Projects | Environmental Molecular Sciences Laboratory

As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website.

Browse current and past research projects supported by the EMSL User Facility.

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Project pages provide details including:

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The EMSL project DOI
Link to project data available in EMSL’s Data Portal
Project type

Deciphering plant-plant, plant-microbe, and plant-soil interactions driving biological invasion in a southwestern desert grassland

Lead Institution

University of Arizona

Principal Investigator

Malak Tfaily

Project type

Large-Scale EMSL Research

Plant invasion is a major component of global change, leading to environmental transformations that alter ecosystem services and associated biogeochemical cycles. The overarching goal of this project…

Deciphering the structure and function of the last unknown major plant organelle - Plasmodesma

Lead Institution

Washington State University

Principal Investigator

Michael Knoblauch

Project type

Large-Scale EMSL Research

Plant tissues exhibit a symplasmic organization; the individual protoplasts are connected to their neighbors via cytoplasmic bridges that extend through pores in the cell walls. These bridges may…

Molecular controls of microbial nitrogen use efficiency in agricultural soils

Lead Institution

United States Department of Agriculture - Agricultural Research Service

Principal Investigator

Amisha Poret-Peterson

Project type

Large-Scale EMSL Research

Microbial nitrogen use efficiency (NUE) reflects the partitioning of organic N taken up between N incorporation into microbial biomass (growth) and N recycled to the environment as inorganic N …

Inferring Kinetic Models for Large-Scale Biochemical Networks

Lead Institution

University of Washington

Principal Investigator

Herbert Sauro

Project type

Large-Scale EMSL Research

Mechanistic models of cell networks that accurately predict changes in input-output dynamics and outcomes upon perturbation have the potential to facilitate a greater understanding of the…

Plant proteome structure-function and pKa prediction augmented with environmental considerations, Deep Learning and integrated datasets

Lead Institution

Johns Hopkins University

Principal Investigator

Carolyn Fitch

Project type

Large-Scale EMSL Research

One of the goals of computational biology is to model cellular behavior. At the crux of this endeavor is the need to understand proteins in their biologically relevant environmental context. In other…

Revealing oxalate-mediated carbon flow through plant-fungal-bacterial rhizosphere interactions as part of a globally important carbon-sequestering biogeochemical process

Lead Institution

Los Alamos National Laboratory

Principal Investigator

Buck Hanson

Project type

Large-Scale EMSL Research

Bacterial and fungal interactions in plant rhizospheres impart a myriad of beneficial functions to plant and soil health as well as playing important roles in biogeochemical cycling. However, the…

Seasonal vertical aerosol profiling for aerosol-cloud-precipitation interactions to advance mountainous hydrological process science

Lead Institution

Los Alamos National Laboratory

Principal Investigator

Allison Aiken

Project type

FICUS Research

Aerosols are central to understanding the water cycle within mountainous regions, but a complete understanding of this role cannot be provided without vertically resolved observations, particularly…

Determination of the Molecular Architecture and Temporal Dynamics that Drive Microbial Lignocellulose Degradation

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Song Feng

Project type

Large-Scale EMSL Research

In order to link phenotypic outcomes to molecular determinants, we have developed an integrated functional profiling platform, PhenoProfiling, that pairs activity-based probes (ABPs) with…

The knowns against the unknowns: Photosynthesis gene discovery through multi-omic survey of photosynthetic mutants during light stress

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Setsuko Wakao

Project type

Large-Scale EMSL Research

To advance genome-based understanding of photosynthesis, we have generated a high-quality, phenotyped photosynthesis mutant library in the model unicellular green alga, Chlamydomonas reinhardtii…

Numerical Modeling of Hydrologic Exchange and Biogeochemistry in Dynamic Rivers

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Timothy Scheibe

Project type

Large-Scale EMSL Research

The River Corridor SFA project (https://www.pnnl.gov/projects/river-corridor) uses a ModEx (integrated models and experiments) approach to study hydrologic exchange fluxes (HEFs) between river…

Disentangling the impacts of particle mixing state on ice nucleation

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Susannah Burrows

Project type

Large-Scale EMSL Research

Atmospheric ice nucleating particles (INPs) are rare particles required to initiate freezing in clouds at temperatures warmer than ca. -38°C, and therefore can have significant impacts on weather and…

Determining mechanisms and rates of microbial plastic biodegradation and the consequences for freshwater carbon cycling

Lead Institution

University of Michigan

Principal Investigator

Melissa Duhaime

Project type

Large-Scale EMSL Research

In recent years, plastic litter has been documented in widespread and diverse marine, freshwater, and even aeolian biomes. It is estimated that 4.8-12.7 million tons of plastics enters the ocean in a…

Coupling X-ray Computed Tomography images with ModEx inspired laboratory manipulation experiment for predicting greenhouse gas fluxes from Terrestrial-Aquatic Interfaces

Lead Institution

Emory University

Principal Investigator

Debjani Sihi

Project type

Large-Scale EMSL Research

The Terrestrial Aquatic Interfaces (TAIs) with dynamic hydrological exchange represent the most biogeochemically active and diverse systems. Frequent hydrological oscillations due to tidal…

Elucidating temporal-spatial patterns in lignocellulose degradation by morphologically distinct anaerobe gut fungi

Lead Institution

Scotland's Rural College

Principal Investigator

Jolanda van Munster

Project type

FICUS Research

Novel mechanisms to directly disassemble raw, untreated lignocellulose, and dispense the need for pre-treatments are essential to advance biotechnology based on lignocellulose conversion into simple…

Microbial impacts on methane emission hot spots from municipal landfills

Lead Institution

University of Waterloo

Principal Investigator

Laura Hug

Project type

FICUS Research

Landfills are responsible for 14% of methane emissions in the U.S., the third highest man-made methane emission source in the country. In Canada, landfills contribute 20% of emitted methane annually…

Histone Methylomics and the Chromatin Landscape of Chlamydomonas reinhardtii

Lead Institution

Donald Danforth Plant Science Center

Principal Investigator

James Umen

Project type

FICUS Research

Our goal is to identify and categorize the SET domain methyltransferase enzymes in the model unicellular green alga Chlamydomonas reinhardtii (Chlamydomonas) that are responsible for histone…

Deploying Advanced Molecular & Cell Free Expression Tools to Accelerate Characterization of Fungal Cellulosomes

Lead Institution

University of California, Santa Barbara

Principal Investigator

Michelle O'Malley

Project type

FICUS Research

This proposal seeks use of EMSL and JGI resources to determine the structure of unique, multi-enzyme cellulosomes made by anaerobic gut fungi. Cellulosomes enable synergistic breakdown of plant…

Linking soil microbial stress metabolism to watershed biogeochemistry under climate change across seasons

Lead Institution

Boston University

Principal Investigator

Jennifer Bhatnagar

Project type

FICUS Research

Air temperatures are rising, while the winter snowpack is shrinking and soil freeze/thaw events are increasing in high latitude ecosystems. The severe thermal perturbations from warming during the…

Elucidating the impacts of viruses on soil organic carbon and greenhouse gas emissions from agricultural peat soils

Lead Institution

University of Amsterdam

Principal Investigator

Paula Dalcin Martins

Project type

FICUS Research

Viruses are the most abundant biological entities on Earth. Despite their abundance, soil viruses are poorly characterized and viral impacts on the biogeochemical cycles in soils are vastly…

Parched: quantifying microbial ecophysiology and the fate of plant carbon during soil dry down

Lead Institution

Lawrence Livermore National Laboratory

Principal Investigator

Steve Blazewicz

Project type

FICUS Research

In seasonally dry grasslands, soil microbes bloom during the plant growing season, survive extreme desiccation (water potential < -35 MPa) during long dry periods, and then rapidly mineralize soil…

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