty acids present in DCY99T. The results of physiological and biochemical tests allowed strain DCY99T to be differentiated phenotypically from other recognized species belonging to the genus Sphingomonas. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Sphingomonas panacis sp. nov. is proposed with the type strain designated as DCY99T (=JCM 30806T =KCTC 42347T).


Sphingomonas panacis Ginseng Polyphasic taxonomy 



This research was supported by the Korea Institute of Planning & Evaluation for Technology in Food, Agriculture, Forestry & Fisheries (KIPET No: 313038-03-2-SB020).

Supplementary material

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  1. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H (2000) Phylogenetic affiliation of the Pseudomonas based on 16S rRNA sequence. Int J Syst Evol Microbiol 50:1563–1589CrossRefPubMedGoogle Scholar
  2. Bauer AW, Kirby WM, Sherris JC, Turck M (1966) Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Path 45:493–496PubMedGoogle Scholar
  3. Bernardet JF, Nakagawa Y, Holmes B (2002) Subcommittee on the taxonomy of Flavobacterium & Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070PubMedGoogle Scholar
  4. Busse HJ, Auling G (1988) Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8CrossRefGoogle Scholar
  5. Chen B, Shen J, Zhang X, Pan F, Yang X, Feng Y (2014) The endophytic bacterium, Sphingomonas SaMR12, improves the potential for zinc phytoremediation by its host, Sedum alfredii. PLoS ONE 9(9):e106826CrossRefPubMedPubMedCentralGoogle Scholar
  6. Choi JE, Ryuk JA, Kim JH, Choi CH, Chun J, Kim YJ, Lee HB (2005) Identification of endophytic bacteria isolated from rusty-colored root of Korean ginseng (Panax ginseng) and its induction. Korean J Med Crop Sci 13:1–5Google Scholar
  7. Christensen WB (1946) Urea decomposition as a means of differentiating Proteus and paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 52:461–466PubMedPubMedCentralGoogle Scholar
  8. Collins MD (1985) Isoprenoid quinone analyses in bacterial classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Academic Press, London, pp 267–287Google Scholar
  9. 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 Evol Microbiol 39:224–229Google Scholar
  10. Fegatella F, Cavicchioli R (2000) Physiological responses to starvation in the marine oligotrophic ultramicrobacterium Sphingomonas sp. Strain RB2256. Appl Environ Microbiol 66(5):2037–2044CrossRefPubMedPubMedCentralGoogle Scholar
  11. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  12. Fida TT, Moreno-Forero SK, Heipieper HJ, Springael D (2013) Physiology and transcriptome of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128 after long-term starvation. Microbiology 159:91807–91817CrossRefGoogle Scholar
  13. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406–416Google Scholar
  14. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  15. Kang MJY, Park CS, Ko SR, In K, Park CS, Lee DY, Yang DC (2011) Characteristics of absorption and accumulation of inorganic germanium in Panax ginseng CA Meyer. J Ginseng Res 35:12–20CrossRefGoogle Scholar
  16. Kim MK, Im WT, Ohta H, Lee M, Lee ST (2005) Sphingopyxis granuli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in alpha-4 subclass of the Proteobacteria. J Microbiol 43:152–157PubMedGoogle Scholar
  17. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH et al (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721CrossRefPubMedGoogle Scholar
  18. Kim YJ, Jeon JN, Jang MG, Kwon WS, Jung SK, Yang DC (2014) Ginsenoside profiles and related gene expression during foliation in Panax ginseng Meyer. J Ginseng Res 38:66–72CrossRefPubMedPubMedCentralGoogle Scholar
  19. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, CambridgeGoogle Scholar
  20. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–176Google Scholar
  21. Lee C, Kim KY, Lee JE, Kim S, Ryu D, Choi JE, An G (2011) Enzymes hydrolyzing structural components and ferrous ion cause rusty-root symptom on ginseng (Panax ginseng). J Microbiol Biotechnol 21(2):192–196CrossRefPubMedGoogle Scholar
  22. 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
  23. Minnikin DE, Odonnell 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
  24. Ohta H, Hattori R, Ushiba Y, Mitsui H, Ito M, Watanabe H, Tonosaki A, Hattori T (2004) Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations. Int J Syst Evol Microbiol 54:2185–2190CrossRefPubMedGoogle Scholar
  25. Rahman M, Punja ZK (2005) Biochemistry of ginseng root tissues affected by rusty root symptoms. Plant Physiol Biochem 43(12):1103–1114CrossRefPubMedGoogle Scholar
  26. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  27. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101, MIDI Inc, Newark, DEGoogle Scholar
  28. Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams and Wilkins, BaltimoreGoogle Scholar
  29. 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 Biomed Sci Appl 745:431–437CrossRefGoogle Scholar
  30. Takeuchi M, Sakane T, Yanagi M, Yamasato K, Hamana K, Yokota A (1995) Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov. Int J Syst Bacteriol 45(2):334–341CrossRefPubMedGoogle Scholar
  31. Takeuchi M, Hamana K, Hiraishi A (2001) Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51:1405–1417CrossRefPubMedGoogle Scholar
  32. Talà A, Lenucci M, Gaballo A, Durante M, Tredici SM, Debowles DA, Pizzolante G, Marcuccio C, Carata E, Piro G, Carpita NC, Mita G, Alifano P (2013) Sphingomonas cynarae sp. nov., a proteobacterium that produces an unusual type of sphingan. Int J Syst Evol Microbiol 63:72–79CrossRefPubMedGoogle Scholar
  33. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefPubMedPubMedCentralGoogle Scholar
  34. 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 25:4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  35. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE et al (1987) Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  36. Xie X, Fu J, Wang H, Liu J (2010) Heavy metal resistance by two bacteria strains isolated from a copper mine tailing in China. Afr J Biotechnol 9(26):4056–4066Google Scholar
  37. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T, Yamamoto H (1990) Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulatacomb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 34(2):99–119CrossRefPubMedGoogle Scholar
  38. Yabuuchi E, Kosako Y, Fujiwara N, Naka T, Matsunaga I, Ogura H, Kobayashi K et al (2002) Emendation of the genus Sphingomonas yabuuchi, 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola. Int J Syst Evol Microbiol 52:1485–1496PubMedGoogle Scholar
  39. Zhang DC, Busse HJ, Liu HC, Zhou YG, Schinner F, Margesin R (2011) Sphingomonas glacialis sp. nov., a psychrophilic bacterium isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 61:587–591CrossRefPubMedGoogle Scholar
  40. Zhou J, Peng M, Zhang R, Li J, Tang X, Xu B, Ding J, Gao Y, Ren J, Huang Z (2015) Characterization of Sphingomonas sp. JB13 exo-inulinase: a novel detergent-, salt-, and protease-tolerant exo-inulinase. Extremophiles 19(2):383–393CrossRefPubMedGoogle Scholar
  41. Ziarati P, Asgarpanah J (2013) Comparing heavy metal contents of Panax Ginseng samples from selected markets in Tehran and Beijing. J Environ Anal Toxicol 3:183Google Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life ScienceKyung Hee UniversityYongin-siRepublic of Korea
  2. 2.Graduate School of Biotechnology, College of Life ScienceKyung Hee UniversityYongin-siRepublic of Korea

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