New transparent soil reveals the secret world of plant roots

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Plant biologists who study the rhizosphere — the narrow region of soil in which roots and microorganisms grow — have never really been able to take a peek at what goes on down there without having to disrupt the plants themselves. The solution, it now seems obvious, is to create transparent soil — and this is exactly what a team of researchers from the U.K. have done. The breakthrough will have implications to root biology, crop genetics, and soil microbiology.

Biologists have tried to use various imaging technologies in the past, such as non-optical scanning, x-ray microtomography, and MRI — but they're not very well suited for imaging biological activity, nor do they allow for the use of fluorescent markers. But the need to study the complex and hidden inner-workings of roots and microorganisms gave rise to a novel idea: Why not develop a translucent substrate suitable for plant growth?


To create their transparent soil, a research team led by Lionel Dupuy and Helen Downie used 350-to-1,600-micron-wide pellets of the synthetic and transparent polymer, Nafion. To heighten its transparency, they saturated it with a special water-based solution that refracted the light. The result: A dynamic, porous, and transparent soil that allowed for the unobstructed 3D imaging of living plants and soil-based microorganisms.

It's hoped that the insights gleaned from the artificial soil will help biologists improve crops, develop better fertilizers, and reveal new ways of preventing outbreaks of food poisoning.

For example, the researchers have already used the transparent soil to analyze how lethal E. coli bacteria interacts with lettuce roots. By using a genetically modified version of the bacteria that has a green fluorescent protein from jellyfish, they were able to see the E. coli interact with the lettuce — something that would have been completely impossible using conventional soil. The scientists now have a better understanding of how the bacteria enters into the food chain.

You can read the entire study at PLOS.

Images via Lionel Dupuy, Ken Loades, and Helen Downie.