Watershed Revival: What will it take to staunch the flow of runoff into the Mississippi Basin? By Anita Neal Harrison. Photography by Robert Llewellyn.

back in 2001, the Environmental Protection Agency developed an action plan aimed at dramatically improving the health of the Gulf of Mexico. Among the plan’s most prominent objectives was reducing the amount of agricultural nutrients — chiefly phosphorous- and nitrogen-rich fertilizers — flowing into the Mississippi River and its tributaries.

Marine scientists and others have long argued that fertilizer runoff was contributing to a vast hypoxic area in the gulf, a “dead zone” where oxygen levels fall too low to support most marine life. Taking steps to limit this runoff, the EPA argued, would likely not kill the dead zone. But it would almost certainly reduce its size. Their action plan set an ambitious decade-and-a-half long goal: to shrink the dead zone from its then average of 4,200 square miles to around 1,900 square miles by 2015.

It’s now 2014. Last summer, researchers estimated that the dead zone encompassed 5,840 square miles — more than three times next year’s target.


What went wrong? University of Missouri researchers, who for years have studied nutrient runoff, say that the EPA plan, while well-intentioned, underestimated both the scale of the problem and the complexity of interventions intended to solve it. Now, they say, a new federally funded, multistate initiative in progress could finally provide workable solutions.

“This is the first time in my memory we have seen such a significant investment of federal funding to do conservation practices on the farm to take care of this issue,” says Shibu Jose, H.E. Garrett Endowed Professor at MU and director of the University’s Center for Agroforestry. “It’s not the first time money has been spent. But I believe it’s the first time so much money has been spent, and in such a large, concerted effort.”

The project, called the Mississippi River Basin Healthy Watersheds Initiative, or MRBI, is funded by the USDA’s Natural Resources Conservation Service, or NRCS. In Missouri, a team led by Jose’s colleague Ranjith Udawatta, an MU associate professor of agroforestry, is monitoring runoff water from a dozen farms, measuring the effectiveness of various conservation practices. The aim is to determine how well the practices keep nutrients and sediment in row-crop fields and out of surface water.

Research teams in 12 other states are doing much the same. The MRBI initiative began in 2010, and already the NRCS has spent $320 million. Additional funding is planned, with monitoring scheduled through 2022.

The investment reflects the seriousness of the problem. Shrinking the Gulf’s dead zone requires making changes throughout the Mississippi River Basin, an area that covers 41 percent of the United States.

The most important changes will affect agriculture. Although agriculture isn’t the dead zone’s sole cause — discharges from sewage treatment plants and fertilizers from suburban lawns also contribute to the problem — “agricultural sources contribute more than 70 percent of the nitrogen and phosphorous delivered to the Gulf,” according to a U.S. Geological Survey report.

A quick geography lesson shows why. Farms within the Mississippi River basin produce close to 80 percent of the world’s feed grains and soybean exports, a phenomenal level of production made possible by millions of tons of nitrogen and phosphorous fertilizer. While some of these nutrients go to crops as intended, much remains mixed in sediment. These are then picked up and carried away during rainstorms. On an average day, some 436,000 tons of sediment flows along the Mississippi’s powerful currents.

Once in the Gulf, the nutrients feed summertime algae blooms larger than some small states. When the algae die, their decomposition sucks oxygen from the water and aquatic animals that can’t escape the area perish.


ancy Rabalais, a professor and the executive director of the Louisiana Universities Marine Consortium, has studied hypoxia in the Gulf of Mexico for close to 30 years. She says it’s impossible to calculate how much fishery production is lost due to hypoxia — in part because there’s no way to calculate what isn’t there, and in part because other factors, such as the cost of diesel and the amount of imported shrimp, also impact fisheries. But, she adds, what is clear is that the ecosystem is stressed.

“It’s not normal for there to be 20,000 square kilometers of bottom water that doesn’t have enough oxygen to support fish and shrimp,” Rabalais says. “It’s a symptom of a sick ecosystem, an ecosystem that provides a lot of resources to people in the Gulf of Mexico.”

And the problem isn’t limited to the Gulf. While still in streams, rivers and lakes, fertilizer nutrients feed algae blooms that hamper recreation, cause fish kills and require extra treatment of local drinking water supplies. Last May, for example, the Des Moines Water Works announced historic nitrate levels at its river intake locations: “This new record follows the continued upward trend of nitrate concentrations since fertilizer use and increased row-crop agriculture began in the mid-1960s,” an agency press release read. “It has been calculated that last week’s nitrate load surpassed last year’s entire nitrate load.”

In Indiana, meanwhile, blue-green algae levels in many of the state’s reservoirs and lakes last summer prompted the Indiana State Department of Health to warn swimmers and boaters who might have come into contact with it. Call your doctor, the agency advised, if experiencing “rashes, eye irritation, nausea, stomachaches or tingling in fingers and toes.”

Outside the Mississippi River basin, a record-setting algae bloom smothered 20 percent — 2,000 square miles — of Lake Erie in 2011. Worldwide, there are more than 400 hypoxic zones today, compared to around 20 before 1950.

The first steps of the Mississippi River Basin Healthy Watersheds Initiative were to identify sensitive or vulnerable watersheds within the vast river basin and to work with farmers in those hotspots to implement conservation practices. As the research progressed, monitoring the impacts of the conservation practices within those targeted watersheds also became a research goal, setting this initiative apart from past efforts.

“The NRCS has funded all sorts of programs to promote planting of trees, planting of grasses, terraces, cover crops and similar practices in the past,” Jose says. “But we’ve not had a monitoring program like this to see what difference does it make for such a large area, particularly in improving water quality.”

The NRCS is partnering with local organizations — mostly soil and water conservation districts in Missouri — to find farmers who are both willing to implement conservation practices and to monitor the effects. Those signing on will receive financial assistance from conservation dollars.

“The idea was, we’re not only going to give you conservation dollars but we want you to show us what benefits we had on water quality and on the landscape,” says Karen Brinkman, an area conservationist for the NRCS in northern Missouri.

This monitoring was something that neither the soil and water conservation boards, nor the NRCS, had any experience with. But Udawatta and Jose did. And they have been doing it for decades.

Runoff Collector

testing the waters
A sheet metal ‘collection tunnel’ channels runoff from a farm field in central Missouri.

Working at the MU Greenley Memorial Research Center in Novelty, Mo., Udawatta has measured the effect that tree and grass buffers have on controlling nitrogen and phosphorous runoff from both grazed and row crop sites. A paper he published in 2011 in the Journal of Environmental Quality reported that on average, grass and agroforestry buffers reduced sediment, total nitrogen and total phosphorous losses by 32, 42 and 46 percent respectively.

For his part, Jose has been working with agroforestry and water quality for over two decades. He is editor-in-chief of Agroforestry Systems and academic editor for PLOS ONE. As a Fulbright Scholar, he lectured and conducted research in Bangladesh. This spring, Jose was appointed to the Forestry Research Advisory Council by Secretary of Agriculture Tom Vilsack. Members of the council present recommendations and advice to the USDA on issues concerning natural resources.

“We knew their commitment to working in agroforestry and how that connected to us, and we also knew what Ranjith was doing at the Greenley [Memorial] Research Center,” Brinkman says by way of explaining what made MU an attractive partner.

The University is providing monitoring for farms located both in north central Missouri and in the Bootheel. Throughout the Mississippi River Basin, the choice of conservation practice will be up to the farmers. They might include sowing cover crops, rotating crops, reducing tillage, terracing, using a variable rate of fertilizer application, or employing grass and tree buffers. The watersheds studied will be small, between three and 12 acres. They will be studied in pairs, with one watershed in each pair serving as the control. Both will have a defined drainage pattern and no drainage from adjacent fields.

To collect the runoff, the MU team is installing wooden berms that channel water into metal collection tunnels. A sensor measures the flow rate and volume of runoff.

In the past, the sensor’s data was stored in a computer at the collection site, and researchers had to depend on the National Weather Service to let them know when a rain event had occurred. But by this summer’s end, technological improvements will allow real-time data uploads straight to the researchers’computers. They’ll be immediately alerted to rain events and will be able to remotely monitor problems — a blocked sensor, for example — from their offices and laboratories at MU.

Collection of runoff samples, meanwhile, is done via an “auto-sampler,” a device that takes sips of water at pre-set intervals. When the remote data transfer system is in place, the researchers will be able to change the length of these intervals from their office computers. After every rain, the scientists go to the field to gather samples and, back at the laboratory, they record sediment, nitrogen and phosphorous concentrations.

For the first three years, the researchers will continue to collect baseline data meant to determine the type and volume of runoff pollutants prior to an intervention. As farmers implement their chosen mitigation strategies, the monitoring will continue to determine how effective these strategies are.

Along with allowing the researchers access to their land, the farmers have also agreed to keep records of land use and conservation efforts. This will entail extra work for them, making the incentives and compensation they receive only fair, Udawatta and Jose say. “They are giving us details on when they did land preparation, applied herbicide, the seeding rate — ” Udawatta says.

“It’s an additional burden for them,” adds Jose.

Still, if the practices prove successful, farmers will be among the beneficiaries. “Identifying the best mitigation strategies will benefit farmers who want to keep valuable topsoil and nutrients on the farm,” Udawatta says. “By slowing or reducing runoff, farmers will be able to employ nutrients and fertilizers more efficiently. This also will create greater crop yields and save money in the process.”

Udawatta and Jose say their data will help them judge both the effectiveness of various runoff-mitigation practices and to develop models to determine how such practices might work on a larger scale.

“We’re excited because we’re getting a chance to scale up some of our own research,” Jose says. “This is a once-in-a-lifetime opportunity. As researchers, we often get to play with small-scale plots, mostly on university experimental farms, but this is expanding that concept on such a large scale, with, hopefully, a very positive outcome: reducing hypoxia in the Gulf of Mexico.”

Corn that fertilizes itself?

the mississippi river basin Healthy Watersheds Initiative is exploring ways to use fertilizer more effectively. But what if researchers found a way for crops to “self-fertilize” instead?

That’s the futuristic approach that University of Missouri Bond Life Sciences Center researchers are advancing with a recent discovery: maize recognition of invasive, but beneficial, bacteria known as rhizobia.

Rhizobia bacteria have a symbiotic relationship with legumes, the plant family that includes soybeans and alfalfa. It works like this: Bacteria infect the roots of legumes and form small nodules. Within these protective bumps, the bacteria receive food from the plant and “fix,” or produce, nitrogen, which the legume then uses to grow. Thanks to this fortunate form of reciprocation— otherwise known as “biological nitrogen fixation” — farmers need to add very little nitrogen to produce healthy soybeans and alfalfa. It also makes the question, “Why can’t this symbiosis work with corn, wheat and other cereal crops?” a tantalizing research topic.

“Virtually since the discovery of nitrogen-fixing rhizobium-legume symbiosis, researchers have dreamed of transferring this capability into nonlegume crop species (for example, corn),” wrote MU biochemist Gary Stacey in the September 5, 2013 issue of the jounal Science.

Until Stacey’s research, scientists thought cereal crops didn’t form a symbiotic relationship with rhizobia bacteria because they lacked the ability to receive the bacteria’s chemical cues.

“Plants don’t have eyes to see, ears to hear or fingers to feel, so the way they communicate with their outside world is by recognizing chemical signals,” says Stacey, the Missouri Soybean Merchandizing Council Endowed Professor of Soybean Biotechnology at MU. “And one of the signals that legumes recognize from rhizobia is a signal we call the NOD factor [so-called because it triggers the root nodules’formation]. The assumption has been that the reason corn cannot nodulate is, in part, because corn doesn’t have the ability to recognize this NOD factor signal.”

Think about a door, Stacey says. With legumes, rhizobia ring the doorbell and get welcomed in. With corn, the assumption was there was no doorbell to ring. What Stacey’s team showed was that there is a doorbell after all, and corn and other flowering plants do, in fact, react to its ring. They just react differently than legumes do. “In the case of legumes, when they recognize the signal, they induce these events that lead to symbiosis,” Stacey says. “In a plant like corn, when it recognizes the signal, what it does is suppress the ability of the plant to protect itself from infection. We believe — and this is strictly hypothesis — that that may in fact have been the original purpose of the signal.”

Stacey explains that relationships such as the one between rhizobia bacteria and legumes are thought to have evolved from “pathogen-host interactions,” in this case pathogens becoming less lethal to prolong their time with their hosts.

“The idea is that rhizobium probably started out as a pathogen and then, as it adapted, it became more and more benign. Eventually, it developed this intimate, symbiotic relationship,” Stacey says. “So our hypothesis is maybe the NOD factor was there initially to allow the bacteria to infect by suppressing the immune response, and only later during the evolution of this interaction did it take on this other role of actually being a symbiotic signal and inducing this symbiotic development.”

Stacey’s discovery is a classic example of how one line of research can lead to discoveries in another. Although he has studied biological nitrogen fixation for decades, this project focused on the back-and-forth contest between plant cells and pathogens — interactions in which pathogens evolve to overcome plants’innate immunity responses as, in turn, plants develop new defenses. In particular, Stacey’s team was looking at “chitin,” the glucose-derivative in cell walls of fungi, and how it elicits a defense response from plants. To the researchers’surprise, they found that chitin structures of certain lengths did not trigger a defense response but actually had the opposite effect: it suppressed immunity. These chitin structures were similar in length to the NOD factor, which is itself a kind of chitin.

“And so when we saw that [the shorter chains of chitin] were suppressing the response, it immediately suggested that we should try the NOD factor,” Stacey says.

The resulting discovery that the NOD factor suppresses the immune response of corn and other flowering plants not only corrected the assumption that these plants cannot recognize the NOD factor, but also revealed a never-before-known aspect of its functionality.

“So, previously, when people talked about the NOD factor, they always talked about it in context with the symbiosis,” Stacey says. “But now you have to say it triggers symbiotic development, but it also suppresses the innate immunity response. … It completely changes how we think about experiments in the future, and we also have to go back and reconsider experiments in the past. But this is a step forward because now we have better understanding and hopefully, it will make it easier ultimately to do what we want to do and that is to make nitrogen-fixing corn.”

If that happens, the benefits won’t just be felt in the Gulf of Mexico, Stacey adds, but will also be a huge advance in overall agricultural sustainability.

“Nitrogen fertilizer is made from fossil fuels, and there are a lot of downsides to fossil fuels,” he says, listing geopolitical issues, high costs and various environmental consequences.

These concerns have caught the interest of the Bill & Melinda Gates Foundation, which has donated $9.8 million to the John Innes Centre in Norwich, UK, to investigate the possibility of initiating a symbiosis between cereal crops and rhizobia bacteria. The foundation has also donated $2.9 million to the Technical University of Madrid and $100,000 to Pivot Bio, Inc. in San Francisco for similar research. All of these projects focus on maize, the most important staple crop for small-scale farmers in Sub-Saharan Africa.

Back in the Mississippi River Basin, MU researchers Shibu Jose and Ranjith Udawatta are familiar with Stacey’s finding and agree that nitrogen-fixing corn would be “big.”

“That’s another piece of the puzzle,” Jose says. “If they can figure out how to fix nitrogen in a plant, that cuts down this issue [of Gulf hypoxia] substantially.”

Reader Comments

Carol wrote on July 29, 2014

Robert Llewellyn's photo at the top is beautiful. Where was it taken? Are we looking north or south?

Grace T Eubanks wrote on August 12, 2014

What an excellent article this is. I'm a Missouri native who tries to keep in touch with home region, even though living on West Cost - and this piece caught my attention and educated me on the problems Mississippi River runoff and the Gulf dead zone. Of course, I'm proud to learn that Mizzou is involved in potential solutions.

Frank Dazzo wrote on August 22, 2014

In relation to Gary Stacey's article on corn fertilized by rhizobia, it is important to indicate that most major cereal crops -- rice, corn, wheat -- already naturally form a beneficial association with soil rhizobia that significantly promote their vegetative and grain production by mechanisms independent of biological nitrogen fixation. Studies show that these symbiotic bacteria enhance rice production by stimulating growth-promoting phytohormones that boost root and shoot architecture, improve photosynthetic efficiency, and elevate plant defense in ways that allow farmers to increase yield under real-world agricultural practices with less dependence on chemical N fertilizer application. See the publication of Yanni et al. 1977 Plant & Soil 194: 99-114 and the dozens of refereed journal publications confirming the natural, beneficial endophytic rhizobia-cereal association. This takes us to the wise words of Leonardo di Vinci, who said "Look first to Nature for the best design before invention".

Frank Dazzo wrote on August 22, 2014

Correction on my previous message: The year of the Plant & Soil publication is 1997 rather than 1977. A substantial followup publication by a multinational group confirming the key finding of a natural endophytic beneficial association between rhizobia and rice on every continent on Earth where rice is grown (Antarctica excluded) is Yanni et al. 2001 Australian Journal of Plant Physiology 28:845-870. Regards -- F. Dazzo

Youssef Garas Yanni wrote on August 23, 2014

Felt like someone is negotiating a problem that is familiar in my country, Egypt, where a tremendous consequences of crazy use of excessive amounts of fertilizers and pesticides. Nitrates can be detected in both Nile water and its attributes and also well-waters near to agricultural areas. We tried hardly to use bio-fertilizers long time ago, rhizobia for legumes, N-fixing cyanobacteria for rice, phosphate dissolvers for most crops etc., trying to diminish the catastrophic consequences of using un-necessary amounts of fertilizers and pesticides. We all the time keep trying to break out this bloody situation. Starting from 1993, we detected the endophytic association between rhizobia and cereals in rice grown in the Nile delta and later extended the work to rhizobia and wheat association in the same area. Many publications on that were mentioned here by Frank Dazzo, our US collaborator in those activities. Although we performed more than 80 extended transitional large scale field experiments in farmers fields in the Nile delta, we still in need to extend our information and make use of our new discoveries a reality in the agriculture landscape in our area, and most importantly, to convince our agronomists, policy makers and healthcare authorities that the matter is serious and if the current recommendations of crop management using only synthetic fertilizers remain on the same track, we are sure going to the middle of nowhere. Did I added an additional experience from other part of the world, and this experience can be helpful to the Missouri concern too?!

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