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DGGE Fragments Oscillate with or Counter to Fluctuations in Cultivable Bacteria Along Wheat Roots

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Abstract

Previously, we showed that bacterial populations oscillate in response to a moving substrate source such as a root tip, resulting in moving wavelike distributions along roots. For this article, we investigated if bacterial communities fluctuate as a whole or if there is a succession in bacterial composition from peak to peak or within peaks. Rhizosphere microbial communities along roots of wheat Triticum aestivum L. were studied in detail (20–25 rhizosphere and bulk soil samples along the total root length) in two related soils by colony enumeration and culture-independent DNA analysis. Similar to our previous findings, the numbers of copiotrophic and oligotrophic bacteria oscillated with significant harmonics along each root, independent of soil moisture or lateral roots. Shifts in amplified eubacterial 16S rDNA fragments from denaturing gradient gel electrophoresis (DGGE) analysis were detected along the roots. The most abundant and intensively amplified fragments fluctuated in phase with colony-forming unit (CFU) oscillations; fewer amplified fragments with less intensive bands fluctuated out of phase or were restricted to certain root zones. The bacterial species richness along the root was negatively correlated with the numbers of oligotrophic bacterial CFUs. Discriminant analyses on DGGE patterns distinguished between soil types, rhizosphere and bulk soil, and waxing and waning phases in the oscillations along roots. Bacterial compositions shifted within oscillations but were repeated from oscillation to oscillation, supporting the idea that the most abundant bacterial taxa were growing and dying over time and consequently in space, whereas other taxa counterfluctuated or hardly responded to the substrate supplied by the passing root tip.

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Acknowledgments

We are thankful to the farmers, Jan Wieringa and Gert Timmer, who provided large quantities of soil, and to Hans Heilig for providing the clones used as synthetic DGGE marker. Financial support was provided by Wageningen UR for A. van Diepeningen in the form of start-up funds for A.H.C. van Bruggen. Additional support came from the graduate school PE&rRC of Wageningen UR to A.M. Semenov for two research periods at Wageningen UR in 2000 and 2001 and a research fellowship from the Nederlandse organisatie voor Wetenschappelijk Onderzoek (NWO) to A.M. Semenov in 2002. V.V. Zelenev received a PhD sandwich fellowship from Wageningen University to study the response of microbial populations to nutrient input.

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Authors and Affiliations

  1. Biological Farming Systems Group, Department of Plant Sciences, Wageningen University and Research Center, Marijkeweg 22, 6709 PG, Wageningen, The Netherlands

    Anne D. van Diepeningen, Oscar J. de Vos & Ariena H. C. van Bruggen

  2. Laboratory for Cultivation of Microorganisms, Institute of Vaccines and Serums, Russian Academy of Science, Maliy Kazenniy per., 5, Moscow, Russia

    Vladimir V. Zelenev

  3. Department of Microbiology, Biological Faculty, Moscow State University, Vorob'evy Gory, 119899, Moscow, Russia

    Alexandre M. Semenov

Authors
  1. Anne D. van Diepeningen
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  2. Oscar J. de Vos
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  3. Vladimir V. Zelenev
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  4. Alexandre M. Semenov
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  5. Ariena H. C. van Bruggen
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Correspondence to Anne D. van Diepeningen.

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van Diepeningen, A.D., de Vos, O.J., Zelenev, V.V. et al. DGGE Fragments Oscillate with or Counter to Fluctuations in Cultivable Bacteria Along Wheat Roots. Microb Ecol 50, 506–517 (2005). https://doi.org/10.1007/s00248-005-0012-7

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