Corporate Banner
Satellite Banner
Scientific Community
Become a Member | Sign in
Home>News>This Article

MSU Leads Largest Soil DNA Sequencing Effort

Published: Thursday, March 13, 2014
Last Updated: Thursday, March 13, 2014
Bookmark and Share
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.

Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,800+ scientific posters on ePosters
  • More than 4,000+ scientific videos on LabTube
  • 35 community eNewsletters

Sign In

Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

MSU to Lead $6.5 Million Research on Disease Resistance in Cucurbits
A national team of 20 scientists led by Michigan State University has been awarded $6.5 million grant to accelerate the development of disease-resistant cucurbit crops through leveraging applied genomics.
Wednesday, October 07, 2015
Perennial Biofuel Crops’ Water Consumption Similar to Corn
A recent study looks at how efficiently “second-generation” biofuel crops—perennial, non-food crops such as switchgrass or native grasses—use rainwater and how these crops affect overall water balance.
Wednesday, July 08, 2015
New, Fossil-fuel-free Process Makes Biodiesel Sustainable
A new fuel-cell concept, developed by a Michigan State University researcher, will allow biodiesel plants to eliminate the creation of hazardous wastes while removing their dependence on fossil fuel from their production process.
Wednesday, May 21, 2014
How Do You Feed 9 Billion People?
An international team of scientists has developed crop models to better forecast food production to feed a growing population in the face of climate change.
Wednesday, June 12, 2013
Hormone could boost plant immune systems
The discovery of a hormone acting like molecular glue could hold a key to bolstering plant immune systems and understanding how plants cope with environmental stress.
Tuesday, October 12, 2010
Researchers discover mechanism protecting plants against freezing
MSU biochemists helps explain how plants protect themselves from freezing temperatures and could lead to discoveries related to plant tolerance for drought and other extreme conditions.
Thursday, September 02, 2010
Scientific News
Red Clover Genome to Help Restore Sustainable Farming
The Genome Analysis Centre (TGAC) in collaboration with IBERS, has sequenced and assembled the DNA of red clover to help breeders improve the beneficial traits of this important forage crop.
Turning up the Tap on Microbes Leads to Better Protein Patenting
Mining millions of proteins could become faster and easier with a new technique that may also transform the enzyme-catalyst industry, according to University of California, Davis, researchers.
Tardigrade's Are DNA Master Thieves
Tardigrades, nearly microscopic animals that can survive the harshest of environments, including outer space, hold the record for the animal that has the most foreign DNA.
GMO Food Animals Should be Judged by Product, Not Process
In a world with a burgeoning demand for meat, milk and eggs, regulatory policies around the use of biotechnologies in agriculture need to be based on the safety and attributes of those foods rather than on the methods used to produce them, says a UC Davis animal scientist.
Cancer-Fighting Tomato Component Traced
The metabolic pathway associated with lycopene, the bioactive red pigment found in tomatoes, has been traced by researchers at the University of Illinois.
TGAC Announces Milestone in Wheat Research
A more complete and accurate wheat genome assembly is being made available to researchers, by The Genome Analysis Centre (TGAC) on 12 November 2015.
Shedding Light on the Origin of the Date Palm
Researchers also find ‘genetic mutation’ that is responsible for dates’ color.
New Way to Find DNA Damage
University of Utah chemists devised a new way to detect chemical damage to DNA that sometimes leads to genetic mutations responsible for many diseases, including various cancers and neurological disorders.
Speeding Up Potato Breeding
A joint project is investigating the potential of drones for speeding up the development of new potato varieties.
Gene Editing Could Enable Pig-To-Human Organ Transplant
The largest number of simultaneous gene edits ever accomplished in the genome could help bridge the gap between organ transplant scarcity and the countless patients who need them.
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,800+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,000+ scientific videos