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Microbial diversity influences nitrogen cycling in rivers

Image of streambed

Seasonal changes affect microbiome communities, genes, and subsurface biogeochemical pathways differently

March 4, 2020
March 4, 2020
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The Science
DOE researchers investigated the role of microbial genetic diversity in two major subsurface biogeochemical processes: nitrification and denitrification. Results show that across different seasons only a few microbe species, namely Nitrosoarchaeum, carry out nitrification functions—demonstrating high resistance to environmental change. However, denitrification genes, which are more broadly distributed in the community, displayed a variety of diversity patterns and abundance dynamics—demonstrating greater microbial interactions as conditions change.

Nitrogen cycling in hyporheic zone
Figure shows nitrogen transformations in the hyporheic zone, where a vast microbiome community influences nutrient cycling. Upper layers, closer to the riverbed contain more oxygen and organic matter. Under these conditions nitrification (orange arrows) occurs. Microbes transform the nitrogen from organic matter through a variety of steps and ultimately deplete the oxygen. As oxygen depletes, denitrification (blue arrows) further transforms nitrogen, resulting in an electron acceptor for catabolism of organic matter.

The Impact
There is little research connecting microbiomes at the genetic level to hydrobiogeochemical modeling. This research helps broaden collective knowledge for a better understanding of the pathways affected by environmental changes. For example, under extreme environmental conditions an entire biochemical pathway could be altered or eliminated if a single step has low genetic diversity such that its loss could not be replaced.

Summary
The Pacific Northwest National Laboratory research team, led by Bill Nelson, found that major environmental processes—specifically nitrification and denitrification—are maintained through a variety of diversity strategies. Historically, the bulk of biogeochemical research has focused on microbial communities at the organismal level. But this research focused on the importance of genetic distribution and diversity.

In their recent PLoS ONE paper, the researchers discuss the roles microbes play in ecological functions; the novelty of the genetic makeup of these microbes; and future research opportunities to determine which organisms are genetically expressing nitrogen cycling functions.

The novelty of this study comes from examining the temporal dynamics of diversity at the gene level. To evaluate all genes in the nitrification and denitrification pathways, novel Hidden Markov Models (HMMs) were developed that can recognize the broad diversity found in environmental samples. They found that while different environmental conditions impair microbiome growth and the gene expression of some populations, at the same time, it can stimulate others. High biodiversity at the organism or genetic level creates more resiliency, and the microbiome community can respond more rapidly to environmental changes.

Contact
Bill Nelson, Pacific Northwest National Laboratory, William.Nelson@pnnl.gov

Funding
This research was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), as part of the Subsurface Biogeochemical Research Scientific Focus Area (SFA) at Pacific Northwest National Laboratory (PNNL).

W.C. Nelson, E.B. Graham, A.R. Crump, S.J. Fansler, E.V. Arntzen, D.W. Kennedy, J.C. Stegen, “Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome”. PLoS ONE 15(1) e0228165 (2020). [DOI: 10.1371/ journal.pone.0228165]

Oxide interfaces in disarray

Microscope image, bright blue background with bright green oxides

Atomic-scale imaging informs interface models for oxygen defect formation during disordering of oxides used in energy and computing.

| PNNL

Exploration of disorder at material interfaces could lead to better device performance

March 3, 2020
March 3, 2020
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The structure of an interface at which two materials meet helps determine the performance of the computers and other devices we use every day. However, understanding and controlling interface disorder at the atomic level is a difficult materials science challenge.

A research team at PNNL and Texas A&M University combined cutting edge imaging and numerical simulations to examine disordering processes in widely used oxide materials. They found that certain oxide interface configurations remain stable in extreme environments, suggesting ways to build better performing, more reliable devices for fuel cells, space-based electronics, and nuclear energy.

Visualizing the disordering process

As reported in Advanced Materials Interfaces (Asymmetric Lattice Disorder Induced at Oxide Interfaces,” DOI: 10.1002/admi.201901944) the team set out to examine interfaces between pyrochlore-like and perovskite oxides, two common classes of functional materials used in energy and computing technologies. While most past work has focused on individual bulk materials, less attention has been paid to interfaces connecting them, as would be the case in a device. In particular, it is not clear how interface features, such as composition, bonding, and possible defects, govern disordering processes.

Funded by PNNL’s Nuclear Process Science Initiative (NPSI), the team employed experimental and theoretical methods to study the interface at different stages of disorder introduced through ion irradiation. They imaged the local structure of the material using high-resolution scanning transmission electron microscopy and convergent beam electron diffraction, which showed that the bulk of the two materials disordered (amorphized) before the interface. After further irradiating the material, they found that a band region near the interface had remained crystalline, while the rest of the structure had become amorphous.

To understand this behavior, the team turned to a technique called electron energy loss spectroscopy, which allowed them to examine the atomic-scale chemistry and defects formed at the interface. Their measurements revealed the presence of substantial amounts of defects called oxygen vacancies, which can greatly affect properties such as magnetism and conductivity. Based on these observations, the team constructed a theoretical model of the interface and explored the effect of different interface configurations on the tendency to form vacancies.

“In our model we are able to systematically vary interface features, such as crystal structure, intermixing, and strain, to see their effect on defect formation. We found that the structure of the materials on both sides of the interface can influence where defects are likely to form first,” explained Steven R. Spurgeon, a PNNL materials scientist. “Our model suggests that by selecting appropriate crystal structures and controlling how they connect, it may be possible to dictate the sequence of defect formation, which would allow us to enhance the properties of these materials.”

The team is exploring other interface structures and chemistries, with an eye toward improving the performance of oxides used in extreme environments.

The study was conducted as part of the NPSI project, “Damage Mechanisms and Defect Formation in Irradiated Model Systems,” led by Spurgeon.

Research Team

Steven Spurgeon (PNNL), Tiffany Kaspar (PNNL), Vaithiyalingam Shutthanandan (Environmental Molecular Sciences Laboratory at PNNL), Jonathan Gigax (Texas A&M), Lin Shao (Texas A&M), Michel Sassi (PNNL).
February 20, 2020

Peeking Into the Lives of Soil Microbiomes

Photo of plant in soil

SoilBox provides in-depth imaging and characterization of soil microbial communities in their native environments.

February 28, 2020
February 25, 2020
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The Science
To better characterize the vast diversity of soil microbes and their interactions, DOE researchers developed a high-tech simulated soil core called SoilBox. This 16.7-centimeter-deep box allows researchers to visualize soil microbes’ complex interactions using different imaging methods and facilitating, for the first time, visualization of the soil microbiome’s organization and community metabolism. Furthermore, SoilBox provides a tool for researchers to observe how soil microbial communities respond to environmental changes and perturbations.

The Impact
The complexity of soil makes spatial imaging of soil microbial communities challenging. Using SoilBox, researchers can now visualize the diversity and metabolic

Graphic of Soilbox
SoilBox allows researchers to characterize and image soil microbiome dynamics at a level of resolution not previously available. This especially applies to how soil microbes respond to environmental shifts.

landscape of the soil microbiome under different environmental conditions, such as soil moisture and temperature. Understanding the basic biology of the soil microbiome is necessary for understanding how native soil systems respond to environmental perturbations such as drought, lack of nutrients, and fire. 

Summary
Soil-dwelling microbes are key players in the overall health of soil ecosystems, performing critical functions like carbon and nutrient cycling. The interplay between the soil microbiome and the soil it inhabits is a dynamic relationship heavily influenced by factors such as soil acidity, organic content, and temperature. The size and distribution of soil particles also affects many soil characteristics, adding to the already complex challenge of accurately describing structure-function relationships of soil microbial communities.

To address the difficulties of studying the soil microbiome in its native state and at a microscale resolution, a team of researchers from Pacific Northwest National Laboratory, led by Arunima Bhattacharjee and Chris Anderton, developed SoilBox. This system represents a soil ecosystem by simulating an ~12-cm-deep soil core; several windows facilitate molecular and optical imaging measurements that are crucial to understanding the nuanced interactions between the soil microbiome and its environment. This novel imaging capability allows scientists to study the dynamic landscape of soil microbial communities as they relate to environmental changes, including nutrient cycling.

This work overcomes the challenge of visualizing the diversity of soil microbial communities in the complex and ever-changing environment of soil. SoilBox will be used in the near future to investigate soil microbial community dynamics.

Contact
Chris Anderton, Pacific Northwest National Laboratory, christopher.anderton@pnnl.gov

Funding
This research was supported by the Department of Energy (DOE) Office of Biological and Environmental Research (BER) and is a contribution of the Scientific Focus Area "Phenotypic response of the soil microbiome to environmental perturbations." Pacific Northwest National Laboratory (PNNL) is operated for the DOE by Battelle Memorial Institute under Contract DE-AC05-76RLO1830. A portion of the research was performed using EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by BER and located at PNNL.

A. Bhattacharjee et al.,“Visualizing microbial community dynamics via a controllable soil environment.” mSystems 5, 1:e00645-19 (2020). https://doi.org/10.1128/mSystems.00645-19.

JANUARY 10, 2020
Web Feature

Clark Recognized for Nuclear Chemistry Research

The world’s largest scientific society honored Sue B. Clark, a PNNL and WSU chemist, for contributions toward resolving our legacy of radioactive waste, advancing nuclear safeguards, and developing landmark nuclear research capabilities.
DECEMBER 11, 2019
Web Feature

PNNL to Lead New Grid Modernization Projects

PNNL will lead three new grid modernization projects funded by the Department of Energy. The projects focus on scalability and usability, networked microgrids, and machine learning for a more resilient, flexible and secure power grid.

PNNL Launches Marine Renewable Energy Database

Logo of Tethys Engineering

PNNL created an online database to share information related to the marine renewable energy industry.

Tethys Engineering addresses industry’s technical and engineering challenges

November 18, 2019
November 18, 2019
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Marine renewable energy (MRE) has the potential to provide 90 gigawatts of power in the United States through waves and tidal and ocean currents.

To harness the ocean’s energy, the MRE industry needs to understand how to address technical and engineering challenges such as efficient power takeoff, device survivability, and grid integration.

PNNL developed Tethys Engineering in September 2019 to allow sharing resources around the deployment of devices in corrosive, high-energy marine environments. The recently launched Tethys Engineering online database includes collected and curated documents surrounding the technical and engineering development of MRE devices. Users can search and filter results to intuitively identify information relevant to developers, researchers, and regulators.

Tethys Engineering includes more than 3,000 journal articles, conference papers, reports, and presentations related to wave, current, salinity gradient, and ocean thermal energy conversion technologies. The database contains information from around the world.

The Tethys Engineering database was created as a companion to the already established Tethys website, which focuses on the environmental effects of the MRE industry.

November 18, 2019