AgBioResearch

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.’”

Like 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 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.”