Smart soils track the formation of pH gradients across the rhizosphere

Abstract

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.

Microcosm Fabrication Platform for Live Microscopy of Plant-Soil Systems

“…The water retention, enabled by the porous PDMS, was similar to sand 36 . This system may not be suitable to control water content in a natural soil (only wet conditions), but is adequate when using artificial soils such as those made of FEP 37 or Nafion™ 14 , which have similar water retention properties.…”

“…Most materials showed capability to provide high quality live images of the rhizosphere. Use of low cost, low refractive index polymers such as FEP produced lower quality data, but the recent methods for functionalising FEP 37 indicated potential for significant improvement of the technique.…”

“…The copyright holder for this preprint this version posted February 27, 2024. ; https://doi.org/10.1101/2024.02.23.581454 doi: bioRxiv preprint (only wet conditions), but is adequate when using artificial soils such as those made of FEP 37 or Nafion™ 14 , which have similar water retention properties.…”

Construction and characterisation of a structured, tuneable, and transparent 3D culture platform for soil bacteria

“…Current transparent soil techniques are based on a limited set of materials because of the combined requirement for low refractive index and transparency. Two materials have been tested in microbial studies, namely Nafion [15,16] and cryolite [17], but fluorinated ethylene propylene (FEP) [31] and hydrogels [32] have been tested in root studies and have potential for application in microbiology. Previous applications of transparent soil methods have been demonstrated in plant science [15,16,18,19] and interkingdom co-culture [17,20].…”

“…Recent developments showed FEP is another promising fluorinated polymer. It was used to combine light sheet imaging and optochemical sensors to image pH gradients induced by root exudation in unsaturated conditions [ 31 ]. However, FEP requires more advanced chemistry to modify its surface properties.…”