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In situ characterization of soil organic carbon-mineral interactions for carbon cycle research

EMSL Project ID


The purpose of this research is to develop a quantitative picture of the impact of increasing global temperatures on organic-soil mineral interactions within the context of both microbial control over mineral formation and immobilization of soluble organic matter (SOM) at soil mineral surfaces. In particular, we will define the stereochemical interactions, binding free energies, and activation barriers that characterize the SOM-mineral and microbe-mineral interfaces for a key set of mineral types and organic compositions. This will be accomplished by integrating in situ TEM capabilities of the Quiet Wing, expanded to incorporate a temperature-controlled, pH-metered, dual inlet flow stage, with the scanned probe imaging and force measurement capabilities available elsewhere in EMSL. These tools will be used to determine nucleation pathways, rates and resulting phases formed on films of both model and natural organic compounds relevant to soils and to measure the binding energies for these organics in contact with iron oxide and phyllosilicates mineral faces. This research addresses the BER mission of understanding of the roles of Earth's biogeochemical systems in determining climate. It uses laboratory experiments on organic-mineral interfaces to understand the interdependency of biogeochemical processes and carbon migration in soils. In addition, it implements EMSL's Quiet Wing facilities advance the frontiers of climate and environmental science and incorporates EMSL's unique in situ liquid phase TEM capabilities.

Project Details

Start Date
End Date


Principal Investigator

James De Yoreo
Pacific Northwest National Laboratory


Nikolla Qafoku
Pacific Northwest National Laboratory

Team Members

Jennifer Soltis
Issaquah School District

Christina Newcomb
Pacific Northwest National Laboratory

Ryan Hufschmid
University of Washington

Nigel Browning
University of Liverpool

Related Publications

Hufschmid RD, CJ Newcomb, JW Grate, JJ De Yoreo, ND Browning, and N Qafoku. 2017. "Direct visualization of aggregate morphology and dynamics in a model soil organic-mineral system." Environmental Science & Technology Letters 4(5):186-191. doi:10.1021/acs.estlett.7b00068
Newcomb C.J., N. Qafoku, J.W. Grate, V.L. Bailey, and J.J. De Yoreo. 2017. "Developing a Molecular Picture of Soil Organic Matter–Mineral Interactions by Quantifying Organo–Mineral Binding." Nature Communications 8. PNNL-SA-121086. doi:10.1038/s41467-017-00407-9
Newcomb CJ, N Qafoku, JW Grate, VL Bailey, and JJ De Yoreo. 2017. "Moving toward a molecular basis for soil organic matter persistence." Nature Geoscience 8:396. doi:10.1038/s41467-017-00407-9