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The Argonne Subsurface Science SFA

Overview: The Argonne Subsurface Biogeochemical Research Program (SBR) Scientific Focus Area (SFA) integrates synchrotron-based biogeochemistry with “now-generation” DNA sequencing techniques and bioinformatics approaches, microbiology, and molecular biology to pursue the long-term scientific goal of elucidating the interplay, at the molecular level, between specific microbial metabolic activities, solution chemistry, and mineralogy contributing to the transformations of minerals, heavy metals, and radioactive elements in subsurface environments. Hypotheses directed toward achieving this goal are tested by experiments that capitalize on unique Argonne capabilities, together with collaborative efforts at other national laboratories (Oak Ridge National Laboratory [ORNL], Pacific Northwest National Laboratory [PNNL], Lawrence Berkeley National Laboratory [LBNL]) focused on field-scale subsurface biogeochemical questions, as well as several academic institutions. The objective for FY 2013-FY 2015 is to characterize coupled biotic-abiotic molecular-scale Fe, S, heavy metal, and radionuclide transformations, integrated over different length scales, to provide knowledge that is necessary for understanding subsurface processes and predicting contaminant reactivity and transport. This objective guides the development and optimization of synchrotron methods for molecular-level measurements pertinent to understanding contaminants, carbon/nutrient forms, and the geochemical character of groundwater in subsurface environments. Argonne SBR SFA research addresses four critical knowledge gaps related to understanding these issues: (1) an in-depth understanding of molecular processes affecting contaminant speciation; (2) an understanding of the role of biogenic and abiotic redox-active products and intermediates in Fe, S, and contaminant transformations; (3) an understanding of mass transfer and microenvironment effects on Fe, S, and contaminant transformations; and (4) an in-depth understanding of the relationship between microbial community dynamics and function and coupled biotic-abiotic controls and their effects on major/minor element cycling and contaminant transformations. Addressing these knowledge gaps has driven the development of 17 specific hypotheses to be tested within the Argonne SBR SFA.

This three-year science plan focuses on the transformation of minerals, uranium, and mercury at different spatial scales and in the context of iron and sulfate reduction in subsurface environments. Experiments at Argonne (Dion Antonopoulos, Max Boyanov, Ted Flynn, Ken Kemner, Ed O’Loughlin, Deirdre Sholto-Douglas), with collaborators from PNNL (Jim Fredrickson, John Zachara), ORNL (Scott Brooks, Dave Watson), LBNL (Ken Williams), Michigan State University (MSU; Terry Marsh), University of Iowa (Michelle Scherer), University of Illinois at Urbana-Champaign (Rob Sanford), Tufts University (Kurt Pennell), University of Tennessee (Frank Loeffler), Stanford University (Craig Criddle, Wei Min Wu), Hamilton College (Mike McCormick), Virginia Commonwealth University (Everett Carpenter), and the Illinois Institute of Technology (IIT; Bhoopesh Mishra, Carlo Segre) will require the integration of microbiology, molecular biology, geochemistry, and physics. Research will emphasize laboratory-based experiments (mixed-batch reactors, thin films for microscopy studies, and columns) with single-crystalline-phase Fe oxide (inclusive of oxides, oxyhydroxides, and hydroxides) powders, fabricated Fe-rich mineral assemblies designed to mimic mineralogical conditions in subsurface environments in the field, Fe oxide thin films, and geomaterial collected from subsurface field environments (down flow from settling ponds at the Y-12 plant at Oak Ridge, Tennessee, groundwater-Columbia river water mixing zone at the Hanford 300 Area at Richland, Washington, and UMTRA sediment at Rifle, Colorado). Inocula for promoting iron- and sulfate-reducing conditions will include (1) monocultures of dissimilatory iron-reducing bacteria (e.g., Geobacter spp., Anaeromyxobacter spp.) and dissimilatory sulfate-reducing bacteria (e.g., Desulfovibrio spp.) representative of organisms identified at these field sites and (2) natural microbial consortia collected from all three of these sites.

The experimental work of the Argonne SBR SFA will drive optimization of techniques at Advanced Photon Source (APS) beamlines and thus increase the availability and productivity of x ray beamlines with the characteristics required for the proposed work. This will include (1) development of x ray fluorescence (XRF) microspectroscopy (spatial resolution ~100 nm) data correction algorithms to enhance capabilities at the XOR Sector 2 insertion device (ID) beamline and (2) optimization of synchrotron-based hard x ray capabilities for in situ investigations of coupled microbiological and geochemical processes in free-flowing columns.

Figure 1. Scope and integration of approaches to study subsurface complexity under the Argonne SFA. The aerial image of the Advanced Photon Source in the background signifies Argonne’s strength in using synchrotron radiation for molecular-level probing and understanding of transformations across each of the relevant length scales.
Figure 2. Experimental platforms and characterization methods at Argonne for accomplishing the objectives of the Argonne SBR SFA.
Team Members:  
Research Manager: Robin Graham (
Research Coordinator: Ken Kemner (
Co-Principal Investigators: Ed O’Loughlin (
  Max Boyanov (
Key Collaborators: M. Scherer, University of Iowa
  T. Marsh, Michigan State University
  R. Sanford, University of Illinois Urbana Champaign
  M. McCormick, Hamilton College
  E. Carpenter, Virginia Commonwealth University
  J. Fredrickson/J. Zachara, Pacific Northwest Natl. Lab
  S. Brooks/D. Watson, Oak Ridge National Laboratory

Research Highlights:




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