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Determination of the genetic diversity of microbial communities using DGGE analysis of PCR-amplified 16S rDNA

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Microbial Mats

Part of the book series: NATO ASI Series ((ASIG,volume 35))

Abstract

Microbial ecosystems contain a large diversity of bacterial species. They are dominated by complex interactions between the different microorganisms, whereby each of the individual species has a specific role in the maintenance of the system. The active communities can efficiently scavenge nutrients from the environment and eliminate toxic compounds. However, not all of the species are active; most of them are dormant until environmental conditions change to favour their growth. Because of the great metabolic diversity and flexible organisation microbial ecosystems can be found nearly everywhere. Examples are the bacterial biofilms in waste water treatment reactors, on ship walls, or the microbial mats, found in hypersaline environments, tidal sediments and hot springs.

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References

  • Amann RI, Binder B. Chisholm SW, Olsen R, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56: 1919–1925

    Google Scholar 

  • Corstjens P, Muyzer G (1993) Phylogenetic analysis of the metal-oxidizing bacteria Leptothrix discophora and Sphaerotilus natans using 16S rDNA sequencing data. System Appl Microbiol 16: 219–223

    Article  Google Scholar 

  • Furhman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356: 148–149

    Article  Google Scholar 

  • Giovannoni SJ (1991) The polymerase chain reaction. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley and sons Ltd, Chichester, pp 177–203

    Google Scholar 

  • Giovannoni SJ, DeLong EF, Olsen GJ, Pace NR (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60–63

    Article  Google Scholar 

  • Höfle M (1992) Bacterioplankton community structure and dynamics after large-scale release of nonindignous bacteria as revealed by low-molecular-weight-RNA analysis. Appl Environ Microbiol 58

    Google Scholar 

  • Huber R, Stetter KO (1992) The order Thermotogales. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleiffer K-H (eds) The Prokaryotes 2nd edition, pp 3809–3815

    Google Scholar 

  • Lee S, Fuhrman JA (1990) DNA hybridization to compare species compositions of natural bacterioplankton assemblages. Appl Environ Microbiol 56: 739–746

    Google Scholar 

  • Lee S, Furhman JA (1991) Spatial and temporal variation of natural bacterioplankton assemblages studied by total genomic DNA cross-hybridization. Limnol Oceanogr 36: 1277–1287

    Article  Google Scholar 

  • Lerman LS, Fischer SG, Hurley I, Silverstein K, Lumelsky N (1984) Sequence-determined DNA separations. Annu Rev Biophys Bioeng 13: 399–423

    Article  Google Scholar 

  • Liesack W, Weyland H, Stackebrandt E (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb Ecol 21: 191–198

    Article  Google Scholar 

  • Muyzer G, de Waal EC, Uitterlinden AG (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

    Google Scholar 

  • Neefs J-M, van de Peer Y, Hendriks L, de Wachter R (1990) Compilation of small ribosomal subunit RNA sequences. Nucleic Acid Res 18: 2237–2317

    Article  Google Scholar 

  • Olsen GJ, Larses N, Woese CR (1991) The ribosomal RNA database project. Nucl Acids Res 19: 2017–2021

    Google Scholar 

  • Pedrós-Alió C (1993) Diversity of bacterioplankton. TREE 8: 86–90

    Google Scholar 

  • Schmidt TM, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173: 4371–4378

    Google Scholar 

  • Stackebrandt E, Liesack W, Goebel BM (1993) Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J 7: 232–236

    Google Scholar 

  • Swofford DL (1991) PAUP: Phylogenetic Analysis Using Parsimony version 3.1, Computer program distibuted by the Illinois Natural History Survey Champaign, Illinois

    Google Scholar 

  • Torsvik V, Goksøyr J, Daae FL (1990) High Diversity in DNA of Soil Bacteria. Appl Environ Microbiol 56: 782–787

    Google Scholar 

  • Ward DM (1989) Molecular probes for analysis of microbial communities. In: Characklis WG, Wilderer PA (eds) Structure and function of biofilms. John Wiley & Sons Ltd, pp 145–163

    Google Scholar 

  • Ward DM, Weiler R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultivated microorganisms in a natural environment. Nature 345: 63–65

    Article  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandier O, Krichevsky MI, Moore C Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approches to bacterial systematics. Int J Syst Bacteriol 37: 463–464

    Article  Google Scholar 

  • Weiler R, Weiler JW, Ward DM (1991) 16S rRNA Sequences of uncultivated Hot Spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA. Appl Environ Microbiol 57: 1146–1151

    Google Scholar 

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© 1994 Springer-Verlag Berlin Heidelberg

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Muyzer, G., de Waal, E.C. (1994). Determination of the genetic diversity of microbial communities using DGGE analysis of PCR-amplified 16S rDNA. In: Stal, L.J., Caumette, P. (eds) Microbial Mats. NATO ASI Series, vol 35. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-78991-5_21

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  • DOI: https://doi.org/10.1007/978-3-642-78991-5_21

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-78993-9

  • Online ISBN: 978-3-642-78991-5

  • eBook Packages: Springer Book Archive

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