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Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms

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Abstract

This review mainly discusses three related topics: the application of ecological theories to soil, the measurement of microbial diversity by molecular techniques and the impact of transgenic plants and microorganisms on genetic diversity of soil. These topics were debated at the Meeting on Soil Emergency held in Erice (Trapani, Italy) in 2001 for the celebration of the 50th anniversary of the Italian Society of Soil Science. Ecological theories have been developed by studying aboveground ecosystems but have neglected the belowground systems, despite the importance of the latter to the global nutrient cycling and to the presence of life on the Earth. Microbial diversity within the soil is crucial to many functions but it has been difficult in the past to determine the major components. Traditional methods of analysis are useful but with the use of molecular methods it is now possible to detect both culturable and unculturable microbial species. Despite these advances, the link between microbial diversity and soil functions is still a major challenge. Generally studies on genetically modified bacteria have not addressed directly the issue of microbial diversity, being mainly focused on their persistence in the environment, colonization ability in the rhizosphere, and survival. Concerns have been raised that transgenic plants might affect microbial communities in addition to environmental factors related to agricultural practice, season, field site and year. Transgenic plant DNA originating from senescent or degraded plant material or pollen has been shown to persist in soil. Horizontal transfer of transgenic plant DNA to bacteria has been shown by the restoration of deleted antibiotic resistance genes under laboratory in filter transformations, in sterile soil or in planta. However, the transformation frequencies under field conditions are supposed to be very low. It is important to underline that the public debate about antibiotic resistant genes in transgenic plants should not divert the attention from the real causes of bacterial resistance to antibiotics, such as the continued abuse and overuse of antibiotics prescribed by physicians and in animal husbandry.

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Acknowledgements

We gratefully acknowledge the support of COST Action 831 for supporting the attendance of authors to the Erice (Trapani, Italy) meeting in 2001. Some of the data presented and discussed in this review by A. Benedetti and P. Nannipieri have been obtained in the research MISA project financed by the Ministero delle Politiche Agericole e Forestali, Italy.

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Authors and Affiliations

  1. Forest Research, Alice Holt Lodge, Farnham, Surrey, GU10 4LH, UK

    J. M. Lynch

  2. Istituto Sperimentale per la Nutrizione delle Piante, Via della Navicella 2–4, 1-00184, Rome, Italy

    A. Benedetti

  3. Institut für Mikrobiologie, Universität Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria

    H. Insam

  4. Department of Agarian Chemistry and Biotechnology, University of Pisa, via del Borghetto, Pisa, Italy

    M. P. Nuti

  5. Institute of Plant Virology, Microbiology and Biosafety, Federal Biological Research Centre for Agriculture and Forestry, Messeweg 11–12, 38104, Braunschweig, Germany

    K. Smalla

  6. Department of Microbiology, University of Bergen, P.O. Box 7800, Jahnebakken 5, 5020, Bergen, Norway

    V. Torsvik

  7. Dipartimento della Scienza del Suolo e Nutrizione della Pianta, P.le delle Cascine 28, 50144, Firenze, Italy

    P. Nannipieri

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  1. J. M. Lynch
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Lynch, J.M., Benedetti, A., Insam, H. et al. Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms. Biol Fertil Soils 40, 363–385 (2004). https://doi.org/10.1007/s00374-004-0784-9

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