Three CALS faculty earn DOE grants to study bioenergy and bioproducts

Three CALS faculty members have earned two grants from the United States Department of Energy to fund research on plants and microbes for bioenergy and bioproducts. Researchers in the University of Wisconsin–Madison Department of Biochemistry and Great Lakes Bioenergy Research Center (GLBRC), led by Professors Brian Fox and John Ralph, will utilize a $2.1 million grant, while Thea Whitman of the Department of Soil Science was awarded $2.3 million.

Brian Fox

Research from Fox and Ralph aims to elucidate the properties of a potentially useful and understudied class of genes and enzymes in important bioenergy crops, such as poplar, sorghum, and switchgrass. Two kinds of enzymes — called acyl-CoA ligases and BAHD acyltransferases — together create a large variety of potentially useful molecules. In a breakthrough application of their methods, the biochemistry group found that very similar genes — predicted to have similar functions — acted very differently.

“Now, we hope to identify the role of a bunch of unknown genes and their corresponding enzymes that are in a class that appears to be important for many reasons,” Ralph explains. “We don’t know much about what they do but the few we have studied have been interesting and useful, so we are excited to explore the rest.”

The potential exists to engineer plants with modified capabilities that can help them produce useful compounds or make them more readily useable for biofuel production. However, without knowing anything about these classes of enzymes — similar to a mechanic not knowing anything about the parts of a car engine — it is difficult if not impossible to understand the breadth of possibilities ahead.

John Ralph

For example, their work in these and related enzymes has already given some exciting results. They’ve been able to create “zip lignin” — lignin being a compound that makes plants woody — to make it easier to convert plant material in precursors for biofuel production. They later found that the gene for zip lignin was already naturally present in poplar trees, the plant they studied, which simulated their interest in carrying out the current study.

Recently, they also found a way synthesize acetaminophen, the active ingredient in Tylenol, from a natural compound derived from plant material. While the application of this process is far from reality with more research needed, it opens up the possibility of a more natural way to make the compound, rather than relying on fossil fuels.

“We’ll hopefully ultimately have functions for all of these enzymes beyond biofuel production, which is of interest to us,” says Rebecca Smith, an assistant scientist in the Ralph Lab. “Once we know what they do we can start designing plants that are better for this or better for that. We’ll also have the structural information to generate good models for other plants and related enzymes in a library or toolkit for other researchers to use.”

Whitman’s project is titled “Dissection of Carbon and Nitrogen Cycles in Post-Fire Soil Environments using a Genome-Informed Experimental Community.” Her lab’s work is focused on how fires affect soil microbes and global biogeochemical cycles, such as those of carbon and nitrogen.

Thea Whitman

The grant will fund work that builds on their previous research, in collaboration with the University of California, Berkeley and the Joint Genome Institute, studying how microbes interact with pyrogenic carbon — which makes up the charcoal left after a forest fire.

They will continue to try to understand what kinds of microbes digest char and how, which microbes and other organisms become reestablished after a fire and why, and how carbon and nitrogen in char remain in and travel through the environment. They have an overall interest in how these aspects impact global stocks of carbon and nitrogen over space and time.

“Most people are aware these days that forest fires are increasing, whether you’re talking about fires in Northern Canada and other parts of the Arctic or in the Amazon very recently,” Whitman explains. “There remain questions about what net effect these fires have on the carbon and nitrogen stocks in soil, which are important from both a climate change perspective and the soils themselves.”

She adds that soils contain more than twice the amount of carbon than living biomass and the atmosphere combined, and the stock is very dynamic. While the input of carbon comes from plants, the majority of the output of carbon is controlled by microbes so the interactions are important to study. Researchers in the lab have engineered a variety of tools they utilize in their work, such as an isolated chamber they can grow plants in that will contain a heavier form of carbon, called an isotope. They can then trace the isotope through the environment after that customized biomass is made into charcoal using another device they call the “charcolator.”

“In this grant we will be able to introduce nitrogen isotopes into those tracing studies,” she says. “Ultimately we are interested in how microbes and the environment interact and how they affect global processes in the context of fire.”