Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
권호 표지

수계 생태계에서의 세균 군집 구조의 분자생물학적 분석

  • 이동훈 (생명공학연구소 유전자원센터 유전자은행) ;
  • 김상종 (서울대학교 미생물학과 및 분자미생물연구센터)
  • Published : 1997.03.01
Download PDF
⟨ Previous Next ⟩

Abstract

16S rRNA를 분석한 연구들은 자연 생태계에서 추출한 핵산을 이용하여 16rRNA 유전자의 염기서열을 분석하거나 특정 DNA probe를 이용한 hybridization 실험이 주류를 이루어 왔다. 특히 PCR 기법이 개발됨에 따라 적은 양의 시료를 대량으로 손쉽게 증폭시킬 수 있어 다양한 분야에 응용되고 있다. 세균 군집의 구조를 이해하는데 있어서 PCR 방법의 적용 대상은 주로 16S rRNA 유전자의 염기서열 해독분야이며 해양 생태계를 대상으로 많은 연구 결과가 보고되었다(11,13,21,26). 한편 자연 생태계의 개별적 미생물 분류룬들을 검출하기 위한 특정 oligonucleotide probe의 개발방법들은 미생물 군집의 유전적 다양성에 대한 정보 파악 이외에 배양이 어려운 혐기성 세균과 같은 특정 세균들의 동정에도 이용되고 있다(3,24,55). 본고에서는 세균 군집의 구조와 다양성을 연구하는데 적용 가능한 rRNA 분석방법들을 수계 생태계를 중심으로 살펴보고자 한다.

Keywords

References

  1. 이학박사학위논문, 서울대학교 소양호 세균군집구조의 분자생태학적 연구 이동훈
  2. J. Appl. Bacteriol. v.58 An assessment of Bacteroides fragilis group organisms as indications of human faecal pollution Allsop, K.;D. J. Stickler
  3. Appl. Environ. Microbiol. v.58 Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilsm Amann, R.;J. Stromely;R. Devereux;R. Key;D.A. Stahl
  4. ASM News v.60 Identification of uncultured bacteria: a challenging task for molecular taxonomists Amann, R.;W. Ludwig;K.H. Schleifer
  5. Appl. Environ. Microbiol. v.62 Phylogenetic analyses of some extrmely holophilic Archaea isolated from Dead Sea Water, determined on the basis of their 16S rRNA sequences. Arahal, D.R.;F.E. Dewhirst;B.J. Paster;B.E. Volcani;A. Ventosa
  6. Appl. Environ. Microbiol. v.62 Phylogenetic analyses of some extremely halophilic Archaea isolated from Dead Sea water, determined on the basis of their 165 rRNA sequences Araha, D.R.;F.E. Dewhirst;B. J. Paster;B.E. Volcani;A. Ventosa
  7. Microbial ecology (3rd) Atals, R.M.;R. Bartha;Benjamin Cummings (ed.)
  8. Mar. Ecol. Prog. Ser. v.10 The ecological role of water-column microbes in the sea Azam, F.;T. Fenchel;J.G. Field;J.S. Gray;L.A. Meyer-Reil;F. Thingstad
  9. Appl. Environ. Microbiol. v.61 Comparison of phenotypical and molecular methods for the identification of bacterial stranis isolated from a deep subsurface environment Boivin-Jahns, V.;A. Bianchi;R. Ruimy;J. Garcin;S. Daumas;R. Christen
  10. Mar. Ecol. Prog. Ser. v.77 Denitrification in the central Baltic: Evidence for $H_2S$-oxidation as motor of denitrification at the oxic-anoxic interface Brettar, I.;G. Rheinheimer
  11. Mar. Ecol. Prog. Ser. v.94 Nitrous oxide producing heterotrophic bacteria from the water column of the cental Baltic: Abundance and molecular identification Brettar, I.;M. G. Hofle
  12. Appl. Environ. Mi-crobiol. v.57 Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing Britshgi, T.B.;S.J. Giovannoni
  13. Proc. Natl. Acad. Sci. USA v.89 Archaea in coastal marine environments DeLong, E.F.
  14. Limnol. Oceanogr v.38 Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages DeLong, E.F.;D.G. Franks;A.L. Aldredge
  15. Syst. Appl. Microbiol. v.15 Genus- and group-specific hybridization probes for determinative and environmental studies of sulfate-reducing bacteria Devereux,R.;M.D. Kane;J. Winfrey;D.A. Stahl
  16. Microb. Ecol. v.32 S cycling: characterization of natural communities of sulfatefreducing bacteria by 16s rRNA sequence comparisons Devereux, R.;M.E. Hines;D.A. Stahl
  17. Appl. Environ. Microbiol. v.59 Design and application of rRNA-targeted oligonucleotide probes for the dissimilatory iron and maganese-reducing bacterium Shewanella puterfaciens DiChristina, T.J.;E.F. DeLong
  18. Nucleic Acids Res. v.14 Collection of published 5S, 5.8S and 4.5S ribosomal RNA sequences Erdmann, V.A.;J. Wolters
  19. Appl. Environ. Microbiol. v.61 Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial specise Farrelly, V.;F.A. Rainey;E. Stackebrandt
  20. Appl. Environ. Microbiol. v.47 Response of marine bacterioplankton to differential filtration and confinement Ferguson, R.L.;E.N. Buckley;A.V. Palumbo
  21. Nature v.356 Novel major archaebacterial group from marine plankton Fuhrman, J.A.;K. McCallum;A.A. Davis
  22. Appl. Environ. Microbiol. v.59 Phylogenetic diversity of substrate marine microbial communities from the Atlantic and Pacific Oceans Fuhrman, J.A.;K. McCallum;A.A. Davis
  23. J. Exp. Mar. Biol. Ecol. v.55 Fluctuation of the communities of heterotrophic bacteria during the decomposition process of phytoplankton Fukami, K.;U. Smidu;N. Taga
  24. Crit. Rev. Environ. Control v.6 Fecal coliform and fecal streptococcus density relationships in waste descharges and receiving waters Geldreich, E.E.
  25. J. Bacteriol. v.170 Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells Giovannoni, S.J.;E.F. DeLong;G.J. Olsen;N.R. Pace
  26. Appl. Envirion. Microbiol. v.56 Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton Giovannoni, S.J.;E.F. DeLong;T.M. Schmidt;N>R. Pace
  27. Nature v.345 Genetic diversity in Sargasso Sea bacterioplankton Giovannoni, S.J.;T.B. Britschgi;C.L. Moyer;K.G. Field
  28. Biometrika v.40 The population frequencies of species and the estimation of the population parameters Good, I. J.
  29. Appl. Environ. Microbiol. v.61 Biodiversity of gas vacuolate bacteria from Antarctic sea ice and water Gosink, J.J.;J.T. Staley
  30. Appl. Environ. Microbiol. v.53 A selective medium for enumeration and recovery of Pseudomonas cepacia biotypes from soil Hagedorn, C.;W.D. Gould;T. R. Bardinelli;D.R. Gustavson
  31. PCR Method Applic. v.1 A simple and sensitive method for detection of mutations in the genomic DNA Hayashi, K.
  32. Nature v.376 Isolation of a hyperthermophilic archaeum predicted by in situ RNA analysis Huber, R.;S. Burggraf;T. Mayer;S.M. Barns;P. Rossnagel;K.O. Stetter
  33. J. Microbiol. Methods v.8 Identification of bacteria by low molecular weight RNA profiles: a new chemotaxonomic approach Hofle, M.G.
  34. Arch. Hydrobiol. Beih. v.31 Taxonomic structure of bacterial communities in mixed cultures as measured by low molecular weight RNA profiles Hofle, M.G.
  35. Appl Environ. Microbiol. v.58 Bacterioplankton community structure and dynamics after large-scale release of nonindigenous bacteria as revealed by low-molecular-weight-RNA analysis Hofle, M.G.
  36. Limnol. Oceanogr v.40 Taxonomic diversity and metabolic activity of microbial communities in the water column of the central Baltic Sea Hofle, M.G.;I. Brettar
  37. Appl. Environ. Microbiol. v.62 Genotyping of heterotrophic bacteria from the central Baltic Sea by use of low-molecular-weight RNA profiles Hofle, M.G.;I. Brettar
  38. Appl. Environ. Microbiol. v.61 Design and evaluation of Bacteroides DNA probes for the specific detection of human fecal pollution Kreader, C. A.
  39. Appl. Environ. Microbiol. v.62 Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphisim Lee, D.-H.;Y.-G. Zo;S.-J. Kim
  40. Mol. Cells v.5 A non-radioactive method for simultaneous detection of single-strand comformation polymorphisms (SSCPs) and heteroduplexes Lee, S.-T.;S.-K. Park;K.-H. Lee-S.A. Holmes;R. A. Spritz
  41. Appl. Environ. Microbiol. v.61 Identification of acquatic Burkholderia(Pseudomonsa) cepacia by hybridization with species-specific rRNA gene probes Leff, L.G.;R.M. Kernan;J.V. McArthur;L.J. Shimkets
  42. Annu. Rev. Biophys. Bioeng. v.13 Sequence-determined DNA separations Lerman, L.S.;S.G. Fischer;I. Hurley;K. Silverstein;N. Lumelsky
  43. Microb. Ecol. v.21 Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria Liesack, W.;H. Weyland;E. Stackebrandt
  44. Microbiol. Rev. v.55 Dissimilatory Fe(Ⅲ) and Mn(Ⅳ) reduction Lovley, D.R.
  45. Arch. Microbiol. v.159 Geobacter metallireducans gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals Lovley, D.R.;S.J. Giovannoni;D.C. White;J.E. Champine;E.J.P. Phillips;Y.A. Gorby;S. Goodwin
  46. Nucleic Acids Res. v.22 The Ribosomal Database project Maidak, B.I.;N. Larsen;M.J. McCaughey;R. Overbeek;G.J. Olsen;K. Fogel;J. Blandy;C.R. Woese
  47. Syst. Appl. Microbiol. v.15 Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions Manz, W.;R. Amann;W. Ludwig;M. Wagner;K. H. Schleifer
  48. FEMS Microbiol. Ecol. v.17 Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments Martinez-Murcia, A.J.;S.G. Acinas;F. Rodriguez-Valera
  49. Appl. Environ. Microbiol. v.60 Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system Moyer, C.L.;F.C. Dobbs;D.M. Karl
  50. Limnol. Oceanogr v.40 Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities Mullins, T.D.;T.B. Britschgi;R.L. Krest;S.J. Giovannoni
  51. Appl. Environ. Microbiol. v.59 Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA Muyzer,G.;E.C. De Waal;A.G. Uitterlinden
  52. Methods Enzymol v.155 Dctection and localization of single base changes by denaturing gradient gel electrophoresis Myer, R. M.;T. Maniatis;L.S. Lerman
  53. Appl. Environ. Microbiol. v.57 Formation of nonculturable Vibrio vulnificus cells and its relationship to the starvation state Oliver, J.D.;L. Nilsson;S. Kjelleberg
  54. Annu. Rev. Microbiol. v.40 Microbial ecology and evolution: a ribosomal RNA approach Olsen, G.J.;D.J. Lane;S.J. Giovanoni;N.R. Pace;D.A. Stahl
  55. Appl. Environ. Microbiol. v.61 A novel approach for monitoring genetically engineered microorganisms by using artificail, stable RNAs. Pitulle C.;K.O.F. Hedenstierna;G.E. Fox
  56. Appl. Environ. Microbiol. v.60 Quantification of methanogenic groups in anaerbic biological reactors by oligonucleotide probe hybridation Raskin, L.;L.K. Poulsen;D.R. Noguera;B.E. Rittmann;D. A. Stahl
  57. Appl. Environ. Microbiol. v.60 Phylogenetic analysis of the hyperthermophiclic pink filament community in Octopus Spring, Yellowstone National Park Reysenbach, A.L.;G.S. Wickham;N.R. Pace
  58. Can. J. Microbiol. v.30 Viable but not recoverable stage of Salmonella enteritidis in aquatic systems Roszak, D.B.;D. J. Grimes;R.R. Colwell
  59. PCR Methods Applic v.2 Modeling of heteroduplex formation during PCR from mixtures of DNA templates Ruano, G.;K.K. Kidd
  60. cremoris. Appl. Environ. Microbiol. v.57 Development and application of oligonucleotide probes fro identification of Lactococcus lactis subsp Salama, M.;W. Sandine;S. Giovannoni
  61. J. Bacteriol. v.173 Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing Schmidt, T.M.;E.F. DeLong;N.R. Pace
  62. Proc. Natl. Acad. Sci. v.86 Attachment of a 40-base pair G+C-rich sequence(GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes Sheffield, V.C.;D.R. Cox;L.S. Lerman;R. M. Myers
  63. Genomics v.16 The sensitivity of single-strand comformation polymorphism analysis for the detection of single base substitutions Sheffield, V.C.;J.S. Beck;A.E. Kwitek;D.W. Sandstrom;E.M. Stone
  64. Nucleic Acids Res. v.18 Compilation of 5S rRNA and 5S rRNA gene sequences Specht, T.;J. Wolters;V.A. Erdmann
  65. Syst. Appl. Microbiol. v.15 Phylogenetic diversity and identification of nonculturable magnetotactic bacteria Spring, S.;R. Amann;W. Ludwig;K.H. Schleifer;N. Petersen
  66. Nucleic Acids Res. v.13 Compilation of tRNA sequences Sprinzel, M.;J. Moll;F. Meissner;T. Hartmann
  67. Science v.224 Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences Stahl, D.A.;D.J. Lane;G.J. Olsen;N.R. Pace
  68. Appl. Environ. Microbiol. v.49 Characterization fo a Yellowstone hot spring microbial community by 5S rRNA sequences Stahl, D.A.;D.J. Lane;G.J. Olsen;N.R. Pace
  69. Annu. Rev. Microbiol. v.39 Measurement of insitu activities of nonphotosynthetic microorganism in aquatic and terrestial habitats Staley, J.T.;A. Konopka
  70. Appl. Environ. Microbiol. v.62 Bias cause by template annealing in the amplificaion of mixtures of 16S rRNA genes by PCR Suzuki, M.T.;S.J. Giovannoni
  71. Appl. Environ. Microbiol. v.62 Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR amplified ribosomal DNA fragments Teske, A.;C. Wawer;G. Muyzer;N.B. Ramsing
  72. FEMS Microbiol. Ecol. v.102 Subgrouping of bacterial populations by celluar fatty acid composition Tompson, I.P.;M.J. Bailey;R.J. Ellis;K.J. Purdy
  73. Appl. Environ. Microbiol. v.59 Probing activated sludge with proteobacteria-specific oligonucleotides: inadequacy of culture-dependent methods of describing microbial community structure Wagner, M.;R. Amann;H. Lemmer;K.H. Schleifer
  74. Adv. Microb. Ecol. v.12 Ribosomal RNA analysis of microorganisms as they occur in nature Ward, D.M.;M.M. Beteson;R. Weller;A.L. Ruff Roberts
  75. Can. Bull. Fish. Aquat. Sci. v.214 Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus Waterbury, J.B.;F.W. Valois;D.G. Franks
  76. Int. J. Syst. Bacteriol. v.37 Report of the ad hoc committee on reconciliation of approaches to bacterial systematics Wayne, L.G.;D.J. Brenner;R.R. Colwell;P.A.D. Grimont;O. Kandler;M.I. Krichevsky;L.H. Moore;R.G.E. Murray;E. Stackebrandt;M.P. Starr;H.G. Truper
  77. Int. Revue ges. Hydrogiol. v.76 The microbial food web and its sensitivity to eutrophication and contaminant enrichment : a cross-system overview Weisse, T.
  78. Syst. Apopl. Microbiol. v.13 The flexibacter-flavobacter connection Woese, C.R.;D. Yang;L. Mandelco;K.O. Stetter
  79. Microbiol. Rev. v.51 Bacterial evolution Woese, C.R.
  80. J. Phycol. v.26 DNA polymorphism within the WH7803 serogroup of marine Synechococcus spp.(Cyanobacteria) Wood, M.A.;D. Townsend
  81. PCR technology: current innovations Non-isotopic singlestrand conformation polymorphism (SSCP) analysis of PCR products Yap, E.P.H.;J.O. McGee;H.G. Griffin;A.M. Griffin (ed.)