Subsurface Biogeochemical Research
science.energy.gov/ber/research/cesd/subsurface-biogeochemical-research/
Advancing a predictive understanding of subsurface environmental processes applicable
to a range of DOE energy and environmental challenges
T
he overarching goal of the Subsurface Biogeochemical Research (SBR) program is to develop robust,
predictive models of subsurface biogeochemical processes to understand the structure and function of complex subsurface systems. SBR supports
a wide range of research activities (described
below) to advance the development of fully
coupled models of subsurface environmental processes. These models incorporate
metabolic modeling of microbial processes;
molecular-scale understanding of geochemical stability, speciation, and biogeochemical reaction kinetics; and diagnostic
signatures of the system response at varying
spatial and temporal scales. State-of-science
understanding codified in models provides
the basis for testing hypotheses, guiding
experimental design, integrating scientific
knowledge on multiple environmental systems
into a common framework, and translating this
information to support informed decision making
and policies.
Research Approach
The SBR activity within the Climate and Environmental Sciences Division of the Office of Biological and Environmental
Research (BER) is advancing a basic understanding of subsurface processes at the intersection of biology, chemistry, and
Current Contaminants of Concern
Contaminants of greatest interest to
the SBR program are those that are
long-lived and mobile, occur at a
number of DOE facilities, and may
pose risks to humans or the environment. They include radionuclides and
metals that are the source material for
or waste products of nuclear research,
reactor operations, and fuel production at DOE facilities.
Radionuclides
•
•
•
•
•
•
•
U
ranium
T
echnetium
P
lutonium
S trontium-90
C
esium-137
I odine-129
N
eptunium-237
Metals
• M
ercury
• C
hromium
Integrative
SBR activities
span multi­scale
­­processes controlling
­contaminant mobility in the
environment.
physics. SBR supports interdisciplinary research in an iterative
cycle of hypothesis generation, experimentation, and modeling
between the laboratory and the field. The current focus is on
elucidating the processes impacting the mobility of contaminant
metals and radionuclides found in the subsurface at Department of Energy (DOE) legacy waste sites. Overall, this scientific
approach is applicable to a wide range of DOE-relevant energy
and environmental challenges including:
• Cleanup of contaminants and stewardship of former
­weapons production sites.
• Underground storage of spent nuclear fuel.
• Carbon cycling and sequestration in the environment.
• Nutrient cycling in the environment in support of sustainable biofuel development.
• Fossil fuel processing and recovery from the deep subsurface.
U.S. Department of Energy Office of Science
Research Activities
Field-Scale Research emphasizes integrative, multi­disciplinary
investigations of key biogeochemical processes that help to validate new insights into the behavior of contaminants derived
at smaller scales or in the laboratory. In situ field studies also
provide the opportunity to test measurement and monitoring tools developed to describe subsurface processes and the
functioning of microbial communities.
Uranium mill tailings site
(Rifle, Colo.)
Integrated Field Research Challenge
(IFRC) Projects. IFRC field sites provide researchers with opportunities to
obtain samples of environmental media
for analysis and to test their laboratoryderived hypotheses under natural conditions at the field scale. These sites also
are used to test and evaluate computer
models describing contaminant mobility
in the environment.
Modeling and High-Performance Computing supports
conceptual and computational models of proc­esses affecting
contaminant transport that help clarify research hypotheses
and guide future research directions. SBR partners with
DOE’s Office of Advanced Scientific Computing Research on
projects of mutual interest, such as the simulation of groundwater reactive transport processes, via the Scientific Discovery through Advanced Computing (SciDAC) program.
Simulation of Pore-Scale Fluid
Flow. [Institute for Ultra-Scale
Visualization, University of
California at Davis]
Geophysics and Geohydrology fosters the development of
novel, high-resolution geophysical techniques for subsurface
research and the deployment of current geophysical techniques in new ways to infer biogeochemical processes affecting contaminant transport across large areas.
Y-12 site (Oak Ridge, Tenn.)
Hanford 300 site (Hanford, Wash.)
Researcher Using
Global Positioning System to
Collect Surface
Electromagnetic Data at
the Rifle IFRC
Site. [Lawrence
Berkeley National
Laboratory]
Molecular-Scale Processes research emphasizes analyses of,
for example, sorption/desorption, precipitation/dissolution,
and redox transformation that can be fully understood only
from detailed, mechanistic, molecular-scale studies. These
process analyses form the basis for understanding the myriad
different mechanisms affecting contaminant transport in the
environment at a multitude of scales.
These molecular-scale research activities are
­leveraged by access to user facilities including:
• Th
e Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory.
• S ynchrotron light sources located at Argonne
National Laboratory, Lawrence Berkeley
National Laboratory, Brookhaven National
Laboratory, and SLAC National Accelerator
Laboratory.
2
Molecular Structure of Shewanella oneidensis
MtrF Decaheme C
­ ytochrome. The structure
provides molecular insight into how reduction
of insoluble substrates (e.g., minerals), soluble
substrates (e.g., flavins), and cytochrome redox
partners might be possible in tandem at different
termini of a trifurcated electron-transport chain on
the cell surface. [Clarke et al. 2011. “Structure of
a Bacterial Cell Surface Decaheme Electron Conduit,” PNAS. DOI: 10.1073/pnas.1017200108.]
Office of Biological and Environmental Research • Climate and Environmental Sciences Division
U.S. Department of Energy Office of Science
Environmental Microbiology and Applied Genomics focuses
on understanding the functioning of subsurface microbial
communities and how their growth and activity affect contaminant fate and transport. Of particular interest are communities involved in metal and radionuclide immobilization or
stabilization processes.
Genome-Enabled Evaluation of Microbial Community
Function and Dynamics. Genome-based techniques are helping to advance a predictive understanding of the function and
activity of microbial communities in the environment.
Geochemistry and Biogeochemistry emphasizes understanding the integral relationships among biological and
geochemical processes influencing contaminant transport
and remediation. Insight gained at the molecular level is
used to interpret
Bacterial
or predict proDissolution
cesses occurring
of Ferrous
at larger scales
Phosphate.
and ultimately
[Pacific Northalong ground­
west National
water flow paths.
Laboratory]
Measurement and Monitoring supports the development of
novel techniques to study contaminant transport processes
and evaluate the potential for long-term success of in situ
remediation concepts. Areas of interest include noninvasive
approaches to delineate subsurface structure, track contaminant migration, detect groundwater flow, and evaluate the
rate and progression of biogeochemical processes.
Experimental Test Plot of Well
Locations at Rifle IFRC Site. Integrative measuring and monitoring techniques are being developed to enhance
predictive descriptions of contaminant
transport in experimental field studies
and natural attenuation processes.
Remediation and Stabilization Research focuses on potentially novel methods to remove, immobilize, or stabilize
contaminants in the subsurface. This research includes the
investigation of both active technologies (physical, chemical,
and biological processes) and passive technologies for intercepting and/or attenuating contaminant concentrations in situ
(barrier systems, natural attenuation).
Scanning Electron
Microscope Image of
Sulfate-Reducing Biofilm.
The biofilm was obtained
from a borehole used for longterm acetate injection during
biostimulation activities.
[Pacific Northwest National
Laboratory, Lawrence Berkeley National Laboratory]
Providing Solutions for Science
and Society
Insights into subsurface processes gleaned from SBR activities
are leading to a predictive understanding of coupled biogeochemical processes in key subsurface environments of interest to DOE. This fundamental knowledge underpins efforts
to predict and control environmental processes—enabling
development of robust strategies to monitor, immobilize, or
remove from the environment contaminants related to former
weapons production and informing science-based approaches
Predicting Microbial Interactions Could Improve
Uranium Bioremediation
Advances in genome sequencing and the capability to
develop genome-scale metabolic models have enabled predictions of microbial interactions. SBR-funded researchers
recently characterized the genomes of dominant microbial
populations and the proteins they expressed during in
situ tests of uranium bioremediation. Changes in microbial metabolism, energy generation, and microbial strain
composition over time reflected the changing geochemical conditions stimulated during the field test. The results
yielded important insights into the functioning of subsurface microbial communities, providing mechanistic
information that can be used to inform models of uranium
bioremediation. This approach enables scientists to study
the mechanistic basis for the growth and functioning of
active microbes in the environment and is applicable not
only to bioremediation but carbon sequestration, nutrient
cycling, and other DOE mission areas.
Office of Biological and Environmental Research • Climate and Environmental Sciences Division
3
U.S. Department of Energy Office of Science
to assess the risks of spent nuclear fuel storage. SBR research
also helps reduce climate model uncertainties in the biogeochemical cycling of carbon in soils and sediments and informs
development of carbon sequestration strategies in terrestrial
or subsurface environments. In support of sustainable biofuels
development, the program’s activities provide improved understanding of coupled plant-microbe-mineral interactions that
impact and control nutrient cycling in soils. Additionally, SBR
research is applicable to manipulative strategies to develop
and enhance the recovery of fossil fuels from deep subsurface
deposits. In short, SBR research provides predictive understanding of subsurface processes that reduces the risk and
cost of developing and managing a variety of DOE-relevant
environmental and energy systems.
Leveraging Other DOE Assets
SBR advances fundamental understanding of environmental
processes through a unique set of BER programs and user facilities. These include the related Terrestrial Ecosystem Science
program, which studies carbon and nutrient cycling, as well
as the Genomic Science program and the microbial genome
sequencing efforts at the DOE Joint Genome Institute. Taking
advantage of revolutionary, genome-enabled, and systems
biology techniques promises a more mechanistic understanding of subsurface microbial metabolism affecting contaminant
transport. The Environmental Molecular Sciences Laboratory
supports an array of co-located experimental and computational capabilities for molecular-level research. Additionally,
synchrotron light sources provide structural and chemical information often unavailable with conventional sources of x-rays.
SBR research also is leveraged with other program offices
within the Office of Science:
• Office of Advanced Scientific Computing Research, Scientific Discovery through Advanced Computing program.
• Office of Basic Energy Sciences, Geosciences program.
Internal DOE and external programs complementing SBR
research or actively leveraging SBR-funded activities include:
• Strategic Environmental Research and Development
Program.
• Advanced Simulation Capability for Environmental Management, DOE Office of Environmental Management.
Funding Opportunities
The SBR program supports mission-oriented research performed by (1) integrated research programs (scientific focus
areas) at national laboratories; (2) university r­ esearchers
with multidisciplinary capabilities; (3) university-based
“exploratory” research for new concepts, tools, and
approaches; and (4) Integrated Field Research Challenge
sites. Funding opportunities are posted at grants.gov.
Additional image credits for p. 1: Field-Scale Research depicting varying sediment layers, courtesy of Pacific Northwest National Laboratory;
Geophysics and Geohydrology depicting Rifle IFRC site, courtesy of Pacific Northwest National Laboratory; Environmental Microbiology and
Applied Genomics depicting GeoChip array, courtesy of Jizhong Zhou, University of Oklahoma.
Contacts and Websites
SBR Program Managers
Paul Bayer, Environmental Science and
Environmental Molecular Sciences Laboratory
[email protected], 301-903-5324
David Lesmes, Geophysics and Geohydrology
[email protected], 301-903-2977
Roland Hirsch, Chemistry and Synchrotron Science
[email protected], 301-903-9009
Arthur Katz, Heavy Element Chemistry
[email protected], 301-903-4932
Websites
Subsurface Biogeochemical Research
(science.energy.gov/ber/research/cesd/subsurfacebiogeochemical-research/)
4
Climate and Environmental Sciences Division
(science.energy.gov/ber/research/cesd/)
DOE Office of Biological and Environmental Research
(science.energy.gov/ber/)
DOE Office of Science (science.energy.gov)
U.S. Department of Energy (energy.gov)
Complex Systems Science for Subsurface Fate and
Transport: Report from the August 2009 Workshop
(science.energy.gov/~/media/ber/pdf/Subsurface_
complexity_03_05_10.pdf )
Subsurface Biogeochemical Research Strategic Plan
(science.energy.gov/~/media/ber/pdf/Subsurface_
biogeochemical_research_strategic_plan.pdf)
Office of Biological and Environmental Research • Climate and Environmental Sciences Division
April 2012