Twenty-Eight Projects Selected for EMSL Large-Scale Research Awards

Twenty-eight principal investigators were recently awarded access to the Environmental Molecular Sciences Laboratory (EMSL) through the Fiscal Year 2025 Large-Scale Research call for proposals. 

The awarded researchers, who hail from as far away as Spain and the Netherlands, will have access to EMSL’s instrumentation and expertise for up to two years. EMSL is a Department of Energy, Office of Science user facility on the Pacific Northwest National Laboratory campus, sponsored by the Biological and Environmental Research program. 

Projects include research that aims to advance climate models, increase carbon sequestration in major bioenergy crops, and understand how environmental stresses change plant cells. 

Read about the researchers who will be starting their projects on Oct. 1. 

Albert Rivas-Ubach

Spanish National Research Council - CSIC 

Determining the Relative Contribution of Bioaerosols Within Complex Samples Through Accurate Metabolite Signatures and Machine Learning 

Current global change scenarios expect to significantly increase the amount of pollen in suspension in the lower atmosphere. In addition, pollen can burst into smaller fragments that are highly efficient as cloud condensation nuclei. However, current climate models still do not incorporate the effects of these particles because of the detection and quantification challenges related to complex aerosol mixtures. In this project, researchers will develop novel analytical and bioinformatic strategies to characterize and quantify complex pollen mixtures present in the atmosphere. This research will lead to a significant advancement in atmospheric chemistry and provide much needed data to improve the accuracy of climate models. 

Hector Garcia Martin

Lawrence Berkeley National Laboratory 

Optimizing P. putida Bioproduction Hosts with Genome-Scale Bayesian 13C Metabolic Flux Analysis 

This project aims to address the critical barrier to progress in biomanufacturing represented by the scarcity of production hosts able to efficiently convert plant biomass into desirable bioproducts. The soil organism Pseudomonas putida KT2440 is a promising host organism for producing valuable small molecules because of its ability to metabolize diverse feedstocks including lignocellulose hydrolysate. Researchers will use EMSL capabilities to identify the key metabolic bottlenecks in Pseudomonas putida KT2440 for producing a sustainable aviation fuel and improve algorithms for flux prediction. Algorithms to predict metabolic fluxes from proteomics would eliminate the necessity to perform expensive, complicated 13C Metabolic Flux Analysis experiments and would enable the prediction of fluxes in situations where microbial communities or multicellular organisms are unviable. 

Elisa Biasin

Pacific Northwest National Laboratory 

Effect of H-Bonding in Biologically Relevant Proton-Coupled Electron Transfer Reactions 

Proton-coupled electron transfer (PCET) reactions are important in metabolic pathways involved in the breakdown, synthesis, and interconversion of molecules such as carbohydrates, lipids, and amino acids. PCET processes are involved in nutrient uptake and transport across cellular membranes and are central to photosynthesis, a process that ultimately leads to the incorporation of carbon dioxide into organic molecules, driving carbon flux through the biosphere. However, there is a lack of understanding of how PCET works, particularly the influence of hydrogen bonding. Through this project, researchers aim to explore PCET in complex systems that can form hydrogen bonds with the surrounding water molecules, leading to improved predictive models and understanding of these reactions. This will enhance our grasp of metabolism, nutrient cycling, biofuel production, and ecosystem dynamics. 

Yang Song

University of Arizona 

Elucidating Environmental Regulation on the Structure and Functional Composition of Microbial Communities Involved in Soil Carbon, Nitrogen, and Phosphorus Cycling Using Metagenomics Analysis and Artificial Intelligence Model 

The predictability of soil carbon–climate feedback remains a significant uncertainty in climate change projections, motivating an increasingly mechanistic representation of microbially mediated soil carbon (C), nitrogen (N), and phosphorus (P) cycling in soil biogeochemical and Earth system models (ESMs). However, these models still struggle to parameterize the complexity of microbially mediated soil C, N, and P cycling and their interactions with changing environments. This project aims to leverage gene-to-ecosystem data from EMSL’s 1000 Soils pilot study to address the impact of environmental heterogeneity on the taxonomic structure of soil microbial communities and their derived potential functional composition related to soil C, N, and P cycling across the contiguous United States (CONUS). Researchers will quantify the structure and functional composition of soil microbial communities across diverse CONUS environments. This research will provide the gene-to-ecosystem-scale dataset across diverse CONUS environments and a novel data integration method for enhancing gene-to-Earth system prediction. 

Min-Yeh Tsai

National Chung Cheng University 

Understanding PTM Impact on Microbial Amyloid Proteins Through Molecular Simulation 

This project aims to delve into the molecular mechanisms of microbial amyloid proteins, particularly focusing on the role of post-translational modifications (PTMs) in these processes. Applying a comprehensive approach, researchers will use a transferable coarse-grained biomolecular simulation package to examine protein–protein interaction properties at interfaces. These interactions are pivotal in various microbial functions such as toxicity, signaling, and biofilm formation in plant-associated microbial communities. Researchers will integrate EMSL’s Python-based workflow with the Associative-memory, Water-mediated, Structure, and Energy Model (AWSEM) to predict protein structures and folding patterns for an intuitive analysis, especially for PTM-specific regulation. 

Hoshin Kim

Pacific Northwest National Laboratory 

Molecular Insight into Active Site Chemistry of Various Monoterpene Synthase Enzymes 

Monoterpene synthases (MTSs) produce natural monoterpene compounds responsible for plant–plant communications and the key ingredients for many industrial applications, including flavor additives, fragrances, and biofuels. MTSs control highly reactive carbocationic intermediates for their challenging reactions in a selective and stereospecific manner. Despite their versatility, there is little understanding of the mechanistic underpinnings of the selectivity and specificity of various MTSs. In this project, researchers plan to apply cutting-edge computational tools for atomistic simulations of enzymatic systems in conjunction with machine-learning-based protein structure predictions to predict several MTSs with unknown structures for precise atomistic simulations, elucidate the regio- and stereoselectivity of these MTSs, and provide findings to experimental collaborators as guidance for the design of enzyme variants. This research is expected to give a complete picture of the active site chemistry of various MTSs and provide a guide to design MTS variants with the desired specificity. 

Elizabeth Bell

National Renewable Energy Laboratory 

Unlocking the Potential of Enzymatic Polyamide Recycling Through Imaging, Tomography, and Chemical Analyses of Polymer Surfaces 

Polyamides (PAs), also known as nylons, are versatile polymers with an increasing annual global consumption: 7.67 million tons were manufactured in 2018 alone. Unfortunately, polyamide production is energy intensive and contributes greatly to greenhouse gas emissions. Polyamides also lack suitable disposal strategies and have limited biodegradability; hence, enzymatic recycling has emerged as a promising alterative recycling route for nylons. 

In this project, researchers will investigate enzymatically deconstructed Polyamide 6 to understand how proteins interact and modify the polyamide surface. The resulting insights into polyamide interfacial catalysis will inspire enzyme engineering approaches and novel surface treatments to improve recycling and give insights into how nylon biodegrades in the natural environment. 

Jaime Barros-Rios

University of Missouri-Columbia 

Tracking the Lignin Biosynthetic Pathway with Cellular Resolution 

Lignin is a complex aromatic polymer produced in plant cell walls and the second-most abundant natural polymer on the planet. It provides mechanical support, facilitates the transport of water and nutrients through the vascular system, and plays an important role in plant responses to biotic and abiotic stresses. Recently, researchers demonstrated the operation of a novel pathway to lignin biosynthesis, suggesting that xylem fiber and vascular bundle cells might follow distinct lignification patterns associated with different enzymatic activities or substrate availabilities. In this project, researchers aim to dissect lignin biosynthesis with precise spatial resolution to contribute fundamental knowledge of plant cell wall biogenesis. Understanding these biochemical processes will help applications to improve stress tolerance and increase carbon sequestration in major bioenergy crops. 

Doug Allen

USDA-ARS/Donald Danforth Plant Science Center 

Assessing Plant–Fungus–Microbe Interactions with SIP-Based Omics to Define the Active Community, Roles, and Functions in Beneficial Relationships for Sustainable Bioenergy Production 

Plants are the foundation of terrestrial life and rely heavily on complex relationships with soil microbes. These interactions are crucial to secure essential nutrients for plant growth and productivity. However, the roles of beneficial functions and the identities of the organisms involved remain to be validated. Investigating these plant–microbe relationships represents the next frontier in enhancing agricultural productivity, a necessity for a sustainable bioeconomy. In this project, researchers will focus on identifying and understanding the microbial communities that assist plants in nutrient uptake from soil, particularly under nutrient-deprived conditions. Efforts are expected to provide important foundational information that can be used to engineer plants and microbes for bioenergy needs. 

Siva Sankari

Stowers Institute for Medical Research 

Determination of the Structures of Plant Nodule-Specific Cysteine-Rich Peptides to Elucidate Their Mechanisms of Action on Nitrogen-Fixing Microbes 

Biological nitrogen fixation (BNF) is a product of a symbiotic relationship between nitrogen-fixing soil bacteria and leguminous plants, where the bacteria provide the plant with fixed nitrogen and the plant provides carbon sources for the bacteria. BNF is a sustainable alternative to chemical fertilizers that cause pollution and leave a large carbon footprint. Some legumes produce nodule-specific cysteine-rich (NCR) peptides, which cause bacteria to undergo terminal differentiation inside the root nodules and enhance nitrogen fixation. 

In this project, researchers aim to improve BNF by engineering NCR peptides into non-NCR-producing legumes to boost nitrogen fixation and crop yield. In order to achieve that, understanding how NCR peptides act on bacteria is crucial. This study will use nuclear magnetic resonance spectroscopy to determine the structures of NCR peptides and understand their interaction with bacterial membranes, helping to design more efficient nitrogen fixation systems. 

Björn Hamberger

Michigan State University 

Probing Terpenoid-Mediated Interactions Between Sorghum Bicolor and Its Microbiome 

Terpenoids, the most abundant class of plant-specialized compounds, play a crucial role in aiding plants to adapt to and interact with other organisms in the environment. 

Terpenoid pathway elucidations and an analysis of the metabolite profile at the host lab at Michigan State University have offered insights into small molecule biosynthesis in the bioenergy crop sorghum. Supplementing the sorghum root microbiome with plant terpenoids was found to induce significant changes in the microbial community composition. In this research, a team will use five activity-based probes (ABPs) containing a terpenoid moiety linked to a fluorescent tag to enhance the understanding of plant–microbe interactions with a focus on terpenoids. This research will provide foundational groundwork for engineering and refining synthetic microbiomes to enhance the resilience and productivity of economically significant biofuel plant species. 

Ronald de Vries

Westerdijk Fungal Biodiversity Institute 

Unraveling the Influence of the Substrate on Stress Response Mechanisms of Fungi (STRESS-FUNG) 

Fungi commonly experience stress in both natural and industrial environments. To overcome these stress conditions, fungi accumulate compatible solutes (e.g., mannitol, trehalose) as protection agents. However, the available carbon source strongly affects the production of such compounds and therefore stress tolerance. In this project, we aim to dissect the influence of the carbon source on the stress response, focusing on three main stress conditions: osmotic, temperature, and oxidative stress. The project may change our scientific understanding of the stress response in fungi and how this impacts biotechnological applications, as stress is a common feature of fungal fermentation. 

Amy Marshall-Colon

University of Illinois at Urbana-Champaign 

High-Resolution Spatial Omics to Investigate Intercellular Signaling and Sink–Source Dynamics in Sorghum and Miscanthus 

The accumulation of bioproducts into the storage organs of bioenergy grasses has great potential to decrease reliance on fossil fuels. Two important bioenergy grasses that hold such potential are Sorghum bicolor and Miscanthus × giganteus. Despite the increase in genomic resources for these crops, there is limited understanding of the multiscale biological and regulatory processes taking place in storage organs, which limits the ability to successfully synthesize and accumulate bioproducts in them. Through this project, researchers aim to expand the sorghum stem atlas by extending an analysis into transitional cell types between the stem, leaf, and nodal roots to learn about the signaling pathway between distinct tissues that are near one another. This research will provide a molecular atlas of sorghum and miscanthus storage organs over development and vastly increase our understanding of grass stem biology. 

Hanjo Hellmann

Washington State University 

Unraveling the Molecular Mechanisms of CRL3BPM E3 Ligase-Mediated Root Development Dynamics 

Researchers have identified a highly conserved ligase known as E3 ligase and further referred to CULLIN3-based (CRLBPM) E3 ligase that is critical for root development and salt stress tolerance. It is currently unknown how the ligase works on a system-wide level to control these processes in plants. CRLBPM marks proteins for degradation and thereby triggers cellular responses. In this project, researchers will unravel on a system-wide level how CRL3BPM impacts root development and what cellular mechanisms depend on this ligase to confer salt-induced stress responses. Because of the conserved nature of the E3 ligase, findings are expected to be widely applicable to plants. 

Sharon Doty

University of Washington 

Molecular Mechanisms of Nitrogen Fixation and Phosphate Solubilization by Endophytes of Populus 

Native poplar plants have a diverse microbiota, some of which can fix dinitrogen gas and solubilize phosphate, potentially providing two key limiting factors to plant growth. To successfully apply endophyte technologies to biomass production, it is necessary to have a greater understanding of the mechanisms by which endophytes provide essential nutrients to the host. In this project, researchers want to determine the molecular mechanisms of nitrogen fixation at the microbial community level and phosphate acquisition at the individual and community levels. 

Jiwei Zhang

University of Minnesota 

Creating a Large-Scale Fungal Gene Regulatory Network That Governs Wood Biomass Decomposition 

In wood decomposer fungi, its saprotrophic lifestyle often requires sophisticated regulation by precisely switching genes “on” and “off” to initiate the corresponding metabolic pathways to coordinate cellular energy distributions for sniffing nutrients, degrading organic matter, and acquiring the carbon nutrients sequestered in plants. Here, we plan to create a genome-wide model regulatory network in the wood decomposer fungus, providing a systematic understanding of the key fungal processes that govern carbon degradation and recycling in terrestrial ecosystems. 

Jocelyn Richardson

Stanford Linear Accelerator Center 

Tracking Potassium Rhizosphere Dynamics During Drought Using Terraforms 

Potassium (K) is essential to plant microbiome health but is often a limiting nutrient in the environment, even when plants are supplied with fertilizer. Additionally, K can mitigate the effects of drought in some plant and microbe species, and the intensity and extent of drought conditions persist globally as a result of climate change. Our understanding of K biogeochemical cycling is limited because of the few techniques capable of visualizing different K chemistries, and the opacity and heterogeneity of soil. In this project, researchers will study the effect of drought on the transformations of K between soil minerals, fungi, bacteria, and plants to visualize the inorganic and organic processes that control rhizosphere K cycling. 

Jorge Vivanco

Colorado State University 

Visualization of Divergent Phosphorous-Solubilization Mechanisms in the Rhizospheres of Wild and Domesticated Crops 

Researchers aim to dissect the complex relationship between plant roots and soil microbes in the context of phosphorus (P) solubilization. They will focus on the spatial distribution of P solubilization and microbial colonization along the root axis in tomatoes and cowpeas, which varies because of root exudate release patterns. The team will establish assays to measure direct P solubilization by roots and indirect solubilization via root-associated microbes. A comparative analysis of wild and cultivated plant varieties will shed light on differing P acquisition strategies, potentially informing new agricultural practices. This research is anticipated to aid in the development of plants with enhanced P uptake capabilities, contributing to the DOE-BER mission of improving nutrient use efficiency and reducing fertilizer dependency. 

Pamela Sullivan

Oregon State University 

How Do Root-Level Hydraulic Regulators in Pseudotsuga menziesii Impact Rhizosphere Processes? 

This project addresses the challenge of understanding how Douglas fir trees manage water use through their roots. By studying molecular changes in root cells and their impact on soil properties, we aim to uncover how different water-use strategies of plant roots affect the surrounding soil environment. This research will help us understand how different environmental stresses change plant cells and how these changes affect the area around the roots and the overall health of the soil. 

Leah Johnson

Los Alamos National Laboratory 

Understanding the Impact of Heat Stress on Bacteria–Fungi Interactions Towards Building Resilient Ecosystems 

As average atmospheric temperatures and heat wave duration and frequency increase globally, it is important to understand the impact of heat stress on soil microbial interactions because of their known contributions to plant resilience and biogeochemical processes. Studying microbial interactions with their environments and hosts from systems that face climate-relevant stressors can provide important insights into how environments will adapt to future climate scenarios. In this project, researchers will evaluate the impact of differential root exudate profiles (heat stress vs. non) on the fungal and bacterial isolates alone and how the exudates influence the interaction phenotypes of the microbial partners. As bacteria and fungi codominate soil microbial communities, this work will provide pivotal knowledge to dissect complex microbial interactions and resilience within broader communities under changing climate conditions. 

Xin Zhang

Pacific Northwest National Laboratory 

Understanding the Effect of Mineral Surface on Soil Carbon Turnover by Probing Soil Organic Matter–Mineral Interactions 

Researchers aim to improve the mechanistic understanding of the soil extracellular enzyme-mediated retention, transformation, and release of soil-mineral-associated organic matter by probing soil organic matter (SOM)–mineral interactions. The team will use a combination of traditional bulk analysis tools and state-of-the-art surface analysis tools to characterize the interaction forces between the mineral surface with both soil extracellular enzymes and enzyme-targeted organic substrates, the conformational change and activities of enzymes, and the decomposition, retention, and release of SOMs to elucidate how organo–mineral–enzyme interactions influence the kinetics and pathways of soil carbon turnover. With a more detailed mechanistic understanding of how organo–mineral and enzyme–mineral interactions regulate soil carbon turnover, scientists can further improve carbon and nutrient cycling modeling from the ecosystem to global scales. 

Vincent Noel

Stanford Linear Accelerator Center 

The Influence of Oscillating Redox Cycles on Colloid Composition and Stability 

Concurrent to rising temperatures and generally increasing drought, mountainous watersheds are experiencing more frequent extreme hydrological events. Episodic wet–dry cycling at solid–water interfaces promotes colloid (1 nm–1 µm) transport, which may facilitate the transport of carbon, micronutrients, and contaminants and further jeopardize water quality. In this project, researchers aim to improve the understanding of the impact of subsequent biogeochemistry driven by hydrological cycle disturbances on colloid chemistry and behavior and to inform predictive models of subsurface micronutrient cycling and transport. 

David Lipson

San Diego State University 

Impacts of Wildfire and Rainfall Variability on Soil Structure and Porosity 

Results from a wildfire/rainfall manipulation experiment in Southern California show that fire and extreme rainfall events alter soil structure and hydrology; wildfire led to reduced carbon storage in larger aggregates and particulate organic matter, while fire and rain intensity interacted to cause complex changes in evapotranspiration and infiltration. To extend these results to a mechanistic and predictive understanding of how wildfire and climate change alter soil structure and hydrology, researchers will test how wildfire and altered rainfall regimes affect the geometry of aggregates and pores in soil from a recently burned semiarid shrubland ecosystem in Southern California. 

Sergey Nizkorodov

University of California, Irvine 

Composition and Transformations of Atmospheric Organic Aerosols from Wildland–Urban Fires 

Researchers will explore the composition and physical properties of organic aerosols (OAs) generated at the wildland–urban interface using fire simulations. With the increasing frequency of wildfires in urban areas due to the warmer climate, significant emissions of poorly characterized OAs result from the combustion of mixed biomass and diverse urban materials. Through molecular characterization, this study will provide insights into source apportionment, formation, aging mechanisms, and the composition of light-absorbing components such as brown carbon within OAs. This research fills a crucial gap, shedding light on these essential OA types and their implications for the atmospheric environment. 

Allan Bertram

The University of British Columbia 

Effect of Atmospheric Aging by Hydroxyl Radicals and Ozone on the Viscosity, Phase Behavior, and Volatility of Biomass Burning Organic Aerosols in the Troposphere 

This project will use EMSL’s desorption electrospray ionization high resolution mass spectrometry and laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry techniques to measure how the chemical composition of forest fire smoke changes with age, and then relate these chemical changes to the changes in the smoke’s physical properties. The team expects to find that the viscosity of smoke particles increases with age and is caused by the molecules becoming larger and more oxidized. 

Andrew Grieshop

North Carolina State University 

Exploring Links Between Biomass-Burning Combustion Conditions and Particle Physicochemical Properties 

Aerosol emissions from biomass burning, including wildfires, play a key role in climate. Fire plume observations find widely ranging particle properties. Variations in combustion conditions, such as temperature, heat flux, and oxygen availability, are critical in dictating primary emission characteristics such as aerosol composition, viscosity, volatility, and optical properties, but are difficult to systematically control. In this project, researchers will use data from combustion systems that enable precise and replicable control of combustion to explore links between combustion conditions and the phases and characteristics of aerosol emissions. This work will address the physical, chemical, and optical properties of biomass-burning aerosols by linking these properties from parametrically varied lab samples to those observed in fire plumes and in transported air masses. 

Cassandra Gaston

University of Miami 

Linking Seasonal and Altitudinal Gradients in African Dust Mixing State with Its Impacts on Clouds and Iron Biogeochemical Cycles 

African dust is transported to the western North Atlantic Basin, impacting aerosol–cloud interactions in addition to depositing critical nutrients to the ocean and Amazon Rainforest. Without knowledge of the dust mixing state, global climate models cannot accurately predict the radiative properties of dust transport or its impact on iron biogeochemical cycles. To address this gap in information, researchers will perform microscopy to analyze atmospheric particles to determine the dust aerosol mixing state. This project will help address the impact of dust on biogeochemical cycles that impact ecosystem health and Earth’s climate. 

Kerri Pratt

University of Michigan 

Characterization of Individual Atmospheric Particle Chemical Composition, Morphology, and Cloud Nucleation Properties in the Remote High Latitudes 

This project will address critical gaps in the understanding of the chemical composition, mixing state, sources, and ice nucleation properties of high-latitude aerosols. Chemical composition, imaging, and ice nucleation particle analyses will be conducted on samples collected in the Arctic and Southern Ocean region. Research is expected to yield significant insights into the understanding of aerosol composition and sources, aerosol aging processes, and cloud ice nucleation properties in high-latitude environments, including the roles of local and transported terrestrial mineral dust in these remote regions.