The Future, Unzipped

John Ralph PhD’82 talks with the easy, garrulous rhythms of his native New Zealand, and often seems amiably close to the edge of laughter.

So he was inclined toward amusement last year when he discovered that some portion of the Internet had misunderstood his latest research. Ralph—a CALS biochemist with joint appointments in biochemistry and biological systems engineering—had just unveiled a way to tweak the lignin that helps give plants their backbone. A kind of a natural plastic or binder, lignin gets in the way of some industrial processes, and Ralph’s team had cracked a complicated puzzle of genetics and chemistry to address the problem. They call it zip-lignin, because the modified lignin comes apart—roughly—like a zipper.

One writer at an influential publication called it “self-destructing” lignin. Not a bad turn of phrase—but not exactly accurate, either. For a geeky science story the news spread far, and by the time it had spread across the Internet, a random blogger could be found complaining about the dangers of walking through forests full of detonating trees.

Turning the misunderstanding into a teachable moment, Ralph went image surfing, and his standard KeyNote talk now contains a picture of a man puzzling over the shattered remains of a tree. “Oh noooo!” the caption reads. “I’ll be peacefully walking in a national park and these dang GM trees are going to be exploding all around me!”

That’s obviously a crazy scenario. But if the technology works as Ralph predicts, the potential changes to biofuels and paper production could rewrite the economics of these industries, and in the process lead to an entirely new natural chemical sector.

“When we talk to people in the biofuels industry, what we are hearing is that creating value from lignin could be game-changing,” says Timothy Donohue, a CALS professor of bacteriology and director of the UW–Madison-based Great Lakes Bioenergy Research Center, where Ralph has a lab. “It could be catalytic.”

After cellulose, lignin is the most abundant organic compound on the planet. Lignin surrounds and shapes our entire lives. Most of us have no idea—yet we are the constant beneficiaries of its strength and binding power.

When plants are growing, it’s the stiffening of the cell wall that creates their visible architecture. Carbohydrate polymers—primarily cellulose and hemicelluloses—and a small amount of protein make up a sort of scaffolding for the construction of plant cell walls. And lignin is the glue, surrounding and encasing this fibrous matrix with a durable and water-resistant polymer—almost like plastic. Some liken lignin to the resin in fiberglass.

Without lignin, the pine cannot soar into the sky, and the woody herb soon succumbs to rot. Found primarily in land plants, a form of lignin has been identified in seaweed, suggesting deep evolutionary origins as much as a billion years ago.

“Lignin is a funny thing,” says Ralph, who was first introduced to lignin chemistry as a young student during a holiday internship at New Zealand’s Forest Research Institute. “People who get into it for a little bit end up staying there the rest of their lives.”

The fascination is born, in part, from its unique chemistry. Enzymes, proteins that catalyze reactions, orchestrate the assembly of complex cell wall carbohydrates from building blocks like xylose and glucose. The types of enzymes present in cells therefore determine the composition of the wall.

Lignin is more enigmatic, says Ralph. Although its parts (called monomers) are assembled using enzymes, the polymerization of these parts into lignin does not require enzymes but instead relies on just the chemistry of the monomers and their radical coupling reactions. “It’s combinatorial, and so you make a polymer in which no two molecules are the same, perhaps anywhere in the whole plant,” says Ralph.

This flexible construction is at the heart of lignin’s toughness, but it’s also a major obstacle for the production of paper and biofuels. Both industries need the high-value carbohydrates, especially the cellulose fraction. And both have to peel away the lignin to get to the treasure inside. A combination of heat, pressure, and caustic soda is standard procedure for liberating cellulose to make paper; bleach removes the remaining lignin. In the biofuels industry, a heat and acid or alkaline treatment is often used to crack the lignin so that it is easier to produce the required simple sugars from cellulose. Leftover lignin is typically burned.

The economic cost of these treatments alone is significant, and lignin pretreatment is at the heart of many of the more egregious environmental costs of paper. On the biofuels side, lowering treatment costs to liberate carbohydrates from lignin could change the very economics of biofuels. In these large-scale, industrial processes, saving a percentage point or two is often worthwhile, but the Holy Grail is a quantum jump.

“Because it’s made this way”—Ralph jams his hands together, crazy-wise, fingers twisted together into a dramatic representation of lignin polymerization—“there is no chemistry or biology that takes it apart in an exquisite way,” he says. “We actually stepped back and thought: How would we like to design lignin? If we could introduce easily cleavable bonds into the backbone, we could break it like a hot knife through butter. How much can you actually mess with this chemistry before the tree falls down?”

Ralph’s team had their eureka moment more than 15 years ago, and have been trying to bring it to life ever since.

With a background in forage production and ruminant nutrition, John Grabber, an agronomist at the USDA–Agricultural Research Services’ Dairy Forage Research Center in Madison, got pulled into lignin chemistry through the barn door. On his family’s dairy farm he grew up with lignin stuck to his boots, though he never knew it. But during graduate school he became interested in how plants are digested by cows. Cell walls are potentially a great source of digestible carbohydrates—most plants contain anywhere from 30 to 90 percent of their mass in their cell walls—but it is entangled with lignin. “You quickly find out that lignin is the main barrier to feed digestion,” he says.

Grabber began working on a model system to understand plant lignification—for corn in particular—in 1989. After meeting at a conference, Grabber joined Ralph and plant physiologist Ronald Hatfield at the Dairy Forage Research Center back in 1992. There were many projects ongoing, but Grabber remained interested in trying to fully understand the structural characteristics of the lignin: how it’s made and how to modify it. In his model system they could make any kind of lignin they wanted to study, and see how the changes affected utilization.

Ralph and Hatfield advocated for the work, helping to find funding and offering their expertise. “If I had worked for somebody else I probably wouldn’t be doing this work,” says Grabber. “John and Ron gave me freedom and support to do it.”

Around the same time, Fachuang Lu joined Ralph’s lab seeking a Ph.D. His journey into lignin chemistry was not, at first, his idea. A native of mainland China, he’d enjoyed a successful undergraduate career in Beijing studying chemical engineering, then found himself assigned by the college to a master’s program in lignin chemistry. Lignin is an ingredient in the slurry of chemicals used in oil drilling, and that was his specialty. In 1989 Lu left Beijing for a teaching position at Guangxi University, but three years later he decided to continue his education. Though he’d never met Ralph, he was fascinated by the chemistry and applied to study in his lab.

As Ralph, Grabber, Hatfield and Lu continued to tinker with lignin chemistry, momentum began to build in the lab. Though lignin created a snowflake universe of different molecules, there were rules of assembly. A complex chemical pathway enabled lignin construction, with a mechanism that remained constant across different families of plants, but with many potential building blocks.

Ralph and his colleagues were the first to detail what was happening to lignin as the controlling genes of the biosynthetic pathway were turned on and off, a task ably completed by a slew of outstanding collaborators worldwide with expertise in biotechnological methods—but who lacked the diagnostic structural tools to determine what the plant was doing in response.

Ralph’s team quickly learned that lignification was somewhat flexible. “We figured that we could engineer lignin well beyond the previously held bounds,” says Ralph. As various pathways and chemical possibilities danced in their heads, it struck them: What if, during lignification, they could persuade the plant to slip in a few monomers that had easily broken chemical bonds? If they did it right, lignin would retain its structural value to the plant, but be easier to deal with chemically.

“In the course of our conversation we realized that if plants could do this, it could really revolutionize how readily you could make paper,” recalls Grabber. Says Ralph: “It’s almost impossible to tell which one of us actually verbalized it first—it is one of those great outcomes of the group dynamic.”

Lu’s particular genius was synthesizing the various complex chemicals needed, particularly a novel monomer-conjugate called coniferyl ferulate. It was the key to the zip-lignin—the teeth of the zipper. “He’s got to be one of the best in terms of making molecules,” says Grabber.

They were thrilled by such a revelation, but, in retrospect, they soon realized it was sort of an obvious idea—one suggested by the underlying chemistry and biochemistry of a pathway that was becoming increasingly well understood. Yet it was a discovery of huge potential value. They dropped into stealth mode and began to work on it. They finished important research and stuck it in drawers—signature research, the kind that, when finally published, would capture journal covers. And yet they sat on it, quietly chipping away for nearly a decade.

It helped that there was a flurry of controversy in the field—what Chemical & Engineering News called “the lignin war.” “Part of the reason we could sit on it was that, at the time, making these kinds of molecules was so far-fetched,” says Grabber. “Probably if we had talked about it, people would have laughed at us.”

But as the idea for zip-lignin grew in principle, it became stronger. Lu, Hatfield and colleague Jane Marita MS’97 PhD’01 found that balsa trees and a fiber crop known as kenaf produced very small amounts of coniferyl ferulate. But even as the idea seemed more and more feasible, Hatfield and Marita couldn’t isolate the gene needed to manufacture coniferyl ferulate because of its very low expression in these plants.

And they got stuck. “At the beginning we were thinking that this is just a fantastic idea, but we really didn’t have that much confidence,” says Lu. “Maybe John [Ralph] had more confidence than me.” So they just kept at it. “Every step you think, yes, we are closer, closer, closer.”

In 2008 Ralph moved his work from the Dairy Forage Research Center into UW labs, with research projects under the recently formed Great Lakes Bioenergy Research Center (GLBRC). The center, launched with a $125 million grant from the U.S. Department of Energy that has since been renewed, was just one manifestation of the money and intellectual heft infusing biofuels research—and for zip-lignin it was a lucky move.

During the center’s first full meeting, Curtis Wilkerson, a plant biologist at GLBRC partner Michigan State University, was sitting in the audience when Ralph took his turn at the podium.

Wilkerson is a cell wall specialist. Though lignin is a third of the wall’s carbon and is essential to the way plants conduct water, he confesses he’d never given it much thought. In a room full of cell wall specialists, Ralph would “likely be the only person talking about lignin,” he says. “It just split that way a long time ago. People like myself had very little exposure to what John was thinking.”

It was this kind of academic silo that a place like GLBRC was supposed to breach. Ralph talked about putting ester bonds into lignins and his team’s long search for the elusive enzyme. Wilkerson saw a solution. Due to recent technical advances, the price of determining all of the expressed enzymes in a plant had become more refined and much less expensive. He offered to use these recent developments to try to find the missing enzyme to enable zip-lignin.

From the previous work, Wilkerson knew essentially the size and shape of the puzzle piece he was looking for. He began, quite literally with Google, trolling through the scientific literature looking for a plant that made a lot of coniferyl ferulate. The Chinese medicinal “dong quai” or Chinese angelica (Angelica sinensis) soon emerged as a candidate. Its roots contained about 2 percent coniferyl ferulate.

The team used knowledge about the likely type of enzyme they were searching for and successfully identified the gene and its enzyme that could produce coniferyl ferulate. The whole search took less than six months.

Would you believe an essential tool for the genetic engineering of poplars is a hole punch? That’s the word from Shawn Mansfield, a molecular biochemist at the University of British Columbia, who took the zip-gene from the Angelica and made it work in poplar, a popular tree in the biomass and forest products industry.

Working from Wilkerson’s gene, the first job was figuring out how to tag the new protein so that it fluoresced during imaging. While not necessary to the function of the genetically modified plant, it essentially allows the scientists to check their work: see where the protein is, how much is there, and if it is behaving as a protein should.
Mansfield’s lab also had to find a way to turn the gene on at the right time and place. It could make all the coniferyl ferulate one wanted, but if it wasn’t made at the right time and tissue, there would be no zip-lignin.

After perfecting these finer points, the gene is inserted into a special bacterium—and then the hole punch finally comes into play. Disks punched from poplar leaves are mixed with bacteria that have been inoculated with a special chemical that stimulates the bacteria to share their DNA around. Then the leaf disks are put in a special growth medium. As many as 12 shoots might emerge off of a single disk, but the lab would select and nurture only one shoot from each disk.

In the end they had about 15 successful transgenic candidates that they grew in the greenhouse and then shipped off to Wilkerson and Ralph for further study. Final selection was made based on the amount of fluorescent yellow the trees gave off, and from a newly devised analytical method developed by Lu and Ralph that was particularly diagnostic for the incorporation of the zip monomer into the lignin polymer.

The team knew that genetically modified organisms are not popular or easily talked about—never mind the exploding trees. The idea of reworking a fundamental building block of the plant world will breed resistance.

Ralph argues that this is already part of nature’s vocabulary: they’ve found their building blocks within the plant kingdom, including mutants that do similar things. And now that they know what they are looking for, Steven Karlen, a member of Ralph’s group, is continuing to find more evidence that Mother Nature is doing it herself. “We managed to persuade plants to do this,” Ralph says. “Chances are that nature has already attempted it and you could actually get there by breeding.”

It’s no surprise that Mansfield, who created the final transgenic tree, argues that there is a role for this kind of technology. “We as scientists should be wise in advocating for the proper use of it,” he cautions. “I would never force it on anybody. I would never try to sway people to think that it is the end-all or be-all for everything.”
But given the growing human population and rising CO2 levels, something like zip-lignin has a definite use in reducing the carbon footprint by reducing processing energy and chemical loads. “That means there are less environmental pollutants that need to be cleaned up afterwards,” Mansfield says.

“Our ecological footprint can be much reduced using these kinds of transgenic trees,” he argues. “The caveat is that we need to be very smart about where and how we plant them.”

Not many things in the natural world can take apart lignin, but any homeowner with a deck knows that fungi are up to the task. A recent analysis of mushroom genomes suggests that fungi evolved this ability about 300 million years ago. This is about the end of the Carboniferous era, when earth’s coal production began to slow down. Coincidence? Perhaps not. Now that wood could rot, it probably slowed the burial of organic carbon via tree trunks and other lignin-rich plants.

Could the discovery of zip-lignin signal another transition, and hasten our move away from fossil fuels laid down in the Carboniferous?

Tim Donohue likes to think so. He likens biofuels now to the early oil industry, when oil was simply being turned into liquid fuel while the by-products were burned or dumped. It took a few decades for inventors to capitalize on this now valuable stream of raw materials to build the modern chemical industry.

“Lignin is about 25 to 30 percent of carbon in the plant. So if we’re going to catalyze an industry that makes clean energy and chemicals from plant biomass, figuring out what to do with the lignin is going to be key,” Donohue says.

People in the industry used to joke that you could do a lot of things with lignin except make money from it. But that may be changing. “The economics and profitability of the industry will be very different if lignin can be turned into valuable compounds,” says Donohue.

One of the early efforts to make use of lignin was in Rothschild, Wisconsin, at a company now known as Borregaard LignoTech. When processed properly, lignin has many uses, from the manufacture of vanilla flavor to additives for concrete. There is even a small amount of it in the battery of your car that allows it to keep recharging.

Jerry Gargulak is research manager at Borregaard LignoTech, and learned about zip-lignin recently in his capacity as a scientific advisor to the GLBRC. Despite its many uses, Gargulak and his colleagues dream about a time when lignin can replace carbon black in tires and be used to build carbon fibers and structural plastics.

Zip-lignin and the ideas behind it could bring this day closer. “It gives us a technology that might yield a more interesting lignin-derived starting material,” Gargulak says. “It could potentially lead to a lot of innovation downstream in lignin technology.” But he emphasizes, “There are a lot of i’s to be dotted and t’s to be crossed.”

This story is just beginning. Zip-lignin has a patent and has excited industrial interest that could be worth significant dollars. Ralph and his colleagues continue working to further refine the process, increasing the percentage of zippable bonds in poplar and also inserting the gene into more plants, such as corn and Brachypodium, both grasses.
And in the basement of the shiny new Wisconsin Energy Institute building, where the GLBRC is based, two massive new nuclear magnetic resonance (NMR) spectrometers work 24/7, providing a level of detail into lignin that Ralph has never had before.

“We spend a lot of time looking at these Rorschach test–like figures,” Ralph says of the information generated from the NMR. “The detail in them is unbelievable. These things have been revolutionizing what we do.”

Uganda: The Benefits of Biogas

Generating enthusiasm for a new kind of technology is key to its long-term success. Rebecca Larson, a CALS professor of biological systems engineering, has already accomplished that goal in Uganda, where students at an elementary school in Lweeza excitedly yell “Biogas! Biogas!” after learning about anaerobic digester systems.

Larson, a UW–Extension biowaste specialist and an expert in agricultural manure management, designs, installs and upgrades small-scale anaerobic digester (AD) systems in developing countries. Her projects are funded by the Wisconsin Energy Institute at UW–Madison and several other sources. Community education and outreach at schools and other installation sites are an important part of these efforts.

Children get excited by the “magic” in her work, she says. “It’s converting something with such a negative connotation as manure into something positive,” Larson notes. In an AD system, this magic is performed by bacteria that break down manure and other organic waste in the absence of oxygen.

The resulting biogas, a form of energy composed of methane and carbon dioxide, can be used directly for cooking, lighting, or heating a building, or it can fuel an engine generator to produce electricity.

Larson’s collaborators in Uganda include Sarah Stefanos and Aleia McCord, graduate students at the Nelson Institute for Environmental Studies who joined forces with fellow students at Makarere University in Kampala to start a company called Waste 2 Energy Ltd.
Along with another company, Green Heat Uganda, which has built a total of 42 digesters, Waste 2 Energy has helped install four AD systems since 2011.

“Most of these digesters are locally built underground dome systems at schools and orphanages,” Larson explains. Lweeza’s elementary school is a perfect example.

The AD systems use food waste, human waste from pit latrines and everything in between. The biogas generated by the digester is run through a pipeline to a kitchen stove where the children’s meals are prepared. Compared to traditional charcoal cooking, the AD systems greatly reduce the school’s greenhouse gas emissions.

Larson and her team are now focusing on enhancing the efficiency and environmental benefits of these systems. Their goals are to improve the digester’s management of human waste, reduce its water needs, increase the amount of energy it produces and generate cheap fertilizer to boost food crop yields.

“Our overall goal is to create a closed-loop and low-cost sustainability package that addresses multiple local user needs,” Larson says.

The beauty of the project is that all these needs can be met by simply adding two new components to the existing systems: heating elements and a solid-liquid separator.

To help visualize the impact of the fertilizer, Larson set up demonstration plots that compare crop yields with and without it. Down the road, a generator could be added to the system to provide electricity in a country where only 9 percent of the population currently has access.

As a next step, Larson hopes to replicate the project’s success in Bolivia. She is finalizing local design plans with Horacio Aguirre-Villegas, her postdoctoral fellow in biological systems engineering, and their collaborators at the Universidad Amazonica de Pando in Cobija.

Give: Hands-On Fieldwork

Before last summer, Vera Swanson’s only exposure to plant sciences had been through classes in introductory biology. That changed big-time when Swanson, a junior majoring in environmental sciences and Russian, signed on to intern at the CALS-based Arlington Agricultural Research Station as a crop scout.

Crop scouts are used in agricultural management to diagnose stress factors in a field—such elements as potentially negative soil and climate conditions, the presence of pests, and threatened crop performance—and determine which management practices are appropriate for the goals of a specific plot. As part of her training, Swanson spent copious hours learning to identify weeds by walking through the fields and the Weed Garden, which displays dozens of invasive plants accompanied by their names.

Swanson paired her internship, which was run through the Department of Agronomy, with an independent research project involving biofuel crops being tested at Arlington. For that work Swanson drew on her growing knowledge of weeds to test the effect of three biofuel crop systems—native prairie, switchgrass and continuous corn—on the soil’s weed seed bank, or the viable seeds present in the soil and its surface. The project involved working one-on-one with research scientists in Randy Jackson’s grassland ecology lab. Jackson is running the crop trials through his affiliation with the UW’s Great Lakes Bioenergy Research Center, housed in the Wisconsin Energy Institute.

The intense focus on plants got Swanson thinking a lot more about soil. “It is such a finite resource, yet so much of what we depend on comes from it—our food, clothing and the materials that we build with,” says Swanson.

It also got her more interested in food systems, to the point where she chose to make horticulture a disciplinary focus within her major and a possible new career direction. “I’d love to work for an organization where I would be able to complement my interests in agriculture, development and language within a global context,” she says.

Swanson’s path exemplifies the power of “beyond classroom” experiences to dramatically shape, and in many cases transform, a student’s education and career goals. These experiences—which include internships, research projects, study abroad, honors thesis stipends, field courses and more—are the hallmark of a CALS education.

“They’re a big part of what makes CALS CALS—and they offer our students a major advantage in both their personal and professional development,” says Sarah Pfatteicher, the college’s associate dean for academic affairs. “Our goal is to ensure that each student can participate in at least four of these important opportunities.”

To help support the CALS Student Experience Fund, visit:

Of Cows and Climate

ON A SUBZERO FEBRUARY day, Mark Powell stops his vehicle on the road a few miles outside Prairie du Sac. He’s been explaining that cows actually enjoy the polar weather—and as if to prove it, a frisky group in the barnyard across the road turns toward us and rushes the fence.

As a USDA soil scientist and CALS professor of soil science, Powell is focused on the ground beneath their hooves. A few years ago he led a survey of manure handling on Wisconsin dairy farms. He and his colleagues knew how much cows left behind—about 17 gallons a day—but had only educated guesses about the ultimate environmental impact of barnyard design. In open yards like this, says Powell, they found that 40 to 60 percent of the manure ends up uncollected. “It just stays there,” he says. In the decade since his survey, the manure challenge has only grown, both in Wisconsin and nationwide. Water quality has been the major concern, but air quality and climate change are gaining.

A few minutes later we turn into the 2,006-acre U.S. Dairy Forage Research Center farm, and the talking points all turn to plumbing. There’s an experimental field fitted to track how well nutrients from manure bond to the soil. Parallel to one barn are nine small yards with different surfaces, each monitored to measure gasses emitted and what washes out with the rainwater.

The manure pit is frozen over, but circumnavigating the complex—shared by CALS and the U.S. Department of Agriculture—we arrive at the southern terminus of the barns. Uncharacteristic ventilation ducts adorn the walls and roofline. Inside are four unique stalls that can contain up to four cows each. The manure trough is lined with trays so that each cow’s waste can be set aside for further experiments. When the cows return from the milking parlor, airtight curtains will drop, isolating each chamber.

Class Act: Energizing the Classroom

When biochemistry senior Hong-En Chen first got involved with a student organization called Energy Hub, she knew she could bring something special to the table.

As the daughter of a preschool teacher, she’d interacted a lot with young children throughout her own childhood and adolescence. While in high school she worked as a teacher and tutor in music, math and reading in both English and Mandarin at the Einstein School in Madison, a private preschool and after-school enrichment center for elementary school students.

Based on her experience, she saw an important niche for Energy Hub: The group could go out to local elementary schools and hold after-school classes about energy.

“When kids are young, they’re like sponges. They absorb a lot of information and are enthusiastic learners,” notes Chen. “When we introduced concepts about energy use, conservation and sustainability, the kids impressed us not only by handling complex material, but also by applying ideas to their everyday lives.”

As outreach director of Energy Hub, Chen got other club members on board to pilot their project, working with second- to fifth-grade students at four Madison elementary schools. Based on that experience, they applied for and received a Wisconsin Idea Fellowship grant to further develop their curriculum during the 2012–2013 school year. They created a 10-week program that is going strong this year.

Hands-on activities are key, says Chen, whether using an educational science toy like Snap Circuits to teach the concepts behind powering lights and fans, or having students divide into the fantasy cities of Greenville and Coaltown to talk about how they, as residents, would use energy from various sources to get through a day. “It was a fun way to get them thinking about the costs and benefits of renewable versus nonrenewable energy sources,” Chen says.

Chen’s thinking a lot about that topic herself. She is researching compounds for solar energy conversion in chemistry professor Song Jin’s lab. And she is considering graduate programs in materials chemistry with an eye toward working in renewable energy research.

Learn more about Energy Hub at

Wisconsin’s “Brown Gold” Rush

Earth’s petroleum stores are dwindling, but a Wisconsin project aims to produce energy from a resource that’s in little danger of running low: cow manure, or “brown gold.”

The University of Wisconsin–Madison and several state companies, funded by a $7 million grant from the USDA Biomass Research and Development Initiative (BRDI), have partnered to pilot the conversion of dairy farm manure into useful product streams—a project that is expected to have significant environmental and economic benefits.

The Accelerated Renewable Energy (ARE) project is in progress at the 5,000-cow Maple Leaf Dairy in Manitowoc County, where animal waste is separated into different streams, or fractions, of processed manure.

After small plant fibers in the manure are separated and anaerobically digested to biogas, liquids from the digestion process are used to fertilize crops, while solids can be converted into useful chemicals and bio-plastics. Larger plant fibers make great animal bedding and mulch, not to mention a starting material for ethanol fermentation.

Meanwhile, at the new Wisconsin Energy Institute at UW–Madison, project co-investigator Troy Runge, a CALS professor of biological systems engineering, is analyzing the ARE project’s separation techniques to improve their efficiency. “We are performing many of the same separations that occur on the farm, but in the controlled environment of
the lab to both measure and optimize the system,” says Runge.

Tom Cox, a project collaborator and a CALS professor of agricultural economics, sees great potential for the initiative. “This is a triple-win situation; we would like to make money by doing the right thing by the environment and society,” he says.

Aicardo Roa-Espinosa MS’85 PhD’89, president of partner SoilNet LLC and an adjunct faculty member in biological systems engineering, developed the manure separation technology behind the project. Roa-Espinosa and Runge will monitor the quality, quantity and composition of biogas produced and analyze processed manure streams to identify chemical constituents. Student researchers will conduct life cycle assessments to evaluate the project’s environmental impact.

The goal for the four-year grant, researchers say, is to improve these manure separation technologies until their sustainability benefits can be realized on a broader commercial scale.

Runge notes that the public-private, multidisciplinary project exemplifies what the university hopes to do with the Wisconsin Energy Institute. “It’s also an example of a project that’s important to Wisconsin,” he says.

Indeed, the project may help farmers manage manure with benefits for both the environment and human health. A 5,000-cow dairy farm like Maple Leaf produces approximately 25 tons of manure per day, which require millions of gallons of water to manage. Although some manure may be used as fertilizer, nutrient imbalances and runoff can create environmental problems. However, manure processed using SoilNet’s technology yields concentrated, homogenized fertilizer that can be applied with greater control over nutrient content.

In addition to its environmental benefits, the cellulosic—or non-food—plant biomass derived from dairy manure avoids the conflict of “food versus fuel.”

That’s a promising basis for exciting innovations at dairy farms. For ARE project leaders, farms are not only the heart of agriculture. They also have the potential to serve as foundations for cellulosic biorefineries that could prove key in supporting a local green economy and a sustainable energy system throughout the region.

Biofuel for Teens

As students in Craig Kohn’s class at Waterford Union High School can tell you, you don’t need a grant or Ph.D. to do scientific research. A question and some curiosity are all that’s needed—along with a sturdy pair of gloves.

Kohn BS’08, who earned degrees in biology and agricultural education at CALS, teaches a class called Biotechnology and Biofuels in which students hunt for bacteria that naturally secrete enzymes called cellulases. Cellulases are named for their ability to break down cellulose, the sugar polymer in plant cell walls that gives stems and leaves their structure.

“Cellulases are important for bioenergy because they are necessary to turn cellulose into a fermentable product that can be made into ethanol and other biofuels,” says Kohn.

To find those cellulase-producing bacteria, Kohn sends students out to collect samples from the compost heaps and animal pens behind their school in a quest known as “bioprospecting.”

Back in the classroom, students drop the samples into test tubes filled with media solution and a strip of filter paper. If cellulases are present, the cellulose-based paper will disintegrate as the enzymes do their work.

That process of discovery excites students. “You see this light in their eyes when they realize that they are participating in science directly, and that their work could lead to actual breakthroughs and results,” Kohn says.

Kohn developed the activity as a participant in “Research Experience for Teachers,” a program at the UW’s Great Lakes Bioenergy Research Center (GLBRC). For his project he shadowed Cameron Currie, a CALS professor of bacteriology and a GLBRC researcher who uses genomic and ecological approaches to study biomass-degrading microbes.

“Teachers are not only learning about current science—they are embedded in the lab,” says John Greenler, GLBRC’s director of education and outreach. “When teachers have that primary experience, they are in a better position to engage their students because they ‘get it.’”

Connor Williams, a high school senior who helped develop the bioprospecting lab with Kohn through his participation in the National FFA Organization (formerly Future Farmers of America), says his favorite element is the hands-on, independent work.

“I learned that answers to biofuel challenges literally can be found right in our backyards,” Williams says. “You just need to know where to look.”

“Red Barns” Go Green

Lofty red barns may be Wisconsin icons, but the real workhorse structure in agriculture today is the post-frame building. You can’t drive very far down a rural road without spotting one being used to house livestock, store and repair equipment, shelter hay or myriad other uses. Virtually every new structure on a modern farm gets built this way, and with good reason. Post-frame buildings are versatile, easy to assemble and affordable.

And now they’re becoming more sustainable, thanks to a “Green Frame” building system being developed by Dave Bohnhoff, a CALS professor of biological systems engineering.

Unlike traditional post-frame construction, Bohnhoff’s system isn’t based on preservative-treated wooden posts embedded into the ground. He uses non-treated wooden “I-posts” affixed to precast concrete piers. The I-posts are sandwiches of dimension lumber and laminated-strand lumber that are structurally and thermally more efficient than timber posts. Another sustainability feature relates to how the frame parts go together. The frame members that tie and brace the vertical posts and roof trusses have reinforced, deep notches at the ends that mate with adjoining pieces. This makes assembly easier, safer and more accurate. It also makes it easy to disassemble and reuse the components when a building outlives its usefulness as the farm enterprise grows and evolves.

Will all of those non-standard parts drive up the cost? Not at all, says Bohnhoff. The beams, connecting pieces and concrete piers can be fabricated on site using materials available in most lumberyards, tools found in any farm shop and basic construction skills.


The Inner Lives of Cows

What do biofuels look like on the Wisconsin landscape? Some might think of corn or switchgrass. But what about that herd of cows?

What you can’t see might fool you. Cows are walking natural biodigesters, says CALS bacteriology professor Garret Suen. Their rumens are filled with rich bacterial communities that break down the cellulose found in feed into nutrients usable by the animal.

“The cow is arguably one of the most efficient cellulose degraders around, and the main reason why is that we’ve domesticated them to be that way through selection,” Suen explains. “What I argue is that we didn’t just domesticate the cow, we domesticated their microbes.”

Efficiently breaking down cellulose into simpler usable materials—a key challenge in biofuel production—is a feat naturally performed primarily by microbes. “A cow couldn’t exist without its bacteria, because it has no way on its own to break down the plants that it eats,” he says.

Suen, a researcher with the Wisconsin Bioenergy Initiative, is exploring the workings of the ruminant system in the hope of harnessing its power for industrial applications. He’s focusing on three strains of bacteria in the rumen that use different strategies to degrade cellulose. Drawing upon his background in both computational biology and genomics, Suen is using next-generation sequencing to hone in on the individual genes, enzymes and other proteins used by each and how they work together.

“Understanding the different ways that nature has come up with to degrade recalcitrant plant material will be very useful,” he says.

To date, Suen’s research group has identified some sets of genes they believe are involved, including some interesting surprises that he isn’t quite ready to share. He recently received a five-year, $750,000 early career award from the U.S. Department of Energy to advance the project. Suen hopes the work could ultimately extend even beyond bioenergy.

“Understanding how the microbes are breaking down these plant biomasses doesn’t only impact biofuels. It also has implications for areas like improving digestibility of feed and nutrient yield for the cow—which could directly affect everything from milk production to feed costs to beef quality,” he says.

Sustainable by Design

THE CHILDREN’S SONG URGES HER TO FLY AWAY HOME, but the ladybug—or ladybeetle, as she’s properly called—is anything but a homebody. After feasting all summer on soybean aphids and other crop pests, the beetles take off from farm fields in search of snug overwintering spots, often winding up in people’s houses. Around Madison, this usually means a journey of five miles or more, says CALS entomology professor Claudio Gratton. But the insects can also fly much farther. In the Southwest, for example, they congregate on mountaintops. “You’ll come upon a bush just dripping with ladybeetles, and you know they probably had to travel 30 miles to get there,” says Tim Meehan, a research scientist working with Gratton who earned his doctorate in
New Mexico.

Those wandering ways got Gratton and Meehan wondering a few years back if the beetles’ lives were touched not just by the soybean fields where they fed, but by the wider world as well. They soon discovered that, indeed, “What the landscape looks like actually makes a big difference,” says Gratton. In experiments across the Midwest, ladybeetles devoured more aphids in fields nestled within a patchwork of woods and grassy pastures than in those surrounded by soybeans and corn as far as a bug’s eye could see.

Although the two still aren’t sure why this is, it led them to ponder another possibility that has big implications for the sustainability of our farmlands. If the chance variation that exists in some farming areas already gives ladybeetles a boost, what if farmlands were purposely designed for diversity? Would the insects dispatch even more aphids? Might they even become tiny tools of sustainability, allowing farmers to spray fewer chemicals?

It takes a lot of imagination to picture such a landscape today, with two-thirds of the Midwest’s cropland blanketed in corn and soybeans. But there is a force that could re-stitch the Corn Belt into a crazy quilt—the push toward ethanol and other types of bioenergy. True, the ethanol blended into gasoline today still comes exclusively from corn kernels. And few “dedicated” bioenergy crops, such as grasses, have been sown so far for making cellulosic ethanol from stalks and stems, or burning in power plants instead of coal.

But bioenergy crops will almost certainly grow widely one day. The goal of the U.S. Department of Energy (DOE) is to replace 30 percent of gasoline and other U.S. transportation fuels with biofuels by 2030. And that, CALS scientists say, offers a chance to reshape our farmlands in an unprecedented way, so they yield not only food and fuel, but also things like ladybeetles and the benefits they provide.

In scientific parlance those benefits are called “ecosystem services”—natural processes we rely on but don’t usually pay for, Meehan says. Pest control by ladybeetles is one service; pollination by native bees, water cleansing, soil formation and even aesthetic beauty are others. Today’s simplified agricultural landscapes excel at producing corn, cotton and other vital commodities in massive amounts, but these may come at the price of water quality, erosion, loss of bird and insect habitat and increased pesticide use, as another study by Meehan and Gratton recently found. The question now is whether switchgrass, willow and other biofuel crops could cut those costs by sowing some plant diversity back into the system.

“The focus now is land use, not just food or fuel or a new crop. How do we use land sustainably?” says Chris Kucharik, a CALS professor of agronomy and environmental studies. “It just so happens that fuel has ignited the debate over sustainable land use right now.”

At the same time, strong forces are working to maintain the status quo. Skyrocketing commodity prices and rising demand for ethanol have led many farmers to put as much land in corn as possible. This year, 92.3 million acres were planted, according to the U.S. Department of Agriculture, four million above last year’s total and the second highest amount since World War II.

Where Are We Now?

TIM DONOHUE HAS SPENT THE LAST FOUR YEARS BUILDING A PIPELINE—but not the kind that springs to mind when we think of fuel.

The professor of bacteriology heads the CALS-led Great Lakes Bioenergy Research Center (GLBRC), founded with $142 million from the U.S. Department of Energy and a groundbreaking charge—to create the next generation of biofuels by harnessing renewable energy from the nonfood plants that are so plentiful all around us: grasses, trees and crop residues.

“We need to create liquid transportation fuels that are more cost-effective, more sustainable and won’t compromise the Earth or our quality of life,” says Donohue. “We’re in the middle of developing ways to generate these new fuels that are essential for powering our daily lives.”

With Michigan State University (MSU) as UW–Madison’s major partner, Donohue has assembled a team that now includes more than 400 researchers and staff and an additional nine member institutions. The effort spans two countries, 11 states and more than 60 individual lab and field facilities.

That’s a lot of brainpower. But the magnitude of the effort is commensurate with the task at hand, Donohue notes.

“We need to be considering everything from roots in the ground to what’s coming out of the nozzle,” Donohue says. “Without such a holistic approach, we won’t be able to demonstrate that this technology is feasible or see the weak spots where we can make improvements.”

What GLBRC has built is a research pipeline, a process that considers all factors that go into developing and implementing cellulosic biofuels—from creating sustainable agricultural landscapes and building better bioenergy crops to innovations in plant biomass processing and converting plant sugars into fuels.

While the promise of creating sustainable plant-based fuels isn’t new, the level of public investment needed to tackle this challenge has only recently emerged. According to the International Energy Agency, the United States leads world spending on biofuels public research, development and demonstration projects, investing $189 million in 2010 alone.

“By relying on fossils fuels, we’re living on energy that arrived on Earth many millions of years ago,” says Steve Slater, GLBRC’s scientific programs manager. “In order to reach a sustainable energy economy, we need to learn to live on the energy that arrives from the sun today. There’s a lot of that solar energy held within plant biomass, if we can figure out how to sustainably convert it to liquid fuels.”

Four years into its five-year grant, GLBRC has made some significant breakthroughs along the research pipeline. Here are some major points of interest.

First Stop: PLANTS

At agricultural research stations in Wisconsin and Michigan, GLBRC researchers tend to tall stands of such biofuel crops as switchgrass and miscanthus, measuring above-ground traits like crop yield and digging down in the dirt to monitor soil microbes and water movement. Sophisticated instruments measure greenhouse gases such as carbon dioxide and nitrous oxide. Researchers count birds and insects to measure biodiversity and use satellite data to capture a watershed-level view of land use patterns.

It’s a lot of information, but each measurement plays a role in determining how these crop contenders would fare as large-scale bioenergy crops.

The leaves and stalks of these potential bioenergy plants are comprised of large quantities of cellulose, the most abundant organic compound on the planet. Cellulose is a polysaccharide, a long chain of tightly linked sugar subunits that must be broken down into simple sugars before they can be processed into biofuel. That alone is difficult—but to make the process even harder, much of a plant’s cellulose is locked within cell walls that form a tough, protective barrier. Breaking past the walls, using enzymes or chemicals to do so, is one of the biggest challenges in creating economically viable cellulosic biofuels.

Plant cell wall structures have evolved over time to fight off pests and disease. The more scientists understand about how the walls are created, the easier it will be to break them apart. DNA sequencing capacity provided by the Department of Energy (DOE) Joint Genome Institute allows plant breeders access to genetic and genomic data that provide clues about how those cell wall layers are built.

While determining the best genetic traits for bioenergy crops is a long-range goal, GLBRC plant researchers already have made important headway when it comes to tackling lignin, one of the toughest compounds that make up plant cell walls. Researchers hope to take it apart to get at the cellulose locked inside and convert small pieces of lignin into valuable co-products. CALS biochemistry professor John Ralph and his team have identified a gene that would allow easily breakable bonds to be incorporated into plant cell walls. They’re calling this new technology Zip-Lignin™ for its ability to break apart—or unzip—the lignin within. By getting lignin out of the way, biomass processing could be completed at lower temperatures. And lower temperatures mean lower overall costs.

And on another track, GLBRC researchers at MSU have located an enzyme that creates a plant oil with unique biodiesel-like properties. Now they’re working to encourage plants to produce more of that oil, which could be used directly as a “drop-in” or ready-to-use diesel replacement.

Beyond the Gas Tank


“One of the most attractive markets this year is a paraffin derivative for lipstick use made from bio-based materials,”
says Baye, a UW–Extension professor of business development who specializes in bioenergy consulting and executive

“The bio-based chemical market is appealing because you get a better return on a more modest amount of feedstock compared to fuels,” he says. “The markets are not as volatile as they are for liquid fuels, and we don’t need major infrastructure, such as pipelines, to move the stuff. We can do it by truck and train.”

Baye has been crunching numbers on bioenergy projects for 27 years, both in his current job and in several private sector positions, including a two-year stint leading an initiative to start up an ethanol plant. Since the mid-1990s he’s also been experimenting with growing biofuel crops—switchgrass, sorghum, aspen and mixed grass stands—on a 240-acre farm in Woodman.

Asked what he thinks Wisconsin will be doing with biomass in the future, he quickly ticks off a dozen projects that already are operating or are on the drawing boards. The tally includes electrical plants fueled by everything from old railroad ties to landfill waste to willow, paper mills that have branched into wood pellets and biodiesel, and municipalities making biogas and fertilizer
from wastewater.

Notably lower on his list: corn-based and cellulosic ethanol.

“We’ll continue to produce liquid fuels from biomass, including corn, as long as the margins are justifiable,” Baye says. “But we don’t have the long growing season they have down South and in the tropics. That’s where you have higher biomass growth rates and yields, and that’s where we’re likely to see most of the biomass-based liquid fuels produced.”

What he does expect to see are lots of multipurpose facilities, where firms supplement their core business with energy and other biomass-based products in order to diversify, cut costs, spur revenues and make use of industrial residues. He cites the paper industry as a prime example.

“A number of our paper plants are planning on bolting on technology platforms to allow them to produce products other than paper,” he says. “A pulp tree may still go to the paper plant, but be converted to something much different than paper.”

He points to a Wisconsin paper mill, Flambeau River Papers, and its planned sister facility, Flambeau River BioFuels, as a national leader. Flambeau River Papers is refining its residual, pulp liquor—a rich red-brown broth left over from the paper-making process—into such value-added products as xylitol, used in making sugar-free gum, and into a binder used for dust control on dirt roads. The paper mill is powered by a biomass-fueled boiler. Flambeau River Biofuels plans on producing biodiesel and industrial lubricants and waxes in a facility scheduled to begin construction in 2012.

This strategy isn’t limited to paper plants. Corn-based ethanol plants are also considering adding processes to improve performance and diversify. Some of the first cellulosic ethanol plants have taken this approach and are eyeing the chemical market too.

Baye also expects to see more biogas digesters—producing methane and generating power and heat—coupled with municipal waste treatment plants to deal with wastewater and industrial residuals laden with organic content from food processors and other manufacturers.

“Municipalities are under pressure to upgrade these plants, which means higher charges,” Baye says. “To minimize these upgrades, they will look to divert the organic material and get a little gift back in the form of biogas. And there are a number of opportunities for them to produce additional, high value products—especially fertilizers.” New regulations addressing phosphorus management will likely accelerate this trend.

Baye says that many such projects will require partnerships between municipalities, local industries and farmers, who will grow switchgrass, sorghum and other bioenergy crops as additional feedstock for the digesters.

And even if Wisconsin doesn’t lead the pack in ethanol production, Baye thinks the Badger State will benefit from any growth in the ethanol industry. The expertise acquired making paper, beer, silage and cheese transfers nicely to the bioenergy business, and it’s a marketable product in and of itself, he points out.

“In the future we probably will be buying cellulosic fuel from other regions, but we’ll be selling them chemicals and enzymes and vats and pumps, technology, legal services and know-how,” Baye says.