메뉴 건너뛰기




Volumn 65, Issue 12, 1999, Pages 5409-5420

Quantification of bias related to the extraction of DNA directly from soils

Author keywords

[No Author keywords available]

Indexed keywords

DNA; EXTRACTION METHOD; SAMPLING BIAS; SOIL MICROORGANISM;

EID: 0032710940     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.12.5409-5420.1999     Document Type: Article
Times cited : (412)

References (60)
  • 1
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
    • (1995) Microbiol. Rev. , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.-H.3
  • 2
    • 0021796885 scopus 로고
    • Separation and purification of bacteria from soil
    • Bakken, L. R. 1985. Separation and purification of bacteria from soil. Appl. Environ. Microbiol. 49:1482-1487.
    • (1985) Appl. Environ. Microbiol. , vol.49 , pp. 1482-1487
    • Bakken, L.R.1
  • 3
    • 0030849809 scopus 로고    scopus 로고
    • Direct extraction of microbial community DNA from humified upland soils
    • Clegg, C. D., K. Ritz, and B. S. Griffiths. 1997. Direct extraction of microbial community DNA from humified upland soils. Lett. Appl. Microbiol. 25: 30-33.
    • (1997) Lett. Appl. Microbiol. , vol.25 , pp. 30-33
    • Clegg, C.D.1    Ritz, K.2    Griffiths, B.S.3
  • 5
    • 0031902077 scopus 로고    scopus 로고
    • Monitoring impact of a pesticide treatment on bacterial soil communities by metabolic and genetic fingerprinting in addition to conventional testing procedures
    • Engelen, B., K. Meinken, F. Von Wintzingerode, H. Heuer, H.-P. Malkomes, and H. Backhaus. 1998. Monitoring impact of a pesticide treatment on bacterial soil communities by metabolic and genetic fingerprinting in addition to conventional testing procedures. Appl. Environ. Microbiol. 64:2814-2821.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 2814-2821
    • Engelen, B.1    Meinken, K.2    Von Wintzingerode, F.3    Heuer, H.4    Malkomes, H.-P.5    Backhaus, H.6
  • 6
    • 0029032318 scopus 로고
    • Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species
    • Farrelly, V., F. A. Rainey, and E. Stackebrandt. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:2798-2801.
    • (1995) Appl. Environ. Microbiol. , vol.61 , pp. 2798-2801
    • Farrelly, V.1    Rainey, F.A.2    Stackebrandt, E.3
  • 7
    • 0025889744 scopus 로고
    • Microbial biomass measured as total lipid phosphate in soils of different organic content
    • Frostegård, Å., A. Tunlid, and E. Bååth. 1991. Microbial biomass measured as total lipid phosphate in soils of different organic content. J. Microbiol. Methods 14:151-163.
    • (1991) J. Microbiol. Methods , vol.14 , pp. 151-163
    • Frostegård, Å.1    Tunlid, A.2    Bååth, E.3
  • 8
    • 0031786144 scopus 로고    scopus 로고
    • The release of genetically engineered micro-organisms and viruses into the environment
    • Giddings, G. 1998. The release of genetically engineered micro-organisms and viruses into the environment. New Phylol. 140:173-184.
    • (1998) New Phylol. , vol.140 , pp. 173-184
    • Giddings, G.1
  • 10
    • 0001726492 scopus 로고
    • Distribution of rare actinomycetes in Japanese soils
    • Hayakawa, M., K. Ishizawa, and H. Nonomura. 1988. Distribution of rare actinomycetes in Japanese soils. J. Ferment. Technol. 66:367-374.
    • (1988) J. Ferment. Technol. , vol.66 , pp. 367-374
    • Hayakawa, M.1    Ishizawa, K.2    Nonomura, H.3
  • 11
    • 0001633459 scopus 로고
    • Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes
    • Hayakawa, M., and H. Nonomura. 1987. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J. Ferment. Technol. 65:501-509.
    • (1987) J. Ferment. Technol. , vol.65 , pp. 501-509
    • Hayakawa, M.1    Nonomura, H.2
  • 12
    • 0001059163 scopus 로고
    • A cobalt-containing medium for sporulation of Streptomyces species
    • Hickey, R. J., and H. D. Tresner. 1952. A cobalt-containing medium for sporulation of Streptomyces species. J. Bacteriol. 64:891-892.
    • (1952) J. Bacteriol. , vol.64 , pp. 891-892
    • Hickey, R.J.1    Tresner, H.D.2
  • 13
    • 0019801255 scopus 로고
    • Restriction analysis of the Streptomyces glaucescens genome by agarose gel electrophoresis
    • Hintermann, G., R. Crameri, T. Kieser, and R. Hütter. 1981. Restriction analysis of the Streptomyces glaucescens genome by agarose gel electrophoresis. Arch. Microbiol. 130:218-222.
    • (1981) Arch. Microbiol. , vol.130 , pp. 218-222
    • Hintermann, G.1    Crameri, R.2    Kieser, T.3    Hütter, R.4
  • 14
    • 0023866522 scopus 로고
    • DNA probe method for the detection of specific microorganisms in the soil bacterial community
    • Holben, W. E., J. K. Jansson, B. K. Chelm, and J. M. Tiedje. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54:703-711.
    • (1988) Appl. Environ. Microbiol. , vol.54 , pp. 703-711
    • Holben, W.E.1    Jansson, J.K.2    Chelm, B.K.3    Tiedje, J.M.4
  • 16
    • 0026631342 scopus 로고
    • Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin
    • Jacobsen, C. S., and O. F. Rasmussen. 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.
    • (1992) Appl. Environ. Microbiol. , vol.58 , pp. 2458-2462
    • Jacobsen, C.S.1    Rasmussen, O.F.2
  • 17
    • 0028165829 scopus 로고
    • Analysis of competition in soil among 2,4-dichlorophenoxyacetic acid-degrading bacteria
    • Ka, J. O., W. E. Holben, and J. M. Tiedje. 1994. Analysis of competition in soil among 2,4-dichlorophenoxyacetic acid-degrading bacteria. Appl. Environ. Microbiol. 60:1121-1128.
    • (1994) Appl. Environ. Microbiol. , vol.60 , pp. 1121-1128
    • Ka, J.O.1    Holben, W.E.2    Tiedje, J.M.3
  • 18
    • 0031842281 scopus 로고    scopus 로고
    • Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil
    • Kuske, C. R., K. L. Banton, D. L. Adorada, P. C. Stark, K. K. Hill, and P. J. Jackson. 1998. Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl. Environ. Microbiol. 64: 2463-2472.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 2463-2472
    • Kuske, C.R.1    Banton, K.L.2    Adorada, D.L.3    Stark, P.C.4    Hill, K.K.5    Jackson, P.J.6
  • 19
    • 0030438385 scopus 로고    scopus 로고
    • Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method
    • Lee, S.-Y., J. Bollinger, D. Bezdicek, and A. Ogram. 1996. Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method. Appl. Environ. Microbiol. 62:3787-3793.
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 3787-3793
    • Lee, S.-Y.1    Bollinger, J.2    Bezdicek, D.3    Ogram, A.4
  • 21
    • 0001093837 scopus 로고    scopus 로고
    • Microbial diversity in soil: The need for a combined approach using molecular and cultivation techniques
    • J. D. Van Elsas, J. T. Trevors, and E. M. H. Wellington (ed.), Marcel Dekker, Inc., New York, N.Y.
    • Liesack, W., P. H. Janssen, F. A. Rainey, N. L. Ward-Rainey, and E. Stackebrandt. 1997. Microbial diversity in soil: the need for a combined approach using molecular and cultivation techniques, p. 375-439. In J. D. Van Elsas, J. T. Trevors, and E. M. H. Wellington (ed.), Modern soil microbiology. Marcel Dekker, Inc., New York, N.Y.
    • (1997) Modern Soil Microbiology , pp. 375-439
    • Liesack, W.1    Janssen, P.H.2    Rainey, F.A.3    Ward-Rainey, N.L.4    Stackebrandt, E.5
  • 22
    • 0026764237 scopus 로고
    • Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment
    • Liesack, W., and E. Stackebrandt. 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.
    • (1992) J. Bacteriol. , vol.174 , pp. 5072-5078
    • Liesack, W.1    Stackebrandt, E.2
  • 23
    • 0028136885 scopus 로고
    • Bacterial gene transfer by natural genetic transformation in the environment
    • Lorentz, M. G., and W. Wackernagel. 1994. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58:563-602.
    • (1994) Microbiol. Rev. , vol.58 , pp. 563-602
    • Lorentz, M.G.1    Wackernagel, W.2
  • 24
    • 0028269319 scopus 로고
    • Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment
    • Moré, M. I., J. B. Herrick, M. C. Silva, W. C. Ghiorse, and E. L. Madsen. 1994. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 60:1572-1580.
    • (1994) Appl. Environ. Microbiol. , vol.60 , pp. 1572-1580
    • Moré, M.I.1    Herrick, J.B.2    Silva, M.C.3    Ghiorse, W.C.4    Madsen, E.L.5
  • 25
    • 0003132082 scopus 로고
    • Specific DNA sequences for detection of soil bacteria
    • J. T. Trevors and J. D. van Elsas (ed.), Springer lab manual. Springer-Verlag, Berlin, Germany
    • Nesme, X., C. Picard, and P. Simonet. 1995. Specific DNA sequences for detection of soil bacteria, p. 111-139. In J. T. Trevors and J. D. van Elsas (ed.), Nucleic acids in the environment, methods and application. Springer lab manual. Springer-Verlag, Berlin, Germany.
    • (1995) Nucleic Acids in the Environment, Methods and Application , pp. 111-139
    • Nesme, X.1    Picard, C.2    Simonet, P.3
  • 26
    • 12744281935 scopus 로고
    • The extraction and purification of microbial DNA from sediments
    • Ogram, A., G. S. Sayler, and T. Barkay. 1987. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7:57-66.
    • (1987) J. Microbiol. Methods , vol.7 , pp. 57-66
    • Ogram, A.1    Sayler, G.S.2    Barkay, T.3
  • 28
    • 0001902087 scopus 로고
    • Viability of soil bacteria: Optimization of the plate-counting technique
    • Olsen, R. A., and L. R. Bakken. 1987. Viability of soil bacteria: optimization of the plate-counting technique. Microb. Ecol. 13:59-74.
    • (1987) Microb. Ecol. , vol.13 , pp. 59-74
    • Olsen, R.A.1    Bakken, L.R.2
  • 29
    • 0026793353 scopus 로고
    • Adsorption of DNA on clay minerals: Protection against DNase I and influence on gene transfer
    • Paget, E., L. Jocteur Monrozier, and P. Simonet. 1992. Adsorption of DNA on clay minerals: protection against DNase I and influence on gene transfer. FEMS Microbiol. Lett. 97:31-40.
    • (1992) FEMS Microbiol. Lett. , vol.97 , pp. 31-40
    • Paget, E.1    Jocteur Monrozier, L.2    Simonet, P.3
  • 30
    • 0030273474 scopus 로고    scopus 로고
    • Isolation of a specific chromosomic DNA sequence of Bacillus anthraciss and its possible use in diagnosis
    • Patra, G., P. Sylvestre, V. Ramisse, J. Thérasse, and J.-L. Guesdon. 1996. Isolation of a specific chromosomic DNA sequence of Bacillus anthraciss and its possible use in diagnosis. FEMS Immunol. Med. Microbiol. 15:223-231.
    • (1996) FEMS Immunol. Med. Microbiol. , vol.15 , pp. 223-231
    • Patra, G.1    Sylvestre, P.2    Ramisse, V.3    Thérasse, J.4    Guesdon, J.-L.5
  • 31
    • 0026745065 scopus 로고
    • Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction
    • Picard, C., C. Ponsonnet, X. Nesme, and P. Simonet. 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 58:2717-2722.
    • (1992) Appl. Environ. Microbiol. , vol.58 , pp. 2717-2722
    • Picard, C.1    Ponsonnet, C.2    Nesme, X.3    Simonet, P.4
  • 33
    • 0027976839 scopus 로고
    • Molecular marker systems for detection of genetically engineered micro-organisms in the environment
    • Prosser, J. 1994. Molecular marker systems for detection of genetically engineered micro-organisms in the environment. Microbiology 140:5-17.
    • (1994) Microbiology , vol.140 , pp. 5-17
    • Prosser, J.1
  • 34
    • 0015991322 scopus 로고
    • Modifications of the diphenylamine reaction giving increased sensitivity and simplicity in the estimation of DNA
    • Richard, G. M. 1974. Modifications of the diphenylamine reaction giving increased sensitivity and simplicity in the estimation of DNA. Anal. Biochem. 57:369-376.
    • (1974) Anal. Biochem. , vol.57 , pp. 369-376
    • Richard, G.M.1
  • 35
    • 0027368569 scopus 로고
    • Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils
    • Romanowski, G., M. G. Lorentz, and W. Wackernagel. 1993. Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils. Appl. Environ. Microbiol. 59:3438-3446.
    • (1993) Appl. Environ. Microbiol. , vol.59 , pp. 3438-3446
    • Romanowski, G.1    Lorentz, M.G.2    Wackernagel, W.3
  • 37
    • 0001023407 scopus 로고
    • Methods for characterization of Streptomyces species
    • Shirling, E. B., and D. Gottlieb. 1966. Methods for characterization of Streptomyces species. Int. J. Syst. Bacteriol. 16:313-340.
    • (1966) Int. J. Syst. Bacteriol. , vol.16 , pp. 313-340
    • Shirling, E.B.1    Gottlieb, D.2
  • 38
    • 0031763367 scopus 로고    scopus 로고
    • Phylogenetic mapping of bacterial morphology
    • Siefert, J. L., and G. E. Fox. 1998. Phylogenetic mapping of bacterial morphology. Microbiology 144:2803-2808.
    • (1998) Microbiology , vol.144 , pp. 2803-2808
    • Siefert, J.L.1    Fox, G.E.2
  • 39
    • 0025190443 scopus 로고
    • Identification of Frankia strains in nodules by hybridization of polymerase chain reaction products with strain-specitic oligonucleotide probes
    • Simonet, P., P. Normand, A. Moiroud, and R. Bardin. 1990. Identification of Frankia strains in nodules by hybridization of polymerase chain reaction products with strain-specitic oligonucleotide probes. Arch. Microbiol. 153: 235-240.
    • (1990) Arch. Microbiol. , vol.153 , pp. 235-240
    • Simonet, P.1    Normand, P.2    Moiroud, A.3    Bardin, R.4
  • 41
    • 0030805071 scopus 로고    scopus 로고
    • Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis
    • Smit, E., P. Leeflang, and K. Wernars. 1997. Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol. Ecol. 23:249-261.
    • (1997) FEMS Microbiol. Ecol. , vol.23 , pp. 249-261
    • Smit, E.1    Leeflang, P.2    Wernars, K.3
  • 42
    • 0023989882 scopus 로고
    • Phylogenetic relationships vs. phenotypic diversity: How to achieve a phylogenetic classification system of the eubacteria
    • Stackebrandt, E. 1988. Phylogenetic relationships vs. phenotypic diversity: how to achieve a phylogenetic classification system of the eubacteria. Can. J. Microbiol. 34:552-556.
    • (1988) Can. J. Microbiol. , vol.34 , pp. 552-556
    • Stackebrandt, E.1
  • 43
    • 0016202002 scopus 로고
    • Simplified approach to identification of aerobic Actinomycetes by thin-layer chromatography
    • Stancek, J. L., and G. D. Roberts. 1974. Simplified approach to identification of aerobic Actinomycetes by thin-layer chromatography. Appl. Microbiol. 28:226-231.
    • (1974) Appl. Microbiol. , vol.28 , pp. 226-231
    • Stancek, J.L.1    Roberts, G.D.2
  • 46
    • 0027202733 scopus 로고
    • Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast
    • Tebbe, C. C. and W. Vahjen. 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.
    • (1993) Appl. Environ. Microbiol. , vol.59 , pp. 2657-2665
    • Tebbe, C.C.1    Vahjen, W.2
  • 47
    • 0030497690 scopus 로고    scopus 로고
    • Total bacterial diversity in soil and sediment communities - A review
    • Torsvik, V., R. Søorheim, and J. Goksøyr. 1996. Total bacterial diversity in soil and sediment communities - a review. J. Ind. Microbiol. 17:170-178.
    • (1996) J. Ind. Microbiol. , vol.17 , pp. 170-178
    • Torsvik, V.1    Søorheim, R.2    Goksøyr, J.3
  • 48
    • 0001894963 scopus 로고
    • Isolation of bacterial DNA from soil
    • Torsvik, V. L. 1980. Isolation of bacterial DNA from soil. Soil. Biol. Biochem. 12:15-21.
    • (1980) Soil. Biol. Biochem. , vol.12 , pp. 15-21
    • Torsvik, V.L.1
  • 49
    • 0025903592 scopus 로고
    • Rapid method for direct extraction of DNA from soil and sediments
    • Tsai, Y.-L., and B. Olson. 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57:1070-1074.
    • (1991) Appl. Environ. Microbiol. , vol.57 , pp. 1070-1074
    • Tsai, Y.-L.1    Olson, B.2
  • 50
    • 0030613148 scopus 로고    scopus 로고
    • Soil DNA extraction and assessment of the fate of Mycobacterium chlorophenolicum strain PCP-1 in different soils by 16S ribosomal RNA gene sequence based most-probable-number PCR and immunofluorescence
    • Van Elsas, J. D., V. Mäntynen, and A. C. Wolters. 1997. Soil DNA extraction and assessment of the fate of Mycobacterium chlorophenolicum strain PCP-1 in different soils by 16S ribosomal RNA gene sequence based most-probable-number PCR and immunofluorescence. Biol. Fert. Soils 24:188-195.
    • (1997) Biol. Fert. Soils , vol.24 , pp. 188-195
    • Van Elsas, J.D.1    Mäntynen, V.2    Wolters, A.C.3
  • 51
    • 0031831891 scopus 로고    scopus 로고
    • Microbiological and molecular biological methods for monitoring microbial inoculants and their effects in the soil environment
    • Van Elsas, J. D., G. F. Duarte, A. S. Rosado, and K. Smalla. 1998. Microbiological and molecular biological methods for monitoring microbial inoculants and their effects in the soil environment. J. Microbiol. Methods 32: 133-154.
    • (1998) J. Microbiol. Methods , vol.32 , pp. 133-154
    • Van Elsas, J.D.1    Duarte, G.F.2    Rosado, A.S.3    Smalla, K.4
  • 54
    • 0025366456 scopus 로고
    • 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community
    • Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 344:63-65.
    • (1990) Nature , vol.344 , pp. 63-65
    • Ward, D.M.1    Weller, R.2    Bateson, M.M.3
  • 55
    • 0030466828 scopus 로고    scopus 로고
    • Sensitive detection of transgenic plant marker gene persistence in soil microcosms
    • Widmer, F., R. J. Seidler, and L. S. Watrud. 1996. Sensitive detection of transgenic plant marker gene persistence in soil microcosms. Mol. Ecol. 5: 603-613.
    • (1996) Mol. Ecol. , vol.5 , pp. 603-613
    • Widmer, F.1    Seidler, R.J.2    Watrud, L.S.3
  • 57
    • 0030748867 scopus 로고    scopus 로고
    • Inhibition and facilitation of nucleic acid amplification
    • Wilson, I. G. 1997. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63:3741-3751.
    • (1997) Appl. Environ. Microbiol. , vol.63 , pp. 3741-3751
    • Wilson, I.G.1
  • 58
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
    • (1987) Microbiol. Rev. , vol.51 , pp. 221-271
    • Woese, C.R.1
  • 59
    • 0040762034 scopus 로고
    • Separation of biomolecules
    • Boris Y. Zaslavsky (ed.), Physical Chemistry and Bioanalytical Applications. Marcel Dekker, Inc., New York, N. Y.
    • Zaslavsky, B. Y. 1995. Separation of biomolecules, p. 503-667. In Boris Y. Zaslavsky (ed.), Aqueous two-phase partitioning. Physical Chemistry and Bioanalytical Applications. Marcel Dekker, Inc., New York, N. Y.
    • (1995) Aqueous Two-phase Partitioning , pp. 503-667
    • Zaslavsky, B.Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.