BER Research Highlights

Search Date: October 17, 2017

17 Records match the search term(s):


December 15, 2008

New Genome-Based Tools Improve Description of Uranium Bioreduction in the Environment

Environmental microbes play an important role in the remediation of contaminants such as uranium by converting them from mobile to immobile forms. However, we do not have accurate or reliable tools to predict the role that microbes will play in remediation of contaminants at a site. Researchers at the University of Massachusetts have developed a genome-enabled approach for assessing the metal-reducing activity of members of the Geobacter family involved in acetate stimulated uranium reduction in the environment. This new approach couples laboratory studies with in silico modeling of microbial metabolism and gene expression (mRNA) analyses from the dominant Geobacter species at a site to explain how the microbes respond to acetate injected into the subsurface to stimulate uranium reduction. The new tools can, for example, provide crucial data on rates of acetate uptake useful in mechanistic, in silico, models of microbial growth and activity. The current study is an example of how genome-enabled studies of environmentally-relevant microbes can lead to more mechanistic descriptions of microbial metabolism in the environment.

Reference: Microbiology, 2008, vol 154:2589-2599.

Contact: Robert T. Anderson, SC-23.1, (301) 903-5549
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


December 01, 2008

Long-Term Bioimmobilization of Chromium in Groundwater Demonstrated at the Hanford Site

As a result of past nuclear processing activities, chromium is a common contaminant in the soils and groundwater at most DOE sites. Chromium in groundwater most commonly exists either as hexavalent chromium, Cr(VI), or trivalent chromium, Cr(III). While Cr(VI) is quite mobile and toxic in groundwater, Cr(III) complexes are much less toxic, and form insoluble and stable precipitates. A multi-institutional research team led by scientists from Lawrence Berkeley National Laboratory (LBNL) conducted field experiments in the 100-H area at the Hanford Site to test the effectiveness of a slow-release glycerol polylactate, or hydrogen release compound (HRC), to see if it would stimulate the existing microbial community to transform Cr(VI) moving in the groundwater into non toxic and insoluble Cr(III). The microbial community initially changed dramatically and then appeared to stabilize to a community with a new composition. In addition, Cr(VI) levels in wells down gradient from the HRC injection wells dropped from more than 150 micrograms/liter to an undetectable level and remained at that level for more than three years. Additional HRC and tracer injection tests are planned to further assess the biogeochemical process changes that occur as a result of HRC injection, to investigate reoxidation of Cr(III) to Cr(VI), and to develop a reactive transport model.

Reference: Environmental Science & Technology, 2008, vol 42(22):8478-8485.

Contact: Paul E. Bayer, SC-23.1, (301) 903-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


November 17, 2008

DOE Biogeochemistry Research Featured in Special Session at the Fall American Geophysical Union Meeting

DOE scientists will present the results of their research during a Biogeosciences session at the fall American Geophysical Union (AGU) meeting from December 15-19, 2008, in San Francisco, CA. This special session, "Geochemical Controls and Microbial Response in Metal Contaminated Environments," will feature presentations on recent findings from studies of microbial responses to mercury contamination and other stresses in contaminated environments. Greater understanding of the fundamental biogeochemical reactions that influence mercury transport and transformation in soils and sediments is needed to enable informed cleanup decisions at DOE sites.

Reference: (link expired)

Contact: Paul Bayer, SC-23.1, (301) 903-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


November 10, 2008

Video on New Supercomputer at the Environmental Molecular Sciences Laboratory (EMSL) to be Shown at the SC08 Conference

A continuously looping video highlighting the availability of the new supercomputer at the Environmental Molecular Sciences Laboratory (EMSL), a DOE scientific user facility located at the Pacific Northwest National Laboratory (PNNL) in Richland, Washington, will be shown during the SC08 Conference from November 15-21, 2008, in Austin, Texas.  The new video shows a speeded up view of how the processor racks for Chinook were assembled within EMSL's raised floor space, while simultaneously informing viewers that Chinook will have 4,620 quad-core processors, 37 tera-Bytes of memory, a peak performance of 163 tera-Bytes, and will be available for users conducting computational research on aerosol formation, bioremediation, catalysis, climate change, hydrogen storage and subsurface science.  The video will be one of the marketing tools about EMSL that will be included in a PNNL booth at the SC08 Conference.  As the premier international conference for high performance computing (HPC), networking, storage and analysis, the SC Conference attracts scientists, engineers, researchers, educators, programmers, system administrators and managers from around the world to hear technical presentations and panel discussions, participate in tutorials, and see new technology demonstrations.  To view the video, go to:  [link expired: https://www.emsl.pnl.gov/emslwebmedia/chinookfinalmedium.wmv].

Contact: Paul Bayer, SC-23.1, (301) 903-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


November 03, 2008

Radiation Resistance of Microbe Could be Due to Activities of Hydrolase Proteins

A research team from Brookhaven National Laboratory the University of Toronto and the Pacific Northwest National Laboratory used state-of-the-art nuclear magnetic resonance (NMR) spectroscopy capabilities at the William R.  Wiley Environmental Molecular Sciences Laboratory (EMSL), a DOE Scientific User Facility located in Richland, Washington, to probe the activity of a hydrolase protein from a microorganism that is highly resistant to radiation.  The microbe, Deinococcus radiodurans, can survive thousands of times more radiation exposure than a human, but the mechanism for this astounding resistance is not understood.  One mechanism could be that a group of proteins called Nudix hydrolases protect cells by binding to specific forms of cellular metabolites called nucleosides.  Using the NMR spectroscopic capabilities at EMSL, the research team was able to study the molecular binding of the Nudix hydrolase DR_0079, with nucleosides in real time.  Unlike other hydrolases, DR_0079 binds to nucleoside diphosphate and converts it into a form that cannot lead to mutations in deoxyribonucleic acid (DNA).  Understanding the molecular basis for the radiation resistant properties of D.  radiondurans could lead to strategies that protect humans from the effects of ionizing radiation, or to novel bioremediation strategies for DOE sites with radionuclide contamination.  The research was supported by the Office of Science, Genome Canada, the Ontario Research and Development Challenge Fund, and the National Institutes of Health Protein Structure Initiative. 

Reference: Buchko GW, O Litvinova, H Robinson, AF Yakunin, and MA Kennedy.  2008.  "Functional and Structural Characterization of DR_0079 from Deinococcus radiodurans, a Novel Nudix Hydrolase with a Preference for Cytosine (Deoxy)Ribonucleoside 5'-Di- and Triphosphates." Biochemistry  47:6571-82.

Contact: Paul Bayer, SC-23.1, (301) 903-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


October 06, 2008

New Model Improves Our Ability to Simulate Contaminant Fate and Transport

Understanding and predicting water flow and contaminant transport at DOE sites is important for developing and monitoring cleanup strategies. Our ability to predict water flow and contaminant transport in unsaturated sediments has been limited by the ability of numerical models to account for the heterogeneity of coarse and fine material layers in those sediments and the scale dependence of hydraulic parameters. A new numerical modeling approach called the Cantor bar model, developed by DOE Office of Science-funded scientists at Oak Ridge National Laboratory (ORNL) and the University of Tennessee, predicts the effective hydraulic parameters of unsaturated flow through thin layers of fine sediment interbedded within a layer of coarse sediments. With additional development, the Cantor bar model should be able to predict the effective hydraulic parameters at various scales. This would be a major step forward in being able to simulate the fate and transport of contaminants at multiple DOE sites. These results were recently published in the Vadose Zone Journal (Tang et al., 7: 493 (2008)).

Contact: Paul Bayer, SC-23.1, (301) 903-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


September 22, 2008

New Field Site at Hanford for Studies of Uranium Transport and Biogeochemistry in Groundwater

A team of DOE Office of Science-supported researchers at PNNL with collaborators from the USGS, INL, LBNL, LANL, and four universities have installed a one-of-a-kind field experimental facility at the Hanford site to study the reactive transport behavior of uranium in a long contaminated groundwater aquifer.  This site is representative of contaminated sites in Hanfords Columbia River corridor. The movement of water in the contaminated aquifer is complex because of close hydrologic coupling with the nearby Columbia River. The behavior of uranium at the site has defied scientific explanation for over ten years, preventing development of an effective remediation strategy to reduce discharges to the Columbia River. The experimental facility is heavily instrumented to characterize and monitor the physical, chemical, biological processes that are thought to control uranium transport at the site. The experimental site will allow scientists to evaluate fundamental field-scale scientific hypotheses on physical, hydrologic, chemical, and biologic factors and processes that control uranium concentrations in site pore- and groundwaters under different hydrologic conditions.

Contact: David Lesmes, SC 23.1, (301)-903-5802
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


September 15, 2008

New Modeling Approach Integrates Geochemical Processes into Field-Scale Simulation of Uranium Mobility in Groundwater at the Hanford Site

Uranium is a persistent groundwater contaminant at many DOE sites due to its adsorption onto mineral surfaces and/or precipitation of various uranium minerals within subsurface materials. These molecular-scale processes often exert a profound influence on uranium mobility at the field scale. One challenge in simulating uranium transport in the subsurface is the difficulty in coupling these molecular-scale geochemical processes controlling uranium concentrations with groundwater transport processes that occur at the field-scale. Researchers at PNNL have developed a modeling approach that incorporates these two types of information derived from laboratory and field experiments. The approach couples molecular-scale, laboratory-derived characterization of uranium geochemical properties with field-scale descriptions of transport processes obtained from tracer experiments. The new approach will be tested as part of the DOE-funded Integrated Field-Scale Subsurface Research Challenge (IFC) site at the Hanford 300 Area .

Citation: Liu, C. Zachara, JM, Qafoku, NP, Wang, Z. (2008), Scale-dependent desorption of uranium from contaminated subsurface sediments. Wat. Resour. Res. vol. 44 (W08413), doi:10.1029/2007WR006478.

Contact: Robert T. Anderson, SC 23.1, (301) 903-5549
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


July 21, 2008

LBNL Researchers Win R&D 100 Award for Phylochip Development

Tools for rapid characterization of complex microbial communities are needed to detect and identify microorganisms in a variety of environmental samples. SC researchers at LBNL have developed a microarray technique known as the Phylochip that can detect and identify thousands of different species of microorganisms very rapidly. The Phylochip provides the capability for unprecedented detection and identification in a device about the size of a quarter. The Phylochip was developed by Gary Andersen, Todd DeSantis, Eoin Brodie and Yvette Piceno from LBNLs Earth Sciences Division. The device has been used to identify airborne bacterial species as part of a biodefense project, to assess microbial communities involved in environmental cleanup projects, and will help to advance the understanding of microbial processes involved in biofuel production and carbon sequestration. The prestigious R&D 100 awards are given in recognition of the top 100 significant technological advances over the past year.

Contact: Robert T. Anderson, SC 23.1, (301) 903-5549; Dan Drell, SC 23.2, (301) 903- 4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.2 Medical Sciences Division, OBER)


July 14, 2008

Geochemical Research Sheds Light on Plutonium Mobility in the Environment

There is a concern that the mobility of plutonium (Pu) in the environment at some DOE legacy waste sites may be increased due to the formation of complexes with the metal-complexing compound ethylenediaminetetraacetic acid (EDTA), which was co-disposed with Pu. At issue is whether EDTA enhances the solubility and therefore the mobility of Pu(IV). Researchers at Pacific Northwest National Laboratory examined the mobility of Pu(IV)-EDTA complexes under common environmental conditions and found that they are not as mobile as previously assumed. The complexation of Pu(IV) with EDTA is affected by competitive complexation reactions with other common inorganic species such as Fe, Al, Ca and Mg. EDTA also readily adsorbs to geologic materials and is biodegraded by microorganisms commonly found in the environment. These other competitive reactions ultimately reduce the potential for EDTA to complex and mobilize Pu in the environment suggesting that Pu(IV)-EDTA complexes are not responsible for the observed mobility of Pu in the environment.

Reference: Journal of Solution Chemistry 37 957-986, 2008.

Contact: Robert T. Anderson, SC-23.1, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.1 Life Sciences Division, OBER)


June 16, 2008

Practical Gas Sampling Method Enables Rapid Evaluation of all Major Dissolved Gases in Groundwater

Researchers at the Oak Ridge National Laboratory recently developed a practical method to sample all major dissolved gases present in groundwater without the need for pumping groundwater to the surface or the need for multiple analytical methods to measure gas concentrations. Traditional dissolved gas sampling techniques in the field are labor intensive, time-consuming efforts. This new passive sampling technique requires little sampling effort, allowing researchers to quickly deploy, retrieve, and analyze gas samples from multiple locations. Concentrations of dissolved gases such as oxygen, hydrogen, nitrogen, carbon dioxide, methane, nitrous oxide, and carbon monoxide yield important information on microbial and chemical processes occurring in the subsurface. Microorganisms profoundly affect the transport of contaminants in the subsurface, and these methods can help identify which microbial processes are active in the subsurface. The sampling device is suspended in a well until it equilibrates with ambient conditions, and then it is removed for analysis in the laboratory. The technique is highly sensitive to trace levels of gases and can provide researchers and modelers with information on active microbial processes in the subsurface. Understanding which microbial processes are active at a specific field site will help in refining simulations of contaminant transport, understanding bioremediation, monitoring natural attenuation processes and devising new techniques to intercept and immobilize contaminants.

Reference: Environmental Science & Technology 42(10) 3766-3772, 2008.

Contact: Robert T. Anderson, SC-23.4, (301) 903-5549
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-23.4 Environmental Remediation Sciences Division, OBER)


June 09, 2008

Learning from Biology

Special Issue of Geobiology Bioenergy Outlines the Implications of Understanding Microbial Metabolism for Environmental Applications and Production

Numerous researchers funded by the DOE Office of Science (SC) contributed to a special issue of Geobiology dedicated to the memory of Terry Beveridge, a world-renowned geomicrobiologist and longtime SC grantee. This special issue is a review of the current state-of-the-science in understanding microbe-metal interactions and a fitting tribute to a respected colleague whose scientific breadth spanned this entire area of science. Advances made over the last few years in understanding microbial metabolism at the microbe-mineral interface are detailed in this special issue. Several groups of bacteria are capable of respiring (breathing) solid-phase materials that reside outside the cell. How cells accomplish this feat is a topic under intensive investigation within SC. Microbes with the ability to reduce inorganic materials extracellularly also reduce electrodes in microbial fuel cells, produce soluble organics with electrochemical properties, and influence mineral precipitation in novel ways. These unique traits have implications for understanding the processes that influence contaminant transport, bioenergy production, microbial biofilm formation, intercellular communication, and biomineral production.

Reference: Geobiology 6(3) June 2008.

Contact: Robert T. Anderson, SC-23.4, (301) 903-5549
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-23.4 Environmental Remediation Sciences Division, OBER)


May 26, 2008

Office of Science Research Yields Understanding of Key Function of Uranium-Reducing Microbe

Biophysical research has provided an important clue about how bacteria move within radionuclide-contaminated sites, where they can reduce and immobilize these contaminants. Scientists at Argonne National Laboratory determined the three-dimensional structure of sensory domains of two proteins involved in movement of the bacterium Geobacter sulfurreducens. These domains are involved in chemotaxis, the means by which bacteria sense where to move to find nutrients or to avoid harmful chemicals. Binding of a stimulant molecule to a sensory domain on the outside of the cell transmits a signal to the interior of the cell, initiating the expression of proteins that enable the cell to move in response to the external stimulation. The Geobacter family is of particular interest because it is a major component of the microbial community in many subsurface environments contaminated by uranium. The Office of Science is supporting research into how Geobacter affects fate and transport of uranium in order to understand how this contamination could be remediated. The information obtained about the structure of the signaling domains will help to understand not only how microbes sense and move toward locations with higher uranium concentrations, but more generally respond to a variety of chemical changes in their environment. The Argonne research was led by Dr. Marianne Schiffer of the Biosciences Division and made use of the Structural Biology Center's protein crystallography stations at the Advanced Photon Source. It was published in the April 11, 2008, issue of the Journal of Molecular Biology.

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.2 Medical Sciences Division, OBER)


May 12, 2008

Three Publications in the April Issue of ES&T Highlight Complex Physical, Chemical and Biological Processes that Influence Contaminant Transport

To more accurately predict the mobility of contaminants in the environment and to devise new remediation techniques, DOE site managers need to understand the complex physical, chemical and biological processes that influence the mobility of metal and radionuclide contaminants in the subsurface. Three Office of Science, BER research activities, reported in the April 15, 2008, issue of Environmental Science & Technology ( ES&T), highlight the factors affecting the fate of radionuclide contaminants in subsurface environments. The articles highlight results obtained from three different DOE sites and demonstrate the importance of understanding complex biogeochemical processes influencing the mobility of radionuclide contaminants in the subsurface. In one article, researchers from the Lawrence Berkeley National Laboratory used a variety of synchrotron-based techniques to evaluate the potential of persistent iron (III) oxides present under reducing-conditions in sediment columns to reoxidize uranium to a more mobile phase. In a second article, researchers from the University of Massachusetts and the Pacific Northwest National Laboratory examined the sorption of oxidized uranium on cell surfaces in uranium-contaminated sediments during biostimulation as a contributing mechanism to immobilizing uranium in situ. In a third article, researchers from the Idaho National Laboratory examined a biological mechanism for stimulating calcite precipitation in subsurface sediments as means to facilitate precipitation, and therefore immobilization, of Sr-90 in subsurface environments.

Contact: Robert T. Anderson, SC-23.4, (301) 903-5549
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-23.4 Environmental Remediation Sciences Division, OBER)


March 10, 2008

Article on Bioimmobilization of Uranium in the Oak Ridge Subsurface Identified as Most Cited Article for 2006 in Environmental Science and Technology

From 2003 to 2006, the Environmental Remediation Sciences Program (ERSP) within the Office of Biological and Environmental Research supported a multi-institutional, field-based research project led by Craig Criddle of Stanford University and Philip Jardine of Oak Ridge National Laboratory (ORNL). A 2006 article describing some of those research efforts authored by Weimin Wu of Stanford University and collaborators from ORNL, Miami University of Ohio, Ecovation Inc., and the Swiss Federal Institute of Aquatic Science and Technology, was recently identified as one of the most cited articles for 2006 in Environmental Science and Technology. The research team conducted field investigations to determine the impact of coupled hydro-, bio- and geo-chemical processes on the immobilization of uranium in the subsurface at the Oak Ridge Y-12 site known as the former S-3 Ponds site. As described in their paper, the team demonstrated that a common form of uranium found in the subsurface at the former S-3 Ponds site could be bioreduced to a less mobile form. Since 2006, long-term monitoring results at this field site indicate that very low aqueous-phase concentrations of uranium can be maintained despite high solid-phase uranium concentrations. This study was also highlighted as a feature article in the January 2008 issue of the popular U.S. EPA newsletter Technology News and Trends. The technical insights from these research findings are being considered in future DOE decision making and remediation efforts at the Oak Ridge site.

Contact: Paul Bayer, SC-23.4, (301) 903-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-23.4 Environmental Remediation Sciences Division, OBER)


March 03, 2008

Hanford Tank Farm Cleanup Contractor Highlights Science Support

In a letter dated February 19, 2008, John Fulton, President and CEO of CH2M Hill Hanford Group, the Hanford tank farm cleanup contractor, expresses his companys appreciation for the technical and administrative support provided by staff from the Pacific Northwest National Laboratory (PNNL) to characterize the release of contaminants from Hanfords tank farms. Mr. Fulton included a list of PNNL scientists who contributed to these efforts, many of whom are, or have been funded by the Office of Science, including the Environmental Remediation Science Program (ERSP) within the Office of Biological and Environmental Research (BER). The list includes John Zachara, the 2007 recipient of the E.O. Lawrence Award and technical co-lead for ERSPs Scientific Focus Area program at PNNL. Mr. Fulton states that, The identified PNNL scientists are a credit to your laboratory [PNNL] and demonstrate the ability of your organization [PNNL] to perform strong fundamental science in support of Hanford issue resolution and decision-making

Contact: David Lesmes, SC-23.4, (301) 903-4902
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-23.4 Environmental Remediation Sciences Division, OBER)


February 25, 2008

New Nanoparticle-Based Sorbent Leads to New Approach to Remove Mercury from Solution

A 6-page paper on a new nanoparticle-based sorbent and method to remove mercury and other toxic metals from solution has attracted significant attention by becoming one of the most accessed articles in Environmental Science and Technology in 2007. A team of scientists led by Wassana Yantasee from the Pacific Northwest National Laboratory and collaborators from Chulalongkorn University, Thailand, and the University of Oregon conducted part of their research in the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility located at PNNL. In the paper, Removal of Heavy Metals from Aqueous Systems with Thiol Functionalized Superparamagentic Nanoparticles, the authors describe how they combined superparamagnetic iron oxide nanoparticles with dimercaptosuccinic acid (DMSA) to create rust-colored particles that possess a very large surface area (114 m2/g) that results in a very large number of binding sites for mercury and other metals. A strong magnet (1.2 Tesla) was then used to separate the particles from a variety of solutions including river water, groundwater, seawater, human blood and plasma. The DMSA-modified particles removed 30 times more mercury than conventional resin-based sorbents, and they removed 99 percent of lead from a solution containing one milligram per liter of the metal in about a minute. The teams work appeared in the July 15, 2007, issue of Environmental Science and Technology. Additional details regarding these exciting findings are available at: [website].

Contact: Paul Bayer, SC-23.4, (301) 903-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-23.4 Environmental Remediation Sciences Division, OBER)