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SEPTEMBER 17, 2020
Web Feature

Not Your Average Refinery

In a new review, PNNL researchers outline how to convert stranded biomass to sustainable fuel using electrochemical reduction reactions in mini-refineries powered by renewable energy.

Study Shows Coastal Wetlands Aid in Carbon Sequestration

data collection in marsh

PNNL scientist, Amy Borde collects data in a marsh on the Columbia River estuary.

Photo: Heida Diefenderfer

Sea-level rise impacts will likely decrease ecosystem carbon stocks

August 13, 2020
August 13, 2020

Tidal marshes, seagrass beds, and tidal forests are exceptional at absorbing and storing carbon. They are referred to as total ecosystem carbon stocks, yet little data exists quantifying how much carbon is absorbed and stored by tidal wetlands in the Pacific Northwest (PNW). Knowing this information is valuable, particularly in the context of sea level rise and with the associated need for Earth system modeling to predict changes at the coast.

The Science

Researchers found that the average total ecosystem carbon stock in the PNW is higher than in other areas of the U.S. and other parts of the world. Marsh carbon stocks, in particular, are twice the global average. Researchers found progressive increases in total ecosystem carbon stocks along the elevation gradient of coastal wetland types common in the PNW: seagrass, low marshes, high marshes, and tidal forests. Total carbon also increased along the salinity gradient, with more carbon occurring in lower salinity areas.

Additionally, this research showed that common methods used to estimate soil carbon actually underestimate soil carbon stocks in coastal wetlands. Soil carbon storage below the depth of 100 centimeters proved to be an important carbon pool in PNW tidal wetlands.

The Impact

The results suggest that long-term sea-level rise impacts, such as tidal inundation and increased soil salinity, will likely decrease ecosystem carbon stocks. This is a concern if wetlands can’t migrate with increased sea level due to being bound by topography and human development.  


This research arose from the Pacific Northwest Blue Carbon Working Group, of which Amy Borde and Heida Diefenderfer of Pacific Northwest National Laboratory’s Coastal Sciences Division are members. The team studied 28 tidal ecosystems across the PNW coast, from Humboldt Bay, California, to Padilla Bay, Washington. They sampled common coastal wetland types that occur along broad gradients of elevation, salinity, and tidal influences, collecting the data necessary to calculate total carbon stocks in both above ground biomass and the soil profile.

In three years of study, the researchers found that most carbon is in the wetland soils not aboveground, and much of it is deeper than one meter—a typical lower limit of sampling. Total ecosystem carbon stocks progressively increased along the terrestrial-aquatic gradient of coastal wetland ecosystems common in the temperate zone including seagrass, low marshes, high marshes, and tidal forests. The findings were reported in “Total Ecosystem Carbon Stocks at the Marine-Terrestrial Interface: Blue Carbon of the Pacific Northwest Coast, USA,” published in the August 2020 online edition of Global Change Biology (DOI: 10.1111/gcb.15248).

Research Team: PNNL’s Amy Borde and Heida Diefenderfer, along with J. Boone Kauffman, Leila Giovanonni, James Kelly, Nicholas Dunstan, and Christopher Janousek (Oregon State University); Craig Cornu and Laura Brophy (Institute for Applied Ecology/Estuary Technical Group); and Jude Apple (Padilla Bay National Estuarine Research Reserve).


The grant award was administered by the Institute of Applied Ecology, and other partners included Oregon State University and the Padilla Bay National Estuarine Research Reserve. This research was supported by the National Oceanic and Atmospheric Administration, through a cooperative agreement with the University of Michigan. 


Kauffman, J Boone, Leila Giovanonni, James Kelly, Nicholas Dunstan, Amy Borde, Heida Diefenderfer, Craig Cornu, Christopher Janousek, Jude Apple, and Laura Brophy. “Total Ecosystem Carbon Stocks at the Marine‐terrestrial Interface: Blue Carbon of the Pacific Northwest Coast, United States.” Global change biology, no. 0 (August 11, 2020). DOI: 10.1111/GCB.15248

August 11, 2020

Making Sense of the 2018 National Biodefense Strategy

July 23, 2020
July 23, 2020
Journal Article

Following the release of the 2018 National Biodefense Strategy, PNNL released a second-generation, publicly available tool—free for use at—that maps out current biodefense responsibilities and brings clarity to the tangle of laws, directives, and agencies that together protect US citizens. The Biodefense Policy Landscape Analysis Tool, or B-PLAT, is affectionately called the “spaghetti monster,” because it visualizes information using spaghetti-like strands to demonstrate relationships between agencies, their specific responsibilities, and the degree of complexity and interconnectedness of the biodefense policy domain.

RA Bartholomew and KM Omberg.  “Making Sense of the 2018 National Biodefense Strategy.” Bulletin of the Atomic Scientists.  January 2019. 

January 18, 2019

A Publicly Available Landscape Analysis Tool for Biodefense Policy

July 23, 2020
July 23, 2020
Journal Article

In 2017, Pacific Northwest National Laboratory chartered an internal effort to capture relevant federal biodefense policy directives and laws in a format conducive to visualization and to better understanding the current state of the US biodefense enterprise.The resulting Biodefense Policy Landscape Analysis Tool (B-PLAT) is publicly available and captures more than 200 enduring biodefense responsibilities assigned by the following directives and laws.


KM Omberg, LR Franklin, DR Jackson, KL Taylor, KL Wahl, A Lesperance,  EM Wynkoop, JAS Gray, OP Leiser, SL Frazar, RM Ozanich , and RA Bartholomew. “A Publicly Available Landscape Analysis Tool for Biodefense.” Health Security. February 16(1): 2018.  DOI:  10.1089/hs.2017.0088

February 1, 2018

NWRTC Notes From the Field (June 2020)

Interviews with public health professionals who are helping to keep us safe

July 20, 2020
July 20, 2020

PNNL's Northwest Regional Technology Center interviews Assistant Chief of Resource Management for Seattle Fire Department Willie Barrington about how his team faced the unknown when the COVID-19 pandemic hit Seattle, Washington.

Research topics

June 25, 2020
JULY 9, 2020
Web Feature

Building a Better Battery—Faster

Researchers at PNNL have developed a software tool that helps universities, small business, and corporate developers to design better batteries with new materials that hold more energy.

Digging into the Details of Phosphorus Availability

Photo of plant with roots under ground

Courtesy of Shutterstock

New root blotting technique visualizes relationship between root growth, microbial activity, and soil nutrients.

July 7, 2020
July 7, 2020

The Science

Phosphorous is an important nutrient for plants. However, the mechanisms used by plants to extract phosphorus from soil and incorporate it into their biomass are not well understood. Now, researchers developed a new technique to visualize the activity and distribution of enzymes that mobilize phosphate around plant roots. Tracking the location of these enzymes can help researchers better understand the chemical dynamics between roots, microbes, and soil that influence how plants get nutrients. The approach could also be applied to other nutrient-cycling enzymes.

Diagram showing rhizosphere blotting nondestructive process
A new root blotting technique produces an imprint of plant roots growing in flat slabs. The paper imprints can then be probed with different fluorescent indicators to visualize both the distribution and activity of phosphate-mobilizing enzymes surrounding the roots.

The Impact

Phosphorus is an essential nutrient for plants and therefore, global demand for phosphorus fertilizers is expected to grow to accommodate the world’s growing population. However, most of these fertilizers are made from rock phosphorus, a non-renewable resource. This research provides new insights into the complex dynamics of phosphorous exchange between soil, microbes, and plant roots. Knowledge from this newly developed approach will help scientists identify strategies to improve phosphorus use efficiency for bioenergy crop production in marginal environments, as well as for agriculture in general.


Soil bacteria, fungi, and plants produce enzymes called phosphatases, which convert organic sources of phosphorus into a form that plants can absorb. Researchers have studied the microbial activity in bulk soil samples, providing information about the overall functional potential of the environment. But to better understand the dynamics between soil, plants, and microbes, more detail is needed. To accomplish that, a team of researchers developed a new technique based on root blotting to reveal phosphatase activity and distribution around plant roots. They grew switchgrass in flat pots or “rhizoboxes” containing soil with pellets of root matter as sources of organic phosphorus. Then, they applied a nitrocellulose membrane to capture proteins around the roots. Finally, the researchers stained the membrane with fluorescent indicators for phosphatase activity and protein concentration. This revealed the spatial distribution of phosphatase around the roots of plants, and highlighted regions of increased phosphatase activity.

This approach could be used to study phosphatase activity over time, as well as other nutrient-cycling enzymes. The combination of membrane extraction, with rapid analysis via fluorescent probes to reveal localization of phosphatase activity in the rhizosphere, offers a new technique for environmental applications. Expanding this approach could enable simultaneous visualization of multiple enzyme types in soil systems.


Development of this method was funded by DOE’s Office of Science, Biological and Environmental Research Program by the Early Career Research Award program (PI: Jim Moran).


V.S. Lin, et al. “Non-destructive spatial analysis of phosphatase activity and total protein distribution in the rhizosphere using a root blotting method.” Soil Biology and Biochemistry, 146 (2020). DOI: 10.1016/j.soilbio.2020.107820

JUNE 30, 2020
Web Feature

'Rooting' for Brachypodium Genes

Plant scientists at Pacific Northwest National Laboratory have garnered the most comprehensive—and first ever—genetic level dataset of the rooting process in a flowering model grass.
APRIL 28, 2020
News Release

A Leap in Using Silicon for Battery Anodes

Researchers at PNNL have come up with a novel way to use silicon as an energy storage ingredient, replacing the graphite in electrodes. Silicon can hold 10 times the electrical charge per gram, but it comes with problems of its own.

Strange water behavior on aluminum oxide

Not all surfaces are created equally

March 16, 2020
March 16, 2020

Researchers adding water to the surface of alumina measured some surprising results. They were preparing the surface of an alumina crystal in ultrahigh vacuum, intending to achieve a hydroxylated surface to approximate another form of aluminum, called gibbsite (α-Al(OH)3). They're interested in gibbsite because it is part of the mix of materials that comprise highly radioactive waste stored in tanks at various former weapons production sites.

At water's interface with a defect-free face of an alumina crystal (oxygen atoms are purple, aluminum atoms are green) researchers, using temperature programmed desorption (TPD) and infrared spectra data, found evidence of molecular water only. Surprisingly, there was no dissolution of the water into its components since the expected hydroxyls (OH) are absent.

The water was supposed to adsorb to the alumina and then immediately dissociate or separate into its components creating hydroxyl or OH components. Surprisingly, the water remained intact, raising important questions regarding the fundamental reactions that govern chemical transformations of aluminum oxides and hydroxides. The new research stems from work at the Interfacial Dynamics in Radioactive Environments and Materials (IDREAM) Energy Frontier Research Center.

The work, led by Pacific Northwest National Laboratory scientists in collaboration with scientists at University of Notre Dame and Georgia Institute of Technology was published in The Journal of Physical Chemistry C in a paper titled, "Molecular Water Adsorption and Reactions on α-Al2O3(0001) and α-Alumina Particles."

Why it matters: Aluminum oxides play an important role in the processing of high-level radioactive waste because they are one of the largest, nonradioactive components of the wastes generated from defense nuclear materials production during the Cold War.

Detailed knowledge of water behavior on aluminum oxide surfaces is key to understanding corrosion and catalytic properties of alumina and other aluminum-based materials in engineering applications.

Summary:Researchers investigated the adsorption and reactions of water on well-characterized alumina under well-controlled experimental conditions: under ultrahigh vacuum (UHV), using temperature programmed desorption (TPD), infrared reflection absorption spectroscopy (IRAS), electron-stimulated desorption (ESD) and other surface science techniques.

They found that water adsorbs on the pristine surface of an alumina crystal α-Al2O3(0001), with no evidence of further reaction. Conversely, when water contacts α-alumina particles under ambient conditions it dissociates and does create hydroxyls on the particles. Dissociation is energetically favorable for both surfaces, but it appears to be hindered on the defect-free surface of alumina, which is counter to some findings in the literature.

Using UHV and IR spectroscopy techniques, which is typically only done on metals, researchers observed the vibration of water when adsorbed on the face of an alumina crystal. Although surface hydroxyls from dissociation of the molecule were expected, no evidence was observed by IRAS used to measure the vibration. But when alumina nanoparticles were exposed to water, a diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) instrument indicated the presence of surface hydroxyls.

What's next? More research is needed to understand why the experiments and theory indicate such different reactivities for this important surface of alumina and to discover if there’s a barrier for water to dissociate and, if so, how to get over that barrier.


This work was supported as part of IDREAM (Interfacial Dynamics in Radioactive Environments and Materials), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The authors acknowledge the Notre Dame Radiation Laboratory, which is supported by DOE BES through Grant DE-FC02-04ER15533.

Sponsors: This work was supported as part of IDREAM (Interfacial Dynamics in Radioactive Environments and Materials), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences and led by Pacific Northwest National Laboratory (PNNL)

User Facilities: The experiments on α-Al2O3(0001) were performed in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research and located at PNNL.

Research Team: Nikolay G. Petrik and Greg A. Kimmel (Pacific Northwest National Laboratory), Thomas M. Orlando and Patricia L. Huestis (Georgia Institute of Technology), Jay A. LaVerne and Alexandr B. Aleksandrov (University of Notre Dame).

Reference: N.G. Petrik, P.L. Huestis, J.A. LaVerne, A.B. Alekandr, T.M. Orlando, G.A. Kimmel. 2018. “Molecular Water Adsorption and Reactions on α-Al2O3(0001) and α-Alumina Particles.” The Journal of Physical Chemistry C2018, 122, 17, 9540-9551 DOI: 10.1021/acs.jpcc.8b01969

November 1, 2019

Aluminum complexes identified via vibrational fingerprints

Findings will allow complex forms of aluminum to be distinguished during aluminum processing

March 16, 2020
March 16, 2020

Dissolved aluminum formed during industrial processing has perplexed chemists by occurring in much greater concentrations than predicted. Efforts to explain the phenomenon have been hampered by an inability to accurately identify the concentrations of each aluminum species present. New research from scientists at the Interfacial Dynamics in Radioactive Environments and Materials (IDREAM) Energy Frontier Research Center sorts out which compounds are present and their concentrations, providing an important new tool with broad applicability.

Raman spectra of solutions composed of an aluminate monomer and two dimeric species. Vibrational bands predicted by ab-initio molecular dynamics (AIMD) shown in red and green. Overlapping IR and Raman bands cause different linear combinations of species to have the same overall spectra, preventing identification.

The work, led by Pacific Northwest National Laboratory scientists in collaboration with scientists at Washington State University and Washington River Protection Solutions, was featured in The Journal of Physical Chemistry B in a paper titled, "Ab Initio Molecular Dynamics Reveal Spectroscopic Siblings and Ion Pairing as New Challenges for Elucidating Prenucleation Aluminum Speciation."

Why it matters: This finding provides support for improved design of aluminum production and separations processes for energy generation and transmission to high level radioactive waste treatment.

Summary: Industrial processing of aluminum for energy production and/or high level radioactive waste clean-up requires dissolving aluminum complexes such as gibbsite (α-Al(OH)3) and boehmite (AlOOH), typically under highly alkaline conditions. Excessively high concentrations of dissolved aluminum could be explained by considering dimeric aluminum species, but spectroscopic evidence to support these species has not been conclusive. Multiple dimeric species are possible, including Al2O(OH)62- and Al2(OH)82-, which have overlapping vibrational bands that prevented unique identification, until now. 

In this work, we used a combination of Raman and infrared (IR) spectroscopies and computational methods (ab-initio molecular dynamics, AIMD) to resolve vibrational band assignments.  Solution phase monomeric Al(OH)4- and dimeric Al as either Al2O(OH)62- or Al2(OH)82- were resolved. In addition, band widths, anharmonic shifts, and average solvent effects were determined, enabling specific band assignments and providing vibrational fingerprints for each species.  Furthermore, solvent effects that are important in such concentrated solutions of electrolytes were determined.  These results provide a basis for improving equilibrium models for boehmite and gibbsite solubilities, which increases confidence in design of industrial aluminum processing schemes.

What's next? The unique identification of aluminum species using vibrational methods will now be applied to concentrated electrolyte solutions containing aluminate to resolve discrepancies in aluminum solubilities under alkaline conditions.


This work is related to the Basic Research Needs for Environmental Management, specifically the Priority Research Direction entitled "Elucidating and Exploiting Complex Speciation and Reactivity Far From Equilibrium".

Sponsors: This work was supported by IDREAM (Interfacial Dynamics in Radioactive Environments and Materials), an Energy Frontier Research Center managed for the U.S. Department of Energy (DOE), Office of Science, Basic Energy Sciences (BES).

User Facilities: A portion of the research was performed at the Environmental and Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE Office of Biological and Environmental Research located at Pacific Northwest National Laboratory.

Research Team: Mateusz Dembowski, Sue B. Clark, Kevin M. Rosso, Gregory K. Schenter, Carolyn I. Pearce (Pacific Northwest National Laboratory), Maxime Pouvreau, Aurora E. Clark (Washington State University), and Jacob G. Reynolds (Washington River Protection Solutions).

Reference: M. Pouvreau, M. Dembowski, S.B. Clark, J.G. Reynolds, K.M. Rosso, G.K. Schenter, C.I. Pearce, A.E. Clark. 2018. "Ab Initio Molecular Dynamics Reveal Spectroscopic Siblings and Ion Pairing as New Challenges for Elucidating Prenucleation Aluminum Speciation." The Journal of Physical Chemistry B. DOI: 10.1021/acs.jpcb.8b04377

January 1, 2019