Getting to the root of the mystery:

New research project could tell us how plants “talk” to microbes in soil


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    Credit: U.S Department of Energy, Ames Laboratory

    To better understand the rhizosphere, the U.S. Department of Energy’s Ames Laboratory is developing a model instrument to look at the biological interactions in the rhizosphere in real time, in the field-- a capability that doesn’t currently exist. The instrument will accomplish this through the use of aptamers, which are short strands of genetic material that can be customized to bind to a wide variety of specific target molecules. With the help of computer software, a 3D image will be created of the targeted biochemicals in the root zone.

Newswise — The field of botany is well over a thousand years old, and the practice of agriculture millennia older than that. Yet surprisingly, little is understood how plant roots interact with soil at a molecular level, a narrow zone around roots of intense microbial activity that scientists call the rhizosphere.

That zone of microbial activity could hold information valuable to understanding how plants stimulate microbes to transform nutrients and promote plant health, resist disease, and adapt to environmental changes and stress.

“It’s an area of science very comparable to the microbiome in the human gut. We are just beginning to learn that human microbiotica play a role not just in our nutrition, but in other areas, like our neurological health,” said Marit Nilsen-Hamilton, an Ames Laboratory scientist and professor in the Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology at Iowa State University. “In the same way with plants, we know that there are many complex processes and interactions going on in the rhizosphere, but we don’t have a clear picture of how they occur.”

To better understand the rhizosphere, Nilsen-Hamilton is leading a new research endeavor at the U.S. Department of Energy’s Ames Laboratory, to develop a model instrument that will enable scientists to look at the biological interactions in the rhizosphere in real time, in the field-- a capability that doesn’t currently exist.

The instrument will accomplish this through the use of aptamers, which are short strands of genetic material that  can be customized to bind to a wide variety of specific target molecules. The aptamers will function as monitors of specific molecules in the rhizosphere.

Sensors that contain aptamers placed in the soil around the root zone will track the molecules in the soil that reflect activity such as signaling between microbes and plants.  With the help of computer software, a 3D image will be created of the targeted biochemicals in the root zone, in addition to tracking changes over time. The instrument, called 4DMAPS (4D analysis of Molecules by APtamers in Soil), will first be developed and tested in a laboratory setting before being implemented in a field environment to investigate the interaction of corn with microbes in the soil by detecting molecules produced by the microbes and plants, such as those produced in response to fungal infection.

Because aptamers can be selected to track most biochemicals, Nilsen-Hamilton envisions the technology being applied in a variety of ways, including crop and environmental monitoring, and medical diagnosis and treatment.

“It could be used to monitor orchards for early signs of stress or disease, or in agricultural research to compare the performance of different types of crops,” she said. “We expect to be able to get a lot of useful biological information from this system.”

In addition to Nilsen-Hamilton, the research team includes Ludovico Cademartiri, Larry Halverson, George Kraus, Pranav Shrotriya, and Olga Zabotina, all contributing scientists at Ames Laboratory, and faculty at Iowa State University. The work is supported by the U.S. Department of Energy Office of Science, to further DOE goals for bioenergy and environmental research.

Ames Laboratory is a U.S. Department of Energy Office of Science national laboratory operated by Iowa State University. Ames Laboratory creates innovative materials, technologies and energy solutions. We use our expertise, unique capabilities and interdisciplinary collaborations to solve global problems.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

 

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