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Newton native helps lead largest DNA sequencing project in history

Portion of research took place in Jasper County

Published: Tuesday, March 18, 2014 11:19 a.m. CDT • Updated: Tuesday, March 18, 2014 11:28 a.m. CDT
Caption
(Ty Rushing/Newton Daily News)
The A.C. and Lela Morris Prairie outside of Newton was a key site in an experiment led by Dr. James Tiedje, a Newton native, and his team in what at the time was the largest DNA sequencing project in history.

Jasper County will now have a permanent place in the scientific community thanks to its native prairie.

A native prairie is a parcel of land still in its original state and that has never been cultivated or developed upon.

Dr. James Tiedje, and a group of other researchers, recently published their research paper “Tackling soil diversity with the assembly of large, complex metagenomes,” in the March issue of Proceedings of the National Academy of Sciences, a scientific serial publication.

At the time the project began, it was the largest DNA sequencing project in history. According to a report by Live Sciences, “DNA sequencing is technology that allows researchers to determine the order of bases in a DNA sequence. The technology can be used to determine the order of bases in genes, chromosomes or an entire genome.”

Tiedje, a 1960 Newton Senior High School graduate and Distinguished Professor at the Center for Microbial Ecology at Michigan State University, helped lead the study and explained why the study was so significant.

“Microbes are on us, in us, a part of all larger organisms, and in our soil, water and air,” Tiedje said. “The overwhelming microbes are beneficial and many of them that live with us and other animals are essential for health. The ones in soil are also essential for providing the nitrogen and phosphorus for plant growth and helping control plant disease. The microbes in soil also produced some of the greenhouse gases. There are about a billion bacteria in every teaspoon of soil.”

Tiedje’s team was co-led by Janet Jansson, of the Lawrence Berkeley National Laboratory in Berkeley, Calif., and had 11 primary science team members and eight additional members for special tasks. He said the team members had backgrounds in molecular microbial biology, computer sciences and some were bioinformatics specialists.

In June 2009, the team visited and sampled from the native prairies of the A.C. and Lela Morris Prairie, just south of the Lake Mariposa Recreation Area near Newton, the Konza Prairie near Manhattan, Kan. and a prairie near Arlington, Wis.

“To find native prairie sites in the Midwest was hard. Most of them had been plowed up, and there are only a few patches left,” Tiedje said.

For the portion of the project conducted in Jasper County, Tiedje partnered with Jasper County Conservation Director Keri Van Zante, who provided some additional information on the Morris Prairie and the extent of the county’s involvement.

“This prairie has been here since the last glaciers left Jasper County, and it, along with other prairie remnants, provides a window into the history of plants, animals and other ecological functions of the past,” Van Zante said.

“Our role in this project was to provide Jim with the management that we were performing on the site during his study — when and where we burned, any invasive species removal,” she continued. “We are proud to be a part of this and hope to be able to help others in similar research projects.”

At all three of the collective sites used for the project, the team managed to generate nearly 400 billion letters of code, or bases of data, which is a staggering amount. Tiedje said it took about three weeks on MSU’s High Performance Computer Center’s machines to process the samples collected in Iowa.

“Another thing about DNA sequencing, is determining each component and knowing what each gene’s functions is and that’s the value of knowing that information,” Tiedje said of the data they collected.

One of the main focal points of the study was to see how much of a role agriculture plays on the soil. Tiedje said they wanted to study the difference between native prairie and land that has been cultivated for farming purposes the last 100 years to see the differences and were surprised by the results.

“What was most striking were the similarities,” Tiedje said. “Overall, there were more similar than different. Over 90 percent of the microbial communities and gene content appear to be the same for the 100 cultivated and native prairie soil communities.”

Tiedje is currently participating in a 10 week study in Australia as a part of the McMaster Fellowship program.

The fellowship “provides support to selected distinguished overseas scientists to work for a period in Commonwealth Scientific and Industrial Research Organization to further strategic research in veterinary science or agriculture.” CSIRO is essentially the Australian version of the U.S. Department of Agriculture.

While he may be thousands of miles away, and he and his team are the toast of the microbiology community, he notes how lucky they were to be able to conduct this experiment and find the results that they did.

“An important part of this was those resources,” Tiedje said of the native prairie. “If they weren’t available, we couldn’t do this kind of thing.”

Senior staff writer Ty Rushing may be contacted at (641) 792-3121, ext. 426, or at trushing@newtondailynews.com.

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