Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Perspective
  • Published:

Problems in monitoring horizontal gene transfer in field trials of transgenic plants

A Corrigendum to this article was published on 01 April 2005

Abstract

Transgenic crops are approved for release in some countries, while many more countries are wrestling with the issue of how to conduct risk assessments. Controls on field trials often include monitoring of horizontal gene transfer (HGT) from crops to surrounding soil microorganisms. Our analysis of antibiotic-resistant bacteria and of the sensitivity of current techniques for monitoring HGT from transgenic plants to soil microorganisms has two major implications for field trial assessments of transgenic crops: first, HGT from transgenic plants to microbes could still have an environmental impact at a frequency approximately a trillion times lower than the current risk assessment literature estimates the frequency to be; and second, current methods of environmental sampling to capture genes or traits in a recombinant are too insensitive for monitoring evolution by HGT. A model for HGT involving iterative short-patch events explains how HGT can occur at high frequencies but be detected at extremely low frequencies.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Evolution of mosaic alleles by molecular massage.
Figure 2: Implicit assumptions in HGT monitoring.

Similar content being viewed by others

References

  1. Harremoës, P. et al. (eds.) Late Lessons from Early Warnings: the Precautionary Principle, 1896–2000 Environmental Issue Report No. 22 (Official Publications of the European Communities, Copenhagen, 2002).

    Google Scholar 

  2. Traavik, T. Environmental risks of genetically engineered vaccines. in Genetically Engineered Organisms Assessing Environmental and Human Health Effects (eds. Letourneau, D.K. & Burrows, B.E.) 331–353 (CRC Press, Boca Raton, 2002).

    Google Scholar 

  3. Conner, A.J., Glare, T.R. & Nap, J.-P. The release of genetically modified crops into the environment Part II. Overview of ecological risk assessment. Plant J. 33, 19–46 (2003).

    Article  PubMed  Google Scholar 

  4. Gasson, M. & Burke, D. Scientific perspectives on regulating the safety of genetically modified foods. Nat. Rev. Genet. 2, 217–222 (2001).

    Article  CAS  PubMed  Google Scholar 

  5. Amábile-Cuevas, C.F. (ed.) Multiple Drug Resistant Bacteria (Horizon Scientific Press, Wymondham, 2003).

    Google Scholar 

  6. Anonymous. Report of the ASM task Force on Antibiotic Resistance. Antimicrob. Agents Chemother. 39, 2–23 (1995).

  7. de la Cruz, F., Garcia-Lobo, J.M. & Davies, J. Antibiotic resistance: how bacterial populations respond to a simple evolutionary force. in Bacterial Resistance to Antimicrobials (eds. Lewis, K., Salyers, A.A., Taber, H.W. & Wax, R.G.) 19–36 (Marcel Dekker, New York and Basel, 2002).

    Google Scholar 

  8. Heinemann, J.A. How antibiotics cause antibiotic resistance. Drug Discov. Today 4, 72–79 (1999).

    Article  CAS  PubMed  Google Scholar 

  9. Levy, S.B. The challenge of antibiotic resistance. Sci. Amer. 278, 32–39 (1998).

    Article  Google Scholar 

  10. Springael, D. & Top, E.M. Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies. Trends Microbiol. 12, 53–58 (2004).

    Article  CAS  PubMed  Google Scholar 

  11. Jain, R., Rivera, M.C. & Lake, J.A. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96, 3801–3806 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Lawrence, J.G. & Roth, J.R. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143, 1843–1860 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Ochman, H., Lawrence, J.G. & Groisman, E.A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304 (2000).

    Article  CAS  PubMed  Google Scholar 

  14. Rujan, R. & Martin, W. How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genet. 17, 113–120 (2001).

    Article  CAS  PubMed  Google Scholar 

  15. Syvanen, M. & Kado, C.I. (eds.) Horizontal Gene Transfer edn. 2 (Academic Press, San Diego, 2002).

    Google Scholar 

  16. Woese, C.R. On the evolution of cells. Proc. Natl. Acad. Sci. USA 99, 8742–8747 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. de Vries, J., Heine, M., Harms, K. & Wackernagel, W. Spread of recombinant DNA by roots and pollen of transgenic potato plants, identified by highly specific biomonitoring using natural transformation of an Acinetobacter sp. Appl. Environ. Microbiol. 69, 4455–4462 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Nielsen, K.M., Bones, A.M., Smalla, K. & van Elas, J.D. Horizontal gene transfer from transgenic plants to terrestrial bacteria—a rare event? FEMS Microbiol. Rev. 22, 79–103 (1998).

    Article  CAS  PubMed  Google Scholar 

  19. Nielsen, K.M., van Elas, J.D. & Smalla, K. Transformation of Acinetobacter sp. strain BD413(pFG4DnptII) with transgenic plant DNA in soil microcosms and effects of kanamycin on selection of transformants. Appl. Environ. Microbiol. 66, 1237–1242 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Kay, E., Vogel, T.M., Bertolla, F., Nalin, R. & Simonet, P. In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria. Appl. Environ. Microbiol. 68, 3345–3351 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Tepfer, D. et al. Homology-dependent DNA transfer from plants to a soil bacterium under laboratory conditions: implications in evolution and horizontal gene transfer. Trans. Res. 12, 425–437 (2003).

    Article  CAS  Google Scholar 

  22. Schluter, K., Futterer, J. & Potrykus, I. 'Horizontal' gene transfer from a transgenic potato line to a bacterial pathogen (Erwinia chrysanthemi) occurs—if at all—at an extremely low frequency. Bio/Technology 13, 1094–1098 (1995).

    Article  CAS  Google Scholar 

  23. Massova, I. & Mobashery, S. Kinship and diversification of bacterial penicillin-binding proteins and beta-lactamases. Antimicrob. Agents Chemother. 42, 1–17 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Hakenbeck, R., Grebe, T., Zähner, D. & Stock, J.B. β-lactam resistance in Streptococcus pneumoniae: penicillin-binding proteins and non-penicillin-binding proteins. Mol. Microbiol. 33, 673–678 (1999).

    Article  CAS  PubMed  Google Scholar 

  25. Spratt, B.G. Resistance to antibiotics mediated by target alterations. Science 264, 388–393 (1994).

    Article  CAS  PubMed  Google Scholar 

  26. Walsh, C. Antibiotics Actions Origins Resistance (ASM Press, Washington, 2003).

    Book  Google Scholar 

  27. Nichol, K.A., Zhanel, G.G. & Hoban, D.J. Penicillin-binding protein 1A, 2B, and 2X alterations in Canadian isolates of penicillin-resistant Streptococcus pneumoniae. Antimicrob. Agents Chemother. 46, 3261–3264 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Hooper, D.C. in Bacterial Resistance to Antimicrobials (eds. Lewis, K. Salyers, A.A., Taber, H.W. & Wax, R.G.) 161–192 (Marcel Dekker, New York, 2002).

    Google Scholar 

  29. Amoroso, A., Demares, D., Mollerach, M., Gutkind, G. & Coyette, J. All detectable high-molecular-mass penicillin-binding proteins are modified in a high-level β-lactam-resistant clinical isolate of Streptococcus mitis. Antimicrob. Agents Chemother. 45, 2075–2081 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Claverys, J.-P., Prudhomme, M.I.M.-B. & Martin, B. Adaptation to the environment: Streptococcus pneumoniae, a paradigm for recombination-mediated genetic plasticity? Mol. Microbiol. 35, 251–259 (2000).

    Article  CAS  PubMed  Google Scholar 

  31. Heinemann, J.A. Horizontal gene transfer between microorganisms. in Encyclopedia of Microbiology edn. 2 (ed. Lederberg, J.) 698–706 (Academic Press, San Diego, 2000).

    Google Scholar 

  32. Marvier, M. Ecology of transgenic crops. Am. Sci. 89, 160–167 (2001).

    Article  Google Scholar 

  33. Doern, G.V. et al. Antimicrobial resistance among clinical isolates of Streptococcus pneumoniae in the United States during 1999–2000, including a comparison of resistance rates since 1994–1995. Antimicrob. Agents Chemother. 45, 1721–1729 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Molbak, L., Licht, T.R., Kvist, T., Kroer, N. & Andersen, S.R. Plasmid transfer from Pseudomonas putida to the indigenous bacteria on alfalfa sprouts: characterization, direct quantification, and in situ location of transconjugant cells. Appl. Environ. Microbiol. 69, 5536–5542 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Lilley, A.K. et al. Population dynamics and gene transfer in genetically modified bacteria in a model microcosm. Mol. Ecol. 12, 3097–3107 (2003).

    Article  CAS  PubMed  Google Scholar 

  36. Anderson, E.S. The ecology of transferable drug resistance in the enterobacteria. Annu. Rev. Microbiol. 22, 131–180 (1968).

    Article  CAS  PubMed  Google Scholar 

  37. Heinemann, J.A., Ankenbauer, R.G. & Amábile-Cuevas, C.F. Do antibiotics maintain antibiotic resistance? Drug Discov. Today 5, 195–204 (2000).

    Article  CAS  PubMed  Google Scholar 

  38. du Plessis, M., Bingen, E. & Klugman, K.P. Analysis of penicillin-binding protein genes of clinical isolates of Streptococcus pneumoniae with reduced susceptibility to amoxicillin. Antimicrob. Agents Chemother. 46, 2349–2367 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Nielsen, K.M. et al. Natural transformation and availability of transforming DNA to Acinetobacter calcoaceticus in soil microcosms. Appl. Environ. Microbiol. 63, 1945–1952 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Gebhard, R. & Smalla, K. Transformation of Acinetobacter sp. strain BD413 by transgenic sugar beet DNA. Appl. Environ. Microbiol. 64, 1550–1554 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Mendelsohn, M., Kough, J., Vaituzis, Z. & Matthews, K. Are Bt crops safe? Nat. Biotechnol. 21, 1003–1009 (2003).

    Article  CAS  PubMed  Google Scholar 

  42. Majewski, J., Zawadzki, P., Pickerill, P., Cohan, F.M. & Dowson, C.G. Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J. Bacteriol. 182, 1016–1023 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Whitman, W.B., Coleman, D.C. & Wiebe, W.J. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95, 6578–6583 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Stokstad, E. Monsanto pulls the plug on genetically modified wheat. Science 304, 1088–1089 (2004).

    Article  CAS  PubMed  Google Scholar 

  45. Knols, B.G.J. & Dicke, M. Bt crop risk assessment in the Netherlands. Nat. Biotechnol. 21, 973–974 (2003).

    Article  CAS  PubMed  Google Scholar 

  46. de Maagd, R.A., Bravo, A. & Crickmore, N. How Bacillus thuringiensis has evolved toxins to colonize the insect world. Trends Genet. 17, 193–199 (2001).

    Article  CAS  PubMed  Google Scholar 

  47. Saxena, D., Flores, S. & Stotzky, G. Insecticidal toxin in root exudates from Bt corn. Nature 402, 480 (1999).

    Article  CAS  PubMed  Google Scholar 

  48. Chowdhury, E.H. et al. Detection of corn intrinsic and recombinant DNA fragments and Cry1Ab protein in the gastrointestinal contents of pigs fed genetically modified corn Bt11. J. Anim. Sci. 81, 2546–2551 (2003).

    Article  CAS  PubMed  Google Scholar 

  49. Keeling, P.J. & Palmer, J.D. Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase. Proc. Natl. Acad. Sci. USA 98, 10745–10750 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Balsalobre, L., Ferrandiz, M.J., Linares, J., Tubau, F. & de la Campa, A.G. Viridans group streptococci are donors in horizontal transfer of topoisomerase IV genes to Streptococcus pneumoniae. Antimicrob. Agents Chemother. 47, 2072–2081 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Kuiper, H.A., Kleter, G.A., Noteborn, H.P.J.M. & Kok, E.J. Assessment of the food safety issues related to genetically modified foods. Plant J. 27, 503–528 (2001).

    Article  CAS  PubMed  Google Scholar 

  52. Curtis, T.P., Sloan, W.T. & Scannell, J.W. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 99, 10494–10499 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Heinemann, J.A., Sparrow, A.D. & Traavik, T. Is confidence in monitoring of GE foods justified? Trends Biotechnol. 22, 331–336 (2004).

    Article  CAS  PubMed  Google Scholar 

  54. Sørensen, S.J., Sørensen, A.H., Hansen, L.H., Oregaard, G. & Veal, D. Direct detection and quantification of horizontal gene transfer by using flow cytometry and GFP as a reporter gene. Curr. Microbiol. 47, 129–133 (2003).

    Article  PubMed  CAS  Google Scholar 

  55. Michael, C. et al. Mobile gene cassettes: a fundamental resource for bacterial evolution. Am. Nat. 164, 1–12 (2004).

    Article  PubMed  Google Scholar 

  56. Nemergut, D.R., Martin, A.P. & Schmidt, S.K. Integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution. Appl. Environ. Microbiol. 70, 1160–1168 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Stokes, H.W. et al. Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA. Appl. Environ. Microbiol. 67, 5240–5246 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Cooper, T.F. & Heinemann, J.A. Post-segregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids. Proc. Natl. Acad. Sci. USA 97, 12543–12648 (2000).

    Google Scholar 

  59. Doolittle, W.F. Phylogenetic classification and the universal tree (taxonomies based on molecular sequences). Science 284, 2124–2130 (1999).

    Article  CAS  PubMed  Google Scholar 

  60. Heinemann, J.A. Genetics of gene transfer between species. Trends Genet. 7, 181–185 (1991).

    Article  CAS  PubMed  Google Scholar 

  61. Maiden, M.C.J., Malorny, B. & Achtman, M. A global gene pool in the neisseriae. Mol. Microbiol. 21, 1297–1298 (1996).

    Article  CAS  PubMed  Google Scholar 

  62. Gibbs, M.J. & Weiller, G.F. Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. Proc. Natl. Acad. Sci. USA 96, 8022–8027 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Prudhomme, M., Libante, V. & Claverys, J.-P. Homologous recombination at the border: insertion-deletions and the trapping of foreign DNA in Streptococcus pneumoniae. Proc. Natl. Acad. Sci. USA 99, 2100–2105 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Denamur, E. et al. Evolutionary implications of the frequent horizontal transfer of mismatch repair genes. Cell 103, 711–721 (2000).

    Article  CAS  PubMed  Google Scholar 

  65. Evans, E. & Alani, E. Roles for mismatch repair factors in regulating genetic recombination. Mol. Cell. Biol. 20, 7839–7844 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Matic, I., Rayssiguier, C. & Radman, M. Interspecies gene exchange in bacteria: the role of SOS and mismatch repair systems in evolution of species. Cell 80, 507–515 (1995).

    Article  CAS  PubMed  Google Scholar 

  67. Rayssiguier, C., Thaler, D.S. & Radman, M. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342, 396–401 (1989).

    Article  CAS  PubMed  Google Scholar 

  68. Cupples, C.G., Cabrera, M., Cruz, C. & Miller, J.H. A set of lacZ mutations in Escherichia coli that allow rapid detection of specific frameshift mutations. Genetics 125, 275–280 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Humayun, M.Z. SOS and Mayday: multiple inducible mutagenic pathways in Escherichia coli. Mol Microbiol 30, 905–910 (1998).

    Article  CAS  PubMed  Google Scholar 

  70. Mihaylova, V.T. et al. Decreased expression of the DNA mismatch repair gene Mlh1 under hypoxic stress in mammalian cells. Mol. Cell. Biol. 23, 3265–3273 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Amann, R., Ludwig, W. & Schleifer, K. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Kaeberlein, T., Lewis, K. & Epstein, S.S. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296, 1127–1129 (2002).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank C. Amábile-Cuevas, H. Cochrane, D. Bean and R. Mann for critical comments on the manuscript. J.A.H. acknowledges support from the Marsden Fund of New Zealand (M1042) and the Brian Mason Trust.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jack A Heinemann.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Heinemann, J., Traavik, T. Problems in monitoring horizontal gene transfer in field trials of transgenic plants. Nat Biotechnol 22, 1105–1109 (2004). https://doi.org/10.1038/nbt1009

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt1009

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing