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Subsurface Biogeochemical Research Program

DOE User Facilities Enabling Science

Empowering an international community of scientists with the most advanced technologies

The U.S. Department of Energy (DOE) Office of Science oversees the construction and operation of some of the nation's most advanced scientific user facilities, located at national laboratories and universities. These include particle and nuclear physics accelerators, synchrotron light sources, neutron scattering facilities, supercomputers and high-speed computer networks, nanoscale science research centers, genome sequencing facilities, and advanced resources in imaging and analysis for biological and environmental systems. Guidelines for submitting proposals for access to these facilities are available from the individual centers.

Presented below are descriptions of some of the most important facilities for the Subsurface Biogeochemical Research (SBR) program.

Environmental Molecular Sciences Laboratory (EMSL)

EMSL Campus
A pine tree root surrounded by a soil fungus imaged by EMSL’s scanning electron microscope and colorized.

By co-locating more than 150 premier experimental instruments and systems with supercomputing capabilities, EMSL is able to make multiple types of capabilities available to single investigators or multidisciplinary teams to study and model molecular to mesoscale hydrobiogeochemical processes. EMSL, located at Pacific Northwest National Laboratory, has helped thousands of researchers use a multidisciplinary, collaborative approach to iterate between theory and experiment to solve important challenges in biogeochemistry and subsurface science, biological interactions and dynamics, and interactions at the interfaces of natural and engineered materials. EMSL’s Terrestrial and Subsurface Ecosystems (TSE) Science Theme focuses on the dynamics of nutrients, metabolites, and contaminants at biogeochemical interfaces in heterogeneous environments across multiple scales.

Joint Genome Institute (JGI)

DOE Joint Genome Institute
ETOP Microfluidics Device [Roy Kaltschmidt, Berkeley Lab]

Sequencing more than one trillion DNA base pairs per year, DOE JGI in Walnut Creek, California, provides state-of-the-art capabilities for genome sequencing and analysis. With more than 1,100 worldwide collaborators on active projects, DOE JGI is the preeminent facility for sequencing plants, microbes, and microbial communities that are foundational to energy and environmental research. DOE JGI’s Community Science Program (CSP) is designed to bring high-throughput sequencing to the scientific community at large.

Facilities Integrating Collaborations for User Science (FICUS)

Facilities Integrating Collaborations for User Science (FICUS) initiative was established to encourage and enable researchers to more easily integrate the expertise and capabilities of multiple user facilities stewarded by the Department of Energy Office of Science into their research. It current participants include the Environmental Molecular Sciences Laboratory (EMSL), the Joint Genome Institute (JGI), the Atmospheric Radiation Measurement (ARM) user facility, National Energy Research Scientific Computing Center (NERSC), and DOE Systems Biology Knowledgebase (KBase).

High-Performance Computing and Data Storage Facilities

DOE provides the SBR community with several high-performance computing and data storage facilities. 

The Molecular Science Computing (MSC)  capability within EMSL provides an integrated production computing environment that supports a wide range of computational activities in environmental molecular research. DOE’s Environmental Systems Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE) provides an archive for subsurface and terrestrial ecosystem science data.

High Performance Computing and Data Storage Facilities

The DOE Office of Advanced Scientific Computing Research (ASCR) supports several Office of Science user facilities for high-performance production computing and data storage. Access to the production computing systems and data storage capabilities are available through several processes. ASCR facilities include:

Synchrotron Light Sources

Structural Biology Resources

Synchrotron light sources at DOE national laboratories enable resolution of the structure of matter from the cellular level down to the atomic and molecular level using approaches not possible with conventional instrumentation. SBR’s primary synchrotron-based research efforts are located at the Advanced Photon Source (APS) at Argonne National Laboratory (ANL) and Stanford Synchrotron Radiation Lightsource at SLAC National Accelerator Laboratory (SLAC).

The ANL Wetland Hydrobiogeochemistry Science Focus Area elucidating the interplay among microbial metabolic activities, solution chemistry, and mineralogy contributing to element and contaminant transformation.

The SLAC Floodplain Hydro-Biogeochemistry Science Focus Area  advancing predictive understanding of uranium subsurface biogeochemistry, fate, and transport.

Biomolecular Characterization and Imaging

Structural Biology Resources

Structural biology and imaging resources—together with today’s systems biology approaches—are key capabilities for understanding the relationship between the genome, structure, function, and environmental interactions of plants and microbes important for energy and environmental missions. As part of its fundamental biology portfolio, the U.S. Department of Energy’s (DOE) Office of Biological and Environmental Research (BER) supports a suite of experimental research technologies, methodologies, instruments, and computational capabilities at DOE facilities. The resolutions and scales provided by these resources enable studying and understanding biological structures and functional processes important to BER-funded investigators and centers. Capabilities of and contact information for each station are described at

  • DE-FOA-0002482 - Integrated Computational and Data Infrastructure for Scientific Discovery
    Now accepting applications. Letters of Intent Due: April 2, 2021, 5:00 p.m. Eastern Time
  • Office of Science Graduate Student Research (SCGSR) Program 2021 Solicitation 1
    Now accepting applications. Pre-Application Due: May 5, 2021, 5:00 p.m. Eastern Time
  • DE-FOA-0002431 – DOE EPSCoR (Experimental Program to Stimulate Competitive Research) Implementation Grants
    Now accepting applications. Pre-Application Due: December 15, 2020, 5:00 p.m. Eastern Time
  • DE-FOA-0002392-Environmental System Science
    Now accepting applications. Pre-Application Due: Dec. 17, 2020, 5:00 p.m. Eastern Time
  • ASCR Leadership Computing Challenge
    Call for Proposals Open. Pre-Proposals Due: January 4, 2021, 5:00 pm Eastern Time
  • Environmental Research Funding: DoD SERDP
    Now accepting applications.
    • Core Solicitation for Environmental Research and Development Proposals. Pre-Proposals Due: Jan. 7, 2021, 2:00 p.m. Eastern Time.
    • SEED Solicitation. Proposals Due: March 4, 2021, 2:00 p.m. Eastern Time. [11/9]
  • DE-FOA-0002431-Established Program To Stimulate Competitive Research (DOE EPSCoR) Implementation Grants
    Now accepting applications. Pre-Application Due: Dec. 15, 2020, 5:00 p.m. Eastern Time
  • Office of Science Graduate Student Research (SCGSR) Program 2020 Solicitation 2
    Now accepting applications. Pre-Application Due: Nov. 12, 2020, 5:00 p.m. Eastern Time
  • See Also:

PI-Submitted Research Highlights for Subsurface Biogeochemical Research Program

Now Featuring

Open Watershed Science by Design Workshop Report

October 2019

EESSD Strategic Plan 2018

Download PDF

Subsurface Biogeochemical Research Overview

November 2019 [PDF]