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Molecular Identification of Microbial Populations in Petroleum-Contaminated Groundwater

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Part of the book series: Methods in Biotechnology ((MIBT,volume 16))

Abstract

In microbiology, morphological observation does not generally provide valuable information for species identification. Identification of microorganisms has therefore relied on physiological characterization, although this method is available only after they are isolated and cultivated in the laboratory. Because over 99% of microorganisms in the natural environment cannot be cultivated by standard techniques, alternative methods are necessary for the detection and identification of a large fraction of natural microbial populations. This is of particular relevance to microorganisms in the anaerobic ecosystem, as each of them requires a specific culture condition according to its specialized ecological niche. In addition, cultivation of anaerobes is generally laborious and time consuming. Culture-independent molecular phylogenetic approaches developed in the last two decades have enabled the detection and identification of such natural microbial populations.

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References

  1. Muyzer, G., Hottentrager, S., Teske, A., and Wawer, C. (1996) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA. A new molecular approach to analyze the genetic diversity of mixed microbial communities, in Molecular Microbial Ecology Manual (Akkermans, A. D. L., van Elsas, J. D., de Bruijn, F. J., eds.), Kluwer Academic Publishing, Dordrecht, pp. 3.4.4.1–3.4.4.22.

    Google Scholar 

  2. Marsh, T. L. (1999) Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Cur. Opin. Microbiol. 2, 323–327.

    Article  CAS  Google Scholar 

  3. 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.

    Article  Google Scholar 

  4. Watanabe, K., Kodama, Y., Syutsubo, K., and Harayama, S. (2000) Molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude-oil-storage cavities. Appl. Environ. Microbiol. 66, 4803–4809.

    Article  PubMed  CAS  Google Scholar 

  5. Akkermans, A. D. L., van Elsas, J. D., and de Bruijn, F. J. (1999) Molecular Microbial Ecology Manual. Kluwer Academic Publishing, Dordrecht.

    Google Scholar 

  6. Snaidr, J., Amann, R., Huber, I., Ludwig, W., and Schleifer, K. H. (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl. Environ. Microbiol. 63, 2884–2896.

    PubMed  CAS  Google Scholar 

  7. 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.

    PubMed  CAS  Google Scholar 

  8. Großkopf, R., Janssen, P. H., and Liesack, W. (1998) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 64, 960–969.

    PubMed  Google Scholar 

  9. Achenbach, L. and Woese, C. (1995) 16S and 23S rRNA-like primers, in Archaea—A Laboratory Manual (Robb, F. T., Sowers, K. R., DasSarma, S., Place, A. R., Schreier, H. J., Fleischmann, E. M. eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 521–523.

    Google Scholar 

  10. Watanabe, K., Kodama, Y., and Harayama, S. (2001) Design and evaluation of RCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. J. Microbiol. Methods 44, 253–262.

    Article  PubMed  CAS  Google Scholar 

  11. Takai, K. and Sako, Y. (1999) A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol. Ecol. 28, 177–188.

    Article  CAS  Google Scholar 

  12. Lane, D. J. (1991) 16S/23S rRNA sequencing, in Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt, E. and Goodfellow, M. eds.). Wiley, New York, pp. 115–175.

    Google Scholar 

  13. Stahl, D. A. and Amann, R. (1991) Development and application of nucleic acid probes, in Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt, E. and Goodfellow, M., eds.), Wiley, New York, pp. 115–175.

    Google Scholar 

  14. DeLong, E. F. (1992) Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89, 5685–5689.

    Article  PubMed  CAS  Google Scholar 

  15. Nübel, U., Engelen, B., Felske, A., Snaidr, J., Wieshuber, A., Amann, R. I., et al. (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178, 5636–5643.

    PubMed  Google Scholar 

  16. Embley, T. M., Finlay, B. J., Thomas, R. H., and Dyal, P. L. (1992) The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont. J. Gen. Microbiol. 138, 1479–1487.

    PubMed  CAS  Google Scholar 

  17. Barns, S. M., Fundyga, R. E., Jeffries, M. W., and Pace, N. R. (1994) Remarkable archaeal diversity detected in Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91, 1609–1613.

    Article  PubMed  CAS  Google Scholar 

  18. Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R., and Stahl, D. A. (1986) Microbial ecology and evolution: a ribosomal rRNA approach. Annu. Rev. Microbiol. 40, 337–365.

    Article  PubMed  CAS  Google Scholar 

  19. Breslauer, K. J., Frank, R., Blocker, H., and Marky, L. A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83, 3746–3750.

    Article  PubMed  CAS  Google Scholar 

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© 2004 Humana Press Inc.

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Watanabe, K., Hamamura, N., Kaku, N. (2004). Molecular Identification of Microbial Populations in Petroleum-Contaminated Groundwater. In: Walker, J.M., Spencer, J.F.T., Ragout de Spencer, A.L. (eds) Environmental Microbiology. Methods in Biotechnology, vol 16. Humana Press. https://doi.org/10.1385/1-59259-765-3:235

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  • DOI: https://doi.org/10.1385/1-59259-765-3:235

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-116-5

  • Online ISBN: 978-1-59259-765-9

  • eBook Packages: Springer Protocols

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