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Call for Exploratory Research Proposals, FY 2025

Submit Letter of Intent


Letters of intent due at 5 p.m. PDT

Proposals must employ one or more of the capabilities highlighted below to advance scientific understanding in the Environmental Molecular Sciences Laboratory’s (EMSL’s) three science areas (biological, environmental, computing). As a guide, at least 30% of the research effort should focus on the highlighted capabilities in terms of requested hours or samples analyzed. Other EMSL instruments and resources may be used to supplement your research plan. Interested users are encouraged to work closely with EMSL scientists when developing the letter of intent (LOI) and subsequent proposal.  

A LOI is required before submitting a proposal, and full proposals may only be submitted by invitation. EMSL utilizes dual anonymous peer review for this call. Full proposals must be anonymized to enable dual anonymous peer review. Successful proposals will include well-described research plans that can be completed within the nine-month project period.  

Exploratory proposals are abbreviated to approximately a third of the duration and budget of a full Large-Scale Research or FICUS proposal. To help accomplish research goals during the 9-month time frame, we encourage PIs to focus the research narrative on one or possibly two subtasks. For proposals that are awarded, we strongly encourage PIs to be ready to ship samples as close as possible to the project start.  

Highlighted Capabilities

  • Single-cell biology capabilities that encompass microscopy, activity-based probing, proteomics, and/or transcriptomics workflows to elucidate intercellular signaling, communication, and ensuing heterogeneity that underpin the phenotypes of microbial systems (Contact: Alex Beliaev)
  • Mass spectrometry-based multiomic workflows supporting the development of high-throughput phenotyping of natural or synthetic metabolic pathways (Contact: Alex Beliaev)
  • Experimental and/or computational analyses to accelerate the annotation of uncharacterized proteins that are highly conserved across fungi with particular emphasis on gene to structure and function workflows of fungal membrane proteins (Contact: James Evans)
  • Applications of deep multiomic characterization of low abundant microorganisms (e.g., bacteria, fungus, viruses) (Contact: Mary Lipton)
  • Post-translational modification analyses that improve the throughput, reproducibility, and sensitivity of or expand the scope of modifications that can be studied (Contact: Paul Piehowski)
  • EMSL is developing capabilities in chemical biology to probe enzyme function and characterize biochemical pathways. EMSL currently has access to (1) a noncanonical fluorogenic probe library to profile amide hydrolase function and (2) photoaffinity probes mimicking plant-derived carbon sources to identify their function and interacting protein targets. EMSL is seeking users to utilize the existing probe library or work with us to develop probes for other activities. (Contact: Sankar Krishnamoorthy)
  • Spatially resolved analyses that utilize mass spectrometry imaging and micro- or nanoscale proteomics to visualize metabolomic pathways at activity sites in microbial systems (Contact: Marija Veličković)
  • Identification and relative quantification of secondary metabolites in complex biological systems such as microbial consortia, soils, and rhizosphere systems using liquid chromatography coupled to dual-high resolution mass spectrometry [Hybrid Orbitrap Exploris 480-21 Tesla Fourier transform ion spectroscopy (FTICR-MS) and tandem mass spectrometry] (Contact: Will Kew)
  • Innovative work leveraging EMSL’s gas chromatography (GC), liquid chromatography (LC), and/or FTICR-MS capabilities for natural organic matter (OM) and/or metabolomic characterization. We welcome smaller scale studies that do not fit into our Large Scale Research/FICUS proposal calls but are too large for limited scope proposals (e.g., 25–100 samples, using a limited set of capabilities). Parties who are interested should contact Emily Graham to discuss scope and capabilities.  
  • Nano- to micron-scale compositional, morphological, and chemical (e.g., oxidation state of C, N, and metals) characterization of mineral-associated OM. Potential methods include (ascending order of length scale probed) scanning/transmission electron microscopy (S/TEM), electron energy loss spectroscopy (EELS), atomic probe tomography (APT), helium ion microscopy (HIM), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), or X-ray photoelectron spectroscopy (XPS) (Contact: Yaobin Xu for S/TEM/EELS, Danny Perea for APT, Shuttha Shutthanandan for HIM, Odeta Qafoku for SEM/EDS, Qian Zhao for XPS). 
  • Spectroscopic characterization of soil organic matter (SOM) and mineral–OM associations. Potential methods include Mössbauer spectroscopy (chemical identity and abundance of nano-Fe oxide/sulfide–OM aggregations), Raman spectroscopy (chemical identification and micrometer-scale imaging of minerals and organics), electron paramagnetic resonance (EPR) [quantitation of humic/fulvic SOM and OM-complexed metal ions, e.g., Fe(III), Mn(II), Cu(II)] and nuclear magnetic resonance (NMR) (identification and quantification of metabolites). (Contact: Eric Walter for EPR, Ravi Kukkadapu for Mössbauer, Brian O’Callahan for Raman, and David Hoyt for NMR)
  • Chemical imaging of the rhizosphere and soil processes using Terraforms platforms. These include micromodels or RhizoChips that explicitly reproduce pore networks obtained from X-ray computed tomography analysis of soils including Molecular Observation Network (MONet) soil cores, bioprinted native soil microbiomes for downstream omics phenotyping, and soil aggregate micromodels. Analysis capabilities include the measurement of microbial consortia and plant dynamics (SubTap platforms); the chemical imaging of soil microbial and root–soil interface processes using optical microscopy, mass spec imaging [matrix-assisted laser desorption/ionization (MALDI), Nanospray desorption electrospray ionization, secondary ion mass spectroscopy (SIMS)], and electron microscopy-EDS; spatial RNA/DNA sampling; and high-throughput metabolomics (SubTap). Micromodels are suitable for microbial incubation and growth (Contact: Arunima Bhattacharjee and Jayde Aufrecht). Submitters planning to propose mineral-printed RhizoChip projects are strongly encouraged to contact Jayde Aufrecht prior to LOI submission to determine if they are in-scope for an Exploratory call project. 
  • Root exudate characterization using EMSL’s ultrasensitive gas and liquid chromatography mass spectrometry methods (GC/LC-MS) and small molecule analytics methods (e.g., FTICR-MS and NMR). Analysis of root exudates collected from field settings using nondestructive in situ sampling techniques is highly encouraged, including trap systems (e.g., glass vials), Rhizon samplers, microdialysis probes, or similar approaches. (Contact: Amir Ahkami). 
  • Investigations of atmospheric processing and ice formation potential of particles from biomass burning using any of the following capabilities: controlled combustion system (Contact: Zezhen Cheng), portable ice nucleation experiment, (Contact: Swarup China and Nurun Nahar Lata), and thermal desorption gas chromatography quadrupole time-of-fight mass spectrometry (Contact: Swarup China). 
  • Investigating vertical profiles of aerosol composition and evaluating their potential to uptake water and act as ice-nucleating particles. Eligible samples are those collected during engineering flights over the ARM Southern Great Plains observatory during summer 2023 and from planned flights in summer 2024 over the Bankhead National Forest in northern Alabama using the Atmospheric Radiation Measurement (ARM) facility’s ArcticShark uncrewed aerial system. Samples can be requested from EMSL. Submitted proposals should describe EMSL-only projects and should not require additional sample collection or related activities from the ARM facility for project completion. (Contact: Swarup China)
  • Tests of innovative approaches for ontology refinement, alignment, and engineering, particularly if integrated with large language models. These tests should focus on the methods’ capacity to bridge or standardize ontologies or data models between the different research communities whose discoveries advance Department of Energy (DOE), Office of Science, Biological and Environmental Research (BER) program mission science, with the ultimate goal of enabling scientists to more easily develop an integrative understanding of biogeochemical and biological processes. (Contact: Montana Smith
  • Investigations seeking to apply, test, and compare advanced methods for overlaying image data to identify areas of interest for detailed sample collections. Accelerated, semiautomated methods [including but not limited to artificial intelligence/machine learning (AI/ML)-based ones] promise to accelerate discoveries from imaging capabilities such as confocal microscopy, fluorescence in situ hybridization, and MALDI. (Contact: Kelly Stratton
  • Investigations seeking to identify and quantify metabolites from NMR spectra. EMSL has developed a semiautomated capability to increase throughput as well as consistency, and datasets with novel or unusual BER-relevant metabolites are of particular interest. (Contact: Kelly Stratton). 
  • Assessment and application of novel computational strategies (including but not limited to artificial learning/machine learning) for converting raw molecular data from high-resolution mass spectrometry into actionable scientific insights. Proposals should focus on improving understanding of biogeochemical and biological processes, and studies focused on processing and annotating data from ‘omics and complex mixtures are of particular interest. (Contacts: Aivett Bilbao and Yuri Corilo)
  • Investigations applying novel computational methods for modeling and simulation of BER-relevant biological systems at molecular and cellular scales. Proposals should leverage newly developed approaches to either simulate complex systems that were not previously tractable; accelerate convergence of molecular simulations; improve accuracy through multiscale modeling; or gain new understanding of molecular behavior and regulation by post-simulation analysis. Studies that would advance ModEx involving EMSL’s experimental capabilities are of particular interest. (Contact: Margaret Cheung and Amity Andersen
  • Computational studies leveraging continuum reactive transport models derived from MONet soil data using EMSL’s upscaling capabilities or studies applying novel statistical or AI/ML based methods to MONet soil data. Proposals should focus on how the work advances capabilities to elucidate hydro-bio-geochemical processes or process parameters. (Contact: Satish Karra)
  • Novel applications of new data science and statistical approaches to analyze and integrate EMSL data, especially in the context of BER-relevant public data resources such as other BER user facilities (Joint Genome Institute, ARM user facility). Studies aiming to integrate data from MONet with public soil, flux, hydrology, and other geospatial data are highly encouraged. (Contact: Kelly Stratton)

Review criteria

User proposals are peer-reviewed against the three criteria listed below. For each criterion, the reviewer rates the proposal Outstanding, Excellent, Good, Fundamentally Sound, or Questionable Impact and provides detailed comments on the quality of the proposal to support each rating, specifically noting 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: Relevance of the proposed research to the missions of EMSL and the Biological and Environmental Research (BER) program (25%) 

EMSL’s mission is to accelerate scientific discovery and pioneer new capabilities to understand biological and environmental processes across temporal and spatial scales. EMSL supports the mission of the Department of Energy, Office of Science, Biological and Environmental Research (BER) program to achieve a predictive understanding of complex biological, Earth, and environmental systems for the nation’s energy and infrastructure sustainability and security. The BER program 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 genetic code into 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 design and reengineering of the 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 the 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. 

Potential Considerations: What is the relationship of the proposed research to EMSL’s and BER’s missions? Does the research significantly advance mission goals and align with the focus topics for EMSL’s science areas as outlined in the most recent Call for Proposals? Will the proposed research advance scientific and/or technological understanding of issues pertaining to one or more EMSL science areas? How well does the project plan represent a unique or innovative application or development of EMSL capabilities?  

Criterion 3: Appropriateness and reasonableness of the request for EMSL resources for the proposed research (25%) 

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 and/or scope of the 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?