BER launches Environmental System Science Program. Visit our new website under construction!

U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

Microbial Protein Structure Altered when Exposed to Soil Mineral Surfaces
Published: May 31, 2016
Posted: October 13, 2016

New findings may improve predictions using decomposition models and shed light on potential changes in protein activity.

The Science
The degradation of soil organic matter by microbes plays an important role in atmospheric carbon levels. A recent study examined how soil minerals could affect the stability of microbial proteins, potentially influencing the rate of carbon dioxide release into the atmosphere.

The Impact
The study shows that interactions with the surface of birnessite, but not other common soil minerals, have the potential to substantially alter the structure of bacterial proteins. These findings shed new light on how protein-mineral interactions could affect degradation rates of soil organic matter.

Soil contains the largest amount of terrestrial carbon on the planet, so a small change in soil carbon can have a large impact on atmospheric carbon dioxide levels. Therefore, understanding how organic carbon is released from soil into the atmosphere is a key question in climate science. Microbes produce enzymes that interact with soil minerals, and these protein-mineral interactions play an important role in the decomposition of soil organic carbon, which is subsequently released into the atmosphere. Not clear, however, is how different soil minerals affect the structure and function of microbial enzymes. To address this question, a team of researchers from the Department of Energy’s (DOE) Environmental Molecular Sciences Laboratory (EMSL), Oregon State University, and Leibniz Zentrum für Agrarlandschaftsforschung conducted molecular dynamics simulations to determine how interactions with surfaces of five common soil minerals affect the structure of a small bacterial protein called Gb1. The team performed simulations using the Cascade high-performance computer at EMSL, a DOE Office of Science user facility. The researchers found the Gb1 structure becomes highly altered due to interactions with Na+-birnessite mineral surfaces, but not kaolinite, montmorillonite, and goethite mineral surfaces. Interactions with birnessite caused the Gb1 protein structure to flatten and partially unravel. These findings shed light on how different soil minerals could affect the stability of microbial enzymes, thereby influencing the degradation rate of soil organic carbon. These insights build on previous, published experimental observations and could lead to more accurate projections of how much carbon dioxide could be released into the atmosphere as a result of microbial decomposition of soil organic matter.

BER PM Contact
Paul Bayer, SC-23.1, 301-903-5324

PI Contact
Amity Andersen
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory

This work was supported by the Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research, including support of the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility; and the “Understanding Molecular-Scale Complexity and Interactions of Soil Organic Matter” Intramural Project at EMSL.

Andersen, A., P. N. Reardon, S. S. Chacon, N. P. Qafoku, N. M. Washton, and M. Kleber. 2016. “Protein-Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure,” Langmuir 32(24), 6194-209. DOI: 10.1021/acs.langmuir.6b01198. (Reference link)

Related Links
EMSL article: Microbial Protein's Structure can be Altered when Exposed to Soil Mineral Surfaces
EMSL article: Abiotic Pathway Makes Organic Nitrogen Compounds Available to Microbes and Plants

Topic Areas:

  • Research Area: Terrestrial Ecosystem Science
  • Research Area: Carbon Cycle, Nutrient Cycling
  • Research Area: DOE Environmental Molecular Sciences Laboratory (EMSL)
  • Research Area: Microbes and Communities
  • Research Area: Computational Biology, Bioinformatics, Modeling
  • Research Area: Structural Biology, Biomolecular Characterization and Imaging

Division: SC-33.1 Earth and Environmental Sciences Division, BER


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

Mar 23, 2021
Molecular Connections from Plants to Fungi to Ants
Lipids transfer energy and serve as an inter-kingdom communication tool in leaf-cutter ants&rsqu [more...]

Mar 19, 2021
Microbes Use Ancient Metabolism to Cycle Phosphorus
Microbial cycling of phosphorus through reduction-oxidation reactions is older and more widespre [more...]

Feb 22, 2021
Warming Soil Means Stronger Microbe Networks
Soil warming leads to more complex, larger, and more connected networks of microbes in those soi [more...]

Jan 27, 2021
Labeling the Thale Cress Metabolites
New data pipeline identifies metabolites following heavy isotope labeling.

Analysis [more...]

Aug 31, 2020
Novel Bacterial Clade Reveals Origin of Form I Rubisco

  • All plant biomass is sourced from the carbon-fixing enzyme Rub [more...]

List all highlights (possible long download time)