Hydrogel-based transparent soils for root phenotyping in vivo

Abstract

Root phenotypes are increasingly explored as predictors of crop performance but are still challenging to characterize. Media that mimic field conditions (e.g., soil, sand) are opaque to most forms of radiation, while transparent media do not provide field-relevant growing conditions and phenotypes. We describe here a "transparent soil" formed by the spherification of hydrogels of biopolymers. It is specifically designed to support root growth in the presence of air, water, and nutrients, and allows the time-resolved phenotyping of roots in vivo by both photography and microscopy. The roots developed by soybean plants in this medium are significantly more similar to those developed in real soil than those developed in hydroponic conditions and do not show signs of hypoxia. Lastly, we show that the granular nature and tunable properties of these hydrogel beads can be leveraged to investigate the response of roots to gradients in water availability and soil stiffness. soil | transparent | hydrogels | plants | microbiome G rowing plants for research is constrained by an apparently necessary compromise. On one hand, media that are representative of field soil (e.g., soil, sand) are opaque to most forms of radiation (1) and offer limited control over heterogeneities that affect the development of roots (e.g., gradients in water availability, nutrient concentrations, mechanical properties, porosity). On the other hand, transparent media (e.g., hydroponics, aeroponics, gels) do not provide field-relevant phenotypes and growing conditions (2).Media that have air-filled, connected pores display several physiologically relevant characteristics of soil, such as aeration and physical interfaces (3). Unfortunately, these porous media are usually opaque to most electromagnetic radiation because each interface changes the direction of propagation of photons, due to refraction and reflection. The magnitude of these deflections increases with the difference between the refractive indices (a physical property of matter dependent on electronic density and susceptibility) of the medium and the material contained in the pores (4). Therefore, a porous medium can become transparent to light if it is fully saturated with a fluid whose refractive index matches that of the porous medium (5).Index matching of granular materials, including hydrogels, was used successfully to study hydrology, soil physics, and fluid dynamics in porous media (6, 7). Nonetheless, the use of this approach to study root development is subject to numerous complex constraints that have made this task notoriously challenging. The medium must be (i) produced simply and inexpensively in large quantities (hectoliters), (ii) nontoxic to plants, (iii) transparent enough in common nutrient solutions to allow for the phenotyping of a whole root system in vivo, and (iv) strong enough to not collapse under its own weight. Furthermore, it should provide water and nutrition to the growing plant and have a fully connected porosity to prevent the formation of air pockets. A rece...

Root Growth Adaptation to Climate Change in Crops

“…Roots are challenging to evaluate in the soil and this has been a major reason for the poor attention that they have been paid in breeding programs in the past. Numerous methods of phenotyping have been used, from laboratory-based methods including the use of soil-free media pots, rhizoboxes, hydroponics or semi-hydroponics media combined with high-throughput digital phenotyping or 3D imaging systems (Walter et al, 2015;Voss-Fels et al, 2018;Jia et al, 2019;Ma et al, 2019;Qiao et al, 2019) to field shovelomics (Trachsel et al, 2011). But still all these methods are generally expensive or/and time-consuming, so better and affordable tools to improve analysis of root traits are still needed.…”

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