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Call for Large-Scale Research Proposals, FY 2024



Projects start

October 1, 2023, 5:00 PDT

The Environmental Molecular Sciences Laboratory (EMSL) Fiscal Year 2024 Call for Large-Scale EMSL Research Proposals seeks leading-edge research activities to advance scientific understanding in each of EMSL’s science areas. The focus topics announced below aim to advance scientific understanding in areas of interest to, or aligned with, those of the Department of Energy (DOE), Office of Science, Biological and Environmental Research (BER) Program, and EMSL.

Researchers from around the world can apply through this call to use EMSL resources and collaborate with EMSL scientists at no cost. Accepted proposals are valid for two years provided that sufficient progress toward the stated goals is accomplished in the first year. Access to EMSL capabilities is competitive and approximately 30 percent of the proposals submitted will be accepted. Proposals will be evaluated according to the five review criteria listed below. Note that proposals that do not adhere to the guidance provided will not be considered.

Focus topic areas

The focus topics for this call are aligned with EMSL’s mission to accelerate scientific discovery and pioneer new capabilities to understand biological and environmental processes across temporal and spatial scales. The topics are organized by EMSL’s three science areas — Environmental Transformations and Interactions (ETI); Functional and Systems Biology (FSB); and Computing, Analytics, and Modeling (CAM).

Environmental Transformations and Interactions Science Area

We seek proposals that use EMSL capabilities to advance mechanistic molecular knowledge of microbial, geochemical, root-driven, and atmospheric processes, and process interdependencies, that control transformations, fate, and transport of C, N, and other nutrients in bedrock, soils, and rhizosphere, and of terrestrial-sourced emissions in the atmosphere. Proposals that develop or refine biogeochemical process models, provide data crucial to improving numerical models, or are part of an explicit MODEX research framework are of particular interest. Studies that are purely computational and that address ETI topical areas should be submitted under one of the 6 CAM science topics. Proposals that leverage samples and analyses performed through the ETI MONet program are particularly encouraged. Learn more about the ETI Science Area on the EMSL website. Contact the ETI Science Area lead, John Bargar if you have questions about these topics.

ETI-1: Molecular mechanisms of soil carbon cycling

Development of mechanistic information of molecular processes governing carbon uptake, stabilization, and release from soils. Topics of interest include microbial processing of organic matter (OM); enhanced stabilization of soil OM; processes occurring in hot spots; and other processes that modify soil C stability, fate, and transport. Soils from urban, agricultural, rangeland/grassland, forest, and wetland systems are appropriate for this topic. Studies that focus explicitly on mechanisms by which roots drive these processes should be submitted under ETI Topic 3.

ETI-2: Atmospheric processing of terrestrial-sourced emissions

Development of mechanistic understanding of processes that influence the behavior of plant- and soil-derived inorganic and biogenic aerosols in the atmosphere. Topics of interest include volatile organic compounds emitted from soil-plant systems; wildfire-generated aerosols; aging processes of aerosols in the atmosphere; physical, chemical, and optical properties of aerosols needed to assess their impact on warm and cold cloud formation and Earth’s radiative budget; and deposition of aerosol that impacts biogeochemical cycles and ecosystem properties. Anthropogenic aerosols that influence these processes are appropriate research subjects. Atmospheric systems above urban, agricultural, rangeland/grassland, forest, wetland, and water, including remote source points that contribute long-range transported aerosols, are appropriate for this call.

ETI-3: Root-soil-microbe interactions

Development of mechanistic understanding of root-microbe-mineral processes in the rhizosphere that influence carbon and nutrient fluxes, support soil and plant function, and help maintain ecosystem services. Topics of interest include coupled molecular and transport processes that facilitate carbon and nutrient retention, transformation, and fluxes; root-microbiome chemical signaling; release and biogeochemical processing of metabolites and photosynthates; characterization and modeling of the spatio-temporal distribution of root exudates at the root-soil interfaces; and responses of microbial communities to these processes. Proposals that primarily address changes in rhizosphere function in response to disturbance events should submit their proposal to ETI Topic 4. 

ETI-4: Molecular and microscale responses to ecosystem drivers

Development of mechanistic molecular knowledge of processes that underpin watershed and atmospheric responses (from bedrock to the top of the troposphere) to transient disturbance events at timescales of hours, days, seasons, and years, (e.g., storms, transient impacts of/responses to wildfires, inundation events, snowmelt, drought, saltwater intrusion, and changes in cold-season climate drivers). Topics of interest include but are not limited to the coupling between hydrological drivers and biogeochemical processes; emissions from plant/soil systems; climate-driven changes in root exudates and subsequent changes in plant-microbe interactions and plant resilience; microbial responses including (meta)transcriptomic signatures, response of mineral-organic associations, and soil OM stability to changes in soil moisture; reactive transport/transformation of carbon, metabolites, major ions, and (micro) nutrients; and changes in the biogeochemical function of terrestrial-aquatic interfaces.

Functional and Systems Biology (FSB) Science Area

We seek proposals utilizing EMSL capabilities for research focused on microbial systems relevant to the sustainable production of biofuels, chemicals and biomaterials, environmental microbiology, and biosystem designs. Learn more about the FSB Science Area on the EMSL website. Contact the FSB Science Area lead, Scott Baker, if you have questions about these topics.

FSB-1: Protein and protein complex structure and function (Principal IRP: SB)

  • The rapid pace of genome sequencing has uncovered a massive catalog of conserved genes encoding proteins of unknown function. The ability to predict, control, and engineer biochemical pathways are reliant on understanding the function of proteins in cellular processes. We seek proposals that structure-function studies targeted at elucidating the biochemical activities or biological activities.
  • Proteins often function in complexes, many of which are not or are poorly characterized. Comprehensive characterization of these complexes can be used to assign function(s) for new and unknown proteins. We seek proposals aimed at characterizing the composition, activities, and location of these complexes.

Overlap with CAM: Reconstruction workflows for protein structure determination and sub-cellular 3-D mapping

FSB-2: Regulatory and biosynthetic pathways (Principal IRP: BP)

  • Understanding the biological circuits in cells is crucial for the simulation or prediction of behavior and the design and engineering of new biological systems for enhanced performance. Projects probing the interconnections and interactions of proteins, and metabolites in the context of environmental nutrient cycling or the production of biofuels, chemicals, or biomaterials are desired.
  • Understanding the metabolic and biosynthetic pathways in natural, designed, and built environmental and biosynthesis systems for the identification and quantification of the functional components of complex systems and probe biological molecules with unknown functions.
  • Our understanding of the regulation of biological circuits is growing but still has gaps. We seek proposals focused on regulatory pathways in microbes involved in environmental nutrient cycling or the production of biofuels, chemicals, or biomaterials.

Overlap with CAM: Processing and integration of multi-omics data for modeling and interpretation

FSB-3: Populations and communities (Principal IRP: CSC)

  • Capturing the breadth and complexity of organism interactions and behaviors across space and time is essential to untangling mechanisms that influence intrinsic microbiome stability and robustness. We seek projects that develop and deploy multi-omics approaches along with high-resolution dynamic imaging to investigate in situ microbial activities controlling key environmental processes.
  • Understanding how individual cell outputs cascade into cumulative, community-level behavior is critical to our ability to predict microbiome function and dynamics. Studies aimed at developing and deploying single-cell measurements to understand how cells in these populations interact and acclimate to internal and external perturbations are desired.
  • The availability of tools and methods for manipulating microbiomes is a critical component for enabling the design of microbiomes with highly improved properties. Projects aiming at building and characterization of engineered consortia, at subspecies/subpopulation resolution, for industrial or environmental applications are encouraged.

Overlap with CAM: We seek computational approaches that facilitate data processing and analysis to integrate molecular measurements at subpopulation and, when possible, at single cell levels.

Computation, Analytics, and Modeling Science Area

The Computing, Analytics, and Modeling (CAM) science area focuses on combining advanced data analytics, visualization, computational modeling, and simulation with state-of-the-art experimental data generation to develop a predictive understanding of biological and environmental systems. Our cohesive approach to integrating experimental and computational methods advances predictive approaches for cellular metabolism toward the production of biofuels and bioproducts as well as material synthesis and degradation (e.g., biomineralization, plant biomass, and plastics) and accelerates research to understand the molecular mechanisms underlying biological and hydro-biogeochemical processes controlling the flux of materials (e.g., carbon, nutrients, and contaminants) in the environment. Please get in touch with Jaydeep Bardhan, CAM Science Area Lead, if you have questions about the following call topics or to discuss your project idea.

CAM-1: Analysis and Modeling for Proteomics

Computation and modeling provide powerful opportunities to enhance discovery in complex proteomic data. Examples include physics-based and AI-enhanced molecular modeling, as well as graphical methods based on databases of protein-protein interactions. Recent AI/ML-based tools such as AlphaFold offer additional transformative possibilities built on protein structure predictions. We seek proposals aimed at achieving a deeper understanding of BER-relevant biological systems by leveraging innovative computational approaches to understand proteomics experiments.

CAM-2: Metatranscriptomics leveraging High-Performance Computing

Metatranscriptomics experiments present important opportunities to understand the responses of microbiomes to environmental perturbations. Typical workflows for such experiments often rely on aligning sample sequences to reference assemblies that are only partial matches, possibly limiting discoveries. New high-performance computing (HPC) capabilities enable full assembly for each sample, thus providing the ideal alignment reference for each sample. We seek proposals in which these new methods may yield important insights into both environmental responses as well as the scientific relevance of traditional approximations.

CAM-3: AI/ML for Mass Spectrometry Data Analysis

Omics studies using hybrid mass spectrometry workflows (e.g., including chromatography, ion mobility spectrometry, or data-independent acquisition) provide valuable insights into molecular regulation, transformation, and activity. Recent advances demonstrate that AI/ML can circumvent long-standing weaknesses of traditional analysis approaches that limit scientific discovery. We seek proposals aimed at leveraging these cutting-edge AI/ML analysis methods to improve the characterization of molecules and their interactions and enhance understanding of complex BER-relevant biological systems.

CAM-4: Bridging Soil Imaging and Modeling

Imaging studies of soil provide detailed structural information relevant to understanding environmental hydro-bio-geochemical processes. We seek proposals aimed at transforming imaging-based structural information into scientific discovery through computational methods that could include the building of simulation models, execution of simulation studies, or AI/ML-based extraction of key quantities of interest.

CAM-5: Novel Data Science and AI/ML Methods

Rapid advances in data science, data integration, and AI/ML could significantly enhance BER science, especially for problems involving complex, heterogeneous data, and data from various types of instrumentation. However, adopting the relevant innovations is frequently stymied by challenges in identifying domain-specific strengths. We seek proposals that will leverage cutting-edge data science and AI/ML approaches in new ways to advance BER science priorities. Methods of particular interest include dimensionality reduction, topological or geometric approaches, Bayesian methods, and approaches designed for noisy, incomplete, or limited training data.

CAM-6: Simulation Modeling from Molecular to Mesoscale

Simulation models can provide essential insights into the structure and function of biological systems, biogeochemical processes, and their regulation, at scales ranging from the molecular to the cellular. We seek proposals that aim to answer BER-relevant questions using molecular, multiscale, or metabolic modeling. Studies involving cryo-electron microscopy (CryoEM) are of particular interest due to the unprecedented insights such experiments can yield into the function and regulation of large biomolecular assemblies.

Highlighted Capabilities

All EMSL instruments and resources are available to users through this call. Applicants are also encouraged to consider emerging cutting-edge capabilities developed by EMSL scientists, including:

  • High-resolution imaging of mineral-associated OM, soil particulate OM, microbial cells, and exudates - EMSL’s Zeiss Orion Helium-ion microscope (HIM) provides high-contrast/depth-of-field morphological information for OM and organic-mineral interfaces at 1 nm resolution in uncoated samples (contact: Shuttha Shutthanandan). EMSL also has deep expertise in transmission electron microscopy of microbial cells (contact: Alice Dohnalkova), scanning electron microscopy with energy-dispersive spectroscopy chemical imaging (Odeta Qafoku) and atomic probe tomography (Mark Wirth) of microbial-inorganic interfaces down to nm scale. Nano-Secondary Ion Mass Spectroscopy provides chemical images with isotopic specificity at trace concentrations and sub-100 nm resolution (Jeremy Bougoure, John Cliff). In combination, these methods provide a comprehensive suite of capabilities for imaging soil OM.  
  • EMSL’s new single-cell transcriptomic workflows elucidate intercellular signaling, communication, and ensuing heterogeneity that underpin the behavior of complex multicellular/multispecies assemblages including microbial communities and host-microbe systems (contact: Alex Beliaev). 
  • Chemical biology – EMSL is developing capabilities in chemical biology to probe enzyme function and characterize biochemical pathways. For example, EMSL recently developed a probe library to broadly profile amidase activity, which targets both canonical (peptide-like) and non-canonical amide hydrolase activity. EMSL is seeking users to utilize this library or work with us to develop probes for other activities (contact: Sankar Krishnamoorthy).
  • EMSL has integrated new capabilities for studying root-system architecture. The first is optical coherence tomography (OCT), a transparent growth medium-based root imaging system (Contact: Amir Ahkami), and the second is x-ray computed tomography (Tamas Varga). These approaches are ideal for non-destructive studies of root development in plants. A new 3D root cartographic platform can be used to image, then index, and prepare samples for collecting 3D chemical information on them by other means, based on the image data (Pubudu Handakumbura).
  • Three-dimensional BGC characterization of soils: EMSL has developed a workflow for high-resolution characterization of intact/undisturbed soil aggregates or cores for morphology (texture, porosity), chemistry (mineralogy, OM, organo-mineral associations), and hydrology (pore network connectivity, flow properties) in three dimensions (3D) using complementary approaches in x-ray computed tomography, mass spectrometry, hydraulics, and related methodologies (contact: Emily GrahamOdeta Qafoku).
  • We encourage proposals that focus on developing artificial intelligence/machine learning-aided methods to mine information from 2-D chemical maps, process multimodal data, help co-register spatial data from different instruments, or expand 2-D chemical information to 3-D space (contact: Jay BardhanTamas Varga).

Review criteria

User proposals are peer-reviewed against the five criteria listed below. For each criterion, the reviewer rates the proposal Outstanding, Excellent, Good, Fundamentally Sound, or Questionable Impact as well as provides detailed comments on the quality of the proposal to support each rating, noting specifically the proposal's strengths and weaknesses. The reviewer also provides overall comments and recommendations to support the ratings given. These scores and comments serve as the starting point for Proposal Review Panel (PRP) discussions. The PRP is responsible for the final score and recommendation to EMSL management.

Criterion 1: Scientific merit and quality of the proposed research (50%)

Potential Considerations: How important is the proposed activity to advancing knowledge and understanding within its own field or across different fields? To what extent does the proposed activity suggest and explore creative and original concepts? How well conceived and organized is the proposed activity?

Criterion 2: Qualifications of the proposed research team to achieve proposal goals and contribute to high-impact science (10%)

Potential Considerations: Does the proposal team, combined with relevant EMSL staff expertise, possess the breadth of skill/knowledge to successfully perform the proposed research and drive progress in this science area? If successful, would the proposed research deliver high-impact products (for example, be publishable in high-impact journals)?

Note: Impact factors are a measure of the average number of citations per published article. Journals with higher impact factors reflect a higher average of citations per article and are considered more influential within their scientific field.

Criterion 3: Relevance of the proposed research to EMSL's mission (10%)

EMSL’s mission is to accelerate scientific discovery and pioneer new capabilities to understand biological and environmental processes across temporal and spatial scales. EMSL leads the scientific community toward a predictive understanding of complex biological and environmental systems to enable sustainable solutions to the nation’s energy and environmental challenges.

EMSL supports the DOE BER program in achieving a predictive understanding of complex biological, Earth, and environmental systems for energy and infrastructure security, independence, and prosperity. BER seeks to understand the biological, biogeochemical, and physical processes that span from molecular and genomics-controlled scales to the regional and global scales that govern changes in watershed dynamics, climate, and the Earth system.

Starting with the genetic information encoded in organisms’ genomes, BER research seeks to discover the principles that guide the translation of the genetic code into the functional proteins and the metabolic and regulatory networks underlying the systems biology of plants and microbes as they respond to and modify their environments. This predictive understanding will enable the design and reengineering of microbes and plants underpinning energy independence and a broad clean energy portfolio, including improved biofuels and bioproducts, improved carbon storage capabilities, and controlled biological transformation of materials such as nutrients and contaminants in the environment.

BER research further advances the fundamental understanding of dynamic, physical, and biogeochemical processes required to systematically develop Earth System models that integrate across the atmosphere, land masses, oceans, sea ice, and subsurface. These predictive tools and approaches are needed to inform policies and plans for ensuring the security and resilience of the Nation’s critical infrastructure and natural resources.

Note: Projects with direct relevance in these areas will have the best chance for selection. Other projects of scientific significance also are welcomed, but the applicant should clearly outline how the project will further a DOE mission or other areas with economic or societal impact.

Potential Considerations: What is the relationship of the proposed research to EMSL's mission? Does the research project significantly advance the mission goals? How well does the project plan represent a unique or innovative application or development of EMSL capabilities?

Criterion 4: Impact of the proposed research on one or more EMSL Science Areas (20%)

Potential Considerations: Will the proposed research advance scientific or technological understanding of issues pertaining to one or more EMSL science areas? To what extent does the proposed research suggest and explore creative and original concepts related to one or more EMSL science areas? How strongly does it relate to the science area's focused topics as outlined in the most recent Call for Proposals? How well will it advance EMSL along the directions specifically outlined in the focused topics?

Criterion 5: Appropriateness and reasonableness of the request for EMSL resources for the proposed research (10%)

Potential Considerations: Are EMSL capabilities and resources essential to performing this research? Are the proposed methods/approaches optimal for achieving the scientific objectives of the proposal? Are the requested resources reasonable and appropriate for the proposed research? Does the complexity or scope of effort justify the duration of the proposed project–including any modifications to EMSL equipment to carry out research? Is the specified work plan practical and achievable for the proposed research project? Is the amount of time requested for each piece of equipment clearly justified and appropriate?