Fall 2019


Tracy Campbell (left), a research assistant in the Department of Agronomy, and research intern Emily Marrs install funnel systems to collect irrigation water in a pea field at Isherwood Farm near Plover, Wis. Photos by Michael P. King

When agronomy professor Chris Kucharik and his wife, Amy, moved into a subdivision in the Town of Burke in 2006, they weren’t surprised to learn their well water contained quite a bit of nitrate. Nitrate is the most widespread groundwater contaminant in Wisconsin, and it’s often associated with agriculture. Their home, located in rural Dane County, is surrounded by current and former farmlands.

Their nitrate level was around 9 parts per million (ppm), below the maximum contaminant level of 10 ppm set by the Environmental Protection Agency. But that still felt too high for them. Fortunately, the house came with a reverse osmosis system that filters out around 70% of the nitrate in their drinking water. Besides changing the filter annually, they didn’t think about it much. Set it and forget it.

Then, in 2013, Amy became pregnant, and they were jolted out of their complacency. It was time to get their drinking water tested again.

“That was at the top of our list of things to do,” recalls Kucharik, a professor of agronomy at CALS. “We rechecked the water samples to make sure the reverse osmosis system was still functioning correctly.”

Professor of agronomy Chris Kucharik at his kitchen table in his Town of Burke, Wis., home.

High levels of nitrate are known to cause health problems in pregnant women and infants, including the life-threatening condition known as blue baby syndrome. In adults, long-term consumption appears to be linked to certain cancers, thyroid problems, and diabetes.

Fortunately for the Kuchariks, their system was doing its job. Unfortunately, nitrate contamination is still a big issue in Wisconsin. There are more than 800,000 private wells in the state, and around 10% of these wells are estimated to have nitrate concentrations exceeding the EPA’s maximum contamination level. In certain agricultural regions, that percentage is reported to be much higher — up near 20–30%.

This issue is one of the reasons why Gov. Tony Evers declared 2019 the Year of Clean Drinking Water in Wisconsin, and it’s why, around the same time, state Assembly Speaker Robin Vos established the Speaker’s Water Quality Task Force. Last summer, Evers specifically called for new rules to help limit nitrate losses from agricultural fields. The goal is to address the source of the nitrate problem — to help understand it and solve it.

It’s a goal Kucharik shares.

“I’ve been worried about this for years,” he says. “Water quality has always been an issue, but it’s coming to a head in many places because more and more residents are becoming concerned that they can’t trust their tap water.”

Kucharik is the developer and steward of a powerful computer model known as Agro-IBIS, which enables him to explore the complex challenges that arise where the interconnected demands for food, water, and energy collide. It can also factor in climate change, a moving target that compounds these challenges.

“Models are tools,” says Kucharik. “They are good for asking big questions. They are good for playing out scenarios of the what-ifs. Using models, we are able to conduct experiments that we can’t conduct in the field [because of the complexity or scale].”

For more than 15 years, Kucharik has been using Agro-IBIS to explore all kinds of difficult questions related to agricultural resiliency and environmental protection. He’s used it to look at the impact of the federal Energy Independence and Security Act of 2007 — which ramped up corn production for ethanol — on the hypoxic area, or dead zone, in the Gulf of Mexico. And he recently wrapped up a big project where his team scrutinized phosphorus levels in the state’s Yahara River watershed.

The plumbing system in the Kuchariks’ home features a reverse osmosis
treatment system, which removes contaminants, such as nitrate.

In recent years, he’s been preparing to bring the model to bear on Wisconsin’s nitrate problem. The project involves field research in the Central Sands region, the state’s “vegetable basket,” to improve the model’s ability to simulate how nitrate flows through the environment.

“We’re trying to understand how the system works, how the nutrient cycles work, a bit better so that we can take that information and use it as validation and calibration data for the model,” says Kucharik. “Then we can look at, if growers irrigate this way, or if they apply fertilizer this way, what is that going to mean to crop production as well as to how much nitrate is being lost out of the system. The model can be used as a tool to understand how different types of management might impact those things at a [regional or statewide] scale as well as under a changing climate.”

Kucharik hopes to provide information that can help guide farmers and policymakers as they develop adaptation strategies to meet water quality goals.

“That’s a big part of what we’re trying to do here,” he says, “to find better solutions for the production of food.”


The idea to develop Agro-IBIS marked a key crossroads on Kucharik’s career path.

Kucharik grew up in West Allis and Slinger, Wisconsin, where, from a young age, he knew he wanted to be a meteorologist. He followed his aspiration to UW–Madison, where he earned bachelor’s and doctoral degrees in atmospheric and oceanic sciences in 1992 and 1997.

During a postdoctoral position at UW–Madison, he worked on a model of global ecosystems and carbon cycling. The model — called IBIS — only included natural landscapes, such as grasslands and forests. Near the end of his postdoc, it struck Kucharik that something was missing.

“There were five or six groups around the world that were doing this [ecosystem] modeling, but nobody was factoring in agriculture, which covers 35–40% of the earth’s ice-free land surface,” says Kucharik.

He then began building his own integrated model of agroecosystems, bringing together traditional crop models and ecosystems models. It was the first model of its kind, notes Kucharik. Before Agro-IBIS, as it came to be known, he could never have predicted that agriculture would be such an integral part of his research program.

“At that point in my career, I had never had a class in agronomy. I didn’t know anything, really, about cropping systems,” notes Kucharik, who is now the chair of the agronomy department. He is also affiliated with other campus units, including the Nelson Institute for Environmental Studies and the Wisconsin Energy Institute.

Agro-IBIS is a process-based model, meaning it tries to account for everything happening in the system, down to the small details. It seeks to simulate all of the processes taking place across the landscape — on both natural and managed lands — factoring in things such as weather, soil type, plant cover type, plant growth rates, irrigation, fertilizer applications, nutrient losses, and surface water and groundwater flow.

“Many [processes in the model] are run at an hourly time step, which means every hour the model is producing new data,” explains Tracy Campbell MS’18, a doctoral student in Kucharik’s lab. “We have to study plant photosynthesis [for a new crop type] over the course of the day, hour by hour, and across a variety of environmental conditions so the model’s simulations can best mimic crop behavior at such a fine temporal scale.”

Sensors are shown at various depths of soil in a field at Isherwood Farm. A clear line is visible between the fertile top soil and the beginning of the sand layer.

Agro-IBIS is ideal for studying complex interacting effects, such as the combined impacts of land management and climate change, and how those interactions can affect crop yields, water quality, soil erosion, and other factors of interest. It can assess these impacts on a field level or on regional, state, and national scales. It can also look at short time frames or long stretches.

“If you’re running a simulation into the future or doing a historical run of 50, 60, 70, or 100 years, it can take a week or two [for the model to complete the run],” notes Kucharik.

The model has grown over time, as Kucharik and his graduate students and scientific collaborators have expanded it to incorporate more phenomena. Over the years, they’ve added new crops (potatoes) and new nutrients (phosphorus), and they’ve integrated it with other helpful models (hydrology).

Today, Agro-IBIS consists of around 50,000 lines of code written in FORTRAN 90. The code looks like concise poetry — with plenty of line breaks and white space — written in some kind of futuristic language that features a lot of numbers and symbols. It seems impenetrable, but it’s not hard to grasp the big picture.

“The code is largely equations that represent the physics, the chemistry, the biophysics, the biogeochemistry that represent our understanding of how the system works,” says Kucharik. The laws of nature, so to speak.

The code also includes the instructions needed to run a simulation. In other words, to query the model with a research question.

“That’s where all the fun starts, when the model starts spitting out data,” says Kucharik.

For years now, Kucharik has been gathering the information needed to ask Agro-IBIS more in-depth questions about nitrate in Wisconsin. To that end, his team is actively involved in three research projects in the Central Sands. They’re gathering field measurements, which are needed to increase their understanding of these agroecosystems on sandy soils, so they can improve and expand the model in this area.


Isherwood Farm sits on a flat expanse of land near Plover, Wisconsin, in the Central Sands. Justin Isherwood, a sixth-generation potato and vegetable farmer, runs the operation with his son, Isaac. A published author with a longtime interest in agriculture and sustainability, the elder Isherwood has been welcoming research on his land since the early 1970s.

“I believe in the place of science, how it alters our methods and improves our lives,” Isherwood says. “It’s been the boon of agriculture.”

Water samples containing nitrate are examined at a testing tent at the Midwest Renewable Energy Association’s Energy Fair in Custer, Wis.

That’s why Isherwood allowed Kucharik and his research team to install 25 lysimeters deep in the sandy soil below his farm fields over the years. The instruments collect the moisture — from irrigation and rain — that soaks down past the root zone of his crop plants.

The Central Sands is one of the nation’s top potato and vegetable producing areas. Encompassing portions of eight counties in the center of the state, the land features a shallow

layer of fertile topsoil — just 10 or 12 inches on Isherwood Farm — underlaid with a large volume of sand and gravel deposited by the state’s most recent glaciers. Water permeates the sand and gravel, creating a large, rain-fed aquifer that farmers utilize to irrigate their crops.

The region is great for growing food, but it’s not without its challenges. The Central Sands has faced serious water quantity problems in the past, and concern is mounting about water quality. Potato and corn require relatively large amounts of nitro- gen-based fertilizer, and some of these nutrients leach down through the soil into the groundwater in the form of nitrate. Nitrate is considered mobile in the soil — it tends to flush through.

“The challenge is the top foot,” says Kevin Masarik MS’03, a doctoral student in Kucharik’s lab. “We need to figure out how to keep nutrients in the top foot of the soil, where plants can take them up and utilize them and prevent them from leaching into the groundwater.”

Masarik is also the state’s groundwater education specialist with the UW–Madison Division of Extension. Through this position, based at UW– Stevens Point, Masarik helps citizens test their well water and advises them on how to address contamination problems. He has access to 30 years of water quality data from private wells around the state. To learn how to deal with such a large data set, he joined Kucharik’s lab, in part, to expand his skills in data analytics and statistics.

“Plus, Chris has been looking at nitrate for a long time,” says Masarik. “That’s one of the reasons why I was excited to work with him.”

On a regular basis, Masarik or his student assistant stops by Isherwood Farm — as well as other participating farms and the Hancock Agricultural Research Station — to pump out the lab’s lysimeters and send the water samples for nitrate testing. The data provide quantitative information about how much nitrate is leaching in various situations, given different crop types, soil properties, nutrient applications, irrigation schedules, and weather events.

This project, now in its fourth year of data collection, has revealed a surprise. The findings show that crops do a pretty good job of capturing nitrate in the root zone during seasons when precipitation is normal to below average. However, wet years still pose challenges.

Kevin Masarik, a doctoral student in the Kucharik Agroecology Lab, injects a dye into his model while giving a presentation on Wisconsin groundwater at the Midwest Renewable Energy Association’s Energy Fair.

“A significant portion of nitrate is actually lost during the period after harvest all the way up until planting the following year,” says Masarik. “During that time, there’s a large portion of nitrogen that’s returned to the soil because of the crop residue [breaking down].”

This was big news to Isherwood, who is excited about this unexpected (and welcome) opportunity for growers to do better.

“Maybe there’s some material that could be sprayed on the residue to slow down its biological decay [until the next growing season],” says Isherwood. “When the problem is revealed, that’s when ingenuity can come into play to help solve it.”

Last summer, Campbell, who joined Kucharik’s lab in 2016, helped launch a new research project at the Hancock station. On most days throughout the growing season, she could be spotted there lugging around a portable LI-COR photosynthesis system. The instrument measures a plant’s rate of photosynthesis — a quantitative way to assess plant growth at a given moment — at various CO2 and light levels.

“It’s nondestructive,” says Campbell. “You just clamp [the leaf chamber] onto a leaf, and it takes around 45 minutes to do the measurements.”

Campbell’s project piggybacked on a field study, led by horticulture assistant professor Yi Wang PhD’12, that is testing out three promising new varieties of potatoes developed through the UW’s potato breeding program. Growers are excited about the new varieties, says Wang, so they will likely be grown on more acreage in the future. She is testing their productivity at five different nitro- gen application rates, comparing them to some more widely grown varieties.

“For this project, I am working to find the optimal ‘N’ rate to grow these varieties,” says Wang. “The hope is maybe these new varieties will need less nitrogen to achieve a good yield compared to their standard counterparts. So that’s the primary objective of the project.” In a related study, she is looking at different irrigation rates for these same varieties.

For Campbell, the goal is to gather information — which she can turn into new parameters and equations and add to Agro-IBIS — about how the new varieties respond to various treatments. At this point, the model already has equations that represent a “generic potato” grown in ideal conditions. When the project is complete, it will be able to answer questions about specific potato varieties under different growing conditions.

Agronomy research assistant Tracy Campbell uses a portable photosynthesis system to assess the growth of potato plants in a research plot at Hancock Agricultural Research Station in Hancock, Wis.

“Those experiments and that data that Tracy’s collecting are the things that we need to put into our models so we can scale up from a plot level to ask, okay, if we started growing one of these new varieties across the whole Central Sands, and managing nitrogen and water this way, these are the large-scale impacts that it would have on water quality,” says Kucharik.

A third project involves looking at how much nitrate is present in irrigation water and whether farmers can factor that into how much nitrogen fertilizer they apply.

“When growers pump groundwater to the surface to irrigate their fields, in a way they’re recycling some of the nitrogen that has been lost earlier, and this is not something new,” says Kucharik. “Now we want to try to credit that so they can maybe reduce the amount of other fertilizer that they’re applying to the crop.”

So far, with data from more than 23 wells, they have found nitrate concentrations ranging from 6 ppm all the way up to 32 ppm, which is quite high and has the potential to make a significant contribution to a crop’s nitrogen needs. Now they are trying to figure out if nitrate levels for wells are consistent over time so farmers can count on this contribution.

“In the future, we may be able to develop guidance on how much N application rates should be reduced based on irrigation water nitrate concentration,” says soil science professor Carrie Laboski, who puts together crop nutrient recommendations for Wisconsin farmers. “We need more data on the consistency of nitrate levels over time along with field trials validating this practice on farms.”


Over the course of his career, it has become more urgent for Kucharik to solve relevant problems and share his results with groups that could benefit.

“Early on, it was satisfying for me to publish my research in journals, and scientists would read that,” says Kucharik. “But it’s very unsatisfying now to know that the people who could actually apply the findings are not really reading that information, so we’re trying to do things to better interface with them.”

Kucharik is now involved in outreach to the state’s growers, a group he finds is constantly motivated to “understand how to do things better.” His goal is to help them envision the future and encourage them to start heading in that direction now, so they won’t be caught off guard by things like new fertilizer regulations or altered weather patterns down the line.

“Chris has made numerous presentations to our grower group,” says Isherwood. “He’s been wanting to take the group in directions that climate science is leading us. That’s very daring, and I’m sure I’m not the only one who appreciates that.”

Kucharik also plans to make himself — and his model — available as a resource to support the state’s water quality efforts during the Year of Clean Drinking Water and beyond, including Gov. Evers’s call for new rules to limit nitrate losses from agricultural fields. To that end, Kucharik has met several times this past year with staff from the Wisconsin Department of Natural Resources (DNR) and the Department of Agriculture, Trade and Consumer Protection to discuss state water quality issues, and he was among a group of CALS researchers who met with DNR Secretary Preston Cole this spring to discuss their water-focused research.

“I want to be as involved as possible,” says Kucharik. “I want the process to be as informed [by science] as possible. Decision-makers and legislators need to make policy at the watershed, region, or state level. A great way that we can help is by sharing model results at broader scales that have some policy relevance to them.”

There’s wide agreement that it won’t be easy to solve the state’s nitrate problem. Kucharik believes it will take a significant transformation of our agricultural systems, including more perennial vegetation on the landscape, such as perennial crops, cover crops, and grasses, as well as reductions in fertilizer applications.

For farmers around the state, there won’t be a one-size-fits-all solution. Adaptations will need to be tailored to individual farms based on their cropping systems, soil, local weather patterns, topography, and hydrology. Solutions may involve adjusting nutrient or irrigation approaches, switching to “low nitrogen” crop varieties, managing crop residues, or crediting nitrate in irrigation water. In most cases, it will likely take a number of things combined.

Kucharik is excited to use Agro-IBIS to help assess which changes will have the biggest impacts — now and into the future — and show the best path forward. The goal, says Kucharik, is twofold: farm resiliency and clean water.

“The model,” he says, “will help us understand the impacts of decision-making and climate change on these goods and services that we rely on as a society.

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