Skip to main content
SpringerLink
Log in

Amplification of ribosomal RNA sequences

  • Chapter
Molecular Microbial Ecology Manual

Abstract

Emergence of the major outlines of bacterial phylogenetic relationships marks a defining advancement in the recent history of microbiology. This was made possible through the work of Woese and his colleagues who pioneered the comparison of rRNA sequences [30]. The ability to measure bacterial phylogenetic relationships, and those among microscopic eukaryotes, has had a direct impact on systematics that extends well into microbial ecology. While the driving force has been basic phylogenetic research, application of molecular techniques based on rRNA sequence comparisons to determinative and environmental microbiology is a blossoming area [9,26].

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Amann RI, Stromley J, Devereux R, Key R, Stahl DA (1992) Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl Environ Microbiol 58: 614–623.

    PubMed  CAS  Google Scholar 

  2. Burggraf S, Stetter KO, Rouviere P, Woese CR (1991) Methanopyrus kandiert: an archaeal methanogen unrelated to all known methanogens System Appl Microbiol 14: 346–351.

    CAS  Google Scholar 

  3. De Rijk P, Neefs JM, Van de Peer Y, De Wächter R (1992) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 18: 4028.

    Google Scholar 

  4. Dobson SJ, Colwell RR, McMeekin TA, Franzmann PD (1993) Direct sequencing of the polymerase chain reaction-amplified 16S rRNA gene of Flavobacterium gondwanense sp. nov. and Flavobacterium salegens sp. nov.: two new species from a hypersaline antarctic lake. Int J Syst Bacteriol 43: 77–83.

    Article  PubMed  CAS  Google Scholar 

  5. Dorsch M, Stackebrandt E (1992) Some modifications in the procedure for direct sequencing of PCR amplified 16S rDNA. J Microbiol Methods 16: 271–279.

    Article  Google Scholar 

  6. Eden PA, Schmidt TM, Blakemore RP, Pace NR (1991) Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA- specific DNA. Int J Syst Bacteriol 41: 324–325.

    Article  PubMed  CAS  Google Scholar 

  7. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC (1989) Isolation and direct complete nucleotide determination of entire genes: characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17: 7843–7853.

    Article  PubMed  CAS  Google Scholar 

  8. Gargas A, Taylor JW (1992) Polymerase chain reaction (PCR) primers for amplifying and sequencing nuclear 18S rDNA from lichenized fungi. Mycologia 84: 589–592.

    Article  CAS  Google Scholar 

  9. Giovannoni S (1991) The polymerase chain reaction. In: Stackebrandt E, Goodfellow M (eds) Nucleic Acids Techniques in Bacterial Systematics, pp. 177–203. John Wiley & Sons, Chichester.

    Google Scholar 

  10. Hiraishi A (1992) Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett Appl Microbiol 15: 210–213.

    Article  PubMed  CAS  Google Scholar 

  11. Innis MA, Gelfand DH (1990) Optimization of PCRs. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR Protocols: A Guide to Methods and Applications, pp. 3–12. Academic Press, Inc. San Diego.

    Google Scholar 

  12. Kwok S (1990) Procedures to minimize PCR-product carry-over. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR Protocols: A Guide to Methods and Applications, pp. 142–145. Academic Press, Inc. San Diego.

    Google Scholar 

  13. Kwok S, Higuchi R (1989) Avoiding false positives with PCR. Nature 339: 237–238.

    Article  PubMed  CAS  Google Scholar 

  14. Lane DJ, (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic Acids Techniques in Bacterial Systematics, pp. 115–147. John Wiley & Sons, Chichester.

    Google Scholar 

  15. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sei USA 82: 6955–6959.

    Article  CAS  Google Scholar 

  16. Larsen N, Olsen GJ, Maidak BL, McCaughey MJ, Overbeek R, Macke TJ, Marsh TL, Woese, CR (1993) The ribosomal databas project. Nucleic Acids Res. 13:3021–3023.

    Article  Google Scholar 

  17. 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  CAS  Google Scholar 

  18. Medlin L, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71: 491–499.

    Article  PubMed  CAS  Google Scholar 

  19. Myers TW, Gelfand DH (1991) Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase. Biochem 30: 7661–7666.

    Article  CAS  Google Scholar 

  20. Mylvaganam S, Dennis, PP (1992) Sequence heterogeneity between two genes encoding16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130: 399–410.

    PubMed  CAS  Google Scholar 

  21. Olsen GJ, Larsen N, Woese CR. (1991) The ribosomal RNA database project. Nucleic Acids Res 19supp: 2017–2021.

    Google Scholar 

  22. Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986) The use of rRNA sequences to characterize natural microbial populations. Adv Microb Ecol 9: 1–55.

    CAS  Google Scholar 

  23. Saiki, RK (1989) The design and optimization of the PCR. In: Erlich HA (ed) PCR Technology: Principles and Applications for DNA Amplification, pp. 7–16. Stockton Press, New York.

    Google Scholar 

  24. Saiki R, Gelfand, DH, Stoffel S, Schraf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-direct enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487–491.

    Article  PubMed  CAS  Google Scholar 

  25. Saris PEJ, Paulin LG, Uhlen M (1990) Direct amplification of DNA from colonies of Bacillus subtilis and Escherichia coli by the polymerase chain reaction. J Microbiol Methods 11: 121–126.

    Article  CAS  Google Scholar 

  26. Stahl DA, Amann R (1991) Development and application of nucleic acid probes. In: Stackebrandt E, Goodfellow M (eds) Nucleic Acids Techniques in Bacterial Systematics, pp. 205–248. John Wiley & Sons, Chichester.

    Google Scholar 

  27. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697–703.

    PubMed  CAS  Google Scholar 

  28. Wilson KH, Blitchington RB, Greene RC (1990) Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. Clinical Microbiol 28: 1942–1946.

    CAS  Google Scholar 

  29. Wisotzkey JD, Jurtshuk P, Fox GE (1990) PCR amplification of 16S rDNA from lyophilized cell cultures facilitates studies in molecular systematics. Curr Microbiol 21: 325–327.

    Article  PubMed  CAS  Google Scholar 

  30. Woese, CR (1987) Bacterial Evolution. Microbiol. Rev. 51: 221–271.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Microbial Ecology and Biotechnology, United States Environmental Protection Agency, 1 Sabine Island Dr., Gulf Breeze, Fl, 32561, USA

    Richard Devereux

  2. Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, NH, 03824, USA

    Stephanie G. Willis

Authors
  1. Richard Devereux
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stephanie G. Willis
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Microbiology, Wageningen Agricultural University, The Netherlands

    Antoon D. L. Akkermans

  2. IPO-DLO, Wageningen, The Netherlands

    Jan Dirk Van Elsas

  3. MSU-DOE Plant Research Lab, NSF Center for Microbial Ecology and Department of Microbiology, Michigan State University, USA

    Frans J. De Bruijn

Rights and permissions

Reprints and permissions

Copyright information

© 1995 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Devereux, R., Willis, S.G. (1995). Amplification of ribosomal RNA sequences. In: Akkermans, A.D.L., Van Elsas, J.D., De Bruijn, F.J. (eds) Molecular Microbial Ecology Manual. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-0351-0_19

Download citation

  • DOI: https://doi.org/10.1007/978-94-011-0351-0_19

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-4156-0

  • Online ISBN: 978-94-011-0351-0

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation