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Learning the Language of Cell Life

Ames Laboratory scientists use genetic markers to discover the rhizosphere.

by Ames Laboratory
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Ames Lab ScientistsMarit Nilsen-Hamilton, an Ames Laboratory scientist and professor in the Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology at Iowa State University, works with her research team to develop methods of non-destructive imaging of biological systems. From left: lab manager and technician Lee Bendickson; graduate research assistant Ivan Geraskin; Marit Nilsen-Hamilton (front), Ames Laboratory scientist George Kraus (back); and graduate research assistant Judhajeet Ray (foreground).Ames LaboratoryIt’s a science lesson so fundamental that we teach it to small children, planting bean seeds in Styrofoam cups: plants take nutrients from the soil to grow.

It is surprising, then, that the complex interchange between the microorganisms in soils and the cellular activities of plants’ root systems, what scientists call the rhizosphere, remains one of science’s great mysteries.

“We want to know how plants and microbes in the soil talk to each other,” 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. “We know they’re communicating with each other, but how? Multicellular communities are vastly more complex than we currently understand. How do we go about finding out?” 

Nilsen-Hamilton said that traditional scientific methodology, taking samples from the environment back to the lab for genetic analysis, gives only part of the total picture of this vital ecological system. 

“It can tell us the population of microbes, the various components of the rhizosphere, and then what the end products are. It’s basically telling us who’s there and how many, but who is doing what? How are they doing it? Do we even know where they’re doing it? We may think we know, but we really don’t, not for sure.” 

The impact of environmental changes on these systems is another question. Variations in temperature, atmosphere, and chemical composition of the soil force plant systems to adapt. Current science, Nilsen-Hamilton says, can only observe changes in the plant-soil system through analysis of the end-products.

“Right now the science is like a person who isn’t a mechanic looking at an operating machine. We can bash it with our fist and observe that it runs faster or slower; but unlike a mechanic, we really don’t understand what we did or why it changed.”

Nilsen-Hamilton, working in partnership with Ames Laboratory, Lawrence Berkeley National Laboratory, Ames Laboratory researcher George Kraus and Iowa State University’s Larry Halverson (Plant Pathology and Microbiology) is on the brink of creating a technology that would allow a clearer look at the entire rhizosphere system through the use of aptamers, short strands of genetic material that bind to a specific target molecule.

“It’s really a type of non-destructive imaging, extended to biological systems,” said Nilsen-Hamilton. “There is a little extra portion of genetic material that we place on the gene, and if we do it properly, it doesn’t affect how the gene functions. On the right gene, it will report on a response to a change in the cell’s environment such as a signal from another cell or more nutrients.  We’ll know when that gene is turned on.”

These “reporters,” called IMAGEtags (Intracellular MultiAptamer GEnetic Tags), are established into a particular species of microbe, or in a particular type of plant cell such as in a root hair, and will allow scientists to track cellular activity when they are in their normal environment.  The reporters allow live-cell imaging with fluorescence microscopy methods and are now being expanded to use with radioactive imaging to “see” through soil.

Nilsen-Hamilton said the IMAGEtags have been developed and proven to work in the lab. The next step is establishing them in soil microbes and plant material and in a controlled soil environment that replicates conditions found in nature.

“These are more defined conditions that are closer to what you would observe in the field than a cell in a dish,” said Nilsen-Hamilton, “and practical application could allow us to understand much more specifically, in real time, how these microbes and plant cells interact.”

The technology could be applied to a number of uses, including agricultural research, environmental monitoring, medical diagnosis and treatment, or anything involving a biological system.