메뉴 건너뛰기




Volumn 7, Issue 3, 2005, Pages 356-364

Serial analysis of V6 ribosomal sequence tags (SARST-V6): A method for efficient, high-throughput analysis of microbial community composition

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA;

EID: 14344266416     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2004.00712.x     Document Type: Article
Times cited : (42)

References (44)
  • 1
    • 0032952591 scopus 로고    scopus 로고
    • Phylogenetic affinity of a wide, vacuolate, nitrate-accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp.
    • Ahmad, A., Barry, J.P., and Nelson, D.C. (1999) Phylogenetic affinity of a wide, vacuolate, nitrate-accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp. Appl Environ Microbiol 65: 270-277.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 270-277
    • Ahmad, A.1    Barry, J.P.2    Nelson, D.C.3
  • 2
    • 0036672093 scopus 로고    scopus 로고
    • Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis
    • Alfreider, A., Vogt, C., and Babel, W. (2002) Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis. Syst Appl Microbiol 25: 232-240.
    • (2002) Syst Appl Microbiol , vol.25 , pp. 232-240
    • Alfreider, A.1    Vogt, C.2    Babel, W.3
  • 4
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • 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.
    • (1995) Microbiol Rev , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 5
    • 0037317253 scopus 로고    scopus 로고
    • In-field spatial variability in the degradation of the phenyl-urea herbicide isoproturon is the result of interactions between degradative sphingomonas spp. & soil pH
    • Bending, G.D., Lincoln, S.D., Sorensen, S.R., Morgan, J.A., Aamand, J., and Walker, A. (2003) In-field spatial variability in the degradation of the phenyl-urea herbicide isoproturon is the result of interactions between degradative sphingomonas spp. & soil pH. Appl Environ Microbiol 69: 827-834.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 827-834
    • Bending, G.D.1    Lincoln, S.D.2    Sorensen, S.R.3    Morgan, J.A.4    Aamand, J.5    Walker, A.6
  • 6
    • 0031449524 scopus 로고    scopus 로고
    • Mechanism of retarded DNA degradation and prokaryotic origin of DNases in nonsterile soils
    • Blum, S.A.E., Lorenz, M.G., and Wackernagel, W. (1997) Mechanism of retarded DNA degradation and prokaryotic origin of DNases in nonsterile soils. Syst Appl Microbiol 20: 513-521.
    • (1997) Syst Appl Microbiol , vol.20 , pp. 513-521
    • Blum, S.A.E.1    Lorenz, M.G.2    Wackernagel, W.3
  • 8
    • 0037251969 scopus 로고    scopus 로고
    • The Ribosomal Database Project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
    • Cole, J.R., Chai, B., Marsh, T.L., Farris, R.J., Wang, Q., Kulam, S.A., et al. (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442-443.
    • (2003) Nucleic Acids Res , vol.31 , pp. 442-443
    • Cole, J.R.1    Chai, B.2    Marsh, T.L.3    Farris, R.J.4    Wang, Q.5    Kulam, S.A.6
  • 9
    • 0037062470 scopus 로고    scopus 로고
    • Novel kingdom-level eukaryotic diversity in anoxic environments
    • Dawson, S.C., and Pace, N.R. (2002) Novel kingdom-level eukaryotic diversity in anoxic environments. Proc Natl Acad Sci USA 99: 8324-8329.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8324-8329
    • Dawson, S.C.1    Pace, N.R.2
  • 10
    • 0035146134 scopus 로고    scopus 로고
    • Novel bacterial lineages at the (sub) division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms
    • Derakshani, M., Lukow, T., and Liesack, W. (2001) Novel bacterial lineages at the (sub) division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Appl Environ Microbiol 67: 623-631.
    • (2001) Appl Environ Microbiol , vol.67 , pp. 623-631
    • Derakshani, M.1    Lukow, T.2    Liesack, W.3
  • 11
    • 0032189023 scopus 로고    scopus 로고
    • Microbial diversity in a hydrocarbon- and chlorinated-solvent- contaminated aquifer undergoing intrinsic bioremediation
    • Dojka, M.A., Hugenholtz, P., Haack, S.K., and Pace, N.R. (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64: 3869-3877.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 3869-3877
    • Dojka, M.A.1    Hugenholtz, P.2    Haack, S.K.3    Pace, N.R.4
  • 12
    • 0034069650 scopus 로고    scopus 로고
    • Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria
    • Dojka, M.A., Harris, J.K., and Pace, N.R. (2000) Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl Environ Microbiol 66: 1617-1621.
    • (2000) Appl Environ Microbiol , vol.66 , pp. 1617-1621
    • Dojka, M.A.1    Harris, J.K.2    Pace, N.R.3
  • 13
    • 0025869974 scopus 로고
    • Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA
    • Eden, P.A., Schmidt, T.M., Blakemore, P.P., and Pace, N.R. (1991) Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA. Int J Syst Bacteriol 41: 324-325.
    • (1991) Int J Syst Bacteriol , vol.41 , pp. 324-325
    • Eden, P.A.1    Schmidt, T.M.2    Blakemore, P.P.3    Pace, N.R.4
  • 15
    • 0037335946 scopus 로고    scopus 로고
    • Community structure of ammonia-oxidizing bacteria within anoxic marine sediments
    • Freitag, T.E., and Prosser, J.I. (2003) Community structure of ammonia-oxidizing bacteria within anoxic marine sediments. Appl Environ Microbiol 69: 1359-1371.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1359-1371
    • Freitag, T.E.1    Prosser, J.I.2
  • 17
    • 0031912606 scopus 로고    scopus 로고
    • Novel division level bacterial diversity in a Yellowstone hot spring
    • Hugenholtz, P., Pitulle, C., Hershberger, K.L., and Pace, N.R. (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180: 366-376.
    • (1998) J Bacteriol , vol.180 , pp. 366-376
    • Hugenholtz, P.1    Pitulle, C.2    Hershberger, K.L.3    Pace, N.R.4
  • 18
    • 0035989439 scopus 로고    scopus 로고
    • Thermodesulfobacterium hydrogeniphilum sp nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a deepsea hydrothermal vent at Guaymas Basin, and emendation of the genus Thermodesulfobacterium
    • Jeanthon, C., L'Haridon, S., Cueff, V., Banta, A., Reysenbach, A.L., and Prieur, D. (2002) Thermodesulfobacterium hydrogeniphilum sp nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a deepsea hydrothermal vent at Guaymas Basin, and emendation of the genus Thermodesulfobacterium. Int J Syst Evol Microbiol 52: 765-772.
    • (2002) Int J Syst Evol Microbiol , vol.52 , pp. 765-772
    • Jeanthon, C.1    L'Haridon, S.2    Cueff, V.3    Banta, A.4    Reysenbach, A.L.5    Prieur, D.6
  • 19
    • 0033831538 scopus 로고    scopus 로고
    • Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater
    • LaPara, T.M., Nakatsu, C.H., Pantea, L., and Alleman, J.E. (2000) Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. Appl Environ Microbiol 66: 3951-3959.
    • (2000) Appl Environ Microbiol , vol.66 , pp. 3951-3959
    • LaPara, T.M.1    Nakatsu, C.H.2    Pantea, L.3    Alleman, J.E.4
  • 20
    • 0004170691 scopus 로고    scopus 로고
    • Amsterdam, the Netherlands; New York, USA: Elsevier
    • Legendre, P., and Legendre, L. (1998) Numerical Ecology. Amsterdam, the Netherlands; New York, USA: Elsevier.
    • (1998) Numerical Ecology
    • Legendre, P.1    Legendre, L.2
  • 21
    • 0035252640 scopus 로고    scopus 로고
    • Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton
    • Lopez-Garcia, P., Rodriguez-Valera, F., Pedros-Alio, C., and Moreira, D. (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409: 603-607.
    • (2001) Nature , vol.409 , pp. 603-607
    • Lopez-Garcia, P.1    Rodriguez-Valera, F.2    Pedros-Alio, C.3    Moreira, D.4
  • 22
    • 0036795787 scopus 로고    scopus 로고
    • Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
    • Loy, A., Lehner, A., Lee, N., Adamczyk, J., Meier, H., Ernst, J., et al. (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68: 5064-5081.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 5064-5081
    • Loy, A.1    Lehner, A.2    Lee, N.3    Adamczyk, J.4    Meier, H.5    Ernst, J.6
  • 23
  • 24
    • 0035318078 scopus 로고    scopus 로고
    • Phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the Cariaco Basin
    • Madrid, V.M., Taylor, G.T., Scranton, M.I., and Chistoserdov, A.Y. (2001) Phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the Cariaco Basin. Appl Environ Microbiol 67: 1663-1674.
    • (2001) Appl Environ Microbiol , vol.67 , pp. 1663-1674
    • Madrid, V.M.1    Taylor, G.T.2    Scranton, M.I.3    Chistoserdov, A.Y.4
  • 25
    • 0032812081 scopus 로고    scopus 로고
    • Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis
    • Moeseneder, M.M., Arrieta, J.M., Muyzer, G., Winter, C., and Herndl, G.J. (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl Environ Microbiol 65: 3518-3525.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 3518-3525
    • Moeseneder, M.M.1    Arrieta, J.M.2    Muyzer, G.3    Winter, C.4    Herndl, G.J.5
  • 26
    • 0035252376 scopus 로고    scopus 로고
    • Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity
    • Moon-van der Staay, S.Y., De Wachter, R., and Vaulot, D. (2001) Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409: 607-610.
    • (2001) Nature , vol.409 , pp. 607-610
    • Moon-van Der Staay, S.Y.1    De Wachter, R.2    Vaulot, D.3
  • 27
    • 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., and Uitterlinden, A.G. (1993) 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: 695-700.
    • (1993) Appl Environ Microbiol , vol.59 , pp. 695-700
    • Muyzer, G.1    De Waal, E.C.2    Uitterlinden, A.G.3
  • 28
    • 0347297590 scopus 로고    scopus 로고
    • Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces
    • Nagashima, K., Hisada, T., Sato, M., and Mochizuki, J. (2003) Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces. Appl Environ Microbiol 69: 1251-1262.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1251-1262
    • Nagashima, K.1    Hisada, T.2    Sato, M.3    Mochizuki, J.4
  • 29
    • 0001494966 scopus 로고
    • Characterization of large, autotrophic Beggiatoa spp. abundant at hydrothermal vents of the Guaymas Basin
    • Nelson, D.C., Wirsen, C.O., and Jannasch, H.W. (1989) Characterization of large, autotrophic Beggiatoa spp. abundant at hydrothermal vents of the Guaymas Basin. Appl Environ Microbiol 55: 2909-2917.
    • (1989) Appl Environ Microbiol , vol.55 , pp. 2909-2917
    • Nelson, D.C.1    Wirsen, C.O.2    Jannasch, H.W.3
  • 30
    • 1142306022 scopus 로고    scopus 로고
    • Serial analysis of ribosomal sequence tags (SARST): A high-throughput method for profiling complex microbial communities
    • Neufeld, J.D., Yu, Z., Lam, W., and Mohn, W.W. (2004) Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities. Environ Microbiol 6: 131-144.
    • (2004) Environ Microbiol , vol.6 , pp. 131-144
    • Neufeld, J.D.1    Yu, Z.2    Lam, W.3    Mohn, W.W.4
  • 31
    • 0035072290 scopus 로고    scopus 로고
    • Molecular characterization of sulfate-reducing bacteria in anaerobic hydrocarbon-degrading consortia and pure cultures using the dissimilatory sulfite reductase (dsrAB) genes
    • Perez-Jimenez, J.R., Young, L.Y., and Kerkhof, L.J. (2001) Molecular characterization of sulfate-reducing bacteria in anaerobic hydrocarbon-degrading consortia and pure cultures using the dissimilatory sulfite reductase (dsrAB) genes. FEMS Microbiol Ecol 35: 145-150.
    • (2001) FEMS Microbiol Ecol , vol.35 , pp. 145-150
    • Perez-Jimenez, J.R.1    Young, L.Y.2    Kerkhof, L.J.3
  • 33
    • 0032933229 scopus 로고    scopus 로고
    • Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments
    • Scala, D.J., and Kerkhof, L.J. (1999) Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments. Appl Environ Microbiol 65: 1681-1687.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 1681-1687
    • Scala, D.J.1    Kerkhof, L.J.2
  • 34
    • 0030067991 scopus 로고    scopus 로고
    • Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
    • Suzuki, M.T., and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
    • (1996) Appl Environ Microbiol , vol.62 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 35
    • 0025797325 scopus 로고
    • Class-IIS restriction enzymes - A review
    • Szybalski, W., Kim, S.C., Hasan, N., and Podhajska, A.J. (1991) Class-IIS restriction enzymes - a review. Gene 100: 13-26.
    • (1991) Gene , vol.100 , pp. 13-26
    • Szybalski, W.1    Kim, S.C.2    Hasan, N.3    Podhajska, A.J.4
  • 36
    • 0002079242 scopus 로고    scopus 로고
    • Complex microbial communities inhabiting sulfide-rich black mud from marine coastal environments
    • Tanner, M.A., Everett, C.L., Coleman, W.J., Yang, M.M., Youvan, D.C. (2000) Complex microbial communities inhabiting sulfide-rich black mud from marine coastal environments. Biotechnology et alia 8: 1-16.
    • (2000) Biotechnology et Alia , vol.8 , pp. 1-16
    • Tanner, M.A.1    Everett, C.L.2    Coleman, W.J.3    Yang, M.M.4    Youvan, D.C.5
  • 37
    • 0008817147 scopus 로고    scopus 로고
    • Phylogenetic position of a large marine Beggiatoa
    • Vol. 22, p. 39, 1999
    • Teske, A. (1999) Phylogenetic position of a large marine Beggiatoa (Vol. 22, p. 39, 1999). Syst Appl Microbiol 22: 492-492.
    • (1999) Syst Appl Microbiol , vol.22 , pp. 492-492
    • Teske, A.1
  • 38
    • 0030066830 scopus 로고    scopus 로고
    • Phylogeny of Thioploca and related filamentous sulfide-oxidizing bacteria
    • Teske, A., Ramsing, N.B., Kuver, J., and Fossing, H. (1996) Phylogeny of Thioploca and related filamentous sulfide-oxidizing bacteria. Syst Appl Microbiol 18: 517-526.
    • (1996) Syst Appl Microbiol , vol.18 , pp. 517-526
    • Teske, A.1    Ramsing, N.B.2    Kuver, J.3    Fossing, H.4
  • 39
    • 0036205605 scopus 로고    scopus 로고
    • Microbial diversity of hydrothermal sediments in the Guaymas Basin: Evidence for anaerobic methanotrophic communities
    • Teske, A., Hinrichs, K.U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S.P., et al. (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68: 1994-2007.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 1994-2007
    • Teske, A.1    Hinrichs, K.U.2    Edgcomb, V.3    De Vera Gomez, A.4    Kysela, D.5    Sylva, S.P.6
  • 41
    • 0030623948 scopus 로고    scopus 로고
    • SEALS: A system for easy analysis of lots of sequences
    • Walker, D.R., and Koonin, E.V. (1997) SEALS: a system for easy analysis of lots of sequences. Proc Int Conf Intell Syst Mol Biol 5: 333-339.
    • (1997) Proc Int Conf Intell Syst Mol Biol , vol.5 , pp. 333-339
    • Walker, D.R.1    Koonin, E.V.2
  • 42
    • 0026067797 scopus 로고
    • 16S ribosomal DNA amplification for phylogenetic study
    • Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697-703.
    • (1991) J Bacteriol , vol.173 , pp. 697-703
    • Weisburg, W.G.1    Barns, S.M.2    Pelletier, D.A.3    Lane, D.J.4
  • 43
    • 0345195995 scopus 로고    scopus 로고
    • Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis
    • von Wintzingerode, F., Göbel, 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.
    • (1997) FEMS Microbiol Rev , vol.21 , pp. 213-229
    • Von Wintzingerode, F.1    Göbel, U.B.2    Stackebrandt, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.