Getting the Scoop on Soil

Raising awareness of the important roles soil plays in everyday life is one of the goals of the United Nations Food and Agriculture Organization, which has dubbed 2015 the "International Year of Soils."

Kurt Steinke (left) and student Christopher Bauer.

While it may seem of little value to the untrained eye, soil is one of the planet’s most precious commodities — and it’s deteriorating at an alarming rate. Unsustainable agricultural practices have led to the degradation of soil around the world, including erosion, loss of structure, changes in salinity and alterations to the complex ecosystems that live beneath our feet. The World Wildlife Foundation estimates that half of the topsoil on the planet has vanished in the past 150 years.

Raising awareness of the important roles soil plays in everyday life is one of the goals of the United Nations Food and Agriculture Organization (FAO), which has dubbed 2015 the “International Year of Soils.” The FAO says that more than 805 million people around the world face hunger and malnutrition. Expected growth in global population will require a 60 percent increase in food production just to keep pace. With one-third of the world’s soil declining in quality, large-scale problems emerge. How will growers respond to these looming challenges? What can be done to reverse the trends and improve land management? Researchers at Michigan State University (MSU) are tackling the problem on an international scale to find long-term answers that help preserve this vital resource.


Paving the way

When discussing soil research at MSU, it is impossible to mention the university’s immense contributions to the field without recognizing James Tiedje, a University Distinguished Professor and the director of the MSU Center for Microbial Ecology. For more than four decades, Tiedje has been unlocking soil’s secrets with the development of new technologies and analysis techniques, broadening the scope of understanding for scientists everywhere.James Tiedje

Throughout his career, Tiedje has seen paradigm shifts in soil studies, starting with the advent of personal computers. They allowed researchers to do modeling work much easier and made it simple to scale up mathematical models derived from experiments. Today Tiedje sequences DNA from soil with the same technology used in human medicine. MSU researchers, including Tiedje, led the largest soil DNA sequencing e?ffort to date, collaborating with scientists at the U.S. Department of Energy Joint Genome Institute and Lawrence Berkeley National Laboratory.

“In the ‘90s, it would take us almost four years to sequence one gene in a microbe,” Tiedje said. “Now we can sequence billions of base pairs a day. The sequencing capacity is tremendous, but the hard part is data analysis because storing and examining that amount of data requires high-performance computers. Our team has developed methods of breaking the data into more interpretable components, suitable for computers here at Michigan State.”

Tiedje calls soil microbiology the greatest frontier in all of biology because it is the most complex, diverse and unknown. Over nearly 3 billion years, microbial evolution has resulted in extremely high genetic diversity in soils. Sequencing e?fforts have decoded some of the mysteries, but scientists are just scratching the surface of identifying and understanding soil microbes and their impacts on agricultural production, the environment, biotechnology and medicine.

“No one knows how many species of bacteria there are,” Tiedje said. “Any particular gram of soil has about 1 billion bacteria, but no more than 0.1 percent of those microbes would be  previously known.”

DNA technology is being used in several of Tiedje’s current projects, including one that is part of the Great Lakes Bioenergy Research Center. It is one of only three national centers funded by the U.S. Department of Energy that focuses on biofuels research, led by the University of Wisconsin-Madison in partnership with MSU. One of its research groups focuses on the rhizosphere, the area of soil around plant roots, which is home to large microbial communities.

Just as humans have microbes that live with us and aid our health, plants also have a microbiome that supports their health and productivity. It improves nutrient access, prevents disease and may provide other benefits not yet discovered. Tiedje’s group is using new high-capacity DNA sequencing to learn how the plant’s microbiome can contribute to cost-e?ffective and sustainable biofuel production. In addition to pinpointing its eff?ect on promoting healthy vegetation, experts are studying how soil plays a part in climate change. A group of MSU researchers is part of a consortium studying warming sites in Alaska and Oklahoma, looking into the soil microbes’ response to an increase in temperature.

“There’s so much carbon in the permafrost in the Arctic and some of the permafrost is melting, so the microbes take over and convert that carbon to carbon dioxide and, in wet areas, to methane,” Tiedje said. “Our major goals are to learn about the temperature sensitivity of microbes using these DNA approaches, and whether their activity has an amplifying or moderating e?ffect on the projected rate of climate warming.”

Soil microbiologists, including those at MSU, have found microbes that can degrade many environmental pollutants. Tiedje’s team is well known for the discovery of bacteria that dechlorinate environmental contaminants, important because many environmental pollutants contain chlorine. This microbial dechlorination process is now implemented in the cleanup of some contaminated groundwater and soil. This process, Tiedje said, is one example of the great microbial diversity that resides in soil.

“’Soil health’ is a general term reflecting the chemical, physical and biological properties that result in effi?cient food production and optimum ecosystem services, such as ensuring good water quality and element cycling,” Tiedje said. “A very important part of soil health is the microbial community, now often termed the microbiome. The new DNA-based methods allow us much more insight into the unknown world. Plants and microbiomes have been living together ever since the first plants evolved, and it makes sense that they have developed to work in harmony. Keeping soil healthy includes ensuring and improving upon that harmony.”


Identifying sustainable solutions

Since her undergraduate days at the University of Colorado, Lisa Tiemann, an assistant professor of soil biology at MSU, has been captivated by soil and the complex interactions that take place underground. She also cites the practical applications of soil investigation on daily life.

“I think soil research is important for a couple of reasons, with the first hopefully being obvious but maybe not as obvious as it should be,” Tiemann said. “Without healthy soils, we can’t survive. We depend on soils for all of the food that we eat. There is some aquaculture, and some people eat fish, but in general we couldn’t survive without soil. I also think there’s a bit of a disconnect, where young people in school aren’t necessarily connected with nature and with the outdoors. I think it’s really the purpose behind this ‘International Year of Soils.’”

Lisa TiemannLike much of Tiedje’s work, Tiemann’s research is largely focused at the microbial level. She is working with her colleagues to gain a firm understanding of soil organic matter and how sustainable land management methods aff­ect nutrients to increase yield and promote soil health. Until recently, researchers did not have a full picture of the diversity of organisms within soil. The technology engineered by Tiedje has revealed a vast ecosystem consisting of thousands of microbial species. One of the keys now, Tiemann said, is to determine the role these species play and the implications they have on humans.

“Over the past 40 years, we’ve doubled the amount of food that we’ve had to produce to keep up with human population growth,” Tiemann said. “In the next 40 years, we have to double it again. We’ve gotten to the point now where there’s not a whole lot more land that we can actually use for farming, so what we need to do now is be more productive. My research is trying to understand how we can manage soil sustainably. In order to do that, we have to understand how soil organic matter is formed and how it’s maintained. Soil organic matter is the cornerstone of fertility.”

Through a grant funded by the National Science Foundation’s Science, Engineering and Education for Sustainability initiative, Tiemann’s research has taken her to the central African nation of Uganda, a country on the equator roughly the size of Oregon. Here she is working to understand the causes of soil organic matter decline and soil fertility loss. The project began in 2012, with Tiemann taking her first trip overseas in January 2013. Running through 2016, the research will give her team insight into the land management practices employed by farmers across the country.

A boom in population coupled with a decrease in fertile soil has put significant stress on Uganda’s available farmland. In the past, if farmers noticed a decline in productivity, they simply moved and farmed a new area. The Uganda National Environment Management Authority estimates, however, that the remaining land that could be used for agriculture will be converted to farmland by 2020 or 2025. Without the financial means to implement inorganic fertilizers, growers are left to biological farming methods and gaining more knowledge of e­ffective land management.

“That’s what we are trying to figure out now,” Tiemann said. “Are there things that people are doing elsewhere, cultural practices that would be acceptable for them to adopt that would help to at least maintain the status quo? There have to be some large, wholesale changes to build soil organic matter back up to what it once was, but if we can at least maintain the status quo and keep them fairly productive, that would be a step in the right direction.”

Tiemann’s team has surveyed local farmers, asking questions that can give researchers a better understanding of how to make recommendations and set feasible goals.

  • What do you do with crop residues?

  • What crops are you most dependent upon?

  • Do you see soil fertility loss as a risk to the future?

  • Are you concerned about population growth?

The answers to these questions are pivotal and shape the suggestions made to growers. Despite the mounting evidence of population putting increased pressure on soils, Tiemann said farmers do not seem concerned. They are, however, interested in methodologies that can help keep their lands producing at current capacity.

“We’ve seen a really big shift to a dependence on maize and the profits they receive from selling maize,” Tiemann said. “That has a lot to do with the soil organic matter depletion. They’ve got two growing seasons, so they are harvesting two crops per year. A lot of these fields are seeing maize harvested twice a year with not much else going back in.”

Although the project’s findings are still in the early stages, the team has made headway through soil testing of a nearby tropical forest conservation park. Analysis of the soil in this undeveloped land provides a picture of the peak of soil fertility in the area. Tiemann said through comparing this ground with the soil used in agriculture, declines in soil organic matter have reached 60 to 80 percent. So what can farmers do to replenish soil organic matter reserves and increase productivity?

Researchers are stressing the importance of cover crops, namely legumes, which will help to increase nitrogen and add other nutrients to the soil. Area farmers have been disposing of crop residues, either burning them or using them as animal feed. Tiemann’s team has discussed returning residues to the fields from which they came in an eff?ort to boost soil organic matter. Another suggestion is to increase the frequency of weeding, which may occur only once or twice per year currently, to improve nutrient uptake for crops by removing competition with weeds. Many of these recommendations are currently being implemented, changing the way Ugandans engage in agriculture with an eye on sustainability. But the work is far from over.

“This summer I’m taking a post-doc and my graduate student with me to Uganda,” Tiemann said. “I’ll be there for probably a month, they’ll be there for maybe six weeks, and then we’ll go back again next summer.”


Hands-on research

One of the only applied soil scientists at MSU, assistant professor of soil fertility and nutrient management Kurt Steinke spends much of his time in the field — literally. In addition to teaching a course on soil fertility and nutrient management to undergraduate and graduate students, Steinke also works with growers across Michigan through a program he leads called MSU Soil Fertility Research, which is partially funded by MSU AgBioResearch and Extension. With the assistance of both graduate and undergraduate students, as well as a research technician, Steinke’s program looks to address grower concerns by providing science-based research and extension information that ultimately promotes “greater yield in the field.”

His program currently works across five cropping systems — corn, wheat, soybeans, sugar beets and potatoes. Planting season typically begins in early to mid-April and may take roughly two months to complete. Although the focus is on soil fertility strategies, Steinke’s team investigates the entire agronomic system and then systematically evaluates individual components, such as planting date, and the impact on plant production.

“One example we are working on is the e?ffect of planting date on wheat production,” Steinke said. “We are looking at the e?ect of planting date in connection with nitrogen rate and nitrogen application timing to increase nutrient use effi?ciency, improve grower profitability and promote environmental stewardship.”

Steinke’s nutrient management methods aim to provide farmers with higher yields and sustainability while improving long-term ecological e?ciency. This involves using the 4R approach — the right fertilizer source at the right rate, right time and with the right placement — to assist Michigan growers in maximizing their resources while simultaneously giving his students access to industry professionals.

“I advise graduate students to begin to understand grower problems, learn grower solutions and, along the way, learn to see and identify grower issues firsthand in the field,” Steinke said. “A lot of graduate students don’t have direct interactions with growers or industry personnel, whereas most of mine do. Students can see firsthand that this isn’t just a problem in their research project. They can see this problem somewhere in a field from northeast to southwest Michigan.”Kurt Steinke and Christopher Bauer

Health is one component of productive soils, so quality land management to maintain or improve soil health is paramount. Technological advances in recent years have changed soil scientists’

understanding of management, forcing researchers such as Steinke to think on a much smaller level. Like Tiemann in Uganda, examining the microbial populations in soil and how management aff?ects them has been a driving force in Steinke’s recent work. It is also the focus of one of his graduate students, Mike Swoish.

Receiving data this past winter from 228 soil samples, Swoish found 26 million unique microbes representing more than 600 microbial genera. The next step is to determine which microbes were found where, under which management regime, and attempt to draw some preliminary conclusions about the impact of management on microbial communities.

“We’ve partnered with some of the technology that Jim Tiedje has brought into the realm of extracting DNA from the soil,” Steinke said. “Once we extract DNA and see what’s present, then it becomes a bigger question: is a more diverse microbial community better for plant production, or is it functionality rather than diversity? We’ve seen some instances where it may not be about microbial biomass but about getting the right microbes in the right spot at the right time to support a healthy system.”

The shift in thinking from simply growing plants to growing two crops, the microbes and the plants, has been a significant change.

“We’re attempting to figure out whether we can feed the soil to then naturally feed the plant,” Steinke said. “So we then apply fertilizer not based on what a plant needs but rather based more on what a microbial community may need. If the microbes are happy and productive, they may be able to cycle more nutrients for plants to use.”

Other technologies have improved accessibility for growers to what were once cost-prohibitive items such as all-in-one nutrient products. When nutrients are applied to a field separately, sizes and densities may vary, and equipment may not evenly distribute the products across the land. A product that contains all of the necessary nutrients in individual prills of fertilizer can be spread consistently.

Slow-release products, a staple of the turfgrass industry for years, have also carved out a spot in agriculture. Housed in a polymer coating, the contents are released over a period of weeks. This allows the nutrients to be available when needed most, rather than immediately and all at once, minimizing losses to rainfall and other environmental factors. These improvements in a?ffordable technology, in conjunction with his team’s research, allow Steinke to provide the most appropriate and sustainable recommendations for Michigan growers.

“We’re one of the only unbiased, third-party sources for nutrient response trials and nutrient recommendation,” Steinke said. “That’s the strength of the land-grant university and the strength of MSU AgBioResearch and Extension. We’re trying to make more progressive recommendations that incorporate these newer technologies without forgetting basic agronomic principles and practices. We are there to help growers stay profitable and use long-term management practices that keep their soil productive.”

This article was published in Futures, a magazine produced twice per year by Michigan State University AgBioResearch. To view past issues of Futures, visit For more information, email Holly Whetstone, editor, at or call 517-355-0123.

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