Carl Bernacchi helping raise the bar for agriculture climate research at Illinois

Photo courtesy of RIPE

When Carl Bernacchi was completing his Ph.D. at the University of Illinois some 20 years ago, Illinois was globally referred to as a “photosynthesis powerhouse.” Today, thanks to Bernacchi and other world-class researchers on Illinois-centric research teams, like the Agroecosystem Sustainability Center (ASC), that agriculture profile has expanded.

“Over the last 10 years, Illinois is starting to accelerate its global profile with regards to ecosystem-scale processes, from mechanism to remote sensing to satellites,” Bernacchi said.

He and contemporary colleague fellow ASC scientist Lisa Ainsworth have been instrumental in building that reputation as internationally recognized research plant physiologists at the USDA Agricultural Research Service (ARS) while also leading research teams in the Departments of Crop Sciences and Plant Biology.

Bernacchi cites strategic hires such as (ASC Director and Blue Waters professor) Kaiyu Guan, Wendy Yang, and D.K. Lee (both ASC scientists) and the collaborative community at Illinois as reasons that reputation has grown exponentially in the last decade.

“I have always seen myself as wearing two different hats that are relatively equal,” Bernacchi said. “One is as a government researcher focusing on government sciences, but also a fully integrated member of an academic environment, where the pillars of strength are collaboration and the full flow of ideas from the spectrum of undergraduate students to administrative staff.”

Bernacchi, who earned bachelor’s and master’s degrees from Bradley University, began his career as a research scientist at the Illinois State Water Survey, an entity that was moved from a governmental organization to a university center and renamed the Prairie Research Institute. 

In 2009, Bernacchi moved to the USDA Photosynthesis Research Unit, a position aligned with his passion of studying how crop interactions with the environment, from the enzyme to the ecosystem scale, affects climate change.

“I am trying to understand how the underlying mechanisms come together to translate into a responsive ecosystem at the canopy or global scale,” Bernacchi explained. “I define myself as an environmental plant physiologist, and that gives me the freedom to maneuver within a very wide space. Over the years, as a result, I have developed a diverse research group.”

Several decades earlier, a group of University of Illinois faculty, understanding the value of collaboration, decided to create the USDA unit and integrate it into campus as a sort of Venn Diagram intersecting university and government priorities. Bernacchi points out that similar USDA centers near colleges and universities don’t often integrate as well as this one does.

“We see ourselves as equal parts USDA and university,” Bernacchi noted. “I think it would be shortsighted to not integrate fully into the community of this campus. As a government scientist, I have the ability to respond quickly to challenges. The academic environment enables me to build collaborations in multiple disciplines to become a member of a much larger community that’s trying to tackle scientific questions well beyond the limits of what our specific units are.”

Photo courtesy of RIPE

Bernacchi’s contributions to the scientific community over the past 15-plus years are numerous. For instance, he was instrumental in developing the Spidercam system, the largest phenotyping system on the planet. It allows researchers to make several measurements on hundreds of thousand plants multiple times per day under different conditions and produces several terabytes of data every 24 hours.

He also built a large-scale experiment that enables researchers to alter the temperature of plants grown under field conditions — the first of its kind and certainly the most versatile in large-scale agricultural systems. The experiment can dial in a heat wave or season-long warming and look at how the crops respond in different levels ranging from the enzymes to the canopy.

With these tools, Bernacchi is helping farmers understand how CO2 not only affects the environment, but also yield.

“There is the notion that elevated CO2 decreases plant water use and increases productivity; however once you layer elevated temperature on top of that, the story gets a little more muddled,” Bernacchi explains. “On its own, elevated CO2 appears to be beneficial for yield. However, when you consider you can’t increase CO2 without elevating temperature, and temperature has an adverse effect on yield, you understand that they offset each other.”

His experiments have revealed that plants typically can rebound from heat waves early in a growing cycle, but if they come later in the growing season, yields take a hit.

“This data sets the ground truth for modeling, remote sensing, and a wide range of different measurements that occur on multiple different scales,” Bernacchi said. “So if you want to model something, you need to have the measurements to know whether the model works.”

That is one of the reasons that Bernacchi’s work is so important to the modelers like Guan and Bin Peng, within ASC.

In 2021, Bernacchi became a founding member of ASC. Under the leadership of Guan, the Center has developed the synergy to respond to current and future environmental challenges related to agriculture, both with regard to the scale of measurements and expertise.

For instance, the Center was instrumental in developing the SMARTFARM project, which uses farms in Champaign County as a test bed for the Midwest Bioenergy Crop Landscape (MRC) Lab to monitor emissions in those fields and make them publicly available. The data could someday be used to develop financial rewards for farmers across the country who practice sustainable farm management.

“One of the biggest limitations that ecosystem science faces is that so much more data is generated from remote sensing and modeling than is being measured directly,” Bernacchi said. “SMARTFARM brings together experts in different scales of measurement, whether it is spatial scales or temporal scales, and compares the results with the models. It is one of the ways that Illinois is now a world leader in crop ecosystem atmosphere interactions. We delve into everything from the mechanisms in the soil that Wendy Yang is doing to the agronomy that DK is doing to ecosystem and canopy scale fluxes that I am doing to the remote sensing and the modeling that Kaiyu and others are doing.”

Three years after its founding, ASC is ready to take flight, with projects like SMARTFARM as its launching pad.

“What SMARTFARM has helped us do is build the machine,” he said. “Now that the machine is running and is well oiled, it doesn’t take much to keep that machine going forward. There are so many ways to leverage this machine, and in 10 years it isn’t hard to imagine a 10-fold increase in ARPA investment in what we are doing here. That kind of investment doesn’t even account for all of the other users of this data that are beyond the boundaries of ASC or beyond the University of Illinois or even the United States.”

One of the tenets of the work is that most of the results are publicly available through Ameriflux, a network of PI-managed sites funded by the U.S. Department of Energy. It measures ecosystem CO2, water, and energy fluxes in North, Central and South America. One of the major anticipated outcomes of Ameriflux is to standardize data collection methods and data analysis. Those methods have so far gathered data in different ways and used different algorithms to tell the statistical story.

Bernacchi pointed out that even as a researcher using USDA ARS funds, he doesn’t have an obligation to participate in Ameriflux or share his team’s results, but he and others within ASC have the greater good in mind. While most Ameriflux contributors have one or two eddy covariance towers (which measure the concentration of gasses and turbulence in the air), Bernacchi’s team has about a dozen such towers that have produced 60-70 site years of data. Those towers take about 10 measurements per second, every second of the day.

“When you start to look at multiple towers in multiple fields with different management practices or different crops, you can start to characterize how changing the landscape alters how the ecosystems transfer carbon, water, energy, and greenhouse gasses with the atmosphere.”

ASC has taken this idea and run with it. Last year, for instance, ASC brought together scientists to strategize about developing a uniform tool to measure nitrous oxide (N2O) — a gas not getting as much attention as CO2 but a major player in agriculture’s role in climate change. The result is a tool called N2Onet, a standardized tool to measure these gasses.

While ASC has facilitated common projects and synergy, each participant has carved his/her own niche. For Bernacchi, that has been measuring temperature differentiation. Historically, if you wanted to know how enzymes change with regards to temperature, it would be done in a test tube. Early in his career, Bernacchi helped change that narrow approach.

Having an interest in photosynthesis and how it responds to parameters, he used genetically modified plants to fine-tune measurements and understand how enzymes respond to changes in temperature in the leaf itself. This gives scientists in vivo abilities instead of just in vitro and helps them understand how most canopy ecosystems respond to temperature. His measurements combined with remote sensing and modeling are helping tell the complete story.

“For someone who does the kind of work that Kaiyu does, having immediate access to ecosystem-scale flux data is useful (instead of having to wait until quality assurance and quality control data is processed nearly a year later),” Bernacchi indicated. “On the other hand, there is always something that is going to create a gap in data. Modeling helps fill in that gap. Combined, you can start to look at what is going on with annual cycles.”

Bernacchi’s work continues to have a major influence on the future. He believes that with temperatures rising in states like Arizona, Florida, and California — which produce over 90 percent of fresh fruits — the Midwest needs to carve out a small portion of its farms to grow food that humans eat, such as tomatoes and kale, in addition to corn and soybeans. To that end, his lab is ramping up efforts in the field of agrivoltaics, which combines agriculture with solar panels.

Whatever future discoveries Bernacchi’s lab will make in the next 20 years, he will benefit from his relationship with his colleagues at ASC.

“From my perspective, having a formalized center where people come together to achieve a common goal, each carrying a very specific charge, has huge benefits,” he said. “It formalizes and streamlines opportunities for collaboration. Under Kaiyu’s leadership, ASC has created a framework of collaboration. We have always collaborated, but now we are doing collaboration with a capital ‘C.’”

Photo courtesy University of Illinois College of ACES

Perhaps at first, it was a case of being in the right place at the right time for Lisa Ainsworth, but in the past 20-plus years, she he has left an indelible mark on the advancement of crop resilience to climate change.

In 2001, USDA Scientist Don Ort along with Steve Long and Evan DeLucia, professors in the Department of Plant Biology, built the Soybean Free Air Concentration Enrichment (SoyFACE) Center in Savoy, Ill., to demonstrate the effects of climate change on crops. Ainsworth, then a Ph.D. student in the Long lab, conducted some of the first experiments at SoyFACE.

Today Ainsworth is in her third decade as a federal scientist under the USDA Agricultural Research Service (ARS). She heads the USDA ARS Global Change & Photosynthesis Unit at SoyFACE and continues to work with the trio of founders, scientists from the University of Illinois and other institutions from around the world, and more recently the team of researchers affiliated with the Agroecosystem Sustainability Center (ASC).

“I think there is tremendous benefit in having long-term funding for mission-driven research in a location that is developing cutting-edge practices,” Ainsworth said. “We have access to all of the equipment, the talent of the university, as well our mission through ARS. I actually think it can be the best of both worlds.”

AT SoyFACE, researchers grow crops with altered climatic conditions, which reflect predicted future changes to our climate (Courtesy SoyFACE)

Ainsworth indicates that more than half of the USDA ARS researchers are on university campuses, which has proven mutually beneficial as an epicenter for research.

“This university is especially good at promoting, encouraging and supporting team science,” Ainsworth said. “There have been a number of these experiments around the world, but none have lasted for as long as the experiment at SoyFACE. It’s just one example of two institutions working together to do more than they could do individually.”

As a Ph.D. student, Ainswoth not only studied photosynthesis and its response to rising CO2 concentrations at SoyFACE, but also did the same with oak trees at an open-top chamber experiment at Cape Canaveral, Fla., and conducted face experiments on ryegrass and clover just outside of Zurich, Switzerland. Following a postdoc experience as a Humboldt Fellow in Germany, she returned to Illinois and has built her career at SoyFACE.

Much like ASC, SoyFACE has thrived not only through the cross-disciplinary environment at the University of Illinois, but also because it is in an area dominated by agriculture.

“Initially, Steve Long came to Illinois from the University of Essex in part to start a FACE experiment,” Ainsworth recalled. “He thought that fields in Central Illinois would be pretty homogenous and a good testbed for this pretty new approach. We have been able to ask questions from a fundamental science perspective, but also from an applied science perspective.”

The mission of the SoyFACE experiment has changed slightly over its two decades — from simply demonstrating the effects of climate change to discovering ways for crops to thrive under futuristic climate conditions, such as increased CO2 and ozone, elevated temperature, and drought. Ainsworth studies genetic variation and crop responses to these elements of climate change and has collaborated with soybean breeders, both inside and outside of ARS.

“If we can identify lines that are more tolerant to ozone and more responsive to CO2, and then understand the genetics that are underpinning those responses, we have the ability to design crops in the future that will produce more,” she said. “We are able to study those responses from molecular mechanisms up to ecosystem-level responses.”

SoyFACE also enables studies on how plant-weed interactions and plant-insect interactions might change in the future.

“Measurements of plant responses to climate change provide critical data to feed into our models of future agricultural productivity,” Ainsworth said. “Plant responses to climate change will also in part determine future atmospheric composition and future climate. SoyFACE and other FACE experiments provide ground truth data that is critical to research efforts to model the Earth’s system.”

The partnership with ASC and Founding Director Kaiyu Guan has, among other things, enhanced the modeling component to the research.

“The goal for ASC is to improve the sustainability of agriculture and that is also fundamental to the research that I do,” Ainsworth said of the partnership. “A big piece of that as we look to the future is adaptation to climate change.”

Ainsworth has worked alongside ASC to improve remote sensing for monitoring nitrogen in crops. Guan has also tested solar induced fluorescence (SIF) under different environmental conditions at SoyFACE.

ASC has brought together teams like Ainsworth’s to collectively tackle some of the grand challenges of sustainability in the 21st century and beyond.

“Kaiyu has brought people together that have very different expertise, but a similar motivation, that is the desire to improve agriculture and to adapt agriculture to climate change that is here already and is impending, and increase its sustainability,” Ainsworth said. “It’s one thing to just increase yields and maybe have more inputs, but that’s not going to help us with the state of the planet. We all understand the need for a systems-level approach to adapt to any change that we make. With Kaiyu at the helm, the sky’s the limit.”

Jonathan Coppess was named the Leonard and Lila Gardner Illinois Farm Bureau Family of Companies Endowed Associate Professor in Agricultural Policy in an investiture ceremony on September 14, 2023. (Photo by Fred Zwicky / University of Illinois Urbana-Champaign)

Jonathan Coppess plays a valuable role in ASC by informing research findings to policymakers and other governmental officials.

The Director of the Gardner Agriculture Policy Program and Associate Professor of Law and Policy for the University of Illinois’ Department of Agricultural and Consumer Economics, grew up on a farm in Ohio. After earning a Juris Doctorate degree from The George Washington University School of Law and practicing law in Chicago, he found his way back to agriculture through the policy space, where today he helps provide a valuable link from research to policy.

Coppess helps provide ASC scientists bridge the gap between research and policy, often interpreting their research to inform policymakers.

“I think ASC scientists, such as Kaiyu’s interest in policy, is phenomenal,” Coppess said. “It’s great to work with a researcher who has the perspective that research can be important for not just the academic value of it, but can also move policy, which can open up new research questions.”

Coppess sees his role as more of an interpreter rather than as an advocate or lobbyist. Although he doesn’t do the basic research, he helps apply research to policy questions, informing policymakers and their staff, farmers, and interest and stakeholder groups. That kind of work has invigorated him.

“For someone that doesn’t have the ability to do the research — but is curious about it and has a fascinated interest in it — I get a chance to find ways to incorporate that research into the work I do in the policy arena,” he said. “The application of research and policy is a challenge at times. Policy moves on a different time frame, but there’s always a need. Trying to figure out how to meet that need is actually fun.”

Coppess brings an impressive resume to his work with ASC. He served as Chief Council for the U.S. Senate Committee on Agriculture, Nutrition, and Forestry and played a lead role in the development of the 2014 Farm Bill. More recently, he served as Special Counsel for the U.S. Senate Committee on Agriculture, Nutrition, and Forestry where he assisted in the development of the Build Back Better Act, legislation that lays the groundwork for climate-smart agriculture and conservation policies. He also volunteered for the U.S. Department of Agriculture’s (UDSA) Agency Review Team as part of the Biden-Harris Transition Team in 2020-21.

On a full-time basis, he engages with farmers and policymakers on agriculture policy both in person and through the farmdoc daily and Policy Matters platforms — all while providing award-winning instruction to University of Illinois students, introducing them to public policy and the principles of policymaking.

Coppess’s road to UIUC, began in 2005, when he decided to pivot from his law practice.

“I’ve always liked politics, government and history and was really interested in some of the work my friends were doing on the Hill in the Senate,” Coppess recalls. “So I decided to try for that and eventually landed a job in the U.S. Senate.”

Coppess spent eight years in Washington, six of them in two stops with the Senate, and two years with the USDA. His experience in legislation and policy making gave him an intimate look at how bills were crafted and negotiated, which ultimately led to his current opportunity at the University of Illinois in 2013.

“They were looking for someone who wanted to focus on agricultural policy,” Coppess recalls. “To say it was a unique opportunity, understates it. It was an amazing chance. I always kind of joke that particularly when you are working in Congress, you’re running 100 miles an hour and everything is about an inch deep. Every day I felt like I was keeping a mental list of questions. One of the things that this position has allowed me to do is to take some deeper dives into policy issues and its development through history.”

His interest in both agriculture and history converged with the publication of his book, The Fault Lines of Farm Policy: A Legislative and Political History of the Farm Bill in 2018.

“The book is the product of all of those questions I had while working on the Hill,” Coppess said. “I just got lost in the history and trying to sort out which thing led to which issue. The regional issues were very clear, but I was struck by how long standing they were and was interested in how it plays out.

Jonathan Coppess’ book, The Fault Lines of Farm Policy: A Legislative and Political History of the Farm Bill, provides perspectives for future policy discussions and more effective policy outcomes. (Courtesy University of Illinois College of ACES) 

“When I was on the committee writing the bill that ultimately became the 2014 Farm Bill, I remember running around counting votes and using different spreadsheets to figure which votes we might gain and lose with a particular amendment. To see how historically these coalitions really accomplished the vote counting and how that, time and again, is a critical factor in how the policy developed, is really interesting.”

Coppess points out that although there is a long history of bipartisanship within the agricultural farm policy arena, much of the divide actually occurs over regional lines.

“The ugly reality of our politics today is that nothing escapes partisanship for long or completely,” he said. “However, there is a lot of crossover appeal where you are helping farmers and low-income families and looking at environmental issues and air and water quality.”

In terms of his work with ASC, he says that modeling, in particular, lends itself to some of these policy questions — especially when it comes to climate change.

“There are some fascinating things that Kaiyu’s research could inform,” Coppess said. “You can present outcomes and scenarios and use this research to open or expand the conversation away from one thing or another to a variety of options.”

After that, Coppess says the goal is to not only let people have a chance to make up their own mind, but also test their ideas. That feedback leads to more discussion and a wider range of ideas, which can be beneficial to the researcher, the policymaker, and the farmer.

“It feeds on itself,” he said. “One conversation leads to another set of questions that could lead to the next six conversations.”

Besides climate change, another hot issue (which is semi-related) is risk assessment, particularly when a farmer decides to change course from his normal practice. All of it gets to the bottom line (dollars and cents).

“The risk issues are huge,” Coppess said. “Change in those practices come with management risks as well as yield variance.”

He notes that policymakers don’t want to be the one to advocate for a policy that has major negative implications for the farmer. The farmer, in turn, is wary of making more bold changes than his neighbor that might risk not being able to pay the mortgage note.

ASC’s modeling and computational capabilities will be particularly helpful to run scenarios on those potential changes and to illustrate some of the challenges, for instance, around climate change and cover cropping. This can help farmers and policymakers shape future decisions.

“Analyzing risk and managing risk is a huge part of what a farmer does year in and year out,” Coppess notes. “Therefore, making sure practices are modified from an informed perspective is really critical. What’s unique to this industry is that if you make a mistake in the farm field, the whole year is gone. We will be able to run scenarios for the farmer and not have to wait five years to see the outcomes because they will have so much research to back it up.”

In addition to informing decisions, those meetings also help support the value of the research in the first place.

“We are helping policymakers understand that when they invest in research, over time we find different ways to use it,” he said. “It’s a good example of how that system plays out. It has value to them. It obviously has value to the university because it helps keep research funding going. It can improve policymakers’ understanding of what research funding can do.”

Coppess is excited to see what impact ASC can play in shaping agriculture going forward and feels fortunate to play a role.

“The opportunity to work directly with researchers and explore how their research findings can inform policy and how we can creatively shape those policies is rewarding,” he said. “It’s been a really amazing journey from working on policy to getting into the weeds of how research can be applied to it.”

Wendy Yang – Professor of Plant Biology (Courtesy University of Illinois News Bureau)

What stood out about the University of Illinois Urbana-Champaign when Wendy Yang interviewed for a tenure-track faculty position in its Department of Plant Biology a decade ago was the institution’s trademark collaborative nature. A decade later, in that environment, she and her collaborators are making their mark in solving some of the globe’s most pressing climate issues.

“I realized immediately that Illinois is a unicorn institution,” she said. “I met world-class scientists in so many disciplines who don’t have egos, who work together and are collaborative with no walls between units on campus. I’ve been here for 10 years and I’m glad that first impression was accurate.”

That collaborative environment was instrumental in the establishment of two major centers headquartered at Illinois, in which Yang is a core figure — the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), now in its seventh year and its second round of funding, and the Agroecosystem Sustainability Center (ASC), now in its third year. Yang is Associate Director of ASC and Sustainability Theme leader for CABBI.

It is that against backdrop where Yang has established her research lab and is working to tackle global climate issues, such as mitigating soil nitrous oxide emissions.

“I’ve been working to understand soil nitrous oxide emissions since even before my first day as a graduate student,” noted Yang, who holds a B.A. from Harvard University and a Ph.D. from University of California-Berkeley. “What piqued my interest has been the fact that it has been a tough challenge for the scientific community for decades. Although scientists have known some of the processes that have produced nitrous oxide emissions since before the 1900s, and there have been hundreds if not thousands of studies on these processes, we still can’t predict these emissions in the field. That’s something we need a better understanding of if we are going to successfully mitigate nitrous oxide emissions from agricultural systems.” 

Yang points out that part of the dilemma is that up until now much of the research to understand drivers of soil nitrous oxide emissions has been done in a controlled environment in laboratories. The U.S. Department of Energy funding through ASC’s SYMFONI and SMARTFARM projects has not only brought the research to the field, but allowed the purchase of 20 chambers distributed throughout the field that automatically measure soil nitrous oxide emissions each hour. 

“When you go outdoors, soil conditions are very complex,” Yang said. “Thanks to this project, we’ve been able to produce unprecedented high-spatial, high-temporal resolution data sets on nitrous oxide emissions. It has been a dream project for me. No one else has been willing or able to invest that much funding in one field, but that’s what we need.”

Her team has discovered that even within the confines of a single field, the nitrous oxide emissions are varied — some places higher and some lower. That, among other things, has helped inform management practices where researchers can target the hot spots. 

The collaborative nature of ASC has meant researchers aren’t doing their work in silos, which has been important in helping make recommendations to farmers in areas such as cover cropping. While Yang’s team is looking at its effects on nitrous oxide emissions, ASC Director Kaiyu Guan, Associate Director Andrew Margenot, and DoKyoung Lee, professor of crop sciences, are also doing cover cropping work and can share their findings with Yang’s group.

“A big challenge, especially for the farmers, is increased volatility in precipitation,” she said. “Not only are we getting more intense spring rainfall, but now we’re also getting  drought  that makes it so difficult to not only manage crop productivity, but also to attain the intended sustainability outcomes of climate-smart agricultural practices.” 

Yang’s group is currently conducting a meta-analysis to evaluate trade offs in the soil carbon benefit from practices versus unintended effects on soil nitrous oxide emissions.  While cover cropping might reduce carbon emissions, it might also increase nitrous oxide emissions, which Yang notes is 300 times better at trapping heat than carbon dioxide. 

“A small increase in nitrous oxide emissions may completely offset the climate change mitigation benefits of the soil carbon gains,” Yang said. “What we have learned from our SMARTFARM research is that greater soil organic carbon availability is part of what makes these nitrous oxide hot spots hot.”

Yang shares Guan’s vision of a future where scientists can not only analyze 20 different spots within a field but scale that up to regions, countries, and even the globe.

“What excites me about Kaiyu’s work is that he is crossing that scale from meters to hundreds of kilometers,” Yang said. “We aim to discover predictive variables that can be remotely sensed and scaled from one field to across regions.” 

In that vein, Yang has taken her studies to the area of the globe that is responsible for the highest naturally produced nitrous oxide emissions — tropical rain forests. That’s because nitrous oxide naturally occurs in soils that lack oxygen. Because the rain often pushes the oxygen out of the soils, it encourages the process of nitrous oxide there. 

“One of the reasons I love studying nitrous oxide is that while there are really important questions we need to address in agricultural systems here, we are also indirectly affecting natural emissions. My work has importance everywhere,” Yang said. 

“When I first started in this field some 20 years ago, we were a bit more concerned about the industrialization of the tropical regions and how the nitrogen deposition we’ve seen in temperate industrialized countries was coming to these tropical areas. We wanted to understand how indirectly fertilizing these areas could change tropical nitrogen cycling. We weren’t considering management of tropical forests, but more so representing those changes in our models. Everything that goes into our Earth system models is crucial for predicting future climate change.”

Part of the challenge in reducing nitrous oxide emissions is reversing the cycle. Half of the increase in atmospheric nitrous oxide concentrations comes from human activity, which has resulted in both increased rains and drought. Yang notes that it directly affects the nitrous oxide emissions that occur naturally not only in rainforests, but elsewhere as well. 

“We expect that as the amount of reactive nitrogen we put into the atmosphere increases, it either rains out or it settles out and it fertilizes even our natural ecosystems,” Yang noted. “So even when humans are not having direct impacts on nitrous oxide emissions through fertilizer application, we are still indirectly fertilizing our natural ecosystems, particularly in areas near industrial activities. There have even been studies which show that near roadways, emissions coming out of the tailpipes of cars end up depositing near the roadways.” 

Image Credit: Wendy Yang

“There is currently a lot of interest in climate smart agriculture with start-up companies emerging and industry leaders pouring funds into this,” Yang added. “I think everyone wants an easy solution, for instance sprinkling microbes on the soil, that would fix our problems for us. However, I think we are realizing that there is a reason why those microbes aren’t surviving naturally or dominating naturally in agricultural soil environments. We need to broaden our focus in developing technologies to reduce the nitrous oxide emissions.”

Which is why it has been important for Yang’s group to work closely with that of Margenot, whose focus is also on soil composition, and with Guan and Jonathan Coppess, who can work closely with politicians on areas such as government subsidies to make these climate practices cost-effective for the farmer. 

Yang is excited about what future collaborations could mean in helping solve these global climate issues. She has been doing team science leadership training through the Carl R. Woese Institute for Genomic Biology. 

“We learned that when you build a team, you need to have team members who work well together, not necessarily just the best and the brightest,” she said. “Our success with CABBI shows that at the University of Illinois we know how to function at that large scale, and we know how to build teams that work well together.” 

While the collaborative nature of ASC shows its benefits in research, it also benefits from being at the heart of the study area – the Midwest – and its understanding of bringing to the table the most applicable piece to the puzzle: the farmers. 

“Through DK and Andrew’s relationships with the farmers, we have insight into the actual challenges of the farmer,” Yang said. “We understand the importance of trying to come up with solutions that are not counterproductive to the livelihoods of the farmers.

“I think one of the strengths of our ASC team is that because we have people looking at the same problem from different angles, we can see the tradeoffs, whereas other people may have blind spots because they are only looking at it from one angle,” she said. “Because at ASC we have people from many disciplines working together as a team, we can holistically address these questions.”

With the core group of ASC researchers, including Yang, transitioning from early-career to mid-career scientists, it produces a unique energy. 

“We are on the upper trajectory in our research programs,” Yang noted. “We are finding a lot of overlap in our visions for not only what we want to accomplish as scientists, but also the impact we want to have on society. One of the exciting parts for me is that when we put all that energy together and it’s all going in the same direction, there is so much we can accomplish. We all have big dreams.”

Margenot profiling soils in coffee agroecosystems in Guatemala. This work, conducted via participatory research with smallholder farmers, seeks to identify means to increase coffee yield and quality to improve smallholder income in a region that is largely economically dependent on this tropical crop.

To find the dirt on Andrew Margenot, you may need to sift through the literal dirt. Currently an associate professor of soil science, Margenot specializes in soil biogeochemistry to understand agroecosystem functions such as nutrient storage and cycling, crop production, contaminant filter and storage, and climate regulation. 

His research team of 40 personnel has approximately 35 active grants, with 80 percent of those projects focused on the Midwest context. The emphasis of this work is on nutrient management, soil organic matter cycling and soil health, involving direct work with stakeholders ranging from USDA NRCS to farmers via a lot of on-farm research.

“We are interested in understanding outcomes of practices: why is a practice working or not for a given outcome of interest?” Margenot explained. “Can we explain those outcomes in order to predict future outcomes? We work with the Agrosystem Sustainability Center (ASC) to assess and explain those outcomes and study the biogeochemical mechanisms that underpin agroecosystem functions.” 

Although the University of Illinois sits in the heart of some of the richest soils in the world, Margenot cut his teeth on high weathered, low fertility soils in the tropics, notably East Africa and Latin America. 

“The soils in these parts of the tropics have low fertility because they are old,” Margenot explained.”It’s like a 95-year-old person.”

Having studied on the coasts, with a bachelor of arts degree  from Connecticut College, majoring in both philosophy and biochemistry and molecular biology, and a PhD in soil biogeochemistry from UC Davis, he thinks there are several misconceptions there about the Midwest.

“ I think that we as a field of research have mistaken ecological simplicity of the Midwestern agricultural landscape with biogeochemical simplicity. It’s not simple, and the problems we face are not easily solvable,” he said.

A current topic of focus is nutrient management, focused both on improving fertilizer use efficiency and how nutrient losses practices can maximize efficiency and minimize losses, and why.

Margenot stands in a soil pit next to Jim Isermann at Isermann Farms in LaSalle Co., IL. The pit profiles the official state of Illinois soil, the Drummer series. Essential to the approach taken by Margenot’s team is start with farmers, be they in the Midwest or in Guatemala or Kenya, to understand the challenges that agroecosystem managers face and how researchers can better align scientific approaches to target real-world solutions.

“As part of that, we build a lot of tools to understand the system and test mechanisms,” he added. “If you don’t have a tool, you have to build it to understand why something is changing.”

Such as finding the right level of phosphorus in the soil to support high crop yields while reducing run-off losses. Margenot calls phosphorus the “Goldilocks nutrient” because it is hard to get it “just right”. Margenot’s team has also discovered that in assessing the nutrient losses to the surface water, researchers have not been accounting for natural losses through eroding streams. 

“A portion of our phosphorus losses are due to practices from 60-80 years ago,” Margenot said. “We call these legacy phosphorus. We have a really poor understanding of legacy nutrient losses, but the problem is that is what is driving our losses today. So it’s an inexact science.”

Although headquartered in central Illinois at the state’s flagship land grant campus, Margenot diversifies his research across fields in northern, central and southern Illinois, the greater Midwest, and in the tropics. 

“In order to make our findings and discoveries applicable globally, we try to understand the why of things,” he said. “Even in Illinois, you go from a very cold climate to the beginning of a nearly  subtropical climate. We tend to be spoiled here because even the ‘lesser’ soils in southern Illinois are still very fertile compared to weathered soils in the tropics.  If we can explain how soils function at a biogeochemical, process-based level, then those same insights can be applied to understand soils and agroecosystem functions anywhere, from the red oxisols of Kenya to the black mollisols of Illinois.”  

Margenot also uses this approach to demonstrate that while one agroecosystem management practice may work well in one context, positive trade-offs  are not necessarily universal. For example, cover crops might increase yield in places with marginal soils like southern Illinois or Missouri, but might not in areas where soils are richer.

“Cover cropping is in some ways a Swiss Army knife: you can customize cover crops for all kinds of outcomes,” he added “Are there benefits of using cover crops to reduce soil erosion by wind or nitrate leaching? Absolutely. That’s what we should be thinking about cover cropping in the ‘flat and black’ in the heart of the Corn Belt. In the rolling ground of the Ohio River Valley that bounds the southern extent of the Corn Belt, we know that cover crops increase yield – in contrast to the central Corn Belt – while  also mitigating soil erosion by gravity.”

A severely eroding streambank in southern Illinois. Streambank erosion is an overlooked but critical contribution to non-point phosphorus and sediment loads to surface waters. Margenot’s team is leading an ASC project to quantify – for the first time – streambank erosion and its contributions to P loads in Illinois. These results will directly inform Illinois and US EPA strategy on improving water quality in the Midwest and the Gulf of Mexico.

That is an example of the kind of innovative research that Margenot and others at ASC hope can improve processes and outcomes in both Illinois and around the globe. They are at the forefront of addressing the growing problems of climate resilience and food security. 

On the microscale, he is teaming with ASC to help update the Illinois Agronomy Handbook, where some of the recommendations are more than 80 years out of date. The project is funded by the National Science Foundation (NSF) and the National Research and Education Network (NREN).

“We aren’t great at keeping up with understanding these systems because we are not keeping up on the basics on how we manage them,” he reasoned. “The amount of phosphorus, potassium, and nitrogen recommended for fertilizer are based on efforts from the 1960s.”

Margenot also notes that much of the recommendation is from sampling the top six inches of the soil. Their updates will include results that will account for soil specific reserves of nutrients at the root level some three to four feet deep. Margenot’s team is applying biogeochemistry to understand fertilizer fate, use and non-fertilizer soil contributions to crop uptake. 

“The idea here is to understand how the biology of soils and native reserves in the subsoil can contribute to crop uptake,” Margenot said. “To me, that’s where agroecology becomes good agronomy, and offers a more biologically inclusive approach to nutrient recommendations to improve the farmer’s bottom line. With co-benefits to water quality. That’s something the traditional agronomy approach has missed, and many ecologists have turned their nose up in favor of more pristine, unmanaged ecosystems. I think the agroecosystem is where the action is at, and frankly, the need.” 

On the environmental side, Margenot’s team is part of an ASC Illinois NREC project, which  is gathering data on erosion of streambanks and resulting phosphorus loading across the major and representative HUC-8 watersheds of Illinois. While studies of Baltic Sea basin states like Germany and Poland, have found that one-third of their entire phosphorus loss have come from eroding stream banks, no such data exists in Illinois. The United States Environmental Protection Agency has mandated that by 2025, states and federal agencies report on progress toward achieving programmatic commitments. This study will directly inform the Illinois Nutrient Loss Reduction Strategy, the report from the State of Illinois. 

“If we have a similar result as our colleagues in the Baltics, we will need to reallocate resources in order to solve the problem,” Margenot said.  

As ASC strives to be a global leader in monitoring and modeling agroecosystems for improving sustainability under climate change, Margenot’s team will be valuable in bringing research to understand the role soil plays.

Magenot concluded, “Applying basic biogeochemistry with a systems approach can provide insights to help close gaps that have only grown over the last 50 years.”

Kaiyu Guan is a researcher with lofty goals – he hopes to monitor, model and ultimately optimize every farmland. Guan aims to achieve these goals in the coming decade or so. He’s a researcher with a mission; of helping create tools so farmers can check on and manage their crops – every single field – in real-time to maintain a healthy and productive growth cycle. But simply reaching that goal isn’t enough. Guan also hopes to achieve co-sustainability of environment quality and food security. It’s quite the task, and he’s been using the supercomputing resources at NCSA to tackle the issues surrounding both aspects of his mission, one piece of research at a time. He’s also in the unique position of being one of the researchers at UIUC who’s had experience using NCSA’s retired supercomputer, Blue Waters, and its new cutting-edge GPU-processing resource, Delta.  

Read more about Blue waters here.