Detection of Nocardia sp. Hl7-1 by PCR during Bioremediation of Crude Oil-Contaminated Soil

원유 오염토양의 Bioremediation과정 동안 PCR을 이용한 Nocardia sp. Hl7-1의 검출

  • Baek, Kyung-Hwa (Environmental Biotechnology Laboratory, Korea Research Institute of Bioscience & Biotechnology, Ecology Laboratory, Ewha Womans University) ;
  • Lee, Young-Ki (Environmental Biotechnology Laboratory, Korea Research Institute of Bioscience & Biotechnology) ;
  • Lee, In-Sook (Ecology Laboratory, Ewha Womans University) ;
  • Oh, Hee-Mock (Environmental Biotechnology Laboratory, Korea Research Institute of Bioscience & Biotechnology) ;
  • Yoon, Byung-Dae (Environmental Biotechnology Laboratory, Korea Research Institute of Bioscience & Biotechnology) ;
  • Kim, Hee-Sik (Environmental Biotechnology Laboratory, Korea Research Institute of Bioscience & Biotechnology)
  • Published : 2004.03.01

Abstract

For the detection of the oil-degrading bacterium, Nocardia sp. Hl7-1, inoculated during the bioremediation of oil-contaminated soil, a species-specific primer was constructed based on the 16S rDNA sequence of this strain. Two forward primers and two reverse primers were designed and tested against both closely and distantly related bacterial strains. All the primers designed were specific to the Nocardia sp. H17-1. Particularly, primer sets NH169F-NH972R and NH575F-NH972R could be used to detect 50 fg of template DNA and TEX>$1.2${\times}$10^4$ CFU/g of sandy soil. These two PCR primer sets successfully detected the H 17-1 strain in the oil-con-laminated soil samples containing heterogeneous DNA. We also conformed the primer specificity by restriction-enzyme cleavage of the PCR products and denaturing gradient gel electrophoresis.

Keywords

16S rDNA;denaturing gradient gel electrophoresis (DGGE);detection;Nocardia sp.;PCR;species-specific primer

References

  1. Biotechnol. Lett. v.23 Specific detection of a oil-degrading bacterium, Corynebacterium sp. IC10, in sand microcosms by PCR using species specific primers based on 16S rRNA gene sequence Lee,J.H.;S.Y.Jung;S.J.Kim
  2. J. Ferment. Bioeng v.84 Production and properties of Lipopeptide biosurfactant from Bacillus subtilis C9 Kim,H.S.;B.D.Yoon;C.H.Lee;H.H.Suh;H.M.Oh;T.Katsuragi;Y.Tani
  3. Kor. J. Biotechnol. v.11 Isolation and characterization of crude oil-degrading strains, Nocardia sp. H17-1 Lee,C.H.;G.S.Kwon;H.S.Kim;H.H.Suh;K.H.Ahn;H.M.Oh;B.D.Yoon
  4. Appl. Environ. Microbiol. v.64 A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pesudomonas (Sensu Stricto) in environmental samples Widmer,F.;R.J.Seidler;P.M.Gillevet;L.S.Watrud;G.D.Di Giovanni
  5. Nucleic Acids Res. v.28 The ribosomal database project (RDP) Maidak,B.L.;N.Larsen;M.J.McCaughey;R.Overbeek;G.J.Olsen;K.Fogel;J.Blandy;C.R.Woses
  6. Soil Biol. Biochem v.26 Mineralization performance of Rhodococcus chlorophenlikcus strain PCP-1 in contaminated soil stimulating on site conditions Briglia,M.;P.J.M.Middeldorp;M.S.Salkinoja Salonen
  7. Appl. Environ. Microbiol. v.64 Survival in soil of different toluene-degrading Pseudomonas strains after solvent shock Huertas,M.J.;E.Duque;S.Marques;J.L.Ramos
  8. Kor. J. Appl. Microbiol. Biotechnol v.25 Microbial degradation of Arabian light crude oil by Acinetobacter sp. A54 Lee,C.H.;H.S.Kim;H.H.Sub;S.H.Choi;H.M.Oh;B.D.Yoon
  9. Environ. Health Perspect v.103 A small circle of knowledge, a large circle of ignorance Alexander,M.
  10. Microbiol. Ecol. v.34 Hybridization analysis of microbial DNA from fuel oil-contaminated and noncontaminated soil Guo,C.;W.Sun;J.B.Harsh;A.Ogram
  11. Appl. Environ. MicroBiol v.59 Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA Muyzer,G.;E.C.De Waal;A.G.Uitterlinden
  12. Appl. Environ. MicroBiol v.63 Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes Zhou,J.A.;V.Palumbo;J.M.Tiedje
  13. Appl. Environ. MicroBiol v.60 Use of molecular tools evaluate the survival of a microorganism injected into an aquifer Thiem,S.M.;M.L.Krumme;R.L.Smith;J.M.Tiedje
  14. Appl. Environ. MicroBiol v.50 Reasons for possible failure of inoculation to enhance biodegradation Goldstein,R.M.;L.M.Mallory;M.alexander