EMSL Selects 19 Projects through 2026 Exploratory Research Call

Integrated Research Platform: Biomolecular Pathways

Hemant Choudhary, Joint BioEnergy Institute

"In situ observation of dynamic lignin structural changes to enhance bioconversion"

This study uses in situ spectroscopic techniques, including nuclear magnetic resonance (NMR), to track lignin’s structural changes during biomass pretreatment and depolymerization. By understanding these transitions, the project aims to optimize processing conditions, prevent inhibitor formation, and advance efficient, scalable biorefineries for improved lignocellulosic feedstock bioconversion and biomass utilization.

Integrated Research Platform: Cell Signaling and Communication

(Listed by principal investigator in alphabetical order)

Armando Bravo, Donald Danforth Plant Science Center

"Arbuscular mycorrhizal fungi acquisition and metabolism of plant lipids"

This project investigates how arbuscular mycorrhizal (AM) fungi acquire and metabolize lipids provided by plants during their nutrient exchange symbiosis. Using proteomics, metabolomics, and advanced imaging techniques, the project aims to identify key lipid transport mechanisms, enzyme functions, and metabolic pathways to strengthen plant-fungal mutualism and enhance microbial-based biotechnologies.

Adam Feist, University of California, San Diego

"Harnessing atmospheric and room temperature plasma (ARTP) mutagenesis to expand functional diversity in automated high-throughput adaptive laboratory evolution"

This project combines ARTP mutagenesis with automated adaptive laboratory evolution (ALE) to accelerate microbial strain optimization for phenotypes important to biomanufacturing. By enhancing functional diversity, the project evaluates ARTP's potential to expand evolutionary design space and optimize workflows for microbial systems engineering in biotechnology.

Rebecca Sherbo, Northeastern University

"Cellular heterogeneity in lithotrophic carbon- and nitrogen-fixing metabolism"

This project explores how chemolithotrophic bacteria, such as Xanthobacter autotrophicus, compatibilize carbon and nitrogen fixation despite their energy-intensive and oxygen-sensitive nature. Using Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) and single-cell proteomics, the project investigates metabolic heterogeneity at the single-cell level, aiming to advance sustainable bioproduction and improve understanding of global biogeochemical cycling.

Rebecca Smith, University of Wisconsin, Madison

"Combining the single cell Sorghum bicolor transcriptome and metabolome to uncover cell-type specific biosynthetic pathways"

This project aims to generate cell-type specific multiomics datasets for Sorghum bicolor using single-cell transcriptomics, proteomics, and spatial metabolomics. By building a detailed cell atlas, the project aims to enable targeted genetic engineering in bioenergy crops, improving biomass yield, biofuel production, and bioproduct synthesis without compromising plant growth or development.

Karen Wawrousek, University of Wyoming

"Using population heterogeneity to identify lipid accumulation pathways in Rhodococcus opacus"

This project investigates how Rhodococcus opacus achieves simultaneous lipid accumulation and growth using an agricultural byproduct. By analyzing cell subpopulations through fluorescence-activated cell sorting (FACS) and multiomics, the project aims to identify metabolic states enabling this phenotype, providing insights for engineering efficient microbial lipid production and advancing economical biofuel development aligned with EMSL and BER missions.

Integrated Research Platform: Structural Biology

Nikhil Malvankar, Yale University

"Seeing is Believing: Correlated imaging of electron transfer and protein structure to identify how BER-relevant bacteria and archaea respire without oxygen-like soluble electron acceptors"

This project investigates how diverse microbial communities interact through extracellular electron transfer via various protein nanowires. Using advanced imaging and analytical techniques to resolve nanowire structures and functions, the project aims to understand and control nanowire-mediated microbial physiology and ecology to harness their potential for energy, biotechnology, and environmental applications.

Integrated Research Platform: Biogeochemical Transformations

(Listed by principal investigator in alphabetical order)

Jennifer Goff, Research Foundation of SUNY

"Redox controls on critical mineral tellurium biogeochemistry in freshwater sediments"

This project addresses tellurium (Te) supply challenges by investigating redox-sensitive pathways for microbial reduction and stabilization of Te as recoverable nanoparticles. Using sediment microcosms, imaging, and sequencing, the project identifies biotic and abiotic processes for Te transformations, advancing strategies for sustainable recovery and expanding EMSL capabilities for critical mineral research.

Zoë Havlena, Los Alamos National Laboratory

"Tracking lanthanide uptake and accumulation in native microbial populations from rare earth mineral bearing sediments"

This project addresses biomining to advance domestic rare earth element (REE) recovery by researching lanthanide accumulation in bacteria from mine wastes and other REE-bearing sediments in New Mexico. By isolating novel strains of bacteria and using high resolution techniques like NanoSIMS, this project aims to uncover biological mechanisms underlying efficient REE sequestration.

Xiaoxu Li, Pacific Northwest National Laboratory

"Advanced characterization of rare earth elements in perovskite phases derived from red mud for optimized recovery of critical minerals"

This project aims to uncover mechanisms behind rare earth element (REE) incorporation in red mud's REE-rich perovskite phases using advanced EMSL imaging tools. By understanding nanoscale partitioning, the project seeks to develop targeted, low-energy extraction methods to recover critical REEs, turning industrial waste into a valuable resource.

Aaron Thompson, University of Georgia

"Reductive isolation of rare earth elements: can common soil organic acids or metallophores facilitate europium(III) reduction?"

This project investigates whether common soil organic compounds can facilitate Eu(III) to Eu(II) reduction under natural conditions, challenging the paradigm of reduction only occurring deep within the Earth. Using advanced analytical techniques, this project explores Eu reduction pathways, enhancing understanding of rare earth biogeochemistry and informing sustainable extraction and contamination mitigation strategies.

Integrated Research Platform: Rhizosphere Function

(Listed by principal investigator in alphabetical order)

Harsh Bais, University of Delaware

"A systems approach to decipher the role of root region specific secretions to microbial association"

This project uses RhizoChip to investigate root secretions and microbial colonization in sorghum, focusing on specific root regions and their association with plant growth-promoting bacteria or synthetic microbial communities (SynCom). Insights will enhance crop engineering for bioenergy, linking root-microbe interactions to improved yield and sustainable energy production.

Cara Santelli, University of Minnesota

"Mechanisms of metal transformation and accumulation by hyperaccumulating plants and soil bacteria within a synthetic rhizosphere environment"

This project investigates how hyperaccumulating plants and soil microbes transform lead (Pb) speciation in the rhizosphere using RhizoChip TerraForms, metabolomic analysis, and transcriptomics. It aims to uncover mechanisms driving Pb mobility and solubility, advancing phytoremediation strategies and critical mineral recovery while enhancing understanding of plant-microbe-metal biogeochemical interactions.

Integrated Research Platform: Terrestrial-Atmospheric Processes

(Listed by principal investigator in alphabetical order)

Kristina Black, National Center for Atmospheric Research

"Uncovering the link between marine biology and cloud formation in high-latitude ocean environments"

This project investigates the link between plankton activity and cloud formation in remote marine environments by analyzing seasonal changes in plankton communities and their contributions to aerosols and ice-nucleating particles. Combining cruise sampling and EMSL analyses, it enhances understanding of atmosphere-biosphere interactions for improved climate and ecosystem modeling. 

Peter DeCarlo, Johns Hopkins University

"Vertical variation of volatile organic compounds and molecular composition of organic aerosols"

This project investigates the vertical distribution of volatile organic compounds (VOCs) and organic aerosols at a coastal site near Baltimore during the Coast-Urban-Rural Atmospheric Gradient Experiment (CoURAGE) campaign. Using advanced EMSL tools, the project explores aerosol composition and its impact on atmospheric interactions, including aerosol-cloud and aerosol-radiation processes, enhancing climate and urban air quality understanding.

Integrated Research Platform: Systems Modeling

(Listed by principal investigator in alphabetical order)

Song Feng, Pacific Northwest National Laboratory

"Exploring AI-informed evolutionary design principles in metabolic control by post-translational modifications and allosteric regulations"

This project combines advanced AI models to uncover evolutionary principles of metabolic regulation through post-translational modifications and allosteric bindings. Using protein sequence, genomic, and interaction interface embeddings, this project aims to predict regulatory sites and motifs, enabling improved genome-scale metabolic models for biosystem design across diverse organisms.

Ganesh Sriram, University of Maryland, College Park

"Understanding the dynamic regulation of metabolism"

This project aims to uncover fundamental principles governing biological systems by studying the Yeast Respiratory Oscillation (YRO), a dynamic metabolic cycle, that draws on the properties of the conserved metabolic network. Using high-quality data, models, and interdisciplinary collaboration, the project seeks to predict metabolic flux, quantify responses to environmental perturbation, and to learn principles that explain metabolic behavior across organisms. This understanding is expected to inform applications in bio-industry and systems biology.

Roelof Versteeg, Subsurface Insights

"Developing a process level understanding of the spectral induced polarization signatures of critical mineral bioleaching"

This project aims to optimize copper slag bioleaching—a sustainable method for critical mineral recovery—by developing spectral induced polarization (SIP) as a real-time diagnostic tool. Through experiments and computational modeling, it explores microbial, geochemical, and hydrological dynamics to advance slag reprocessing, support domestic mineral supply chains, and strengthen U.S. energy and economic security.

Chao Zeng, Pacific Northwest National Laboratory

"Predictive microbial–mineral interaction models for lithium bioleaching"

This project aims to optimize lithium bioleaching by linking microbial genomic and metabolic traits to environmental factors governing lithium release in porous media. The project combines genomic analysis, metabolic modeling, and flow-through experiments with AI-driven workflows to predict lithium mobilization efficiency and refine sustainable extraction strategies using selected microbial strains.