Microbial Ecology

, Volume 52, Issue 1, pp 151–158 | Cite as

Three-dimensional Microorganization of the Soil–Root–Microbe System

  • Debbie S. Feeney
  • John W. Crawford
  • Tim Daniell
  • Paul D. Hallett
  • Naoise Nunan
  • Karl Ritz
  • Mark Rivers
  • Iain M. YoungEmail author


Soils contain the greatest reservoir of biodiversity on Earth, and the functionality of the soil ecosystem sustains the rest of the terrestrial biosphere. This functionality results from complex interactions between biological and physical processes that are strongly modulated by the soil physical structure. Using a novel combination of biochemical and biophysical indicators and synchrotron microtomography, we have discovered that soil microbes and plant roots microengineer their habitats by changing the porosity and clustering properties (i.e., spatial correlation) of the soil pores. Our results indicate that biota act to significantly alter their habitat toward a more porous, ordered, and aggregated structure that has important consequences for functional properties, including transport processes. These observations support the hypothesis that the soil–plant–microbe complex is self-organized.


Rhizosphere Soil Fungal Biomass Soil Aggregate Water Repellency Physical Habitat 
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.



Portions of this work were performed at GeoSoilEnviroCARS (Sector 13), APS, Argonne National Laboratory. GeoSoilEnviroCARS is supported by the National Science Foundation–Earth Sciences (EAR-0217473), Department of Energy-Geosciences (DE-FG02-94ER14466), and the State of Illinois. Use of APS was supported by the US Department of Energy, Basic Energy Sciences, Office of Science, under contract no. W-31-109-Eng-38. We acknowledge funding from the Biotechnological Biological Research Council (BBSRC; grant number D20454), the Natural Environment Research Council, and the University of Abertay. KR gratefully acknowledges the support in the form of an International Scientific Interchange Scheme (ISIS) grant from the BBSRC.


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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Debbie S. Feeney
    • 1
  • John W. Crawford
    • 1
  • Tim Daniell
    • 2
  • Paul D. Hallett
    • 2
  • Naoise Nunan
    • 3
  • Karl Ritz
    • 4
  • Mark Rivers
    • 5
  • Iain M. Young
    • 1
    Email author
  1. 1.Scottish Informatics Mathematics Biology and Statistics (SIMBIOS) CentreUniversity of AbertayDundeeUK
  2. 2.Scottish Crop Research InstituteDundeeUK
  3. 3.CNRS, Laboratoire de Biogéochimie des Milieux Continentaux, Bâtiment EGER, aîle B, INRA INA-PGThiverval-GrignonFrance
  4. 4.National Soil Resources InstituteCranfield UniversityBedfordshireUK
  5. 5.APS/CARS-CATThe University of Chicago, c/o Argonne National LaboratoryArgonneUSA

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