Ten Months, Twenty Projects, and Countless Scientific Advancements

The Environmental Molecular Sciences Laboratory (EMSL) selected 20 recipients of funding from its annual Exploratory Call. Over the next 10 months, researchers and teams from across the country will evaluate resources for carbon storage, model water systems, examine biological systems as bioenergy sources, and more.

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

EMSL offers 150 instruments at no cost to proposal awardees. These instruments include the in-house-developed nanoPOTS technology as well as transmission and scanning electron microscopes, X-ray photoelectron spectroscopy, Fourier-transform ion cyclotron resonance mass spectrometry, X-ray diffraction, Mössbauer spectroscopy, nanoSIMS, atom probe tomography, X-ray computed tomography, confocal Raman microspectroscopy, nuclear magnetic resonance spectroscopy, and matrix-assisted laser desorption ionization as a mass spectrometry, known as MALDI, to name a few.

The awarded projects include the following:

Maruti K. Mudunuru 

Pacific Northwest National Laboratory

ModEx benchmark: artificial intelligence for benchmarking model-experiment integration workflows

This research uses field datasets to accurately estimate the 3D permeability field for modeling river water intrusion and tracer transport into the subsurface. Accurate estimation of the permeability field is essential for a predictive understanding of the infiltration process and for developing realistic subsurface process models for natural and engineered systems.

Kate Hanna Kucharzyk 

Battelle Columbus

SynThetic biolOgy driven approach to Repurpose polyaMides (STORM)

Nylon-6 (PA6) is a polyamide polymer abundant in clothing, ropes, fabrics, and automobile parts, and the United States annually consumes ~0.5 million metric tons. To divert these materials from landfills and incinerators, researchers will use synthetic biology approaches to efficiently degrade and upcycle PA6 into high-value monomers.

Qiang Guan 

Kent State University

AlphaEnzyme: predicting enzyme functions directly from AlphaFold encoding

Predicting the function of enzymes helps us understand the metabolic potentials of microbes and microbiomes. With the help of large training sets of protein structures and EMSL’s supercomputer, the team proposes building a machine learning pipeline that is capable of quickly generating intermediate representation of proteins to enable prediction of enzyme functions.

Karen Sanguinet 

Washington State University

Understanding cell wall remodeling processes of grass root system formation and function for sustainable biofuel production

This research aims to unearth molecular cues that underlie cell wall remodeling during root hair emergence and lateral root initiation. Further understanding of these root traits is key to improving bioenergy crop sustainability and increasing feedstock production in marginal environments.

Erin Clarissa Rooney 

University of Tennessee

Employing synthetic soil environments to test the impact of freeze-thaw and pore geometry on iron, phosphorus, and carbon interactions in permafrost-affected soil

Arctic warming is accelerating permafrost thaw, exposing previously frozen soil to repeated freeze-thaw cycles. The project will assess the role of pore geometry on geochemical transformations and redox gradients. Results will help determine how the pore-scale effects of freeze-thaw may alter redox chemistry, nutrient availability, and carbon loss in a warming Arctic.

Daniel David Gregory 

University of Toronto

Detailed analysis of sulfur isotopic signatures via atom probe tomography

Under low oxygen conditions, some organisms use sulfate for respiration instead of oxygen. When this occurs, sulfide is expelled, reacting with iron to form pyrite. This project aims to further understand the sulfur cycle by obtaining nanoscale S-isotope analyses of pyrite. 

Lisamarie Windham-Myers 

U.S. Geological Survey

Pore-scale evidence of tidal wetland soil carbon stabilization

At a mechanistic level, the scientific community needs to better understand the capacity of vegetated coastal ecosystems to preserve organic carbon. This study will couple physical, ecological, and chemical observations spatially—within neighboring but geomorphically distinct tidal marsh soils—to prioritize sampling for future landscape model development.

Idowu Ademola Atoloye 

North Carolina A&T State University

Composition and adsorption mechanism of metabolites produced by roots of different hemp varieties grown in a synthetic soil habitat

Understanding the interactions between plant organic molecules and soil minerals is critical in biogeochemical processes. This project will use rhizosphere-on-a-chip to clarify the intricate and mechanistic processes of the adsorptive interaction of root exudates and soil minerals.

Sabeeha Sabanali Merchant 

University of California, Berkeley

Stoichiometry changes to photosynthetic structures in algae in response to environmental stimuli and genetic engineering

As light and carbon dioxide availability changes, plants and algae employ short-term acclimation strategies to maximize photosynthetic yield and minimize potential cell damage. This project intends to define the compositional dynamics in the photosynthetic apparatus so that we can better understand similar adjustments in genetically engineered algae for eventual use in bioproduct production.

Amy Marshall-Colon 

University of Illinois at Urbana-Champaign

Developing a protocol for spatial metabolomics to investigate cell types in the Sorghum bicolor stem

Engineering sorghum bicolor stems to accumulate bioproducts could decrease the burden on conversion groups in the biofuel industry. This project seeks to expand our understanding of stem cell types and the metabolic dynamics between them, thus creating a molecular atlas of sorghum stem development and increasing our understanding of grass stem biology.

Amy Schmid 

Duke University

Modeling microbial community metabolic interactions in hypersaline ecosystems

Hypersaline microbial communities have the potential to teach us about general principles of community resilience to environmental perturbation. However, the mechanisms of metabolic interactions within these microbial communities remain largely uncharacterized. The proposed research will use metabolomics methods to investigate how hypersaline microbial communities interact to maintain stability despite changes in salinity and nutrient availability. 

Pavlo Bohutskyi 

Pacific Northwest National Laboratory

Revealing the secretome and enriching the function of newly established hyperthermophilic microbial communities with superior cellulolytic and hemicellulolytic activities

The project continues research into developing a novel biological process based on the superior hydrolytic and metabolic capabilities of the hyperthermophilic microbial communities proliferating at temperatures of 70 degrees Celsius and above. This innovative process aims to significantly improve carbon conversion efficiency and to reduce the overall processing time, thereby minimizing capital and operating costs.

Anne Melissa Gothmann 

St. Olaf College

An improved understanding of coral skeletons as environmental proxies and biomaterials by mapping organics and water at the nanoscale

This project will develop a baseline nanoscale understanding of organic matter and water in an existing sample set of natural and cultured coral skeletons. The fundamental results would be a stepping stone for understanding how nanoscale patterns in organics and water in coral skeletons vary in direct response to changing environmental conditions.

Jean Carlos Rodriguez Ramos 

United States Department of Agriculture - Agricultural Research Service Water Management Research

Root modulation of soil pore architecture as a potential driver of divergent C accrual between two cover crop types

Agricultural cover crops can affect the longer-term stabilization of soil organic carbon, but details of how they do it remain understudied. This project will build on a current soil biological health assessment using data on how cover crop species differentially modulate soil properties important for soil carbon accrual and sequestration.

Charles James Werth 

University of Texas at Austin

Spatial architecture of extracellular electron shuttle production for iron cycling in a model soil habitat

This project will create a specialized microfluidic soil habitat to test the hypothesis that bacteria will spatially segregate in a model soil system according to the location and reduction potential of different solid-phase ferric iron minerals present and the quantity and type of extracellular electron shuttles they produce.

Marcus Bernard Foston 

Washington University in St. Louis

Characterization of novel synthetic biological materials

Synthetic biology and genome engineering allow us to harness the machinery of nature to produce synthetic biological materials. In this project, researchers seek to redesign recombinant chimeric proteins based on proteins found in mussel feet so that they produce hydrogels with enhanced properties for applications that require underwater adhesives. 

Michael Enoch Green 

City College of New York

Proton paths in biological systems: composition, stability, and requirements for transmitting protons

This project will use structures from known proton transmitters to calculate the energy for proton paths. The aim is to find paths that allow protons to proceed without major energy barriers and determine whether there are general properties found in configurations of these successful paths.

Matthew Owen Schrenk 

Michigan State University

Microbial distributions related to carbon retention, heavy metals, and pore structure in serpentine soils

Terranes of rock formations known as serpentinites are an understudied site of key biogeochemical transformations that are also being considered as sites for carbon capture and storage. This research seeks to create large-scale biogeochemical models that can predict microbial activities in serpentine soils and their response to environmental change.

Benjamin Gilbert 

Lawrence Berkeley National Laboratory

Rhizosphere promoted rock weathering and nutrient cycling in deep shale fractures

This project seeks to determine the geologic, biological, and biochemical structure of the rhizosphere that develops in deep shale fractures and correlate that information with geochemical signatures of shale weathering. The work could enable unprecedented insight into the earliest stages of plant-influenced bedrock weathering and soil formation.

Bjoern Robert Hamberger 

Michigan State University

Identification of root-specific terpenoids, mediators in plant-microbe interactions in the rhizosphere

This project aims to establish biological relevance and tools for predicting and shaping the microbiome to increase plant resilience. Researchers will accomplish this by increasing their fundamental understanding of the sorghum root microbiome and its expression of terpene metabolism.