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

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An Erratum to this article was published on 03 March 2016

Abstract

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 (C18:1 ω7c:/C18:1 ω6c) 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).

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References

  • 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 50:1563–1589

    Article  CAS  PubMed  Google Scholar 

  • Bauer AW, Kirby WM, Sherris JC, Turck M (1966) Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Path 45:493–496

    CAS  PubMed  Google Scholar 

  • 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 52:1049–1070

    CAS  PubMed  Google Scholar 

  • Busse HJ, Auling G (1988) Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8

    Article  CAS  Google Scholar 

  • 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):e106826

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 13:1–5

    Google Scholar 

  • 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 52:461–466

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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 267–287

  • 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 39:224–229

    Google Scholar 

  • Fegatella F, Cavicchioli R (2000) Physiological responses to starvation in the marine oligotrophic ultramicrobacterium Sphingomonas sp. Strain RB2256. Appl Environ Microbiol 66(5):2037–2044

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • 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 159:91807–91817

    Article  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406–416

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • 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 35:12–20

    Article  CAS  Google Scholar 

  • 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 43:152–157

    CAS  PubMed  Google Scholar 

  • 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 62:716–721

    Article  CAS  PubMed  Google Scholar 

  • 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 38:66–72

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–176

  • 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):192–196

    Article  CAS  PubMed  Google Scholar 

  • 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 39:159–167

    Article  CAS  Google Scholar 

  • 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 2:233–241

    Article  CAS  Google Scholar 

  • 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 54:2185–2190

    Article  CAS  PubMed  Google Scholar 

  • Rahman M, Punja ZK (2005) Biochemistry of ginseng root tissues affected by rusty root symptoms. Plant Physiol Biochem 43(12):1103–1114

    Article  CAS  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101, MIDI Inc, Newark, DE

  • Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams and Wilkins, Baltimore

  • 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 745:431–437

    Article  CAS  Google Scholar 

  • 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):334–341

    Article  CAS  PubMed  Google Scholar 

  • 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 51:1405–1417

    Article  CAS  PubMed  Google Scholar 

  • 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 63:72–79

    Article  PubMed  Google Scholar 

  • 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 28:2731–2739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 25:4876–4882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 37:463–464

    Article  Google Scholar 

  • 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):4056–4066

    CAS  Google Scholar 

  • 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):99–119

    Article  CAS  PubMed  Google Scholar 

  • 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 52:1485–1496

    CAS  PubMed  Google Scholar 

  • 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 61:587–591

    Article  CAS  PubMed  Google Scholar 

  • 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):383–393

    Article  CAS  PubMed  Google Scholar 

  • Ziarati P, Asgarpanah J (2013) Comparing heavy metal contents of Panax Ginseng samples from selected markets in Tehran and Beijing. J Environ Anal Toxicol 3:183

    Google Scholar 

Download references

Acknowledgments

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

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Authors and Affiliations

  1. Department of Oriental Medicine Biotechnology, Ginseng Bank, College of Life Science, Kyung Hee University, Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea

    Priyanka Singh, Yeon-Ju Kim, Van-An Hoang & Deok-Chun Yang

  2. Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea

    Mohamed El-Agamy Farh & Deok-Chun Yang

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  1. Priyanka Singh
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  2. Yeon-Ju Kim
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Correspondence to Yeon-Ju Kim or Deok-Chun Yang.

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Singh, P., Kim, YJ., Hoang, VA. et al. Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng. Antonie van Leeuwenhoek 108, 711–720 (2015). https://doi.org/10.1007/s10482-015-0527-y

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