3d images

Optical instrument to provide the clearest 3D images of the rhizosphere to date

An interdisciplinary team of researchers from the Georgia Institute of Technology has received a $2 million federal grant to create tools that will provide the clearest three-dimensional images yet of the chemical and biomolecular interactions between plants and the soil in which they grow. .

A few centimeters underground, the rhizosphere – the thin strip of soil that comprises the soil-root interface – has so far been difficult to visualize on site. If scientists can build instruments that capture clearer pictures in real time of the physical associations of root-attached microbes, as well as the chemical oxygen-carbon-nitrogen exchanges they mediate, it could help mitigate the effects of climate change. and lead to the development of more sustainable fuels and fertilizers.

“From a microbiological perspective, we listed the microbes present in the root zone and their abundance,” said Joel Kostka, a professor in the School of Biological Sciences and the School of Earth and Earth Sciences. atmosphere of Georgia Tech. “But there has been very little work to understand their dynamics in real ground conditions.”

Kostka, who also serves as an associate chair for research in biological sciences, joins Marcus Cicerone, professor in the School of Chemistry and Biochemistry and principal investigator for the new grant from the Office of Biological and Environmental Research at the U.S. Department of energy. The research team also includes Francisco Robles, assistant professor in the Wallace H. Coulter Department of Biomedical Engineering, and Lily Cheung, assistant professor in the School of Chemical and Biomolecular Engineering at the College of Engineering.

Together, the researchers plan to produce a new optical instrument that will provide 3D images of dynamic metabolic processes with chemical specificity, meaning it will be able to identify carbon sources (sugars, organic acids) exuded by roots. plants and the nitrogen-rich compounds supplied to the root by nitrogen-fixing microbes (diazotrophs). The instrument will be built with commercially available components and with simplicity in mind so that it can be easily operated by bioenergy research centers and Department of Energy (DOE) field sites.

A ‘hot spot for germs’ In 3D

A better understanding of the metabolic processes that occur in the rhizosphere will help the DOE develop a broader range of sustainable products like new types of biofertilizers and biofuels. The research will also help create practices for better crop management – ​​and help researchers use plants and soil as more efficient carbon sinks that sequester greenhouse gases from the atmosphere into the soil.

“The problem is that we don’t know much about free-living bacteria in the soil because we can’t get in there and look,” Cicerone said. “The DOE wanted someone to build an instrument that would allow them to image or gather information about metabolic processes, the interaction – the metabolic interactions between microbes and plants, in real time.”

Kostka adds that the rhizosphere is “a hot spot for microbes.”

“It’s often where the plant communicates with the outside world,” he explained. “Our goal is to develop an instrument that they (the DOE) can use to better understand these interactions between plants and microbes and how these can be modified, for example, to optimize crop production, agricultural production, biofuels and biomass production. And that’s the long-term goal for us.

How light is scattered, muffled and covered with earth

Cicerone says the visibility problem with the ground involves how photons – or particles of light – scatter once they hit the ground. He compares it to someone putting a red light on the back of their thumb.

“You turn your thumb, your thumb turns red, right? So the light passes, but most of it scatters. The unscattered light contains the spatial information, but it’s so weak that you can’t detect it with the naked eye and you lose spatial information. The same thing happens with floors. You get a lot of light scattering and you lose spatial information,” Cicerone said.

Cicerone and Robles would build instruments that focused light into the ground and were “exquisitely sensitive to the tiny amount of light that scatters only when it hits its target.” Assessing this light will help scientists learn even more about chemical processes in the rhizosphere.

The visibility improvements will be implemented in optical techniques with names such as coherent Raman scattering and optical coherence tomography, which are commonly used for noninvasive imaging of thin biological material, such as the retina of the eye – or the smallest of plant roots.

“We learn two things from the light coming out of the sample. The amount of light that comes out tells you about the refractive index of the material, and the change in frequency of the light tells you about the chemical makeup of the material,” Cicerone explained.

It is by imaging and then optimizing these microbe-plant interactions that the DOE aims to design more sustainable products and practices, based on the chemistry to be learned from the team’s new optical instruments.

“This is a three-year funded project, and we hope at the end of the three years to have an experimental system, where we can do something that no one else can do,” Cicerone added. “And that’s that we can follow the biochemistry under the ground, on the spot, in real time, to clearly see what’s going on there and find out what microbes are actually doing under natural conditions. At this point, we can start manipulating the biology, start doing the experiments that the DOE is primarily interested in. »