Microcosm fabrication platform for live microscopy of plant-soil systems

Our ability to fully understand how plants acquire water and nutrients from the soil is constrained by the limitations of current technologies. Soil structures and properties are complex, dynamic, and profoundly modified by root and microbial secretions. Detailed descriptions of soil properties are rarely available to the researcher because natural soil is opaque, making direct observations challenging. To address these experimental difficulties, microcosm systems dedicated to live imaging of rhizosphere processes in highly controlled environmental conditions were developed. The system is based on fluorinated granular materials with low refractive indices, termed transparent soils. Microcosm chambers were assembled using poly(dimethyl siloxane) parts (PDMS) fabricated by injection moulding and subsequently joined to glass slides. The control of liquid fluxes in the microcosm was achieved by syringes passing through the PDMS parts or through custom made PDMS sponges. The platform was tested for live imaging experiments using Light Sheet Fluorescence microscopy. Results demonstrated that the platform is suitable for a diverse range of experiments, including live observation of plant roots, split-soil systems and investigations into the effects of soil heterogeneity, controlled water content experiments, and dye tracer monitoring. The technique was used to quantify the increase in infiltration rate due to the presence of roots in soil. This study demonstrates the potential of combining new materials and microfabrication techniques to overcome current limitations on plant-soil interaction research.