Call for Exploratory Research Proposals, FY 2026

• Single-cell proteomic and/or transcriptomic workflows (nanoPOTS/nanoSPLIT/splitSEQ) to quantitatively characterize phenotypic heterogeneity and spatial organization and to delineate cell–cell interactions underpinning the functioning of multicellular and/or multispecies microbial systems (Contacts: James Fulcher and Alex Beliaev). 
• High-fidelity cell separation and isolation techniques (i.e., fluorescence-activated cell sorting [FACS], laser capture microdissection [LCM], nano dispensing) that enable downstream integration of multimodal measurements such as high-resolution imaging, chemical/spectroscopic analyses, and single-cell omics. We invite Biological and Environmental Research (BER)-mission-aligned proposals that deepen the understanding of environmental microbes and microbiomes central to the bioprocessing of materials and products of economic value. Of particular interest are proposals exploring biological pathways (including but not limited to catabolic and biosynthetic reactions) and organisms participating in critical material transformations, transport, and acquisition, as well as proposals addressing questions related to microbe–mineral interactions (Contacts: Scott Lea and Alex Beliaev). 
• To support the development of new high-throughput cell phenotyping workflows, EMSL is introducing advanced capabilities in atmospheric and room temperature plasma (ARTP) mutagenesis. This innovative technique enables the rapid and effective creation of genetically diverse libraries across a wide range of microbial hosts. We invite proposals that systematically examine and characterize the impact of ARTP on microorganisms relevant to the DOE BER mission (e.g., CMM recovery and extraction, economically feasible production of biomaterials and chemicals), focusing on aspects such as mutation frequency and mutation types. These investigations will support the efficient development of downstream phenotyping protocols as well as provide data for artificial intelligence/machine learning (AI/ML)-enabled strain engineering strategies (Contacts: Erin Bredeweg and Alex Beliaev). 
• We invite proposals that leverage EMSL’s capabilities in cell-free protein expression and high-throughput mass spectrometry (MS) for parallel same-sample metabolite and protein quantification in low complexity samples to support the development of workflows enabling enzyme/pathway kinetic studies (Contacts: Paul Piehowski, James Evans, and Alex Beliaev). 
• Experimental (e.g., cell-free expression, cryogenic electron microscopy [cryo-EM], native mass spectrometry, etc.) and/or computational (e.g., OpenFold, Boltz-1, molecular dynamics, etc.) workflows 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 proteins (Contact: James Evans). 
• Applications of spectroscopic and atomic imaging to resolve structural and biochemical interactions between environmental microbes and critical materials or between proteins or protein complexes and interfaces in plant or microbial systems (Contact: Scott Lea). 
• Applications of deep multiomic characterization of microorganisms involved in bioprocess and metabolic pathways applicable for biomanufacturing and biotransformation in the bioeconomy aligning with BER mission and strategy (e.g., bacteria, fungi, algae). Specific emphasis on statistics-driven data integration of different analytical types (e.g., nuclear magnetic resonance [NMR] and MS approaches) (Contact: Mary Lipton). 
• Applications of deep multiomic characterization that expand the knowledge of microbiomes and the fundamentals of how microbes interact in these systems (including interkingdom interactions). Specific highlighted capabilities include the integration of global omics (proteomics, metabolomics by NMR and MS techniques) and statistical approaches to data integration (Contact: Mary Lipton). 
• MS-based discovery analysis for mapping post-translational modification (PTM) analyses in microbial systems with an emphasis on the impact of protein phosphorylation and acetylation on metabolic pathway regulation, growth rates, and bioproduct production (Contact: Paul Piehowski). 
• Spatially resolved analyses that use metabolome-informed proteome imaging (MIPI) to visualize biological pathways in complex systems. These analyses use matrix-assisted laser desorption/ionization (MALDI) MS imaging and micro- or nanoscale proteomics (microPOTS or nanoPOTS) to visualize biological pathways at activity hotspots in microbial systems (Contact: Marija Veličković). 
• Identification and relative quantification of secondary metabolites, especially siderophores and other metal coordinating species, in complex biological systems such as microbial consortia using liquid chromatography (LC) coupled to dual-high resolution MS (hybrid Fourier transform Orbitrap Exploris 480-21 Tesla ion cyclotron resonance mass spectrometry [FTICR-MS]) (Contact: Will Kew). 
• Innovative work to understand biogeochemical processes in BER-relevant environments, including but not limited to soils, sediments, surface water, groundwater, permafrost, and peatlands. Proposals must leverage EMSL’s gas chromatography (GC), pyrolysis gas chromatography (PyGC), LC, and/or FTICR-MS capabilities for natural organic matter (OM) and/or metabolomic characterization. Interested parties are encouraged to contact Emily Graham to discuss scope and capabilities. 
• Nano- to microscale compositional, morphological, and chemical characterization of mineral-associated OM, including minerals containing CMMs. Potential methods include scanning/transmission electron microscopy (S/TEM), electron energy loss spectroscopy (EELS), atomic probe tomography (APT), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), or X-ray photoelectron spectroscopy (XPS) (Contacts: Yaobin Xu for S/TEM/EELS, Danny Perea for APT, Shuttha Shutthanandan for XPS, Odeta Qafoku for SEM/EDS.) 
• Spectroscopic characterization of soil organic matter (SOM) and mineral–OM associations (including CMMs). Potential methods include Mössbauer, Raman, electron paramagnetic resonance (EPR), and NMR spectroscopy. (Contacts: Eric Walter for EPR, Ravi Kukkadapu for Mössbauer, Brian O’Callahan for Raman, and David Hoyt for NMR). 
• Chemical imaging of rhizosphere, soil, and sediment processes using TerraForms, including micromodels, RhizoChips, and Pore2Chip platforms, and/or RhizoMAP capabilities. TerraForms reproduce pore networks and can include bioprinted native soil microbes, soil aggregates, and minerals. The development and use of TerraForms to study CMM and rare earth element solubilization and transport in porous media are highly encouraged. (Contacts: Arunima Bhattacharjee and Jayde Aufrecht; Dušan Veličković for RhizoMap). Parties interested in mineral-printed RhizoChip capabilities are strongly encouraged to contact Jayde Aufrecht prior to LOI submission. 
• Stable isotope probing coupled with laser ablation–isotope ratio mass spectrometry (LA-IRMS) to spatially map the trajectory of root-exuded carbon in the rhizosphere and surrounding soil (50 to 150 µm spatial resolution of datapoints from in situ samples) (Contacts: Vimal Balasubramanian and Sophie Lehmann). 
• Root exudate characterization using EMSL’s ultrasensitive gas and LC MS methods and small-molecule analytics methods (e.g., NMR). The development/use of novel capabilities for high-throughput collection and analysis of root exudates from field settings is highly encouraged, including trap systems, Rhizon samplers, microdialysis probes, or similar approaches (Contact: Amir Ahkami). 
• Investigations of atmospheric processing and ice formation potential of particles from biomass burning and biological and field-collected atmospheric particles using any of the following capabilities: controlled combustion system (Contact: Zezhen Cheng), freezing assay system (Nurun Nahar Lata), ice-nucleating particle concentration measurements at warm temperatures (Gourihar Kulkarni), portable ice nucleation experiment (Swarup China), and thermal desorption GC quadrupole time-of-fight MS (Swarup China). 
• Atmospheric aerosol particle characterization using sum frequency generation (SFG) to study heterogeneous chemistry (Contact: Zheming Wang) 
• Measurement of vertical composition profiles of atmospheric aerosols and their potential to uptake water and act as ice-nucleating particles. Samples must be from flights over the Bankhead National Forest using the Atmospheric Radiation Measurement facility’s ArcticShark uncrewed aerial system in summer 2024 and planned flights during summer 2025. Proposals that require additional sample collection or related activities from the ARM facility will not be eligible (Contact: Swarup China). 
• Assessment and application of novel computational strategies for incorporating molecular data into existing biogeochemical, watershed, and Earth system models. Submitters are encouraged to propose parameterizations of Molecular Observation Network (MONet) data that could improve reaction networks, or thermodynamic or kinetic pool representations within existing model frameworks. The use of AI models or other strategies for estimating, extrapolating, or scaling MONet parameters with the context of watershed and Earth system frameworks is also encouraged. Submitters should articulate how the proposed work will enable the utilization of MONet data in larger-scale model frameworks (Contacts: Arjun Chakrawal and Satish Karra). Proposals may utilize the numerical tools available in EMSL’s PFLOTRAN Carbon Reaction Sandbox (Contact: Glenn Hammond) or Pore2Chip/Chip2Flow workflows (Contact: Maruti Mudunuru).
• 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 DOE, Office of Science, 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 the multimodal integration of imaging data with other data streams. For instance, overlaying MS-based imaging data with abundance or concentration data can identify areas of interest for detailed sample collections. Accelerated, semiautomated methods (including but not limited to 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, particularly leveraging AI/ML, for converting raw molecular data from high-resolution MS into actionable scientific insights. Proposals should focus on improving our 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 the 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 the convergence of molecular simulations; improve accuracy through multiscale modeling, advanced sampling methods, or coupled atomistic–coarse-grained simulations; or gain new understanding of molecular behavior and regulation by post-simulation analysis. Studies that would advance model–experiment integration (ModEx) involving EMSL’s experimental capabilities are of particular interest (Contacts: 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 hydrobiogeochemical 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 (e.g., using MAGI to integrate EMSL metabolomic data with genome data from the Joint Genome Institute). Studies aiming to integrate MONet data with public soil, flux, hydrology, and other geospatial data are highly encouraged (Contact: Kelly Stratton). 
• Identifying, modeling, and/or optimizing proteins that bind critical materials or small molecules containing them (view the definitions). Investigations seeking to test new models’ capabilities for predicting the behavior of such proteins are also of interest, e.g., protein language models or genome language models (Contact: Satish Karra). Studies that would validate findings through experimental capabilities are encouraged but not required. 
• Investigations leveraging genome-scale metabolic models (GSMMs) to understand experimental results or develop novel experimental designs. Studies requiring model refinement using EMSL data and/or JGI data are of special interest, as are studies leveraging novel methodologies for model creation and refinement (Contacts: Satish Karra and Niaz Chowdhury). 
• EMSL is introducing a new Makerspace capability. Users can leverage the Makerspace to build physical prototypes to help them answer research questions in BER-relevant science areas. The capabilities will include 3-D printers (resin, high temperature, filament), laser engravers and cutters (CO₂, ultraviolet [UV]), collaborative robotic equipment and liquid handlers, shared collaboration and storage spaces, dedicated design computers, and more. Example use cases include developing micrometer-resolution laser-etched 3-D models of soils to study processes using a reduced complexity experimental setup or developing custom field-deployable aerosol capture devices to study rhizosphere processes. Our 3-D printers could be used to print biologically compatible vessels to study perturbations of microbial growth, or interfaces to capture the headspace of a 96 well plate. Users can access the capabilities remotely in collaboration with on-site staff, or they can opt to join us here at EMSL (travel and accommodations not provided). Contact Kim DeSousa or the Integrated Research Platform leader in your scientific domain. 

Contacts 

For questions about the proposal submission process, please contact User Program Services. 

For technical help with NEXUS, please contact NEXUS Support. 

For scientific questions, contact the EMSL staff identified in the focus topics or highlighted capabilities of the proposal call.