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Subsurface Biogeochemical Research Program

Benefits of Subsurface Biogeochemical Research for U.S. Water, Environmental, and Energy Security

Research funded by the Subsurface Biogeochemical Research (SBR) program, as well as SBR’s direct predecessor programs (Environmental Remediation Sciences Program, Natural and Accelerated Bioremediation Program, and Subsurface Science Program), in watershed and subsurface system science has produced world-leading discoveries and impacts in multiple scientific fields, new capabilities, and leading expertise for more than 30 years. Through tight iteration among observations, experiments, and modeling, SBR obtains a systems-level understanding of how watersheds function, from the subsurface through land surface vegetation. Understanding how watersheds function as integrated hydrobiogeochemical systems is key for addressing the many energy and environmental challenges facing the United States, including contaminant cleanup, clean water availability, nutrient availability for sustainable biofuel crops, safe subsurface storage of energy and nuclear byproducts, and recovery of subsurface energy resources. Examples of recent SBR-funded discoveries and accomplishments in various research areas include:

Watershed and Subsurface System Modeling and Simulation

  • Simulation across continental scales demonstrates that groundwater flow is key for understanding evapotranspiration from vegetation.
  • Integrated genomic information into parallelized reactive transport models to more accurately define biogeochemical reaction pathways catalyzed by subsurface microbial communities and water table dynamics.
  • Mechanistic modeling studies demonstrate molecular through watershed controls on long-term uranium and iodide plume behavior.

Contaminant Transport and Transformation

  • Used a combination of high-performance computer modeling and chemical analyses to solve a 40-year challenge in identifying the genes in anaerobic bacteria that methylate mercury and regulate ecosystem-scale mercury transport.
  • Multiple studies provide fundamental understanding of plutonium hydrobiogeochemistry in the Hanford Site (Richland, Washington) subsurface, enabling better decision making by the Department of Energy’s (DOE) Office of Environmental Management on long-term stewardship of contaminated groundwater and soils at this DOE site.
  • Comprehensively elucidated uranium’s extremely complex environmental biogeochemical cycle within diverse subsurface environments ranging from sand-dominated systems to fractured bedrock systems. This process understanding has been incorporated into predictive fate and transport models.

Water Quality and Availability

  • Three new field-scale study sites located (a) across a headwater catchment, (b) over an extended river reach, and (c) within a flood-plain river corridor are providing unprecedented new insights on surface water–groundwater hydrobiogeochemical interactions controlling watershed water quality and availability.
  • Demonstrated that variable water release patterns from an upstream dam drive dynamic mixing of groundwater with surface water within the Columbia River, enabling microbial communities in the sediments to catalyze biogeochemical cycling of elements and nutrients.
  • Demonstrated that when metal-laden (e.g., lead and arsenic) mine wastes become buried in stream sediments—such as from the Gold King Mine spill into the Animas River in Colorado—anaerobic microorganisms are likely to drive long-term remobilization of these metals into the stream.

Subsurface Hydrobiogeochemistry

  • Multiple studies demonstrate that incorporating hydrobiogeochemical process understanding into parallelized reactive transport model codes enables predictive understanding of microbially mediated biogeochemical reactions in natural heterogeneous media.
  • Integrated numerical models of subsurface biogeochemical processes and microbial population dynamics with hydrologic transport models to describe and predict chemical and nutrient movements and water fluxes in subsurface environments under natural and manipulated conditions.

Nutrient Availability and Elemental Cycling

  • Multiple studies demonstrate the importance of “hot spots” and “hot moments” in controlling fluxes of key elements (e.g., iron and carbon) and contaminant transformations at field-relevant scales.
  • Identified novel nitrate-reducing bacteria from the subsurface, and subsequent studies changed the conceptual model of nitrogen cycling.
  • Discovered that in alkaline aquifers, some bacteria can use elemental sulfur to indirectly reduce iron, which can then indirectly affect contaminant mobility in the subsurface.

Subsurface Microbiology

  • Demonstrated for the first time that Archaea isolated from groundwater have clustered regularly interspaced palindromic repeats (CRISPR)–CRISPR-associated protein-9 (Cas9) systems.
  • Significantly expanded the known microbial “tree of life” using genomic methods and bioinformatics.
  • Identified completely functional nanobacterial-sized cells from groundwater and thereby determined the smallest size limit for a living cell.
  • Identified uncultivatable bacteria from the subsurface using metagenomics approaches and determined their roles in modulating subsurface biogeochemical processes.


  • Used new, highly sensitive analytical capabilities at DOE’s Environmental Molecular Sciences Laboratory and DOE light source user facilities to reveal unique chemical forms and species of elements associated with bacterial and mineral surfaces, thereby providing a scientific basis for predicting the behavior of these elements and associated contaminants.


  • Used hydrogeophysical methodologies to characterize microbial communities and their activity in the subsurface.
  • Identified subtleties of water movement in subsurface environments and anomalous contaminant migration patterns using new geophysical approaches.

A detailed timeline of scientific advances and other programmatic activities is available.

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