EMSL Selects 15 Projects for Exploratory Research in 2025

Fifteen researchers from across the world were selected by the Environmental Molecular Sciences Laboratory (EMSL) to conduct nine-month Exploratory Research projects in 2025.

The call sought proposals that address at least one of EMSL’s three scientific focus areas: Environmental Transformations and Interactions, Functional and Systems Biology, and Computing Analytics and Modeling. EMSL used an anonymized peer review process for this call.

EMSL, a Department of Energy Office of Science user facility, offers more than 150 instruments, resources, and expertise at no cost to proposal awardees. EMSL is sponsored by the Office of Science’s Biological and Environmental Research program.

Leveraging EMSL’s capabilities, including mass spectrometry, artificial intelligence, and microfluidic technologies, the principal investigators and their teams will take on some of the greatest challenges facing biological and environmental science.

The awarded projects include the following:

Avni Malhotra 

Pacific Northwest National Laboratory

AI-Based Harmonization of Soil Data

One major obstacle to predictive soil modeling is the lack of standardized global soil data. Soil data are collected globally using different methods and reported with disparate variable names and units. Soil data harmonization requires human annotation that is extremely labor intensive and prone to errors. This project aims to develop a generative artificial-intelligence-based workflow for harmonizing disparate soil datasets into a standardized database.

Navid H. Jafari

Texas A&M University 

Fusion of X-ray Computed Tomography and Optical Coherence Tomography Techniques for Root Analysis Across Coastal Environmental Sites

A team of researchers aims to develop and validate an artificial intelligence/machine learning model to fuse data types for plant roots and surrounding sediments in a coastal wetland environment. They plan to perform micro X-ray computed tomography and optical coherence tomography scans on live to dead roots before using the model to fuse data types for segmenting live, dead, and decaying roots; root architecture; pore structure; and sediment density.

Anirban Pal

West Texas A&M University

Probing Ice Nucleation Ability of Soot Particles from Biomass Burning via Computational and Experimental Methods

A team of researchers will explore the use of atomistic simulations to study multiple heterogeneous ice nucleation processes. They aim to examine whether the ice-nucleating ability of soot increases with packing due to the presence of smaller pores where pore condensation freezing can occur. They also aim to examine whether the ice-nucleating ability of a single soot monomer decreases with decreasing size due to the increased curvature and not due to the decreased surface area.

Maggie R. Wagner

Kansas Biological Survey & Center for Ecological Research

Spatially Resolved Profiling of Root-Exuded Metabolites and Bacterial Colonization in Contrasting Maize Genotypes

Existing root exudate research typically ignores the variation within root systems, by either focusing on a tiny subset of the system or lumping it into one monolithic sample. To address this knowledge gap, a team of researchers will spatiotemporally characterize root exudate composition and variation among maize genotypes, and link spatially resolved exudate profiles to microbiome variation. They plan to use the TerraForms SubTap system for plant growth to complete these aims.

Matthew Posewitz 

Colorado School of Mines

Carbon-Dioxide Sensing, Ultrafast Photoautotrophic Growth, and the Physiological Roles of Protein Carbamylation in the High-Productivity Marine Alga Picochlorum celeri

Researchers are studying an industrially important alga called Picochlorum celeri, which has among the most rapid photosynthetic growth rates reported in seawater when supplemented with CO₂. However, P. celeri does not have a highly efficient carbon-concentrating mechanism and grows very slowly at air levels of CO₂. To better understand how this alga senses and responds to CO₂ levels, a research team will investigate whether a process called lysine carbamylation influences enzyme activities beyond Rubisco, which aids in photosynthesis and CO₂ use.

Itamar Shabtai 

Connecticut Agricultural Experiment Station

Quantifying Calcium-Induced Surface Attachment and Deposition of Microbial (Necro)mass on Mineral Surfaces in the Rhizosphere

This project aims to increase the understanding of the chemical and biological mechanisms involved in calcium-driven surface colonization of microbes in soils. A team of researchers will grow maize in soil microcosms to study the microbe–mineral interface that develops during the exudate-enhanced dissolution of calcium orthosilicate (wollastonite) or basalt rock powder.

Pamela Peralta-Yahya

Georgia Institute of Technology 

Toward a Kinetic Model of a Synthetic Formate Fixation Pathway

The goal of this project is to acquire timed, targeted metabolomics data from an engineered 10-enzyme synthetic pathway that fixes formate, a more biologically accessible form of CO₂, into the industrially relevant amino acid serine. The kinetic parameters established from this study should be applicable to the long-term future development of in vivo whole-cell models.

Linnea Honeker 

Lawrence Livermore National Laboratory

Using Meta-omics and Machine Learning to Predict Soil Organic Carbon Transformations Following Seasonal Moisture Changes in a Mediterranean Grassland

In this project, researchers will explore new integration and data management methods to advance the understanding of connections within complex multivariate omics datasets. With chemical and compound data provided by EMSL on the state and structure of carbon in our soils, the team will link microbial composition and function to soil carbon dynamics and advance our ability to predict soil responses.

Gerard Hopfgartner 

University of Geneva

Advancing Structural Elucidation of Lipids in Environmental Samples

A team of researchers aim to develop and demonstrate automated software approaches for novel mass spectrometry (MS) fragmentation techniques. These techniques have been shown to generate fragment-richer MS/MS spectra compared to those of classical methods. The software will enable automated improved lipid annotation for large sets of samples.

Jennifer Bhatnagar 

Boston University

FIRE-OAK: Fire and Urbanization Impacts on Rhizospheres and Root Exudates in California Oak Woodlands

This study aims to explore how post-fire-resprouting oaks exchange carbon and nitrogen with fire-adapted rhizosphere mutualists, such as ectomycorrhizal fungi, and how this process is affected by urbanization and forest fragmentation. The study will test the hypothesis that rhizosphere mutualists decline, root exudation increases, and plant pathogens flourish at forest edges, ultimately slowing post-fire forest recovery in urbanizing agro-forest landscapes.

Pavlo Bohutskyi 

Pacific Northwest National Laboratory

Unraveling Host–Phage Interaction Heterogeneity at Single-Cell Resolution Using a Small-Genome Model Organism

This innovative research aims to develop a “Google Earth”-like platform for tracking and visualizing how pathogens and hosts evolve together from the macro- to nanoscale at a glance, advancing our understanding of how to predict and prepare for biological threats to public health. Using a tractable model system, researchers will leverage EMSL’s cutting-edge single-cell RNA sequencing technology alongside high-resolution bulk RNA sequencing to capture the diverse ways hosts respond to viral infections, ultimately improving the accuracy of predictive models.

Sophie Comer-Warner

University of Birmingham

Unraveling Drivers of Stream Microbial-Biogeochemical Cycling Along a Land-Use Gradient: From Localized Processes to Ecosystem-Wide Effects

There is a lack of research on how land-use gradients affect dissolved organic matter chemodiversity and create subsequent changes to the microbial community structure and riverine greenhouse gas fluxes. Additionally, the association between riparian zones and in-stream processes is not generally considered so that riparian and hyporheic sediments, which are both hotspots of river corridor biogeochemical turnover, are rarely studied together at the same site. In this project, researchers aim to disentangle these complex drivers of biogeochemical cycles by generating in-depth characterization of the dissolved organic matter and metabolite pools available for biogeochemical cycling.

Ilenne Del Valle Kessra 

Oak Ridge National Laboratory

Measuring ICE-Mediated Horizontal Gene Transfer in the Rhizosphere Using a Dual Reporter System

Engineered horizontal gene transfer (HGT) is a promising strategy for microbiome engineering to improve plant health and sustainability. However, there is a lack of information about how environmental factors affect the effectiveness of DNA transfer. A team of researchers will leverage TerraForms and analytical and imaging capabilities to study how soil physical properties influence the transfer of an integrative and conjugative element (ICE) between gram-positive bacteria. By mapping the exudate diffusion in a RhizoChip simulating a sandy soil, we can understand how soil texture alters the rate of ICE-mediated HGT.

Laura Bartley 

Washington State University

Testing Hypotheses in Bioenergy Plant Development with Activity-Based Probes

In this project, researchers will apply activity-based protein profiling (ABPP) to identify the kinases and lignin biosynthesis enzymes that are differentially labeled in bioenergy-crop-relevant grass samples. ABPPs are covalent inhibitors that label active enzymes in a sample for subsequent isolation or visualization. The team will use ABPPs to distinguish which regulators and other enzymes are functioning in plant organ development and cell wall synthesis.

Gregg Beckham

National Renewable Energy Laboratory

Aerobic Polyethylene Deconstruction to Oxygenated Compounds for Biological Upgrading

In this project, researchers are developing an integrated chemical and biological process for the aerobic deconstruction of polyethylene into oxygenated compounds suitable for microbial upgrading. Polyethylene is the most abundant thermoplastic polymer, yet current recycling technologies are inadequate for its efficient and selective upcycling. By optimizing reaction conditions, the research team aims to maximize yields of oxygenates such as dicarboxylic acids, which can serve as feedstocks for downstream bioconversion processes.