SBR Figure 1

Figure 1: The gray region in the figure illustrates the scope of the Argonne SBR SFA. Specifically identified are (1) the molecular- to core-scale biogeochemical processes that are the primary focus of the SBR SFA, (2) the unique strengths of the Argonne synchrotron-based and genomic- based approaches that we use to understand biogeochemical processes at these scales, and (3) first attempts to use reactive transport modeling approaches to assist in the design and interpretation of biogeochemical experiments.


Water is vital for sustaining life on Earth; its movement, whether through oceans, lakes, rivers, streams, or underground, is responsible for transporting most of the biologically catalyzed and many of the chemically reactive elements that cycle through the environment. The movements of water and the constituents dissolved in it, along with the biogeochemically catalyzed transformations of those constituents, determine the mobility of contaminants, atmospheric greenhouse gas (e.g., CO2, CH4, and N2O) emissions, carbon cycling and sequestration in subsurface environments, nutrient (e.g., carbon and nitrogen) mobility, and the quality of water itself. Iron (Fe) is a highly abundant element in the lithosphere; its biogeochemistry in many aquatic and terrestrial environments is driven largely by microbial activity. In Fe-rich soils and sediments, particularly, Fe redox cycling by microorganisms is a significant component of major and minor elemental cycling and energy flux. Similarly, sulfur (S) is commonly found in groundwater; its transformations, often driven by microbially catalyzed redox reactions, can also greatly affect the cycling of elements. Redox-dynamic environments where Fe or S biogeochemical cycling can be a major driver of other elemental cycles include terrestrial-aquatic interfaces and subsurface environments (e.g., marshes, wetlands, floodplains, soil aggregates, plant root-soil interfaces, and locations where groundwater and surface waters mix). These environments are often part of polar, temperate, or tropical systems containing continuously or temporarily water-saturated soils and sediments. Although much is known about the respective biogeochemical cycles of Fe and S, the interplay between the two cycles is less understood. Thus, understanding the interplay of the Fe and S biogeochemical cycles with the water cycle is critical for prediction of the mobility of contaminants; atmospheric greenhouse gas emissions; carbon cycling and sequestration in subsurface environments; and nutrient mobility in near-surface and subsurface polar, temperate, or tropical systems.

The objective of the Argonne Subsurface Biogeochemical Research Program (SBR) Scientific Focus Area (SFA) is to identify and understand coupled biotic-abiotic molecular- to core-scale transformations of Fe and S within redox-dynamic environments and understand the effects of Fe and S biogeochemistry on transformation and mobility of major/minor elements and contaminants. To accomplish this objective, the Argonne SBR SFA integrates two unique strengths at Argonne — the Advanced Photon Source (APS) for synchrotron-based interrogation of systems and next-generation DNA sequencing and bioinformatics approaches for microbial community and metabolic pathway analysis — with biogeochemistry and microbial ecology. Drawing on these strengths, we pursue the long-term scientific goal of elucidating the interplay, from the molecular to core scale, between specific microbial metabolic activities, solution chemistry, and mineralogy contributing to the transformations of Fe, S, nutrients, and contaminants in subsurface environments. Addressing this objective contributes directly to the goal of the United States Department of Energy (DOE), Office of Biological and Environmental Research (BER), Climate and Environmental Sciences Division (CESD) to “advance fundamental understanding of coupled biogeochemical processes in complex subsurface environments to enable system-level environmental prediction and decision support” ( (DOE 2012). In addition, the work of the Argonne SBR SFA specifically addresses the SBR priority of “understanding and predicting biogeochemical processes in subsurface environments” (DOE 2012). By focusing research efforts on understanding the effects of coupled Fe and S biogeochemical cycles on carbon, nutrient, and contaminant transport, the Argonne SBR SFA will continue contributing to the CESD’s identified core capability (DOE 2012) that includes “focused research on key Earth system processes that represent significant uncertainties and currently limit predictive understanding.” Similarly, by continuing the well-integrated use of synchrotron radiation at the APS to investigate coupled Fe and S biogeochemical processes, the Argonne SBR SFA will contribute to CESD’s identified core capabilities and needs for “exploiting synchrotron radiation light sources provided by the SC Office of Basic Energy Sciences” (DOE 2012) and providing “foundational knowledge of these molecular scale processes” (DOE 2014).

Hypotheses directed toward achieving the goal of the Argonne SBR SFA are tested by experiments that capitalize on the talents of Argonne researchers and unique Argonne capabilities. Other members of the Argonne SBR SFA are research scientists at several additional institutions; they bring diverse, relevant expertise and established track records of collaborative and integrated multidisciplinary research for experiments investigating hydrological and biogeochemical processes at multiple spatial and temporal scales, in both field and laboratory settings. All members of the Argonne SBR SFA share a long-term vision of ultimately integrating the new knowledge generated by the SFA into future multiscale modeling approaches to understand and predict relevant environmental processes. Argonne SBR SFA research addresses four critical knowledge gaps related to accomplishing this goal: (1) an in-depth understanding of the molecular processes affecting Fe, S, and contaminant speciation in dynamic redox environments; (2) an understanding of the role of biogenic and abiotic redox-active products and intermediates in Fe, S, and contaminant transformations; (3) a mechanistic understanding of the factors controlling the mass transfer of Fe, S, and contaminants in heterogeneous media; and (4) an in-depth understanding of the relationship of 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 14 specific hypotheses to be tested within the Argonne SBR SFA.

At the core of our Science Plan are sophisticated molecular speciation measurements, performed at the APS, and omics analyses, using next-generation sequencing and bioinformatics approaches, that provide insights into biogeochemical reaction mechanisms and pathways as components of larger reaction networks driven by microbial communities. This 3‑yr science plan focuses on Fe and S redox transformations, driven by microbial communities, and their effects on the transformation of major and minor elements, nutrients, and contaminants at different spatial scales. Experiments at Argonne (Dion Antonopoulos, Ted Flynn, Ken Kemner, Ed O’Loughlin, Julie Jastrow, Jack Gilbert) — in collaboration with the Bulgarian Academy of Sciences (Max Boyanov); Illinois Institute of Technology (Bhoopesh Mishra, Carlo Segre); University of Iowa (Michelle Scherer, Drew Latta); Korean Institute of Science and Technology (Man-Jae Kwon); North Central College, Naperville, Illinois (Silvia Alvarez-Clare); Hope College, Holland, Michigan (Aaron Best, Graham Peasley); and Pacific Northwest National Laboratory (Jim Fredrickson, John Zachara, Chongxuan Liu, Tim Schiebe, Kevin Rosso) — will require the integration of microbial ecology, microbiology, molecular biology, geochemistry, physics, and modeling approaches. Members of the Argonne SBR SFA team represent expertise in all of these disciplines. Research will emphasize laboratory-based experiments with single-crystalline-phase Fe oxides (including oxides, oxyhydroxides, and hydroxides) and Fe-containing clays (e.g., smectite, illite, chlorite), fabricated Fe-rich mineral assemblies designed to mimic mineralogical conditions in subsurface environments in the field, and geomaterial collected from field environments (e.g., groundwater-Columbia river water mixing zone at the Hanford 300 Area at Richland, Washington, and arctic, temperate, and tropical sites [obtained from no-cost collaborators]). Inocula for promoting bioreducing or biooxidizing conditions will include (1) monocultures of well-characterized organisms representing dominant genera with recognized roles in Fe and S redox transformations (e.g., Geobacter spp., Shewanella spp., Desulfitobacterium spp., Desulfovibrio spp., Desulfotomaculum spp. Thiobacillus spp., Acidithiobacillus spp.), and (2) natural microbial consortia collected from all of these sites. To improve our ability to identify cryptic biogeochemical processes within larger complex reaction networks, we will use model minerals with mixed microbial communities to reduce the complexity of the mineralogical aspects of the system. Similarly, we will use model microbial monocultures to reduce the complexity of the microbial aspects of the system.

In addition to the unique molecular-scale electronic and chemical information provided by measurements at the APS, the experimental work of the Argonne SBR SFA will drive optimization of techniques at APS beamlines, thus increasing the availability and productivity of x‑ray beamlines with the characteristics required for the proposed work and benefitting the larger international synchrotron-based biogeochemistry research community. The focus will be on optimization of synchrotron-based hard x‑ray capabilities for in situ investigations of coupled microbiological and geochemical processes in free-flowing columns. Additional developments of hard x‑ray Raman approaches for bulk sample analysis of C and N chemistries in natural samples will also benefit CESD research activities.



Contact: PI: Ken Kemner,, Ed O’Loughlin