Transparent Soil-Like Substances Open a Window On Soil Ecology

By using two different transparent soil substitutes, scientists have shown that soil bacteria rely on fungi to help them survive dry periods, according to a study led by Caltech postdoctoral scholar.

The findings of the study, published in eLife, indicate that soil-like substrates may enable researchers to observe the complex interactions of the myriad microscopic creatures that live in soil. This ability is crucial to help us better understand the role that soil and soil microbes play in healthy ecosystems.

Millions of microscopic organisms, such as fungi and bacteria, live in soil. They are essential for healthy ecosystems because they support the growth of plants and capture and store carbon from the atmosphere. But studying these processes in real soil can be challenging.

“To advance the study of soil processes, we used transparent soil substitutes that allowed us to use microscopes and other experimental techniques to see and measure the activity of soil bacteria and determine how this activity depends on the fungi,” said lead author Kriti Sharma, who completed the study as a doctoral student at the University of North Carolina at Chapel Hill and is now a postdoctoral scholar at Caltech in Pasadena.

In the experiments, Sharma and collaborators from Vienna successfully grew soil bacteria and fungi in two transparent soil substitutes. One was a synthetic substance called Nafion and the other was a naturally occurring crystal called cryolite. They also demonstrated that it was possible to observe living microbes in these substitutes using a microscope and to measure the organisms’ overall metabolic activity and uptake of carbon using a technique called Raman microspectroscopy.

Next, according to the eLife report, they used the soil substitutes to study what happens to bacteria when soil goes from being dried out to wet again. The experiments showed that while many soil bacteria die or become inactive when soil dries out, bacteria living close to dead fungi remain active and use the fungi as a source for carbon.

“In this way, fungi promote the activity of soil bacteria in changing environmental conditions,” Sharma said.

The transparent soil systems reported in the study will likely be used by many other researchers who study soil ecology, adds senior author Elizabeth Shank, associate professor of systems biology in the Department of Microbiology and Physiological Systems at the University of Massachusetts Medical School in Worcester, Massachusetts.

“For example, they could be used to explore how interactions between bacteria, fungi, and other microscopic creatures living in soil help support the growth of crops,” said Shank. “Or, to better understand how carbon is stored and released from soil, which may be critical to combating climate change. Overall, these transparent soil substitutes are powerful tools that will help us answer many outstanding questions in soil microbial ecology.”