Microcosm fabrication platform for live microscopy of plant-soil systems

Biological processes in soil pores are critical to crop nutrition and productivity, but live observations of these processes at that scale have been difficult to accomplish. To address this challenge, we have developed new techniques for the fabrication of microcosms dedicated to live imaging of the rhizosphere which incorporate the ability to control water content in transparent soil. Chambers were assembled using poly(dimethyl siloxane) (PDMS) parts 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. We then tested various low refractive index materials for the fabrication of transparent soils and carried out live microscopy using Fluorescence Light Sheet microscopy. The proposed fabrication techniques are modular and enabled the construction of a wide range of experimental systems, including split chamber systems for the control of water content in soil, heterogeneous distribution of water content, monitoring of dye tracers, and live observation of plant roots. Using the techniques, we show how plant roots increase water infiltration through increased permeability of dry soil layers. This study therefore establishes that material property control and microfabrication in model rhizosphere systems can greatly enhance our understanding of plant-soil interactions. ### Competing Interest Statement Some materials used in the study were donated by AGC Inc.