Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo

Helen F. Downie, Tracy A. Valentine, Wilfred Otten, Andrew J. Spiers, Lionel X. Dupuy

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    Abstract

    The recently developed transparent soil consists of particles of Nafion, a polymer with a low refractive index (RI), which is prepared by milling and chemical treatment for use as a soil analogue. After the addition of a RI-matched solution, confocal imaging can be carried out in vivo and without destructive sampling. In a previous study, we showed that the new substrate provides a good approximation of plant growth conditions found in natural soils. In this paper, we present further development of the techniques for detailed quantitative analysis of images of root-microbe interactions in situ. Using this system it was possible for the first time to analyse bacterial distribution along the roots and in the bulk substrate in vivo. These findings indicate that the coupling of transparent soil with light microscopy is an important advance towards the discovery of the mechanisms of microbial colonisation of the rhizosphere.
    Original languageEnglish
    Article numbere970421
    Number of pages4
    JournalPlant Signaling & Behavior
    Volume9
    Issue number10
    DOIs
    Publication statusPublished - 1 Oct 2014

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    microcosm
    refractive index
    soil
    substrate
    quantitative analysis
    rhizosphere
    microscopy
    colonization
    polymer
    sampling

    Cite this

    Downie, Helen F. ; Valentine, Tracy A. ; Otten, Wilfred ; Spiers, Andrew J. ; Dupuy, Lionel X. / Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo. In: Plant Signaling & Behavior. 2014 ; Vol. 9, No. 10.
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    abstract = "The recently developed transparent soil consists of particles of Nafion, a polymer with a low refractive index (RI), which is prepared by milling and chemical treatment for use as a soil analogue. After the addition of a RI-matched solution, confocal imaging can be carried out in vivo and without destructive sampling. In a previous study, we showed that the new substrate provides a good approximation of plant growth conditions found in natural soils. In this paper, we present further development of the techniques for detailed quantitative analysis of images of root-microbe interactions in situ. Using this system it was possible for the first time to analyse bacterial distribution along the roots and in the bulk substrate in vivo. These findings indicate that the coupling of transparent soil with light microscopy is an important advance towards the discovery of the mechanisms of microbial colonisation of the rhizosphere.",
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    Downie, HF, Valentine, TA, Otten, W, Spiers, AJ & Dupuy, LX 2014, 'Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo', Plant Signaling & Behavior, vol. 9, no. 10, e970421. https://doi.org/10.4161/15592316.2014.970421

    Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo. / Downie, Helen F.; Valentine, Tracy A.; Otten, Wilfred; Spiers, Andrew J.; Dupuy, Lionel X.

    In: Plant Signaling & Behavior, Vol. 9, No. 10, e970421, 01.10.2014.

    Research output: Contribution to journal › Article

    TY - JOUR

    T1 - Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo

    AU - Downie, Helen F.

    AU - Valentine, Tracy A.

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    AU - Spiers, Andrew J.

    AU - Dupuy, Lionel X.

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    AB - The recently developed transparent soil consists of particles of Nafion, a polymer with a low refractive index (RI), which is prepared by milling and chemical treatment for use as a soil analogue. After the addition of a RI-matched solution, confocal imaging can be carried out in vivo and without destructive sampling. In a previous study, we showed that the new substrate provides a good approximation of plant growth conditions found in natural soils. In this paper, we present further development of the techniques for detailed quantitative analysis of images of root-microbe interactions in situ. Using this system it was possible for the first time to analyse bacterial distribution along the roots and in the bulk substrate in vivo. These findings indicate that the coupling of transparent soil with light microscopy is an important advance towards the discovery of the mechanisms of microbial colonisation of the rhizosphere.

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    Downie HF, Valentine TA, Otten W, Spiers AJ, Dupuy LX. Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo. Plant Signaling & Behavior. 2014 Oct 1;9(10). e970421. https://doi.org/10.4161/15592316.2014.970421

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