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The Microbes and Molecules Beneath Your Feet

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What has dirt got to do with you.  Dirt, also known as soil, is so much more than something you want to keep out of the house.

At the Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy (DOE) Office of Science User Facility at Pacific Northwest National Laboratory, researchers study the complex properties of dirt and its interactions at a molecular level because of soil’s importance to our lives – so important that the United Nations has declared 2015 to be the “International Year of Soils” to raise awareness of soil’s significance. EMSL provides researchers from across the U.S. and other countries with leadership and access to its expertise, including more than 150 experimental instruments and its supercomputer – Cascade – for typically no cost to scientists from academia, government labs, and industry.

At the Department of Energy’s EMSL, scientists from around the world conduct experimental and theoretical research to understand the environment on a molecular level.
Photo courtesy of Dave Anderson, EMSL

To carry out investigations into the complexities of soil science, research teams and individual investigators from outside institutions working alongside EMSL scientists have been applying EMSL’s scientific and computational capabilities and developing new methods of analyzing and characterizing the composition of soils to help better understand them and how they contribute to processes important to DOE.

Most recently, EMSL has coordinated with another DOE Office of Science User Facility, the Joint Genome Institute (JGI), which is managed by the Lawrence Berkeley National Laboratory, to enable scientists to leverage opportunities in genomics research at JGI and molecular characterization at EMSL at the same time. The JGI-EMSL Collaborative Science Initiative (JECSI) is supporting a number of user projects, including two that are led by outside researchers working with EMSL and with JGI scientists and equipment on soil studies.

One group led by Virginia Rich from the University of Arizona monitors carbon cycling at a permafrost site in sub-arctic Sweden. Permafrost acts as a big “freezer,” currently storing twice the carbon the atmosphere contains. As this freezer thaws from climate change, its carbon will become available to microbes that convert carbon to simpler compounds; these simpler compounds include the greenhouse gases carbon dioxide, carbon monoxide, and methane that could further drive global warming. Understanding carbon cycling in this frozen environment is critical to determining how thawing will impact climate change.

The roots of a common Mediterranean grass, Avena fatua, are the focus of a second joint JECSI study led by Mary Firestone from the University of California, Berkeley. Firestone’s team follows carbon as it moves from the grass roots into soil microbes, then into the surrounding area. A closer look at the root/microbe interaction may explain the decomposing and dispersing mechanisms responsible for spreading carbon in the soil and, in turn, this knowledge will help to better project the soil’s response to environmental changes.

EMSL, the Environmental Molecular Sciences Laboratory, is a Department of Energy national scientific user facility located at PNNL.

Photo courtesy of EMSL

Among EMSL’s regular user projects, one study being led by Johannes Lehmann from Cornell University is examining fires and the resultant char (the blackened remains of trees and shrubs), to address concerns about soil carbon storage. Char is a form of carbon that can be sequestered in soil. Soils contain a surprising amount of char, and the slower it breaks down, the longer carbon stays in soil. Scientists are analyzing the distribution of char carbon at a fine scale to understand the interactions that drive decomposition and retention of char. The answers could then help predict if adding char will change the amount of carbon stored in soil.

Malak Tfaily from EMSL is supporting a PNNL team investigating the effects of environmental changes that have occurred over a 17-year period. By transplanting soil to new locations, and then comparing changes in the genes of microbes at these different locations, scientists can identify adaptations in the structure and function of microbial communities, along with changes in soil chemistry caused by relocation to hotter, drier or cooler, wetter locations – effectively mimicking climate changes.

These examples illustrate how applying EMSL’s unique tools and expertise are providing an in-depth understanding of how soils are changing in response to environmental and climate changes. That, in turn, will better prepare us for the challenges ahead. That’s why, at EMSL, it’s a joy to dig for answers.

Contacts and sources:
Sandra Allen McLean

 Environmental Molecular Sciences Laboratory (EMSL),


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