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Volumn 53, Issue 3, 2005, Pages 339-348

Improvements for comparative analysis of changes in diversity of microbial communities using internal standards in PCR-DGGE

Author keywords

Complex microbial communities; DNA extraction; Internal standards; PCR DGGE; Relative comparison

Indexed keywords

FLUORESCENT DYE; PRIMER DNA;

EID: 22044449755     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.femsec.2005.01.001     Document Type: Article
Times cited : (33)

References (31)
  • 1
    • 0030613231 scopus 로고    scopus 로고
    • Population structure and physiological changes within a hot spring microbial mat community following disturbance
    • M.J. Ferris, S.C. Nold, N.P. Revsbech, and D.M. Ward Population structure and physiological changes within a hot spring microbial mat community following disturbance Appl. Environ. Microbiol. 63 4 1997 1367 1374
    • (1997) Appl. Environ. Microbiol. , vol.63 , Issue.4 , pp. 1367-1374
    • Ferris, M.J.1    Nold, S.C.2    Revsbech, N.P.3    Ward, D.M.4
  • 2
    • 0031959006 scopus 로고    scopus 로고
    • Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology
    • G. Muyzer, and K. Smalla Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology Antonie Van Leeuwenhoek Int. J. General Molecular Microbiol 73 1 1998 127 141
    • (1998) Antonie Van Leeuwenhoek Int. J. General Molecular Microbiol , vol.73 , Issue.1 , pp. 127-141
    • Muyzer, G.1    Smalla, K.2
  • 3
    • 0033050123 scopus 로고    scopus 로고
    • Detritus-dependent development of the microbial community in an experimental system: Qualitative analysis by denaturing gradient gel electrophoresis
    • E.J. van Hannen, W. Mooij, M.P. van Agterveld, H.J. Gons, and H.J. Laanbroek Detritus-dependent development of the microbial community in an experimental system: Qualitative analysis by denaturing gradient gel electrophoresis Appl. Environ. Microbiol. 65 6 1999 2478 2484
    • (1999) Appl. Environ. Microbiol. , vol.65 , Issue.6 , pp. 2478-2484
    • Van Hannen, E.J.1    Mooij, W.2    Van Agterveld, M.P.3    Gons, H.J.4    Laanbroek, H.J.5
  • 5
    • 0033950632 scopus 로고    scopus 로고
    • Successional changes in the genetic diversity of a marine bacterial assemblage during confinement
    • H. Schafer, P. Servais, and G. Muyzer Successional changes in the genetic diversity of a marine bacterial assemblage during confinement Arch. Microbiol. 173 2 2000 138 145
    • (2000) Arch. Microbiol. , vol.173 , Issue.2 , pp. 138-145
    • Schafer, H.1    Servais, P.2    Muyzer, G.3
  • 6
    • 0029551398 scopus 로고
    • Molecular methods to study the organization of microbial communities
    • G. Muyzer, and N.B. Ramsing Molecular methods to study the organization of microbial communities Water Sci. Technol. 32 8 1995 1 9
    • (1995) Water Sci. Technol. , vol.32 , Issue.8 , pp. 1-9
    • Muyzer, G.1    Ramsing, N.B.2
  • 7
    • 0030698675 scopus 로고    scopus 로고
    • Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs
    • T. Vallaeys, E. Topp, G. Muyzer, V. Macheret, G. Laguerre, and A. Rigaud Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs FEMS Microbiol. Ecol. 24 3 1997 279 285
    • (1997) FEMS Microbiol. Ecol. , vol.24 , Issue.3 , pp. 279-285
    • Vallaeys, T.1    Topp, E.2    Muyzer, G.3    MacHeret, V.4    Laguerre, G.5    Rigaud, A.6
  • 8
    • 0034857157 scopus 로고    scopus 로고
    • A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis
    • H. Sekiguchi, N. Tomioka, T. Nakahara, and H. Uchiyama A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis Biotechnol. Lett. 23 15 2001 1205 1208
    • (2001) Biotechnol. Lett. , vol.23 , Issue.15 , pp. 1205-1208
    • Sekiguchi, H.1    Tomioka, N.2    Nakahara, T.3    Uchiyama, H.4
  • 9
    • 2542509415 scopus 로고    scopus 로고
    • Quantifying microbial diversity: Morphotypes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats
    • U. Nubel, F. Garcia-Pichel, M. Kuhl, and G. Muyzer Quantifying microbial diversity: Morphotypes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats Appl. Environ. Microbiol. 65 2 1999 422 430
    • (1999) Appl. Environ. Microbiol. , vol.65 , Issue.2 , pp. 422-430
    • Nubel, U.1    Garcia-Pichel, F.2    Kuhl, M.3    Muyzer, G.4
  • 10
    • 0343416244 scopus 로고    scopus 로고
    • Competitive PCR-DGGE analysis of bacterial mixtures an internal standard and an appraisal of template enumeration accuracy
    • J. Bruggemann, J.R. Stephen, Y.J. Chang, S.J. Macnaughton, G.A. Kowalchuk, and E. Kline Competitive PCR-DGGE analysis of bacterial mixtures an internal standard and an appraisal of template enumeration accuracy J. Microbiol. Meth. 40 2 2000 111 123
    • (2000) J. Microbiol. Meth. , vol.40 , Issue.2 , pp. 111-123
    • Bruggemann, J.1    Stephen, J.R.2    Chang, Y.J.3    MacNaughton, S.J.4    Kowalchuk, G.A.5    Kline, E.6
  • 11
    • 0345195995 scopus 로고    scopus 로고
    • Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis
    • F. von Wintzingerode, U.B. Gobel, and E. Stackebrandt Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis FEMS Microbiol. Rev. 21 3 1997 213 229
    • (1997) FEMS Microbiol. Rev. , vol.21 , Issue.3 , pp. 213-229
    • Von Wintzingerode, F.1    Gobel, U.B.2    Stackebrandt, E.3
  • 12
    • 0028976428 scopus 로고
    • Survival and activity of pseudomonas sp strain b13(fr1) in a marine microcosm determined by quantitative PCR and an ribosomal-RNA-targeting probe and its effect on the indigenous bacterioplankton
    • T.D. Leser, M. Boye, and N.B. Hendriksen Survival and activity of pseudomonas sp strain b13(fr1) in a marine microcosm determined by quantitative PCR and an ribosomal-RNA-targeting probe and its effect on the indigenous bacterioplankton Appl. Environ. Microbiol. 61 4 1995 1201 1207
    • (1995) Appl. Environ. Microbiol. , vol.61 , Issue.4 , pp. 1201-1207
    • Leser, T.D.1    Boye, M.2    Hendriksen, N.B.3
  • 13
    • 0030067991 scopus 로고    scopus 로고
    • Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
    • M.T. Suzuki, and S.J. Giovannoni Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR Appl. Environ. Microbiol. 62 2 1996 625 630
    • (1996) Appl. Environ. Microbiol. , vol.62 , Issue.2 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 14
    • 0035018373 scopus 로고    scopus 로고
    • Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia
    • R.M. Niemi, I. Heiskanen, K. Wallenius, and K. Lindstrom Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia J. Microbiol. Meth. 45 3 2001 155 165
    • (2001) J. Microbiol. Meth. , vol.45 , Issue.3 , pp. 155-165
    • Niemi, R.M.1    Heiskanen, I.2    Wallenius, K.3    Lindstrom, K.4
  • 15
    • 0033860832 scopus 로고    scopus 로고
    • RpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity
    • I. Dahllof, H. Baillie, and S. Kjelleberg rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity Appl. Environ. Microbiol. 66 8 2000 3376 3380
    • (2000) Appl. Environ. Microbiol. , vol.66 , Issue.8 , pp. 3376-3380
    • Dahllof, I.1    Baillie, H.2    Kjelleberg, S.3
  • 16
    • 1842511510 scopus 로고    scopus 로고
    • Effects of zinc pyrithione and copper pyrithione on microbial community function and structure in sediments
    • D.G. Petersen, I. Dahllof, and L.P. Nielsen Effects of zinc pyrithione and copper pyrithione on microbial community function and structure in sediments Environ. Toxicol. Chem. 23 4 2004 921 928
    • (2004) Environ. Toxicol. Chem. , vol.23 , Issue.4 , pp. 921-928
    • Petersen, D.G.1    Dahllof, I.2    Nielsen, L.P.3
  • 17
    • 0035370087 scopus 로고    scopus 로고
    • The identification of microorganisms by fluorescence in situ hybridisation
    • R. Amann, B.M. Fuchs, and S. Behrens The identification of microorganisms by fluorescence in situ hybridisation Curr. Opin. Biotechnol. 12 3 2001 231 236
    • (2001) Curr. Opin. Biotechnol. , vol.12 , Issue.3 , pp. 231-236
    • Amann, R.1    Fuchs, B.M.2    Behrens, S.3
  • 18
    • 0036624813 scopus 로고    scopus 로고
    • Molecular community analysis of microbial diversity
    • I. Dahllof Molecular community analysis of microbial diversity Curr. Opin. Biotechnol. 13 3 2002 213 217
    • (2002) Curr. Opin. Biotechnol. , vol.13 , Issue.3 , pp. 213-217
    • Dahllof, I.1
  • 19
    • 1842509857 scopus 로고    scopus 로고
    • Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR
    • K.L. Mumy, and R.H. Findlay Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR J. Microbiol. Meth. 57 2004 259 268
    • (2004) J. Microbiol. Meth. , vol.57 , pp. 259-268
    • Mumy, K.L.1    Findlay, R.H.2
  • 20
    • 0028946084 scopus 로고
    • Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation
    • R.I. Amann, W. Ludwig, and K.H. Schleifer Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation Microbiol. Rev. 59 1 1995 143 169
    • (1995) Microbiol. Rev. , vol.59 , Issue.1 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 21
    • 0031982528 scopus 로고    scopus 로고
    • Microbial evolution, diversity, and ecology: A decade of ribosomal RNA analysis of uncultivated microorganisms
    • I.M. Head, J.R. Saunders, and R.W. Pickup Microbial evolution, diversity, and ecology: A decade of ribosomal RNA analysis of uncultivated microorganisms Microb. Ecol. 35 1 1998 1 21
    • (1998) Microb. Ecol. , vol.35 , Issue.1 , pp. 1-21
    • Head, I.M.1    Saunders, J.R.2    Pickup, R.W.3
  • 22
    • 0032703237 scopus 로고    scopus 로고
    • Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples
    • D.N. Miller, J.E. Bryant, E.L. Madsen, and W.C. Ghiorse Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples Appl. Environ. Microbiol. 65 11 1999 4715 4724
    • (1999) Appl. Environ. Microbiol. , vol.65 , Issue.11 , pp. 4715-4724
    • Miller, D.N.1    Bryant, J.E.2    Madsen, E.L.3    Ghiorse, W.C.4
  • 23
    • 0028269319 scopus 로고
    • Quantitative cell-lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment
    • M.I. More, J.B. Herrick, M.C. Silva, W.C. Ghiorse, and E.L. Madsen Quantitative cell-lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment Appl. Environ. Microbiol. 60 5 1994 1572 1580
    • (1994) Appl. Environ. Microbiol. , vol.60 , Issue.5 , pp. 1572-1580
    • More, M.I.1    Herrick, J.B.2    Silva, M.C.3    Ghiorse, W.C.4    Madsen, E.L.5
  • 24
    • 0033928875 scopus 로고    scopus 로고
    • Application of polymerase chain reaction-denaturing gradient gel electrophoresis for comparison of direct and indirect extraction methods of soil DNA used for microbial community fingerprinting
    • J. Kozdroj, and J.D. van Elsas Application of polymerase chain reaction-denaturing gradient gel electrophoresis for comparison of direct and indirect extraction methods of soil DNA used for microbial community fingerprinting Biol. Fertil. Soils 31 5 2000 372 378
    • (2000) Biol. Fertil. Soils , vol.31 , Issue.5 , pp. 372-378
    • Kozdroj, J.1    Van Elsas, J.D.2
  • 25
    • 0031842162 scopus 로고    scopus 로고
    • Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region
    • M.C. Hansen, T. Tolker-Nielsen, M. Givskov, and S. Molin Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region FEMS Microbiol. Ecol. 26 2 1998 141 149
    • (1998) FEMS Microbiol. Ecol. , vol.26 , Issue.2 , pp. 141-149
    • Hansen, M.C.1    Tolker-Nielsen, T.2    Givskov, M.3    Molin, S.4
  • 26
    • 0031711754 scopus 로고    scopus 로고
    • Bias in template-to-product ratios in multitemplate PCR
    • M.F. Polz, and C.M. Cavanaugh Bias in template-to-product ratios in multitemplate PCR Appl. Environ. Microbiol. 64 10 1998 3724 3730
    • (1998) Appl. Environ. Microbiol. , vol.64 , Issue.10 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 27
    • 0029660135 scopus 로고    scopus 로고
    • Phylogenetic analysis of the bacterial communities in marine sediments
    • J.P. Gray, and R.P. Herwig Phylogenetic analysis of the bacterial communities in marine sediments Appl. Environ. Microbiol. 62 11 1996 4049 4059
    • (1996) Appl. Environ. Microbiol. , vol.62 , Issue.11 , pp. 4049-4059
    • Gray, J.P.1    Herwig, R.P.2
  • 28
    • 0029900986 scopus 로고    scopus 로고
    • Human colonic biota studied by ribosomal DNA sequence analysis
    • K.H. Wilson, and R.B. Blitchington Human colonic biota studied by ribosomal DNA sequence analysis Appl. Environ. Microbiol. 62 7 1996 2273 2278
    • (1996) Appl. Environ. Microbiol. , vol.62 , Issue.7 , pp. 2273-2278
    • Wilson, K.H.1    Blitchington, R.B.2
  • 29
    • 0031732597 scopus 로고    scopus 로고
    • Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription PCR in temperature gradient gel electrophoresis fingerprints
    • A. Felske, A.D.L. Akkermans, and W.M. De Vos Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription PCR in temperature gradient gel electrophoresis fingerprints Appl. Environ. Microbiol. 64 11 1998 4581 4587
    • (1998) Appl. Environ. Microbiol. , vol.64 , Issue.11 , pp. 4581-4587
    • Felske, A.1    Akkermans, A.D.L.2    De Vos, W.M.3
  • 30
    • 0026794170 scopus 로고
    • Differential amplification of ribosomal-rRNA genes by polymerase chain-reaction
    • A.L. Reysenbach, L.J. Giver, G.S. Wickham, and N.R. Pace Differential amplification of ribosomal-rRNA genes by polymerase chain-reaction Appl. Environ. Microbiol. 58 10 1992 3417 3418
    • (1992) Appl. Environ. Microbiol. , vol.58 , Issue.10 , pp. 3417-3418
    • Reysenbach, A.L.1    Giver, L.J.2    Wickham, G.S.3    Pace, N.R.4
  • 31
    • 0036008787 scopus 로고    scopus 로고
    • Enumeration of total bacteria and bacteria with genes for proteolytic activity in pure cultures and in environmental samples by quantitative PCR mediated amplification
    • H.J. Bach, J Tomanova, M. Schloter, and J.C. Munch Enumeration of total bacteria and bacteria with genes for proteolytic activity in pure cultures and in environmental samples by quantitative PCR mediated amplification J. Microbiol. Meth. 49 3 2002 235 245
    • (2002) J. Microbiol. Meth. , vol.49 , Issue.3 , pp. 235-245
    • Bach, H.J.1    Tomanova, J.2    Schloter, M.3    Munch, J.C.4


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