Tracking Microorganisms and Genes in the Environment

  • Ronald M. Atlas
  • Gary S. Sayler
Part of the Basic Life Sciences book series (BLSC, volume 45)


Many concerns have been expressed about the possible hazards resulting from the release into natural environments of genetically engineered microorganisms (GEMs) derived from recombinant DNA (rDNA) technology (7, 15, 42). These concerns center around the possibilities that GEMs, or host cells into which rDNA might move, could demonstrate pathogenicity, causing disease in plants or animals, or that GEMs or subsequent hosts for the rDNA could have detrimental effects on natural ecosystems. Many different disaster scenarios have been postulated, ranging from a deadly “Andromeda strain” pathogen produced by rDNA technology causing massive mortalities, to the release of a GEM altering the world climate. Many similar concerns were raised in the early 1970s when the technology for producing GEMs was first developed, leading to the Asilomar Conference in February 1975, and the development of guidelines and oversight by the Recombinant Advisory Committee (RAC) of the National Institutes of Health (NIH) for the safe handling of GEMs.


rDNA Sequence Gene Probe Fluorescent Antibody Specific Gene Probe Colony Hybridization 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Atlas, R.M. (1982) Enumeration and estimation of biomass of microbial components in the biosphere. In Experimental Microbial Ecology, R.G. Burns and J.H. Slater, eds. Blackwell Science Publishers, Oxford, England, pp. 84–102.Google Scholar
  2. 2.
    Barkay, T., and G. Sayler (1987) Gene probes as a tool for the detection of specific genomes in the environment. American Society for Testing and Materials special publication on Biotechnology Risk Assessment (in press).Google Scholar
  3. 3.
    Barkay, T., D.L. Fouts, and B.H. Olson (1985) The preparation of a DNA gene probe for the detection of mercury resistance genes in Gram-negative bacterial communities. Appl. Environ. Microbiol. 49:686–692.PubMedGoogle Scholar
  4. 4.
    Berent, S.L., M. Mahmoudi, R.M. Torczynski, P.W. Bragg, and A.P. Bollon (1985) Comparison of oligonucleotide and long DNA fragments as probes in DNA and RNA dot, Southern, Northern, colony and plaque hybridizations. Biotechniques 3:208.Google Scholar
  5. 5.
    Blackburn, J.W., R.K. Jain, and G.S. Sayler (1987) The molecular microbial ecology of a naphthalene-degrading genotype in activated sludge. Environ. Sci. Technol., Vol. 21 (in press).Google Scholar
  6. 6.
    Bohlool, B.B., and E.L. Schmidt (1980) The immunofluorescence approach in microbial ecology. In Advances in Microbial Ecology, Vol. 4, M. Alexander, ed. Plenum Press, New York. pp. 203–241.CrossRefGoogle Scholar
  7. 7.
    Brown, T.H., R.K. Colwell, R.E. Lenski, B.R. Levin, M. Lloyd, P.J. Regal, and D. Simberloff (1984) Report on workshop on possible ecological and evolutionary impacts of bioengineered organisms released into the environment. Bull. Ecol. Soc. Am. 65:436.Google Scholar
  8. 8.
    Curtiss, III, R.(1976) Genetic manipulation of microorganisms: Potential benefits. Annu. Rev. Microbiol. 30:507–533.PubMedCrossRefGoogle Scholar
  9. 9.
    Drahos, D.J., B.C. Hemming, and S. McPherson (1986) Tracking recombinant organisms in the environment: β-galactosidase as a selectable non-antibiotic marker for fluorescent pseudomonads. Bio/Technology 4:439–444.CrossRefGoogle Scholar
  10. 10.
    Ford, S., S.C. Simpson, and B.H. Olson (1987) Evaluation of strategies for the detection of specific DNA sequences by colony hybridization in Gram-positive and Gram-negative microorganisms. Abstracts of the Annual Meeting, American Society for Microbiology, Atlanta, Georgia, Q129.Google Scholar
  11. 11.
    Forster, A.C., J.L. Mclnnes, D.C. Skingle, and R. H. Symons (1985) Non-radioactive hybridization probes prepared by the chemical labelling of DNA and RNA with a novel reagent, photobiotin. Nucl. Acids Res. 13:745–761.PubMedCrossRefGoogle Scholar
  12. 12.
    Frederickson, J.K., D.F. Bezdicek, F.E. Brockman, and S.W. Li (1987) Enumeration of Tn5 mutant bacteria in soil by MPN-DNA hybridization and antibiotic resistance. Applied Environ. Microbiol. (in press).Google Scholar
  13. 13.
    Glaser, D., T. Keith, P. Riley, G. Chambers, J. Manning, S. Hatting, and R. Evans (1985) Monitoring techniques for genetically engineered microorganisms. In Research Needs in Biotechnology and the Environment, NTIS Order PB86-158979/REB, U.S. Environmental Protection Agency, Washington, D.C.Google Scholar
  14. 14.
    Grunstein, M., and D.S. Hogness (1975) Colony hybridization: A method for the isolation of cloned DNAs that contain a specific gene. Proc. Natl. Acad. Sci., USA 72:3961–3965.PubMedCrossRefGoogle Scholar
  15. 15.
    Halvorson, H.O., D. Pramer, and M. Rogul (1985) Engineered Organisms in the Environment: Scientific Issues, American Society for Microbiology, Washington, D.C.Google Scholar
  16. 16.
    Hanahan, D., and M. Meselson (1980) Plasmid screening at high colony density. Gene 10:63–67.PubMedCrossRefGoogle Scholar
  17. 17.
    Holben, W.E., J.R. Jannson, B.K. Chelm, and J.M. Tiedje (1987) Methods for assessing the fate of genetically engineered microorganisms in soil. Abstracts of the Annual Meeting, American Society for Microbiology, Atlanta, Georgia, Q131.Google Scholar
  18. 18.
    Jain, R.K., and G.S. Sayler (1987) Problems and potential for in situ treatment of environmental pollutants by engineered microorganisms. Microbiol. Sci. 4:59–63.PubMedGoogle Scholar
  19. 19.
    Jain, R.K., R.S. Burlage, and G.S. Sayler (1987) Methods for detecting recombinant DNA in the environment. CRC Crit. Rev. Biotechnol. (in press).Google Scholar
  20. 20.
    Jain, R.K., G.S. Sayler, J.T. Wilson, L. Houston, and D. Pacia (1987) Maintenance and stability of introduced genotypes in ground-water aquifer material. Appl. Environ. Microbiol. 53:996–1002.PubMedGoogle Scholar
  21. 21.
    Jannson, J.R., W. Holben, B.K. Chelm, and J.M. Tiedje (1987) Fate of genetically engineered Pseudomonads added to soil cores. Abstracts of the Annual Meeting, American Society for Microbiology, Atlanta, Georgia, Q132.Google Scholar
  22. 22.
    Leary, J.J., D.J. Brigati, and D.C. Ward (1983) Rapid and sensitive colorimetric method for visualizing biotin-labeled DNA probes hybridized to DNA or RNA immobilized on nitrocellulose: Bio-blots. Proc. Natl. Acad. Sci., USA 80:4045–4049.PubMedCrossRefGoogle Scholar
  23. 23.
    Levin, M.A., R. Seidler, A.W. Bourquin, J.W. Fowle, III, and T. Barkay (1986) EPA developing methods to assess environmental release. Bio/Technology 5:38–45.CrossRefGoogle Scholar
  24. 24.
    Levine, M.M., J.B. Kaper, H. Lockman, R.E. Black, M.L. Clements, and S. Falkow (1983) Recombinant DNA risk assessment studies in man: Efficacy of poorly mobilizable plasmids in biologic containment. Recomb. DNA Tech. Bull. 6:89–97.PubMedGoogle Scholar
  25. 25.
    Lewin, R. (1983) Genetic probes become even sharper. Science 221:1167.PubMedCrossRefGoogle Scholar
  26. 26.
    Liang, L.N., J.L. Sinclair, L.M. Mallory, and M. Alexander (1982) Fate in model ecosystems of microbial species of potential use in genetic engineering. Appl. Environ. Microbiol. 44:708–714.PubMedGoogle Scholar
  27. 27.
    Lo, R.C., and L.A. Cameron (1976) A simple immunological detection method for the direct screening of genes from clone banks. Biochem. Cell Biol. 64:73.CrossRefGoogle Scholar
  28. 28.
    McCormick, D. (1986) Detection technology: The key to environmental biotechnology. Bio/Technology 4:419–422.CrossRefGoogle Scholar
  29. 29.
    Meinkoth, J., and G. Wahl (1984) Hybridization of nucleic acids immobilized on solid supports. Anal. Biochem. 138:267–271.PubMedCrossRefGoogle Scholar
  30. 30.
    Miller, E.C., U. Juhl, and J.A. Miller (1966) Nucleic acid guanine: Reaction with the carcinogen N-acetoxy-2-acetylaminofluorene. Science 153:1125–1127.PubMedCrossRefGoogle Scholar
  31. 31.
    Moseley, S.L., U. Huq, A.R.M.A. Alim, M. So, M. Samadpourmotalebi, and S. Falkow (1980) Detection of enterotoxigenic Escherichia coli by DNA colony hybridization. J. Infect. Dis. 142:892–898.PubMedCrossRefGoogle Scholar
  32. 32.
    Ogram, A., G.S. Sayler, and T. Barkay (1988) DNA extraction and purification from sediments. J. Micro. Meth. (in press).Google Scholar
  33. 33.
    Omenn, G.S. (1986) Controlled testing and monitoring methods for microorganisms. In Biotechnology Risk Assessment: Issues and Methods for Environmental Introductions, J. Fiksel and V.T. Covello, eds. Pergamon Press, New York, pp. 144–162.Google Scholar
  34. 34.
    Pettigrew, C., and G.S. Sayler (1986) The use of DNA:DNA colony hybridization in the rapid isolation of 4-chlorobiphenyl degradative bacterial phenotypes. J. Microbiol. Meth. 5:205–213.CrossRefGoogle Scholar
  35. 35.
    Renz, M. (1983) Polynucleotide-histone H1 complexes as probes for blot hybridization. EMBO J. 2:817–821.PubMedGoogle Scholar
  36. 36.
    Renz, M., and C. Kurz (1984) A colorimetric method for DNA hybridization. Nucl. Acids Res. 12:3435–3444.PubMedCrossRefGoogle Scholar
  37. 37.
    Rigby, P.W.J., M. Dieckmann, C. Rhodes, and P. Berg (1977) Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J. Mol. Biol. 113:237–251.PubMedCrossRefGoogle Scholar
  38. 38.
    Sayler, G.S., and G. Stacey (1986) Methods for evaluation of microorganism properties. In Biotechnology Risk Assessment: Issues and Methods for Environmental Introductions, J. Fiksel and V.T. Covello, eds. Pergamon Press, New York, pp. 35–58.Google Scholar
  39. 39.
    Sayler, G.S., C. Harris, C. Pettigrew, D. Pacia, A. Breen, and K.M. Sirotkin (1987b) Evaluating the maintenance and effects of genetically engineered microorganisms. Dev. Indust. Microbiol. 27:135–149.Google Scholar
  40. 40.
    Sayler, G.S., M.S. Shields, A. Breen, E.T. Tedford, S. Hooper, K.M. Sirotkin, and J.W. Davis (1985) Application of DNA:DNA colony hybridization to the detection of catabolic genotypes in environmental samples. Appl. Environ. Microbiol. 49:1295–1303.PubMedGoogle Scholar
  41. 41.
    Sayler, G.S., R.K. Jain, L. Houston, A. Ogram, C.A. Pettigrew, J.W. Blackburn, and W.S. Riggsby (1987a) Applications for DNA probes in biodegradation research. In Contemporary Microbial Ecology, Proceedings of the Fourth International Symposium on Microbial Ecology (in press).Google Scholar
  42. 42.
    Sharpies, F.E. (1983) Spread of organisms with novel genotypes: Thoughts from an ecological perspective. Recomb. DNA Tech Bull. 6:43–56.Google Scholar
  43. 43.
    Steffan, R.J., and R.M. Atlas (1987) Use of specific gene probes for the detection of Pseudomonas cepacia DC102 in sediments. In Abstracts of the Annual Meeting of the American Society for Microbiology, Atlanta, Georgia, Abstr. Q130.Google Scholar
  44. 44.
    Steffan, R.J., J. Goksoyr, and R.M. Atlas (1986) Isolation of bacterial DNA from Ohio River sediments. Annual Meeting, American Society for Microbiology, Washington, D.C., Q-144.Google Scholar
  45. 45.
    Stotzky, G., and V.N. Krasovsky (1981) Ecological factors that affect the survival, establishment, growth, and genetic recombination of microbes in natural habitats. In Molecular Biology, Pathogenicity, and Ecology of Bacterial Plasmids, S.B. Levy, U.C. Clowes, and E.L. Koenig, eds. Plenum Press, New York, pp. 31–42.CrossRefGoogle Scholar
  46. 46.
    Stotzky, G., and H. Babich (1986) Survival of, and genetic transfer by, genetically engineered bacteria in natural environments. In Advances in Applied Microbiology, Vol. 31, A.I. Laskin, ed. Academic Press, Inc., New York, pp. 93–138.Google Scholar
  47. 47.
    Tchen, P., R. Fuchs, E. Sage, and M. Leng (1984) Chemically modified nucleic acids as immunodetectable probes in hybridization experiments. Proc. Natl. Acad. Sci., USA 81:3466–3470.PubMedCrossRefGoogle Scholar
  48. 48.
    Torsvik, V.L. (1980) Isolation of bacterial DNA from soil. Soil Biol. Biochem. 12:15–21.CrossRefGoogle Scholar
  49. 49.
    Trevors, J.T., T. Barkay, and A.W. Bourquin (1987) Gene transfer among bacteria in soil and aquatic environments: A review. Can. J. Microbiol. 33:191–198.CrossRefGoogle Scholar
  50. 50.
    Van Voris, P., J.K. Fredrickson, and M. Ligotke (1987) Terrestrial microcosms and containment systems to evaluate ecosystem effects of genetically engineered microorganisms. In Annual Meeting of the American Society for Microbiology, Atlanta, Georgia.Google Scholar
  51. 51.
    Yates, J.R., J.H. Lobos, and D.S. Holmes (1986) The use of genetic probes to detect microorganisms in biomining operations. J. Indust. Microbiol. 1:129–135.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1988

Authors and Affiliations

  • Ronald M. Atlas
    • 1
  • Gary S. Sayler
    • 2
  1. 1.Department of BiologyUniversity of LouisvilleLouisvilleUSA
  2. 2.Graduate Ecology ProgramUniversity of TennesseeKnoxvilleUSA

Personalised recommendations