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30 Projects Awarded Funding from EMSL

Researchers will develop tools to mitigate climate change and engineer bioproducts 

Genoa Blankenship |
globe in forest

Researchers who have been awarded Large-Scale Research funding from EMSL will have access to EMSL instrumentation in the user facility's three science areas. (Photo provided by iStock) 

Scientists from across the globe are working on 30 projects to develop tools and processes to improve plant, crops, and bioproducts, as well as mitigate climate change.  

This international effort to tackle the world’s greatest scientific hurdles is funded through the Environmental Molecular Sciences Laboratory (EMSL) Fiscal Year 2023 Call for Large-Scale Research Proposals. EMSL is a Department of Energy, Office of Science user facility sponsored by the Biological and Environmental Research (BER) program. Scientists with Large-Scale Research project funding have up to two years of access to EMSL’s world-class expertise and instrumentation.  

The awarded projects support research in EMSL’s three science areas—environmental, biological, and computational sciences. Featured among the projects are investigations into global carbon cycling, plastic pollution, greenhouse gas emissions, and aerosols. 

“We are thrilled to welcome new and returning users from universities and national laboratories to collaborate with EMSL on cutting-edge science,” said Nikki Powell, deputy of EMSL User Services. “This proposal funding provides researchers with the opportunity to delve into unprecedented areas of science using some of our most highly specialized instrumentation alongside EMSL research staff.” 

EMSL offers 150 instruments and resources to researchers who submit a successful research proposal, some of which include the Tahoma supercomputer, high-resolution micro-X-ray computed tomography to characterize plant roots, and the cell-free expression pipeline to synthesize proteins. 

The awarded projects include:  

Melissa DuhaimeMelissa Duhaime

University of Michigan

Determining mechanisms and rates of microbial plastic
biodegradation and the consequences for freshwater
carbon cycling

Knowledge gaps regarding microbe–plastic interactions have limited innovation in plastics recycling and engineering of systems for plastic pollution bioremediation. Through this project, researchers will use EMSL’s multi-omics, metabolic modeling, and advanced microscopy capabilities to determine the mechanisms and rates of polyethylene and biodegradable polymer degradation in natural aquatic communities.

Erik Wright Erik Wright

University of Pittsburgh

Illuminating emergent properties underlying complex carbon degradation within communities of soil microorganisms

Soil microorganisms play a key role in global carbon cycling by degrading complex carbon molecules. Carbon degradation requires the contributions of multiple different soil microorganisms. This research aims to identify the set of small molecules that govern community assembly and the collective degradation of complex carbon molecules.

Song FengFeng Song


Pacific Northwest National Laboratory

Determination of the molecular architecture and temporal dynamics that drive microbial lignocellulose degradation

This project aims to generate information that aids in the development of rationally engineered communities expressing phenotypes.
Researchers will apply multi-omics analyses using a biology-informed, data-driven model and kinetic assays specific to lignocellulolytic activity levels to isolate and analyze microbes that degrade lignocellulose.

Lyle Whyte Lyle Whyte

McGill University 

Cellular controls on carbon source–sink dynamics in deglaciated soils

Researchers seek to identify the microbial taxa and carbon pools that drive the carbon cycle in deglaciated soils of different ages. The expected outcome is to determine how predicted changes in the Arctic climate will shape future carbon source–sink dynamics by affecting underlying cellular processes.

Steven HallamSteven Hallam

University of British Columbia 

Mass-spectral 'fingerprinting' of technical and native lignin substrates for improved biological funneling and enzyme discovery

Lignin derived from plant biomass is a potentially valuable resource for renewable energy and materials production. To address the challenges of lignin deconstruction, researchers will combine the biological and chemical signatures of transformed lignin to design, build, and test standardized workflows to compare biological treatments across lignin types. This will guide assembly of more efficient biotechnology platforms for energy and materials production.

Amy Marshall-Colon Amy Marshall Colon

University of Illinois at Urbana-Champaign

Uncovering dynamic changes in metabolism and signaling across cell types in the Sorghum bicolor stem using multi-omics

Sorghum is a bioenergy crop that produces a large quantity of biomass that can be processed into ethanol for biofuels. This project will use EMSL’s capabilities in multi-omics to build gene regulatory networks that direct experimental efforts to improve stem traits. 

Francisco Javier CejudoFrancisco Cejudo

Universidad de Sevilla

The thiol redox proteome dynamics in Arabidopsis thaliana in response to light

Plant performance relies on regulatory mechanisms that allow the rapid adaptation of their metabolism to light, which is the key stimulus for growth and development of photosynthetic organisms. This research will develop new tools to improve crop acclimation, given that climatic change is expected to affect Earth’s vegetation.

Kendall Corbin Kendall Corbin

University of Kentucky

Unraveling the biochemical and metabolic networks controlling bacterial cellulose biosynthesis 

The project aims to unravel the complex relationship between gene function, metabolic pathways, and phenotype through
the integration of structural, biochemical, and ‘omics datasets. The comprehensive molecular-level information generated from this project will have broad application for the metabolic engineering of cellulose-producing bacteria.

James Umen James Umen

Donald Danforth Plant Science Center

Structural and functional dissection of a cell cycle
chromatin switch in green algae

Chlamydomonas reinhardtii will be used to develop a structural model for cell cycle control by a conserved chromatin-associated regulator, the retinoblastoma tumor suppressor complex. This data will provide a foundational resource on how cell growth is linked to cell cycle progression during the Chlamydomonas life cycle.

Michael Knoblauch Michael Knoblauch

Washington State University

Deciphering the structure and function of the last unknown major plant organelle – Plasmodesma

EMSL’s sample preparation technology and cryo-electron tomography will be used to reveal in-situ structure of plasmodesmata, which is a nanoscale pore that is essential to plant performance. The combination of structural and functional data will be used to fundamentally refine current models.

Suping Zhou Suping Zhao

Tennessee State University

Developing the proteome network regulating structure and function of root development of switchgrass on marginal lands

Researchers will select drought- and AI-treated biomass switchgrass to profile proteomes in each distinct type of cell found in root tips. Results are expected to advance understanding of the biological processes that regulate and coordinate cell division, cell differentiation, and cell growth in the root tip. 

Setsuko Wakao Setsuko Wakao

Lawrence Berkeley National Laboratory

The knowns against the unknowns: Photosynthesis gene discovery through multi-omic survey of photosynthetic

This research tackles a high-risk challenge of identifying novel gene functions related to photosynthesis using a large-scale mutant library. Researchers aim
to gain insight into the functions of unknown-function genes through mining multi-omic patterns across mutants and wildtypes during perturbation with photosynthetic stress.

Paul DeMott Paul DeMott

Colorado State University

Single-particle characterization for interpreting ice-nucleating particle measurements in the SAIL field study

This project will use single-particle characterizations of aerosol samples to associate aerosol composition with simultaneous measurements of ice-nucleating particles (INPs). A synthesized description of INPs and their relationships to aerosol regimes will result, which are
useful for modeling studies of aerosol–cloud–precipitation interactions in weather and climate models.

Claudio Mazzoleni Claudio Mazzoleni

Michigan Technological University

Transformations of organic coatings in light-absorbing aerosols released by biomass burning and associated impacts on the interactions with clouds

This project will use EMSL’s analytical capabilities to study the interactions of black-carbon-containing particles with clouds, including how these interactions drive direct and indirect radiative forcing, modify cloud microphysical properties, and govern the wet removal and transformations of black-carbon-containing particles.

Susannah Burrows Susannah Burrows

Pacific Northwest National Laboratory

Disentangling the impacts of particle mixing state on ice nucleation

This project will exploit a unique combination of EMSL capabilities to quantify droplet freezing under different conditions and to characterize the bulk and surface chemistry of individual particles and atmospheric ice-nucleating
particles to test theoretical model predictions of the impacts of particle mixing state on ice nucleation.

Alexander LaskinAlexander Laskin

Purdue University

Probing atmospheric nanoplastics: An unrecognized urban source of airborne particles

Environmental nanoplastic (EnvNP) particles are inadequately
characterized pollutants with significant adverse effects on aquatic and atmospheric systems. A range of particle analysis and chemical imaging techniques hosted by EMSL will be used for extensive analysis of EnvNP particles collected in field and focused laboratory studies.

Debjani Sihi  Debjani Sihi

Emory University

Coupling X-ray computed tomography images with ModEx inspired laboratory manipulation experiment for predicting greenhouse gas fluxes from terrestrial–aquatic interfaces

This project will generate fine-scale data to validate a computational tool to advance modeling from fine-scale processes to ecosystem-scale functions to improve understanding of multiscale Earth system dynamics and processes. EMSL capabilities will be used to evaluate how redox heterogeneity across soil microsites influences greenhouse gas emissions from terrestrial–aquatic interfaces.

Jean-Thomas Cornelis Jean-Thomas Cornelis

University of British Columbia

Elucidating the effects of root responses to moderate soil nutrient limitation on mineral bioweathering processes

This project aims to advance understanding of soil controls on root exudation and their influence on bioweathering and the formation of organo-mineral associations. The research will catalyze the fundamental understanding of soil–plant feedback processes to propose new land management strategies that optimize soil nutrient acquisition and carbon storage.

Amisha Poret-Peterson Amisha Poret Peterson

U.S. Department of Agriculture - Agricultural Research Service

Molecular controls of microbial nitrogen use efficiency in agricultural soils

Using stable isotope probing and tracing experiments, this project tests the hypothesis that biomass-amended soils will have higher microbial nitrogen use efficiency than unamended soils. This work provides mechanistic understanding of microbial processes involved in nutrient cycling and carbon sequestration in agricultural soil systems.

Daniel Knopf Daniel Knopf

State University of New York at Stony Brook

Towards aerosol-ice formation closure: Chemical imaging investigation of aerosol and ice-nucleating particles

This project applies chemical imaging to identify the physicochemical properties associated with soil-dust particles that make up ice-nucleating particles. This research will result in improved ice-nucleating particle parameterizations and contribute to the predictive understanding of cloud formation and the hydrological cycle.

Buck Hanson Buck Hanson

Los Alamos National Laboratory

Revealing oxalate-mediated carbon flow through plant–fungal–bacterial rhizosphere interactions as part of a globally important carbon-sequestering biogeochemical process

This research will investigate the role of the plant root exudate oxalate in shaping bacterial-fungal-plant interactions in soil. Understanding how nutrients that plants secrete into soils influences microbial activities will advance strategies that aim to improve the management of plants for biofuel production, soil carbon sequestration, and soil fertility.

Kerri Pratt Kerri Pratt

University of Michigan

Identification of individual particle chemical composition, morphology, and ice nucleation properties in the Arctic

This project addresses gaps in understanding of Arctic aerosol chemical composition, mixing state, sources, and ice nucleation properties through chemical imaging and ice nucleation particle analysis. This work will provide insight into how natural and anthropogenic emissions and atmospheric processing are driving aerosol interactions with radiation, fog, and clouds.

Malak Tfaily Malak Tfaily

University of Arizona

Deciphering plant–plant, plant–microbe, and plant–soil interactions driving biological invasion in a southwestern desert grassland

Plant invasion is a major component of global change, leading to environmental transformations that alter
ecosystem services and associated biogeochemical cycles. This project aims to achieve a mechanistic understanding
of the role that belowground microbes play in conjunction with the plant metabolome to promote plant invasion.

Tim Scheibe Tim Scheibe

Pacific Northwest National Laboratory

Numerical modeling of hydrologic exchange and biogeochemistry in dynamic rivers

This project utilizes EMSL computational resources to support high-resolution numerical modeling and machine learning analyses at river corridor, watershed, and basin scales. Researchers will model groundwater–surface water interactions in the Hanford Reach of the Columbia River and watershed processes in the Yakima River Basin.

Bojana Ginovska Bojana Ginovska

Pacific Northwest National Laboratory

Computational mechanistic studies of methyl-coenzyme M reductase enzyme

Methyl-coenzyme M reductase (MCR) is an enzyme in the methane biological conversion by microbial communities with sulfate- or nitrate-reducing bacteria. MCRs achieve a catalytic bias toward using/producing methane though changes in protein confinement of substrates.
Researchers will use computational approaches to explore how the protein environment contributes to the reactivity.

Pernilla Wittung-Stafshede Pernilla Wittung Stafshede

Chalmers University of Technology

Novel artificial intelligence approach to unravel complex protein folding landscapes: toward a better bioeconomy

Most proteins must fold to function. Today, researchers can predict structures of folded proteins but not their folding reactions. This project will uniquely combine artificial intelligence/machine learning code with experimental folding data to predict protein folding processes with atomistic detail. The AI developed from model systems will then be applied to enzymes used in bioeconomy processes.

Marcel Baer Marcel Baer

Pacific Northwest National Laboratory

Atomistic simulations of the discriminatory power of desaturase

Desaturases catalyze regiospecific dehydrogenation of fatty acids. This project will use multiscale modeling to reveal atomistic details of how the metalloenzyme controls this process. This may help understand mechanisms governing carbon allocation and lipid synthesis that are keys to understanding and manipulating levels of lipid accumulation in plants.

Herbert Sauro Herbert Sauro

University of Washington

Inferring kinetic models for large-scale biochemical networks

This project will develop an iterative model ensemble approach for model building that incorporates existing knowledge
and is designed explicitly for hypothesis generation. Adversarial machine learning will be used to evaluate the ability of this method to recapitulate the benchmark models.

Carolyn Fitch Carolyn Fitch

Johns Hopkins University

Plant proteome structure-function and pKa prediction augmented with environmental considerations, deep learning, and integrated datasets

Researchers will investigate determinants of pKa values for protein groups with low-accuracy prediction and that are often triggers of biological function. Solvation and environmental influences will be systematically addressed. These studies will contribute to developing and applying computational algorithms to the levels needed to model biological systems.

Hoshin Kim Hoshin Kim

Pacific Northwest National Laboratory

Understanding product selectivity of monoterpene synthases using atomistic simulations

This research uses computational tools to conduct atomistic simulations of enzymatic systems to understand the chemistry and mechanisms of monoterpene synthases (MTSs). MTSs catalyze biosynthesis of monoterpenes, which play a pivotal role in plant–plant communications and act as a key ingredient in industrial applications, including flavor additives, fragrances,
and biofuels.