Thirteen Projects Funded through FICUS Program

Researchers representing 13 projects were recently awarded funding through the Facilities Integrating Collaborations for User Science (FICUS) program.

FICUS provides researchers with access to resources at multiple DOE user facilities through a single proposal. Awarded principal investigators and their research teams will receive access to instrumentation, resources, and expertise at the Environmental Molecular Sciences Laboratory (EMSL), Joint Genome Institute, and the Atmospheric Radiation Measurement user facility, which are Department of Energy (DOE), Office of Science Biological and Environmental Research program user facilities.

Additionally, the awarded projects have access to the Bio-SANS beamline through the Center for Structural Molecular Biology at Oak Ridge National Laboratory and the eBERlight program offered by the Advanced Photon Source at Argonne National Laboratory.

Among the research focuses are projects centered around aerosol sources, soil microbes in Arctic greenhouse gas cycling, carbon allocation in the peatland methane cycle, and carbon use efficiency to predict soil organic carbon accumulation.

Meet this year’s awarded principal investigators.

Chongai Kuang

Brookhaven National Laboratory

Quantifying the Integrated Terrestrial Controls on Aerosol Sources, Transformations, and Climate Impacts in the Southeastern United States

A team of researchers, led by Brookhaven National Laboratory’s Chongai Kuang, is studying how land influences particle sources and movement in the atmospheric boundary layer above forests. Using ARM’s mobile facility at Bankhead National Forest in northwestern Alabama, the team will examine how biological aerosol particles and biogenic volatile organic compounds are vertically distributed in the atmosphere and how those distributions change with the seasons. These experiments will shed light on how forests affect the dynamics of atmospheric particles. Measurements taken will be combined with surface and tower observations in a detailed model to understand how land–atmosphere interactions control airborne particles. EMSL’s aerosol capabilities, including nanospray desorption electrospray ionization, focused ion beam-scanning electron microscopy, and size- and time-resolved aerosol collection, will be used to help analyze the collected particle samples.

Jason Surratt

University of North Carolina at Chapel Hill

Chemical Characterization of Secondary Organic Aerosol from Isoprene-Derived Epoxydiols with Altitude at the DOE ARM Bankhead National Forest (BNF) Site During Spring and Summer 2025

University of North Carolina at Chapel Hill’s Jason Surratt is leading a project looking at how varied altitude affects the composition of secondary organic aerosol (SOA), particularly from the acid-driven multiphase chemistry of isoprene-derived epoxydiols (IEPOX). Aerosol samples will be collected at different altitudes in spring and summer 2025 using EMSL’s STAC onboard ARM’s Tethered-Balloon System at BNF. EMSL’s TRAVIS platform will be deployed to analyze volatile organic compounds (VOCs), and EMSL microscopy and mass spectrometry will be used to characterize aerosol composition and physiochemical properties. This research is designed to improve mechanistic representations of IEPOX-derived SOA within Earth system models.

Daniel Knopf

State University of New York at Stony Brook

Acquiring Vertical Profiles of Aerosol and Ice-Nucleating Particles for Aerosol–Ice Formation Closure

Atmospheric ice formation is considered a significant challenge in atmospheric sciences because of the lack of understanding of how aerosol particles acting as ice-nucleating particles (INPs) cause ice crystal formation. A multi-institutional team is conducting experiments using particle samples collected at ARM’s SGP and BNF sites at varying altitudes to assess the predictive understanding of ice formation to benefit cloud and climate models. Researchers will use EMSL’s microspectroscopic analytical techniques to characterize the physicochemical properties of individual INPs and to determine the corresponding freezing rates.

Steven Hallam

The University of British Columbia

Targeted Multi-omics of Metabolically Active Microbial Populations in Anaerobic Digesters Bioaugmented with Carbon-Based Conductive Materials

Metabolic interactions play a key role in producing renewable natural gas (RNG) composed primarily of methane from biomass in anaerobic digestion (AD) environments. The electron flow between putative syntrophic acetate-oxidizing bacteria (SAOB) and methanogenic archaea can support methane production from hydrogen and carbon dioxide in AD environments, but identifying specific populations of SAOB from primary sequence information has proven somewhat elusive. Conductive carbon materials have been shown to enhance methane production in AD environments and may promote interactions between SAOB and hydrogentrophic methanogens for more energy efficient conversion of biomass into RNG. In this project, we will build on previous EMSL research combining activity-dependent cell sorting and stable isotope probing with multi-omics (DNA, RNA, and protein) to identify interactions between active SAOB and methanogenic archaea driving more efficient RNG production. The results from this work will identify novel lineages of SAOB relevant to municipal-scale biomass conversion and provide quantitative information useful in the development of more refined process models.

Lukas Kohl

University of Eastern Finland

Growth Efficiency and Carbon Allocation in the Peatland Methane Cycle

Microbial methane oxidation is an important process that reduces the amount of methane emitted by peatlands and wetlands. In this project, researchers will conduct a pioneering experiment that addresses two key questions regarding this process. First, they will study how many methane-oxidizing microorganisms grow per amount of methane oxidized, which determines how efficiently microorganisms can reduce methane emissions. They also will study how much methane is converted into organic matter, including both long-lived and easily decomposable and leachable forms.

Using JGI’s quantitative stable isotope probing method, the team will address how much growth can be observed in methane-oxidizing microorganisms. The team will use EMSL’s analytical platforms to determine the rates of methane oxidation and its transformation into various forms of organic matter. Together, these results will allow researchers to make better predictions of how methane emissions from natural ecosystems will respond to changes in climate, land use, and other anthropogenic impacts in the future.

Steven Van Doren

University of Missouri-Columbia

Structural Mechanisms of Enzyme Regulation to Open the Tap of Plant Oil Synthesis

In this FICUS project, a team of researchers will characterize key energy-capturing protein complexes from plants. The catalytic protein assemblies from the enzyme ACCase act as gatekeepers that control the production of new fatty acids in chloroplasts, seeds, and leaves. The goal is to boost oil production using pennycress, a promising biofuel crop that can grow during the winter. In the chloroplasts of most plants, this target enzyme combines multiple catalytic and regulatory protein components, but it’s unknown how these components of ACCase fit together. Through the project, researchers will focus on components of the biotin carboxylase (BC) half of ACCase and seek a structural understanding of different combinations of the protein parts of BC. They will also test combinations of the proteins in pennycress. The team believes structural insights will provide ideas of how the reaction of BC gets sped up or slowed down. This information should suggest where to make precision alterations of BC components that could speed up BC and oil synthesis in crops such as pennycress.

Devin Rippner

United States Department of Agriculture - Agricultural Research Service

Long-Term Crop Rotations Alter Soil Function and Prairie Carbon Dynamics to Depth in Midwestern Cropping Systems

Over the past 150 years, the tallgrass prairie biome of central North America has been rapidly replaced by annual cropping systems, transforming the region into one of the world’s most productive grain areas. The productivity of this region is in large part attributed to the nutrient-rich soil organic matter (SOM) that accumulated from millenia of prairie growth. However, much of this native SOM has been lost over the last 150 years, raising concerns about the sustainability of current agricultural practices. This study aims to address how the conversion of the tallgrass prairie biome to corn-based cropping systems in the U.S. Midwest has affected soil hydrobiogeochemical functioning and SOM content, form, source, and age. Research will link long-term agricultural management practices spanning 149 years at the proposed 2025 sampling and hydrobiogeochemical functions above and below the typical plow layer at macro- and microscales. The results of this work will inform our understanding of how the legacy of the tallgrass prairie biome of central North America and the current U.S. Corn Belt influences soil hydrobiogeochemical function and soil carbon stability today.

Jenni Hultman

Natural Resources Institute Finland

Illuminating the Role and Function of Soil Microbes in Arctic Greenhouse Gas Cycling through Systems Biology Multi-omics Approaches

Global warming is more pronounced in the Arctic regions than the rest of the globe, with recent estimates predicting the Arctic warming four times faster compared to the global average. Arctic soils contain more than half of the global soil organic carbon stock, and the role of tundra soils in greenhouse gas (GHG) emissions—particularly, methane, carbon dioxide, and nitrous oxide—is predicted to increase in the future. However, it is still unclear how rapid environmental changes will influence these ecosystems. Additionally, high altitudes have the potential for further substantial positive feedbacks to climate warming. Microbes are in charge of almost all the global biogeochemical processes contributing to life on Earth, including those involved in the production of GHGs, yet many of these processes are not well understood. In this project, researchers will integrate detailed information on the local landscape, ecology, microclimate, and microbial activities to reveal the role of these systems in controlling GHG fluxes.

Luke Thompson

Cornell University

Single-Cell Analysis of Symbiont Physiology and Development Using Fluorescent Protein-Tagged Cell Identity Lines to Optimize Therapeutic Molecule Delivery to Economically Important Tree Crops

This project seeks to optimize the delivery of biologically derived therapeutics, such as antibacterial proteins, to tree crops important to the DOE using a developing biotechnology called The Symbiont. The Symbiont utilizes the growth-stimulating and DNA-altering abilities of the bacteria Agrobacterium tumefaciens to develop biofactory-like organs physically attached to host plants without the time-consuming process of developing, regulating, and growing full transgenics (GMOs).

Margaret Frank

Cornell University

Multi-omics Discovery of Long-Distance Mobile Signals Involved in Vascular Plant Carbon Partitioning

Intercellular communication in vascular plants is fundamental to understanding biomass allocation, particularly in the context of carbon accumulation and partitioning between root and shoot systems. Despite significant advancements, a comprehensive view of the molecular signals governing this process is still lacking. This project addresses this gap by employing a multidisciplinary, multi-omics approach integrating genomics, proteomics, and advanced imaging techniques. Research will involve identifying and functionally characterizing mobile signals, including RNAs, proteins, and hormones. By capitalizing on recent advancements at EMSL and JGI in super-resolution RNA and hormone imaging, untargeted RNA and protein profiling, and targeted RNA and protein profiling, researchers aim to identify the long-distance movement of RNAs and proteins and unravel their potential signaling functions in coordinating root/shoot biomass allocation through altered plant architecture. By elucidating the genetic basis of long-distance signaling pathways related to biomass accumulation, researchers plan to forge a path for the development of clean, renewable biofuels and bioproducts.

Kaitlin Rempfert

Pacific Northwest National Laboratory

Unpacking the Metabolic Basis of Carbon Use Efficiency to Understand and Predict Soil Organic Carbon Accumulation

Microbial carbon use efficiency (CUE) measures how effectively microbial communities convert carbon substrates into biomass. As microbial growth influences soil organic carbon (SOC), CUE is critical for understanding soil–climate interactions. Yet, the mechanisms behind CUE are unclear, which limit the accuracy of carbon cycle models. Through this project, researchers seek to uncover the metabolic basis of CUE by combining isotope-based growth measurements with multi-omics profiling across different soil conditions, including depth, season, and moisture. By connecting CUE with microbial traits and environmental data, this research aims to improve predictions of SOC responses to environmental changes, specifically as they relate to climate change.

Cristina Howard-Varona

The Ohio State University

Environmental Virus–Microbe Interactions: Regulation, Functions, and Ecosystem Outputs of Diverse Virocells

This project aims to better understand the properties of environmental virus–host interactions that are not yet well understood, including transcriptional regulation, high-resolution virus–host recognition, and intra- and extracellular mechanisms of viral resistance in environmental bacteria. Using high-throughput sequencing techniques, high-resolution electron microscopy, and multi-omics of different flavors of viral infections, this project will elucidate virus and bacterium transcription factors and their binding sites, bacterial receptors for viruses and how those change structurally during complete or partial resistance, and the intra- and extracellular mechanisms by which environmental bacteria fight viruses with varying degrees of success. Overall, the goal is to improve the mechanistic understanding of environmental virus–bacterium interactions.

Erin Nuccio

Lawrence Livermore National Laboratory

Context-Dependent Mycorrhizal Resource Exchange and N Sustainability for Bioenergy Grasses

Mutualistic relationships between arbuscular mycorrhizal fungi (AMF) and plants improve carbon allocation, stress resilience, and plant productivity. In this project, researchers will explore how different AMF guilds affect nitrogen cycling and resource exchange with the bioenergy crop switchgrass (Panicum virgatum) using advanced isotopic and metagenomic techniques. The goal of this research is to understand the metabolic interactions between soil microbes and AMF to improve bioenergy production and carbon sequestration efforts.