Environmental System Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Availability of User Facilities and Other Specialized Resources

DOE has responsibility for User Facilities (https://science.osti.gov/User-Facilities) and programs that offer unique and complementary resources in support of research in environmental system science. Applicants are encouraged to consider using or collaborating with these experimental, observational, and computational facilities/capabilities, which have existing and dedicated financial support, to leverage their capabilities, including archived samples and long-term data sets.

Potential applicants are encouraged to consider use of these resources/user facilities in developing their applications. The applicant must certify via written documentation (e.g., letter of support) that user program coordinators, site/capability coordinators/managers, and/or advisory panels find the proposed research within their mission and would support the access or use if selected for an award. Some User Facilities have a separate proposal process, but applicants to this FOA should still provide a letter from that facility indicating the proposed interaction would be within scope of their capabilities pending successful selection through their respective process. This documentation should be in the form of a letter of agreement, signed by an individual with authority to commit the expertise/resources of the collaborating institution/project/program, and submitted with the application.

Examples of available user facilities and other specialized resources include:

DOE User Facilities and Resources

ResourceDescription
Atmospheric Radiation Measurement (ARM) User FacilityThe Atmospheric Radiation Measurement (ARM) User Facility (https://www.arm.gov) provides the research community with strategically located in situ and remote sensing observatories designed to improve the understanding and representation, in climate and Earth system models, of clouds and aerosols as well as their interactions and coupling with the Earth’s surface. ARM operates three fixed sites: the Southern Great Plains (SGP) in Oklahoma; the North Slope of Alaska (NSA) in Barrow, AK; and the Eastern North Atlantic (ENA) in the Azores (https://www.arm.gov/capabilities/observatories). ARM also has three mobile facilities (https://www.arm.gov/capabilities/observatories/amf) and an aerial facility (https://www.arm.gov/capabilities/observatories/aaf). All ARM data is available at no cost to scientific users through the ARM archive (https://www.arm.gov/data/). Deployment of the ARM Mobile Facility or ARM Aerial Facility to a specific location or large campaigns at fixed ARM sites is requested through an annual ARM facility user proposal process. Smaller campaigns (such as deployment of user-owned instruments to ARM facilities or requests for intensive or special operation of existing ARM instruments) are requested through an ARM facility user proposal process (https://www.arm.gov/research/campaigns) and reviewed quarterly.
Environmental Molecular Sciences Laboratory (EMSL)The Environmental Molecular Sciences Laboratory (EMSL) is a U. S. Department of Energy Office of Science User Facility (https://www.emsl.pnnl.gov), sponsored by the Biological and Environmental (BER) program. Scientists around the world submit proposals to use EMSL's world-class laboratory space, expertise, and equipment to gain predictive understanding of the molecular and atomic processes that control biological and ecosystem functions. We conduct fundamental environmental research by studying environmental (physiochemical, hydrological, biogeochemical), microbial, vegetative, soil, and ecological processes in above- and belowground ecosystems, the atmosphere, and their interfaces. In fundamental biological research, EMSL focuses on revealing the connections between protein structure and function, biochemical pathways, and complex cellular phenotypic responses to improve strategies for biofuels and biobased products production. To aid in developing a predictive understanding of biological and environmental systems, EMSL supports computing research advancing the use of data analytics, visualization, and modeling and simulation on increasingly complex multimodal experimental data. EMSL capabilities are available at no charge through a user proposal process (https://www.emsl.pnnl.gov/proposals). Applicants are also encouraged to explore the Facilities Integrating Collaborations for User Science (FICUS) program between EMSL and other user facilities (https://www.emsl.pnnl.gov/ficus), through which multiple facilities can be accessed with one proposal.
Energy Exascale Earth System Model (E3SM)DOE’s Energy Exascale Earth System Model (E3SM) is a coupled earth system model including all earth components (i.e., atmosphere, ocean, land, rivers, sea ice, and land ice) and their interactions with human components, designed to run on DOE high-performance computers and to address energy-related science questions, including water availability, carbon and nutrient cycles, sea-level changes, and coastal inundations. E3SM’s land model (ELM) foci include hydrology, water management, soil nutrients, dynamic vegetation (using the FATES model), crops and agricultural practice, land-use, land-cover, and disturbance effects. Version 1 of the model was released in 2018 (including codes, output and analysis codes), and the development codes are open-access. An AGU E3SM Special Collection features 50 papers documenting the development of new model features released in E3SM v1 and those being integrated into E3SM v2. Training materials/tools for new users are available at https://e3sm.org/resources/. To learn more about E3SM, see https://E3SM.org.
Environmental Systems Science – Data Infrastructure for a Virtual Ecosystem (ESS-DIVE)ESS-DIVE is a data repository for Earth and environmental science data that is funded by the Data Management program within BER's Earth and Environmental Systems Sciences Division. Maintained and managed at Lawrence Berkeley National Laboratory, ESS-DIVE archives and publicly shares data obtained from observational, experimental, and modeling research funded by the ESS program. ESS-DIVE allows data contributors to obtain digital object identifiers (DOIs) that can be used to cite and track usage of the data. For more information, see https://ess-dive.lbl.gov.
High Performance Computing CentersDOE supports high performance computing centers, which provide compute cycles and data storage through a proposal process to the scientific user community. These resources include the Molecular Science Computing (MSC) capability at EMSL (https://www.emsl.pnl.gov/emslweb/capabilities/computing/), the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory (https://www.nersc.gov), and the Oak Ridge Leadership Computing Facility (OLCF) at Oak Ridge National Laboratory (https://www.olcf.ornl.gov).
Joint Genome InstituteThe DOE Joint Genome Institute (JGI) User Facility, located at the Integrative Genomics Building on the Lawrence Berkeley National Laboratory campus in California provides the scientific community access to high-throughput sequencing and analysis, DNA synthesis, and metabolomics capabilities for microbial, plant, microbial community, and other (non-pathogen) targets. JGI provides the national and international scientific community access to massive-scale DNA sequencing to underpin modern systems biology research and provide fundamental data on key genes that may link to biological functions, including microbial metabolic pathways and enzymes that are used to generate fuel molecules, affect plant biomass formation, degrade contaminants, or capture CO2 to support further discovery in DOE mission areas (https://www.jgi.doe.gov). These resources are available at no charge through a user proposal process (see https://proposals.jgi.doe.gov). Applicants are also encouraged to explore the Facilities Integrating Collaborations for User Science (FICUS) initiative between JGI and EMSL, through which capabilities at these (and potentially other) User Facilities can be combined (https://jgi.doe.gov/user-program-info/community-science-program/how-to-propose-a-csp-project/emsl). Through these programs, the Department of Energy aims to advance genome science-based innovative research exploiting a range of capabilities.
KBaseThe U.S Department of Energy Systems Biology Knowledgebase (KBase) (https://www.kbase.us) is an open-source software and data platform designed to meet the grand challenge of systems biology—predicting and designing biological function from the biomolecular (small scale) to the ecological (large scale). KBase is available for anyone to use. KBase enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large-scale analyses on scalable computing infrastructure; and combine experimental evidence and conclusions that lead to accurate models of plant and microbial physiology and community dynamics. The KBase platform has (1) extensible analytical capabilities (2) a web-browser-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; (3) access to extensive computational resources; and (4) a software development kit allowing the community to add functionality to the system. Science done within KBase can be linked to from peer-reviewed publications, and the KBase Narratives associated with these experiments are available to be copied, re-run, and extended by all.
NMDCThe National Microbiome Data Collaborative (NMDC) https://microbiomedata.org is an integrated microbiome data ecosystem hosting high-quality, consistently processed multi-omics microbiome data to enable data sharing, management and cross-comparison studies in accordance with the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. Community-driven standards developed by the Open Biological and Biomedical Ontology (OBO) Foundry (e.g., the Environment Ontology (EnvO)) and the Genomic Standards Consortium (GSC) (e.g., the Minimum Information about any (x) Sequence (MIxS)) are applied to all project metadata, and support the NMDC metadata schema (https://github.com/microbiomedata/nmdc-metadata). The NMDC hosts a variety of interoperable and reusable annotated microbiome data products processed through open-source analytic workflows (documentation: https://nmdc-workflowdocumentation.readthedocs.io) including metagenome, metatranscriptome, metaproteome, and metabolome data. The DOE User Facilities, the Joint Genome Institute (JGI) and Environmental Molecular Sciences Laboratory (EMSL), serve complementary microbiome infrastructure (e.g., IMG/M and GOLD) and are integrated with the NMDC, while KBase can provide advanced bioinformatics capabilities leveraging NMDC data. For the pilot phase, the NMDC is developing infrastructure for all stages of the digital data lifecycle including capture, analysis, sharing, and preservation to support data management. Applicants are strongly encouraged to work with NMDC staff to ensure their data aligns with the NMDC metadata schema and for the generation of multiomic data products for inclusion in the NMDC.
Neutron Beam FacilitiesDOE provides the scientific community access to high flux neutron sources that are capable of providing structural and chemical information often unavailable using other technologies. DOE has two such facilities at the Oak Ridge National Laboratory, the Spallation Neutron Source (SNS; https://neutrons.ornl.gov/sns/) and the High Flux Isotope Reactor (HFIR; https://neutrons.ornl.gov/hfir/). Use of the neutron sources is available at no charge through a user proposal process.
Synchrotron Light SourcesDOE provides the scientific community access to synchrotron light sources that are capable of providing structural and chemical information often unavailable with conventional sources of x- rays. Use of each synchrotron light source is available at no charge through its user proposal process. Information about each DOE synchrotron user facility can be found at: Argonne National Laboratory (https://www.aps.anl.gov); Brookhaven National Laboratory (https://www.bnl.gov/ps/); Lawrence Berkeley National Laboratory (https://www.als.lbl.gov/); and Stanford Synchrotron Radiation Laboratory (https://www-ssrl.slac.stanford.edu). For more information about the BER-supported biology beamline resources at the synchrotron and neutron facilities, visit: https://www.berstructuralbioportal.org.

 

DOE-Supported Community Resources

ResourceDescription
AmeriFlux NetworkThe AmeriFlux Network gathers and shares long-term carbon, water and energy flux measurements and site metadata collected by hundreds of sites that span a spectrum of climate and ecosystems across the Americas. The AmeriFlux Network ensures the availability of the continuous, long-term ecosystem measurements necessary to build effective models and multi-site syntheses, while maximizing insight through robust, site-specific, independent research programs. Information on the availability of long-term flux data and contact information for the Network and individual AmeriFlux sites is available at: https://ameriflux.lbl.gov.
Center for Accelerator Mass Spectrometry (CAMS)The Center for Accelerator Mass Spectrometry (CAMS) at Lawrence Livermore National Laboratory provides AMS capabilities on a cost-recovery basis to the scientific community. CAMS provides technical and analytical support for 14C applications in several existing research projects in carbon cycle science. Radiocarbon measurements can be used to determine the ‘age’ and rate of change of carbon stocks or as a biogeochemical tracer to elucidate processes and pathways for carbon cycling studies. Additionally, CAMS offers routine sample processing and AMS measurement capabilities for 7Be, 10Be, 26Al, and 36Cl. These isotopes are commonly applied to date the exposure and burial of Earth-surface materials, quantify erosion rates, and trace numerous soil production and landscape evolution processes. More information on the applicability of CAMS capability to environmental systems science is available at https://cams.llnl.gov/cams-competencies/terrestrial-carbon-cycle and https://cams.llnl.gov/cams-competencies/earth-system-processes.
Fine-Root Ecology Database (FRED)The Fine-Root Ecology Database (FRED) gathers observations of root traits from across the world into a common framework, freely available to empiricists and modelers alike. FRED facilitates the quantification of fine-root trait variation within and among species and across environments, as well as the improved representation and parameterization of fine-root processes in terrestrial biosphere models. A new version of FRED is now available. FRED 3.0 houses more than 330 root traits that span 150,000 observations made at locations across the world, and includes ancillary data on associated site, vegetation, edaphic, and climatic conditions. A new interactive user interface allows root trait observations to be filtered according to the scientific interests of the user. More information can be found at: https://roots.ornl.gov.
IDEAS-WatershedsThe Interoperable Design of Extreme-Scale Application Software (IDEAS) – Watersheds project is accelerating watershed science through the development and support of a sustainable community-driven software ecosystem of interoperable components and libraries. This flexible modeling capacity is an important part of the growing ESS community cyberinfrastructure that supports the integration of diverse and complex environmental datasets with multi-scale, multi-physics models. The IDEAS-Watersheds project aims to develop a sustainable software ecosystem of numerical codes to address a variety of hydro-biogeochemistry questions across a range of temporal and spatial scales. Planning, development and performance enhancements to codes within the IDEAS-Watersheds project are guided through materials posted on the Better Scientific Software site (https://bssw.io). Through use cases that are aligned with the SFAs, the IDEAS-Watersheds project is leveraging advances in software development methodologies and design, establishing multi-scale workflows, and exploring the bridging of fine-scale mechanistic models to watersheds and river basin/regional-scale models and analyses. For more information, see: https://ideas-watersheds.github.io.
International Land Model BenchmarkingInternational Land Model Benchmarking (ILAMB) is both a coordination project and a software tool for systematic evaluation of land surface/ecosystem models. The ILAMB tool scores the performance of multiple models or multiple model versions through comparison with observational data based on a variety of evaluation metrics, and it generates graphical plots and maps to facilitate diagnosis of differences between model results and reference data. The two goals of ILAMB are to facilitate model improvement and to inform design of new measurement campaigns that generate data to better constrain models. More information can be found at https://www.ilamb.org.
LeafWeb

LeafWeb is an automated online tool for leaf photosynthesis and fluorescence analyses. It applies the principle of SErvices in Exchange for Data Sharing (SEEDS). By using LeafWeb, users agree to share their data with the broad scientific community with proper credits and acknowledgement of data contribution. LeafWeb accepts the submission of standard leaf gas exchange and Pulse Amplitude Modulated (PAM) fluorometry measurements. After passing initial format and quality checks, the data are then analyzed with standard mechanistic models to estimate key biochemical and physiological photosynthetic parameters that are used in plant science research and carbon cycle models. The obtained parameters are then reported back to the user. For more information, visit https://www.leafweb.org.

Mercury Aqueous Speciation Database (AQUA-MER)AQUA-MER contains a curated database of thermodynamic stability constants of mercury in aqueous solutions. In addition, it calculates speciation profiles as a function of pH given input concentrations of chemicals, using the well-known program, PHREEQC, from the U.S. Geological Survey (USGS), and it provides a computational chemistry toolkit for thermodynamics constants calculations and more. See: https://aquamer.ornl.gov.
Worldwide Hydro-biogeochemical Observation Network for Dynamic River Systems (WHONDRS)WHONDRS is a research consortium that aims to understand coupled hydrologic, biogeochemical, and microbial function within river corridors, with an emphasis on increasing accessibility of resources and knowledge throughout the research life cycle. WHONDRS seeks to galvanize a global community around understanding river corridors from local to global scales and ultimately to provide the scientific basis for improved prediction and management of dynamic river corridors throughout the world. The science of WHONDRS is often driven by collaborator and community interests/needs across all types of river corridors, spanning inland, urban, and coastal systems. Through collaborations, WHONDRS implements river corridor field campaigns that embody integrated, coordinated, open, and networked (ICON) science principles. Field campaigns range from local-scale intensive sampling to multi-biome global-scale efforts. In all cases, campaigns use standardized sampling kits and are designed to generate FAIR data relevant to integrated hydro-biogeochemical models. Sampling supplies, shipping, analysis, and data management are provided by WHONDRS and through collaborations with BER user facilities, including EMSL and JGI. WHONDRS can also facilitate the design and implementation of collaborator-led highly distributed, community-enabled campaigns. WHONDRS data for each campaign depend on collaborator needs and often include ultra-high resolution organic matter chemistry, small metabolite concentrations, microbial community potential and expressed functions, respiration rates, aqueous chemistry, sediment texture and mineralogy, surface water hydrology, water isotopes, and many others. Data are often complemented with collaborator-generated data and all are georeferenced such that they can be further augmented and contextualized with public geospatial data. High dimensionality and consistency of the collective data lends itself to the application of machine learning as well as integration with mechanistic numerical models to enable distributed modeling efforts. For more information, see: https://whondrs.pnnl.gov.

 

Research Efforts in Critical Ecosystems

ResourceDescription
Next Generation Ecosystem Experiment – Arctic (NGEE-Arctic)DOE supports process studies and modeling to assess carbon cycle dynamics in high-latitude terrestrial ecosystems. The NGEE Arctic project focuses on permafrost ecology in a warming Arctic, and how associated changes in biogeochemical processes, disturbance ecology, and vegetation dynamics will affect feedbacks to the climate system. Fundamental knowledge gained in these investigations will improve representation of ecosystem dynamics, subsurface biogeochemistry, and atmosphere processes in regional and global models, and improve predictions of climate change in tundra ecosystems. Field sites for the NGEE Arctic project exist at locations in Alaska. More information on the study and information for contacting NGEE Arctic project staff to discuss collaborative research are described on the project web site (https://ngee.ornl.gov).
Next Generation Ecosystem Experiment – Tropics (NGEE-Tropics)The Next Generation Ecosystem Experiment - Tropics (NGEE-Tropics) supports modeling and process-based studies for tropical forest ecosystems. Research is focused in three primary research focus areas: tree ecophysiological responses to drought and elevated temperature stress; forest community assembly across moisture, nutrient and disturbance gradients; and forest-atmosphere water, carbon, and energy fluxes at landscape to regional scales. Scientific advances in these areas result in improved Earth system model (ESM) representation of vegetation dynamics, coupled biogeochemical cycles, and feedbacks to Earth’s climate system. NGEE-Tropics field sites are located in Puerto Rico, Panama, the Brazilian Amazon, and additional pantropically distributed sites. Additional information on NGEE-Tropics activities, the collaborative team, and institutional partners can be found on the project’s website: (https://ngee-tropics.lbl.gov)
Spruce and Peatland Responses Under Changing Environments (SPRUCE) DOE supports an experiment to assess the response of northern boreal and peatland ecosystems to increases in temperature and elevated atmospheric CO2 concentrations. The SPRUCE experiment is being operated for a planned decade of operation (2016-2025) at the Marcell Experimental Forest in northern Minnesota. More information on the study, a listing of currently funded collaborators, and the method for contacting SPRUCE project staff is described on the project web site (https://mnspruce.ornl.gov). New collaborators must discuss potential research interests with project participants to avoid duplication of effort and to ensure available space within the SPRUCE footprint. SPRUCE hosts an abundance of cooperative research efforts focused on peat matrix processes (e.g., microbial community responses including metagenomic analyses, methane biogeochemistry and process, etc.) and may not be able to accommodate new research in this area at this time. However, the SPRUCE project has recently begun hosting new effort focused on cold hardiness characteristics of vegetation. Empirical disciplines not represented by the group of established collaborators or modelers interested in interacting with an established group are encouraged to discuss research opportunities with the SPRUCE group.
Coastal Observations, Mechanisms, and Predictions Across Systems and Scales – Field, Measurements, and Experiments (COMPASS-FME)The Coastal Observations, Mechanisms, and Predictions Across Systems and Scales – Field, Measurements, and Experiments (COMPASS-FME) pilot study is a multi-institutional effort to understand the interactions of waters, soils, microbes, and plants within coastal Terrestrial-Aquatic Interfaces (TAIs) to inform the development, testing, and application of multiscale, hierarchical models. COMPASS-FME is being piloted at select sites in the Chesapeake Bay and Lake Erie regions, focused on the fluxes and transformations of carbon, nutrients, and redox-sensitive elements in ecosystems influenced by coastal water exchange; these gaseous, aqueous, and particulate fluxes and transformations must be mechanistically resolved to enable coupling between land, wetland, and open-water systems in regional models and ultimately Earth system models. https://compass.pnnl.gov/FME/COMPASSFME

 

ESS-Supported National Laboratory Research

ResourceLaboratoryMore Information and Contacts
Soil Carbon Response to Environmental ChangeArgonne National Laboratoryhttps://ess.science.energy.gov/anl-sfa/
Wetland Hydro-biogeochemistryArgonne National Laboratoryhttps://ess.science.energy.gov/anl-wetland-sfa/
Belowground BiogeochemistryLawrence Berkeley National Laboratoryhttps://ess.science.energy.gov/lbnl-sfa/
Watershed FunctionLawrence Berkeley National Laboratoryhttps://ess.science.energy.gov/lbnl-watershed-function-sfa/
Biogeochemistry of ActinidesLawrence Livermore National Laboratoryhttps://ess.science.energy.gov/llnl-actinides-sfa/
Critical Interfaces BiogeochemistryOak Ridge National Laboratoryhttps://ess.science.energy.gov/ornl-mercury-sfa/
FACE-Model Data SynthesisOak Ridge National Laboratoryhttps://ess.science.energy.gov/face/
Terrestrial Ecosystem ScienceOak Ridge National Laboratoryhttps://ess.science.energy.gov/terrestrial-ecosystem-science-sfa/
River CorridorPacific Northwest National Laboratoryhttps://ess.science.energy.gov/pnnl-hydrobiogeochemistry-sfa/
Floodplain Hydro-BiogeochemistryPacific Northwest National Laboratoryhttps://ess.science.energy.gov/slac-floodplain-sfa/