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Subsurface Biogeochemical Research Program

DOE User Facilities Enabling Science

Environmental Molecular Sciences Laboratory

EMSL Campus
The rhizosphere is a critical zone where plant roots, microbes, and minerals interface and where biogeochemical weathering provides nutrients to plants. Shown here is a pine tree root surrounded by a soil fungus imaged by EMSL’s scanning electron microscope and colorized.

The mission of the Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy (DOE) scientific user facility, is to lead molecular-level discoveries for DOE and its Office of Biological and Environmental Research that translate to predictive understanding and accelerated solutions for the nation’s energy and environmental challenges.

EMSL’s scientists and unique, state-of-the-art capabilities can help users gain a predictive understanding of the molecular-to-mesoscale processes in environmental, climate, biological, and energy systems. EMSL offers access to more than 60 premier experimental and computational systems, including many one-of-a-kind analytical instruments for studying atomic to molecular to larger-scale processes and a data management and storage platform with associated computation, modeling, and simulation capacities. EMSL scientists collaborate with users to generate impactful and timely results.

Terrestrial and Subsurface Ecosystems
EMSL’s Terrestrial and Subsurface Ecosystems (TSE) Science Theme encompasses a holistic view of belowground processes including carbon and nutrient cycling among plants, soil, water, and the atmosphere and the fate and transport of contaminants. Developing a mechanistic understanding of biogeochemical and microbial processes in soils and the subsurface, and linking those processes via pore-scale hydrological models, leads to improved strategies for sustainable approaches to land use and contaminant remediation.

New capabilities in TSE include advanced spectrometric and spectroscopic techniques to characterize organic matter in soil and groundwater; in situ tomographic imaging for studying intact roots and nutrient allocation; enhanced pore- to intermediate-scale capabilities in unsaturated porous media; and multiscale reactive transport models.

EMSL Campus
Research on uranium-contaminated wetlands leveraged helium ion microscopy capabilities in EMSL’s Quiet Wing to image biogenic nano-iron oxides oriented along a root recovered from a wetland plant from the Savannah River Site. Scientists Daniel Kaplan, Savanah River National Laboratory, and Peter Jaffe, Princeton University, conducted the research, and Bruce Arey, EMSL technologist, took the colorized image.

Research Capabilities
Users can access more than 150 premier and accompanying instruments and systems distributed among these scientific capabilities:

  1. Subsurface Flow and Transport
    Using EMSL’s subsurface flow and transport capability, researchers can develop remediation strategies for a variety of contaminants by integrating theory, experiment, and numerical simulation prior to field-scale studies. This capability gives users access to all the tools necessary for designing and conducting a subsurface flow and transport experiment. These tools include customized microfluidic cells, intermediate-scale flow cells, simulation programs, and analytical instruments from chromatographs to spectrometers.
    See instruments for this capability.
  2. Microscopy
    Instruments in the microscopy capability image at high resolution and provide complementary chemical, structural, and phase information. In situ imaging in native environments and imaging dynamic processes with high temporal resolution are possible on some instruments. Electron microscopes are available with tomography, cryo, scanning, environmental, and dynamic imaging capabilities. EMSL has focused ion beam/scanning electron microscopy capabilities for specialized sample preparation and three-dimensional topographic and chemical imaging.
    See instruments for this capability.
  3. Cell Isolation and Systems Analysis (CISA)
    EMSL resources are available for detecting and isolating distinct cells from complex populations, including environmental microbial communities or plant tissues, for further single-cell and other analyses. Coupled with other EMSL capabilities, CISA provides a systems biology approach for molecular-level understanding of individual cells and cell communities’ dynamics and functions.
    See instruments for this capability.
  4. Mass Spectrometry
    EMSL’s world-class mass spectrometry capabilities provide compositional and structural information at the molecular level to allow systems biology and complex mixture studies in microbial communities; climate-relevant elemental cycling; and contaminant, mineral, microbe, and fluid interactions. Available cutting-edge proteomics tools and methods facilitate advanced global proteomics research and allow detailed visualization and analyses of cellular proteins in  large samples and at both the peptide and intact protein levels.
    See instruments for this capability.  
  5. Spectroscopy and Diffraction
    Atomic-scale spatial and high-energy resolution spectrometers and diffractometers allow users to investigate molecular-level solid, liquid, and gaseous interactions through structural, chemical, and compositional analysis in novel fundamental research.
    See instruments for this capability.
  6. Nuclear Magnetic Resonance and Electron Paramagnetic Resonance Spectroscopy
    EMSL offers unique and custom NMR and EPR tools, including probes for specialized research, to study catalytic, advanced material, geochemical, and biological systems in their near-native state and in real time. EMSL’s NMR spectrometers range from 300 MHz to 850 MHz for high-field liquid-state, solid-state, and micro-imaging techniques. W- and X-band pulsed EPR spectrometry for probing metal centers in biological and materials systems are also available.
    See instruments for this capability.
  7. Molecular Science Computing
    EMSL is home to Cascade, a 3.4 petaflop supercomputer specially designed for modeling and simulation of cellular processes, microbial interactions, elemental cycling, reactive transport, computational chemistry, and materials science. This capability includes NWChem, one of DOE’s premier open-source computational chemistry software suites, and Aurora, a 15.8 petabyte data storage system.
    See instruments for this capability.

Unique Facilities
One of only a few such user facilities worldwide, RadEMSL houses a collection of experimental tools uniquely suited for actinide chemistry studies. It is equipped with advanced spectroscopic and imaging instrumentation to provide the molecular-level chemical speciation information needed to develop mechanistic models of radionuclide chemical behavior under environmental conditions. RadEMSL offers nuclear magnetic resonance capabilities and surface science capabilities, such X-ray photoelectron spectroscopy, electron microscopy, electron microprobe, transmission electron microscopy, scanning electron microscopy, and more.
See instruments at this facility.

Quiet Wing
EMSL’s Quiet Wing is a specialized environment for the study of atmospheric, biological, environmental, biogeochemical, surface, and material sciences. It is among the most advanced quiet laboratories in the world and was designed to help accelerate critical science by allowing state-of-the-art ultrasensitive microscopy equipment to operate at optimal resolution. A temperature-controlled facility, the wing’s design eliminates or reduces to a minimum the vibrations, acoustics, and electromagnetic noise that can interfere with the resolution of ultrasensitive scientific instrumentation. The 9,500-square-foot facility features eight quiet laboratory cells and a sample preparation area. The wing currently houses seven premier microscopy instruments and has room for one more.
See the instruments in this facility.

EMSL Campus
EMSL post-doctoral research assistants Tzu-Yung “Terry” Lin (center) and Jared Shaw work with EMSL’s new high resolution and mass accuracy mass spectrometry capability, or HRMAC. HRMAC’s higher-resolution and mass accuracy measurements ensure identification of molecular constituents in complex samples and materials and will be used to characterize complex environmental and biological materials.

New Instrumentation
EMSL and BER are investing in the development of two new instruments and are considering development of a plant phenomics facility that will enable researchers to advance their understanding of biosystems and their design. Capabilities under development include:

  • Dynamic transmission electron microscope. With its pulsed electron source, this instrument will provide unprecedented in situ imaging of the structural dynamics of proteins with sub-molecular detail on the nanosecond to ,microsecond time scale. Upon completion, this capability will significantly advance the understanding of dynamic biological processes, such as enzymatic reactions, cell signaling, protein-protein interactions, and interfacial electron transfer.
  • High Resolution and Mass Accuracy Capability (HRMAC). The nearly complete HRMAC project will provide unequivocal abilities to identify molecular species in complex systems. Also referred to as the 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS), HRMAC will enable the study of previously intractable sample types and the resolution of difficult scientific problems. Application to specific microbial and plant proteomics and metabolomics, atmospheric aerosol, imaging, natural organic matter, and biofuel challenges are planned.
  • Plant phenotyping. To enable EMSL users and staff to leverage existing omics and imaging capabilities in exploring and exploiting the vast resources available in plant genomics databases, EMSL is currently considering options for a plant phenotyping pipeline for high-throughput, noninvasive screening of plant germplasm.

Researchers may submit a general proposal to use EMSL capabilities through the EMSL website at any time. DOE’s EMSL supports both open and proprietary research proposals, all of which are externally peer reviewed. In addition to general proposals, EMSL issues an annual Science Theme call and periodic calls for specific types of proposals.

More than half of EMSL’s 700 annual users are from academia; the rest are from DOE national laboratories, other federally sponsored labs, and industry.

Visiting Scientist Program and Fellowships
DOE’s EMSL seeks to attract new, highly qualified users and honor their major contributions through fellowships and awards:

For more information about EMSL, contact:
Paul Bayer
Climate and Environmental Sciences Division
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research

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