Xylome’s quest to lower the cost of cellulosic ethanol

Monday, May 23rd, 2016

In their lab on a 20-acre prairie in Madison, Wisconsin, Xylome scientists are busy tinkering with the yeasts that live in the bellies of wood-boring beetles. A spin-off from the Great Lakes Bioenergy Research Center (GLBRC), Xylome is lowering the cost of making ethanol by creating new yeast strains that more efficiently convert cellulosic biomass to fuel.

While the early stages of biofuel manufacturing focused on fermenting corn grain to ethanol, corn is not the only available feedstock for making biofuel. Cellulosic biomass – i.e., wood, perennial grasses, and the non-food portion of plants – offers another, arguably more sustainable feedstock for fuels.


Tom Jeffries (L) and Tom Kelleher (R) conduct R&D and provide research services from Xylome’s labs at University Research Park, Madison, WI.

And yet developing an economically viable cellulosic biofuel pipeline remains a technically challenging endeavor. Compared to corn, the sugars in cellulosic biomass are much more difficult to access and convert to fuel. The sugar xylose, in particular, which accounts for up to 20 –30% of the dry weight of non-food plants, is notoriously difficult to ferment.

“In order to make ethanol out of cellulosic biomass economically,” says Tom Jeffries, Xylome founder and UW–Madison professor emeritus of microbiology and bacteriology, “the technical problem of how to ferment xylose needed to be solved. It’s a problem I’ve worked on for decades.”

It’s also a problem that got a lift in 2006, when Louisiana State University biologist Meredith Blackwell discovered xylose-fermenting yeasts in the guts of wood-boring beetles. Well-acquainted with Jeffries’ research, Blackwell sent him samples of a particularly interesting yeast species she named Spathaspora passalidarum, and it has been the focus of his work ever since.

“These yeasts inhabit the mid-gut,” says Jeffries, “where they consume the sugars the beetles chew on. They have a huge capacity for degrading not only xylose and other complex sugars, but also cellulose.”

Engineering S. passalidarum to even more effectively ferment xylose and other plant sugars is the work that defines Xylome.

Sequencing the S. passalidarum genome and deepening their understanding of the yeasts’ physiology and biochemistry has allowed Xylome scientists to increase the rate and efficiency of the yeast’s ability to ferment sugars, including xylose, to ethanol.

“We don’t introduce any extraneous genes in this process,” says Jeffries. “We take a native organism with a desirable capability, modify the organism’s genes in useful ways, and put them back into the cell. And it’s working! They’re hardy organisms – it’s not difficult to scale up the process.”


A microscopic image of one of Jeffries’ yeast strains.

Jeffries emphasizes that Xylome is not focused on establishing new biofuel facilities. Existing ethanol plants, he says, are already built just where they need to be – in the middle of fields, adjacent to railroad tracks, and on rivers.

“Ethanol plants have easy access to feedstocks, transport, and towns that can provide labor. They’ve obtained air and water permits and have community acceptance and support – all very important things!” Jeffries says. “And none of these things has to change when a plant shifts from processing grain to processing cellulosic feedstocks if you have the right fermentation capability.”

Xylome’s first-generation product, a cellulose- and xylose-fermenting yeast strain developed with GLBRC support, will debut at the International Fuel Ethanol Workshop & Expo in June 2016. And Jeffries is confident that Xylome’s product will go a long way in helping grain ethanol producers enter the market for second-generation, cellulosic fuels and chemicals.

GLBRC is one of three Department of Energy Bioenergy Research Centers created to make transformational breakthroughs and build the foundation of new cellulosic biofuels technology. For more information on GLBRC, visit www.glbrc.org or visit us on twitter @glbioenergy.

This story was originally published on the Great Lakes Bioenergy Research Center News site.

Panda poop study provides insights into microbiome, reproductive troubles

Wednesday, May 18th, 2016

A stomachache can put a real damper on your love life — especially if you’re a giant panda.

One minute it’s breeding season and you’re happily dining on fresh bamboo leaves, the next you’re left clutching your stomach while your gastrointestinal lining passes through your system. It exits your body as a thick, gooey, gelatinous mass.

Le Le stalk

Le Le, a male giant panda at the Memphis Zoo, feeds on a bamboo stalk. Researchers analyzed the percentage of feeding time Le Le and his female zoo mate, Ya Ya, spent feeding on bamboo leaves relative to stalks. Photo: Candace Williams

This is exactly what seems to happen to captive giant pandas, and the researchers behind a new study published in Frontiers in Microbiology are beginning to suspect it may play a role in their struggles to reproduce.

“We think they are sloughing off the internal mucous membrane of their gastrointestinal tract and because of this, they get really sick, which coincides with gestation,” says Garret Suen, a University of Wisconsin–Madison professor of bacteriology and co-author of the panda poop and feeding behavior study. “The pandas stop eating and they produce these painful, membranous fecal pellets.”

No one quite understands why these gelatinous masses, called mucoids, happen but Suen and his co-authors believe bamboo may be a factor. Evolutionarily speaking, giant pandas are not built to eat a sole diet of bamboo. As bears, their digestive systems are designed to break down meat and small amounts of plant material, yet in the wild and in captivity these bears are exclusively herbivorous. The study suggests this may lead to digestive troubles that could negatively affect panda pregnancy. It motivated the researchers to take a closer look at the gut bacteria involved.

“Gastrointestinal diseases are a major cause of mortality in wild and captive pandas but scientists understand very little about their digestive process,” says co-author Ashli Brown Johnson, state chemist and Mississippi State University associate professor of biochemistry, molecular biology, entomology and plant pathology. “By studying the microbial community in the panda’s gastrointestinal tract, we gain a better understanding of panda nutrition, which could help improve the health and reproduction of the endangered species.”


Garret Suen

Suen, an Alfred Toepfer Faculty Fellow, also has other motivations. A renaissance man of the microbiome, his lab studies the gut bacteria of everything from cows to sloths to pandas. His interests are both fundamental and applied. For example, understanding how animals and their microbes break down fibrous plant materials could aid in more efficient production of biofuels. It could also lend insights into human digestive diseases.

For the study, Suen, Brown Johnson and co-first authors Candace Williams and Kim Dill-McFarland enlisted help from the Memphis Zoo, which has collected feeding behavior on its two giant pandas — Le Le (male) and Ya Ya (female) — since 2003. Williams, who conducted the work as a Ph.D. student in Brown Johnson’s lab, had also performed her master’s degree work at the zoo, watching the pandas feed for 12 hours a day.

Using data recorded by trained zoo docents, the research team analyzed how much time Ya Ya and Le Le spent feeding on both bamboo stalks and leaves. They saw dramatic shifts in eating behavior: The pandas ate leaves less than one percent of the time in winter and spring, but by August — when mucoids became more prevalent — nearly 60 percent of their feeding time was spent eating leaves.

Every summer, in captivity and in the wild, pandas switch from eating primarily the woody stalks of bamboo to the leaves. It is at this transition — which also coincides with when most female pandas become pregnant — that their digestion appears to go awry. In July and August, pandas pass more mucoids, cease eating, become lethargic, and express their discomfort and pain.

“If it’s happening every three to four days, and the pandas stop eating for half to a whole day — when they normally spend their whole day eating — that’s a lot,” says Dill-McFarland, a Ph.D. student in Suen’s lab.

leaf and culm

A fecal sample from a giant panda, showing a mix of bamboo stalk and leaves. Pandas eat up to a third of their body weight in bamboo every day. Photo: Candace Williams

The researchers studied bowel movements the pandas made in February 2013, during the season when pandas don’t normally have mucosal poop, and between June 29 and Aug. 22, 2014, when they more frequently pass mucoids. During this time, zookeepers collected the mucoids as well as the regular feces the bears produced immediately prior to and immediately after these events.

The team studied five normal fecal samples from Ya Ya and one mucoid, and 13 regular bowel movements from Le Le and five mucoids. The samples arrived from the zoo like “chicken breasts wrapped in foil,” says Dill-McFarland.

Williams traveled to Madison to learn from Suen and Dill-McFarland how to analyze the microbial composition of panda poop. Regular panda poop resembles shredded bamboo stalks and was a challenge for the researchers to process. The mucoids were gooey, smelled “ghastly” (says Williams) and presented their own challenges.

The team found the panda poop had unusually low bacterial diversity relative to other herbivores, though the mix of bacteria changed day to day. The diversity dropped even lower right before mucoids, but then spiked in the mucoids themselves, which contained a different population of microbes than regular poop. In particular, they were made up of bacteria typically found in the gut lining.

They also found bacteria in the mucoids associated with dysfunctional digestion in humans, called Actinobacteria.

“What we think might be happening is that their diet is causing a strong internal reaction, leading to an inflammatory response,” says Suen. “Pandas are basically shedding their gastrointestinal lining to allow for the replacement of those microbes. It’s kind of like resetting the microbiome.”

While researchers can’t be certain why pandas experience this resetting, it is clear their diet is rough on the animals. At 220 to 275 pounds, pandas eat up to a third of their body weight in bamboo every day. It passes quickly through their digestive systems, which does not give the microbes in their guts much time to break things down. This is entirely different from other animals adapted to consuming plant matter, like cows, whose rumen microbes take up to 24 hours digesting the complex carbohydrates found in plants.

“I’m very interested in animals that eat way more than should be necessary to maintain their body size, and on the flip side, in animals that eat way less than should be required to maintain their body size,” says Suen.


tubes of feces from badgers, porcupines, lemurs and more sit on top of a lab freezer. Photo: Kelly Tyrrell, UW-Madison

The study does not provide solutions to prevent the gastrointestinal distress pandas experience, which Williams says is very hard to watch. Whether pandas feed on stalks or leaves appears related to chemical changes in the bamboo leaves themselves, a strategy some plants use to prevent herbivores from munching on them. And meat is out of the question.

“It’s gotten to the point where if you try to feed them meat, they get violently ill,” says Suen.

But the study does give scientists a place to start.

“Until recently, the gut microbiome hasn’t really played a role in the management of animals,” says Williams. “Having a balanced gut is important, and it’s also important that we know these things, especially about such unique animals. I strive to let people know how important the gut microbiome really is and the impact it has on reproduction, health and even immune function.”

That Ya Ya produced just a single mucoid is one limitation of the analysis, as is her unusual breeding cycle. However, pandas are incredibly difficult to study, the researchers say, and data of this kind are rare.

Additional researchers from Mississippi State University and the Memphis Zoological Society contributed to the study, which was funded by the United States Forest Service’s International Programs, the Memphis Zoological Society, the United States Department of Agriculture’s National Institute of Food and Agriculture, the Mississippi Agricultural and Forestry Experiment Station, and the Leo Seal Family Foundation.

This story was originally published on the UW-Madison News site.

UW expert at White House summit

Thursday, May 12th, 2016

On Friday, May 13, the White House Office of Science and Technology Policy will host an event on microbiomes – communities of microorganisms that live on and in people, plants, soil, oceans and the atmosphere. Microbiomes maintain healthy function of these ecosystems, influencing diverse features of the planet – human health, climate change and food security.

During the event, the administration will announce steps to advance the understanding of microbiome behavior and enable protection and restoration of healthy microbiome function, including by investigating fundamental principles that govern microbiomes across diverse ecosystems, and developing new tools to study microbiomes.

Lending expertise to the summit will be UW-Madison bacteriology Professor Timothy Donohue. Donohue directs the Department of Energy-supported Great Lakes Bioenergy Research Center and is an expert on biofuels and bio-based renewable energy technologies. Donohue can talk about microbiome research in general and, more specifically, how it might inform strategies for devising alternative fuel technologies. He can be reached at (608) 770-1283.

For Theo Loo, an unintimidated, humble approach to solving global problems

Tuesday, May 10th, 2016

mt-st-helensBig problems don’t intimidate UW-Madison senior Theo Loo.

And big ideas, it seems, come naturally.

One of eight undergraduate Wisconsin Idea Fellows at the Morgridge Center for Public Service this year, Loo is wrapping up the latest stage in his multi-year community-based study on water quality and access in rural South Africa.

And when he’s not on the ground in South Africa, you can find him back in Madison hard at work developing a potentially revolutionary approach to HIV diagnostic testing —one that would cost perhaps just 1% of current tests.

Loo, humble in sharing credit at every step, says his persistence comes from his passion for the work.

“I truly enjoy research,” Loo says. “It would definitely be a chore to go into lab or write grants and papers if I did not enjoy my workplace and research subject.”

Loo credits Global Health Institute Director Dr. Jonathan Patz’s Health Impact Assessment of Global Environmental Change course for changing his perspective on research back in 2013.

When Loo took the class, his assessment group paired with Dr. Michael Bell, director of the Center for Integrated Agricultural Systems, studying waterborne disease and land use in the eastern rural South Africa village of KuManzimdaka.

south africa

Sunrise on the rural eastern cape of South Africa

But when the class ended, Loo didn’t feel like his work was done.

“There were definitely long-term opportunities that transcended the class,” Loo said. “It kind of seemed like a shame that we had put a whole semester into doing this project, and I knew we hadn’t really produced a solution to the problem.”

Loo’s friend and 2014-15 Wisconsin Idea Fellow Kayla Sippl suggested he should apply for the fellowship. He did, partnering with Dr. Bell as his faculty mentor and South Africa-based Indwe Trust NPC as his community partner. His waterborne disease community-based research project was accepted as one of six 2015-16 Wisconsin Idea Fellowship projects.

But Loo knew to be successful, his project needed strong community input.

Recognizing what you don’t know

Valerie Stull, a PhD student in the Nelson Institute and a teaching assistant for Dr. Patz’s health impact assessment course, says Loo’s humble approach to community-based research has been critical to the project.

“One of the weaknesses I see in many undergraduates is the inability to recognize what they don’t know,” said Stull. “Theo recognized what he didn’t know right away, and he took special care to consult the appropriate people before his research trip.”

And when Loo landed in South Africa last summer, he took special care to talk with everyone. Literally.

“I actually went to every single household,” said Loo. “I went to every single child, mother and father and asked them what they thought their primary problem was in the village.”

KuManzimdaka’s residents face health issues directly tied to decades of apartheid in South Africa. Loo says the community was pushed into the foothills of a rocky mountain range that’s not conducive to livestock management or grazing or farming. And their water sources are springs contaminated by animal waste that are often kilometers away.

Some people walk up to six hours to collect water.

rocky hillside

A contaminated spring at the bottom of a rocky hillside

In addition to community dialogues, Loo performed water quality tests (confirming that the water was, in fact, badly contaminated) and conducted extensive mapping that helped identify infrastructure and terrain. The data and experiences he gathered told him the village needed a serious long-term solution. But Loo said it didn’t feel right to abandon the village with just a data set and a few distant solutions.

“Yeah, it would be hard to go,” said Loo. “I feel so morally conflicted and wrong if I went to the community and said, ‘You have this problem. You have this water issue problem. We’re going to give this data to the South African government and just kind of leave.’”

So with his partners in South Africa, Loo is proposing a series of “water plazas” that will help collect and store rain water within the community for the near term. A crowdfunding campaign has been established for the project.

“We’re hoping that can mitigate the situation until they have a more permanent solution,” said Loo. “I think I have a big responsibility in that. I think I have to help them out somehow until the longer-term issue gets resolved.”

A novel mechanism

“The goal for all of us should be to live a life of consequence. And he’s making that happen,” said Dr. Bell. Theo Loo, in fact, is making that happen a couple times over.

Two years ago, Loo and his friend Nico set off on a road trip from Madison for Colorado. “We were stuck in the car together for 14 hours. We needed to make it productive.”

By the time they reached the Rockies, the pair had developed a rough idea to revolutionize HIV diagnostic testing. “We just kind of played in back and forth until we had something tangible.”

When they returned to Madison, the pair approached Dr. David Beebe and Dr. Scott Berry at the Wisconsin Institutes for Medical Research, who funded the idea with seed money.

Here’s the issue: Patients with HIV need regular testing to determine the amount of the virus in their blood. A sudden increase in virus loads can indicate that the patient needs a change in treatment. But according to Loo, only 25 percent of patients living in low-resource settings have access to the test, which usually cost $24-44 per test. On top of that, the test requires complex equipment that can cost hundreds of thousands of dollars, involves intensive training and requires steady electricity.

The new simpler test costs just one dollar.

“It’s just as good as the other ones,” said Loo. “And it’s also really rapid. So fast, cheap, reliable and accurate.”

So how does it work?

“The chemicals you use for HIV diagnostic testing are really expensive,” Loo said. “We’re cutting down the re-agents and the materials used by 95 percent. So it’s nano-scale.”


A homemade incubator Theo Loo used for his research in South Africa

“It’s certainly exciting that no one is looking at the approaches that we’re looking at.”

A cheaper test, along with a cheaper and simplified quantification device in development, could very likely mean better HIV treatment for potentially millions around the world. And that’s exactly what Loo has in mind.

“It’s a novel mechanism. So we’re going to try to patent that and try to bring this product widespread throughout the world.”

In April, Loo traveled to Berkeley, Cal., to share his work at the Clinton Global Initiative -University—an annual summit showcasing top research and global solutions from university students. Loo said the event inspired him to keep pushing further.

“The main takeaway for me was not a business card, funding, or tidbit of knowledge, but the urge to do more,” said Loo of the event. “It inspired me to further my research and apply my skills to improve global health.”

The very best sense of the Wisconsin Idea

Loo is heading back to northern California for a longer stay in the fall—he’ll be attending graduate school at the University of California-Berkeley where he plans to continue his work. In fact, he wants to combine his water quality work with the HIV diagnostic research.

“I didn’t want to just be there for a few weeks, leave and never see them again,” said Loo of his time in South Africa. “I wanted to make it into a long-term project.”

Loo knows it’s ambitious, but he hopes his water project can establish a replicable blueprint for water quality and access solutions across all of rural South Africa—covering nearly 20 million people.

Theo Loo’s unintimidated, humble persistence to fight some of the world’s most pressing challenges is both inspiring and motivating.

“He just has such a passion for really doing something good,” said Dr. Bell. “Really the very best sense of the Wisconsin idea.”

This story was originally published on the Morgridge Center News site.

Microbiomes new research frontier – Audio

Friday, March 4th, 2016

Microbiomes new research frontier

Garret Suen, Assistant Professor
Department of Bacteriology
UW-Madison College of Agricultural and Life Sciences
(608) 890-3971

3:03 – Total Time
0:14 – What is a microbiome
0:30 – Microbiomes large and small
0:41 – Life driven by microbiomes
1:10 – Cow rumen a microbiome
1:50 – Powerful new technology
2:29 – Will touch medicine and agriculture
2:55 – Lead out


 Sevie Kenyon: The new frontier of microbiomes. We are visiting today with Garret Suen, department of Bacteriology, University of Wisconsin-Madison in the College of Agricultural and Life Sciences and I’m Sevie Kenyon. Garret, start out by defining for us, what is a microbiome?

Garret Suen: A microbiome is the collection of all microbes that lives within a given environment. So what we are talking about, are all the bacteria, all the archaea, all the fungi, and all of the viruses that live within any type of community. Continue reading

Tim Donohue, the power of microbes and the pull of Rockaway Beach

Monday, February 1st, 2016

Tim Donohue, director of the Great Lakes Bioenergy Research Center (GLBRC) and UW-Madison professor of bacteriology, says microbiology is enjoying a renaissance period: “Innovation in biology and microbiology can help provide food, health, and energy for a growing population while also ensuring that future generations have access to resources they need to thrive on the planet. That prospect really excites me.”

Long before Tim Donohue became a bacteriology professor and the director of the Great Lakes Bioenergy Research Center (GLBRC), he was a teenage beach cleaner and would-be biologist growing up on the boardwalk of New York City’s Rockaway Beach.

“I was fascinated by the change in the seasons, the tides, the weather, the wildlife,” Donohue says of those early years. “Exposure to the ocean really led me to biology.”

Rockaway, the largest urban beach in the U.S., fed Donohue’s interest in science but it also gave him the cash he needed for college. As a young man, Donohue held two summer jobs, performing routine vehicle maintenance for the National Park Service during the day and emptying Rockaway’s trashcans as the sun set every night.

“I was the first child in our family to go to college,” Donohue says. “My mother had a sixth grade education, my father had an eighth grade education. I think there was probably an implicit expectation that I would go to college, but the idea of me becoming a scientist, getting a Ph.D., that was not really on the table.”

As a college student at the Polytechnic Institute of Brooklyn in the early 1970s, Donohue  met Professor Ron Melnick, who introduced him to the world of microbes. The most ancient form of life on earth, microbes are microscopic, single-cell organisms such as bacteria, fungi, and viruses. Donohue’s love of all things biology had found a tiny new focus.

“I was just fascinated by the power of microbes,” Donohue says, “and by their global impact on our everyday lives. They shaped this planet’s history, they’re central to many of the foods we eat, and they have a huge impact – sometimes positive, sometimes negative – on our bodies and agriculture.”

Melnick also encouraged Donohue to begin working in his lab or, as Donohue puts it, “to drive the car instead of just reading the driver’s manual.” Donohue definitely drove that car, heading to the Pennsylvania State University to pursue a doctorate in microbiology and then on to the University of Illinois at Urbana-Champaign for a post-doctoral research fellowship.

Now a professor of bacteriology at the University of Wisconsin–Madison, Donohue likes to describe his research as “unlocking the secrets” of microbes.

“Microbes have been doing interesting chemistry on this planet for billions of years,” Donohue says. “We can learn a lot from studying how they do what they do.”

Individual bacteria use different strategies to obtain the energy and nutrients they need to live. Some microbes harvest sun light, others have a sweet tooth and prefer to eat sugars. Some digest aromatics, while still others grow by using energy from splitting hydrogen.

“We knew about many of these different processes when I was a student”, Donohue says, “but now, with genomics tools such as DNA sequencing, we can see the actual blueprints of these processes.”

Possessing these exact blueprints gives scientists the information they need to design new pathways that coax bacteria to perform new and desirable tasks.

“In our GLBRC projects, we’re trying to re-task native pathways and engineer next-generation microbial factories that can manufacture valuable fuels and chemicals from renewable wastes.”

While biofuel production is one area of research that will continue to gain from advances in microbiology, the field of microbiology is exceptionally wide-ranging, and enjoying what Donohue calls a “renaissance period.”

Donohue was recently among a group of leading scientists who published a call for a new, government-led “Unified Microbiome Initiative” in the scientific journals Science andNature. A more coordinated research effort, the authors argue, would go a long way toward harnessing the power of microbes to benefit agriculture and energy production and help address issues such as climate change and disease.

“We’re really at an inflection point,” Donohue says. “Innovation in biology and microbiology can help provide food, health, and energy for a growing population while also ensuring that future generations have access to resources they need to thrive on the planet. That prospect really excites me.”

Donohue, who has published in collaboration with other researchers for much of his career, is a firm believer in coordinated, cross-disciplinary research. As director of the GLBRC, he oversees a team representing a wide array of disciplines and specialties collaborating to overcome a major energy challenge: developing a robust and environmentally sustainable pipeline for biofuels.

“It’s been eye-opening for me to see how GLBRC’s team approach has allowed us to make advances much faster than I ever imagined,” Donohue says. “I never thought we would’ve accumulated the body of knowledge, produced the number of papers, and generated the amount of intellectual property that we have.”

In early 2015, GLBRC reported the filing of its 100th patent application. And to date, the Center has published approximately 850 papers, many of which represent collaborations with researchers from over 32 U.S. states and 24 countries.

Tim Donohue, son of New York City’s so-called Irish Riviera, now occupies an office with a view of the west end of UW–Madison’s campus and is candid about drawing inspiration from the Wisconsin Idea, or the notion that the university should improve people’s lives well beyond the classroom.

“GLBRC really is a proud contributor to the Wisconsin Idea,” Donohue says. “We are doing relevant research that will benefit the state, the region, and the country. It’s been an honor to be a part of this work.”

The GLBRC is one of three Department of Energy Bioenergy Research Centers created to make transformational breakthroughs and build the foundation of new cellulosic biofuels technology. For more information on the GLBRC, visit www.glbrc.org or visit us on twitter @glbioenergy.

This story was originally published on the Great Lakes Bioenergy Research Center news page.

Researchers collaborate to break down lignin and advance biofuels

Thursday, January 14th, 2016

To tackle what many consider the next frontier in biofuels research, the Great Lakes Bioenergy Research Center (GLBRC) recently joined forces with the Joint BioEnergy Institute (JBEI) in Emeryville, California. The focus of their collaboration? Lignin, a glue-like compound in the cell wall of most living plants that gives them their sturdiness.

While lignin accounts for up to one third of plant carbon, it’s also the most difficult part to break down and remains a formidable obstacle to accessing the valuable sugars contained within biomass. As a result, the biofuels and paper industries mostly treat it as a waste product, isolating it to be burned or discarded.

GLBRC lignin Kate Helmich

Kate Helmich analyzes bacterial enzymes called LigF and LigE that break particular chemical bonds within larger lignin molecules.

But GLBRC and JBEI researchers hope to change all that by bringing their collective expertise to the challenge of unraveling lignin’s strong and unique molecular bonds. With two new studies already complete, the payoff for their effort could be significant.

“If we can convert lignin from an undesirable byproduct into a starting material for advanced biofuels and other lucrative chemicals,” says Tim Donohue, GLBRC director and UW–Madison professor of bacteriology, “we would dramatically change the economics of tomorrow’s biorefineries.”

The researchers began by studying bacterial enzymes that cleave specific chemical bonds inside larger lignin molecules with the idea of creating a single new enzyme to break down lignin. That turned out to be a difficult task, however, because lignin molecules are similar to snowflakes: they have a multitude of spatial configurations, even within a single plant, and each of them requires a different approach to deconstruction.

“Making a single enzyme would be like trying to make a glove that’s designed for your left hand fit on your right hand,” explains Kate Helmich, co-first author of one of the studies and a recent PhD graduate of UW–Madison’s biochemistry department. “Our two hands are different configurations of the same fingers, and lignin is like a chain of many different hands. Degrading that entire chain would require an enzyme, or glove, that can attach to both the left and the right hands within it.”

Nature has instead evolved multiple, highly specialized bacterial enzymes that work in concert to break down lignin, each of them cleaving different sets of chemical bonds in the complex molecule.

Though a single lignin-cracking “master hybrid enzyme” remains elusive, the study informs future enzyme engineering efforts and sets the stage for more GLBRC and JBEI collaborations to convert lignin and other parts of plant biomass into biofuels and valuable chemicals.

GLBRC’s Helmich and Daniel Gall share first authorship, ​with JBEI’s Jose Henrique Pereira, on a paper recently published in the Journal of Biological Chemistry; and former GLBRC researcher and Rice University professor George Phillips, Jr. is senior author. In a sister study led by JBEI (currently slated for publication), the team reports new insights into bacterial enzymes that could someday help produce aromatic compounds of great interest to the chemical industry from lignin.

“It is exciting to see that our collaboration has resulted in the simultaneous publication of these two important papers,” Donohue says. “Collaboration is at the center of everything we do at GLBRC. We look forward to doing more of this mutually beneficial work with JBEI and other academic and industrial partners to advance the growing biofuels industry.”

GLBRC is one of three Department of Energy-funded Bioenergy Research Centers created to make transformational breakthroughs that will form the foundation of new cellulosic biofuels technology. For more information on the GLBRC, visit www.glbrc.org.

This story was originally published on the Great Lakes Bioenergy Research Center website.

Scientists: Harnessing microbes could help solve hunger, health, chemical and energy problems

Thursday, October 29th, 2015

While scientists learn more with each passing study about the way the invisible lives of fungi, bacteria, viruses and other microscopic organisms intersect with much larger plants and animals as well as the planet, Tim Donohue and a group of prominent scientists want to make sure researchers don’t miss the giant forest for the tiny trees.

Donohue, a UW–Madison bacteriology professor and director of the Great Lakes Bioenergy Research Center, joined 17 other scientists from around the world and representing a wide range of disciplines on Oct. 28 to lay out a case for an organized approach to harnessing the power of microbes to tackle many of the world’s most pressing problems.

Tim Donohue, professor of bacteriology

Tim Donohue

Led by Jeff F. Miller, a microbiology professor at the University of California, Los Angeles, in the journal Science, and microbiologist Nicole Dubilier of Germany’s Max Planck Institute for Marine Microbiology, in Nature, the authors proposed a Unified Microbiome Initiative to supply key knowledge and techniques to address sustainable agriculture, chemical and energy production, climate change, disease and more.

Discoveries ancient and modern illustrate the importance of microbes.

The geological record provides evidence of how ancestors of today’s microbes helped shape our planet. Microbes provide the oxygen we breathe, break down contaminants in water, help us digest and absorb nutrients in our food, and pass nitrogen in soil to hungry plants.

Yeast leavens bread and ferments beer, but also has a hand in the production of insulin, vaccines and industrial chemicals. Viruses may help guide normal development in animals, are a source of gene exchange in the oceans, and have stepped up as powerful tools for the study of genetics and delivery of gene therapies.

But much of what researchers have learned about the specific workings of the ubiquitous little “bugs” remains walled up within each microbe or group of microbes’ home range — or the particular branch of science practiced by the experts, according to Donohue.

“A variety of people in the academic community, the private sector and the federal government really feel it’s time to take the analysis of microbial communities to the next level,” he says. “That means moving beyond using genome sequences to obtain a census of which microbes are where, and tackling the next big challenge: understanding what communities of microbes are doing in different environments.”

A Unified Microbiome Initiative could help collect and process enormous amounts of information about dozens or hundreds or thousands of types of microbes that are born, eat, excrete, fight, die and evolve together — all the while making a fundamental difference in the environment they inhabit.

“What we need is an influx of people from other fields to work with the biochemists and microbiologists and engineers who have typically studied microbes in isolation,” Donohue says.

If scientists could accurately model communities of microbes, and anticipate how changes at the microscopic level make for changes visible on the human scale, they can anticipate problems and use microbes to create next-generationsolutions to grand societal problems.

“That has enormous potential for the health of the planet and the health of people. It could make personalized medicine work. It could create new energy sources and be the catalyst for next-generation bio-based manufacturing. It could grow food and provide clean water,” Donohue says. “Twenty years from now we may look back at this as a watershed time where we began to take information on microbes and use them as predictors of human health and influencers of planetary activities on a new scale.”

That would require organization and support for research that develops tools for exploring microbial communities and put those tools in the hands of multidisciplinary teams of scientists and engineers, according to the researchers writing in Nature and Science.

Donohue sees enthusiasm from U.S. governmental agencies and major private research philanthropic organizations for a collective push like the BRAIN Initiative, launched in 2013 by the White House’s Office of Science and Technology Policy (OSTP) to advance neuroscience. The initiative incorporates hundreds of millions of dollars in research supported by federal agencies, the pharmaceutical and medical imaging industries, and nonprofits like the Kavli Foundation.

OSTP and the Kavli Foundation have separately organized recent meetings where scientists fleshed out a vision of a Unified Microbiome Initiative.

“It’s important that this be an international effort,” Donohue says. “This is a problem the United States has the brain power and the resources to be a leader in. But to do it right, it is critical that we take advantage of the expertise that exists around the globe. Because these are problems — medicine, energy, food — we face collectively.”

UW–Madison — where researchers are investigating the roles microbes play in lifelong health, plant productivity, wastewater treatment, manufacturing and more — is uniquely positioned to play a role in a concerted effort to broaden the way science studies and makes use of microbes.

“We have expertise in every arena that needs to be pulled in to contribute, beginning with a world-class cadre of microbiologists and a spirit of collaboration,” Donohue says. “Our medical school, veterinary school, strong engineering, agricultural experts, leaders in oceanography — if we can find a way here to connect teams of these people with researchers in analytics and computation, we can be a model for the country and the world.”

This story was originally published on the UW News site.

Mycologist says our close relatives break the bounds of biology

Monday, October 26th, 2015

The mushroom nicknamed “death cap” made headlines this summer when it poisoned Syrian refugees fleeing through Eastern Europe.

But it was cooperation, not toxicity, that attracted Anne Pringle to Amanita phalloides. The fungus consumes carbon compounds released by tree roots, says the UW-Madison associate professor of botany and bacteriology, and in return helps the roots absorb soil nutrients. “I was interested in the evolution of cooperation,” she says, “and fungi and plants are models for understanding how symbiotic species interact — how the relationship is policed and maintained.”


The European Amanita phalloides (“death cap”) mushroom. Photo: Archenzo/Creative Commons. Banner photo: The hallucinogenic toadstool Amanita muscaria is also invading new terrain. Photo courtesy of Rytas Vilgalys.

Long before the Syrian refugees were poisoned, Pringle says, immigrants in California were dying as the death cap expanded its range along the West Coast. “A. phalloides poisoning is a really unpleasant way to go,” she says. “There’s intestinal distress, diarrhea. Then you feel fine during a ‘honeymoon’ that lasts several hours or more. Death can come through liver and kidney failure.”

In large swaths of California, she says, “the mushrooms are so abundant, it’s hard to believe they’re simply a neutral addition to the landscape.”

Fungi are essential recyclers of material and members of ecosystems, but they are “a cryptic part of biodiversity, largely hidden in the soil,” Pringle says. “We don’t have a fungicide that is species specific, and if you drenched its habitat with fungicide, would that be effective and safe for the environment?”

Fungi as a group are poorly known, says Pringle, who was an associate professor of organismic and evolutionary biology at Harvard University before coming to Wisconsin. “The fungi are basically a jungle of species. There are an estimated one to 10 million species, and we have names for 100,000, which suggests how little we know. You can go outside and pick up some soil, put it in a gene sequencer, and you will see a heck of a lot of species that do not match anything seen before.”

Pringle’s studies of spore dispersal show that fungi actually have some mobility. “Typically, people think fungi just release spores passively to the wind or water,” she says, “but it seems that they have evolved a mechanism to make sure the spores are released when they are most likely to spread.”

Pringle, along with Damon Smith and Mehdi Kabbage, two UW-Madison assistant professors of plant pathology, is studying the spring-like mechanism that parasitic soybean fungi use to catapult their spores into the wind. Such a mechanism, she says, “challenges the idea of fungi as passive entities.”


Anne Pringle

Pringle says fungi are puzzling. “If there is a rule in biology, I can think about how it does not apply to fungi. They challenge our preconceptions of how biology works.”

The overall oddness of fungi appears in the genes. In almost all organisms, every cell contains identical genes — it is a difference in gene activation that distinguishes a blood cell from a nerve cell. “But in fungi, one part looks very different genetically from another,” Pringle says, “so the entity you call an individual from a physical perspective encompasses many different genetic individuals. What is going on?”

Cooperation, not competition, is the archetypal relationship between fungi and many of their hosts, especially plants, Pringle says. “How you think about biology is shaped by the organisms you work with. If you think about fungi, you start with symbiosis.”

The goal of her ecological studies, she says, “is to slowly chip away at this overwhelming amount of not-knowledge. How does the pattern of fungal biodiversity vary across regions, and across the planet? How are species being moved? What does extinction look like in the fungal kingdom?”

Many people are surprised to find that the genomes of fungi and people are so closely related, Pringle observes. “If biology is to be true, we have to build rules that work for the whole of life. Maybe there are no general rules, and if that’s true, that’s also interesting. Understanding these issues is a critical part of our job, and it gets me up every day. If we are going to search for life on other planets, we need to think about how the entire spectrum of life works.”

This story was originally published on the UW-Madison News site.

Ancestors of land plants were wired to make the leap to shore

Tuesday, October 6th, 2015
liverworts, moss, fern

Liverwort plants, pictured here with moss and a fern, are an ancient lineage of land plant. Fossils suggest they may have been some of the first plants to colonize land 450 million years ago. Photo: Jean-Michel Ane lab, UW-Madison.

When the algal ancestor of modern land plants made the transition from aquatic environments to an inhospitable shore 450 million years ago, it changed the world by dramatically altering climate and setting the stage for the vast array of terrestrial life.

The genetic and developmental innovations plants used to make the leap to land have been enduring secrets of nature. Now, an international team of researchers, writing in the Proceedings of the National Academy of Sciences (PNAS), reveals that the aquatic algae from which terrestrial plant life first arose were genetically pre-adapted to form the symbiotic relationships with microorganisms that most land plants need to acquire nutrients from the soil.

The finding is important because it begins to flesh out the story of how the first land plants evolved from freshwater algae, formed critical symbiotic partnerships with microorganisms like fungi and bacteria, and made the world’s land masses habitable. What’s more, it could help with the development of biofuels. Understanding the genetic pathways involved could allow agronomists to unlock similar genes that are likely conserved in plants such as cereals and green algae, which are promising biofuel stock but require substantial amounts of chemical fertilizer.

“We were expecting that these mechanisms arose with land plants,” explains Jean-Michel Ane, a University of Wisconsin-Madison professor of bacteriology and agronomy and the senior author of the PNAS report. “The surprise was finding in algae the mechanisms we know allow plants to interact with symbiotic fungi.”

The discovery shows that the algae knew how to interact with beneficial microbes while it was still in the water, observes Pierre-Marc Delaux, who conducted the research as a postdoctoral fellow at UW-Madison and is now at the John Innes Centre in the U.K. “Without the development of this pre-adapted capability in algae, the Earth would be a very different place today,” says Delaux.

Jean-Michel Ane

Jean-Michel Ane

Many plant species depend on symbiotic relationships with microorganisms to thrive. The most famous are legumes and their beneficial association with nitrogen-fixing bacteria. Other plant species depend on relationships with fungi to chemically convert minerals in soil to forms that benefit the plant, notes Ane.

The efficient acquisition of mineral nutrients, says Ane, was likely one of the primary challenges for the earliest land plants.

“The association between plants, algae and fungi probably played a really important role in the ability of plants to colonize land,” he says. “In fact, many of us think early plants were able to colonize lands because they evolved the ability to associate with beneficial fungi.”

The genes required to encourage symbiosis between plants and microbes likely arose in a common ancestor of green algae and land plants, says Ane.

Prior to the new study, little was know about the associations between algae and fungi. The genetic pathways plants use to form a symbiosis with fungi were known in land plants called liverworts and hornworts, ancient lineages sister to all other land plant lineages. Liverworts thrive in damp environments worldwide and the oldest known liverwort fossils provide the earliest evidence of plants colonizing land.

“We had found these mechanisms in liverworts, but not algae previously,” explains Ane.

And while microorganisms had been found before in association with algae, they were believed to be pathogens, not symbionts. “Nobody had studied associations in these freshwater algae. We think some of these associations may be beneficial.”

Genetic features in plants, animals and microbes tend to be preserved and repurposed through evolutionary history. Discovering these pathways allowing associations with beneficial microbes in green algae and in cereals, which now require significant amounts of chemical fertilizer, could enable the engineering in plants of more efficient nutrient acquisition — significantly reducing the need for chemical fertilizers for food and bioenergy production.

The study was supported by grants from the National Science Foundation, UW-Madison and the Bill & Melinda Gates Foundation.

This story was originally published on the UW-Madison News site.