EMSL Awards Funding to 32 Large-Scale Research Projects
Scientists using EMSL instruments and expertise to further research in aerosols, wildfires, and drought.
The Environmental Molecular Sciences Laboratory (EMSL) has awarded funding to 32 Large-Scale Research projects. (Photo provided by Adobe)
Researchers representing 32 different projects have been awarded Fiscal Year 2024 Large-Scale Research (LSR) project funding from the Environmental Molecular Sciences Laboratory (EMSL), a Department of Energy, Office of Science user facility sponsored by the Biological and Environmental Research (BER) program.
The awarded projects support research in EMSL’s three science areas—environmental, biological, and computational sciences. Featured among the projects are studies looking at atmospheric aerosols, wildfires, and drought.
Scientists with LSR project funding have up to two years of access to EMSL’s world-class expertise and instrumentation.
The awardees include:
Assessing the selective bioweathering of minerals by fungi in soil ecosystems
Rebecca Lybrand
University of California, Davis
Researchers will use EMSL’s high-resolution microscopy and mass spectrometry to automate mineral identification and produce scanning electron microscopy images to confirm the presence or absence of fungi on identified mineral grains. The method will provide a means to assess fungal-mineral interactions as a function of mineral type, which will advance understanding of how fungi selectively weather minerals in natural soil conditions.
Alex Tat-Shing Chow
The Chinese University of Hong Kong
A team of scientists will conduct watershed-scale wildfire experiments at the Department of Energy’s Savannah River site to improve understanding of the effects of wildfires and post-fire rainstorms on the fates of pyrogenic organic carbon and nitrogen in burned terrestrial and aquatic ecosystems. EMSL’s mass spectrometry and nuclear magnetic resonance resources will be used to determine the molecular structure and composition of samples collected from the wildfire experiments.
Bradley Tebo
University of Washington
To visualize molecular-level interactions between a protein and its mineral product, researchers will use advanced visual proteomics approaches to solve geochemical and geomicrobiological questions about how manganese mineralization is staged by a manganese-oxidizing bacterial enzyme within the biomolecular matrix of the mature outer layer of spores known as the exosporium.
Visualizing the cellular and molecular bases underlying desiccation tolerance
Marisa Otegui 
University of Wisconsin, Madison
Using EMSL’s cryo-electron microscopy imaging approaches, researchers will analyze mature pollen grains of Pennisetum typhoides and Arabidopsis thaliana (desiccation tolerant) and energy sorghum (desiccation-sensitive) to reveal the cellular and molecular strategies that allow them to survive desiccation. Understanding the cellular and molecular traits that underlie pollen desiccation tolerance will support efforts to engineer bioenergy grass crops with higher reproductive capacity in a warming planet.
Cellular and chloroplast recycling pathways in maize leaf cells under low nitrogen conditions
Marisa Otegui
University of Wisconsin, Madison
Understanding the cellular pathways that mediate nitrogen recycling and remobilization in leaves is critical for the bioenergy crop production. In this project, researchers will explore how two different photosynthetic cell types of a carbon-compound leaf degrade and recycle cellular components, including chloroplasts, under low nitrogen conditions. The goal of this research is to provide fundamental knowledge for the sustainable production of bioenergy crops by improving understanding about nutrient recycling, increasing yields in low nutrient soils, and minimizing fertilizer requirements and pollution.
Epidermal plastid reprograming during microbial colonization
Jean Greenberg
University of Chicago
Using a recently developed fast and accurate method for isolating intact sensory plastids from leaves and roots, researchers will investigate the metabolite, lipid, and membrane proteome reprogramming of epidermal plastids during microbial interactions.
Steven Burgess
University of Illinois at Urbana-Champaign
Researchers are studying Rubisco—an enzyme present in plant chloroplasts which is important for crop production. Understanding the evolution and properties of this enzyme has the potential to inform strain improvement efforts for photosynthetic biomass production with important for energy security and bioproduction.
Understanding the impact of drought on native cell wall nanoarchitecture of engineered plants via multi-dimensional solid-state NMR and cryo-TEM
Jennifer Mortimer
University of Adelaide and Lawrence Berkeley National Laboratory
Drought affects plant growth and quality. There is some evidence that a plant’s tolerance to drought can improve with modifications to the plant cell wall. However, it is not understood how these changes enable drought tolerance at a molecular level. This research will provide a framework for developing breeding strategies for biomass crops with improved drought tolerance. Scientists will explore the impact of temporal drought treatments on cell wall architecture to understand the role of the 3D lignin-xylan-cellulose interactions in response to drought.
Jennifer Teschler
Pivot Bio, Inc.
Nitrogen-fixing soil bacteria can replace synthetic fertilizers to provide plants with nitrogen, which is an essential nutrient, in a more ecological way. Scientists at Pivot Bio have identified two plant associated nitrogen-fixing bacteria and edited key genes to enhance nitrogen fixation and excretion. In this project, the team plans to further characterize how these microbes associate with the roots and deliver nitrogen to the plant.
Manipulating chloroplast metabolism by controlling ferredoxin dependent electron distribution
Daniela Strenkert
Michigan State University
Through this project, researchers will gain insights into how green algae regulate metabolic reactions in response to changes in their environment via Ferredoxins, which are small iron–sulfur proteins that mediate electron transfer.
Sabeeha Merchant
University of California, Berkeley
Researchers will develop proteomics methods to determine the number of protein molecules per cell for each component of the machinery that is responsible for carbon fixation and the capture of light energy. The results will provide an understanding of compositional variation in protein complexes in response to the environment and will be used to refine metabolic models.
Unraveling spatial and temporal dynamics of microbial necromass destabilization
Courtney Creamer
U.S. Geological Survey
This project addresses the importance of mineral associations and organic chemistry in necromass destabilization, transport, and re-association with minerals. EMSL’s time-of-flight secondary ion mass spectrometry (ToF-SIMS), isotope ratio mass spectrometry, and ultra-high-resolution mass spectrometry will be employed to provide insight into important insights into the poorly understood process of necromass destabilization.
Molecular scale investigations of the interaction of soil organic N with soil minerals
Yuan Liu
Michigan State University
Researchers will use a combination of EMSL instrumentation, including ToF-SIMS, nanoscale secondary ion mass spectrometry (NanoSIMS), and atomic force microscopy to directly characterize the binding mechanisms and strengths of amino acids absorbed to mineral surfaces. Research results will provide mechanistic and improved predictive understanding of the interactions of soil organic nitrogen compounds with minerals, which will have important implications for managing soil organic nitrogen and nutrients in agricultural ecosystems.
Rhizosphere Microbial Metabolism and Viral Dynamics for Improving Tall Wheatgrass Drought Tolerance
Sneha Couvillion
Pacific Northwest National Laboratory
A team of researchers are using experimental and modeling approaches to examine the effect of drought-altered exudate composition on rhizosphere microbial metabolism, gene expression and microbial host-virus dynamics. The multi-omic characterization of the key microbial taxa, expressed genes and bioactive metabolites involved will enable a mechanistic understanding of plant-microbe feedbacks during drought and inform the development of microbial or metabolite-based solutions to enhance plant performance.
Elucidating the Ice Formation and Transformation Pathways in Aerosols at Atomic Resolution
Jingshan Du
Pacific Northwest National Laboratory
This research aims to elucidate the nucleation, phase transformation, and melting pathways of ice nanocrystals at an unprecedented resolution and to pave the way for a new level of research on ice in earth and biological systems, shedding light on environmental, surface chemical, and cryobiological technologies.
The Influence of Particle Phase State on the Growth Kinetics of Secondary Organic Aerosols
Rahul Zaveri
Pacific Northwest National Laboratory
Researchers will investigate the influence of particle phase state on the growth of secondary organic aerosols by observing the evolution of particle size distribution, viscosity, morphology, volatility, and molecular composition with EMSL’s single particle mass spectrometer, electron microscopy, and nanospray desorption electrospray ionization high-resolution mass spectrometry.
Frank Keutsch
Harvard University
To investigate aerosols in the stratosphere and upper troposphere and resulting ice nucleation and climate impacts, researchers will study the chemical composition, morphology, and ice nucleation propensity of aerosol particles collected using the NASA WB-57 high-altitude research aircraft. Offline measurements with microscopy and spectroscopy techniques will be conducted at EMSL.
Chandan Sarangi
Indian Institute of Technology, Madras
Using EMSL’s multi-modal chemical imaging and spectroscopy capabilities, this project addresses uncertainties about the fundamental properties of polluted dust layers by characterizing the chemical speciation, morphology and mixing state of individual aerosol particles sampled over the Indian Himalayas. Results from this work will enable improvements in remote sensing algorithms as well as in fine tuning the relevant aerosol modules in Earth system and climate prediction models to reduce uncertainties about polluted dust's impact on weather and hydroclimate over the Indian sub-continent.
The role of biopolymers in controlling kinetics of mineral growth via particle aggregation
Dongsheng Li
Pacific Northwest National Laboratory
Building on previous work, researchers will use EMSL capabilities to explore the impact of biomolecules and small molecule protein-mimetics on mineral growth via particle aggregation. This research will utilize a combination of oxide minerals—hematite, anatase, and rutile with well-characterized surfaces and a class of synthetic organic ligands, known as peptoids, that enable the systematic variations in each of the ligand characteristics.
Nutrient and contaminant incorporation in amorphous intermediates during carbonate nucleation and growth in biogeochemical systems
Sebastien Kerisit
Pacific Northwest National Laboratory
Through this research, scientists will use a variety of EMSL instrumentation, including nuclear magnetic resonance, scanning electron microscopy, and the Tahoma scientific computing resources to develop a quantitative understanding of nutrient and contaminant incorporation in amorphous intermediates and crystalline end-products that leads to accurate predictions of the bioavailability of nutrients and the fate of contaminants in biogeochemical systems.
iTopS: integrative topological scores with functional molecular modeling
Mihaela Sardiu
University of Kansas Medical Center
This project aims to produce a novel computational prototype to synthesize and visualize the structural models of higher-order protein complexes derived from the existing empirical data and the relative protein abundance of these complex assemblies from many organisms.
Soil-based carbon dioxide sorption: Image analysis, numerical modeling, and deep learning
Behzad Ghanbarian
Kansas State University
Modeling carbon dioxide storage in soils will provide deep insights on how much soil-based CO2 adsorption can help fight climate change. To advance knowledge of soil-based CO2 sorption, researchers leading this project will analyze soil images available through the Molecular Observation Network (MONet). The team will develop deep learning models to predict CO2 adsorption and desorption in soils.
Scale-bridging soil imaging and modeling using physics-informed machine learning
Kalyana B. Nakshatrala
University of Houston
This project develops a physics-informed machine learning methodology to upscale soil structural information. The proposed machine-learning-based framework provides a science-based approach to transfer information across scales. Thus, it facilitates an improved mechanistic understanding of hydrobiogeochemical processes from pore scale to watershed scales.
Eugene Ilton
Pacific Northwest National Laboratory
In this project, researchers will develop an automated workflow that will integrate artificial intelligence and machine learning methods with electronic spectroscopy and computational chemistry to efficiently explore the configurational space of micronutrients/impurities in host minerals, proteins, and soils. This work will provide a deeper molecular-level understanding of the biogeochemical cycling of micronutrients and the effect of impurities on the stability of carbon in soils.
Physics-guided Machine Learning for Protein Modeling and Design
Armita Nourmohammad
University of Washington
Researchers are creating novel physics-guided machine learning models with graph neural networks to learn symmetry-aware representations for protein interfaces. This approach opens a new path toward interpretable computational models for proteins to describe how biological properties and function emerge from protein subunits.
Nitrogen Fixation by Nitrogenase
Simone Raugei
Pacific Northwest National Laboratory
Building on previous combined experimental/computational investigations, scientists will further explore the electronic rearrangements upon electron and proton delivery to the catalytic cofactor and upon nitrogen activation and reduction.
Exploring gas migration and diffusion pathways in CODH/ACS using molecular simulations
Simone Raugei
Pacific Northwest National Laboratory
The purpose of the project is to computationally characterize the diffusion channels and escape routes for carbon monoxide and carbon dioxide in a variety of monoxide dehydrogenase and acetyl-coenzyme A synthase (ACS) complexes. ACS is an enzymatic complex with potential industrial applications.
Understanding structure-function relationship in enzymes by designing artificial enzymes
Bojana Ginovska
Pacific Northwest National Laboratory
In this project, researchers will study how the protein environment affects functionality by designing an artificial enzyme. The team will investigate an artificial enzyme that converts carbon dioxide to formate in an aqueous solution. Researchers will use computational chemistry tools to understand how the protein scaffold activates the molecular complex in water and then redesign the enzyme for higher activity.
Investigation of Copper Binding in A Metal-chelating Plant Protein
Ritimukta Sarangi
Stanford Linear Accelerator Center
Cellular metal chelation is a vital plant stress response mechanism that enables plants to survive in metal-polluted soils, which could be valuable in crop engineering for agricultural use and phytoremediation of metal-polluted soils. The study of metal-chelating proteins is crucial in understanding these biological processes. This project aims to uncover the mechanism of copper ion binding in a metal-chelating protein that is involved in peptide cyclization reactions.
Real-time detection of biogeochemical hotspots within saturated sediments
Kevin Roche
Boise State University
This project will identify the mechanisms controlling the flux of greenhouse gases from bulk oxic river sediments by simultaneously observing anoxic microzones and anoxic gas fluxes in microfluidic experiments. These results are critical for incorporating fine-scale reaction heterogeneity into whole river biogeochemical models, and they will improve estimates of greenhouse gas fluxes from freshwater ecosystems to the atmosphere.
Imaging the Spatial Effects of Hydraulic Redistribution on Root Exudation
Richard Marinos
University at Buffalo, State University of New York
Researchers aim to understand how plant hydraulic redistribution alters the transfer of carbon from plants to soils during periods of water stress and what effect this has on soil carbon cycling. This work will advance mechanistic understanding of ecosystem resilience to drought.
Microbial diversity, complexity, and dynamics within a ‘grass-to-glass’ profile at a late iron age archaeological site, and as a function of climatic variables
Carolyn Pearce
Pacific Northwest National Laboratory
We propose to systematically analyze the microbial consortia that are enriched on rock surfaces as a function of depth through a ‘grass-to-glass’ profile using samples obtained during the excavation of a late iron age Swedish vitrified hillfort, an ancient copper mine in Israel, and an obsidian flow at the Newberry volcano. The research represents habitat analogs for disposed radioactive waste glass to inform how microbial processes might influence long-term glass waste form durability.