Influence of soil structure on the spread of Pseudomonas fluorescens in soil at microscale

Archana Juyal, Wilfred Otten, Philippe C. Baveye, Thilo Eickhorst*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    20 Citations (Scopus)
    66 Downloads (Pure)


    For over a half a century, researchers have been aware of the fact that the physical and chemical characteristics of microenvironments in soils strongly influence the activity, growth, and metabolism of microorganisms. However, many aspects of the effect of soil physical characteristics, such as the pore geometry, remain poorly understood. Therefore, the objective of the present research was to determine the influence of soil pore characteristics on the spread of bacteria, observed at the scale relevant to microbes. Pseudomonas fluorescens was introduced in columns filled with 1–2 mm soil aggregates, packed at different bulk densities.. Soil microcosms were scanned at 10.87 μm voxel resolution using X‐ray computed tomography (CT) to characterize the geometry of pores. Thin sections were prepared to determine the spread and colonization of bacteria. The results showed that average bacterial cell density was 174 cells mm−2 in soil with bulk density of 1.3 g cm−3 and 99 cells mm−2 in soil with bulk density of 1.5 g cm−3. Soil porosity and solid‐pore interfaces influence the spread of bacteria and their colonization of the pore space at lower bulk density, resulting in relatively higher bacterial densities in larger pore spaces. The study also demonstrates that thin sectioning of resin impregnated soil samples can be combined with X‐ray CT to visualize bacterial colonization of a 3D pore volume. This research therefore represents a significant step towards understanding how environmental change and soil management impact bacterial diversity in soils.
    Original languageEnglish
    Pages (from-to)141-153
    Number of pages13
    JournalEuropean Journal of Soil Science
    Issue number1
    Early online date24 Apr 2020
    Publication statusPublished - 4 Jan 2021


    • Bacterial spread
    • Fluorescence microscopy
    • Pore geometry
    • Soil thin sections
    • X-ray computed tomography


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