Skip to main content
SpringerLink
Log in

Cupriavidus yeoncheonense sp. nov., isolated from soil of ginseng

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A novel bacterial strain, DCY86T (=KCTC 42053T = JCM 19890T) was isolated from soil of a ginseng field in Yeoncheon province (38°04′00″N 126°57′00″E), Republic of Korea using a serial dilution method. Strain DCY86T was observed to be Gram-stain negative, strictly aerobic, to grow optimally at 25–30 °C, at pH 7–7.5 and on tryptic soya agar medium. The cells were found to be sensitive to ceftazidine and tetracycline. Based on 16S rRNA gene sequence comparisons, strain DCY86T was found to be most closely related to Cupriavidus basilensis LMG 18990T (98.48 %), Cupriavidus numazensis LMG 26411T (98.34 %), Cupriavidus pinatabonesis KCTC 22125T (98.34 %) and Cupriavidus laharis KCTC 22126T (98.00 %). The G+C content was determined to be 64.23 mol %. The only isoprenoid quinone detected in strain DCY86T was ubiquinone Q-8. The major polar lipids were identified as diphosphatidylglycerol, phosphtidylethanolamine, phosphatidylglycerol, unidentified aminophosphoglycolipids and unidentified phospholipids. The major fatty acids were identified as C16:0 summed feature 3 (C16:1 ω7c/ω6c and/or iso-C15 : 0 2-OH) and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). These data support the affiliation of strain DCY86T to the genus Cupriavidus. Strain DCY86T was also found to be able to solubilize phosphate and produce siderophores. The results of physiological and biochemical tests enabled strain DCY86T to be differentiated genotypically and phenotypically from the recognized species of the genus Cupriaividus. Therefore, the novel isolate can be considered to represent a novel species, for which the name Cupriavidus yeoncheonense sp. nov. is proposed here. The type strain is DCY86T (=KCTC 42053T = JCM 19890T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Amadou C, Pascal G, Mangenot S, Glew M, Bontemps C, Capela D, Carrère S, Cruveiller S, Dossat S, Lajus A, Marchetti M, Poinsot V, Rouy R, Servin B, Saad M, Schenowitz C, Barbe V, Batut J, Médigue C, Masson-Boivin C (2008) Genome sequence of the β-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res 18:1472–1483

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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 Subcommittee on the taxonomy of Flavobacterium & Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002) 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

    Article  Google Scholar 

  • Chen WM, Laevens S, Lee TM, Coenye T, De Vos P, Mergeay M, Vandamme P (2001) Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 51:1729–1735

    Article  CAS  PubMed  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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Coenye T, Falsen E, Vancanneyt M, Hoste B, Govan JR, Kersters K, Vandamme P (1999) Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov. Int J Syst Bacteriol 49:405–413

    Article  PubMed  Google Scholar 

  • Coenye T, Goris J, De Vos P, Vandamme P, LiPuma JJ (2003) Classification of Ralstonia pickettii-like isolates from the environment and clinical samples as Ralstonia insidiosa sp. nov. Int J Syst Evol Microbiol 53:1075–1080

    Article  CAS  PubMed  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

    Google Scholar 

  • Cowan ST, Steel KJ (1974) Manual for the identification of medical bacteria, 3rd edn. Cambridge University Press, Cambridge

    Google Scholar 

  • Cuadrado V, Gomila M, Merini L, Giulietti AM, Moore ER (2010) Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 60:2606–2612

    Article  CAS  PubMed  Google Scholar 

  • 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 39:224–229

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  • 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 61:793–796

    PubMed Central  CAS  PubMed  Google Scholar 

  • Goris J, De Vos P, Coenye T, Hoste B, Janssens D, Brim H, Diels L, Mergeay M, Kersters K et al (2001) Classification of metal-resistant bacteria from industrial biotopes as Ralstonia campinensis sp. nov., Ralstonia metallidurans sp. nov. and Ralstonia basilensis Steinle et al. 1998 emend. Int J Syst Evol Microbiol 51:1773–1782

    Article  CAS  PubMed  Google Scholar 

  • 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 

  • 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 

  • Kimura M (1984) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Google Scholar 

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

    Google Scholar 

  • Lourdes MA, Jesús CM, Paulina ES (2013) Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb nov. Int J Syst Evol Microbiol 63:208–211

    Article  Google Scholar 

  • Makkar NS, Casida LE (1987) Cupriavidus necator gen. nov., sp. nov.; a Nonobligate bacterial predator of bacteria in soil†. Int J Syst Bacteriol 37:323–326

    Article  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 

  • Monchy S, Benotmane MA, Janssen P, Vallaeys T, Taghavi S, van der Lelie D, Mergeay M (2007) Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals. J Bacteriol 189:7417–7425

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pikovskaya RI (1948) Mobilization of phosphorus in soil in connection with vital activity of some microbial species. Microbiologia 17:362–370

    CAS  Google Scholar 

  • Sahin N, Isik K, Tamer AU, Goodfellow M (2000) Taxonomic position of “Pseudomonas oxalaticus” strain ox14T (DSM 1105T) (Khambata and Bhat, 1953) and its description in the genus Ralstonia as Ralstonia oxalatica comb. nov. Syst Appl Microbiol 23:206–209

    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 

  • Santos PEI, Martínez-Aguilar L, López-Lara IM, Mellado JC (2012) Cupriavidus alkaliphilus sp. nov., a new species associated with agricultural plants that grow in alkaline soils. Syst Appl Microbiol 5:310–314

    Article  Google Scholar 

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

    Google Scholar 

  • Sato Y, Nishihara H, Yoshida M, Watanabe M, Rondal JD, Concepcion RN, Ohta H (2006) Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines. Int J Syst Evol Microbiol 56:973–978

    Article  CAS  PubMed  Google Scholar 

  • Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56

    Article  CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Steinle P, Stucki G, Stettler R, Hanselmann KW (1998) Aerobic mineralization of 2,6-dichlorophenol by Ralstonia sp. strain RK1. Appl Environ Microbiol 64:2566–2571

    PubMed Central  CAS  PubMed  Google Scholar 

  • Steinle P, Stucki G, Stettler R, Hanselmann KW (1999) Validation of publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Evol Microbiol 49:1325–1326

    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  PubMed Central  CAS  PubMed  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  PubMed Central  CAS  PubMed  Google Scholar 

  • Vandamme P, Coenye T (2004) Taxonomy of the genus Cupriavidus: a tale of lost and found. Int J Syst Evol Microbiol 54:2285–2289

    Article  PubMed  Google Scholar 

  • Vandamme P, Goris J, Coenye T, Hoste B, Janssens D, Kersters K, De Vos P, Falsen E (1999) Assignment of centers for disease control group IVc-2 to the genus Ralstonia as Ralstonia paucula sp. nov. Int J Syst Bacteriol 49:663–669

    Article  PubMed  Google Scholar 

  • Vaneechoutte M, Kampfer P, De Baere T, Falsen E, Verschraegen G (2004) Wautersia gen. nov., a novel genus accommodating the phylogenetic lineage including Ralstonia eutropha and related species, and proposal of Ralstonia [Pseudomonas] syzygii (Roberts et al. 1990) comb. nov. Int J Syst Evol Microbiol 54:317–327

    Article  PubMed  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 

  • Yabuuchi E, Kosako Y, Yano I, Hotta H, Nishiuchi Y (1995) Transfer of two Burkholderia and an Alcaligenes species to Ralstonia gen. nov.: proposal of Ralstonia pickettii (Ralston, Palleroni and Doudoroff 1973) comb. nov., Ralstonia solanacearum (Smith 1896) comb. nov. and Ralstonia eutropha (Davis 1969) comb nov. Microbiol Immunol 39:897–904

    Article  CAS  PubMed  Google Scholar 

  • Zhang YB, Monchy S, Greenberg B, Mergeay M, Gang O, Taghavi S, van del Lelie D (2009) ArsR arsenic-resistance regulatory protein from Cupriavidus metallidurans CH34. Antonie Leeuwenhoek 96:161–170

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This research was supported by Korea Institute of Planning & Evaluation for Technology in Food, Agriculture, Forestry & Fisheries (KIPET No. : 313038-03-2-SB010) and Next-Generation BioGreen 21 Program (SSAC, Grant#: PJ009529032014), Republic of Korea.

Author information

Authors and Affiliations

  1. Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University, Seocheon-dong, Giheung-gu, Gyeonggi-do, Yongin-si, 446-701, Republic of Korea

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

  2. Graduate School of Biotechnology, Ginseng Genetic Resource Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Republic of Korea

    Yeon-Ju Kim, Johan Sukweenadhi, Mohamed El-Agamy Farh & Deok-Chun Yang

Authors
  1. Priyanka Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yeon-Ju Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ngoc-Lan Nguyen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Van-An Hoang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Johan Sukweenadhi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Mohamed El-Agamy Farh
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Deok-Chun Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Yeon-Ju Kim or Deok-Chun Yang.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1 (JPG 309 kb)

ESM 1 (JPG 309 kb)

ESM 1 (JPG 309 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Singh, P., Kim, YJ., Nguyen, NL. et al. Cupriavidus yeoncheonense sp. nov., isolated from soil of ginseng. Antonie van Leeuwenhoek 107, 749–758 (2015). https://doi.org/10.1007/s10482-014-0369-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-014-0369-z

Keywords

Search

Navigation