• A Review on the Current Methods for Extracting DNA from Soil and Sediment Environmental Samples
  • Yoo, Keun-Je;Lee, Jae-Jin;Park, Joon-Hong;
  • School of Civil and Environmental Engineering, Yonsei University;School of Civil and Environmental Engineering, Yonsei University;School of Civil and Environmental Engineering, Yonsei University;
  • 토양 및 퇴적토 환경 시료로부터 DNA 추출하는 방법에 대한 고찰
  • 유근제;이재진;박준홍;
  • 연세대학교 토목환경공학과;연세대학교 토목환경공학과;연세대학교 토목환경공학과;
References
  • 1. 서장선, 김상효, 엄명호, 2000, 토양미생물 다양성과 Biomass에 의한 토양건전성 평가, 한국유기농업, 2(7)135-148
  •  
  • 2. 이영재, 한인숙, 1998, Superscale Plasmid DNA Preparation Using Wizard Plus Maxipreps Kit, MEDLIS, 17, 136-140
  •  
  • 3. Alm, E.W., Zheng, D., and Raskin, L., 2000, The presence of humic substances and DNA in RNA extracts affects hybridization results, Appl. Environ. Microbiol, 66, 4547-4554
  •  
  • 4. Alpini, G., Phillips, J.O., Vroman, B., and Larusso, N.F., 1994, Recent advances in the isolation of liver cells, Hepatology, 20, 494-514
  •  
  • 5. Amann, R.I., Ludwig, W., and Schleifer, K.H., 1995, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiol. Rev, 59, 143-169
  •  
  • 6. Bakkern, L.R., 1985, Separation and purification of bacteria from soil, Appl. Environ. Microbiol. 49, 1482-1487
  •  
  • 7. Bakken, L.R. and Lindahl, V., 1995, Recovery of bacterial cells from soil, Nucleic Acids in the Environment: Methods and Applications, Springer-Verlag, Heidelberg, Germany, 9-27
  •  
  • 8. Brosch, R., Gordon, S.V., Billault, A., Garnier, T., Eiglmeier, K., Soravito, C., Barrell, B.G., and Cole, S.T., 1998, Use of a Mycobacterium tuberculosis H37Rv bacterial artificial chromosome library for genome mapping, sequencing and comparative genomics, Infect. Immun, 66, 2221-2229
  •  
  • 9. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., and Ritchie, D.A., 1992, Amplication of DNA from native populations of soil bacteria by using the polymerase chain reaction, Appl. Environ. Microbiol, 58, 3413-3416
  •  
  • 10. Burgmann, H., Pesaro, M., Widmer, F., and Zeyer, J., 2001, A strategy for optimizing quality and quality of DNA extracted from soil, J. Microbiol. Methods, 45, 7-20
  •  
  • 11. Chandler, D.P., Stults, J.R., Cebula, S., Schuck, B.L., Weaver, D. W., Anderson, K.K., Egholm, M., and Brockman, F.J., 2000, Affinity purification of DNA and RNA from environmental samples with peptide nucleic acid clamps, Appl. Environ. Microtiol, 66, 3438-3445
  •  
  • 12. Courtois, S., Frostegard, A., Goransson, P., Depret, G., Jeanin, P., and Simonet, P., 2001, Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation, Environ. Microbiol, 3, 431-439
  •  
  • 13. Courtois, S., Cappellano, C.M., Ball, M., Francou, F.X., Normand, P., Helynck, G., Martinez, A., Kolvek, S.J., Hopke, J., Osburne, M.S., August, P.R., Nalin, R., Guerineau, M., Jeannin, P., Simonet, P., and Pernodet, J.L., 2003, Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products, Appl. Environ. Microbiol, 69, 49-55
  •  
  • 14. Curtis, T.P., Sloan, W.T., and Scannell, J.W., 2002, Estimating prokaryotic diversity and its limits, Proc. Natl. Acad. Sci. USA 99, 10494-10499
  •  
  • 15. Diaz-Perez, S.V., Alatriste-Mondtagon, F., Hernandez, R., Birren, B., and Gunsalus, R.P., 1997, Bacterial artificial chromosome (BAC) library as a tool for physical mapping of the archaeon Methanosarcina thermophila TM-1, Microb. Comp. Genomics, 2, 275-286
  •  
  • 16. Degrange, V. and Bardin, R., 1995, Detection and counting of nitrobacter populations in soil by PCR, Appl. Environ. Microbiol. 61, 2093-2098
  •  
  • 17. Dewar, K., Sabbagh, L., Cardinal, G., Veilleux, F., Sanschagrin, F., Birren, B., and Levesque, R.C., 1998, Pseudomonas aeruginosa PAO1 bacterial artificial chromosomes: strategies for mapping, screening, and sequencing 100kb loci of the 5.9 Mb genome, Microb. Comp. Genomics, 3, 105-117
  •  
  • 18. Edhcomb, V.P., McDonald, J.H., Devereux, R., and Smith, D.W., 1999, Estimation of bacterial cell numbers in humic acidrich salt marsh sediments with probes directed to 16S ribosomal DNA, Appl. Environ. Microbiol, 65, 1516-1523
  •  
  • 19. Faegri, V., Torsvik, V.L., and Goksoyr, J., 1977, Bacterial and fungal activities in soil: separation of bacteria and fugi by a rapid fractionated centrifugation technique, Soil Biol. Biochem, 9, 105-112
  •  
  • 20. Frostegard, A., Courtois, S., Ramisse, V., Clerc, S., Bernillon, D., Le Gall, F., Jeannin, P., Nesme, X., and Simonet, P., 1999, Quantification of bias related to the extraction of DNA directly from soils, Appl. Environ. Microbiol, 65, 5409-5420
  •  
  • 21. Hary, M., Gambier, B., and Garnier Sillam, E., 2000, Soil conservation for DNA preservation for bacterial molecular studies, Eur. J. Soil Biol, 36, 51-55
  •  
  • 22. Hattori, T., 1988, aggregates as microhabitats of microorganisms, Biol. Fertil. Soils 6, 189-203
  •  
  • 23. Henne, A., Daniel, R., Schmitz, R.A., and Gottschalk, G., 1999, Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate, Appl. Environ. Microbiol, 65, 3901-3907
  •  
  • 24. Herron, P.R. and Wellington, E.M.H., 1990, New method for extraction of Streptomycete spores from soil and application to the study of lysogeny in sterile amended and non sterile soil, Appl. Environ. Microbiol, 56, 1406-1412
  •  
  • 25. Heuer, H., Krsek, M., Baker, P., Smalla, K., and Wellington, E.M., 1997, Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients, APPl. Environ. Microbiol, 63, 3233-3241
  •  
  • 26. Holben, W.E., Jansson, J.K., Chelm, B.K., and Tiedje, J.M., 1988, DNA probe method for the detection of specific microorganisms in the soil bacterial community, Appl. Environ. Microbial, 54, 703-711
  •  
  • 27. Hugenholtz, P., Goebel, B.M., and Pace, N.R., 1998, Impact of culture independent studies on the emerging phylogenetic view of bacterial diversity, J. Bacteriol, 180, 4765-4774
  •  
  • 28. Hurt, R., Qiu, X., Wu, L., Roh, Y., Palumbo, A.V., Tiedje, J.M., and Zhou, Z., 2001, Simultaneous Recovery of RNA and DNA from Soils and Sediments, Appl. Environ. Microbiol, 67, 4495-4503
  •  
  • 29. Jackson, C.R., Harper, J.P., Willoughby, D., Roden, E.E., and Churchill, P.F., 1997, A simple efficient method for the separation of humic substances and DNA from environmental samples, Appl. Environ. Microbiol, 63, 4993-4995
  •  
  • 30. Jacobsen, C.S. and Rasmussen, O.F., 1992, Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin, Appl. Environ. Microbiol, 58, 2458-2462
  •  
  • 31. Jacobsen, C.S., 1995, Microscale detection of specific bacterial DNA in soil with a magnetic capture-hybridization and PCR amplication assay, Appl. Environ. Microbiol, 61, 3347-3352
  •  
  • 32. Krsek, M. and Wellington, E.M., 1999, Comparison of different methods for the isolation and purification of total community DNA from soil (In Process Citation), J. Microbiol. Methods, 39, 1-16
  •  
  • 33. Kuske, C.R., Banton, K.L., Adorada, D.L., Stark, P.C., Hill, K. K., and Jackson, P.J., 1998, Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil, Appl. Environ. Microbiol, 64, 2463-2472
  •  
  • 34. Lamontagne, M.G., Michel, F.C., Holden, P.A., and Reddy, C.A., 2002, Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis, J. Microbiol. Methods, 49, 255-264
  •  
  • 35. Leff, L.G., Dana, J.R., McArthur, J.V., and Shimkets, L.J., 1995, Comparison of methods of DNA extraction from stream sediments, Appl. Environ. Microbiol, 61, 1141-1143
  •  
  • 36. Liesack, W., Weyland H., and Stackebrandt, E., 1991, Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria, Microb. Ecol, 21, 191-198
  •  
  • 37. Liesack, W. and Stackebrandt, E., 1992, Occurrence of novel groups of the domain bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment, J. Bacteriol, 174, 5072-5078
  •  
  • 38. Lindahl, V. and Bakken, L.R., 1995, Evaluation of methods for extraction of bacterial from soil, FEMS Microbiol. Ecol, 16, 135-142
  •  
  • 39. Lee, Y.S., Bollinger, J., Bezdicek, D., and Ogram, A., 1996, Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method, Appl. Environ. Microbiol, 62, 3787-3793
  •  
  • 40. Maarit Niemi, R., Heiskanen, I., Wallenius, K., and Lindstrom, K., 2001, Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia, J. Microbiol. Methods, 45, 155-165
  •  
  • 41. Martin-Laurent, F., philippot, L., Hallet, S., Chaussod, R., Germon, J.C., Soulas, G., and Catroux, G., 2001, DNA extraction from soils: old bias for new microbial diversity analysis methods, Appl. Environ. Microbiol, 67, 2354-2359
  •  
  • 42. Mayr, C., Winding, A., and Hendriksen, N. B., 1999, Community level physiological profile of soil bacteria unaffected by extraction method, J. Microbiol. Methods, 36, 29-33
  •  
  • 43. McDonalds, R.M., 1986, Sampling soil microfloras: dispersion of soil by ion exchange and extraction of specific microorganisms from suspension by elutriation, Soil Biol. Biochem, 18, 399-406
  •  
  • 44. Miller, D.N., Bryant, J.E., Madsen, E.L., Ghiorse, W.C., and Madsen, E.L., 1994, Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment, Appl. Environ. Microbiol, 60, 1572-1580
  •  
  • 45. Miller, D.N., 2001, Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soils and sediments, J. Microbiol. Methods, 44, 49-58
  •  
  • 46. More, M.I., Herrick, J.B., Silva, M.C., Ghiorse, W.C., and Madsen, E.L., 1994, Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment, Appl. Envriron. Microbiol, 60, 1572-1580
  •  
  • 47. Nalin, R., Normand, P., Simonet, P., and Domenach, A.M., 1999, Polymerase chain reaction and hybridization on DNA extracted from soil as a tool for Frankia spp. Population distribution studies in soil, Can. J. Bot. 77, 1239-1247
  •  
  • 48. Ogram, A., Sayler, G.S., and Barkay, T., 1987, The extraction and purification of microbialDNA from sediments, J. Microbiol. Metholds, 7, 57-66
  •  
  • 49. Orsini, M. and Romano-Spica, V., 2001, A microwave-based method for nucleic acid isolation from environmental samples, Lett. Appl. Microbiol, 33, 17-20
  •  
  • 50. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., and Simonet, P., 1992, Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction, Appl. Environ. Microbiol, 58, 2717-2722
  •  
  • 51. Pillai, S.D., Josephson, K.L., Bailey, R.L., Gerba, C.P., and Pepper, I. L., 1991, Rapid method for processing soil samples for polymerase chain reaction amplification of specific gene sequences, Appl. Environ. Microbiol, 57, 2283-2286
  •  
  • 52. Porteous, L.A. and Armstrong, J.L., 1991, Recovery of bulk DNA from soil by a rapid, small-scale extraction method, Curr. Microbiol, 22, 345-348
  •  
  • 53. Porteous, L.A., Sidler, R.J., and Watrud, L.S., 1997, An improved method for purifying DNA from soil for polymerase chain reaction amplification and molecular ecology applications, Mol. Ecol, 6, 787-791
  •  
  • 54. Purdy, K.J., Embley, T.M., Takii, S., and Nedwell, D.B., 1996, Rapid extraction of DNA and rDNA from sediments by a novel hydroxyapatite spin-column method, Appl. Environ. Microbiol, 62, 3905-3907
  •  
  • 55. Ramsay, A.J., 1984, Extraction of bacteria from soil: efficiency of shaking or ultrasonication as indicated by direct counts and autoradiography, Soil Biol. Biochem, 16, 457-481
  •  
  • 56. Ranjard, L., Poly, F., Combrisson, J., Richaume, A., and Nazaret, S., 1998, A single procedure to recover DNA from the surface or inside aggregates and in various size fractions of soil suitable for PCR-based assays of bacterial communities, Eur. J. Soil Biol, 34, 89-97
  •  
  • 57. Rochelle, P.A., Fry, J.C., Parkes, R.J., and Weightman, A.J., 1992, DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities, Fems. Microbiol. Lett, 79, 59-65
  •  
  • 58. Rondon, M.R., Raffel, S.J., Goodman, R.M., and Handelsman, R., 1999, Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus, Proc. Natl. Acad. Sci. USA 96, 6451-6455
  •  
  • 59. Rondon, M.R., August, P.R., Bettermann, A.D., Brady, S.F., Grossman, T.H., Liles, M.R., Loiacono, K.A., Lynch, B.A., MacNeil, I.A., Minor, C., Tiong, C.L., Gilman, M., Osburne, M. S., Clardy, J., Handelsman, J., and Goodman, R.M., 2000, Cloning the soil metagenome: a strategy for accessing he genetic and fuctional diversity of uncultured microorganisms, Appl. Eviron. Microbiol, 66, 2541-2547
  •  
  • 60. Roose-Amsaleg, C.L., Garnier-Sillam, E., and Harry, M., 2001, Extraction and purification of microbial DNA from soil and sediment samples, Appl. Soil Ecol, 18, 47-60
  •  
  • 61. Saano, A., Tas, E., Pippola, S., Lindstrom, K., and Van Elsas, J.D., 1995, Extraction and analysis of microbial DNA from soil, in: Nucleic Acids in the Environment: Methods and Applications, Springer-Verlag, Heidelberg, Germany, 49-67
  •  
  • 62. Selenska, S. and Klingmuller, W., 1991, DNA recovery and direct detection of Tn5 sequences from soil, Lett. Appl. Microbiol, 13, 21-24
  •  
  • 63. Simonet, P., Capellano, A., Navarro, E., Bardin, R., and Moiroud, A., 1984, An improved method for lysis of Frankia with achromopeptidase allows detection of new plasmids, Can. J. Microbiol, 30, 1292-1295
  •  
  • 64. Simonet, P., Grosjean, M.C., Misra, A.K., Nazaret, S., Cournoyer, B., and Normand, P., 1991, Frankia genus-specific characterization by polymerase chain reaction, Apple. Environ. Microbiol, 57, 3278-3286
  •  
  • 65. Steffan, R.J., Goksoyr, J., Bej, A.K., and Atlas, R.M., 1988, Recovery of DNA from soils and sediments, Appl. Environ. Microbiol, 54, 2908-2915
  •  
  • 66. Sylvia, D.M, Fuhrmann, J.J, Hartel, P.G, and Zuberer, D.A, 2005, Principles and Applications of Soil Microbiology, 동화기술교역, 경기도, p. 26-38, p. 54-69, p. 85-98
  •  
  • 67. Tebbe, C.C. and Vahjen, W., 1993, Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast, Appl. Environ. Microbiol, 59, 2657-2665
  •  
  • 68. Tien, C.C., Chao, C.C., and Chao, W.L., 1999, Methods for DNA extraction from various soils: a comparison, Appl. Environ. Microbiol, 59, 2657-2665
  •  
  • 69. Tien, C.C., Chao, C.C., and Chao, W.L., 1999, Methods for DNA extraction from various soils: a comparison, J. Appl. Microbiol, 86, 937-943
  •  
  • 70. Torsvik, V.L. and Goksoyr, J., 1978, Determination of bacterial DNA in soil, Soil Biol. Biochem, 10, 7-12
  •  
  • 71. Torsvik, V.L., 1980, Isolation of bacterial DNA form soil, Soil Biol. Biochem. 10, 15-21
  •  
  • 72. Torsvik, V., Goksoyr, J., and Daae, F.L., 1990, High diversity in DNA of soil bacteria, Appl. Environ. Microbiol, 56, 782-787
  •  
  • 73. Torsvik, V.L., Daae, F.L., and Goksoyr, J., 1995, Extraction, purification, and analysis of DNA from soil bacteria, in: Nucleic Acids in the Environment: Metholds and Applicationos, Springer-Verlag, Heidelberg, Germany, 29-48
  •  
  • 74. Tsai, Y.L. and Olson, B.H., 1991, Rapid method for direct extraction of DNA from soil and sediments, Appl. Environ. Microbiol, 57, 1070-1074
  •  
  • 75. Tsai, Y.L., Park, M.J., and Olson, B.H., 1991, Rapid method for direct extraction of mRNA from seeded soils, Appl. Environ. Microbiol, 57, 765-768
  •  
  • 76. Turpin, P.E., Maycroft, K.A., Rowlands, C.L., and Wellington, E.M., 1993, An ion-exchange based extraction method for the detection of salmonellas in soil, J. Appl. Bacteriol, 74, 181-190
  •  
  • 77. Von Wintzingerode, F., Gobel, U.B., and Stackebrandt, E., 1997, Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis, Fems. Microbiol. Rev, 21, 213-229
  •  
  • 78. Von Wintzingerode, F., Gobel, U.B., and Stackebrandt, E., 1997, Determmination of microbial diversiry in environmental samples: pitfalls of PCR-based rRNA analysis, Fems. Microbiol. Rev, 21, 213-229
  •  
  • 79. Wilson, I.G., 1997, Inhibition and facilitation of nucleic acid amplification, Appl. Environ. Microbiol, 63, 3741-3751
  •  
  • 80. Young, C.C., Burghoff, R.L., Keim, J.G., Minak-Berbero, V., Lute, J.R., and Hinton, S.M., 1993, Polyvinylpyrrolidone-agarose gel electrophoresis purification of polymerase chain reaction amplifiable DNA from soils, Appl. Environ. Microbiol, 59, 1972-1974
  •  
  • 81. Zhou, J., Bruns, M.A., and Tiedje, J.M., 1996, DNA recovery from soils of diverse composition, Appl. Environ. Microbiol, 62, 316-322
  •  

This Article

  • 2009; 14(3): 57-67

    Published on Jun 30, 2009

  • Received on May 8, 2009
  • Revised on May 20, 2009
  • Accepted on Jun 24, 2009

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