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Environmental Transformations and Interactions
Functional and Systems Biology

Thirteen Scientists Awarded FICUS Program Funding

Environmental and biological research to be conducted at DOE user facilities.

Genoa Blankenship |
FICUS: Facilities Integrating Collaborations for User Science, EMSL, ARM, U.S. Department of Energy

The Facilities Integrating Collaborations for User Science (FICUS) Program provides access to Department of Energy user facilities, including EMSL, JGI, and ARM. (Graphic by Stephanie King | Pacific Northwest National Laboratory)

Scientists representing 13 projects have been awarded funding through the Facilities Integrating Collaborations for User Science (FICUS) program to conduct biological and environmental research at Department of Energy (DOE) user facilities.

The 9-year-old FICUS program, supported by the DOE Office of Science’s Biological and Environmental Research program, enables researchers to use scientific instrumentation and to work with experts at no cost following selection through a competitive proposal process.

The Fiscal Year 2024 awarded projects range from understanding glacial carbon cycling in the wake of changing climate to research that will aid in the development of improved fungal cell factory biotechnological applications.

Research teams from 11 projects will use resources at the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI). Several of the projects also were awarded access to the Bio-SANS beamline through the Center for Structural Molecular Biology (CSMB) at Oak Ridge National Laboratory and the Advanced Photon Source (APS) at Argonne National Laboratory.

The focus topic areas for projects conducted with these facilities include:

  • Biofuels, biomaterials, and bioproducts
  • Hydro-biogeochemistry
  • Inter-organismal interactions
  • Novel applications of molecular techniques

Two projects will use capabilities at EMSL and the Atmospheric Radiation Measurement (ARM) user facility to study land–atmosphere processes and aerosol–cloud interactions.

Projects in collaboration with EMSL and JGI

Multiscale multimodal analysis of brown rot fungal decay mechanisms for improved biomimetic lignocellulosic biorefinery processes

Joseph E. Jakes Joseph Jakes

United States Forest Service

Researchers will use resources at EMSL, JGI, and APS to produce accumulative transcriptomic, chemical, composition, structural, and mechanical data that will be used to identify different decay stages in wood with their associated decay mechanisms and cell wall modifications.

Systems analysis of embolism resiliency in grasses for biofuel production under marginal environments

Andrei Smertenko Andrei Smertenko

Washington State University

Water flows from roots to shoots through vessels composed of hollow dead cells. Specialized regions in the cell wall, known as pits, conduct water between vessels. Drought causes embolism of vessels leading to blockage of water movement. Pits contribute to the embolism spread between the vessels. This project aims at developing technology for containing embolism by optimizing pit morphology.

Functional and structural analysis of microbial expansin-related proteins that loosen lignocellulosic and chitin fiber networks 

Emma MasterEmma Master

University of Toronto

This project brings together functional genomics, structural biology, and advanced techniques in material science to evaluate the untapped potential of microbial expansin-related proteins in the production of bio-based chemicals and materials.

Expanding synthetic biology tools by deeper understanding of Aspergillus niger primary metabolism

Ronald de Vries Ronald de Vries

Westerdijk Fungal Biodiversity Institute

A deep understanding of metabolism is crucial for efficient and effective metabolic engineering strategies to develop novel or improved fungal cell factories for a range of biotechnological applications. In this project, researchers will use EMSL and JGI capabilities to discover and characterize novel enzymes and to obtain a new level of understanding of primary carbon metabolism in fungi.

(Eco)Physiology of methanogens of the phylum Thermoproteota

Roland Hatzenpichler Roland Hatzenpichler

Montana State University

In this project, scientists will study the physiology of newly discovered methanogens both in culture and in their native habitat. The team will address how these cells vary their gene expression and metabolomes under changing physiochemical and thermodynamic conditions.

Integrating microbial meta-omics, isotopes and methane metabolites to connect belowground microbial processes to aboveground methane emissions in seasonally inundated Amazonian floodplain forests

Scott Saleska Scott Saleska

University of Arizona

This project builds on the first continuous whole-ecosystem measurements of methane emissions, via eddy covariance methods, from a seasonal inundated floodplain forest in the Amazon. Researchers will use metagenome and metatranscriptome sequencing and metabolomics to mechanistically identify the distribution of methane production and consumption activity in soils and tree stems, and how these components shift between wet and dry season in seasonally inundated forests, and between a floodplain forest and an upland terra firme forest.

Linking multi-organism-environment interactions across lab and field scales to estimate viral contributions to soil carbon cycling

Amy Zimmerman Amy Zimmerman

Pacific Northwest National Laboratory       

Researchers will conduct complementary field and laboratory-based experiments to generate the data necessary for baseline estimates of when and how much viruses contribute to soil carbon cycling. The team will generate some of the first quantitative data about rates of viral production in soil, shifts in soil carbon pools as a result of viral predation, and the degree to which natural soil viral communities vary over time.

The role of microbial predation and cooperation on soil carbon pathways measured through multi-omics

Bram Stone Bram Stone

Pacific Northwest National Laboratory 

Researchers will conduct labeled isotope tracer incubations to follow the movement of plant and microbial carbon under different moisture and predator manipulations. Data from this experiment will be used to combine soil carbon processing more rigorously with organismal interactions. These data will thus address the critical knowledge gap of how and when microbial interactions accelerate soil carbon cycling.

Structural and biochemical characterization of glycosyltransferase 47 family proteins from Spirodela to enable predictive biology

Samantha Ziegler Samantha Ziegler

National Renewable Energy Laboratory

In this project, researchers are comprehensively studying cell wall synthesis enzymes found in the duckweed Spirodela polyrhiza to create a database that can be used to predict the functionality of similar proteins in other organisms. The data generated from this proposal will be used to create designer plants, with specified cell wall structures for bioproduction.

A high-resolution view of the plant–microbe–mineral interactions affecting C-cycling in thawed permafrost soils

Jessica Ernakovich Jessica Ernakovich

University of New Hampshire

Researchers aim to determine how plants, microbial activity, and organo-mineral associations influence permafrost soil carbon balance. Findings will be integrated into a modeling framework to resolve the interactions among plants, microbes, and minerals, which are critical to advancing fundamental understanding of biogeochemical processes in a warming and thawing Arctic.

Opening the black box of glacial carbon cycling—providing fundamental insight into impacts of a changing climate

Heidi Smith Heid Smith

Montana State University

Roughly 104 petagrams of organic carbon are stored within ice worldwide. Glacial carbon originates from new atmospherically deposited material (including black carbon from wildfires) and in situ production by microorganisms. The metabolic strategies of carbon transformation within glacial systems are not well understood, yet critically affect adjacent and downstream aquatic ecosystems. This research will link microbial processing of discrete sources of organic carbon and its concomitant compositional shifts. 

Projects in collaboration with EMSL and ARM

Characterization of organosulfates and organonitrates in vertically resolved aerosols over the Southern Great Plains

Haofei Zhang Haofei Zhang

University of California, Riverside (UCR)

Researchers will conduct a field campaign at the Southern Great Plains Atmospheric Radiation Measurement site and use the tethered balloon systems to collect vertically resolved aerosol samples. The samples will be analyzed using EMSL’s nanospray desorption electrospray ionization  coupled to a high-resolution mass spectrometer and UCR’s ion mobility spectrometry mass spectrometer. The results could provide key insights into aerosol–cloud interactions and help understand their effects on aerosols and on climate.

Vertical distribution of aerosol properties during TRACER

Rajan Chakrabarty Rajan Chakrabarty

Washington University in St. Louis

This project will provide the vertical distribution of physico-chemical properties of individual atmospheric particles collected by ARM’s tethered balloon system as part of the TRACER campaign. The results of this research will provide critical feedback for further development and evaluation of the particle-resolved atmospheric models.