메뉴 건너뛰기




Volumn 55, Issue 1, 2003, Pages 155-164

Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: A cautionary tale

Author keywords

16S rRNA; Anaerobic sediments; Deep biosphere; DGGE; DNA extraction; PCR bias

Indexed keywords

RIBOSOME DNA; RIBOSOME RNA;

EID: 0142091782     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7012(03)00140-4     Document Type: Article
Times cited : (211)

References (38)
  • 1
    • 0036682224 scopus 로고    scopus 로고
    • PRIMROSE: A computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database
    • Ashelford K.E., Weightman A.J., Fry J.C. PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res. 30:2002;3481-3489.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3481-3489
    • Ashelford, K.E.1    Weightman, A.J.2    Fry, J.C.3
  • 2
    • 0031149569 scopus 로고    scopus 로고
    • Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries
    • Chandler D.P., Fredrickson J.K., Brockman F.J. Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6:1997;475-482.
    • (1997) Mol. Ecol. , vol.6 , pp. 475-482
    • Chandler, D.P.1    Fredrickson, J.K.2    Brockman, F.J.3
  • 4
    • 0026755238 scopus 로고
    • Archaea in coastal marine environments
    • DeLong E.F. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. U. S. A. 89:1992;5685-5689.
    • (1992) Proc. Natl. Acad. Sci. U. S. A. , vol.89 , pp. 5685-5689
    • DeLong, E.F.1
  • 5
    • 0034468557 scopus 로고    scopus 로고
    • Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and RNA-based microbial community composition
    • Griffiths R.I., Whiteley A.S., O'Donnell A.G., Bailey M.J. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and RNA-based microbial community composition. Appl. Environ. Microbiol. 66:2000;5488-5491.
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 5488-5491
    • Griffiths, R.I.1    Whiteley, A.S.2    O'Donnell, A.G.3    Bailey, M.J.4
  • 6
    • 0031912606 scopus 로고    scopus 로고
    • Novel division level bacterial diversity in a Yelowstone hot spring
    • Hugenholtz P., Pitulle C., Hershberger K.L., Pace N.R. Novel division level bacterial diversity in a Yelowstone hot spring. J. Bacteriol. 180:1998;366-376.
    • (1998) J. Bacteriol. , vol.180 , pp. 366-376
    • Hugenholtz, P.1    Pitulle, C.2    Hershberger, K.L.3    Pace, N.R.4
  • 7
    • 0343725734 scopus 로고    scopus 로고
    • Extraction and purification of DNA from organic rich subsurface sediments (ODP Leg 169S)
    • Juniper S.K., Cambon M.A., Lesongeur F., Barbier G. Extraction and purification of DNA from organic rich subsurface sediments (ODP Leg 169S). Mar. Geol. 174:2001;241-247.
    • (2001) Mar. Geol. , vol.174 , pp. 241-247
    • Juniper, S.K.1    Cambon, M.A.2    Lesongeur, F.3    Barbier, G.4
  • 9
    • 0032882298 scopus 로고    scopus 로고
    • Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench
    • Li L., Kato C., Horikoshi K. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar. Biotechnol. 1:1999;391-400.
    • (1999) Mar. Biotechnol. , vol.1 , pp. 391-400
    • Li, L.1    Kato, C.2    Horikoshi, K.3
  • 11
    • 0037225001 scopus 로고    scopus 로고
    • Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts
    • Lueders T., Friedrich M.W. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl. Environ. Microbiol. 69:2003;320-326.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 320-326
    • Lueders, T.1    Friedrich, M.W.2
  • 13
    • 0034535113 scopus 로고    scopus 로고
    • Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis
    • Marchesi J.R., Weightman A.J., Cragg B.A., Parkes R.J., Fry J.C. Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol. Ecol. 34:2001;221-228.
    • (2001) FEMS Microbiol. Ecol. , vol.34 , pp. 221-228
    • Marchesi, J.R.1    Weightman, A.J.2    Cragg, B.A.3    Parkes, R.J.4    Fry, J.C.5
  • 14
  • 15
    • 0029020740 scopus 로고
    • PCR bias in amplification of androgen receptor alleles, a trinucleotide repeat marker used in clonality studies
    • Mutter G.L., Boynton K.A. PCR bias in amplification of androgen receptor alleles, a trinucleotide repeat marker used in clonality studies. Nucleic Acids Res. 23:1995;1411-1418.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 1411-1418
    • Mutter, G.L.1    Boynton, K.A.2
  • 16
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
    • Muyzer G., De Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:1993;695-700.
    • (1993) Appl. Environ. Microbiol. , vol.59 , pp. 695-700
    • Muyzer, G.1    De Waal, E.C.2    Uitterlinden, A.G.3
  • 19
    • 0029161663 scopus 로고
    • A combined ecological and physiological approach to studying sulphate reduction within deep marine sediment layers
    • Parkes R.J., Cragg B.A., Bale S.J., Goodman K., Fry J.C. A combined ecological and physiological approach to studying sulphate reduction within deep marine sediment layers. J. Microbiol. Methods. 23:1995;235-249.
    • (1995) J. Microbiol. Methods , vol.23 , pp. 235-249
    • Parkes, R.J.1    Cragg, B.A.2    Bale, S.J.3    Goodman, K.4    Fry, J.C.5
  • 20
    • 0347794946 scopus 로고    scopus 로고
    • Recent studies on bacterial populations and processes in subseafloor sediments: A review
    • Parkes R.J., Cragg B.A., Wellesbury P. Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol. J. 8:2000;11-28.
    • (2000) Hydrogeol. J. , vol.8 , pp. 11-28
    • Parkes, R.J.1    Cragg, B.A.2    Wellesbury, P.3
  • 21
    • 0031711754 scopus 로고    scopus 로고
    • Bias in template-to-product ratios in multitemplate PCR
    • Polz M.F., Cavanaugh C.M. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:1998;3724-3730.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 23
    • 0027121460 scopus 로고
    • DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities
    • Rochelle P.A., Fry J.C., Parkes R.J., Weightman A.J. DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities. FEMS Microbiol. Lett. 100:1992;59-66.
    • (1992) FEMS Microbiol. Lett. , vol.100 , pp. 59-66
    • Rochelle, P.A.1    Fry, J.C.2    Parkes, R.J.3    Weightman, A.J.4
  • 24
    • 0026768316 scopus 로고
    • DNase I treatment of Taq DNA polymerase for complete PCR decontamination
    • Rochelle P.A., Weightman A.J., Fry J.C. DNase I treatment of Taq DNA polymerase for complete PCR decontamination. BioTechniques. 13:1992;520.
    • (1992) BioTechniques , vol.13 , pp. 520
    • Rochelle, P.A.1    Weightman, A.J.2    Fry, J.C.3
  • 25
    • 0028019502 scopus 로고
    • Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence diversity
    • Rochelle P.A., Cragg B.A., Fry J.C., Parkes R.J., Weightman A.J. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence diversity. FEMS Microbiol. Ecol. 15:1994;215-226.
    • (1994) FEMS Microbiol. Ecol. , vol.15 , pp. 215-226
    • Rochelle, P.A.1    Cragg, B.A.2    Fry, J.C.3    Parkes, R.J.4    Weightman, A.J.5
  • 26
    • 0034882012 scopus 로고    scopus 로고
    • Extraction and purification of microbial DNA from soil and sediment samples
    • Roose-Amsaleg C.L., Garnier-Sillam E., Harry M. Extraction and purification of microbial DNA from soil and sediment samples. Appl. Soil Ecol. 18:2001;47-60.
    • (2001) Appl. Soil Ecol. , vol.18 , pp. 47-60
    • Roose-Amsaleg, C.L.1    Garnier-Sillam, E.2    Harry, M.3
  • 27
    • 0142074115 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis in marine microbial ecology
    • J.H. Paul. London: Academic Press
    • Schäfer H., Muyzer G. Denaturing gradient gel electrophoresis in marine microbial ecology. Paul J.H. Marine Microbiology. Methods in Microbiology. vol. 30:2001;425-468 Academic Press, London.
    • (2001) Marine Microbiology. Methods in Microbiology , vol.30 , pp. 425-468
    • Schäfer, H.1    Muyzer, G.2
  • 28
    • 0035431143 scopus 로고    scopus 로고
    • Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling
    • Schmalenberger A., Schwieger F., Tebbe C.C. Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl. Environ. Microbiol. 67:2001;3557-3563.
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 3557-3563
    • Schmalenberger, A.1    Schwieger, F.2    Tebbe, C.C.3
  • 29
    • 0029805297 scopus 로고    scopus 로고
    • Molecular diversity of soil and marine 16S rDNA sequences related to Beta-subgroup ammonia-oxidizing bacteria
    • Stephen J.R., McCaig A.E., Smith Z., Prosser J.I., Embley T.M. Molecular diversity of soil and marine 16S rDNA sequences related to Beta-subgroup ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 62:1996;4147-4154.
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 4147-4154
    • Stephen, J.R.1    McCaig, A.E.2    Smith, Z.3    Prosser, J.I.4    Embley, T.M.5
  • 31
    • 0031904685 scopus 로고    scopus 로고
    • Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants
    • Tanner M.A., Goebel B.M., Dojka M.A., Pace N.R. Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Appl. Environ. Microbiol. 64:1998;3110-3113.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3110-3113
    • Tanner, M.A.1    Goebel, B.M.2    Dojka, M.A.3    Pace, N.R.4
  • 33
    • 0025903592 scopus 로고
    • Rapid method for direct extraction of DNA from soil and sediments
    • Tsai Y.L., Olson B.H. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57:1991;1070-1074.
    • (1991) Appl. Environ. Microbiol. , vol.57 , pp. 1070-1074
    • Tsai, Y.L.1    Olson, B.H.2
  • 34
    • 0345195995 scopus 로고    scopus 로고
    • Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis
    • von Wintzingerode F., Göbel U.B., Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:1997;213-229.
    • (1997) FEMS Microbiol. Rev. , vol.21 , pp. 213-229
    • Von Wintzingerode, F.1    Göbel, U.B.2    Stackebrandt, E.3
  • 35
    • 0036135250 scopus 로고    scopus 로고
    • Grassland management regimens reduce small-scale heterogeneity and species diversity of Beta-Proteobacterial ammonia oxidizer populations
    • Webster G., Embley T.M., Prosser J.I. Grassland management regimens reduce small-scale heterogeneity and species diversity of Beta-Proteobacterial ammonia oxidizer populations. Appl. Environ. Microbiol. 68:2002;20-30.
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 20-30
    • Webster, G.1    Embley, T.M.2    Prosser, J.I.3
  • 36
    • 0036806079 scopus 로고    scopus 로고
    • Geomicrobiology of deep, low organic carbon sediments in the Woodlark Basin, Pacific Ocean
    • Wellesbury P., Mather I., Parkes R.J. Geomicrobiology of deep, low organic carbon sediments in the Woodlark Basin, Pacific Ocean. FEMS Microbiol. Ecol. 42:2002;59-70.
    • (2002) FEMS Microbiol. Ecol. , vol.42 , pp. 59-70
    • Wellesbury, P.1    Mather, I.2    Parkes, R.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.