Smart soils track the formation of pH gradients across the rhizosphere

Aims: Our understanding of the rhizosphere is limited by the lack of techniques for in situ live microscopy. Current techniques are either destructive or unsuitable for observing chemical changes within the pore space. To address this limitation, we have developed artificial substrates, termed smart soils, that enable the acquisition and 3D reconstruction of chemical sensors attached to soil particles. Methods: The transparency of smart soils was achieved using polymer particles with refractive index matching that of water. The surface of the particles was modified both to retain water and act as a local sensor to report on pore space pH via fluorescence emissions. Multispectral signals were acquired from the particles using a light sheet microscope, and machine learning algorithms predicted the changes and spatial distribution in pH at the surface of the smart soil particles. Results: The technique was able to predict pH live and in situ within ± 0.5 units of the true pH value. pH distribution could be reconstructed across a volume of several cubic centimetres around plant roots at 10 μm resolution. Using smart soils of different composition, we revealed how root exudation and pore structure create variability in chemical properties. Conclusion: Smart soils captured the pH gradients forming around a growing plant root. Future developments of the technology could include the fine tuning of soil physicochemical properties, the addition of chemical sensors and improved data processing. Hence, this technology could play a critical role in advancing our understanding of complex rhizosphere processes. © 2023, The Author(s).Funding: This work was funded by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant agreement No. 647857-SENSOILS). We also acknowledge the funding from the Spanish Ministry of Science and Innovation (MICINN) under de project MICROCROWD (PID2020-112950RR-I00). Researchers at the James Hutton Institute also receive financial support from the Rural & Environment Science & Analytical Services Division of the Scottish Government