The Environmental Molecular Sciences Division (EMSD) and the Environmental Molecular Sciences Laboratory (EMSL), the user facility PNNL manages, support the US Department of Energy (DOE) Biological and Environmental Research (BER) program’s mission to achieve fundamental understanding and prediction of complex biological, Earth, and environmental systems for energy and infrastructure security.

EMSD is working toward three large-scale strategic science objectives.

  • Digital Phenome Platform (DigiPhen): Engineering biology from biomolecules to organisms. This project is focused on creating methods for predictive modeling of protein function, pathway identification, and phenotype.
  • Molecular Observation Network (MONet): Modeling from elements to ecosystems. This project creates a national molecular-level ecosystem/watershed/coastal monitoring network.
  • Modeling and Data Sciences Capability (MDS): Visualizing all biological and environmental data. This project focuses on developing a BER-dedicated capability that provides mid-range high-performance computing for data-model integration and multiscale modeling.

The foundation for these long-term platforms is EMSD/EMSL's seven integrated research platforms.

Biogeochemical Transformations

Biogeochemical Transformation composite image

The interplay of geology, chemistry, and biology among Earth systems is critically important for keeping Earth’s air and water clean and plants healthy. Our biogeochemical transformations expertise crosses scientific boundaries to investigate how nutrients, contaminants, aerosols, and other chemical compounds move and change in the environment. With new information on how these exchanges occur, we can develop and improve predictive models to anticipate and manage their effects on both human and natural systems.

The Biogeochemical Transformations Integrated Research Platform helps researchers answer fundamental questions about chemical, physical, hydrologic, microbial, and atmospheric interactions that affect the transformation and mobility of critical nutrients, contaminants, aerosols, particles, and compounds within the environment. We use the latest platforms and approaches to gain new insights into the physiochemical effects of nutrient cycling in the environment, the interactions between metabolic pathways, and the dynamics of microbial communities. From molecular structures and activity, to cellular and community-scale processes, we seek to improve scientific understanding of microbial metabolism and nutrient cycling in the environment.

 

 

 

Ecosystem Interfaces

Isotope and Chemical Analysis composite illustration

The interface between ecosystems is often highly dynamic with increased rates of biogeochemical reactions and fluxes. Understanding process controls present at these interfaces can help elucidate large scale nutrient dynamics, identify rate-controlling reactions, and evaluate the magnitude of external forcing on the broader connectivity between ecosystems. Our ecosystem interface platform uses multiple laboratory and field techniques to quantify key biogeochemical fluxes between critical zone, aquatic, atmospheric, and deep subsurface boundaries. With this knowledge, we can help refine global biogeochemical models and improve accuracy of predicted ecosystem responses to environmental perturbations.  

We quantify nutrient exchange between ecosystems using various chemical, chemical imaging, and stable isotope analyses. By analyzing a range of spatial scales (e.g., nanometer to centimeter and larger), we can uncover the mechanistic drivers and controls of pertinent environmental fluxes. We leverage the analyses we employ to inform landscape and larger-scale models and evaluate how fluxes respond to environmental changes.

 

 

 

Plant and Ecosystem Phenotyping

Molecular Plant Phenotyping composite illustration

What genetic and environmental variables help one plant thrive while another fails? In a world faced with increasingly stretched resources, we need ways to grow food and bioenergy crops under sustainable conditions, using as little water, arable soil, and fertilizer as possible. Plant and ecosystem phenotyping investigates interactions between genes and the environment at the molecular level to understand, predict, and control plant traits at the plant-system scale. It also probes the complex interactions between plants and the environment, including microbes, soil, and the atmosphere, that lead to specific plant traits. With this understanding, we can grow targeted crops or engineer plants with desirable attributes such as drought tolerance or disease resistance.

Our Plant and Ecosystem Phenotyping Integrated Research Platform focuses on characterizing and modeling plant phenotypes at the molecular to organismal scale. We characterize cellular biomolecules and correlate microscopic molecular changes (internal phenotypes) of plants with macroscopic observations (external phenotypes) to identify characteristics that regulate their growth and sustainability. We achieve ultra-precise observations using integrated multi-omics (at the single-cell, distinct cell-types, and whole tissue levels), quantitative imaging, synthetic biology, computational biology, stable isotope probing, and high-throughput phenotyping approaches.

For root phenotyping, we study how different components of the root system evolve—how they branch and angle, develop during plant growth, and respond to environmental changes. We also characterize the rhizosphere and phyllosphere microbiome structure and function, including soil properties and plant-microbe interactions.

 

 

 

 

 

Structural Biology

Molecular Bioimaging composition illustration

All living systems rely on the tiniest of cellular functions to maintain health and vigor. When these functions break from disease or other stresses, the whole organism suffers. Structural biology allows us to study the relationships between cellular proteins, how they communicate, and their functions. With a better understanding of these cellular roles, we can look for ways to improve crops for food, biofuels, and bioproducts in a resource-constrained future.

Our Structural Biology Integrated Research Platform focuses on examining the assembly, structure, and function of proteins and protein complexes at the nanoscale, down to Ångströms, across space and time. With high-resolution images, we can see details in the molecular organization of a biosystem in three-dimensions. We can also map the chemical processes involved in micronutrient exchange both within and between cells and their environment, revealing links between proteins' structural and biochemical dynamics, protein complexes, and other biomolecules. These views help us understand how changes in morphology and composition affect biological systems.

 

 

 

 

Biomolecular Pathways

Functional Omics composite illustration

Essential biological molecules—like proteins, lipids, RNA, and metabolites—create the language of gene expression and energy exchange that leads to healthy cells, organisms, and living systems. Our Biomolecular Pathways Integrated Research Platform connects these biomolecules to their communication signals, biological roles, and energy functions to better explain and understand the trillions of small interactions that make up the world as we know it. This essential knowledge provides an enhanced understanding of cellular communication to improve resource use and create a more resilient environment.

The collective biomolecules in plants, fungi, and microbes determine an organism’s structure, function, and dynamics. We have developed integrated capabilities to quantify the functional components of complex systems and probe biological molecules with unknown functions through increasing the rate, dynamic range, and resolution by which we analyze proteins and metabolites. Our accelerated throughput—with integrated transcriptomics, proteomics, and metabolomics—provides ultrasensitive measurements that explain the molecular mechanisms behind biological processes. With this capability, our research community explores biological complexity and diversity in the quest for more efficient biofuel production and robust environmental nutrient cycling predictions.

 

 

 

Cell Signaling and Communications

Cellular Dynamics composite illustration

Billions of cells, each with a one-of-a-kind role and behavior, make up living systems. Our expertise in systems biology, functional genomics, and biochemistry, enhanced by the state-of-the-art capabilities in high-resolution imaging and single-cell multi-omic measurements helps untangle the mechanisms by which cells communicate and exchange chemical signals. Quantitative studies of how individual cells grow and interact with their neighbors or hosts provide a critical understanding of molecular-level events underpinning complex biological systems' behaviors and their responses to the changing environment.

Expertise in the Cell Signaling and Communications Integrated Research Platform allows us to localize and isolate individual cells from complex biological samples for further structural and functional analyses. Researchers can then observe the live, intact cells and measure their unique responses over time to capture minute differences in cellular functions and outputs. Our technical capabilities enable labeling and characterization of subcellular structures and molecules in real time to quantify how, when, and where organisms exchange molecular signals and nutrients to foster interactions. As we begin to better understand and differentiate single-cell behavior, we are poised to predict functional outputs of interconnected biological systems as a function of their environment, thus enabling an informed design of organisms and communities with highly improved environmental and industrial properties for biosecurity and health applications.

 

 

 

 

Systems Modeling and Data Sciences

Systems Modeling and Data Sciences illustration

The foundation for advancing scientific discovery is data. Improved means of producing, storing, and analyzing it is the key to expanding our knowledge of the world. With over 25 years of computing expertise, we are a leader in high-performance computing, software creation, and modeling development. One of our primary science missions includes advancing the prediction and control of biological and environmental systems by developing approaches for advanced data analysis, data integration, multiscale modeling, and simulation of processes across scales. 

Our Systems Modeling and Data Sciences Integrated Research Platform has two focuses. We use computational models of protein structure and function, metabolic modeling, and machine learning approaches to associate genotype with phenotype, understand the biological processes that control nutrient flux, and enable predictive approaches to biodesign and biofuel/bioproduct production. We also trace the flow of materials, like carbon, nutrients, and contaminants, in the environment to see how biological and hydrobiogeological processes change ecosystem function.

 

 

 

 

Other Research

Scientists at EMSD also support non-BER-funded research projects that use EMSL’s capabilities. Our scientists are leading or have led projects funded by:

  • the National Science Foundation, including the Center for Sustainable Nanotechnology
  • the National Institutes of Health, including the Pacific Northwest Center for Cryo-EM
  • DOE’s Basic Energy Sciences program
  • DOE’s Office of Energy Efficiency and Renewable Energy, including Next Generation Cathodes, Battery Materials Research, and Advanced Manufacturing Office
  • NASA