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MSU Leads Largest Soil DNA Sequencing Effort

Published: Thursday, March 13, 2014
Last Updated: Thursday, March 13, 2014
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Study also created a new analytic approach, which makes interpreting the data much easier.

Scientists from Michigan State University have led the largest soil DNA sequencing effort to date, which sheds light on one of the planet’s largest microbial populations.

Considering that a single spoonful of soil holds hundreds of billions of microbial cells, encompassing thousands of species, it’s no wonder that the daunting task of an accurate census has never been undertaken.

MSU scientists, working with colleagues from the U.S. Department of Energy Joint Genome Institute and Lawrence Berkeley National Laboratory, published their findings in the current issue of Proceedings of the National Academy of Sciences.

“It’s one of the most diverse microbial habitats on Earth, yet we know surprisingly little about the identities and functions of the microbes inhabiting soil,” said Jim Tiedje, MSU Distinguished Professor of microbiology and molecular genetics and of plant, soil and microbial sciences, and one of the co-authors.

Since the release of the first human genome, the applications of DNA sequencing have been extended as a powerful diagnostic technique for gauging the health of the planet’s diverse ecological niches and their responsiveness to change. The team’s results provide a simple, elegant solution to sifting through the deluge of information gleaned, as well as a sobering reality check on just how hard a challenge these environments will be.

The team compared microbial populations of different soils sampled from Midwestern cornfields, under continuous cultivation for 100 years, with those sourced from pristine expanses of prairie.

“The Great Plains represents the largest expanse of the world’s most fertile soils, which makes it important as a reference site and for understanding the biological basis and ecosystem services of its microbial community,” Tiedje said. “It sequesters the most carbon of any soil system in the U.S. and produces large amounts of biomass annually, which is key for biofuels, food security and carbon sequestration.”

As part of the study, the researchers created a new analytic approach, which makes interpreting the data much easier. They offered a data management “democratization” that empowers scientists who don’t have access to cloud- and high-performance computing, to analyze the data

It’s comparable to how large jpeg files are shared over the Internet, a process that sheds a substantial amount of data without compromising the image, said C. Titus Brown, MSU assistant professor in bioinformatics.

“I think this can lead to a fundamental shift in thinking,” he said. “We are actually converting standard, heavyweight approaches in biological sequence analysis to an ultra-efficient streaming approach.”

Even though the study provided 400 billion bases of data, however, it was still insufficient to interrogate the microbial players in the localized soil sample deeply enough, confirming that much more data are needed to study the content of soil metagenomes comprehensively, said Adina Chuang Howe, MSU postdoctoral student of bioinformatics and lead author.

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