Mechanistic modelling of bioavailability
: putting soil microbiology in its pore scale context

  • Jennifer Blair

    Student thesis: Doctoral Thesis


    The soil-microbe complex was investigated in terms of the relationship between the physical soil structure and related functional characteristics. The use of CT scanning technology provided a means of obtaining high-resolution digital reconstructions of the internal soil structures in three dimensions thus allowing, for the first time, the internal architecture of soil to be investigated. The investigation of soil structure was facilitated through the development of a theoretical modelling framework that acted as a virtual laboratory. A suite of metrics was implemented within the modelling framework to allow the quantification of the physical soil structure. The analysis of a range of CT imaged soil structures via the quantification metrics showed that the micro-structure of soil can span a range of porosities and textures. The metric values obtained for individual structures characterise the features of the structures that play an influential role in mediating the functional value of a sample.

    A model that simulates soil structure in three dimensions from two-dimensional data is shown to reproduce the key structural characteristics of soil at the micro-scale. Data extracted from the CT imaged soil samples were extracted to parameterise the model and thus the simulated soil structures were validated against the original CT imaged structure using the quantification metrics. In general, the model adequately reconstructed the variation found across the CT imaged samples. However, for low porosity samples the complex pore architectures were not captured.

    The soil structures were used to simulated oxygen transport through the microenvironment to microbial active sites thus allowing the examination of the impact of physical structure on microbial respiration. The results presented show that soil structure is the determining factor in bulk respiration of the soil microenvironment.
    Date of AwardMar 2007
    Original languageEnglish
    SponsorsBiotechnology and Biological Sciences Research Council
    SupervisorJohn W. Crawford (Supervisor) & Iain M. Young (Supervisor)

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