Call for Large-Scale Research Proposals, FY 2026

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).

Call responders are encouraged to propose LSR projects that leverage Molecular Observation Network (MONet) soil function resources to enhance the scope and scale of hypotheses that can be tested. There are two primary avenues to do this:

1. Standardized MONet data could be obtained from samples collected at the authors’ field site(s) at the beginning of an awarded LSR project as one component of the proposed suite of measurements. MONet data types include soil organic matter (SOM) composition, microbial community structure, pore network structure, hydraulic properties, and biogeochemical parameters.
2. Existing MONet data could be used to perform meta-analyses and/or as modeling inputs to address regional- and contiguous United States (CONUS)-scale science questions.

Environmental Transformations and Interactions (ETI) Science Area

EMSL seeks proposals that would use EMSL expertise and experimental capabilities to elaborate foundational molecular and microscale soil/sediment microbial and root-driven processes that govern the transformations and cycling of carbon, nutrients, and minerals in belowground terrestrial ecosystems down to bedrock (including watershed, coastal, and urban). EMSL also invites proposals that address the molecular chemistry and behavior of terrestrially sourced aerosols and volatile organic compounds (VOCs) from the land surface up to the boundary layer. This call addresses the need to develop improved understanding and representations of these processes to help reduce the uncertainty in simulations of Earth and atmospheric systems. Proposals should identify specific knowledge gaps and testable hypotheses to address the uncertainties in terrestrial ecosystem, ecohydrological, atmospheric, or Earth system contexts.

Studies that are primarily computational and that address ETI topical areas (including, but not limited to, studies focused on data analytics) should be submitted under one of the CAM science topics. Proposals focused primarily on the behavior of terrestrial anthropogenic contaminants, food crop production, aquatic processes, land/forest management, or artificial systems are ineligible. Learn more about the ETI Science Area. Contact the ETI Science Area Leader, John Bargar, with questions about these topics.

ETI-1: Molecular mechanisms of carbon cycling in soils and sediments (IRP: Biogeochemical Transformations, Emily Graham)

Elaboration of mechanistic information of molecular processes governing carbon uptake, transport, stabilization, and release from soils and sediments. Topics of interest include microbial processing of organic matter (OM); stabilization of SOM; nano- to micrometer-scale characterization of mineral-associated OM; processes occurring in biogeochemical hot spots; and other processes that modify soil C stability, fate, and transport. Soils from urban, agricultural, rangeland/grassland, forest, subalpine and alpine, and wetland systems are appropriate for this topic. Proposals that leverage MONet data or would use MONet sampling as part of the research scope are encouraged. Studies that focus primarily on mechanisms by which roots drive these processes should be submitted under ETI Topic 3.

ETI-2: Atmospheric processing of terrestrial emissions (IRP: Terrestrial–Atmospheric Processes, Swarup China)

Development of mechanistic understandings of the molecular and physical processes that influence the behavior of plant- and soil-derived emissions as well as direct anthropogenic emissions including VOCs and aerosols in the atmosphere. Topics of interest include emissions and atmospheric processing of VOCs and particles from soils; biomass burning and plants; spatiotemporal and compositional heterogeneity of biogenic and anthropogenic aerosols; airborne aerosol aging processes; experimental–molecular-modeling studies of aerosol reactivity, new aerosol particle formation, and heterogeneous ice nucleation; physical, chemical, and optical properties of aerosols and their impacts on warm and cold cloud formation; and the deposition of aerosols that impact biogeochemical cycles and ecosystem properties. Interactions between biogenic and 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 generate long-range transported aerosols, are appropriate for this call. Investigations that couple molecular modeling with experimentation to investigate VOC and aerosol particle chemistry are encouraged.

ETI-3: Rhizosphere interactions across scales (IRP: Rhizosphere Function, Amir Ahkami)

Elaboration of rhizosphere processes at molecular and micrometer scales. EMSL seeks proposals that aim to mechanistically link the physical, chemical, and biological processes taking place at different spatial (nanometers to centimeters) and temporal (minutes to months to years) scales in the rhizosphere. Proposals that upscale these processes in the context of the soil profile in a changing environment are encouraged. Topics of interest include (but are not limited to) root–microbe–soil interactions; rhizodeposition that influences carbon and nutrient fluxes; coupled molecular and transport processes that facilitate carbon and nutrient retention, transformation, and release; root-microbiome chemical signaling; linking rhizosphere structure (including root phenotypes) and function; studying carbon, nutrient, and metabolite flow in the rhizosphere using stable isotope labeling; targeted and untargeted spatiotemporal metabolomic characterization of exudates at root–soil interfaces; and responses of rhizosphere processes and microbial communities to rhizodeposition. Proposals that integrate 2-D and 3-D rhizosphere imaging (physical and/or chemical), multiomics, and sensing technologies with root phenotyping are encouraged. Samples collected from field experiments are encouraged.

ETI-4: Molecular and microscale responses to ecosystem disturbances (All ETI IRPs)

Elaboration of watershed biogeochemical and/or atmospheric responses to disturbance events at timescales of hours, days, seasons, or multiple years. Disturbance events include but are not limited to major precipitation events, wildfires, inundation, drought, and saltwater intrusion. Topics of interest include processes controlling carbon, metabolite, nutrient, and micronutrient cycling, transport, uptake, and release; coupling between watershed and biogeochemical processes; volatile atmospheric emissions from terrestrial systems; root exudation, plant–microbe interactions, and ecosystem resilience; and OM stability. Proposals that leverage MONet data or would use MONet sampling as part of the research scope are encouraged.

Overlap with CAM: Proposals under one of the four ETI topics mentioned above that would test, develop, or utilize innovative methods for the coanalysis of 2-D and 3-D chemical images using artificial intelligence (AI) or machine learning (ML) approaches to enable the mining of molecular information from images, the processing of multimodal data, coregistering spatial molecular data from different instruments, or expanding 2-D chemical information to 3-D space are of particular interest (Contact: Satish Karra).

Functional and Systems Biology (FSB) Science Area

EMSL invites proposals that utilize EMSL expertise and experimental capabilities for research focused on biological systems relevant to the sustainable production of bioproducts, environmental microbiology, and biosystem design. Proposals aimed at uncovering insights into nutrient cycling and bioproduct production within fungal, algal, and microbial systems, as well as microbial communities, are desired. Focus areas include elucidating protein function with structure-mechanistic studies; enhancing the understanding of biological circuits by investigating protein, metabolite, and lipid interactions; and capturing the complexity of individual cell behaviors within microbial communities. Learn more about the FSB Science Area. Contact the FSB Science Area Leader, Kristin Burnum-Johnson, if you have questions about these topics.

FSB-1: Protein and protein complex structure and function (IRP: Structural Biology, Scott Lea)

• 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 relies on understanding the function of proteins in cellular processes. EMSL seeks proposals that target structure-mechanistic studies that elucidate the biochemical or biological functions of fungi, algae, and microbes essential to nutrient cycling or the production of bioproducts.
• The 1000 Fungal Proteins project aims to utilize structural biology resources, both experimental and computational (including simulation, data analytics, and informatics), to accelerate the annotation of proteins of unknown function that are highly conserved across the fungal kingdom. User samples can enter the structural biology pipeline within the 1000 Fungal Proteins project at various points, including users who already have proteins or metabolites highly purified and available for shipment to those users who only have a gene sequence (such as those found in the Joint Genome Institute’s [JGI’s] Mycocosm) and would utilize EMSL’s computational or experimental workflows from gene to structure.
• Proteins often function in complexes, many of which are not or are only poorly characterized. Comprehensive characterization of these complexes can be used to assign function(s) for new and unknown proteins. EMSL seeks proposals aimed at characterizing the composition, activities, and locations of complexes that regulate biochemical pathways in fungal, algal, and microbial systems.
• Knowledge of molecular assembly and cellular component organization and behavior in time and space can provide unique clues about function and reveal opportunities for pathway engineering in fungal, algal, and microbial systems. EMSL seeks proposals that focus on the characterization of the spatiotemporal relationships between proteins, protein complexes, and subcellular ultrastructure.

Overlap with CAM: Proposals are of particular interest where they would advance AI/ML and reconstruction workflows for protein structure determination and functional annotation (Contact: Satish Karra).

FSB-2: Regulatory and biosynthetic pathways (IRP: Biomolecular Pathways, Mary Lipton)

• 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 biological processes that mitigate the interconnections and interactions of proteins, metabolites, and lipids in the context of environmental nutrient cycling or the production of bioproducts in biological systems including but not limited to fungi, algae, microbes, and microbial communities are desired.
• The quantification of the functional components of complex systems involved in metabolic and biosynthetic pathways is crucial to understanding how these pathways are regulated and controlled. Projects aimed at the quantitative characterization and integration of biomolecules central to these pathways in or the connection of these processes with environmental systems, including but not limited to fungi, algae, microbes, and microbial communities including viruses, are desired.
• The understanding of the regulation of biological circuits is growing but still has gaps. Proposals focused on the elucidation of regulatory pathways in microbes, fungi, algae, and microbes (including viruses and microbial communities) involved in environmental nutrient cycling or the production of bioproducts are desired.

Overlap with CAM: Proposals are of particular interest where they would advance the processing and integration of multiomics data for modeling and interpretation (Contact: Kelly Stratton).

FSB-3: Structure and function of natural microbial communities, engineered consortia, and host–microbe systems (IRP: Cell Signaling and Communications, Alex Beliaev)

• Capturing the breadth and complexity of individual cell behaviors as part of multiorganism communities or populations across space and time is essential to untangling mechanisms that influence intrinsic microbiome properties and cumulative outputs. EMSL seeks projects that develop and deploy multiomics approaches along with high-resolution dynamic imaging to investigate the in situ function, diversity, and dynamics of multicellular systems comprising microbial, fungal, algal, and viral cells, such as environmental microbiomes, engineered microbial consortia, and host–microbe associations.
• Delineating mechanisms of intercellular interactions, signaling, and resource-sharing processes is critical to understanding how individual organisms affect neighboring cells and affect community-level behavior. Studies leveraging high-resolution and/or single-cell measurements to understand how cells in microbial populations interact as a function of 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 the building and characterization of engineered microbial consortia, at single-cell and /or subpopulation resolution, for industrial or environmental applications are encouraged.

Overlap with CAM: Of particular interest are proposals advancing computational approaches that facilitate data processing and analysis to integrate molecular measurements at the subpopulation and, when possible, single-cell levels.

Computing, Analytics, and Modeling (CAM) 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. EMSL follows a cohesive approach to integrating experimental and computational methods with data analytics, visualization advances, and predictive approaches for cellular metabolism towards the production of 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 other constituents) in the environment. As part of EMSL’s strategic science objective MIDAS (Modeling, Integration, and Data Agents for Science), proposals seeking to test novel foundation models, language models, and AI-based agents in the context of advancing BER mission science are of general interest. Researchers with questions about the following call topics or interested in discussing project concepts are encouraged to contact Jaydeep Bardhan, CAM Science Area Leader.

CAM-1: Data-driven modeling of soil samples (IRP: Systems Modeling, Satish Karra)

Data-driven approaches including statistical methods and the recent advances in AI/ML enable the “learning” of unknown processes in a system from data. EMSL seeks proposals to apply and test statistical/AI/ML methods that elucidate the underlying hydro-biogeochemical processes or process parameters (e.g., constitutive model parameters) from soil data. Hybrid approaches that combine statistical/AI/ML methods and mechanistic models (e.g., combining balance-law-based partial differential equations with ML) are also of interest. Data-driven models for bridging scales and that enable using information from one scale to another (e.g., molecular to pore or pore to continuum scales) are also of particular interest.

Overlap with ETI: Proposals are of particular interest if they would integrate multiple types of data in the EMSL MONet data resource or if they focus on bio-/ecointegration (e.g., incorporating metabolic or other biological models).

CAM-2: Advanced data analytics and data integration methods (IRP: Data Transformations, Kelly Stratton)

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, generating interpretable and actionable results can be challenging. Proposals that will leverage cutting-edge data science and statistical approaches and make use of existing data resources in new ways to advance BER science priorities are therefore encouraged. Methods of particular interest include dimensionality reduction, data integration, incorporation of pathway information from existing public data and metadata resources (including but not limited to NMDC, KEGG, STRING, etc.), topological or geometric approaches, Bayesian methods, and approaches designed for noisy, incomplete, or limited training data.

Overlap with FSB: Proposals are of particular interest where they would provide new insights into regulatory and biosynthetic pathways by leveraging existing BER domain-science repositories (e.g., JGI and ESS-DIVE).

CAM-3: Data science and statistical/AI/ML methods to advance data analysis and visualization of spatially resolved molecular information in microbial communities (IRP: Data Transformations, Kelly Stratton)

Spatially resolved molecular information (metabolic, lipidomic, proteomic, transcriptomic) generated from microbial communities and, particularly, 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. Complementary imaging studies of soil—for instance, X-ray computed tomography (XCT)—provide detailed structural information relevant to understanding environmental biogeochemical processes. Techniques to integrate these types of data frequently generated by EMSL represent an emerging research area of great potential for BER mission science. Proposals aimed at testing innovative methods to transform imaging-based structural information into scientific discovery through computational image analysis, data integration, and visualization, with the aim of enhancing capabilities to understand complex BER-relevant systems, are of particular interest.

Overlap with FSB: Proposals are of particular interest where they would leverage EMSL data to develop new insights into natural microbial communities, engineered consortia, or host–microbe systems.

Overlap with ETI: Proposals are of particular interest where they would furnish new insights into rhizosphere processes, structure, and function or into the spatial elements of responses to environmental disturbances.

CAM-4: Methods for modeling biological systems at the cellular and community levels (IRP: Systems Modeling, Satish Karra)

Cutting-edge capabilities for modeling cellular behavior and microbial communities have shown substantial promise for understanding and controlling biological processes and the genotype–phenotype relationship. However, until recently, the effort and expertise required to build such models have prohibited their widespread use, but the growth in automation capabilities motivates improvements in understanding the creation, use, and refinement of cellular and community models. Proposals leveraging existing genome-scale metabolic models to advance bio-/ecodata integration or innovative methods to reduce barriers to creating such models are therefore of particular interest, as are proposals that would advance the use of EMSL experimental capabilities to create, refine, and validate cellular and community models.

Overlap with FSB: Proposals are of particular interest where they advance model–experiment (ModEx) cycles for interrogating specific pathways or accelerate ModEx cycles through the automation of model creation, curation, and refinement.

Overlap with ETI: Proposals are of particular interest where they advance the understanding of rhizosphere processes or carbon cycling in soil.

CAM-5: Advancing AI/ML for the modeling and simulation of biological and environmental molecules (IRP: Systems Modeling, Satish Karra)

AI and ML are enabling simulation studies to reach unprecedented time and length scales through predictive models for multiscale problems and to provide new insights into molecular structure–function relationships through the analysis of simulation data. Proposals that leverage AI/ML in novel ways to simulate complex systems that were not previously tractable, to accelerate the convergence of molecular simulations, to improve accuracy through multiscale modeling, or to gain new understanding of molecular behavior and regulation by post-simulation analysis are of particular interest, as are proposals that advance the coupling of modeling and EMSL experimental capabilities.

Overlap with FSB: Proposals are of particular interest where they would advance functional understanding of specific protein complexes or their roles in novel (or potentially important) pathways.

Overlap with ETI: Proposals are of particular interest where they would advance or accelerate ModEx cycles, enhancing the understanding of multiscale environmental processes influenced by soil chemistry, aerosols, or VOCs.

CAM-6: Methods for molecular identification and function annotation (IRP: Data Transformations, Kelly Stratton)

Advances in statistics, data science, and simulation have led to powerful new tools for identifying molecules and for predicting the properties and functions of biological molecules, including proteins, nucleic acids, small molecules, and lipids. However, the relevance and value of many data analytics tools for BER science remain relatively unrecognized because of domain-expertise barriers between the developers of data analytics methods and domain scientists. Studies testing new identification and functional-annotation approaches to problems central to BER science priorities are therefore encouraged. Proposals in this topic area should focus on advancing bio/ecodata integration by leveraging large-scale public datasets (e.g., JGI, ESS-DIVE) to provide new insights into EMSL data and/or by leveraging EMSL data to advance the state of the art, for example, enhancing predictions or inference of protein regulation (by post-translational modifications, protein–protein interactions, protein–nucleic-acid interactions, and protein–small-molecule interactions) using environmental context.

Overlap with FSB: Proposals are of particular interest where they would advance the identification or characterization of functional protein complexes, of novel pathways, or of microbial communities or host–microbe systems.

Overlap with ETI: Proposals are of particular interest where the methods would advance the understanding of molecular mechanisms of soil systems, terrestrial emissions and their atmospheric processing, or rhizosphere processes.