BER Research Highlights

Search Date: October 19, 2017

161 Records match the search term(s):


April 13, 2017

Identifying the Important Contributors to Model Variability in a Multiprocess Model

Researchers define a new sensitivity index to quantify the uncertainty contribution from each process under model structural uncertainty.

The Science
Earth system models consist of multiple processes, each of them being a submodel in the integrated system model. A research team, including scientists at Florida State University, Pacific Northwest National Laboratory, and Oak Ridge National Laboratory, derived a new process sensitivity index to rank the importance of each process in a system model with multiple choices of each process model.

The Impact
The new process sensitivity index tackles the model uncertainty in a rigorous mathematical way, which has not been dealt with in conventional sensitivity analyses. Accounting for model structural uncertainty in complex multiphysics, multiprocess models has been a long-recognized need in the modeling community.

Summary
Most of the processes in a multiprocess model could be conceptualized in multiple ways, leading to multiple alternative models of a system. One question often asked is which process contributed to the most variability or uncertainty in the system model outputs. Global sensitivity analysis methods are an important and often used venue for quantifying such contributions and identifying the targets for efficient uncertainty reduction. However, existing methods of global sensitivity analysis only consider variability in the model parameters and are not capable of handling variability that arises from conceptualization of one or more processes. This research developed a new method to isolate the contribution of each process to the overall variability in model outputs by integrating model averaging concepts with a variance-based global sensitivity analysis. The researchers derived a process sensitivity index as a measure of relative process importance, which accounts for variability caused by both process models and their parameters. They demonstrated the new method with a hypothetical groundwater reactive transport modeling case that considers alternative physical heterogeneity and surface recharge submodels. However, the new process sensitivity index is generally applicable to a wide range of problems in hydrologic and biogeochemical problems in Earth system models. This research offers an advanced systematic approach to prioritizing model inspired experiments.

Contacts (BER PM)
David Lesmes
Subsurface Biogeochemical Research Program
David.Lesmes@science.doe.gov (301-903-2977)

Daniel Stover
Terrestrial Ecosystem Science Program
Daniel.Stover@science.doe.gov (301-903-0289)

(PI Contacts)
Ming Ye, Florida State University, mye@fsu.edu
Xingyuan Chen, Pacific Northwest National Laboratory (PNNL), Xingyuan.Chen@pnnl.gov
Anthony P. Walker, Oak Ridge National Laboratory (ORNL), walkerap@ornl.gov

Funding
This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological Research, Early Career Award and PNNL Subsurface Science Research Scientific Focus Area and ORNL Terrestrial Ecosystem Science Scientific Focus Area.

Publication
Dai, H., M. Ye, A. P. Walker, and X. Chen. 2017. “A New Process Sensitivity Index to Identify Important System Processes Under Process Model Uncertainty and Parametric Uncertainty,” Water Resources Research 53(4), 3746-90. [DOI: 10.1002/2016WR019715]. (Reference link)

Topic Areas:

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


January 25, 2017

Building Confidence in Hydrologic Models

Model intercomparison project evaluates performance of seven different integrated hydrology models for solving challenge benchmarks.

The Science 
Understanding water availability and quality for large-scale surface and groundwater systems requires simulation and many numerical models have been developed by scientists to address these needs. A suite of common hydrologic benchmark challenges was developed and seven different modeling teams from the U.S. and Europe exercised their models to achieve the benchmarks to  better understand how each of the models and model outputs agree and differ.

The Impact
Model intercomparison benchmark challenges build confidence in the choice of model used for a specific scientific question or application and they illuminate the implications of model choice because they force modeling teams to better understand the strengths and weaknesses of their own and competing models. This understanding leads to more reliable simulations and improves integrated hydrologic modeling.

Summary
Following up on a first integrated hydrologic model intercomparison project several years ago, seven teams of modelers, including two teams supported by the Interoperable Design for Extreme-scale Application Software (IDEAS) project, participated in a second intercomparison project. Teams met at a workshop in Bonn, Germany, and designed a series of three model intercomparison benchmark challenges. The challenges were designed to focus on different aspects of integrated hydrology, including a hillslope-scale catchment, subsurface structural inclusions and layering, and a field study of hydrology on a small ditch with simple but data-informed topography. Parameters were standardized, but each team used their own model, including differences in model physics, coupling, and algorithms. Results were collected, stimulating detailed conversations to explain similarities and differences across the suite of models. While each of the codes share a common underlying core capability, they are focused on different applications and scales, and have their own strengths and weaknesses. This type of effort leads to improvement in all the codes, and improves the modeling community’s understanding of simulating integrated surface and groundwater systems hydrology.

Contacts
Ethan Coon
Oak Ridge National Laboratory
coonet@ornl.gov

Reed Maxwell
Colorado School of Mines
rmaxwell@mines.edu

Funding
Funding was provided by the DOE Office of Biological and Environmental Research, Subsurface Biogeochemistry Research (SBR) activity to the Interoperable Design for Extreme-scale Application Software (IDEAS) project.

Publications
S. Kollet, M. Sulis, R.M. Maxwell, C. Paniconi, M. Putti, G. Bertoldi, E.T. Coon, E. Cordano, S. Endrizzi, E. Kikinzon, E. Mouche, C. Mugler, Y.-J. Park, J.C. Refsgaard, S. Stisen, and E. Sudicky. “The integrated hydrologic model intercomparison project, IH-MIP2: A second set of benchmark results to diagnose integrated hydrology and feedbacks.” Water Resour. Res., 53, 867-890. (2017). [DOI: 10.1002/2016WR019191.] (Reference link)

Topic Areas:

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


January 25, 2017

Using Microbial Community Gene Expression to Highlight Key Biogeochemical Processes

A study of gene expression in an aquifer reveals unexpectedly diverse microbial metabolism in biogeochemical hot spots.

The Science
Researchers conducted a study of naturally reduced zones (NRZs)—biogeochemical hot spots—in the Rifle, Colo., aquifer, a legacy Department of Energy uranium mill site. They performed a state-of-the-art analysis of gene expression in the aquifer’s microbial communities, elucidating metabolic pathways and organisms underlying observed biogeochemical phases as well as revealing unexpected metabolic activities.

The Impact
NRZs, organic-rich deposits heterogeneously distributed in alluvial aquifers, modulate aquifer redox status and influence the speciation and mobility of metals. Overall, NRZs have an outsized effect on groundwater geochemistry. This study’s results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.

Summary
Organic matter deposits in alluvial aquifers have been shown to result in the formation of NRZs, which can modulate aquifer redox status and influence the speciation and mobility of metals, significantly affecting groundwater geochemistry. In this study, researchers sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (or NRZs) in a shallow alluvial aquifer at the Rifle site. The researchers conducted an anaerobic microcosm experiment in which NRZ sediments served as the sole source of electron donors and microorganisms. Biogeochemical data indicated that native organic matter decomposition occurred in different phases, beginning with the mineralization of dissolved organic matter (DOM) to carbon dioxide (CO2) during the first week of incubation. This was followed by a pulse of acetogenesis that dominated carbon flux after two weeks. DOM depletion over time was strongly correlated with increases in the expression of many genes associated with heterotrophy (e.g., amino acid, fatty acid, and carbohydrate metabolism) belonging to a Hydrogenophaga strain that accounted for a relatively large percentage (roughly 8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO2 fixation, dihydrogen (H2) oxidation, sulfur compound oxidation, and denitrification. The acetogenesis pulse appeared to have been collectively catalyzed by a number of different organisms and metabolisms, most prominently pyruvate:ferredoxin oxidoreductase.  Unexpected genes were identified among the most highly expressed (more than 98th percentile) transcripts, including acetone carboxylase and cell-wall-associated hydrolases with unknown substrates.  Many of the most highly expressed hydrolases belonged to a Ca. Bathyarchaeota strain and may have been associated with recycling of bacterial biomass. Overall, these results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.

Contacts (BER PM)
David Lesmes
SC-23
david.lesmes@science.doe.gov

(PI Contact)
Harry R. Beller
Senior Scientist, Lawrence Berkeley National Laboratory
HRBeller@lbl.gov

Funding
This work was supported as part of the Subsurface Biogeochemical Research Scientific Focus Area funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE-AC02-05CH11231. This work used the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley, supported by the National Institutes of Health S10 instrumentation grants S10RR029668 and S10RR027303.  

Publication
Jewell, T. N. M., U. Karaoz, M. Bill, R. Chakraborty, E. L. Brodie, K. H. Williams, and H. R. Beller. 2017. “Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer,” Frontiers in Microbiology, DOI: 10.3389/fmicb.2017.00040. (Reference link)

Topic Areas:

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


January 24, 2017

Sorption to Organic Matter Controls Uranium Mobility

Organic matter controls uranium mobility.

The Science  
A new multi-technique study using X-ray absorption spectroscopy at the Stanford Synchrotron Radiation Laboratory (SSRL) and Nano-Secondary Ion Mass Spectroscopy (NanoSIMS) at the Environmental Molecular Science Laboratory (EMSL), an Office of Science User Facility, has revealed crisp new details about the mechanisms of uranium binding in sediments. Surfaces of natural organic matter bind uranium more strongly than minerals under field-relevant conditions.

The Impact
Uranium is less stable and more easily remobilized when bound to surfaces of organic matter and mineral as compared to being incorporated with mineral precipitates. This new finding implies that reduced uranium is much more reactive and able to participate in repeated biogeochemical cycling than previously thought to be the case.

Summary
Uranium is an important carbon-neutral energy source and major subsurface contaminant at DOE legacy sites. Anoxic sediments, which are common in alluvial aquifers, are important concentrators of uranium, where it accumulates in the tetravalent state, U(IV). Uranium-laden sediments pose risks as ‘secondary sources’ from which uranium can be re-released to aquifers, prolonging its impact on local water supplies. In spite of its importance, little is known about the speciation of U(IV) in these geochemical environments. Uranium analysis is challenged by its low concentrations and the tremendous chemical and physical complexity of natural sediments. U(IV) binds to both organic matter and minerals, which can be co-associated at the scale of 10s to 100s of nanometers. Because of the multiplicity and similarity of binding sites present in samples, “standby” analytical techniques such as X-ray absorption spectroscopy are challenged to distinguish the molecular structure of U(IV) in these natural sediments. The molecular nature of accumulated U(IV) is however a first-order question, as the susceptibility of uranium to oxidative mobilization is mediated by its structure.  

In an SSRL-based study, Bone et al (2017) overcame these challenges by combining X-ray absorption spectroscopy, NanoSIMS, and STXM measurements to characterize the local structure and nanoscale localization of uranium and the character of organic functional groups. This work showed that complexes of U(IV) adsorb on organic carbon and organic carbon-coated clays in an organic-rich natural substrate under field-relevant conditions. Furthermore, whereas previous research assumed that U(IV) speciation is dictated by the mode of reduction (i.e., whether reduction is mediated by microbes or by inorganic reductants), this work demonstrated that precipitation of U(IV) minerals, such as UO2, can be inhibited simply by decreasing the total concentration of U, while maintaining the same concentration of sorbent. This conclusion is significant because UO2 (uraninite) and other minerals are much more stable and more readily remobilized than surface-complexed forms of U(IV). Thus, the number and type of organic and mineral surface binding sites that are available have a profound influence on U(IV) behavior. Projections of U transport and bioavailability, and thus its threat to human and ecosystem health, must consider U(IV) adsorption to organic matter within the local sediment environment.

Contacts (BER PM)
Roland Hirsch
DOE Office of Biological and Environmental Research, Climate and Environmental Sciences Division
roland.hirsch@science.doe.gov

(PI Contact)
John Bargar
SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Laboratory
Bargar@slac.stanford.edu

Funding
Funding was provided by the DOE Office of Biological and Environmental Research, Subsurface Biogeochemistry Research (SBR) activity to the SLAC Science Focus Area under contract DE-AC02-76SF00515 to SLAC. Use of SSRL is supported by the U.S. DOE, Office of Basic Energy Sciences. A portion of the research was performed using EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research (located at PNNL). Research described in this paper was performed at beamline 10ID-1 the CLS, which is supported by NSERC, CIHR, NRC, WEDC, the University of Saskatchewan, and the Province of Saskatchewan. The authors thank Ann Marshall for assistance in collecting TEM images at the Stanford Nano Shared Facilities.

Publications
Bone SE, Dynes JJ, Cliff J, & Bargar JR “Uranium(IV) adsorption by natural organic matter in sediments.” Proceedings of the National Academy of Sciences of the United States of America 114(4), 711-716. [10.1073/pnas.1611918114] (Reference link)

Topic Areas:

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


December 22, 2016

Metagenomics Leads to New CRISPR-Cas Systems

Researchers discover the first CRISPR-Cas9 system in archaea.

The Science
Using large amounts of metagenomic data generated by the Department of Energy’s Joint Genome Institute (DOE JGI), researchers analyzed 155 million protein coding genes from uncultivated microbial communities. This work led to the discovery of the first CRISPR- (clustered regularly interspaced short palindromic repeats) Cas9 protein in the archaeal domain, as well as two previously unknown simple bacterial CRISPR-Cas systems.

The Impact
Microbes play key roles in the planet’s cycles, and characterizing them helps researchers work toward solutions for energy and environmental challenges. Examining environmental microbial communities has enabled access to an unprecedented diversity of genomes and CRISPR-Cas systems that have many applications, including biological research. The combined computational-experimental approach that was successful in this study can be used to investigate nearly all environments where life exists.

Summary
Microbes heavily influence the planet’s cycles, but only a fraction have been identified. Characterizing the abundant but largely unknown extent of microbial diversity can help researchers develop solutions to energy and environmental challenges. In microbes, CRISPR-Cas systems provide a form of adaptive immunity, and these gene-editing tools are the foundation of versatile technologies revolutionizing research. Thus far, CRISPR-Cas technology has been based only on systems from isolated bacteria. In a study led by longtime DOE JGI collaborator Jill Banfield of the University of California, Berkeley, researchers discovered, for the first time, a CRISPR-Cas9 system in archaea, as well as simple CRISPR-Cas systems in uncultivable bacteria. To identify these new CRISPR-Cas systems, the team harnessed more than a decade’s worth of metagenomic data from samples sequenced and analyzed by DOE JGI, a DOE Office of Science user facility. The CasX and CasY proteins were found in bacteria from groundwater and sediment samples. The archaeal Cas9 was identified in samples taken from the Iron Mountain Superfund site as part of Banfield’s pioneering metagenomics work with DOE JGI. Both CasX and CasY are among some of the most compact systems ever identified. This application of metagenomics validates studies of CRISPR-Cas proteins using living organisms.

Contacts
Daniel Drell, Ph.D.
Program Manager
Biological Systems Science Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
daniel.drell@science.doe.gov

David Lesmes, Ph.D.
Program Manager
Climate and Environmental Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
david.lesmes@science.doe.gov

Jill Banfield
University of California, Berkeley
jbanfield@berkeley.edu

Funding
DOE Office of Science, National Science Foundation, EMBO, German Science Foundation, Paul Allen Institute, and Howard Hughes Medical Institute 

Publication
Burstein, D., et al., “New CRISPR-Cas systems from uncultivated microbes.” Nature (2016). [DOI: 10.1038/nature21059] (Reference link)

Related Links

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER,SC-23.2 Biological Systems Science Division, BER



An artistic representation of the Tree of Life, with the many groups of bacteria and archaea at the upper left and eukaryotes, which include humans, at the lower right. Department of Energy Joint Genome Institute scientists are using gene-editing tools to explore microbial “dark matter.” [Artistic representation of Fig. 1 from Hug et al., “A new view of the tree of life.” Nature Microbiology 1 (2016). DOI: 10.1038/nmicrobiol.2016.48. Courtesy of Jill Banfield, University of California, Berkeley]



December 14, 2016

Clay Minerals and Metal Oxides Can Change How Uranium Travels Through Sediments

The molecular form of reduced uranium in the subsurface is affected by common sediment constituents.

The Science 
Clay minerals are ubiquitous native components of sediments and soils, as well as a material used in the engineered barriers of spent nuclear fuel storage facilities. A recent study examined the molecular form of uranium(IV) in the presence of montmorillonite clays and found that they can inhibit the predicted precipitation of the mineral uraninite.

The Impact
The effect of environmental surfaces on the form of reduced uranium is currently not accounted for in computational models. This study used state-of-the-art spectroscopy techniques to provide the molecular-level information needed for accurate prediction of uranium transport in subsurface environments.

Summary
Uranium mobility in the subsurface depends strongly on its oxidation state, with U(IV) being significantly less soluble than U(VI). However, solubility also depends on the contaminant’s molecular form, which can be affected by adsorption to the surface of minerals, bacterial membranes, and other constituents in the surrounding environment. Researchers examined the ability of montmorillonite clay minerals to adsorb U(IV) resulting from the reduction of U(VI) and compared it to that of iron and titanium oxide surfaces. The valence and molecular structure of U was tracked by synchrotron x-ray absorption spectroscopy. Findings showed that at low clay surface:U ratios, the reduction of U(VI) in the presence of SYn-1 montmorillonite leads to the formation of the mineral uraninite (UO2). However, at high clay surface:U ratios (more typical of environmental conditions), a significant fraction of the resulting U(IV) is present as adsorbed U(IV) ions (up to 50% of total U). The threshold U(IV) surface coverage above which uraninite formation begins was determined to be significantly lower for montmorillonite than for iron or titanium oxides, suggesting that metal oxides may play a more important role than clay minerals in stabilizing the nonuraninite species observed in natural sediments.

Contacts (BER PM)
Dr. Roland F. Hirsch
Program Officer, U.S. DOE Office of Science
roland.hirsch@science.doe.gov; (301) 903-9009

(PI Contact)
Dr. Kenneth M. Kemner
Argonne National Laboratory
kemner@anl.gov; (630) 252-1163

Funding
This research is part of the Subsurface Science Scientific Focus Area at Argonne National Laboratory (ANL), which is supported by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research, Subsurface Biogeochemical Research program. Use of the Electron Microscopy Center at ANL and the Advanced Photon Source is supported by DOE’s Office of Science, Office of Basic Energy Sciences. MRCAT/EnviroCAT operations are supported by DOE and the MRCAT/EnviroCAT member institutions. All work at ANL was under contract DE-AC02-06CH11357.

Publication
M. I. Boyanov, D. E. Latta, M. M. Scherer, E. J. O’Loughlin, and K. M. Kemner, “Surface area effects on the reduction of UVI in the presence of synthetic montmorillonite.” Chemical Geology (2017). [DOI: 10.1016/j.chemgeo.2016.12.016] (Reference link)

Related Links
Subsurface Science Scientific Focus Area at Argonne National Laboratory

Topic Areas:

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



Redox transformations that affect the environmental mobility of metal or radionuclide contaminants typically occur in the presence of mineral or biological surfaces. [Image courtesy of Argonne National Laboratory]



October 25, 2016

Future Climate Warming Induces Emergence of New Hydrologic Regimes of Surface Water Resources in the Conterminous United States

Global warming poses great challenges to the future U.S. surface water supply.

The Science  
Future climate change projections often focus on average trends over time, or zero in on changes in extreme events. When evaluating climate change impacts, however, it is often important to consider additional parameters, such as changes in the seasonality of runoff. This study evaluates whether the overall pattern of surface water supply in a given watershed has shifted significantly away from historical conditions—that is, when it is projected to enter a new “hydrological regime”— using a statistical technique, and finds that more than 40% of the continental United States land area is likely to experience a significant hydrological regime shift by the end of the 21st century.

The Impact
Many human and natural systems have evolved in the context of a relatively stable climate, so it is important to understand when and where climate change could push systems across thresholds that would result in rapid, nonlinear changes. This study assessed changes in the probability distributions of surface water resources in large (HUC-4) sub-basins across the United States under a range of future climate projections. The research found that each 1°C increase in global mean temperature was associated with an 11-17% increase in land area experiencing a new hydrologic regime, which could pose significant challenges to water resource managers. Northern California and the Pacific Northwest are projected to experience these regime shifts by 2030, earlier than other US regions.

Summary
Researchers at the Department of Energy’s Pacific Northwest National Laboratory (PNNL) analyzed runoff projections from the Variable Infiltration Capacity (VIC) hydrological model which was driven by 97 downscaled and bias-corrected Coupled Model Intercomparison Project Phase 5 (CMIP5) climate projections over the conterminous United States (CONUS). A statistical technique based on the two-sample Kolmogorov-Smirnov test was used to determine the year in which the summer and winter surface runoff in each sub-basin shifted to a new regime in each of these projections, compared to the simulated historical hydroclimate from 1970-1999. They found that the overall land area experiencing a significant hydrologic regime shift followed a linear relationship with respect to global mean temperature, with 11-17% more lands experiencing statistically significant changes in winter and summer runoff across all scenarios and models considered. Further decomposition showed that the emergence of new runoff regimes is typically dominated by changes in variability, rather than shifts in average runoff, and that these runoff regime shifts are driven by an increase in the year-to-year variability of precipitation across many future climate scenarios.

Contacts (BER PM)
Robert Vallario
Integrated Assessment Research Program
Bob.Vallario@science.doe.gov

David Lesmes and Paul Bayer
Subsurface Biogeochemical Research
David.Lesmes@science.doe.gov and Paul.Bayer@science.doe.gov

(PI Contacts)
Maoyi Huang
Pacific Northwest National Laboratory
Maoyi.Huang@pnnl.gov

Funding
This study was conducted with support from the US Department of Energy’s Office of Science, Office of Biological and Environmental Research (BER) for the Subsurface Biogeochemical Research (SBR) program through the PNNL SBR SFA, and the BER’s Integrated Assessment Research Program for the Regional Integrated Assessment Modeling project (RIAM).

Publications
Leng, G., et al., “Emergence of new hydrologic regimes of surface water resources in the conterminous United States under future warming,” Environmental Research Letters, 11(11):114003, (2016). DOI:10.1088/1748-9326/11/11/114003 (Reference link)

Topic Areas:

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


October 24, 2016

Metabolic Handoffs Among Microbial Community Members Drive Biogeochemical Cycles

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.

The Science
2,540 genomes that represent the majority of known bacterial phyla and 47 new phylum-level lineages were reconstructed from sediment and groundwater collected from a semi-arid floodplain near Rifle, CO. Analyses showed that inter-organism interactions are required to turn the carbon, sulfur and nitrogen biogeochemical cycles and revealed that complex patterns of community assembly are likely key to ecosystem functioning and resilience.

The Impact
The research almost doubled the number of major bacterial groups and provided detailed information about the ecosystem roles of organisms from these groups. The research dramatically increased understanding of subsurface biology and motivates new approaches to ecosystem modeling. The genomes represent a treasure-trove that will be mined for biotechnology.

Summary
The subterranean world hosts up to one fifth of all biomass, including microbial communities that drive transformations central to Earth’s biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Terabase-scale cultivation-independent metagenomics was applied to aquifer sediments and groundwater and 2,540 high-quality near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla were constructed.  Some of these genomes derive from 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system were used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, it was shown that few organisms within the community conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.

BER PM Contact
David Lesmes, SC-23.1, 301-903-2977

Contact
Susan Hubbard
Lawrence Berkeley National Laboratory
sshubbard@lbl.gov

Funding: This work was supported by Lawrence Berkeley National Laboratory’s Sustainable Systems Scientific Focus Area funded by the US Department of Energy, Office of Science, Office of Biological and Environmental Research.  Terabase-scale sequencing critical for this work was provided by the Joint Genome Institute via Community Science Program allocations.

Publication
K. Anantharaman, C. T. Brown, L. A. Hug, I.Sharon, C. J. Castelle, A. J. Probst, B. C. Thomas, A. Singh, M. J. Wilkins, U. Karaoz, E. L. Brodie, K. H. Williams, S. S. Hubbard, and J. F. Banfield. “Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system”. Nature Communications 7, ncomms13219 (2016). [DOI: 10.1038/ncomms13219]. (Reference link)

Topic Areas:

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



Tree showing all of bacterial diversity that is now represented by genomes, with the major lineages indicated by wedges. Research on the microbiology of the Rifle aquifer has provided new genomic information within previously identified groups (black wedges). In addition, many major bacterial groups were first identified and via study of the Rifle site (red and purple wedges). Red wedges indicate many major lineages that were first identified in the current study. Colored dots indicate the genomically predicted roles of members of these newly defined bacterial lineages in geochemical cycling. Remarkably, few major bacterial lineages have not been genomically sampled at this site (olive green wedges). [Image courtesy of Anantharaman et al. 2016. DOI: 10.1038/ncomms13219. Reprinted under CC by 4.0.]



October 12, 2016

Unraveling the Molecular Complexity of Cellular Machines and Environmental Processes

State-of-the-art mass spectrometer delivers unprecedented capability to users.

The Science
Two recent studies demonstrate the enormous potential for scientists to explore extremely complex molecular mixtures and systems frequently encountered in environmental, biological, atmospheric, and energy research.

The Impact
The Environmental Molecular Sciences Laboratory (EMSL), a Department of Energy Office of Science user facility, has an unprecedented ability to routinely analyze large intact proteins, precisely measure the fine structure of isotopes, and extract more information from complex natural organic matter mixtures. One of the world’s most powerful mass spectrometry instruments, a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T FTICR MS), is now available to the scientific community. Illustrating the power of this new instrument for biogeochemical research, EMSL scientists were able to make over 8,000 molecular formula assignments from dissolved organic matter mixtures using the 21T FTICR MS. In another study, EMSL users rapidly identified and discovered new types of metal-binding molecules known as siderophores, which are produced by bacterial cells.

Summary
As the highest-performance mass spectrometry technique, the FTICR MS has become increasingly valuable in recent years for various research applications. The FTICR MS determines the mass-to-charge ratio of ions by measuring the frequency at which ions rotate in a magnetic field, providing ultra-high resolution and mass measurement accuracy. The 21T FTICR MS, which is one of only two in the world with this high magnetic field strength, went online at EMSL in 2015. In a recent study, a team of EMSL scientists evaluated performance gains produced by this high magnetic field strength. They found this next-generation instrument empowers routine analysis of large intact proteins, precisely measures the fine structure of isotopes, and elicits more information than ever before from complex natural organic matter mixtures. The initial performance characterization of the 21T FTICR MS demonstrates enormous potential for future applications to extremely complex molecular mixtures and systems frequently encountered in environmental, biological, atmospheric, and energy research. Moreover, this unprecedented level of mass resolution and accuracy will help promote widespread use of top-down proteomics—an approach that enables accurate characterization of different protein variants with different biological activity. As a result, this transformative instrument will enable users from around the world to tackle previously intractable questions related to atmospheric, terrestrial, and subsurface processes; microbial communities; biofuel development; and environmental remediation.

BER PM Contact
Paul Bayer, SC-23.1, 301-903-5324

PI Contact
Ljiljana Paša-Tolic
Environmental Molecular Sciences Laboratory
ljiljana.pasatolic@pnnl.gov

Funding
This work was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research, including support of the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility, and the "High Resolution and Mass Accuracy Capability" development project at EMSL.

Publications
J. B. Shaw, T.-Y. Lin, F. E Leach III, A. V. Tolmachev, N. Tolic, E. W. Robinson, D. W. Koppenaal, and L. Paša-Tolic, “21 Tesla Fourier transform ion cyclotron resonance mass spectrometer greatly expands mass spectrometry toolbox.” Journal of the American Society for Mass Spectrometry 27(12), 1929-36 (2016). DOI: 10.1007/s13361-016-1507-9. (Reference link)

L. R. Walker, M. M. Tfaily, J. B. Shaw, N. J. Hess, L. Pasa-Tolic, and D. W. Koppenaal, “Unambiguous identification and discovery of bacterial siderophores by direct injection 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry.” Metallomics (2017). DOI: 10.1039/c6mt00201c. (Reference link)

Related Links
Unraveling Molecular Complexity of Natural Systems
Top-down Proteomics: Onward and Upward

Topic Areas:

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



The 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer will propel the future direction of environmental, biological, atmospheric, and energy research. [Image courtesy Pacific Northwest National Laboratory]



September 01, 2016

Reconciling Observations and Global Models of Terrestrial Water Fluxes

Water table depth and groundwater flow are key to understanding the amount of water that plants transmit to the atmosphere.

The Science
Plants are one of the largest water users on land, and, through transpiration, they move more water into the atmosphere than streams or rivers move across the landscape. Unlike stream flow, which can be easily observed, measuring and simulating the amount of water plants transmit to the atmosphere is a significant challenge. A new modeling study using high-performance computers (HPCs) shows that lateral groundwater flow, not included in previous modeling approaches, may be the missing link to predicting how important plant water use is to the total hydrologic system.

The Impact
The relative importance of plant transpiration remains one of the largest uncertainties in balancing water at continental scales. Improving the large-scale simulation of plant transpiration will enable scientists to better predict hydrologic response and manage water resources, as well as predict and understand how much freshwater is available globally.

Summary
Using integrated hydrologic simulations that couple vegetation and land-energy processes with surface and subsurface hydrology, the researchers studied the relative importance of transpiration as a fraction of all of the water moving from the land surface to the atmosphere (commonly referred to as transpiration partitioning) at the continental scale. They found that both the total flux of water and transpiration partitioning are connected to water table depth. Because of this connection, including groundwater flow in the model increases transpiration partitioning from 47±13% to 62±12%. This finding suggests that groundwater flow, which is generally simplified or excluded from other continental-scale simulations, may provide a missing link to reconciling observations and global models of terrestrial water fluxes.

BER PM Contact
David Lesmes, SC-23.1, 301-903-2977
Paul Bayer, SC-23.1, 301-903-5324

Contact
Reed Maxwell
Colorado School of Mines
Rmaxwell@mines.edu

Laura Condon
Syracuse University
lecondon@syr.edu

Funding
This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research and Office of Advanced Scientific Computing through the Interoperable Design of Extreme-scale Application Software (IDEAS) project. Simulations were made possible through support from Yellowstone at the National Center for Atmospheric Research Computational and Information Systems Laboratory.

Publication
Maxwell, R. M., and L. E. Condon. 2016. “Connections Between Groundwater Flow and Transpiration Partitioning,” Science, DOI: 10.1126/science.aaf7891. (Reference link)

Topic Areas:

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



Modeling Water Movement. This conceptual diagram compares two approaches for modeling water movement above and below the land surface. Traditional land surface models simplify the system by solving it as a set of discrete columns without lateral groundwater flow, while integrated hydrologic models connect three-dimensional flow in the subsurface with processes at the land surface. [Image courtesy Laura Condon, Syracuse University; Mary Michael Forrester and Reed Maxwell, Colorado School of Mines]



Connecting Water, Plant Function, and Scale. A mosaic of plant and water images making up a single leaf overlaid on the continental United States illustrates the connection between water, plant function, and scale. Continental-scale simulations reconcile previous stand and global scale approaches and link lateral groundwater flow to transpiration partitioning. [Image courtesy Mary Michael Forrester, Colorado School of Mines]



August 26, 2016

A Novel Iron-Loving Bacterium from the Deep Subsurface

New research has uncovered the bacterium Orenia metallireducens, a microorganism from 2 km deep underground capable of reducing iron.

The Science                       
A novel microorganism capable of withstanding high temperatures and briny water was isolated from a geological formation located two kilometers deep within the Illinois Basin. This bacterium, dubbed Orenia metallireducens, has many distinctive properties that allow it to reduce iron minerals such as goethite and hematite. These findings expand current knowledge of how bacteria survive in the deep, hostile environments of the terrestrial subsurface and provide further insights into how life might exist on other planetary bodies.

The Impact
The discovery of O. metallireducens expands current knowledge of the metabolic diversity of bacteria that inhabit the subsurface. Previously thought to be largely sterile, researchers now know that microbial life dwells deep within the fractures and pore spaces of rocks that make up Earth’s crust. These bacteria drive many of the biogeochemical cycles that occur within the subsurface, driving the dissolution and precipitation of minerals as well as the breakdown of organic matter. Understanding the microbially driven mechanisms behind these geochemical transformations is essential for parameterizing Earth system models that seek to quantify the flux of carbon between the atmosphere, soil, and subsurface.

Summary
The microbial reduction of ferric iron minerals is widespread in both terrestrial and marine environments and is potentially one of the earliest forms of metabolisms to evolve on Earth. Due to the abundance of ferric minerals in Earth’s crust, Fe(III) reduction is of global environmental significance, particularly in the subsurface where it contributes to water quality, contaminant fate and transport, and the biogeochemical cycling of carbon. Taking groundwater that was sampled from two kilometers deep underground, researchers isolated a novel member of the phylum Firmicutes, named Orenia metallireducens strain Z6. They found O. metallireducens to have numerous unique properties, including the ability to reduce ferric iron minerals across a broad range of temperature, pH, and salinity. O. metallireducens also lacks the c-type cytochromes that are typically present in bacteria capable of reducing ferric iron such as Geobacter and Shewanella species. The researchers also found that O. metallireducens is the only member of the order Halanaerobiales capable of reducing crystalline iron minerals such as goethite and hematite. This study’s results significantly expand the scope of phylogenetic affiliations, metabolic capabilities, and catalytic mechanisms that are known for iron-reducing microorganisms.

Contacts (BER PM)
Dr. Roland F. Hirsch
Program Manager, U.S. Department of Energy Office of Science
roland.hirsch@science.doe.gov; 301-903-9009

(PI Contact)
Dr. Kenneth M. Kemner
Argonne National Laboratory
kemner@anl.gov; 630-252-1163

Funding
This research is part of the Subsurface Science Scientific Focus Area at Argonne National Laboratory (ANL), which is supported by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research, Subsurface Biogeochemical Research program. Use of the Electron Microscopy Center at Argonne and the Advanced Photon Source is supported by DOE’s Office of Science, Office of Basic Energy Sciences. MRCAT/EnviroCAT operations are supported by DOE and the MRCAT/EnviroCAT member institutions. All work at ANL was performed under contract DE-AC02-06CH11357. This work, including the efforts of Y. Dong, R.A. Sanford, R. A. Locke, Jr., and B. W. Fouke, was funded under DE-FC26-05NT42588. Parts of this work, including the efforts of Y. Dong, R. A. Sanford, J. Y. Chang, and B. W. Fouke, was also funded by National Aeronautics and Space Administration (NNA13AA91A).

Publication
Dong, Y., R. A. Sanford, M. I. Boyanov, K. M. Kemner, T. M. Flynn, E. J. O’Loughlin, Y.-J. Chang, R. A. Locke Jr., J. R. Weber, S. M. Egan, R. I. Mackie, I. Cann, and B. W. Fouke. 2016. “Orenia metallireducens sp. nov. strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface,” Applied and Environmental Microbiology 82(21), 6440-453. DOI:10.1128/aem.02382-16. (Reference link)

Related Links
Subsurface Science Scientific Focus Area at Argonne National Laboratory

Topic Areas:

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



Photo Micrograph of Orenia metallireducens Strain Z6. Inset focus shows peritrichous pili produced by the organism. This bacterium was isolated from groundwater sampled from 2 km deep within the Illinois Basin and can reduce crystalline forms of ferric iron such as goethite and hematite. [Image courtesy Yiran Dong, University of Illinois at Urbana-Champaign]



July 28, 2016

Microbial Respiration in Deep Subsurface Contributes Significant Greenhouse Gas Fluxes to Atmosphere

CO2 production from soils between 2 m and 3.5 m in depth contributes ˜17% of total gas fluxes in a semiarid floodplain.

The Science
Most carbon dioxide (CO2) fluxes leaving the soil surface are commonly attributed to root and microbial respiration occurring at shallow depths (< 1 m). Less understood are respiration rates in the deeper subsurface (> 1-m depth), which contains a large inventory of organic carbon and supports an abundance of microorganisms. In this study, vertical profiles of CO2 concentrations in pore gases, measured from the soil surface down to the water table in a semiarid floodplain, were shown to have significant contributions from microbial respiration in the deeper subsurface or vadose zone, well below the rooting depth and above the water table.

The Impact
The deeper vadose zone was shown to contribute a significant amount of CO2 to the total floodplain—approximately 17% of the surface CO2 flux originates from depths between 2 m and 3.5 m. These contributions are not typically accounted for in Earth system models.

Summary
CO2 fluxes from soils are often assumed to originate within shallow soil horizons (< 1-m depth), whereas relatively little is known about respiration rates at greater depths. Scientists compared measured and calculated CO2 fluxes at the Rifle floodplain along the Colorado River, and measured CO2 production rates of floodplain sediments to determine the relative importance of deeper vadose zone respiration. Calculations based on measured CO2 gradients and estimated effective diffusion coefficients yielded fluxes that are generally consistent with measurements obtained at the soil surface (326 g C m-2 yr-1). CO2 production from the 2 to 3.5-m depth interval was calculated to contribute 17% of the total floodplain respiration, with rates that were larger than some parts of the shallower vadose zone and underlying aquifer. Microbial respiration rates determined from laboratory incubation tests of the sediments support this conclusion. The deeper unsaturated zone typically maintains intermediate water and air saturations, lacks extreme temperatures and salinities, and is annually resupplied with organic carbon from snowmelt-driven recharge and by water table decline. This combination of favorable conditions supports deeper unsaturated zone microbial respiration throughout the year.

BER PM Contact
David Lesmes, SC-23.1, 301-903-2977

PI Contact
Susan Hubbard
Lawrence Berkeley National Laboratory
sshubbard@lbl.gov

Funding
This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Subsurface Biogeochemical Research program.

Publication
T. K. Tokunaga, Y. Kim, M. E. Conrad, M. Bill, C. Hobson, K. H. Williams, W. Dong, J. Wan, M. J. Robbins, P. E. Long, B. Faybishenko, J. N. Christensen, and S. S. Hubbard, “Deep vadose zone respiration contributions to carbon dioxide fluxes from a semiarid floodplain,” Vadose Zone Journal 15(7) (2016). [DOI: 10.2136/vzj2016.02.0014]. (Reference link)

Topic Areas:

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



Left: Rifle, Colorado, floodplain vadose zone profile. Middle: Instrumentation for monitoring pore water and gas profiles down to 3.5-m depth. Right: Respiration profiles sustained by organic carbon carried in infiltration water. [Image courtesy Tokunaga, T. K., et al. 2016. Vadose Zone Journal. [DOI: 10.2136/vzj2016.02.0014]



July 27, 2016

Mercury Methylation Genes involved in Additional Microbial Metabolic Pathways

The work supports the hypothesis that the function of HgcA and HgcB is linked to one-carbon metabolism of the acetyl-CoA pathway.

The Science
Comparative proteomics of the global response of Geobacter sulfurreducens PCA following the deletion of mercury methylation genes demonstrates that these genes are involved in other cellular metabolic pathways.

The Impact
This study is the first to compare differences in the proteomes of several strains of G. sulfurreducens PCA, demonstrating that the deletion of the genes for mercury methylation leads to impacts on other key metabolic processes in these strains. This work supports the hypothesis that the function of HgcA and HgcB is linked to one-carbon (C1) metabolism through the folate branch of the acetyl-CoA pathway by providing methyl groups required for mercury methylation.

Summary
In this study, shotgun proteomics was used to compare global proteome profiles between wild-type G. sulfurreducens PCA and two mutant strains in which DhgcAB is deficient in two genes known to be essential for the biosynthesis of methylmercury toxin, and DomcBESTZ is deficient in five outer membrane c-type cytochromes and thus impaired in its ability for dissimilatory metal ion reduction. The team delineated the global response of G. sulfurreducens PCA in both mutants and identified cellular networks and metabolic pathways that were affected by the loss of these genes. Deletion of hgcAB increased the relative abundances of proteins implicated in extracellular electron transfer, including most of the c-type cytochromes, PilA-C and OmpB, whereas deletion of omcBESTZ significantly increased relative abundances of various methyltransferases, suggesting that a loss of dissimilatory reduction capacity results in elevated activity among C1 metabolic pathways. These results support the hypothesis that the function of HgcA and HgcB is linked to C1 metabolism through the folate branch of the acetyl-CoA pathway by providing methyl groups required for mercury methylation.

Contact (BER PM)
Paul Bayer
DOE Office of Biological and Environmental Research
Paul.Bayer@science.doe.gov (301-903-5324)

(PI Contact)
Baohua Gu
Oak Ridge National Laboratory
gub1@ornl.gov (865-574-7286)

Funding
This research was funded by the Office of Biological and Environmental Research within the U.S. Department of Energy’s Office of Science, as part of the Mercury Science Focus Area project at Oak Ridge National Laboratory.

Publication
Qian, C., A. Johs, H. Chen, B. F. Mann, X. Lu, P.E. Abraham, R. L. Hettich, and B. Gu. 2016. “Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in Geobacter sulfurreducens PCA,” Journal of Proteome Research 15(10), 3340-49. DOI: 10.1021/acs.jproteome.6b00263. (Reference link)

Topic Areas:

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


July 15, 2016

Molecular Probes Developed for Mercury Methylating Genes

The new tools will enable researchers to more quickly detect and quantify microbes with these genes in the environment.

The Science
Researchers have developed deoxyribonucleic acid (DNA) and messenger ribonucleic acid (mRNA) probes to not only identify microbes that carry the genes for mercury (Hg) methylation, but also to quantify the extent to which specific types of microbes contribute to the methylation process.

The Impact
The neurotoxin methylmercury (MeHg) poses a serious risk to human health. MeHg production in nature is associated with anaerobic microbes. The development of DNA and mRNA probes represents a substantial improvement over previous work to develop both qualitative and quantitative primers for Hg-methylating genes. These new primers take into consideration the different degrees of methylation potential for specific types of microbes, which ranges from ~10% in the Archaea to ~90% in some Deltaproteobacterial species. These findings will enable a more realistic understanding of possible MeHg generation levels that may occur in a given environment, with the resulting data enabling more accurate risk management assessments.

Summary
Two genes, hgcA and hgcB, are essential for microbial Hg methylation. Detecting and estimating their abundance in microbes in conjunction with quantifying Hg species and other geochemical factors is critical in determining potential hotspots of MeHg generation in at-risk environments. Scientists at Oak Ridge National Laboratory led a team that identified a broad range of degenerate polymerase chain reaction (PCR) primers spanning known hgcAB genes to determine the presence of both genes in diverse environments. These broad-range primers were tested against an extensive set of pure cultures with published genomes that are known to methylate mercury, including 13 Deltaproteobacteria, nine Firmicutes, and nine methanogenic Archaea. For all these types of microbes, the primers not only consistently identified the methylating genes, but they enabled the team to quantify the extent to which each type of microbe methylates Hg. Environmental samples were further used to validate the primers and determine corrective calculations for DNA extraction and PCR amplification efficiencies. Taken together, these findings will enable a more realistic picture of possible MeHg generation levels that may occur in a given environment.

Contact (BER PM)
Paul Bayer
DOE Office of Biological and Environmental Research
Paul.Bayer@science.doe.gov (301-903-5324)

(PI Contact)
Dwayne Elias
Oak Ridge National Laboratory
eliasda@ornl.gov (865-574-0956)

Funding
This research was funded by the Office of Biological and Environmental Research within the U.S. Department of Energy’s Office of Science, as part of the Mercury Science Focus Area project at Oak Ridge National Laboratory.

Publication
G. A. Christensen, A. M. Wymore, A. J. King, M. Podar, R. A. Hurt Jr., E. U. Santillan, A. Soren, C. C. Brandt, S. D. Brown, A. V. Palumbo, J. D. Wall, C. C. Gilmour, and D. A. Elias, “Development and validation of broad-range qualitative and clade-specific quantitative molecular probes for assessing mercury methylation in the environment.” Applied and Environmental Microbiology (2016). DOI:10.1128/ AEM.01271-16. (Reference link)

Topic Areas:

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



New molecular tool probes for genes linked to toxic methylmercury. [Image courtesy Oak Ridge National Laboratory]



June 18, 2016

How Wetlands Naturally Clean Up Contaminants

Highly ordered iron nanoparticles found closely associated with wetland plant roots in the rhizosphere may be key to immobilizing uranium in wetlands.

The Science
Wetland environments are effective at mitigating migration of many groundwater contaminants because of their unique combination of geochemistry, microbiology, and hydrology. A recent study showed iron nanoparticles enriched near wetland plants roots bind natural organic matter to greatly immobilize uranium and possibly other contaminants.

The Impact
This study provides a new perspective on geochemical processes responsible for the observed enrichment of uranium in wetlands. Moreover, the findings shed light on a natural process of environmental remediation that potentially could be harnessed for strategies aimed at immobilizing a wide variety of groundwater contaminants.

Summary
Wetlands inhibit migration of groundwater contaminants through a series of biogeochemical processes that enhance the soil’s capacity to immobilize toxic metals. Past evidence has suggested that the root-impacted soil zone, known as the rhizosphere, might play an important role in contaminant immobilization in wetlands. Plants have adapted to grow in these waterlogged environments by transporting oxygen into the rhizosphere, thereby promoting oxidation of dissolved ferrous iron (Fe(II)) to form ferric iron (Fe(III)) oxyhydroxide and soluble uranium ( precipitates on the root surface, referred to as plaques). A recent study examined whether this type of Fe(II)/Fe(III) cycling in wetlands could participate in immobilizing U(VI)—a highly soluble form of uranium. To explore this possibility, researchers from Savannah River National Laboratory, Environmental Molecular Sciences Laboratory (EMSL), University of Georgia, U.S. Environmental Protection Agency, and Princeton University collected soil samples containing roots from the Tims Branch wetland on the Savannah River Site, a nuclear processing facility in South Carolina. The team characterized subsamples near and far from the roots using wet chemistry and various types of spectroscopy and microscopy. Mössbauer spectroscopy, X-ray computed tomography, transmission electron microscopy, helium ion microscopy, and scanning electron microscopy with energy-dispersive X-ray spectroscopy were conducted at EMSL, a Department of Energy user facility. The analysis revealed wetland rhizosphere soil is enriched in Fe(III) nanoparticles. Moreover, U(VI) is concentrated in root plaques containing Fe(III)-oxyhydroxide precipitates. These results suggest dissolved Fe(II) from the wetland environment enters the rhizosphere and precipitates as Fe(III) nanoparticles capable of binding U(VI). Taken together, the findings suggest plant roots create biogeochemical conditions conducive to the formation of iron nanoparticles, which, in turn, play an important role in uranium enrichment and contaminant immobilization in wetlands.

BER PM Contact
Paul Bayer, SC-23.1, 301-903-5324

PI Contacts
Daniel Kaplan
Savannah River National Laboratory
daniel.kaplan@srnl.doe.gov

Ravi Kukkadapu
Environmental Molecular Sciences Laboratory
Ravi.Kukkadapu@pnnl.gov

Funding
This work was supported by the U.S. Department of Energy (DOE), Office of Science, Offices of Basic Energy Sciences and Biological and Environmental Research, including support of the Environmental Molecular Sciences Laboratory, a DOE Office of Science user facility, and Subsurface Biogeochemical Research program; and Princeton University.

Publication
Kaplan, D. I., R. Kukkadapu, J. C. Seaman, B. W. Arey, A. C. Dohnalkova, S. Buettner, D. Li, T. Varga, K. G. Scheckel, and P. R. Jaffé. 2016. “Iron Mineralogy and Uranium-Binding Environment in the Rhizosphere of a Wetland Soil,” Science of the Total Environment 569-570, 53-64. DOI: 10.1016/j.scitotenv.2016.06.120. (Reference link)

Related Links
EMSL News

Topic Areas:

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


May 11, 2016

Snowmelt-Induced Hydrologic Perturbations Drive Dynamic Biogeochemical Behavior in a Shallow Aquifer

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western United States.

The Science                                              
Researchers used a high-resolution sampling approach to track subsurface biogeochemical shifts during an annual period of water table fluctuation in a riparian aquifer near Rifle, Colorado. This work provided the first description of microbiological and geochemical responses to increased dissolved oxygen concentrations within the aquifer across a six-month period, revealing how local sediment heterogeneity was responsible for dramatically different shifts in both groundwater chemistry and microbial community structures. Simultaneously, the implementation of a computational framework for predicting biogeochemical behavior throughout the site indicated that seasonal “background” subsurface processes and responses could be successfully modeled.

The Impact
This work resulted in a new understanding of how biogeochemical processes in riparian zones may respond to seasonal hydrologic fluctuations linked to snowmelt discharge. While subsurface regions previously were assumed to be relatively stable ecosystems, the new data indicated that dynamic geochemical and microbiological shifts occur on annual cycles, with implications for carbon cycling, metal mobility, and contaminant sequestration. Additionally, the aquifer site near Rifle is a potential template for riparian aquifers throughout the semi-arid inner mountain western United States, allowing these results to be extrapolated across larger scales. The successful implementation of a modeling framework offers one such approach for this up-scaling and will enable a greater understanding of potential shifts in biogeochemical processes under future climate change scenarios.

Summary
Various regions of the aquifer responded differently to the snowmelt-driven hydrologic perturbation based on redox state, with dissolved oxygen penetrating deeply into oxidized regions, and being rapidly consumed via abiotic reactions in naturally reduced regions, liberating Fe2+ and U6+ species. Microbial community composition varied across spatial and temporal scales. During periods of elevated river stage associated with increasing dissolved oxygen concentrations in the aquifer, microbial community composition favored putative chemolithoautotrophs and heterotrophs, while putative fermenters within the candidate phyla radiation (CPR) were greatly enriched (e.g., members of the Microgenomates and Parcubacteria) during water table fall. Reactive transport modeling was able to capture the dynamic behavior of both the geochemistry and microbiology at the site during the fluctuating hydrology, suggesting that a predictive framework can be developed to better understand biogeochemical responses to future hydrologic dynamics.

Contacts
(BER PM)
David Lesmes, SC-23.1, 301-903-2977
Paul Bayer, SC-23.1, 301-903-5324

(PI Contact)
Michael J. Wilkins
The Ohio State University
wilkins.231@osu.edu

Funding
This work was supported as part of the Genomes to Watershed Scientific Focus Area at Lawrence Berkeley National Laboratory, which is funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DEAC02-05CH11231.

Publications
Danczak, R. E., S. B. Yabusaki, K. H. Williams, Y. Fang, C. Hobson, and M. J. Wilkins. 2016. “Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors Across a Shallow Riparian Aquifer,” Frontiers in Earth Science 4(57). DOI: 10.3389/feart.2016.00057. (Reference link).

Topic Areas:

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


April 11, 2016

A New View of the Tree of Life

Access to a wealth of environments and the ability to reconstruct genomes for previously unknown and uncultured lineages has greatly expanded understanding of the diversity of life on earth.

The Science
A comprehensive three domain tree of life was constructed from all lineages for which sequenced genomes are available. The tree highlights the diversity contained in candidate phyla: lineages with no cultivated representatives for which genome sequences are derived from environmental surveys.

The Impact
The tree of life is one of the most important organizing principles in biology. The new depiction will be useful not only to biologists who study microbial ecology, but also to biochemists searching for novel genes and researchers studying evolution and earth history. This updated view highlights the weight of diversity found within the bacteria and within lineages with no cultured representatives.

Summary
This tree presents a new view of the diversity of life from a genome perspective. Exploration of new environments and deeper sequencing of well-studied systems continue to uncover new organisms and lineages on the tree. To construct a comprehensive tree of life, researchers gathered 3,085 genomes representing all genera for which genomes are available and including over 1,000 newly reconstructed genomes targeting candidate phyla representatives. Sample sites for new genomes included extreme environments like Chile’s Atacama Desert salt flats and Yellowstone National Park hot springs, but also more common environments such as groundwater, estuarine sediment, meadow soil, and dolphin oral microbiomes. The tree inferred from this genomic perspective shows the predominance of bacterial diversity compared to the divergence seen in the Archaea and Eukarya.  Collapsing the tree based on sequence divergence rather than taxonomy highlighted the amount of diversity found within candidate phyla, emphasizing the importance of environmental surveys for discovery of organisms not tractable in laboratory experiments.

Contacts (BER PM)
Todd Anderson
Todd.Anderson@science.doe.gov

David Lesmes
David.Lesmes@science.doi.gov

(PI Contact)
Jillian Banfield
University of California Berkeley
jbanfield@berkeley.edu

Funding
This research was largely supported by Lawrence Berkeley National Laboratory’s (LBNL) Genomes to Watershed Scientific Focus Area funded by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research (BER) under contract DE-AC02-05CH11231. Additional support was provided by LBNL EFRC award DE-AC02-05CH11231; National Aeronautics and Space Administration NESSF grant 12 PLANET12R-0025 and National Science Foundation DEB grant 1406956; DOE BER grant DOE-SC10010566; Office of Naval Research grants N00014-07-1-0287, N00014-10-1-0233, and N00014-11-1-0918; and the Thomas C. and Joan M. Merigan Endowment at Stanford University. In addition, funding was provided by the Ministry of Economy, Trade, and Industry of Japan, and metagenome sequence was generated by DOE’s Joint Genome Institute via the Community Science Program.

Publication
Hug, L. A., B. J. Baker, K. Anantharaman, C. T. Brown, A. J. Probst, C. J. Castelle, C. N. Butterfield, A. W. Hernsdorf, Y. Amano, K. Ise, Y. Suzuki, N. Dudek, D. A. Relman, K. M. Finstad, R. Amundson, B. C. Thomas, and J. F. Banfield. 2016. “A New View of the Tree of Life,” Nature Microbiology 1(16048), DOI: 10.1038/nmicrobiol.2016.48. (Reference link)

Topic Areas:

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


April 01, 2016

Managing Complexity in Simulations of Land-Surface and Near-Surface Processes

New multiphysics software framework facilitates more realistic, process-based simulations of environmental systems.

The Science  
A new approach has been developed and demonstrated for managing the rapidly increasing complexity of simulations of environmental systems in the critical zone near the land surface. The multiphysics Arcos framework combines modern software design principles in a novel way to create flexibly configured simulators, thus enabling significantly more complex and realistic simulations that combine many individual ecohydrological and biogeochemical processes.

The Impact
As simulations of environmental systems grow in complexity by incorporating more and more ecohydrological and biogeochemical process representations, adding new process understanding while ensuring that individual and coupled-process simulations are reliable has become increasingly difficult. A new multiphysics framework helps tame this runaway complexity, making process-rich simulations easier to develop, test, combine with data, and reconfigure for different numerical experiments. This approach to developing models provides a more natural way for scientists to collaborate on increasingly complex models and helps build confidence in the resulting simulations.

Summary
The Arcos system is based on two graph representations that interact to provide a flexible and extensible framework. The first graph is a process tree representation that defines the coupling among various environmental process representations denoted as process kernels (PKs). Two or more PKs are coupled together through multiprocess coordinators. The second graph defines how the mass and energy balances depend on primary variables (unknowns to be solved for) through a series of intermediate variables. Formal representation of these dependencies in a graph structure makes it easier to substitute new constitutive models and ensures that intermediate variables are always current and consistent among different PKs. Taken together, these two graphs make it possible to define which PKs are to be used and how they are to be coupled at run time. Such a flexibly configured and hierarchical structure is critical to systematically building up complexity supported by rigorous testing and evaluation against observations.

Contacts (BER PM)
David Lesmes and Paul Bayer
SC-23.1
David.Lesmes@science.doe.gov, 301-903-0289; and Paul.Bayer@science.doe.gov, 301-903-1678

(PI Contact)
Ethan T. Coon
Los Alamos National Laboratory
ecoon@lanl.gov; 505-665-8289

Funding
This research was supported by the Interoperable Design of Extreme-scale Application Software (IDEAS) project funded by the U.S. Department of Energy, Office of Science. This work was also supported by Los Alamos National Laboratory’s Laboratory Directed Research and Development Predicting Climate Impacts and Feedbacks in the Terrestrial Arctic project (LDRD201200068DR).

Publication
Coon, E. T., J. D. Moulton, and S. L. Painter. 2016. “Managing Complexity in Simulations of Land Surface and Near-Surface Processes,” Environmental Modelling and Software 78(C), 134-49. DOI: 10.1016/j.envsoft.2015.12.017. (Reference link)

Topic Areas:

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


March 31, 2016

Mercury and Methylmercury Dynamics in an Industrially Contaminated Stream

Algal biofilms found to be major generators of toxic methylmercury in streams.

The Science
Detailed monitoring of changing mercury (Hg) and methylmercury (MeHg) concentrations in a creek during baseflow and flood events indicates that MeHg is produced within the stream and further suggests that algal biofilms, also called periphyton, are major sources of MeHg production.

The Impact
These findings may explain why past improvements in overall stream water quality have not resulted in concomitant improvements in MeHg concentrations in water and in fish. Additionally, future alterations to stream management practices or climate that alter periphyton abundance, activity, or composition may have unintended negative consequences that could influence MeHg production within the creek.

Summary
Sediments and floodplain soils in the East Fork Poplar Creek (EFPC) watershed in Oak Ridge, Tennessee, are contaminated with high levels of Hg from an industrial source at the headwaters. While baseflow conditions have been monitored, concentrations of Hg and MeHg during high-flow storm events (when the stream is more hydrologically connected to the floodplain) had not yet been assessed. This study evaluates EFPC baseflow and event-driven Hg and MeHg dynamics 5 km upstream of the confluence with Poplar Creek to determine the importance of hydrology to instream concentrations and downstream loads, and to ascertain if dynamics are comparable to systems without an industrial Hg source. Particulate Hg (HgP) and MeHg were positively correlated with discharge (r2=0.64 and 0.58, respectively) and total suspended sediment (r2=0.97 and 0.89, respectively). Dissolved Hg (HgD) also increased with increasing flow (r2=0.18) and was associated with increases in dissolved organic carbon (DOC; r2=0.65) similar to dynamics observed in uncontaminated systems. Dissolved MeHg (MeHgD) decreased with increases in discharge (r2=0.23) and was not related to DOC concentrations (p=0.56), dynamics comparable to relatively uncontaminated watersheds with a small percentage of wetlands (<10%). While stormflows exert a dominant control on HgP, MeHgP, and HgD concentrations and loads, baseflows were associated with the highest MeHgD concentration (0.38 ng/L) and represented the majority of the annual MeHgD load.

BER PM Contact
Paul Bayer, SC-23.1, 301-903-5324

PI Contact
Scott C. Brooks
Oak Ridge National Laboratory
brookssc@ornl.gov

Funding
This work was supported by the U.S. Department of Energy’s (DOE) Subsurface Biogeochemical Research program within DOE’s Office of Science Office of Biological and Environmental Research. The isotope(s) used in this research were supplied by DOE’s Isotope Program within DOE’s Office of Science Office of Nuclear Physics.

Publication
Riscassi, A., C. Miller, and S. Brooks. “Seasonal and flow-driven dynamics of particulate and dissolved mercury and methylmercury in a stream impacted by an industrial mercury source.” Environ. Toxicol. Chem. (2015). [DOI:10.1002/etc.3310]. (Reference link)

Topic Areas:

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



Dissolved mercury increases during high flow events in streams. [Image courtesy Oak Ridge National Laboratory]



February 02, 2016

Metal Monouranates Found to be Highly Stable

A less common form of uranium may hold the key to remediation efforts.

The Science
A recent study examined in unprecedented detail the structural and thermodynamic properties of uranium (U(V))-containing compounds called metal monouranates. Metal monouranates are of considerable interest because of their relevance to nuclear technology.

The Impact
The new findings on this understudied form of uranium help complete the picture of uranium solid-state chemistry and could improve models of and strategies for minimizing the environmental impact of uranium contamination.

Summary
Uranium poses a serious risk to groundwater contamination at the Department of Energy’s (DOE) Hanford Site and other locations worldwide. Its chemistry is complex because uranium can exist in several different oxidation states, each having different properties. Remediation strategies have focused on developing approaches for converting the highly soluble U(VI) form of uranium into the less soluble U(IV) form, which poses less risk of contamination due to its lower mobility in groundwater and soil. While much research has focused on these two forms of uranium, remediation efforts have been limited by the lack of knowledge about the intermediate U(V) form. To address this question, a team of researchers recently examined in unprecedented detail the structural and thermodynamic properties of U(V)-containing compounds called metal monouranates. U(V)-containing monouranates allow in-depth structural and stability investigations. The research team used a variety of advanced structural and spectroscopic techniques combined with calorimetric measurements and computational modeling. Mossbauer and X-ray photoelectron spectroscopy (XPS) analyses were performed at the RadEMSL radiochemistry facility at the Environmental Molecular Sciences Laboratory (EMSL), a DOE national scientific user facility. This project received major support from the DOE Energy Frontier Research Center, “Materials Science of Actinides.” It was led by the University of California, Davis, and included participation by a team of scientists from Pacific Northwest National Laboratory; Los Alamos National Laboratory; Argonne National Laboratory; and Lawrence Berkeley National Laboratory; as well as the Nuclear Energy Center of the Negev, Israel; University of California, Berkeley; University of Michigan; and University of Chicago. The research team confirmed the presence of U(V) in the thermodynamically stable metal monouranates CrUO4 and FeUO4. The structural and thermodynamic behavior of U5+ elucidated in this work is relevant to applications in the nuclear industry and radioactive waste disposal. For example, the thermodynamic studies suggest these compounds are highly stable, making them potentially useful in precipitating uranium from oxidizing aqueous environments.

BER PM Contact
Paul Bayer, SC-23.1, 301-903-5324

PI Contact
Alexandra Navrotsky
University of California, Davis
anavrotsky@ucdavis.edu

Funding
This work was supported by DOE’s Office of Science, Office of Biological and Environmental Research, including support of EMSL, a DOE Office of Science user facility. Major funding was provided by the DOE Energy Frontier Research Center, Materials Science of Actinides, under DOE’s Office of Basic Energy Sciences. This work also was supported by the National Science Foundation, DOE GeoSciences program, and the Laboratory-Directed Research and Development Program at Los Alamos National Laboratory.

Publication
Guo, X., et al. “U(V) in metal urinates: a combined experimental and theoretical study of MgUO4, CrUO4 and FeUO4.” Dalton Trans. 45, 4622–32 (2016). [DOI: 10.1039/c6dt00066e]. (Reference link)

Related Links
EMSL website

Topic Areas:

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


November 25, 2015

Uranium Accumulated in Anoxic Sediments Threatens Groundwater Quality at Contaminated Department of Energy Sites

Anoxic, organic-rich sediments in the subsurface retain enough uranium to sustain a groundwater plume for centuries.

The Science  
Sediment cores sampled at “high resolution” for the first time (~10-cm depth intervals) from wells on a uranium contaminated floodplain near Rifle, Colorado, revealed that uranium has accumulated exclusively within organic-enriched sulfidic sediments. Molecular investigations of uranium and sulfur at this Department of Energy site indicated that uranium was present in a non-crystalline reduced (tetravalent) form and that even the interior parts of these sediment bodies are oxidized on an annual basis.

The Impact
Release of uranium from anoxic, organic-enriched sediment bodies, defined through these detailed, centimeter-scaled investigations, could sustain a contaminant groundwater plume for centuries. Similar types of sulfidic, organic-enriched sediment bodies exist in other uranium contaminated aquifers in the upper Colorado River Basin, meaning that these findings could offer regionally important explanations to uranium behavior. These new results highlight the need for better understanding of the vulnerability of anoxic, organic-rich sediments in this region to climate perturbations.

Summary
Uranium mobility is regulated by its chemical state; the reduced form, U(IV), is much less soluble than the oxidized U(VI). Consequently, oxidation of anoxic sediments could allow uranium to enter the aquifer at the Rifle site with a long-term impact on groundwater quality. The co-occurrence of uranium, sulfur, and organic carbon in the Rifle subsurface suggests that sulfate reduction coupled to microbial carbon oxidation is an important regulator of uranium retention in this floodplain. Sulfur was only found to accumulate in groundwater saturated fine-grained materials with an elevated organic carbon content, supporting the conclusion that reducing conditions, induced by the low permeability and microbial oxygen consumption, promote sulfide formation and uranium retention. The co-existence of multiple sulfur species (sulfate, elemental sulfur, mackinawite, greigite, and pyrite) throughout the reduced zone, suggests redox cycling of these materials, which implies oxidative release of uranium occurs. Uranium was found to be associated with both organic carbon and sulfur, respectively. Therefore, the study concluded that uranium reduction and retention in these sediments resulted from abiotic reduction by iron sulfides, potentially enhanced by organic matter shuttling electrons, as well as via biotic reduction through respiratory and enzymatic activity coupled to organic matter decomposition.

Contacts (BER PM)
Roland F. Hirsch, SC-23.2, roland.hirsch@science.doe.gov, 301-903-9009

(PI Contact)
John Bargar
Stanford Synchrotron Radiation Lightsource
SLAC National Accelerator Laboratory
bargar@slac.stanford.edu

Funding
This work was supported as part of the SLAC Scientific Focus Area (SFA), which is funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Subsurface Biogeochemical Research (SBR) program under subcontract DE-AC02-76SF00515. Logistical support was provided by the Rifle field research program of the Lawrence Berkeley National Laboratory, through SBR funding to the Sustainable Systems SFA under contract DE-AC02-05CH11231. Portions of the work were performed at the Stanford Synchrotron Radiation Lightsource at the SLAC National Accelerator Laboratory.

Publication
Janot, N.,et al. 2016. “Physico-Chemical Heterogeneity of Organic-Rich Sediments in the Rifle Aquifer, CO: Impact on Uranium Biogeochemistry,” Environmental Science and Technology 50(1), 46-53. DOI: 10.1021/acs.est.5b03208. (Reference link)

Topic Areas:

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


November 17, 2015

Calcium and Phosphate Can Affect How Uranium Contamination Travels Through the Environment

The molecular form and the oxidation of subsurface uranium are affected by common groundwater constituents.

The Science  
Calcium and phosphate are environmental components found in animal bone, various minerals, and groundwater. A recent study has demonstrated that these ions slow down the oxidation of subsurface-relevant uranium species and change the oxidized form of uranium into a more stable mineral.

The Impact
The effect of environmental factors like calcium and phosphate on transformations of some newly discovered forms of uranium found in groundwater are currently unknown. This study determined uranium valence and molecular structure using state-of-the-art spectroscopy techniques to provide information necessary for accurately predicting uranium transport.

Summary
The mobility of uranium in subsurface environments depends strongly on its oxidation state, with chemically reduced UIV phases being significantly less soluble than UIV minerals. A team of scientists from Argonne National Laboratory, Illinois Institute of Technology, and Bulgarian Academy of Sciences compared the oxidation kinetics and mechanisms of two potential products of UIV reduction in natural systems: a nanoparticulate UO2 phase and an amorphous UIV-Ca-PO4 phase. The valence and molecular structure of uranium was tracked by synchrotron x-ray absorption spectroscopy. Similar oxidation rates for the two phases were observed in solutions equilibrated with atmospheric O2 and CO2. Addition of up to 400 µM Ca and PO4 decreased the oxidation rate by an order of magnitude for both UO2 and UIV-phosphate. In the absence of Ca or PO4, the product of UO2 oxidation was Na-uranyl oxyhydroxide, whereas the product of UIV-Ca-PO4 oxidation was a UIV-phosphate phase (autunite). In the presence of Ca or PO4, the oxidation proceeded to UIV-phosphate for both pre-oxidation forms of UIV. Addition of Ca or PO4 changed the mechanism of oxidation by causing the formation of a passivation layer on the particle surfaces.

Contacts (BER PM)
Roland F. Hirsch, roland.hirsch@science.doe.gov, 301-903-9009

(PI Contact)
Kenneth M. Kemner
Argonne National Laboratory
kemner@anl.gov, 630-252-1163

Funding
This research is part of the Subsurface Science Scientific Focus Area at Argonne National Laboratory (ANL), which is supported by the U.S. Department of Energy’s (DOE) Subsurface Biogeochemical Research Program, Office of Biological and Environmental Research, Office of Science. Use of the Electron Microscopy Center and Advanced Photon Source at ANL is supported by DOE’s Office of Science, Office of Basic Energy Sciences. MRCAT/EnviroCAT operations are supported by DOE and the MRCAT/EnviroCAT member institutions. All work at ANL was under Contract DE-AC02-06CH11357.

Publications
Latta, D. E., K. M. Kemner, B. Mishra, and M. I. Boyanov. 2016. “Effects of Calcium and Phosphate on Uranium(IV) Oxidation: Comparison Between Nanoparticulate Uraninite and Amorphous UIV–Phosphate,” Geochimica et Cosmochimica Acta 174, 122–42. DOI: 10.1016/j.gca.2015.11.010. (Reference link)  

Related Links
Subsurface Science Scientific Focus Area at Argonne National Laboratory.

Topic Areas:

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


October 09, 2015

Global Prevalence and Distribution of Genes and Microbes involved in Mercury Methylation

It is well known that the methylation of mercury (Hg) is mediated by bacteria and produces neurotoxic methylmercury (MeHg), which is also highly bioaccumulative in living organisms. However, the specific environments or locations in which MeHg is created are not well understood or identified. The recent finding of the specific genes (hgcAB) involved in Hg methylation provides a potential tool for scientists to identify the specific environments or locations where MeHg is created. Because the hgcAB genes are highly conserved, a team of scientists from Oak Ridge National Laboratory, Smithsonian Environmental Research Center, and Texas A&M University realized that they had a foundation for broadly evaluating spatial and niche-specific patterns of microbial Hg-methylation potential in natural environments. The team primarily used assembled and annotated data publicly available from the Department of Energy’s Joint Genome Institute to query hgcAB diversity and distribution in >3,500 publically available microbial metagenomes, encompassing a broad range of global environments. The hgcAB genes were found in nearly all anaerobic, but not aerobic, environments including oxygenated layers of the open ocean. Critically, hgcAB was effectively absent in ~1500 human and mammalian microbiomes, suggesting a low risk of endogenous MeHg production. New potential methylation habitats were identified, including invertebrate digestive tracts, thawing permafrost, coastal “dead zones,” soils, sediments, and extreme environments, suggesting multiple routes for MeHg entry into food webs. Several new taxonomic groups capable of Hg methylation emerged, including lineages having no cultured representatives. Phylogenetic analysis points to an evolutionary relationship between hgcA and genes encoding the corrinoid iron-sulfur proteins functioning in the ancient Wood-Ljungdahl carbon fixation pathway, suggesting that methanogenic archaea may have been the first to perform these biotransformations.

References: Podar, M., C. C. Gilmour, C. C. Brandt, A. Soren, S. D. Brown, B. R. Crable, A. V. Palumbo, A. C. Somenahally, and D. A. Elias. 2015. “Global Prevalence and Distribution of Genes and Microorganisms involved in Mercury-Methylation,” Science Advances 1(9), e1500675.  DOI: 10.1126/sciadv.1500675. (Reference link)
See also ORNL News Release.

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

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


October 08, 2015

Detecting Technetium in Groundwater

Novel approach uses salt-based sensor.

The Science
Technetium-99 (99Tc) is a long-lived radionuclide byproduct of the nuclear fuel cycle, making it a major risk driver at former nuclear weapons production sites that requires onsite monitoring. A novel approach has been demonstrated that uses highly selective and sensitive platinum salt to detect and quantify the highly soluble pertechnetate (TcO4-) anion in groundwater.

The Impact
The new anion recognition approach has potential for the development of a field-deployable and highly accurate sensor for monitoring TcO4- in groundwater, river water, and watersheds. This work could have a broad impact on remediation efforts, paving the way for the development of similar salts for detection of other important environmental contaminants.

Summary
When exposed to moderately oxidizing conditions, 99Tc is readily converted to pertechnetate (TcO4-), a highly soluble anion that can migrate into groundwater and the environment. Existing methods for onsite monitoring of TcO4- in groundwater require a complicated series of analytical steps due to the low selectivity and sensitivity of Tc. A team of scientists from Pacific Northwest National Laboratory (PNNL), Environmental Molecular Sciences Laboratory [EMSL; a U.S. Department of Energy (DOE) user facility], University of Cincinnati, and Florida State University searched for a suitable material for sensing TcO4- in water. The team evaluated simple salts of transition metal complexes that change in color and luminescence properties upon exposure to the Tc anion using the SPEX Fluorolog 2 fluorimeter at EMSL. They found one specific platinum salt that undergoes a dramatic color and brightness change upon exposure to TcO4-; the salt was highly sensitive and enables detection of TcO4- at levels well below the drinking water standard established by the U.S. Environmental Protection Agency. Modeling and simulation work using EMSL’s Cascade supercomputer enabled the team to determine that the high selectivity was due to the unique electronic structure of the platinum salt. Unlike currently available methods for TcO4- sensing, the new approach does not require separation, concentration, or other pretreatment steps. Thus, the rapid, sensitive, and accurate TcO4- sensing system is ideal for real-time deployment at contaminated sites. Future implementation of this type of ion recognition system has great potential for remediation efforts and could be essential in addressing a broad range of environmental and health concerns.

BER PM Contact:
Paul Bayer, SC-23.1, 301-903-5324

PI Contacts:
Sayandev Chatterjee
PNNL
sayandev.chatterjee@pnnl.gov

Tatiana Levitskaia
PNNL
tatiana.levistkaia@pnnl.gov

Funding
This work was supported by DOE’s Office of Science, Office of Biological and Environmental Research and Office of Basic Energy Sciences, including support of EMSL; PNNL’s Laboratory-Directed Research and Development Program; National Science Foundation; and Office of Environmental Management Sciences Program.

Publications
Chatterjee, S., A. E. Norton, M. K. Edwards, J. M. Peterson, S. D. Taylor, S. A. Bryan, A. Andersen, N. Govind, T. E. Albrecht-Schmitt, W. B. Connick, and T. G. Levitskaia. 2015. “Highly Selective Colorimetric and Luminescence Response of a Square-Planar Platinum(II) Terpyridyl Complex to Aqueous TcO4–,” Inorganic Chemistry 54(20), 9914–23. DOI:   10.1021/acs.inorgchem.5b01664. (Reference link)

Related Links
EMSL article

Topic Areas:

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


October 02, 2015

Potential for Reoxidation of Iron-Chromium Precipitates by Manganese Oxide

Reductive immobilization of hexavalent chromium (Cr(VI)), often forming Fe-Cr precipitates, is a frequent remediation alternative, yet the relationship between the conditions of precipitate formation, the structural and chemical properties of the precipitates, and the rate and extent of precipitate oxidation by Mn oxides is needed. This study provided a systematic investigation of the rates of Cr(VI) reduction by both abiotic minerals and a chromium reducing bacterium, the properties of the resulting Fe-Cr precipitates, and the susceptibility for reoxidation and remobilization of Cr(VI) upon precipitate exposure to the manganese oxide birnessite.

The properties of the resulting Fe-Cr solids and their behavior upon exposure to birnessite differed significantly. In microcosms where Cr(VI) was reduced by Desulfovibrio vulgaris strain RCH1, and where hematite or Al-goethite were present as iron sources, there was significant initial loss of Cr(VI) in a pattern consistent with adsorption, and significant Cr(VI) was found in the resulting solids. The solid formed when Cr(VI) was reduced by FeS contained a high proportion of Cr(III) and was poorly crystalline. Reaction between birnessite and the abiotically formed Cr(III) solids led to production of significant dissolved Cr(VI) compared to the no-birnessite controls. This pattern was not observed in the solids generated by microbial Cr(VI) reduction, and could be due to re-reduction of any Cr(VI) generated upon oxidation by birnessite via active bacteria or microbial enzymes.

The results of this study suggest that Fe-Cr precipitates formed in groundwater remediation may remain stable only in the presence of active anaerobic microbial reduction. If exposed to environmentally common Mn oxides such as birnessite in the absence of microbial activity, there is the potential for rapid (re)formation of dissolved Cr(VI) above regulatory levels.

Citation:
Butler, E. C., Chen, L., Hansel, C. M., Krumholz, L. R., Elwood Madden, A. S., Lan, Y. (2015), Biological versus mineralogical chromium reduction: Potential for reoxidation by manganese oxide, Environ. Sci.: Processes Impacts 17, 1930-1940, DOI: 10.1039/C5EM00286A.

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

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



Abiotic reduction of Cr(VI) by FeS and reduced nontronite led to precipitates that released significant Cr(VI) when exposed to birnessite. Figure reproduced from Environ. Sci.: Processes Impacts 17 (2016), 1930–1940 (DOI: 10.1039/C5EM00286A) with permission from the Royal Society of Chemistry.



September 27, 2015

Colloid Deposit Morphology Controls Permeability in Porous Media

Processes occurring in soils and aquifers play a crucial role in contaminant remediation and carbon cycling. The flow of water through porous media like soils and aquifers is essential for contaminant remediation and carbon cycling and depends on the permeability, which determines how much water flows for a given hydraulic driving force. Widely recognized is that colloids (fine particles including soils, chemical precipitates, and bacteria) often control permeability and that colloid deposit morphology (the structure of deposited colloids) is a fundamental aspect of permeability. Until recently, however, no experimental techniques were available to measure colloid deposit morphology within porous media. A recent study, led by the University of Colorado Denver in collaboration with Lawrence Berkeley National Laboratory, used a custom-designed experimental apparatus to perform a series of experiments using static light scattering (SLS) to characterize colloid deposit morphology within refractive index matched (RIM) porous media during flow through a column. Real-time measurements of permeability, specific deposit, and deposit morphology were conducted with initially clean porous media at various ionic strengths and water velocities. Decreased permeability (i.e., increased clogging) correlated with colloid deposit morphology, specifically with lower fractal dimension and smaller radius of gyration. These observations suggest a deposition scenario in which large and uniform aggregates become deposits, reducing porosity, and lead to higher fluid shear forces, which then decompose the deposits, filling the pore space with small and dendritic fragments of aggregate. Accordingly, for the first time, observations are available to quantify the relationship between the macroscopic variables of ionic strength and water velocity and the pore-scale variables of colloid deposit morphology, which can be conceptualized as an emergent property of the system. This research paves the way for future studies to quantify the complex feedback process between flow, chemistry, and biology in soils and aquifers.

Reference: Roth, E. J., B. Gilbert, and D. C. Mays. 2015. “Colloid Deposit Morphology and Clogging in Porous Media: Fundamental Insights Through Investigation of Deposit Fractal Dimension,” Environmental Science and Technology 49(20), 12263–70. DOI: 10.1021/acs.est.5b03212. (Reference link)

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

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



Permeability, which is crucial in groundwater remediation, depends on colloidal deposit morphology. A novel application of static light scattering has enabled first-of-their-kind, real-time, in situ measurements of deposit morphology as a fractal dimension during column filtration experiments. [Image courtesy Roth, Gilbert, and Mays 2015]



June 19, 2015

New Molecular Insights into the Structural Mechanism of Uraninite Oxidation

Molecular-scale information reveals non-classical diffusion behavior during the initial stages of uranium dioxide corrosion.

The Science
Density-functional theory and X-ray based methods sensitive to surface atomic structure and oxidation state [crystal truncation rod (CTR), X-ray diffraction, and X-ray photoelectron spectroscopy (XPS)] were used to determine the behavior of the natural cleavage surface of uraninite (UO2) in water at ambient conditions. Oxygen was found to react strongly with UO2. However, rather than following classical diffusion patterns, oxygen self-organized as interstitial atoms within the mineral lattice of every third atomic layer.

The Impact
Uranium dioxide occurs naturally in anoxic sediments, is the desired product of in situ bioremediation of uranium-contaminated aquifers, and is likely to control uranium release from such sediments over the long term. These surprising insights indicate that UO2 oxidation is far more complicated that previously known and offer a new conceptual molecular-scale framework for understanding UO2 fate in the environment.  

Summary
CTR X-ray diffraction measurements of a polished UO2 (111) surface exposed to atmospheric oxygen revealed a periodic, oscillatory structure of the oxidation front perpendicular to the mineral-water interface. This behavior could be explained by quantum mechanic considerations of the electron-transfer from U 5f orbitals to O 2p orbitals, assuming at least partial contribution from hemi-uranyl (resembling half of the UO22+ uranyl cation, i.e., with only a single short U-O bond) termination groups at the mineral surface, which favor the incorporation of interstitial oxygens into slab 3 of the UO2 lattice. The presence of hemi-uranyl termination groups was supported by XPS analyses revealing that both U(V) and U(VI) were present at the mineral surface, suggesting a mixed termination of the oxidized surface with hemi-uranyl, hydroxyl, and molecular water. The ordered oscillatory oxidation front with a three-layer periodicity observed is distinct from previously proposed models of oxidative corrosion under vacuum and offers important molecular-scale insights into UO2 oxidation under ambient conditions.

Contact (BER PM)
Roland F. Hirsch, SC-23.2, roland.hirsch@science.doe.gov, 301-903-9009

(PI Contact)
John Bargar
SSRL, SLAC National Accelerator Laboratory
bargar@slac.stanford.edu

Funding
Support was provided by the U.S. Department of Energy (DOE), Office of Science, Biological and Environmental Research (BER), Subsurface Biogeochemical Research activity, through the SLAC Scientific Focus Area program (Contract No. DE-AC02-76SF00515); and by the Geosciences Research Program at Pacific Northwest National Laboratory (PNNL), funded by DOE’s Office of Basic Energy Sciences (BES). XPS data were collected in the Radiochemistry Annex at the Environmental Molecular Sciences Laboratory, a DOE user facility located at PNNL. A portion of the DFT study was also performed using the computational resources of EMSL. GeoSoilEnviroCARS is supported by the National Science Foundation-Earth Sciences (EAR-1128799) and BES GeoSciences (DE-FG02-94ER14466). This research used resources at the Advanced Photon Source, a DOE user facility.

Publication
Stubbs, J. E.,et al. 2015. “UO2 Oxidative Corrosion by Nonclassical Diffusion,” Physical Review Letters 114, 246103. DOI: 10.1103/PhysRevLett.114.246103. (Reference link)

Related Links
ANL Highlight

Topic Areas:

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


May 12, 2015

Using Natural Microbial Communities as Biosensors for Environmental Contaminants

Microbial communities are highly attuned to changes in environmental conditions, rapidly sensing and responding to shifts in temperature, pH, nutrient availability, toxin levels, and dozens of other variables. For decades, scientists have studied the abilities of microbes to survive exposure to (and in some cases make use of) environmental contaminants such as heavy metals, radionuclides, and hydrocarbons. However, microbial communities can contain hundreds of different species, and this complexity makes it extremely difficult to quantitatively measure community-level responses to contaminant exposure. In a new study, a team of researchers from Lawrence Berkeley National Laboratory’s ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies) science focus area developed a new computational approach for the analysis and computational modeling of microbial community responses to environmental contaminants. Using direct sequencing of DNA from environmental samples, the team examined the microbial community of a subsurface aquifer in Oak Ridge, Tennessee, that had been contaminated with uranium, nitrate, and a variety of other compounds. Drawing on this data, a modeling framework was constructed to enable prediction of the types and amounts of contaminants that had been experienced by the microbial community based on known physiological characteristics of detected bacterial species. The predictions of this model strongly correlated with amounts of uranium, nitrate, and a variety of other geochemical factors measured at the sampling sites. To test the utility of this approach using an independent dataset, the team applied the model to microbial DNA samples collected during the Deepwater Horizon oil spill in 2010. Again, the model accurately predicted which samples had experienced oil contamination based on microbial DNA sequences and suggested that the community fingerprint retained a “memory” of exposure even after oil was no longer detectable. The results of this study provide a powerful new approach for not only the identification of contaminants in environmental samples, but also the microbial processes that are acting on them and potentially impacting their movement and/or longevity in the environment.

Reference: Smith, M. B., A. M. Rocha, C. S. Smillie, S. W. Oleson, C. J. Paradis, L. Wu, J. H. Campbell, J. L. Fortney, T. L. Mehlhorn, K. A. Lowe, J. E. Earles, J. Phillips, S. M. Techtmann, D. C. Joyner, S. P. Preheim, M. S. Sanders, J. Yang, M. A. Mueller, S. C. Brooks, D. B. Watson, P. Zhang, Z. He, E. A. Dubinsky, P. D. Adams, A. P. Arkin, M. W. Fields, J. Zhou, E. J. Alm, and T. C. Hazen. 2015. “Natural Bacterial Communities as Quantitative Biosensors,” mBio 6(3), e00326-15. DOI: 10.1128/mBio.00326-15. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 27, 2015

Microbes Use Tiny Magnets as Batteries

Understanding subsurface electron flow is vital in understanding elemental cycling and remediating subsurface pollutants, including those from recent energy technologies and historic waste sites. Research into the flow of electrons can show how certain minerals and bacteria work together via reduction-oxidation reactions to shape the geochemical landscape at Earth’s near surface and possibly halt toxins from spreading. The scientific challenge is how to unravel complex communities of organisms and mineral assemblages in nature into key cooperative subsystems that can be studied in the laboratory to determine how they work. In a recent study, scientists at the University of Tuebingen, University of Manchester, and Pacific Northwest National Laboratory discovered that during the day, one species of bacteria withdraws electrons from the iron-based mineral magnetite. At night, another species adds electrons back to the mineral, where the electrons reside until the daytime bacteria are active. The phototrophic Fe(II)-oxidizing Rhodopseudomonas palustris TIE-1 and the anaerobic Fe(III)-reducing Geobacter sulfurreducens work together to use magnetite's iron ions as both electron sources and sinks under different day and night conditions. The researchers used a host of instruments to make this discovery, including transmission electron microscopy resources at the Department of Energy’s Environmental Molecular Sciences Laboratory. The research shows that the common iron oxide mineral magnetite can serve as a naturally occurring battery for two very different types of bacteria that depend on iron to survive, revealing that a single mineral can serve as a platform for microbial diversity in nature.

Reference: Byrne, J. M., N. Klueglein, C. Pearce, K. M. Rosso, E. Appel, and A. Kappler. 2015. “Redox Cycling of Fe(II) and Fe(III) in Magnetite by Fe-Metabolizing Bacteria,” Science 347(6229),1473–76. DOI: 10.1126/science.aaa4834. (Reference link)

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

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



In the subsurface environment, below the water level, iron-oxidizing bacteria strip electrons from the naturally occurring battery (left); the reducing bacteria, which are active at night, add electrons, effectively recharging the battery (right). [Image courtesy University of Tuebingen]



March 03, 2015

Immobilization of Heavy Metals via Two Parallel Pathways During In Situ Bioremediation

Bioreduction is being actively investigated as an effective strategy for subsurface remediation and long-term management of Department of Energy (DOE) sites contaminated by metals and radionuclides [i.e., uranium (VI)]. These strategies require manipulation of the subsurface, usually through injection of chemicals (e.g., electron donor), which mix at varying scales with the contaminant to stimulate metal-reducing bacteria. Evidence from DOE field experiments suggests that mixing limitations of substrates at all scales may affect biological growth and activity for U(VI) reduction.

To study the effects of mixing on U(VI) reduction, researchers used selenite, Se(IV), instead of U(VI) in the lab because Se(IV) is easier to handle and microbial reduction of Se(IV) and U(VI) is similar in that two immobilization pathways are involved. In one pathway, the soluble contaminant [Se(IV) or U(VI)] is biologically reduced to a solid [Se0 or U(IV)]. In the other pathway, sulfate, which is commonly present in groundwater, is first biologically reduced to sulfide; this product then abiotically reacts with the soluble contaminant [Se(IV) or U(VI)] to form a solid [selenium sulfide or U(IV)]. While the first pathway is well understood, the second pathway has not been widely studied. Another unique aspect of this study is that researchers investigated mixing and reaction in a microfluidic flow cell with realistic pore geometry and flow conditions that mimic the transverse-mixing dominated reaction zone along the margins of a selenite plume undergoing bioremediation due to injected electron donors in the presence of background sulfate. Microbial and chemical reaction products were characterized using advanced microscopic and spectroscopic methods. A continuum-scale reactive transport model also was developed to simulate this experiment.

Results demonstrate that engineering remediation of metal-contaminated sites via electron-donor addition can lead to secondary and abiotic reactions that can immobilize metals, in addition to previously studied biotic reactions. The improved understanding of selenite immobilization as well as the improved model can help in the design of in situ bioremediation processes for groundwater contaminated by selenite or other contaminants [e.g., U(IV)] that can be immobilized via similar pathways.

Reference: Tang, Y., C. J. Werth, R. A. Sanford, R. Singh, K. Michelson, M. Nobu, W. Liu, and A.J. Valocchi. 2015. “Immobilization of Selenite via Two Parallel Pathways During In Situ Bioremediation,” Environmental Science and Technology 49, 4543–50. DOI: 10.1021/es506107r. (Reference link)

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

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


February 15, 2015

Newly Identified Archaea Involved in Anaerobic Carbon Cycling

Archaea, a domain of single-celled microorganisms, represent a significant fraction of Earth’s biodiversity, yet much less is known about Archaea than bacteria. One reason for this lack of knowledge is relatively poor genome sampling, which has limited accuracy for the Archaeal phylogenetic tree. To obtain a better understanding of the diversity and physiological functions of members of the Archaea domain, a team of scientists from the University of California, Berkeley, The Ohio State University, Columbia University, Lawrence Berkeley National Laboratory, the Department of Energy’s (DOE) Joint Genome Institute, Pacific Northwest National Laboratory, and DOE Environmental Molecular Sciences Laboratory used genome-resolved metagenomics analyses to investigate the diversity, genome sizes, metabolic capabilities, and potential environmental niches of Archaea from the Rifle, Colorado, uranium mill tailings site. The team used DOE JGI to sequence DNA from Rifle sediment and groundwater samples, and they not only identified new sequences for more than 150 Archaea but were able to reconstruct the complete genomes of two Archaea that were demonstrated to be representative of two different phyla. Transcriptomic studies conducted using EMSL capabilities on one of these microbes demonstrate that they have small genomes and limited metabolic capabilities; however, these metabolic capabilities are associated with carbon and hydrogen metabolism. These results suggest that these Archaea are either symbionts or parasites that depend on other organisms for some of their metabolic requirements. This research approximately doubled the known genomic diversity of Archaea, reconstructed the first complete genomes for Archaea using cultivation-independent methods, and enabled an extensive revision of the Archaeal tree of life. In addition, these findings can be incorporated into genome-resolved ecosystem models to more accurately reflect the role played by Archaea in the global carbon cycle.

References: Castelle, C. J., K. C. Wrighton, B. C. Thomas, L. A. Hug, C. T. Brown, M. J. Wilkins, K. R. Frischkorn, S. G. Tringe, A. Singh, L. M. Markillie, R. C. Taylor, K. H. Williams, and J. F. Banfield. “Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling,” Current Biology 25(6), 690-701. DOI: 10.1016/j.cub.2015.01.014. (Reference link)
(See also)

Contact: Paul E. Bayer, SC-23.1, (301) 903-5324, Dan Drell, SC-23.2, (301) 903-4742, David Lesmes, SC 23.1, (301) 903-2977, Pablo Rabinowicz, SC-23.2 (301) 903-0379
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER,SC-23.2 Biological Systems Science Division, BER


December 24, 2014

Carbonate Minerals Could Immobilize Neptunium in Groundwater

The radioactive metallic element neptunium (Np) is created when uranium (U)-based nuclear fuel is burned in electricity-producing commercial reactors and in plutonium-producing reactors operated for military purposes. Np(V) has been accidentally released to the environment at former Department of Energy (DOE) weapons production sites as well as other locations through a variety of circumstances. Because Np(V) has a high aqueous solubility, it is readily transported in groundwater. Predictions for the transport of Np(V) in groundwater are based on studies of U(VI), in part because U(VI) is easier and cheaper to study. However, there are major differences in the crystal chemistry of Np(V) and U(VI), suggesting they might be incorporated into mineral structures differently, and thereby immobilized in groundwater differently. In a recent study, researchers from the University of Notre Dame and Pacific Northwest National Laboratory examined factors that impact the structural incorporation of Np(V) and U(VI) ions into carbonate and sulfate minerals. Using spectroscopic and imaging instruments in RadEMSL, a radiochemistry facility at DOE’s Environmental Molecular Sciences Laboraty, the team found that carbonate minerals incorporated both ions at far higher levels than sulfate minerals. In addition, they found that Np(V) and U(VI) are incorporated into carbonate minerals at dramatically different levels, and that Np(V) can be readily incorporated into carbonate minerals, thereby reducing its mobility in groundwater.

Reference: Balboni, E., J. M. Morrison, Z. Wang, M. H. Engelhard, and P. C. Burns. 2015. "Incorporation of Np(V) and U(VI) in Carbonate and Sulfate Minerals Crystallized from Aqueous Solution," Geochimica et Cosmochimica Acta 151,133-49. DOI: 10.1016/j.gca.2014.10.027. (Reference link)
(See also)

Contact: Paul E. Bayer, SC-23.1, (301) 903-5324, Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

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


September 30, 2014

Visualizing Mercury on Surface of Freshwater Particulates

Suspended particulates are primarily responsible for the transport of mercury and toxic methylmercury in freshwater systems; however, little is known about how mercury interacts with particulates. Mercury interactions with phytoplankton and colloidal minerals, two common types of particulates known to be involved in binding and transporting mercury, were studied by a team of scientists from Oak Ridge National Laboratory and Argonne National Laboratory using X-ray fluorescence (XRF) spectroscopy. Using samples from a mercury-contaminated freshwater system, the team found that mercury is mostly found on the outer surface of phytoplankton cells (diatoms) and that it is heterogeneously distributed on mineral particles rich in iron oxides and natural organic matter (NOM). The findings confirm that suspended particles, especially diatoms and NOM-coated oxide minerals, are important sinks for mercury in freshwater systems.

Reference: Gu, B., B. Mishra, C. Miller, W. Wang, B. Lai, S. C. Brooks, K. M. Kemner, and L. Liang. 2014. “X-Ray Fluorescence Mapping of Mercury on Suspended Mineral Particles and Diatoms in a Contaminated Freshwater System,” Biogeosciences Discussion 11, 7521-40. DOI:10.5194/bgd-11-7521-2014. (Reference link)

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

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


May 30, 2014

How Sulfur Affects Chemistry of Iron in the Environment

Substantial amounts of iron are present in many subsurface environments. This element has a significant effect on both the biogeochemical cycling of carbon and the fate and transport of trace environmental contaminants, because it is readily transformed among several reactive species. The interactions of subsurface iron with various naturally occurring bacteria have a major influence on its environmental impacts, but these interactions are not well understood. Scientists at Argonne National Laboratory and three partner universities have identified a key role for sulfur in how bacteria affect the speciation of subsurface iron. They determined that bacteria unable to reduce ferric iron directly under alkaline conditions can do so indirectly. The bacteria do this by reducing elemental sulfur to sulfide ion, which then reduces the ferric iron in the goethite to ferrous iron. In addition, this ferrous iron can reduce other metal species such as uranyl ion, thus affecting their solubility. The researchers determined that this process is common in alkaline environments such aquifers, especially those in arid regions. This new understanding of this environmental role of iron will enable progress in a wide range of areas, from modeling of potential carbon capture systems to understanding speciation of contaminants such as uranium and arsenic.

References: Flynn, T. M., E. J. O’Loughlin, B. Mishra, T. J. DiChristina, and K. M. Kemner. 2014. “Sulfur-Mediated Electron Shuttling During Bacterial Iron Reduction,”, Science 344, 1039-42. DOI: 10.1126/science.1252066. (Reference link)

Friedrich, M. W., and K. W. Finster. 2014. “How Sulfur Beats Iron,” Science 344, 974-75. DOI: 10.1126/science.1255442. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, roland.hirsch@science.doe.gov, 301-903-9009.

Topic Areas:

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


May 15, 2014

Stimulating Bacteria to Immobilize Chromium in Groundwater

Hexavalent chromium is a major contaminant in numerous soil and groundwater systems worldwide, in particular at Department of Energy sites due to former weapons production and reprocessing activities and wastes from electroplating processes, and from industrial efforts to reduce corrosion in steel pipes. Although hexavalent chromium is readily transported in groundwater, reduction to a less mobile form involves the interaction of hexavalent chromium with certain minerals and microorganisms. Specifically, iron-reducing bacteria can convert the oxidized form of iron in clay minerals (ferric iron) into the reduced form of iron (ferrous iron) that can then reduce hexavalent chromium to much less mobile trivalent chromium. Efforts to understand the specific details of this process were recently reported by a team of scientists from Miami University and the Environmental Molecular Sciences Laboratory (EMSL), using EMSL’s ultra-sensitive microscopy and spectroscopy capabilities. Starting with the iron-reducing bacterium Geobacter sulfurreducens and ferric iron-containing clay minerals, the team found that they could provide a specific nutrient to the bacteria that would significantly stimulate the bacteria to reduce ferric to ferrous iron. The resulting ferrous iron was able to reduce hexavalent chromium, and it reduced the chromium even faster as the temperature of the system was increased. In addition to demonstrating a possible way to reduce the transport of hexavalent chromium in groundwater, the team also determined the kinetics of these reactions. These kinetic parameters can now be incorporated into models to improve predictions of the transport of hexavalent chromium in subsurface environments.

Reference: Bishop, M. E., P. Glasser, H. Dong, B. Arey, and L. Kovarik. 2014. “Reduction and Immobilization of Hexavalent Chromium by Microbially Reduced Fe-bearing Clay Minerals,” Geochimica et Cosmochimica Acta 133, 186-203. DOI: 10.1016/j.gca.2014.02.040. (Reference link)

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

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


January 09, 2014

Chemical View of Single Uranium Atoms Attached to Mineral Surfaces

Uranium fission currently provides a significant portion of the world’s low-carbon energy. Mining of uranium ores, fuel processing, nuclear accidents, and spent fuel disposal all have resulted in the release of uranium to the environment. Furthermore, because of its chemistry, uranium is often enriched in fossil fuel ores (e.g., kerogens and black shales). Accurate modelling of uranium transport is paramount to understanding the risks from uranium release in the environment. Current models assume that reduction of U6+ to U4+ in bioreduced sediments results in the precipitation of the insoluble mineral uraninite (UO2). However, researchers at Argonne National Laboratory have shown that mineral surfaces have a significant role in stabilizing U4+ as isolated, adsorbed U4+ atoms at low U:surface ratios that are more typical of contaminated sites. Using two model minerals, rutile (TiO2) and magnetite (Fe3O4), the researchers found that the surface area threshold at which U4+ forms single-atom surface complexes and the stability of these complexes over time is dependent on the mineral chemistry. Adsorbed U4+ was produced by reactions representative of both biotic and abiotic U6+ reduction pathways, suggesting that non-uraninite U4+ associated with minerals may account for a significant portion of the U4+ balance in sediments. The results indicate the need to include such forms of U4+ in reactive transport models to better predict uranium mobility in the environment.

Reference: Latta, D. E., B. Mishra, R. E. Cook, K. M. Kemner, and M. I. Boyanov. 2014. “Stable U(IV) Complexes Form at High-Affinity Mineral Surface Sites,” Environmental Science and Technology 48(3), 1683-91. DOI: 10.1021/es4047389. (Reference link)

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

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


January 03, 2014

Watershed-Scale Fungal Communities in a Co-Contaminated System

The legacy of the Department of Energy’s former weapons production activities includes comingled plumes of uranium and very high levels of nitrate in groundwater and soils. At contaminated sites with high nitrate concentrations, anaerobic microbes are known to reduce the nitrate through metabolic respiration. In contrast, the role and importance of fungi, which are abundant in groundwater and soils and are also metal resistant and involved in biogeochemical cycling of carbon, nutrients and metals, is not well understood. To address this gap in understanding, a team of scientists from the Georgia Institute of Technology, Florida State University, and Oak Ridge National Laboratory used quantitative and semi-quantitative molecular techniques to characterize the abundance, distribution, and diversity of fungi in a nitrate and uranium contaminated watershed. The team found that members of the Ascomycota phylum dominated the watershed, and that the community composition varied as a function of the pH gradient. In addition, they discovered that one fungal species is able to reduce nitrate to nitrous oxide, a potent greenhouse gas.

Reference: Jasrotia, P., S. J. Green, A. Ganion, W. A. Overholt, O. Prakash, D. Wafula, D. Hubbard, D. B. Watson, C. W. Schadt, S. C. Brooks, and J. E. Kostka. 2014. “Watershed-Scale Fungal Community Characterization Along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate,” Applied and Environmental Microbiology 80(6), 1810-20. DOI:10.1128/AEM.03423-13. (Reference link)

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

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


November 15, 2013

Revealing Pathways that Drive Metabolism in Sulfate-Reducing Bacteria

Sulfate-reducing bacteria (SRB), commonly found in oxygen-deprived habitats, are known for their involvement in the corrosion of metals and the formation of toxic sulfide; however, they also are involved in controlling the transformations and transport of a number of toxic metal contaminants in soils and groundwater. Effective use of SRBs to control metal contaminants requires a better understanding of their bioenergetic pathways for sulfate reduction. A team of scientists from the University of Missouri, Oak Ridge National Laboratory, and Environmental Molecular Sciences Laboratory (EMSL) used a mutant form of an SRB, Desulfovibrio alaskensis, to test the hypothesis that the sulfate reduction that occurs in the cell’s interior cytoplasm relies on a flow of electrons from the cell’s periplasm, found between the cell’s two exterior membranes. The researchers characterized bacterial growth and examined gene expression using proteomic and transcriptomic analyses at EMSL. Their results indicate that a protein that spans the inner membrane from the periplasm to the cytoplasm and another protein found only in the periplasm are essential for transferring electrons from the periplasm to the cytoplasm to drive sulfate reduction. These research results also are consistent with another recently discovered biochemical pathway involving hydrogen cycling that increases the efficiency of energy use in many SRBs. Together, these findings could be important in designing pathways for biofuels production.

Reference: Keller, K. L., B. J. Rapp-Giles, E. S. Semkiw, I. Porat, S. D. Brown, and J. D. Wall. 2014. “A New Model for Electron Flow for Sulfate Reduction in Desulfovibrio alaskensis G20,” Applied and Environmental Microbiology 80(3), 855-68. DOI:10.1128/AEM.02963-13. (Reference link)

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

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


November 09, 2013

First Quantification of Total Thiols on Bacteria and Natural Organic Matter in Environmental Samples

Organic thiols react and form complexes with some toxic soft metals such as mercury in both biotic and abiotic systems. However, a clear understanding of these interactions is currently limited because quantifying thiols in environmental matrices is difficult due to their low abundance, susceptibility to oxidation, and measurement interference by non-thiol compounds in samples. A team of scientists from Oak Ridge National Laboratory has developed a fluorescence-labeling method to determine total thiols directly on gram-negative bacterial cells and natural organic matter (NOM) in environmental samples. The method is highly selective and can quantify thiols at submicromolar concentration levels. The direct quantification of organic thiols on NOM and bacterial cells is needed to enable a mechanistic understanding of soft metal and biota interactions, metal speciation, and bioavailability.

Reference: Rao, B., C. Simpson, H. Lin, L. Liang, and B. Gu. 2014. “Determination of Thiol Functional Groups on Bacteria and Natural Organic Matter in Environmental Systems,” Talanta 119, 240-47. (Reference link)

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

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


August 04, 2013

Multiple Species of Bacteria Convert Elemental Mercury to Toxic Methylmercury

Methylmercury is a known neurotoxin that poses a significant health risk to humans. A number of anaerobic bacterial species methylate oxidized mercury to methylmercury, but only one species has been shown to methylate elemental mercury. Because elemental mercury has been considered to be relatively inert and is volatile, remediation approaches have focused on converting toxic forms of mercury into elemental mercury that would then bubble out of surface water and dissipate. Now, scientists from Oak Ridge National Laboratory report that multiple species of bacteria can methylate elemental mercury. Moreover, some species can both oxidize and methylate elemental mercury, others require the presence of a specific amino acid to perform these conversions, and still others can only oxidize elemental mercury. These findings suggest that both methylating and non-methylating bacteria can enhance the formation of methylmercury in anaerobic environments. A more complete understanding of the variety of microbial processes involved in mercury cycling clarifies the challenges associated with cleaning up mercury-contaminated water and sediments.

Reference: Hu, H., H. Lin, W. Zheng, S. J. Tomanicek, A. Johs, X. Feng, D. A. Elias, L. Liang, and B. Gu. 2013. “Oxidation and Methylation of Dissolved Elemental Mercury by Anaerobic Bacteria,” Nature Geoscience 6, 751–54. DOI: 10.1038/NGEO1894. (Reference link)

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

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


August 02, 2013

How Phosphate Ion Influences Cycling of Carbon and Iron in the Environment

Subsurface microbes convert iron among several chemical species. These forms of iron can influence the immobilization and release of contaminant metals such as uranium as well as sequestration of carbon. Predictive understanding of the processes involved in these transformations is limited by a lack of knowledge of the impact of many other chemical species commonly found with iron in the subsurface. New research by scientists at Argonne National Laboratory and collaborating universities has provided knowledge of how phosphate ion incorporated in iron-containing minerals affects the speciation of iron and cycling of carbonate ion (a common form of carbon in the subsurface). These scientists determined that the phosphate bound or occluded within the Fe(III)-containing particles has a significant impact on the minerals produced by the iron-reducing bacterium Shewanella putrefaciens . In the absence of phosphate, the Fe(III) is largely converted to magnetite, but when phosphate is present within the Fe(III) particles, a significant amount of a reactive iron-containing species known as green rust is produced. Green rust is highly effective in reducing and immobilizing contaminants such as radionuclides and toxic metals. This study therefore provides key information for understanding how to efficiently use Shewanella to treat contaminated environments.

Reference: O'Loughlin, E. J., M. I. Boyanov, T. M. Flynn, C. Gorski, S. M. Hofmann, M. L. McCormick, M. M. Scherer, and K. M. Kemner. 2013. “Effects of Bound Phosphate on the Bioreduction of Lepidocrocite (γ-FeOOH) and Maghemite (γ-Fe2O3) and Formation of Secondary Minerals,” Environmental Science and Technology 47 , 9157–66. DOI: 10.1021/es400627j. (Reference link)

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

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


May 14, 2013

Microbial Membrane Protein Extracts Electrons from Iron Nanoparticles

Iron plays a vital role in environmental biogeochemistry, exchanging electrons with microorganisms to transform more soluble Fe(II) to less soluble Fe(III). The iron cycle is also coupled to the climatically relevant carbon and nitrogen cycles, as well as other elemental cycles. By pulling apart the kinetics and detailed interactions between iron particles and microorganisms, researchers hope to gain insights into which aspects of these processes are important at larger scales. A team of scientists from Pacific Northwest and Lawrence Berkeley National Laboratories used stopped-flow spectrometry and micro X-ray diffraction at the Environmental Molecular Sciences Laboratory (EMSL) and X-ray absorption and magnetic circular dichroism spectroscopies at the Advanced Light Source (ALS) to investigate the oxidation kinetics of iron nanoparticles exposed to a bacterial protein, decaheme c-type cytochrome (Mto). When MtoA from Sideroxydans lithotrophicus was exposed to iron nanoparticles, the MtoA extracted electrons from the structural Fe(II) in the nanoparticles starting at the surface and then continuing to the interior, leaving behind the Fe(III) and not damaging the crystal structure. The team intends to further investigate this process using proteins known to transfer electrons in other environmentally relevant microorganisms, and using other types of iron-containing minerals. This research provides the first quantitative insights into the transfer of electrons from minerals to microbes, and provides a clear picture of how microorganisms accelerate or control iron biogeochemistry and cycling in natural systems. This knowledge sheds light on elemental cycling processes coupled to the iron cycle, including carbon, nitrogen, sulfur, and other metals.

Reference: Liu, J., C. I. Pearce, C. Liu, Z. Wang, L. Shi, E. Arenholz, and K. M. Rosso. 2013. “Fe3-xTixO4 Nanoparticles as Tunable Probes of Microbial Metal Oxidation,” Journal of the American Chemical Society 135(24), 8896–907. DOI: 10.1021/ja4015343. (Reference link)

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

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


April 26, 2013

Influence of Magnetite Composition on Environmental Mercury Speciation

Mercury exists in several different forms in the environment, and some of these forms are quite toxic. Research is being conducted to gain a fuller understanding of how different forms of mercury interact with minerals and how these interactions influence mercury’s conversion into hazardous forms, or, conversely, its reduction to volatile metallic mercury. New studies of the behavior of mercury (II; the generally soluble, oxidized form of mercury) have shown that the common iron-containing mineral magnetite with a large proportion of ferrous (reduced) iron is effective in converting mercury (II) into mercury metal. If chloride ion was present in significant concentrations (as it often is in natural environments), then the mercury was reduced more slowly, and some of it was in the metastable mercury (I) chloride form. The studies, carried out by scientists at the University of Iowa, Argonne National Laboratory, and Illinois Institute of Technology, used X-ray spectroscopy stations at Argonne’s Advanced Photon Source to study the changing forms of mercury.

Reference: Pasakarnis, T. S., M. I. Boyanov, K. M. Kemner, B. Mishra, E. J. O’Loughlin, G. Parkin, and M. M. Scherer. 2013. “Influence of Chloride and Fe(II) Content on the Reduction of Hg(II) by Magnetite,” Environmental Science and Technology, DOI: 10.1021/es304761u. (Reference link)

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

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


April 24, 2013

Plutonium Sorption over 10 Orders of Magnitude

Plutonium (Pu) adsorption to and desorption from mineral surfaces plays a major role in controlling its mobility in the environment. However, laboratory measurements of Pu sorption are typically conducted at much higher concentrations (10-6 to 10-10 M) than found in subsurface water (< 10-12 M). As a result, there is a concern that Pu behavior determined in lab measurements might not be representative of sorption occurring under actual subsurface conditions. A new study carried out at Lawrence Livermore National Laboratory (LLNL) overcomes this obstacle. It provides measurements of the sorption of dissolved Pu (V) onto surfaces of a common clay mineral (Na-montmorillonite) over an unprecedentedly large range of initial plutonium solution concentrations (10-6 to 10-16 M). Concentration measurements at the low end of this range were made possible by the unique capabilities of the Center for Accelerator Mass Spectrometry at LLNL. The team's results indicate that the plutonium adsorption behavior on montmorillonite was linear over the range of concentrations studied, indicating that plutonium sorption behavior from laboratory studies at higher concentrations can be extrapolated to sorption behavior at low, environmentally relevant concentrations.

Reference: Begg, J., M. Zavarin, P. Zhao, S. Tumey, B. A. Powell, and A. B. Kersting. 2013. "Pu(V) and Pu(IV) Sorption to Montmorillonite," Environmental Science and Technology, DOI: 10.1021/es305257s. (Reference link)

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

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


April 03, 2013

Analyzing the Complexity of Interactions with Mineral Surfaces

Minerals have a profound effect on the fate and transport of contaminants in subsurface environments. Surface complexation modeling (SCM) enables predictions of adsorption over a broader range of conditions than can be accommodated by adsorption isotherm equations or ion exchange models. A newly published review article discusses the current status of SCM and its applications to a range of systems. The main focus is on multidentate surface complexes, formed when an ion or molecule in solution binds to two or more adjacent active sites on the surface. Spectroscopic measurements often provide evidence for the presence of multidentate surface complexes, but there has been ambiguity and confusion in the literature regarding the best ways to incorporate such complexes into SCM. The article describes and evaluates several approaches to modeling these interactions and discusses examples of model applications, as well as the need for improvements in textbooks, computer programs, and the clarity of future publications to bridge the gap between theory and practice in SCM. This section is illustrated by a modeling discussion of surface complexation of uranium (VI) on the mineral goethite, a system that is a research focus of the Department of Energy's Office of Biological and Environmental Research (BER). Many of the experimental results referenced in this review were obtained in BER research projects. The article concludes with advice for SCM users.

Reference: Wang, Z., and D. E. Giammar. 2013. "Mass Action Expressions for Bidentate Adsorption in Surface Complexation Modeling: Theory and Practice," Environmental Science and Technology 47(9), 3982–96. DOI: 10.1021/es305180e. (Reference link)

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

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


March 25, 2013

Impurities in Natural Minerals Can Affect Uranium Mobility

Uranium groundwater contamination resulted from mining for use as an energy source, as well as from past enrichment and weapons production activities at U.S. Department of Energy (DOE) sites. Understanding the impact of uranium contamination on water sources and developing appropriate remediation strategies are needed both to protect public safety and to continue the use of uranium in a balanced energy portfolio. Ground­water travels underground through a complex mixture of soils and sediments. A magnetic iron oxide mineral, magnetite, is commonly found in these sediments. Magnetite can significantly slow uranium migration, acting like a “rechargeable battery” for continued uranium removal from groundwater. It performs this task by sequestering the uranium as nanoparticles of uranium dioxide within underground sediments. Researchers at Argonne National Laboratory (ANL) and Pacific Northwest National Laboratory now have found that titanium, a common impurity in these natural magnetic iron minerals, obstructs the formation of the uraninite nanoparticles, resulting in the formation of novel molecular-sized uranium-titanium structures. This previously unknown association of uranium with titanium affects uranium’s mobility in subsurface groundwater. Incorporating this knowledge into ongoing modeling efforts will improve scientists’ ability to predict future migration of subsurface contaminant plumes and provide detailed information needed for long-term stewardship of DOE legacy sites. The researchers used ANL’s Advanced Photon Source to study how uranium interacts with magnetite within the complex subsurface chemical environment.

Reference: Latta, D. E., C. I. Pearce, K. M. Rosso , K. M. Kemner, and M. I. Boyanov. 2013. “Reaction of UVI with Titanium-Substituted Magnetite: Influence of Ti on UIV Speciation,” Environmental Science and Technology 47(9), 421–30. DOI: 10.1021/es303383n. (Reference link)

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

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


March 04, 2013

Understanding How Uranium Changes in Subsurface Environments

The U.S. Department of Energy has a long-term responsibility to contain uranium leaked into the environment at mining and processing sites. Uranium has a complex chemistry that determines whether it is immobilized or moves out of a contaminated area, potentially into water supplies. New research on the transformation of uranium (VI) to uranium (IV)—the most common oxidation states of the element—discovered that bacterial biomass in the ground impacts this transition. Studies were carried out at the Rifle (Colorado) Integrated Field Research Challenge site, by scientists from the SLAC National Accelerator Laboratory and Berkeley Lab, to determine how uranium (VI) exposed to natural conditions at the site behaved and to determine the underlying controlling biological and chemical mechanisms. The experiments showed that uranium (IV) unexpectedly was present both as a monomeric, biomass-associated uranium (IV) species and, to a much lesser extent, as nanoparticles of uraninite (UO2). The researchers attribute the presence of the former to the binding of uranium (IV) to phosphate groups in biomass following the chemical transformation of uranium (VI) to uranium (IV) by reaction with iron sulfides or bacterial enzymes. Since a substantial portion of the uranium is found in this form, models of uranium transport in contaminated subsurface environments need to recognize the existence of multiple pathways for reduction of uranium (VI), including the biological factors identified in this research.

Reference: Bargar, J. R., et al. 2013. “Uranium Redox Transition Pathways in Acetate-Amended Sediments,” Proceedings of the National Academy of Sciences USA, DOI: 10.1073/pnas.1219198110. (Reference link)

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

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


February 07, 2013

Genetic Basis for Bacterial Mercury Methylation

Methylmercury is a potent neurotoxin produced from inorganic mercury by anaerobic bacteria in natural environments. Until now, however, the genes and proteins involved have remained unidentified. A team of scientists from Oak Ridge National Laboratory and collaborators from the Universities of Missouri and Tennessee identified a two-gene cluster required for mercury methylation by Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA. In both bacteria, deletion of either or both genes resulted in the elimination of their ability to methylate mercury. Among bacteria and archaea with sequenced genomes, related genes (orthologs) are present in confirmed methylators but absent in non-methylators, suggesting a common mercury methylation pathway in all methylating bacteria and archaea sequenced to date.

Reference: Parks, J. M., A. Johs, M. Podar, R. Bridou, R. A. Hurt, S. D. Smith, S. J. Tomanicek, Y. Qian, S. D. Brown, C. C. Brandt, A. V. Palumbo, J. C. Smith, J. D. Wall, D. A. Elias, and L. Liang. 2013. “The Genetic Basis for Bacterial Mercury Methylation,” Science 339, 1332–35. DOI: 10.1126/science.1230667. (Reference link)

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

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


August 10, 2012

Improved Approach for Modeling Pu Behavior in the Environment

The presence of plutonium (Pu) in the environment due to anthropogenic activity remains a serious problem. Predicting Pu transport and fate requires an understanding of biogeochemical processes that are particularly complicated in the case of Pu. Detailed Pu characterization is difficult because its very low environmental concentrations make most experimental approaches difficult to use. Extrapolation from higher Pu concentration studies in the laboratory are subject to concentration-related artifacts. Researchers at Lawrence Livermore National Laboratory recently explored an alternate course of ab initio simulations to study aqueous actinide ions. They tested a number of approaches to simulate the highly insoluble species Pu (IV), using a comparison of ab initio electronic structure methods applied to a benchmark case under environmentally relevant concentrations and neutral pH. They proposed the use of the extension of density functional theory that explicitly includes onsite interactions as a method to improve the calculation. The application of this method combined with additional derived parameters was proposed as an overall approach for largescale dynamical simulations of Pu (IV) chemistry.

Reference: Huang, P., M. Zavarin, and A. B. Kersting. 2012. "Ab initio Structure and Energetics of Pu(OH)4 and Pu(OH)4(H2O)n Clusters: Comparison Between Density Functional and Multi-Reference Theories," Chemical Physics Letters 543, 193–98. (Reference link)

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

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


August 01, 2012

How Iron in Minerals Affects Subsurface Uranium

Subsurface minerals help control the chemical form of contaminants such as uranium (U). The redox (reduction and oxidation) state of soils and sediments exists on a continuum from oxidized to reduced and can affect the mobility of uranium plumes. Under oxidized conditions, U is rather soluble as a uranyl ion in the U6+ valence state, whereas under reducing conditions U can become immobilized in the less-soluble U4+ valence state. Researchers at the University of Iowa and Argonne National Laboratory have found that a complex mixture of ferrous iron (Fe2+)-bearing minerals in a naturally reduced soil is capable of reducing and immobilizing uranium. Using Mössbauer spectroscopy at the University of Iowa and synchrotron x-ray absorption spectroscopy at the Advanced Photon Source at Argonne, the researchers found that uranium was reduced by Fe2+ in clay minerals and by a less-common, transient, and highly reactive Fe2+-mineral called green rust. The researchers also observed that the reduced U4+ atoms formed a product different from the uraninite mineral (UO2) commonly observed in laboratory studies, providing evidence for the diversity in chemical speciation of reduced U in natural systems. This study provides detailed information necessary for understanding toxic and radioactive contaminant mobility which will contribute to the long-term stewardship of U.S. Department of Energy legacy sites.

Reference: Latta, D. E., M. I. Boyanov, K. M. Kemner, E. J. O'Loughlin, and M. M. Scherer. 2012. "Abiotic Reduction of Uranium by Fe(II) in Soil," Applied Geochemistry 27, 1512–24. (Reference link)

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

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


August 01, 2012

Novel Bioremediation Strategy for Degrading Contaminants

Microbes continue to offer surprises by their range of capabilities and versatility. When studying a microbe in its natural environment for a particular application, scientists often find that it also does something quite different and useful. A new study of the basic biological processes of methane-producing bacteria (methanotrophs) found that Methylocystis strain SB2 can also grow on acetate or ethanol and degrade a wide range of halogenated hydrocarbons. A specific pollutant-degrading protein, particulate methane monooxygenase (pMMO), attacked pollutants of interest while the bacteria used ethanol to grow. Ethanol added to contaminated groundwater enhances the ability of the groundwater to “flush” pollutants such as trichloroethylene and tetrachloroethylene. The authors suggest that the resulting aqueous ethanol-pollutant solution can be passed through a methanotrophic bioreactor where both ethanol and the pollutants are removed by a bacterium like Methylocystis strain SB2. The study, which began as a project to understand how methanotrophs that produce a metal-binding compound (methanobactin) affect the behavior of copper and mercury in the environment, led to new discoveries that could provide novel bioremediation strategies.

Reference: Jagadevan, S., and J. D. Semrau. 2012. “Priority Pollutant Degradation by the Facultative Methanotroph, Methylocystis Strain SB2,” Applied Microbiology and Biotechnology, DOI: 10.1007/s00253-012-4310-y. (Reference link).

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

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


June 08, 2012

Bacteria Affect Rock Weathering

In their effort to derive energy from iron, bacteria may set off a cascade of reactions that reduce rocks to soil and free biologically important minerals. These findings from a team at the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory are based on a model microbial community called the Straub culture, a lithotrophic culture or literally an “eater of rock,” that can turn non-carbon sources such as iron into energy. This energy is produced via a biochemical pathway driven by a series of electron exchanges, which, in the case of the Straub culture, is initiated by taking an electron from, or oxidizing, iron. To gain insight into how lithotrophs behave in the environment, the Straub culture was incubated with media containing fine particles of an iron-rich mica called biotite. After two weeks, Mössbauer spectroscopy was used to compare a biotite control to biotite incubated with the Straub culture to quantify how much iron exists in what oxidation states in the sample. In the biotite, Mössbauer confirmed that the microbes did oxidize iron from Fe(II) to Fe(III). Transmission electron microscopy revealed that this oxidation affected the biotite structure, leading to changes that resemble those observed in nature. This work offers new insight into the roles of microbes in soil production and in the biogeochemical cycling of minerals (e.g., iron oxidation) and suggests that microbes have a direct effect on rock weathering.

Reference: Shelobolina, E. S., H. Xu, H. Konishi, R. K. Kukkadapu, T. Wu, M. Blothe, and E. E. Roden. 2012. "Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite," Applied and Environmental Microbiology 78(16), 5746–52. DOI: 10.1128/AEM.01034-12. (Reference link)

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

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


May 10, 2012

Electron Gradients in Biofilms

Microbes play a key role in determining the chemical form of metal and radioactive contaminants in the environment. They shuttle electrons back and forth with metal ions, often over long distances. Researchers at the University of Minnesota have found new evidence for how this happens by examining how the thickness of a biofilm produced by Geobacter sulfurreducens affects electron transfer. They used spectroscopic methods involving ultraviolet and visible light with a potentiometric system that exposes the biofilm to a controlled voltage. The investigators discovered that a gradient of electrons developed if the biofilm grew beyond a few cell thicknesses. This gradient was identified when an increased potential, i.e., an increased pull on the electrons produced by a more positive electrode, could not increase the rate electrons travelled out of the thicker biofilm. Unlike thin biofilms where only a small percentage of cytochromes retained electrons, the thicker biofilm showed a substantial number of cytochromes still retained electrons, even when subjected to increased voltage. These results will be helpful in developing new interaction models of metallic contaminants with microbial communities in the environment, particularly in light of the fact that previous studies have led to significantly different descriptions of how the electron transfer process works.

Reference: Liu, Y., and D. R. Bond. 2012. “Long-Distance Electron Transfer by G. sulfurreducens Biofilms Results in Accumulation of Reduced c-Type Cytochromes,” ChemSusChem 5(6), 1047–1053. DOI: 10.1002/cssc.201100734. (Reference link)

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

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


May 10, 2012

Mercury Methylating Bacteria Widespread in Contaminated Streams

Mercury has become a global pollutant due to its release into the atmosphere during coal burning and into freshwater systems as part of agricultural runoff and direct industrial discharge. Once in freshwater systems, specific types of microorganisms are known to transform mercury into methylmercury (MeHg), a highly toxic form of mercury. Scientists from Oak Ridge National Laboratory (ORNL) recently examined the microbial communities from the sediments of six different surface streams in Oak Ridge, Tennessee, to identify bacteria that could be contributing to MeHg production. Using 16S rRNA pyrosequencing, the researchers correlated the presence of a group of known MeHg producers, the Deltaproteobacteria, with MeHg in all of the Hg contaminated streams. Within the Deltaproteobacteria group, Desulfobulbus species are considered to be prime candidates for being involved in Hg methylation in these streams.

Reference: Mosher, J. J., T. A. Vishnivetskaya, D. A. Elias, M. Podar, S. C. Brooks, S. D. Brown, C. C. Brandt, and A. V. Palumbo. 2012. "Characterization of the Deltaproteobacteria in Contaminated and Uncontaminated Stream Sediments and Identification of Potential Mercury Methylators," Aquatic Microbial Ecology 66, 271–82. (Reference link)

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

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


September 14, 2011

How Bacteria Influence Speciation (and Mobility) of Mercury in the Environment

Significant amounts of mercury have contaminated some DOE cleanup sites, such as the Oak Ridge Reservation. Mercury mobility is strongly dependent on its chemical form, with the elemental metal being volatile and hence mobile in the environment, while oxidized forms are much less mobile (though more toxic). New research at Argonne National Laboratory has provided improved understanding of the role of bacteria in controlling the chemical form of mercury in subsurface environments. The research group used x-ray absorption spectroscopy experiments at the Advanced Photon Source to study the sorption of oxidized HgII to Bacillus subtilis, a bacterium commonly found in soils. They found that HgII sorbs to bacterial cells via both high-affinity sulfhydryl binding groups and low-affinity carboxyl groups on the cell surfaces. The HgII that is sorbed to cells via the sulfhydryl groups remains unavailable for reduction by magnetite, a reactive iron-containing mineral often found in sediments, even after two months of reaction time. These results identify a mechanism by which mercury might be immobilized in the environment and help provide a clearer picture of the complex system of interactions of mercury in the subsurface.

Reference: Mishra, B., E. J. O'Loughlin, M. I. Boyanov, and K. M. Kemner. 2011. "Binding of Hg(II) to High-Affinity Sites on Bacteria Inhibits Reduction to Hg(0) by Mixed Fe(II/III) Phases," Environmental Science and Technology 45(22), 9597–9603. DOI: 10.1021/es201820c. (Reference link)

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

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


September 12, 2011

Understanding How Environmental Microbes Make Uranium Less Soluble

Uranium is one of the major contaminants at DOE cleanup sites. It was usually released into the environment as the highly soluble uranyl ion (uranium (VI)). This ion interacts with bacteria and minerals in the ground to form reduced uranium (IV), notably in the mineral uraninite, a form that is much less soluble than uranium (VI). Less soluble uranium (IV) species are less likely to be moved out of the initially contaminated zone and into nearby rivers or aquifers by groundwater. New research has shown that biologically produced uraninite in a natural underground environment dissolves much more slowly than uraninite prepared in the laboratory. Researchers have developed a model showing that the slower dissolution is due to the presence of biomass that limits the reoxidation rate of the uranium (IV) in uraninite and diffusion of oxidized uranium into the groundwater. This understanding will be used in developing improved models of uranium transport in contaminated environments. Field studies were carried out at the Old Rifle, Colorado, Integrated Field Research Challenge site, while experiments to determine the forms of uranium present were conducted at the Stanford Synchrotron Radiation Lightsource.

Reference: Campbell, K. M., et al. 2011. "Oxidative Dissolution of Biogenic Uraninite in Groundwater at Old Rifle, CO," Environmental Science and Technology 45, 8748–54. DOI: 10.1021/es200482f. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


August 07, 2011

Microbial Nanowires Exhibit Metal-like Conductivity

Recent reports indicate that common anaerobic subsurface microbes respire metal-containing minerals and radionuclide contaminants via appendages, known as "nanowires," on their cell surface. These nanowires facilitate electron transport from central metabolism inside the cell to electron acceptors on the outside of the cell. New results from a DOE team led by the University of Massachusetts show that microbial pili composed of natural proteins exhibit metal-like conductivity in the absence of cytochromes and function as "nanowires," a finding that could have far-reaching biotechnological and bioelectronic implications. Researchers have shown that they could manipulate biofilms grown in microbial fuel cells, "tuning" electrical conductance depending on the expression of specific genes associated with pili ("nanowire") production. Furthermore, X-ray diffraction and electrical studies of purified "nanowire" filaments attribute the electron-conducting behavior to the molecular structure of the pili that results in close alignment of aromatic groups within the amino acid components facilitating p-orbital overlap and charge delocalization. The data help to explain how these microorganisms respire solid minerals and radionuclide contaminants in anaerobic subsurface environments and has far-reaching implications for nanomaterial biodesign and biotechnology.

Reference: Malvankar, N. S., M. Vargas, K. P. Nevin, A. E. Franks, C. Leang, B. Kim, K. Inoue, T. Mester, S. F. Covalla, J. P. Johnson, V. M. Rotello, M. T. Tuominen, and D. R. Lovley. 2011. "Tunable Metallic-Like Conductivity in Microbial Nanowire Networks," Nature Nanotechnology, DOI: 10.1038/NNANO.2011.119. (Reference link)

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

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


May 31, 2011

Extracellular Polymeric Substances Stop Migration of Subsurface Contaminants

Subsurface uranium is a significant contaminant at U.S. Department of Energy sites. Remediation solutions include immobilizing contaminants to prevent them from reaching groundwater. Using a model organism isolated from a uranium seep of the Columbia River, scientists recently quantified how extracellular polymeric substances (EPS) in subsurface environments can be used to immobilize heavy metal and radionuclide contaminants such as uranium [U(VI)]. In geologic systems, EPS can help bind microbes to mineral surfaces, influence cellular metabolism, and influence the fate and transport of contaminants. Using a novel biofuel reactor designed by scientists from the Environmental Molecular Sciences Laboratory (EMSL), the team prepared biofilms of a Shewanella species that produces EPS, and quantitatively analyzed the contribution of EPS to U(VI) immobilization. Using EMSL’s nuclear magnetic resonance capabilities to analyze chemical residues in EPS samples and cryogenic fluorescence spectroscopy to obtain sensitive U(VI) measurements, they tested the reactivity of loosely associated EPS and bound EPS with U(VI). The scientists found that, when reduced, the isolated cell-free EPS fractions could reduce U(VI) and the bound EPS contributed significantly to its immobilization, primarily through redox-active proteins. For loosely associated EPS, sorption of U(VI) was attributed predominantly to reaction with polysaccharides. These results could lead to the development of improved remediation techniques for subsurface contaminants.

Reference: Cao, B., B. Ahmed, D. W. Kennedy, Z. Wang, L. Shi, M. J. Marshall, J. K. Fredrickson, N. G. Isern, P. D. Majors, and H. Beyenal. 2011. "Contribution of Extracellular Polymeric Substances from Shewanella sp. HRCR-1 Biofilms to U(VI) Immobilization," Environmental Science and Technology, DOI: 10.1021/es200095j. (Reference Link)

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

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


May 23, 2011

Microbial Wires Could Generate Energy or Immobilize Environmental Contaminants

A team of researchers from the University of East Anglia and Pacific Northwest National Laboratory have determined, for the first time, the molecular structure of the proteins that enable the bacterium Shewanella oneidensis to transfer an electrical charge. The bacteria survive in oxygen-free environments by constructing small wires that extend through the cell wall and contact minerals—a process called iron respiration or “breathing rocks.” Proteins within these wires pass electrons outward to create an electrical charge. Using resources at the Environmental Molecular Sciences Laboratory (EMSL), including X-ray crystallography, the scientists gained new insights about how these proteins work together to move electrons from the inside to the outside of a cell. Identifying the molecular structure of these proteins is a key step toward potentially using microbes as a source of electricity; for example, by connecting them to electrodes to create microbial fuel cells. Because the bacteria also trap and transform the minerals they contact, the new information could advance the development of microbe-based agents for use in environmental remediation such as cleaning up legacy radioactive waste. EMSL is a Department of Energy national scientific user facility.

Reference: Clarke, T. A., M. J. Edwards, A. J. Gates, A. Hall, G. F. White, J. Bradley, C. Reardon, L. Shi, A. S. Beliaev, M. J. Marshall, Z. Wang, N. J. Watmough, J. Fredrickson, J. Zachara, J. N. Butt, and D. J. Richardson. 2011. "Structure of a Bacterial Cell Surface Decaheme Electron Conduit," Proceedings of the National Academy of Sciences of the United States, DOI 10.1073/pnas.1017200108. (Reference Link)

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

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


May 11, 2011

Fungus Study Offers Insights About Biogeochemical Cycling, Bioremediation

Users at the DOE Environmental Molecular Sciences Laboratory (EMSL) have helped fill a gap in the research community's knowledge about the role of fungi and manganese (Mn) oxides in biogeochemical cycling and bioremediation. Mn is a contaminant commonly found in coal mine drainage. Though high concentrations of soluble Mn, such as the reduced Mn(II) ion, can be problematic, Mn oxides, whose formation is readily stimulated by bacteria and fungi, can be quite helpful. These highly reactive compounds play a role in the cycling of nutrients and carbon in the soil and water, and, importantly, they can serve as bioremediating agents by scavenging metals. Previous Mn studies have centered on bacteria, but the role of fungi in Mn(II) oxidation and subsequent Mn oxide formation is just as important. The research team fully characterized the Mn oxides produced by four different species of fungi isolated from coal mine drainage treatment systems in central Pennsylvania by integrating a broad suite of microscopy and spectroscopy tools, including high-resolution transmission electron microscopy (HR-TEM) equipped with energy-dispersive X-ray spectroscopy at EMSL and X-ray absorption spectroscopy at the Stanford Synchrotron Radiation Lightsource. Their studies revealed that the species, growth conditions, and cellular structures of fungi influence the size, morphology, and structure—and, therefore, reactivity—of the Mn oxides. Their results underline the importance of species diversity in biogeochemical cycling and bioremediation. This project was funded by the National Science Foundation. Portions of the work were performed at EMSL, a national scientific user facility located at Pacific Northwest National Laboratory.

Reference: Santelli, C. M., S. M. Webb, A. C. Dohnalkova, and C. M. Hansel. 2011. "Diversity of Mn Oxides Produced by Mn(II)-Oxidizing Fungi," Geochimica et Cosmochimica Acta 75(10), 2762–76. (Reference Link)

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

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


May 05, 2011

Specialized Atomic Force Microscope Enables Studies of Mineral-Fluid Interfaces in Supercritical Carbon Dioxide

Among the options for reducing the emission of greenhouse gases such as carbon dioxide to the atmosphere is the injection of supercritical CO2 into the deep subsurface for long-term storage. However, some scientists wonder whether ongoing geochemical processes in the subsurface will ensure that the supercritical CO2 would remain sequestered. Efforts to study these processes require instrumentation that can handle samples at supercritical CO2 pressure and temperatures. In response to this need, a team of scientists from the Environmental Molecular Sciences Laboratory (EMSL), a DOE scientific user facility in Richland, WA, Wright State University, and Lawrence Berkeley National Laboratory has developed a high-pressure atomic force microscope (AFM) that enables the first-ever measurements of the atomic-scale topography of solid surfaces that are in contact with supercritical carbon dioxide (scCO2) fluids. Obtaining in situ, atomic-scale information about mineral-fluid interfaces at high pressure is particularly useful for understanding geochemical processes relevant to carbon sequestration. The ability to take in situ images as a function of time allows researchers to measure atomic-scale reaction rates by visualizing the dynamic processes that occur on the mineral surface and eliminates the need to alter experimental conditions between images. The new apparatus significantly extends the ability to make AFM measurements in environmental conditions not previously possible (in either commercial AFM instruments or in the few specially designed hydrothermal AFMs), and is designed to handle pressures up to 100 atmospheres at temperatures up to approximately 350 degrees Kelvin. The research team demonstrated the new microscope by imaging the disappearance of a hydrated calcium carbonate film on the calcite mineral surface in scCO2. The team met the technical challenge of maintaining precise control of pressure and temperature in the fluid cell, which is necessary to mitigate noise associated with density changes in a compressible fluid. The new apparatus can be used to study other gaseous or aqueous high-pressure solid-fluid chemical processes in addition to geochemical processes. For more information on this new capability, see: this highlight.

Reference: Lea, A. S., S. R. Higgins, K. G. Knauss, and K. M. Rosso. 2011. "A High-Pressure Atomic Force Microscope for Imaging in Supercritical Carbon Dioxide," Review of Scientific Instruments 82, 043709; DOI:10.1063/1.3580603. (Reference Link)

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

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


April 19, 2011

New Insights into Processes Impacting Plutonium (Pu) Mobility in the Environment

Reduced iron, Fe(II), found in numerous subsurface environments, is a reductant for a variety of redox-active actinide contaminants, such as Pu, found at DOE sites. Changing the redox state of actinide contaminants can profoundly decrease or increase their mobility by decreasing or increasing their solubility. A key question is whether solid-phase minerals facilitate these Fe(II) reactions by providing a "template" for potential reaction products that drives a more thermodynamically favorable reaction. A research team led by Pacific Northwest National Laboratory demonstrated the heterogeneous reduction of sparingly soluble Pu(IV) to aqueous Pu(III) by Fe(II) in the presence of goethite, a common iron mineral. Experimental data and thermodynamic calculations show how differences in the free energy of various possible solid-phase Fe(III) reaction products on the iron mineral surface can influence the extent of the reduction reaction and the production of aqueous Pu(III). Heterogeneous reduction reactions by Fe(II) have been demonstrated with other actinides such as uranium and technetium, but this study presents the first experimental evidence of enhanced heterogeneous reduction of plutonium by Fe(II) in the presence of an iron mineral. The work is an example of a surface catalyzed reduction mechanism that is not fully captured in current contaminant fate and transport models but is needed to more fully describe the potential mobility of Pu in the environment.

Reference: Felmy, A. R., D. A. Moore, K. M. Rosso, O. Qafoku, D. Rai, E. C. Buck, and E. S. Ilton. 2011. "Heterogeneous Reduction of PuO2 with Fe(II): Importance of the Fe(III) Reaction Product," Environmental Science and Technology, 45, 3952–58. DOI: 10.1021/es104212g. (Reference link)

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

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


March 03, 2011

Microbes Limit Technetium Movement in Groundwater

A legacy of DOE's former weapons production activities is the contamination of groundwater by radionuclides such as technetium (Tc). Tc-99 found in Hanford site groundwater is a mobile and long-lived fission product whose mobility can be retarded by subsurface minerals containing reduced or ferrous iron. Scientists from Pacific Northwest National Laboratory (PNNL) have now found that several species of microbes can increase the amount of reduced iron in the subsurface as part of their metabolic processes and that this additional reduced iron significantly reduces the mobility of Tc. Using a variety of instruments available at the Environmental Molecular Sciences Laboratory and the Advanced Photon Source, DOE scientific user facilities at PNNL and Argonne National Laboratory, respectively, the team found that Tc was 10 times less soluble when it came in contact with microbially generated reduced iron. This research provides a basis for a conceptual approach to limit the movement of Tc in groundwater at DOE sites.

Reference: Plymale, A. E., J. K. Fredrickson, J. M. Zachara, A. C. Dohnalkova, S. M. Heald, D. A. Moore, D. W. Kennedy, M. J. Marshall, C. Wang, C. T. Resch, and P. Nachimuthu. 2011. Environmental Science and Technology 45, 951-7.

Contact: Robert T. Anderson, SC 23.1, (301) 903-5549, Paul E. Bayer, SC-23.1, (301) 903-5324
Topic Areas:

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


March 03, 2011

New Insight into the Mechanism of Plutonium Transport in the Environment

The potential migration of plutonium in the environment is a concern at DOE sites such as the Hanford Nuclear Reservation and the Nevada Test Site, as well as an issue in nuclear waste disposal for nuclear energy development. Using a number of transmission electron microscopy techniques Lawrence Livermore National Laboratory researchers and collaborating Clemson University scientists have provided important new understanding of the formation and the biogeochemical mechanisms controlling plutonium migration. Once thought immobile in the subsurface, it has been recently recognized that plutonium is capable of being transported with the colloidal faction of groundwater. The researchers examined the interaction of plutonium nanocolloids with environmentally relevant minerals such as iron-containing goethite and silicon-containing quartz. The studies revealed the molecular basis of potential binding through epitaxial growth between the plutonium nanocolloids and colloid goethite that may be a possible mechanism for enhanced plutonium transport. The results improve our understanding of how molecular-scale behavior at the mineral-water interface may facilitate transport of plutonium at the field scale, providing important molecular-level input to improve contaminant transport models and the prediction of plutonium behavior.

Reference: Powell, B. A., Z. Dai, M. Zavarin, P. Zhao, and A. B. Kersting. 2011. "Stabilization of Plutonium Nano-Colloids by Epitaxial Distortion on Mineral Surfaces," Environmental Science and Technology 45, 2698–2703. DOI:dx.doi.org/10.1021/es1033487. (Reference link)

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

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


March 03, 2011

New Method for Uranium Remediation in Acidic Waste Plumes

Acidic uranium (U) groundwater plumes resulted from acid extraction of plutonium during the Cold War and from U mining and milling operations. A sustainable remediation method is not yet available. DOE scientists from Lawrence Berkeley National Laboratory are exploring the use of humic acids (HA) to immobilize U in groundwater under acidic conditions. When acidic groundwater (pH below 5.0) is treated with humic acid, U can adsorb onto aquifer sediments rapidly, strongly, and practically irreversibly. Using historically contaminated sediments from the DOE Savannah River site, column-leaching experiments show that with humic acid treatment, 99% of the contaminant U was immobilized at pH < 4.5 under normal groundwater flow rates, suggesting that humic acid treatment is a promising in situ remediation method for acidic U waste plumes. As a remediation reagent, humic acids are resistant to biodegradation, cost-effective, nontoxic, and easily introducible into the subsurface.

Reference: Wan, J., W. Dong, and T. K. Tokunaga. 2011. "Method To Attenuate U(VI) Mobility in Acidic Waste Plumes Using Humic Acids," Environmental Science and Technology, 45(6), 2331–37. DOI: 10.1021/es103864t. (Reference link)

Contact: David Lesmes, SC 23.1, (301) 903-2977
Topic Areas:

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


March 03, 2011

New Model Improves Prediction of Contaminant Movement

The conventional approach for monitoring contaminant movement in groundwater is to drill monitoring boreholes and watch the groundwater for contaminants—a time-consuming and expensive approach subject to uncertainties regarding the direction or depth of contaminant movement. Moreover, in areas of high rainfall or recharge, contaminant movement can be greatly influenced by significant recharge events. A team of scientists from Lawrence Berkeley National Laboratory, Oak Ridge National Laboratory, and the University of Tennessee collaborated to develop a modeling approach that couples time-lapse electrical resistivity data with hydrogeochemical data and processes. The team validated the model using data from a location within DOE’s Oak Ridge Integrated Field Research Challenge site in Oak Ridge, TN, demonstrating that they could accurately simulate recharge events for this location using this coupled approach. Estimates from this model are now being used to constrain the site-wide model.

Reference: Kowalsky, M. B., E. Gasperikova, S. Finsterle, D. Watson, G. Baker, and S. S. Hubbard. 2011. "Coupled Modeling of Hydrogeochemical and Electrical Resistivity Data for Exploring the Impact of Recharge on Subsurface Contamination," Water Resources Research doi:10.1029/2009WR008947.

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

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


March 03, 2011

Predicting Microbial Interactions Could Improve Uranium Bioremediation

Advances in genome sequencing and the capability to develop genome-scale metabolic models have enabled the ability to predict microbial interactions. An analysis of two microbes known to compete in situ during tests of uranium bioremediation predicts how life strategies and growth rates for each are altered by substrate and nutrient availability and the implications of these interactions on uranium bioremediation strategies. DOE researchers from the University of Massachusetts and University of Toronto working with metabolic models for two metal-reducing microorganisms (Rhodoferax and Geobacter) present in the subsurface at a uranium bioremediation test site in Rifle, CO, explain how the introduction of acetate and the availability of ammonium impacts growth rates and the life strategies of these two organisms. Acetate addition in the absence of ammonium favors Geobacter metabolism consistent with field observations. However, the models predict that Rhodoferax metabolism should be favored in the presence of ammonium due to a higher overall growth rate. The results help explain field observations of decreased uranium bioreduction activity in areas with elevated ammonium concentrations. Unlike Geobacter species, Rhodoferax species are not known to reduce uranium indicating ammonium concentration as an important design criterion for uranium bioremediation.

Reference: Zhuang, K., M. Izallalen, P. Mouser, H. Richter, C. Risso, R. Mahadevan, and D. R. Lovley. 2011. The ISME Journal 5, 305-16.

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

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


February 07, 2011

Dual Role for Organic Matter in Mercury Cycling and Toxicity

Mercury from worldwide industrialization is a widely recognized global pollutant. Concern over mercury is due to the bioaccumulation of the highly toxic methylmercury. Methylmercury is created by microbes through the conversion of inorganic mercury, Hg(II), under anaerobic conditions, such as those found in stream sediments. However, dissolved organic matter (DOM), which is ubiquitous in soils and aquatic sediments, forms strong complexes with Hg(II), influencing the microbial production of methylmercury. A research team from Oak Ridge National Laboratory (ORNL) has found that low concentrations of DOM reduce Hg(II), and that high concentrations of DOM forms complexes with Hg. The authors propose that the dual nature of DOM activity is due to the redox state of sulfur in DOM and the DOM:Hg ratio which affect the transformation of Hg and the potential microbial production of toxic methylmercury. These findings provide greater understanding of the potential transformations of Hg that are occurring not only in the mercury-contaminated East Fork Poplar Creek stream sediments on the Y-12 complex in Oak Ridge but in the sediments of many other mercury-contaminated streams worldwide.

Reference: Gu, B., Y. Bian, C. L. Miller, W. Dong, X. Jiang, and L. Liang. 2011. "Mercury Reduction and Complexation by Natural Organic Matter in Anoxic Environments," Proceedings of the National Academy of Sciences USA DOI:10.1073/pnas.1008747108.

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

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


January 26, 2011

Modeling How Uranium Sticks to Soils

Determining how radioactive material sticks to soil and affects its movement into nearby water sources is a major challenge for cleaning up nuclear waste sites. This waste, which may include uranium, can be diffuse as well as difficult to isolate and remove. To reduce the cost and complexity of complete removal, innovative and inexpensive methods are needed to expedite cleanup efforts around the world, especially in sites with vast areas of contamination. Scientists at Pacific Northwest National Laboratory discovered that the surface of a common soil mineral, aluminum oxide, adheres to uranium, making it less mobile. The researchers assembled a detailed picture of how uranium adheres to the mineral surface using a computational model. By modeling the behavior of uranium in a complex subsurface environment, they were able to show that uranium sticks to the surface of aluminum oxide without changing it in any way and that a more acidic environment improves how well the two stick together. This cluster model approach allows for a straightforward comparison between different sorption mechanisms, and predictions can be directly related to X-ray adsorption experiment measurements. This approach can be used to model surface reactivity and be further utilized in other complex model systems. It also may lead to efficient, more affordable solutions for cleaning contaminated ground.

Reference: Glezakou, V., and W. A. de Jong. 2011. “Cluster-Models for Uranyl(VI) Adsorption on α-Alumina,” The Journal of Physical Chemistry A 115(7), 1257–63. DOI: 10.1021/jp1092509. (Reference link) (See also)

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



Computational modeling of uranium oxide ions with aluminum oxide provides insights that are contributing to development of a cheap and effective way to clean up nuclear waste sites. more...

Image Credit: Pacific Northwest National Laboratory



December 06, 2010

A New Mechanism for Microbial Community Metabolism

Outside of laboratories, microbial species rarely exist in isolation. Many important environmental processes are actually mediated by complex communities of microbes. In many cases, two or more species have evolved to perform a cooperative metabolic activity that would be energetically unfavorable for either organism acting independently. Research published in the December 3 issue of Science and led by DOE scientist Derek Lovley of the University of Massachusetts, Amherst, describes a new mechanism by which the bacterium Geobacter metallireducens consumes ethanol, an important intermediate compound in oxygen free soils and sediments, in cooperation with a second organism Geobacter sulfureducens. For this reaction to yield energy for either partner, electrons produced from ethanol oxidation must be rapidly consumed. Although it was previously assumed that the first organism uses a hydrogen production mechanism to pass electrons to its partner, the authors have discovered that electrons are instead directly fed to G. sulfureducens via conductive "nanowires" called pili on the cell surface, resulting in much more efficient collaborative growth. These results provide important new clues on the fundamentals used by microbes to mediate important environmental processes such as carbon cycling and contaminant transformation and suggest intriguing new approaches to direct generation of electricity in microbial fuel cell systems.

Reference: Summers, Z.M., H. E. Fogarty, C. Leang, A. E. Franks, N. S. Malvankar, and D. R. Lovley. 2010. "Direct Electron Exchange Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria," Science 330:1413-15.

Contact: Dan Drell, SC-23.2, (301) 903-4742
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Division: SC-23.2 Biological Systems Science Division, BER


December 06, 2010

New Approach for Studying Microbes in their Native Environment

Advances in proteomics techniques are enabling scientists to understand the mechanisms of in situ microbial metabolism associated with DOE relevant environmental processes, including site remediation and carbon sequestration. A multidisciplinary team of DOE researchers working at a field research site in Rifle, Colorado, has developed proteomic techniques to track changes in expressed metabolic pathways for environmentally relevant and dominant metal- and sulfate-reducing bacteria during tests of in situ uranium bioremediation. The team is developing these new techniques to advance the study of microorganisms in their natural environment and to mechanistically link microbial metabolism with changes in geochemistry observed in natural sediments. These approaches are advancing a more predictive understanding of biogeochemical processes associated with in situ uranium bioremediation but are also applicable to a broad range of DOE environmental challenges.

Reference: Callister, S.J., M.J. Wilkins, C.D. Nicora, K.H. Williams, J.F. Banfield, N.C. Verberkmoes, R.L. Hettich, L. N'Guessan, P.J. Mouser, H. Elifantz, R.D. Smith, D.R. Lovley, M.S. Lipton, and P.E. Long. 2010. "Analysis of Biostimulated Microbial Communities From Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles," Environmental Science & Technology. ASAP Article. DOI: 10.12021/ES101029f, Published on the web Nov-8-2010.

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

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


November 22, 2010

Interactions of Bacteria with Uranium in the Environment

Uranium in the 6+ oxidation state is quite soluble and can thus move rapidly in uranium-contaminated subsurface environments. In contrast, uranium in the 4+ state is highly insoluble, and is therefore less likely to move the subsurface environment. New research has identified important aspects of how bacteria reduce uranium 6+ to uranium 4+, showing that the latter is produced in a variety of forms, not just in the expected, simple form of uraninite (UO2). The authors of the new study used a variety of techniques at the Stanford Synchrotron Radiation Lightsource (SSRL) to characterize the products of uranium reduction in various microbial cultures, including x-ray absorption spectroscopy (XAS). The XAS experiments showed that many of the uranium 4+ products lacked the spectral peak characteristic of uraninite. Instead, a variety of complex solids involving uranium and phosphate, and in some cases also calcium were identified, as well as solids in which uranium 4+ is bound to the surface of the bacterial biomass. These results will be helpful in modeling the mobility of uranium species at contaminated DOE sites. The research was led by Rizlan Bernier-Latmani of the École Polytechnique Fédérale de Lausanne in Switzerland, and involved scientists at SSRL. It is just published online in Environmental Science & Technology.

Reference: Bernier-Latmani, R., et al. 2010. "Non-uraninite Products of Microbial U(VI) Reduction," Environmental Science & Technology, online November 11, 2010. DOI: 10.1021/es101675a

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

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


November 22, 2010

New Roles for Microbes in the Mercury/Methyl Mercury Cycle

Mercury is a global pollutant released into the atmosphere during coal burning and into freshwater systems froma agricultural runoff and industrial discharge. Once in freshwater systems, microorganisms, known as d-proteobacteria, create methylmercury (MeHg), a highly toxic form of mercury that accumulates in biological systems. High concentrations of MeHg are detected in biota in the East Fork Poplar Creek in Oak Ridge, Tennessee, even though mercury producing weapons production activities at the Y-12 National Security complex were discontinued many years ago. Oak Ridge National Laboratory scientists recently characterized the impacts of mercury and uranium contamination on the diversity and structure of bacterial populations from the East Fork Poplar Creek and other nearby streams. The team sampled 6 different streams at select times over a year and demonstrated that specific microbial groupings (Verrucomicrobia and e-proteobacteria groupings) were most closely correlated with high MeHg levels, even though no bacteria in these groupings are known to have any role in MeHg generation. This is the first study to indicate an influence of MeHg on an existing microbial community, and suggests that bacteria within the Verrucomicrobia and the e-proteobacteria groupings have an important, but yet to be determined role in the overall Hg/MeHg cycle.

Reference: Vishnivetskaya T. A., J.J. Mosher, A. V. Palumbo, Z. K. Yang, M. Podar, S. D. Brown, S.C. Brooks, B. Gu, G. R. Southworth, M. M. Drake, C. C. Brandt, and D. A. Elias. 2010. "Mercury and Other Heavy Metals Influence Bacterial Community Structure in Contaminated Tennessee Streams," Applied and Environmental Microbiology, published online ahead of print on 5 November 2010, doi:10.1128/AEM.01715-10.

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

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


October 12, 2010

New Models of Uranium Migration at the Hanford Site Shed Light on its Persistance

Three recent modeling studies shed light on the importance of the coupled physical, chemical, and geological factors that have caused a uranium plume at the Hanford 300 Area to persist over three decades. In contrast, legacy models of the site predicted that natural flushing of the aquifer would reduce the uranium concentration in the groundwater to drinking water standards within 10 years. These new simulations, performed by different teams, ranged in duration from a few days to 20 years and in spatial scale from laboratory columns to a massive 3-D field-scale simulation of the Hanford 300 Area. The smaller scale experiments elucidated the importance of various geochemical factors that control the adsorption and release of uranium from sediments. The field scale simulations executed on ORNL’s Jaguar supercomputer (Hammond and Lichtner, 2010), tested how pore scale processes couple with larger scale factors to control the evolution of the uranium plume over longer time periods. The results indicate that rapid fluctuations in the Columbia River stage combined with the slow release of bound uranium from contaminated sediment are the primary cause for the persistent uranium plume at the Hanford 300 Area. These DOE funded modeling studies are guiding the design of additional field and laboratory investigations to better understand the spatial and temporal dynamics of the plume and to inform future remediation efforts at the site.

References: Hammond, G. E., and P. C. Lichtner. 2010. "Field-scale model for the natural attenuation of uranium at the Hanford 300 Area using high-performance computing," Water Resour. Res., 46, W09527, doi: 10.1029/2009WR008819.

Ma, R., C. Zheng, H. Prommer, J. Greskowiak, C. Liu, J. Zachara, and M. Rockhold. 2010. "A field-scale reactive transport model for U(VI) migration influenced by coupled multirate mass transfer and surface complexation reactions," Water Resour. Res., 46, W05509, doi: 10.1029/2009WR008168.

Greskowiak, J., H. Prommer, C. Liu, V. E. A. Post, R. Ma, C. Zheng, and J. M. Zachara. 2010. "Comparison of parameter sensitivities between laboratory and field-scale model of uranium transport in a dual domain, distributed rate reactive system," Water Resour. Res., 46, W05509, doi: 10.1029/2009WR008781.

Contact: Robert T. Anderson, SC 23.1, (301) 903-5549, David Lesmes, SC 23.1, (301) 903-2977
Topic Areas:

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


September 07, 2010

A New Approach to Understand Complex Microbial Communities

Microorganisms control the rates of numerous processes in the environment including contaminant degradation and biogeochemical cycling of carbon and other nutrients; however, they rarely perform these functions alone or in isolation. Microorganisms exist in communities whose dynamic activities and responses to environmental influences remain poorly understood. Building on the increasing availability of microbial species whose genomes have been sequenced, researchers at Oak Ridge National Laboratory developed a model system of three microbial species to probe the details of microbial community interactions and physiology. Co-cultures containing a Clostridia, Desulfovibrio and Geobacter species were used to examine carbon and energy flow in an anaerobic microbial community. The availability of genomic information for each microbe enabled the use of powerful techniques for analysis of gene and protein expression to understand the dynamic shifts in metabolism resulting from environmental changes and/or association or competition within the microbial community. The model system is applicable to numerous environmental processes where fermentative production of simple organic acids (by Clostridia) drives microbial metabolism such as sulfate-reduction (by Desulfovibrio) or iron reduction (by Geobacter). This project will advance our predictive understanding of microbial community interactions in a manner not previously possible and will increase our understanding of environmental processes relevant to DOE such as carbon and nutrient cycling in soils and contaminant biotransformation in contaminated groundwater.

Reference: Miller, L. D., J. J. Mosher, A. Venkateswaran, Z. K. Yang, A. V. Palumbo, T. J. Phelps, M. Podar, C. W. Schadt, and M. Keller. 2010. Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments. BMC Microbiology. 10:149

Contact: Robert T. Anderson, SC 23.1, (301) 903-5549, Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

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


September 07, 2010

Uranium Isotopes Tell a Fractionating Story

Uranium is a risk-driving contaminant at many DOE sites and its mobility in groundwater is influenced by both geochemical and biological processes. Methods are needed to identify which biogeochemical processes influence uranium mobility so that we can develop more robust contaminant transport models. Researchers at the University of Illinois, Pacific Northwest National Laboratory and Lawrence Berkeley National Laboratory have developed an isotopic method based on U-238/U-235 ratios that can be used to distinguish between microbe-mediated (preferentially U-238) versus chemical (either isotope) reduction of uranium in contaminated subsurface environments. In the laboratory, soluble uranium [U(VI)] can be reduced to an insoluble species [U(IV)] either enzymatically, by microorganisms, or chemically, by species such as Fe(II) or sulfide. To accurately model the transport of uranium in groundwater, methods are needed that discriminate between enzymatic and chemical reduction of uranium. At a field research site in Colorado, stimulation of subsurface microbial communities produces a decrease in the concentration of soluble uranium co-incident with an increase in uranium-reducing microorganisms and the production of chemical reductants such as Fe(II) and sulfide. Samples collected during these tests indicated a preferential shift in the U-238/U-235 ratios consistent with an enzymatic reduction process. The results indicate that isotopic methods can be used to distinguish between biotic and abiotic processes influencing uranium reduction under bioremediation conditions and/or natural attenuation conditions in the environment. The technique is important in the development of more robust models of contaminant transport in groundwater at uranium-contaminated sites.

Reference: C.J. Bopp IV, C.C. Lundstrom, T.M. Johnson, R.A. Sanford, P.E. Long, K.H. Williams. (2010) "Uranium 238U/235U Isotope Ratios as Indicators of Reduction: Results from an in situ Biostimulation Experiment at Rifle, Colorado, U.S.A.," Environ. Sci. Technol. 44(15):5927-5933.

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

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


June 28, 2010

DOE Mass Spectrometry on Cover of Chemical & Engineering News

Mass spectrometry is a critical technique for analysis of complex biological systems. The technique is essential for DOE’s research into biofuel production and plays an important role in studying such diverse areas as low dose radiation biology, environmental contamination, and microbial capture of carbon dioxide. The Pacific Northwest National Laboratory (PNNL) has carried out much pioneering research in mass spectrometry and its application in systems biology. The June 21, 2010 issue of Chemical & Engineering News includes new developments at PNNL in its cover story on high resolution mass spectrometry. The cover photo shows Yehia Ibrahim at a high performance time-of-flight mass spectrometer in PNNL’s Environmental Molecular Sciences Laboratory (EMSL). Comments by PNNL scientist Richard D. Smith on the impact of the new technologies, being developed in part with American Reinvestment and Recovery Act (ARRA) funding through EMSL, are included in the story. The article also mentions the collaboration between the EMSL and the National High Magnetic Field Laboratory at Florida State University under a separate effort to develop the newest generation of mass spectrometric instruments.

Reference: Celia Henry Arnaud, “High-Res Mass Spec: Mass spectrometry users have more choices for high resolving power, from conventional ion cyclotron resonance to newer time of flight”, Chemical & Engineering News, June 21, 2010, pages 10–15.

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

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


June 07, 2010

Bacteria Produce Distinct Form of Reduced Uranium

Some gram-negative microorganisms are known to reduce soluble uranium to insoluble uraninite [UO2(s)] forming the basis for in situ bioremediation or natural attenuation techniques for uranium in contaminated groundwater. But do all bacteria produce the same forms of reduced uranium? New results indicate that some gram-positive bacteria such as Desulfitobacteria, common to subsurface environments, also reduce soluble uranium but produce a mononuclear uranium species that differs from the commonly observed uraninite mineral form produced by gram-negative bacteria. Researchers from the Georgia Institute of Technology and Argonne National Laboratory working at the Advanced Photon Source (APS) show that Desulfitobacteria produce a form of reduced uranium that is likely coordinated with light atom shells such as C/N/O or S/P rather than the commonly observed uraninite mineral structure [UO2(s)]. The chemical identity of uranium species in subsurface environments is crucial to modeling the biogeochemical processes controlling contaminant transport at DOE sites. These results suggest that these alternate forms of reduced uranium also need to be characterized to be able to accurately predict uranium mobility/stability in reduced environments.

Reference: KE Fletcher, MI Boyanov, SH Thomas, Q. Wu, KM Kemner, FE Loeffler, (2010) Environ. Sci. Technol., 44(12): 4705-4709

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

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


June 07, 2010

Elemental Composition of Glass Used to Capture Nuclear Waste Makes a Difference

To better understand the structure and durability of aluminoborosilicate glass used to capture nuclear waste, Pacific Northwest National Laboratory scientists conducted systematic experiments with aluminum, boron, sodium and silicon, the four major components of nuclear waste glass. The team synthesized glasses with different concentrations of these elements and then, using the solid-state nuclear magnetic resonance capabilities at DOE's Environmental Molecular Sciences Laboratory at PNNL, along with flow-through dissolution experiments, they investigated how structural changes in the glass affected their dissolution as a function of pH and temperature. Results indicate that the dissolution rate for glass is controlled by rupturing the aluminum to oxygen bond or the silicon to oxygen bond. Determining how glass breaks and dissolves is paramount for improving the prediction of nuclear waste release from glass and it advances fundamental understanding of how minerals weather and cycle these elements in subsurface environments.

Reference: Pierce EM, LR Reed, WJ Shaw, BP McGrail, JP Icenhower, CF Windisch, Jr, EA Cordova, and J Broady. 2010. "Experimental Determination of the Effect of the Ratio of B/Al on Glass Dissolution along the Nepheline (NaAlSiO4)-Malinkoite (NaBSiO4) Join." Geochimica et Cosmochimica Acta 74(9):2634-2654.

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

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


June 07, 2010

Microorganisms "Breathe" Humic Particulates

Organic matter in the soil, such as humic substances, plays a key role in determining the fate and transport of radioactive and heavy metal contaminants in the subsurface. Just-published research has demonstrated for the first time that particulate humic substances can serve as electron carriers for anaerobic metabolism by microorganisms. The humic substances act to shuttle electrons between the microorganisms and iron oxide minerals. Recent reports have suggested that microbial communities in sedimentary environments may be networked via nanowires or other bacterial appendages (or secretions) capable of accepting and donating electrons derived from microbial metabolism. Thus, these redox active humic particulates, in coordination with appropriate mineral phases, could be an integral component of these microbial networks, and have a significant role in determining the chemical form - and the resulting mobility - of contaminants of interest to DOE. The research is published in the June 2010 issue of Nature Geoscience. It was conducted by DOE-funded scientists at the University of Wisconsin, Madison, and at laboratories in Germany.

Reference: E.E. Roden, A. Kappler, I. Bauer, J. Jiang, A. Paul, R. Stoesser, H. Konishi, H. Xu, (2010), Nature Geoscience, 3:417-421.

Contact: Robert T. Anderson, SC 23.1, (301) 903-5549, Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER,SC-23.2 Biological Systems Science Division


May 24, 2010

New Method to Study Microbial "First Responder" Proteins

Proteins found in the surface membranes of cells are essential for maintaining normal biological functions in cells, and often are the "first responders" to environmental stimuli. But membrane proteins can be low in abundance and insoluble, making them challenging to quantify and purify. To meet this challenge, scientists at Pacific Northwest National Laboratory developed a strategy to quantify and purify proteins on the surface membranes of cells. Using capabilities at the Environmental Molecular Sciences Laboratory (EMSL), a team of scientists enriched surface membrane proteins expressed by the bacterium Shewanella oneidensis MR-1, using a membrane-impermeable chemical probe. By linking this method with post-digestion stable isotope labeling, surface proteins could be quantified. Armed with this technique, scientists can better study the function of many bacterial membrane proteins.

Reference: Zhang H, RN Brown, W-J Qian, ME Monroe, SO Purvine, RJ Moore, MA Gritsenko, L Shi, MF Romine, JK Fredrickson, L Paaa-Tolic, RD Smith, and MS Lipton. 2010. "Quantitative Analysis of Cell Surface Membrane Proteins using Membrane-Impermeable Chemical Probe Coupled with 18O Labeling." Journal of Proteome Research 9:2160-2169.

Contact: Marvin Stodolsky, SC-23.2, (301) 903-4475, Paul E. Bayer, SC-23.1, (301) 903-5324, Robert T. Anderson, SC 23.1, (301) 903-5549
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER,SC-23.2 Biological Systems Science Division


May 10, 2010

Unraveling the Microbial Mechanism for Mercury Resistance

Some microbes can metabolize inorganic and organic mercury to less toxic forms using the MerR protein. Using small-angle X-ray scattering (SAXS) complemented by molecular dynamics simulations, a scientific team from the Universities of Tennessee, Georgia and California at San Francisco and Oak Ridge National Laboratory determined that when a single mercury ion binds to the MerR protein a structural change is induced. This structural change turns on the DNA transcription machinery for several other proteins and enzymes involved in removing the toxic mercury from the cell. Understanding the mechanism by which the proteins in these microorganisms bind to and metabolize mercury could be useful for identifying biological strategies for removing or transforming mercury in groundwater or soils.

Reference: Guo, H-B., A. Johs, J.M. Parks, L. Olliff, S.M. Miller, A.O. Summers, L. Liang and J.C. Smith. 2010. "Structure and Conformational Dynamics of the Metalloregulator MerR upon Binding of Hg(II)." Journal of Molecular Biology 398: 555-568.

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

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


May 03, 2010

Stressful Living in Contaminated Groundwater

Microorganisms are the primary drivers of key subsurface geochemical processes but we only have limited understanding of the composition and function of the microbial communities involved. "Metagenomic" sequencing is providing insights into the metabolic capabilities of these microbial communities and microbial adaptations to environmental changes. A multi-institutional team from the University of Oklahoma, Oak Ridge and Lawrence Berkeley National Laboratories, and the DOE Joint Genome Institute has now sequenced microbial community DNA isolated from groundwater at a site with low pH and high levels of uranium, technetium, nitrate, and organic solvents. The analysis reveals a significant reduction in microbial diversity from background and an overabundance of genes that confer tolerance for nitrate, heavy metals, and organic solvents. In addition, the overabundance of genes for DNA recombination and repair suggests the presence of lateral gene transfer induced by exposure to extreme environmental conditions. These results expand our understanding of how microbial communities adapt to and influence the fate of environmental contaminants.

Reference: Hemme, C.L., Y. Deng, T.J. Gentry, M.W. Fields, L. Wu, S. Barua, K. Barry, S.G. Tringe, D.B. Watson, Z. He, T.C. Hazen, J.M. Tiedje, E.M. Rubin, and J. Zhou. 2010. "Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community." ISME Journal 4: 660-672.

Contact: Joseph Graber, SC-23.2, (301) 903-1239, Paul E. Bayer, SC-23.1, (301) 903-5324
Topic Areas:

Division: SC-23 BER


May 03, 2010

Subsurface Biogeobatteries: Geophysics meets Microbiology

Tracking subsurface microbial activity can be an important component in developing bioremediation or natural attenuation strategies but often requires costly drilling. New research on the production of electrical current by electrochemically reduced sediments in subsurface contaminant plumes formed as a result of microbial activity coupled to the production of reduced iron and sulfur minerals may provide a cheaper tracking alternative. Although known for some time, a research team led by the Colorado School of Mines developed a theoretical basis for linking the production of current to microbial activity in contaminated environments. The work lays a theoretical basis for "self-potential" (SP) techniques to map areas of microbially-mediated electrical anomalies in subsurface environments. SP can be a practical surface-deployed method to track the extent of microbial activity in subsurface environments.

Reference: Revil A, Mendonca, CA, Atekwana, EA, Kulessa B, Hubbard, SS, Bohlen, KJ. "Understanding Biogeobatteries: Where geophysics meets microbiology," Journal of Geophysical Research-Biogeosciences, 115:G00G02, doi:10.1029/2009JG001065 (2010).

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

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


April 26, 2010

Hydrogel-Encapsulated Soil: A New Tool to Measure Contaminant-Soil Interactions in the Subsurface

Measuring the transformation of contaminants such as radionuclides and heavy metals in the subsurface over time remains an important but difficult challenge. A team of scientists from Oak Ridge National Laboratory (ORNL) has developed a novel and powerful approach for encapsulating soils and sediments in polyacrylamide hydrogels called PELCAPs. The PELCAPs can be placed in the subsurface for extended periods of time, readily retrieved, and non-destructively assayed to observe and measure many water-solid contaminant interactions under natural groundwater flow conditions. The team showed that when PELCAPs were placed in a subsurface environment with uranium contaminated groundwater, uranium was adsorbed by the soils in the PELCAPs. The PELCAPs could be resampled over several years, the transformation of uranium-contaminated soil could be readily determined, and the hydrogel remained inert and fully functional. Finally, many different soils (limestone, Portland cement paste, activated charcoal and other materials) could be encapsulated for extended periods of time in the hydrogel. PELCAPs represent an important new tool for measuring contaminant-soil interactions in the subsurface.

Reference: Spalding, B., S.C. Brooks and D.B. Watson. 2010. "Hydrogel-Encapsulated Soil: A Tool to measure Contaminant Attenuation In Situ." Environmental Science & Technology 44(8):3-47-3051.

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

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


March 08, 2010

New Insight Into How Iron Oxide Minerals Influence Transport of Uranium in Subsurface

Iron-oxide minerals play a critical role in determining the mobility of subsurface contaminants such as uranium at DOE cleanup sites. Understanding how the surface reactivity of these minerals changes over time is critical to understanding uranium transport. Researchers funded by DOE and NSF at SLAC National Accelerator Laboratory and Stanford University have developed a new structural model that accounts for gaps in the mineral structure of ferrihydrite as it transforms to the more stable mineral hematite and shows that these gaps are likely to be important sites for the binding of contaminants such as uranium. Synchrotron-based studies led to a detailed analysis of the changes occurring in the mineral structure of ferrihydrite as it is converted to hematite. The research also produced new information about the interaction of microbes with these minerals and how these interactions influence the chemical form of uranium.

Reference: F. Marc Michel, Vidal Barrón, José Torrent, María P. Morales, Carlos J. Serna, Jean-François Boily, Qingsong Liu, Andrea Ambrosini, A. Cristina Cismasu, and Gordon E. Brown, Jr. "Ordered ferrimagnetic form of ferrihydrite reveals links among structure, composition, and magnetism," Proceedings of the National Academy of Sciences, 107: 2787-2792 (2010).

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

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


February 01, 2010

New Gene Tools Help Predict Microbial Growth in the Subsurface

Environmental microbes modify their growth and activity in response to changing nutrients in largely unknown ways. This complicates the development and use of predictive models of microbial metabolism in the environment. New gene expression tools now enable researchers to determine whether microbes are actively taking up phosphate for growth or not. The new tools developed by researchers at the University of Massachusetts, Lawrence Berkeley National Laboratory, Pacific Northwest National Laboratories, the J. Craig Venter Institute and the University of California-Berkeley enables researchers to assess phosphate bioavailability from the microbe's "point of view" and to use the information to calibrate and revise models of microbial growth in the environment and to directly test nutrient formulations for their bioavailability potential. These tools were tested during in situ field tests of uranium bioremediation and add to a growing set of tools advancing a predictive understanding of microbial communities in the environment. These new results were reported online at The ISME Journal (10 December 2009:1-14).

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

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


January 19, 2010

Electrodes Tap into Microbial Activity During Uranium Bioremediation

Microbes in subsurface environments can be used to remediate uranium-contaminated sites but scientists have not been able to monitor the progress of bioremediation without physically taking samples. Now, researchers from Lawrence Berkeley National Laboratory, Ruhr University, Pacific Northwest National Laboratory, and the University of Massachusetts have adapted microbial fuel cell techniques to the detection of microbial activity in the environment. Electrodes placed into the subsurface during uranium bioremediation provide a signal that correlates with acetate availability (a microbial energy source) demonstrating a new method to monitor microbial activity in the environment. The results suggest that electrical signals could be used to monitor the progress of bioremediation processes and provide real-time data for use in predictive models of microbial metabolism during uranium bioremediation. These techniques are not specific to uranium bioremediation and in fact could be used to detect microbial activity in a host of different environmental settings thereby allowing researchers to directly examine rates of microbial processes in environment. The results are reported in the latest addition of Environmental Science and Technology (2010) 44:47-54.

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

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


January 19, 2010

New Technique for Studying Biogeochemical Transformation on Uranium

Understanding the fate and transport of uranium in subsurface environments is a major concern for planning remediation of contamination at the DOE cleanup sites. Yet it is very difficult to study the biogeochemical processes that impact uranium mobility in these environments. Research at the Argonne National Laboratory has now led to a realistic laboratory-based approach that uses sediments from field contaminated locations in microcosms prepared and maintained under conditions that closely match those in the field. Tests of the new technique were carried out using sediment samples from the Oak Ridge National Laboratory Integrated Field-Research Challenge site. The microcosms were maintained under anaerobic (no oxygen) conditions to ensure that microbial activity would match that in the sampled subsurface field site. Changes in chemical characteristics of the uranium in each microcosm were determined periodically over an eleven month period using x-ray absorption spectroscopy beamlines at the Advanced Photon Source. Analysis of the results of these experiments, along with biochemical and geochemical data, indicates that at least two distinct processes are taking place that gradually transform the highly mobile uranium (VI) to highly immobile uranium (IV). The research has just been published in Environmental Science & Technology.

Reference: S.D. Kelly, et al., "Uranium transformations in static microcosms", Environ. Sci. Technol. 2010 44(1), 236-242.

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

Division: SC-23.2 Biological Systems Science Division, BER


November 02, 2009

Protein Sequences Help Scientists Decipher Uranium Bioremediation Processes

Native microbes in subsurface environments interact with contaminants, play a role in modifying contaminant mobility in the subsurface environment and can be used as part of biology-based remediation strategies. A multi-disciplinary, multi-institution team of investigators working at a field research site in Rifle, CO, (a former uranium mill tailings site managed by the DOE Office of Legacy Management) characterized the genomes of the dominant microbial populations and the proteins they expressed (proteomics), demonstrating that an understanding of cell metabolism can be used to diagnose the status of subsurface microbial communities involved in uranium bioremediation and as monitors of environmental processes in general. Changes in microbial central metabolism, energy generation and microbial strain composition over time reflected the changing geochemical conditions stimulated in situ during the field test. The results yielded important insights into the functioning of subsurface microbial communities, providing mechanistic information that can used to inform models of uranium bioremediation. This "proteogenomic" approach enables scientists to study the mechanistic basis for the growth and functioning of active microbes and microbial communities in the environment.

Reference: Appl. Environ. Microbiol., 2009, 75(20): 6591-6599

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

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


October 13, 2009

Visualizing Microbial Activity in the Subsurface

The transport of metal and radionuclide contaminants in groundwater can be greatly influenced by microbial activity. Geophysical methods provide a way to detect microbial activity across larger spatial scales in subsurface environments than can be accomplished by point source drilling-intensive techniques. Detection of in situ microbial activity is important for developing realistic conceptual models of contaminant fate and transport at DOE sites. Results obtained from researchers at Lawrence Berkeley National Laboratory, Pacific Northwest National Laboratory and the University of California at Berkeley working at a field test site in Rifle, CO show that geophysics techniques can detect geochemical changes attributable to specific microbial activities in the subsurface across large spatial areas at field sites. These techniques provide a more spatially resolved assessment of microbial activity in the subsurface and can be used to inform conceptual and quantitative models of contaminant transport in the subsurface.

Reference: Environ. Sci. Technol., 2009, 43(17): 6717-6723

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

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


August 24, 2009

Common Mineral Alters Fate of Mercury in Contaminated Sediments

Mercury (Hg) contamination is a significant environmental concern due to its toxicity and is one of the most challenging remediation challenges at DOE's Oak Ridge site.  Ionic mercury (Hg[II]) can be transformed by anaerobic bacteria in anoxic soils and sediments to methylmercury (MeHg), a potent neurotoxin.  MeHg accumulates in ecological food chains and can be readily detected in fish tissues in contaminated streams and rivers. Reducing the levels of Hg(II) in contaminated soils decreases the potential for forming MeHg.  Researchers at Rutgers University and Pacific Northwest National Laboratory show that Hg(II) can be reduced to elemental Hg(0) by magnetite, a mineral commonly found in anoxic sediments.  The results demonstrate a potentially important mechanism of Hg(II) reduction needed to better understand the fate of Hg in contaminated environments and improve predictions of MeHg production in anoxic sediments.   

Reference:  Environ. Sci. Technol., 2009, 43(14): 5307-5313 

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

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


August 03, 2009

Six DOE Science-Funded Research Articles Published in July 15th Edition of ES&T

Subsurface contamination stemming from post Cold War Era uranium processing remains one of DOE's most problematic remediation challenges.  DOE's Office of Biological and Environmental Research (BER) funds basic interdisciplinary research on the fate and transport of priority metal and radionuclide contaminants in the subsurface at DOE sites.  Six separate BER-funded research articles appear in the latest edition of the journal Environmental Science & Technology, an authoritative source of environmental process science read by a broad range of environmental researchers and professionals.  The articles discuss a range of findings including new mechanisms of mercury reduction; uranium sorption to nanosized iron minerals; mobility of nanosized zerovalent iron; a new uranium immobilization technique; and computer simulations of biomass development, mineral transformation, and changes in local hydrology and geochemistry during field tests of in situ uranium bioremediation.  These findings advance understanding of the coupled physical, chemical and biological processes impacting the mobility of priority contaminants at DOE sites so that decision-making for environmental remediation and long term stewardship can be informed by science-based information.

Reference: Environ. Sci. Technol., 2009, 43(14):5161-5550.

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

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


July 13, 2009

Clay Minerals Affect Technetium (99Tc) Mobility in the Environment

99Tc is a major risk driver at DOE sites due to its long half life, high solubility and potential for possible uptake into the food chain as a phosphate analog.  Researchers at Miami University-Ohio, Pacific Northwest National Laboratory and Argonne National Laboratory have found that ferrous iron, produced by metal reducing bacteria, within clay minerals, can readily reduce 99Tc to an insoluble form thereby removing it from solution.  Once reduced much of the immobilized 99Tc remains physically protected from potential oxidants, that would otherwise remobilize the contaminant, inside clay particle aggregates.  99Tc is a product of nuclear reactions and is found in the subsurface at some DOE sites due to inadvertent disposal of wastes stemming from Cold War era production of nuclear weapons.  Clay minerals are common components of soils and sediments. The results indicate that bioreduced clay minerals could naturally play an important role in reducing 99Tc mobility at key biologically active interfaces in soils and sediments in the environment or within bioremediation strategies aimed at limiting 99Tc transport in groundwater at contaminated sites.

Reference: Chemical Geology, 2009, 264:127-138.

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

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


April 27, 2009

PNNL Scientist Chosen as the Henry Darcy Distinguished Lecturer

Each year an outstanding groundwater professional is chosen by a panel of scientists and engineers as the National Ground Water Research and Education Foundation's (NGWREF) Darcy Lecturer to share his or her work with their peers and students at universities throughout the country and internationally. The 2010 honoree, the 24th and the first from a DOE Laboratory, is Dr. Timothy Scheibe, a staff scientist in the Hydrology Technical Group at Pacific Northwest National Laboratory. Scheibe has made major contributions to the field of groundwater modeling. His multidisciplinary and integrative approaches to computational modeling have brought new insights into the scaling of geochemical processes affecting contaminant transport and innovative methods to couple genome-based mechanistic understanding of biological processes with traditional groundwater modeling codes.

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

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


April 06, 2009

LBNL Earth Scientist Named Geological Society Distinguished Lecturer

Dr. Susan Hubbard, a staff scientist in the Earth Sciences Division at Lawrence Berkeley National Laboratory, has been chosen to serve as the 2010 Geological Society of America's (GSA) Birdsall-Dreiss Lecturer. The endowed lectureship is made to one person annually by the GSA Hydrogeology Division based on two criteria. The nominee must be (1) a renowned scientist whose publication record and research have had national and international impact in the field of hydrogeology and (2) an outstanding speaker. Hubbard is the 32nd GSA Birdsall-Dreiss Lecturer, and the first from a DOE national laboratory. Hubbard has made major contributions to the field of hydrogeophysics through her research, which is sponsored by DOE's Office of Biological and Environmental Research.

Contact: David Lesmes, SC 23.1, (301) 903-2977.
Topic Areas:

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


March 09, 2009

Genomics Improves Contaminant Transport Simulations

Microbes profoundly affect the mobility of contaminants in the environment, but current transport models oversimplify predictions of microbial activity in situ. DOE-funded researchers at Pacific Northwest National Laboratory and the universities of Toronto and Massachusetts have coupled a genome-scale metabolic model of a uranium-reducing microorganism, Geobacter sulfurreducens, to the reactive transport code HYDROGEOCHEM to better predict the in situ bioremediation of uranium at the Rifle, Colorado, test site. This enabled the researchers to integrate field tests and laboratory investigations and to demonstrate important advances between current empirical methods of simulating microbial activity and the new genome-scale metabolic modeling approach. The new, genome-based approach better predicts the coupled physical, chemical, and biological processes influencing the mobility of contaminants in the environment. The approach can be extended to other natural environments and other microbes or microbial communities. It also demonstrates the importance of studying environmentally relevant microbes to describe important microbially mediated processes in the environment.

Reference: Microbial Biotechnology., 2009, 2 (2): 274-286.

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

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


January 19, 2009

Organic Carbon Supply Influences Uranium Bioremediation

Addition of organic carbon compounds to uranium-contaminated environments stimulates the activity of microorganisms resulting in the removal of uranium from groundwater.  Researchers at LBNL have shown that competing biogeochemical reactions driven by the rate of organic carbon supply strongly influence uranium mobility during biostimulation and must be carefully optimized to ensure the sustainability of the remediation technique.  At low organic carbon supply rates, desorption of uranium from sediments increases soluble uranium concentrations while higher rates stimulate conditions necessary for removal of soluble uranium via microbial bioreduction in laboratory column experiments.  Further increases in organic carbon supply rate lead to formation of uranium-carbonate complexes that may drive uranium reoxidation thereby increasing soluble uranium concentrations. The results illustrate that uranium bioremediation processes are more complicated than previously thought and organic carbon supply rates will need to be optimized to balance several competing biogeochemical processes to ensure uranium immobilization over long time frames. 

Reference: Environ. Sci. Technol., 2008, 42(23): 8901-8907.

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

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


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)


December 10, 2007

Current Understanding of Subsurface Transport Processes at the Hanford Site Captured in Special Section of the Vadose Zone Journal

The November 20, 2007, online edition of the Vadose Zone Journal contains a Special Section on the current understanding of subsurface transport processes, including contaminant transport processes, that occur at the Hanford Site. The 14 articles in this Special Section and an introductory review of research activities in subsurface reactive transport modeling were made possible through the support of the Environmental Remediation Sciences Division (ERSD) within the Office of Biological and Environmental Research, Office of Science (SC). Funding to support the research activities described in the articles was provided both by ERSD within SC, and by the Remediation and Closure Science Project funded by the DOE Office of Environmental Management (EM) through the Richland Operations Office. A November 27, 2007, EurekAlert ([website]) entitled Where Does Stored Nuclear Waste Go? contains an overview of the Special Section.

Reference: Vadose Zone Journal, 6(4) November 2007.

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)


February 12, 2007

ERSD Researcher Receives E.O. Lawrence Award

John Zachara, senior chief scientist for environmental chemistry in the Chemical and Materials Sciences Division at the Pacific Northwest National Laboratory (PNNL) has been announced by DOE as a winner of the prestigious Ernest Orlando Lawrence award. The E.O. Lawrence award honors scientists and engineers at mid-career for exceptional contributions to research and technology development in support of DOE missions, and consists of a gold medal, a citation, and an honorarium of $50,000. Dr. Zachara's many contributions to understanding the geochemical mechanisms affecting the transport of metals and radionuclides in contaminated subsurface environments at DOE sites have provided the scientific basis needed for making sound decisions for environmental remediation in support of DOE's cleanup mission. His work with 99Tc, U, Cr and in particular his contributions on understanding the fate of 137Cs in contaminant plumes underneath the tanks at Hanford have led to new conceptual models on the mobility of these contaminants in the subsurface and contributed to substantially reduced cost estimates for remediation. Dr. Zachara has been a long-time principal investigator funded by the research programs within the Environmental Remediation Sciences Division (ERSD) within the Office of Science. He is the lead investigator for several research projects, and he is currently leading a major $3M/year field research project recently funded by ERSD at the Hanford 300 Area. The award will be presented to Dr. Zachara, and seven other winners representing other areas of science, at a ceremony in Washington, DC, in the spring of 2007.

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)


January 15, 2007

EMSL Magnetic Resonance Users Quantify Radiation Damage in Actinide Waste Containment Material

Users of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) have improved the fundamental understanding and predictive models that support the informative evaluation of the long-term stability of materials proposed for immobilization of actinide wastes. Scientists from the University of Cambridge and Pacific Northwest National Laboratory (PNNL) presented research in an article in this week's Nature (Vol 445, pg 190-193) that analyzes the impacts of alpha-emitters on the crystalline structure of zircon. These results measured significantly more atoms displaced by each alpha-disintegration in zircon than had previously been estimated. The authors were also able to show that damage in synthetic plutonium-doped zircon samples is likely to be consistent with damage resulting from long-term, lower-level exposure experienced by naturally occurring, uranium-containing zircons. Portions of this research were conducted using the EMSL, a DOE national scientific user facility at PNNL. EMSL scientists collaborated on the development of triple containment rotor technology and provided user access for the radiological nuclear magnetic resonance magic-angle spinning analysis. This publication highlights how EMSL's unique capabilities attract international users and collaborators and promote high-impact science.

Contact: Paul Bayer, 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)


January 15, 2007

Three Multidisciplinary Field Projects Selected for Subsurface Contaminant Transport Research

The Office of Science (SC) has selected three field-based projects for conducting research on the microbiological, chemical, and physical processes affecting the fate and transport of DOE contaminants in the subsurface. These five year, $3M/year awards will fund multi-disciplinary and multi-institutional teams of scientists working at DOE sites to make significant advances in the conceptual understanding and computational simulation of coupled subsurface processes affecting contaminant transport at the field scale. These projects also will provide soil and groundwater samples and site access to scientists within the Biological and Environmental Research program to further test small-scale, laboratory-derived hypotheses at larger scales in the field under environmentally relevant conditions. The three field sites are located on the Oak Ridge Reservation, at the Hanford 300 Area, and at a Uranium Mill Tailings Remedial Action (UMTRA) site in Rifle, Colorado. The lead scientists for these projects have coordinated with the Office of Environmental Management and Office of Legacy Management offices to align the planned basic science research to support subsurface cleanup and/or long term stewardship decisions at the sites.

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 27, 2006

New Solicitations Issued by the BERs Environmental Remediation Science Division (ERSD)

The ERSD has issued 2 solicitations calling for research on the fate and transport of DOE-relevant contaminant metals and radionuclides in the subsurface. The first solicitation, the Environmental Remediation Science Program (ERSP) represents the merger of the previous NABIR and EMSP programs and will focus on understanding the biogeochemical factors controlling the transport behavior of contaminants in the subsurface in order to develop novel remediation concepts and/or address long term stewardship concerns. The second solicitation, the ERSP-Integrated Field-Scale Subsurface Research Challenge will enable large, multi-disciplinary teams of researchers to resolve key gaps in the understanding of subsurface contaminant transport at the field scale at a DOE site. The two solicitations compliment each other and provide a programmatic mechanism whereby laboratory-derived, molecular scale mechanisms controlling subsurface contaminant transport can be evaluated not only at intermediate scales and but also at the field scale under in situ conditions at a DOE site.

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)


February 27, 2006

EMSL Featured at AAAS with Symposium, Exhibit

The William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) was featured at the American Association for the Advancement of Science (AAAS) meeting in St. Louis February 16-20. EMSL Director Allison Campbell and BERs Mike Kuperberg organized a symposium February 17 entitled "Unique Tools for Unique Science: Profiling a DOE National Scientific User Facility." The symposium described EMSL's Scientific Grand Challenges and included presentations by Biogeochemistry Grand Challenge leader John Zachara, PNNL; and Membrane Biology Grand Challenge leader Himadri Pakrasi, Washington University. EMSL also had a booth at the meeting that gave Campbell and staff the opportunity to showcase EMSL's capabilities, science themes, and accessibility. Office of Science Director Raymond Orbach was one of the booth visitors.

Contact: Mike Kuperberg, 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)


October 10, 2005

Darsh Wasan to Receive Alpha Chi Sigma Award for Chemical Engineering Research

Darsh Wasan, Professor of Chemical Engineering and holder of the Motorola Chair at the Illinois Institute of Technology, will receive the Alpha Chi Sigma Award of the American Institute of Chemical Engineers (AIChE) for 2005. The award recognizes his outstanding accomplishments in chemical engineering research and will be presented at the AIChE Annual Meeting in Cincinnati on October 30. Dr Wasan's research into the mechanisms that cause foaming of radioactive wastes during treatment has been supported by the Environmental Management Science Program (EMSP) in the Environmental Remediation Sciences Division since 1997. This research has led to new techniques for characterizing surface properties of particle suspensions. The mechanisms of formation and stabilization of foams in the wastes have been determined using the new technologies, and new antifoaming agents have been designed and used in DOE facilities at the Savannah River Site as a result of the EMSP research.

Contact: Roland F. Hirsch, SC-23.4, (301) 903-9009
Topic Areas:

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


May 23, 2005

An Electrifying Discovery

NABIR-supported researcher Dr. Derek R. Lovley of the University of Massachusetts, Amherst, has made a remarkable discovery that will be published in the journal Nature in mid-June. Dr. Lovleys group has found that the metal-reducing microorganism Geobacter produces nanotube projections called pili on the outer cell surface that appear to function as electron conducting nanowires. The data indicates these conductive pili are conduits by which Geobacter transfers electrons onto iron oxides during the process of dissimilatory iron reduction. This is of importance because Geobacter species are detected as a dominant species in the subsurface during stimulated uranium bioremediation, where iron oxide reduction is a dominant process. Discovery of this fundamental mechanism of microbial metal reduction could lead to better models for subsurface bioremediation processes but may also have implications for the electronics field because the conducting pili can be mass produced and pili composition can be altered via genetic manipulation.

Contact: Arthur Katz, SC-23.1, (301) 903-4932
Topic Areas:

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


February 07, 2005

New Understanding of Role of Colloids in Contaminant Transport at Hanford

Scientists at Washington State University (WSU) have published a research paper describing new results about the stability of natural colloids from the DOE Hanford Reservation. They found that these colloids do form stable suspensions that gradually aggregate into particles that settle out of suspension in the electrolyte solutions. They conclude that due to the very long travel times of water through the Hanford vadose zone most colloids will aggregate and be removed from the water column before reaching groundwater levels. Colloidal particles are a major concern at several DOE sites as they may facilitate transport of radionuclides that have been released into the subsurface environment at these sites. Significant transport could occur if the colloidal particles that contain radionuclides were to form colloid suspensions that are stable for a long enough period of time that water flowing through the area could move the suspension into an aquifer. The research team, led by Dr Markus Flury of the Center for Multiphase Environmental Research at WSU, studied the behavior of Hanford colloids in electrolyte solutions representative of the composition of waters in the Hanford vadose (unsaturated) zone. The research is funded by the Environmental Remediation Sciences Division of the Biological and Environmental Research program.

Contact: Roland F. Hirsch, SC-73, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-73 Medical Sciences Division, OBER)


November 22, 2004

Walter J. Weber, Jr., Honored with Festshrift Issue of Environmental Science & Technology

The November 15, 2004, issue of the American Chemical Society journal Environmental Science & Technology honors Dr. Walter J. Weber, Jr, Distinguished University Professor of Civil and Environmental Engineering at the University of Michigan. Dr. Weber has been a faculty member at the University for more than 40 years and is director of the Concentrations in Environmental Sustainability (ConsEnSus) program there. He has been a Principal Investigator in the Environmental Management Science Program since its inception in 1996, with his current research in this program focused on engineered natural geosorbents for immobilizing environmental contaminants. The journal features a photograph of Dr. Weber on the cover, an article "Walter J. Weber, Jr.'s Unique Legacy," and a dozen research papers by his present and former students. The article is available at http://pubs.acs.org/subscribe/journals/esthag-a/38/i22/pdf/111504feature_petkewich.pdf

Contact: Roland F. Hirsch, SC-73, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-73 Medical Sciences Division, OBER)


October 25, 2004

Monitoring Nanoscale Changes Within and Around Single Microbes From Environmental Samples

Research results from the Natural and Accelerated Bioremediation Research program (NABIR) researchers, Dr. Kenneth M. Kemner of Argonne National Laboratory (ANL), Dr. Kenneth H. Nealson of the University of Southern California, and colleagues appear in the October 22, 2004, issue of Science. Using a microprobe technology at the Advanced Photon Source (APS), Dr. Kemner and colleagues document changes in morphology and elemental composition of both planktonic (i.e. free-swimming) and surface adhered, single bacteria before and after exposure to high concentrations of toxic Cr(VI). Dr. Kemner uses highly focused synchrotron-based x-rays to probe biogeochemical processes occurring at the microbe-mineral interface. The analytical technique developed by Kemner is noninvasive and allows the researchers to interrogate living, hydrated biological samples at the nanometer scale (150nm). The results show that surface adhered bacteria tolerate chromium better than planktonic cells and accumulate elements such as calcium and phosphorus associated with the production of extracellular polysaccharide (EPS). X-ray absorption near-edge spectroscopy (XANES) analyses of surface adhered bacteria implied that Cr(VI) was reduced to Cr(III) within the EPS layer. Several differences also were observed in the distribution of transition metal abundance within surface adhered cells relative to planktonic cells. These results demonstrate that it is now possible to monitor nanoscale changes in elemental composition and redox chemistry within and around a single bacterial cell, an ability that could prove invaluable during investigations of biogeochemical processes in the environment.

Contact: Robert T. Anderson, SC-75, (301) 903-5549
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


August 02, 2004

Environmental Remediation Sciences Researcher in Nature

NABIR-program researcher Dr. Jonathan R. Lloyd of the University of Manchester/UK recently published results of a study on anaerobic metal-reducing microorganisms and their impact on arsenic mobilization. The article, published in the journal Nature [430:68-71 (2004)], details how metal-reducing organisms may be involved in the mobilization of toxic arsenic within the groundwaters of West Bengal, India and Bangladesh. Dr. Lloyd and coworkers are the first to show a potential direct link between the stimulation of metal and arsenic-reducing bacteria and the mobilization of arsenic in actual aquifer sediments from the affected areas. Understanding the biogeochemical mechanisms of arsenic mobilization in these environments is a step towards identifying techniques to remove and/or prevent arsenic migration in groundwater.

Contact: Robert T. Anderson, SC-75, (301) 903-5549
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


July 26, 2004

Environmental Remediation Sciences and Genomics:GTL Researcher in the News

Dr. Derek Lovley of the University of Massachusetts was recently highlighted in a syndicated Knight-Ridder newspaper article for his work with the microbial Geobacter species. Geobacter species conserve energy to support growth via the enzymatic reduction of metals such as iron and uranium. Lovley's group, in collaboration with PNNL researcher Philip E. Long, demonstrated that native Geobacters are associated with the in situ removal of uranium from contaminated groundwater. This bio-based, in situ technique could lead to more cost effective means to remove contaminant metals from groundwater. In addition to its potential as a remediation tool, the novel attributes of Geobacter metabolism that enable it to reduce solid phase metals also enable it to reduce electrodes and produce electricity when cultured in microbial fuel cells. While the power outputs are small from such cells the efficiency of the process is quite high. Lovley maintains that further advances should enable practical use of microbial fuel cells for low power energy needs.

Contact: Robert T. Anderson, SC-75, (301) 903-5549
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


July 26, 2004

Langmuir Lecture Award Given to Environmental Remediation Sciences Researcher

Dr Darsh Wasan has been selected to give one of two 2004 Langmuir Lectures of the American Chemical Society (ACS) Division of Colloid and Surface Chemistry at the ACS National Meeting in Philadelphia on August 24. Dr. Wasan holds the Motorola Chair in Chemical Engineering at Illinois Institute of Technology, where he also is Vice President for International Affairs. His lecture will be on liquid interfaces, including disperse systems. He is carrying out research in this area in the Environmental Management Science Program. His project is focused on understanding foaming in radioactive waste streams. In the course of this research he has developed solutions to foaming problems that have been implemented in waste processing at the DOE Savannah River Site.

Contact: Roland F. Hirsch, SC-73, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-73 Medical Sciences Division, OBER)


February 18, 2004

New Optical Sensor Technology Measures Key Environmental Contaminants

Detection and measurement of amounts of traces of toxic chemicals is a necessary first step in the cleanup of environmental contamination. However, there are very few analytical techniques that have sufficient sensitivity to measure the low levels of many contaminants at the sites for which DOE is responsible for cleanup. Office of Science research at the National Institute for Standards and Technology (NIST) has demon­strated the suitability of a recently developed technique, cavity ring-down spectro­scopy, for measuring trace amounts of chemicals such as trichloroethylene (TCE) in the field. TCE is a major subsurface contaminant at several DOE sites. Its migration will have to be monitored at these sites for many years into the future. The NIST technique also shows promise for laboratory studies of the adsorption of molecules on surfaces, as a means of understanding chemical reactions such as those catalyzed by the surface. The studies by Andrew Pipino's research group at NIST was funded by the Biological and Environmental Research Environmental Management Science Program. An article about the fundamental concept has just been published in the Journal of Chemical Physics.

Contact: Roland F. Hirsch, SC-73, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-73 Medical Sciences Division, OBER)


February 11, 2004

New Method to Predict Behavior of Glasses Honored with American Ceramic Society Award

Existing thermochemical models of glasses containing high level radioactive waste are inadequate to allow prediction of key properties of these glasses, such as their behavior in the melters used for producing glasses for storage of the wastes. Research supported by the Environmental Management Science Program (EMSP) at the Oak Ridge National Laboratory (ORNL) has led to improved models of high level waste glasses that will find application in both the production of the glasses and in studying the potential for loss of radionuclides through leaching from the glasses. The scientist directing this project, Dr. Theodore Besmann of the ORNL Surface Processing and Mechanics Group, will receive the Spriggs Phase Equilibria Award from the American Ceramic Society at its Annual Meeting in April 2004 for his research paper titled "Thermochemical Modeling of Oxide Glasses," which is based on his EMSP-funded research.

Contact: Roland F. Hirsch, SC-73, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-73 Medical Sciences Division, OBER)


November 26, 2003

EMSL Supercomputer Ranked Number 5 in Top 500

On November 16, 2003, the Top 500 list of fastest supercomputers in the world was released. The new Hewlett-Packard (HP) supercomputer that was recently installed at the Environmental Molecular Sciences Laboratory (EMSL) in Richland, Washington, was ranked number 5 in the top 500 list. The ranking of top supercomputers is based on their performance running a benchmark called Linpack, which is a method to measure a machine's ability to solve a set of dense linear equations. The new 11.8 teraflop HP system at the EMSL consists of nearly 2,000 1.5 GHz Intel® Itanium®-2 processors. The EMSL is a National Scientific User Facility located at the Pacific Northwest National Laboratory. The new HP system was specifically designed for users seeking large-scale environmental, biological, and chemical science computational capabilities. Allocations of time on the HP system are therefore granted in large blocks to multi-institutional research teams on a competitive proposal basis. Further information on the EMSL is available at [website].

Contact: Paul E. Bayer, SC-75, (301) 903-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


November 05, 2003

Subsurface Microbial Community Stimulated to Immobilize Uranium Plume

The first demonstration of a feasible process for the in situ immobilization of uranium as a bioremediation strategy was conducted by a team of scientists from the University of Massachusetts, the Pacific Northwest National Laboratory, the University of Tennessee, and several other institutions. Under field conditions, the team demonstrated that microorganisms can be stimulated to immobilize uranium in the subsurface. This interdisciplinary research was published in the October issue of Applied and Environmental Microbiology and featured in an on-line Science Update for the international journal Nature on October 13, 2003. The team conducted a two month field study and demonstrated that by adding acetate to the subsurface, they could stimulate the growth and proportion of Geobacter species within the subsurface microbial community. At the same time, the concentration of uranium (U) in the ground water was greatly reduced. During this first field experiment, uranium reduction was not maintained due to the onset of sulfate reduction and a corresponding change in the microbial community. However, a second field experiment has now successfully addressed the sulfate reduction problem by increasing the acetate concentration.

Contact: P. Bayer, SC-75, 3-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


October 15, 2003

Kristin Bowman-James to Receive American Chemical Society Midwest Award

The 2003 Midwest Regional Award of the American Chemical Society will be presented to Dr. Kristin Bowman-James, Professor of Chemistry at the University of Kansas. Dr. Bowman-James is being honored for noteworthy contributions to the design of large molecules that selectively bind metals or negatively-charged ions, and is considered a leading expert in this field known as supramolecular chemistry. Her research is funded by the Environmental Management Science Program (EMSP) of the Office of Biological and Environmental Research. The EMSP support was recently renewed, with a focus on finding supramolecular agents capable of selectively extracting sulfate ions from radioactive waste mixtures. Removal of sulfate ions from these mixtures would reduce the volume of high-level wastes that must be stored for long periods of time. The research is being carried out in collaboration with scientists at the University of Texas, Austin, and the Oak Ridge National Laboratory.

Contact: Roland F. Hirsch, SC-73, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-73 Medical Sciences Division, OBER)


August 06, 2003

Natural and Accelerated Bioremediation Research (NABIR) Highlighted in the San Francisco Chronicle

The July 14 edition of the San Francisco Chronicle featured an article in the Science section devoted to bioremediation research funded by the Office of Science NABIR program. "Mining bacteria's appetite for toxic waste : Researchers try to clean nuclear sites with microbes," was authored by well-known science writer, David Perlman. The article noted that scientists are exploiting the "unusual appetites" of some microbes as a way to clean up nuclear sites. Dr. Craig Criddle, an environmental engineer at Stanford University, is working with microorganisms that can convert soluble uranium into an insoluble form. Criddle's work includes research at the NABIR Field Research Center at the Oak Ridge Reservation. In collaboration with ORNL scientists, he is identifying and controlling environmental factors that might inhibit or enhance the process of uranium precipitation. Criddle hopes that "after bacteria consume radioactive waste, the uranium can be separated from water like sand, and gathered like a common mineral." The article also describes NABIR funded research by Dr. Derek Lovley of the University of Massachusetts at Amherst. Lovley is currently performing a field experiment at a Uranium Mill Tailing Remedial Action (UMTRA) site in Rifle, CO. The goal of the experiment is to enhance the growth of naturally-occurring microbes called Geobacter to bioremediate uranium-polluted ground water at the site. The article noted that genomes of several species of Geobacter have been sequenced by The Institute for Genomic Research and the DOE Joint Genome Institute. The genome sequencing was funded by the DOE Microbial Genome and Genomes to Life Programs.

Contact: Anna Palmisano, SC-75, 301-903-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


August 06, 2003

Theoretical Modeling of High-Level Radioactive Waste Components Featured on Cover of Journal of Physical Chemistry

Scientists at Pacific Northwest National Laboratory (PNNL) and Notre Dame Radiation Laboratory (NDRL) have developed a new computational model of the interactions between solvent molecules and negatively charged ions (anions), particularly those composed of a central atom surrounded by multiple oxygen atoms (oxyanions). Several oxyanions are significant components of the contents of the high-level radioactive waste tanks at the Hanford and Savannah River sites; however, existing models were unable to predict the thermodynamic properties of these species with the accuracy needed for cleanup applications. The PNNL and NDRL scientists found that the errors in these models could be reduced significantly by using a better description of size and geometry of the cluster of solvent molecules surrounding a dissolved oxyanion. For example, in an aqueous solution, the central nitrogen atom in a nitrate ion has a much larger radius and the oxygen atoms much smaller radii than previously assumed. Examination of the electrostatic potential around a dissolved nitrate ion, and of the interactions between the nitrate ion and the surrounding water molecules, showed that the new description is more consistent with the fundamental chemical interactions that govern oxyanion solvation than previous models. The new model can reliably predict the free energy of solvation of several oxyanions of interest in high-level radioactive waste, including perchlorate, formate, nitrate, and nitrite. This information is needed for predicting the evolution the chemistry of the wastes, both during storage in tanks and during treatment and processing. These results were published in the July 31, 2003 issue of the Journal of Physical Chemistry A, which also features a diagram of the new model of the nitrate ion on the cover. This work was supported by the Environmental Management Science Program and made use of the Molecular Science Computing Facility at the William R. Wiley Environmental Molecular Sciences Laboratory at PNNL.

Contact: Roland F. Hirsch, SC-73, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-73 Medical Sciences Division, OBER)


July 03, 2003

Trees Preserve History of Contaminant Exposure

There is disagreement on whether analysis of annual rings from trees growing in contaminated areas provides information on a tree's contaminant exposure history. Tracy Punshon at the University of Georgia's Savannah River Ecology Laboratory (SREL) used synchrotron x-ray microanalysis at Brookhaven's National Synchrotron Light Source on extracted cores from black willow trees to show that this past disagreement is due in part to an inability to determine the spatial distribution of metals in tree core samples. This novel analytic approach enables the study of the in situ distribution, concentration, and chemical binding environment of metals in environmental samples  a far more informative technique than traditional wet-chemistry methods, which involve drying, grinding and digestion of samples in acids. Punshon's work shows that trees from metal-contaminated areas do have a signature of metals in their annual rings that corresponds with historic information on the timing of contaminant exposure. However, a tree can only be used as an indicator of its contaminant history if it has not experienced excessive toxicity. Over time, trees can adapt to their environment, enabling them to avoid high-level pockets of contaminants, reducing the amount of contaminant they take up. Knowing this may help scientists to more accurately interpret tree ring data in the future.

Contact: Henry Shaw, SC-75, 301-903-3947
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


June 04, 2003

Natural and Accelerated Bioremediation Research (NABIR) Highlighted at the Annual Meeting of the American Society of Microbiology (ASM)

The ASM meeting, which drew over 15,000 attendees, was held in Washington, D.C., on May 19-22. NABIR funded research was presented in six invited talks and over 45 additional scientific papers. NABIR researchers reported their findings in a full-day session entitled Bioreduction of metals and bioremediation of metal-contaminated soils, as well as sessions on Subsurface microbiology, Environmental restoration microbiology, Molecular microbial ecology and others. Highlights included research by Dr. Joel Kostka (Florida State University) who has identified novel metal reducing microorganisms from acidic, contaminated subsurface sediments at the NABIR Field Research Center at the Oak Ridge Reservation. These microbes are unique and unrelated to any previously cultured metal reducers. Uranium and nitric acid were co-disposed at a number of DOE sites, so the identification of an acid-tolerant metal-reducing microbe is of great importance to bioremediation at those sites. Another highlight was a report by Dr. Ray Wildung (PNNL) on an interesting offshoot of his NABIR-funded research on reduction of the pertechnetate ion (Tc(VII)O4-) by Shewanella putrefaciens. The ion is widely used in imaging; however, the chemical reductant (SnCl2) used in commercial synthesis may result in a number of potentially undesirable competitive ions and reaction products. Dr. Wildung demonstrated the feasibility of using Shewanella isolated from a subsurface environment for an enzymatic reduction of Tc avoiding the potential problems and meeting the medical imaging requirements. Two government patents have been issued for the process and for a prototype kit for hospitals. This project exemplifies how basic research may impact several different fields; in this case, both environmental remediation and medical science.

Contact: Anna Palmisano, SC-75, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


June 04, 2003

Office of Science Research Shines at American Society for Microbiology Annual Meeting

The annual meeting of the American Society for Microbiology was held in Washington, DC, the week of May 19. In a meeting that was, overall, dominated by medical microbiology, Office of Science research comprised about 11% of all posters present (some 200 out of a total of about 1800 posters) and about 10% of all oral presentations (nearly 40 of just under 400 presentations). Office of Science staff co-chaired (Marvin Frazier, SC-72; Sharlene Weatherwax, SC-14; Dan Drell, SC-72) or spoke (Ari Patrinos, SC-70) at scientific sessions as did SC-funded scientists. Office of Science research programs that were represented included the Microbial Genome Program, the Natural and Accelerated Bioremediation Research Program, the Genomes to Life Program, the Environmental Management Science Program, and the Biotechnological Investigations-Oceans Margin Program. Many other presentations at the meeting represented research not directly funded by SC, but enabled by SC's support for the genomic sequencing of a large number of microbial genomes now being used for a diverse array of experiments.

Contact: Dan Drell, SC-72, 301-903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


March 26, 2003

Highlights from the Sixth Annual DOE Natural and Accelerated Bioremediation Research (NABIR) Program Grantee/Contractor Meeting

The sixth annual NABIR grantee/contractor meeting was held in Warrenton, VA, on March 17-19, 2003. Over 140 attendees participated including bioremediation researchers from universities and DOE National Laboratories, as well as program managers from the Office of Science and the Office of Environmental Management. The NABIR program supports fundamental research on natural attenuation and immobilization of radionuclides and metals in subsurface environments to decrease risk to humans and the environment. Special sessions were devoted to 1) Numerical modeling in the NABIR program; 2) Research at the Uranium Mill Tailings Remedial Action (UMTRA) sites; 3) Lateral gene transfer in microbial communities, and 4) Functional biodiversity of subsurface microorganisms. One highlight of the meeting was a session devoted to research findings from the NABIR Field Research Center at the Oak Ridge National Laboratory. During this session, a team of investigators from Oregon State University and the University of Oklahoma described how they have performed over 60 push-pull experiments within the contaminated area. These experiments probe the in situ activities of naturally occurring microorganisms and their potential to precipitate uranium and technetium by microbially-mediated reduction. Results revealed that Uranium(VI) could be reduced to the insoluble Uranium(IV) in areas where nitrate (a common co-contaminant) was in low concentration. The reduction of technetium, however, was unaffected by the presence of nitrate. These important findings will lead to the design of more effective remedial strategies for uranium and technetium at contaminated DOE sites.

Contact: Anna Palmisano, SC-75, (301) 903-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


February 26, 2003

EMSP Researcher Elected to National Academy of Engineering

Linda M. Abriola, Horace Williams King Professor of Civil and Environmental Engineering at the University of Michigan, Ann Arbor, has been elected to The National Academy of Engineering in recognition of her contributions to advancing our knowledge of contaminant fate and transport in groundwater and subsurface systems. Professor Abriola has been supported by the Environmental Management Science Program since 1996 for research on the migration and entrapment of dense, non-aqueous liquids in heterogeneous porous media. In addition, she served on the NABIR Subcommittee for BERAC. Election to the National Academy of Engineering is among the highest professional distinctions accorded an engineer. Academy membership honors those who have made "important contributions to engineering theory and practice, including significant contributions to the literature of engineering theory and practice," and those who have demonstrated accomplishment in "the pioneering of new fields of engineering, making major advancements in traditional fields of engineering, or developing/implementing innovative approaches to engineering education."

Contact: Henry Shaw, SC-75, (301) 903-3947
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


February 05, 2003

Department of Energy (DOE) Scientists Rank Among Highly Cited Researchers in Environmental Studies

The Institute for Scientific Information (ISI) has released its January 2003 list of 247 highly cited researchers whose work has formed or changed the course of research in the environmental sciences (http://www.highlycited.com/). This prestigious list is international in scope and includes nine researchers, within academia or the DOE laboratories, who are currently supported by research programs in the Environmental Remediation Sciences Division within the Office of Biological and Environmental Research. ISI uses its extensive citation indices to track and assess the influence of researchers papers on the scientific community. Its recognition of these scientists and engineers indicates the impact of DOEsupported research on environmental science and environmental remediation. Highly cited DOE laboratory investigators include:

Highly cited university investigators include:

Contact: Brendlyn Faison, SC-75, (301)-903-0042
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


October 30, 2002

Bioremediation Field Experiment Successfully Removes Uranium from Contaminated Ground Water

Researchers in the Natural and Accelerated Bioremediation Research (NABIR) program have demonstrated that a novel bioremediation strategy precipitates uranium from ground water at a Uranium Mill Tailings Remedial Action (UMTRA) site in Rifle, Colorado. Until now, there have been no cost-effective mechanisms for preventing uranium contamination from migrating with ground water and threatening important water resources. Researchers from the University of Massachusetts discovered that microorganisms from the genus Geobacter effectively strip uranium from contaminated ground water by transferring electrons onto uranium. This electron transfer process converts soluble uranium to an insoluble form that precipitates from the ground water. To stimulate the activity of Geobacter at the Old Rifle site, an interdisciplinary team of researchers from the University of Massachusetts, the Pacific Northwest National Laboratory, and the UMTRA program added a dilute solution of acetate (i.e. vinegar) to the ground water. From mid-June through mid-August, more than 70% of the uranium was precipitated from the ground water within the treatment zone. In some areas, uranium concentrations were below UMTRAs maximum contaminant level (MCL) of 0.044mg/L. The Geobacter species responsible for uranium removal at the Old Rifle site is also being investigated in the Genomes to Life Program to better understand the mechanisms by which Geobacter transforms radionuclides such as uranium.

Contact: Paul Bayer, SC-75, (301) 903-5324 and Anna Palmisano, SC-75, (301) 903-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


October 09, 2002

Researcher Honored for Work in Biological Chemistry

Yi Lu, associate professor of chemistry, biochemistry, and biophysics at the University of Illinois Urbana-Champaign, has been recognized twice recently for his pioneering work related to the development of DNA-based sensors for metal or radionuclide contaminants. His scientific efforts, supported in part by BER's Natural and Accelerated Bioremediation Research Program (NABIR), earned him a first-runner-up certificate in the Elsevier Bioelectronics and Biosensors competition at the World Congress on Biosensors in Kyoto, Japan, in May 2002. His prize-winning work will be described in a special issue of the journal Biosensors and Bioelectronics sometime in 2003. More recently, the philanthropic Howard Hughes Medical Institute awarded Dr. Lu a prestigious and sizeable grant in support of his science education efforts, designating him one of its first group of HHMI Professors. The full story of the HHMI award appeared in the 30 September 2002 issue of Chemical and Engineering News (pp. 32-33). Dr. Lu's NABIR project focuses on the use of combinatorial chemistry in the development of DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides. He has identified several catalytic DNAs for use within small, field-portable sensors for various toxic heavy metals. These DNA biosensors are highly sensitive, selective, shelf-stable, and cost-effective; and have been demonstrated useful in both fluorometric and colorimetric analysis of natural and municipal waters. Further work will enable their use as on-site or remote analytical tools, to obtain quantitative measurements of contamination, in real time. This research is applicable both to DOE's current bioremediation efforts and subsequent long-term stewardship.

Contact: Brendlyn Faison, SC-75, 3-0042
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


September 18, 2002

Enzyme Activity Boosted by Entrapping in a Nanoporous Support

The Pacific Northwest National Laboratory (PNNL) researchers have discovered that modifying the surfaces of the pores of the silica particles with carboxylate groups enhanced the activity of the enzyme organophosphorus hydrolase (OPH), which is widely used for treating poisonous agents. The researchers have demonstrated that immobilizing an enzyme in a functionalized nanoporous silica support increases the activity of the enzyme by a factor of four over the enzyme in an unfunctionalized support. Immobilization of enzymes enables their use in applications ranging from continuous treatment of environmental contaminants to use in biosensors. The activity of an immobilized enzyme generally is lower than that of the enzyme in solution. The carboxylate groups attract the OPH and hold it within the pores of the silica without affecting the activity of the enzyme solving this problem. The PNNL group is led by Eric J. Ackerman and Jun Liu. The research has just been published on line in the Journal of the American Chemical Society and was selected to be highlighted in the Science & Technology section of the September 9, 2002, issue of Chemical & Engineering News.

Contact: Marvin Frazier, SC-72, 3-5468
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


September 18, 2002

NABIR Research Published in Nature Shows Bacterial Transformation of Uranium Results in Nanometer Size Particles

This finding has important implications for uraninite reactivity and fate because these tiny particles may be transported in an aqueous environment, rather than immobilized, as previously assumed. Dr. Ken Kemner, a Natural and Accelerated Bioremediation Research Program investigator at ANL, is a senior author on a brief communication in the September 12, 2002 issue of the premier scientific journal Nature: "Radionuclide contamination: Nanometre-size products of uranium bioreduction," (Y. Suzuki et al., Nature 419:134, 2002). The research showed that uraninite (UO2) particles formed from uranium in sediments by bacterial reduction are typically less than 2 nanometers in size. This pioneering work lies at the interface between geology and biology. These results will help to fine-tune the control of microbial processes designed to remediate DOE's contaminated sites, and will contribute to basic understanding of the uranium biogeochemistry in nature worldwide. Kemner is a recipient of both the Presidential Early Career and the DOE Early Career Scientist Awards.

Contact: Brendlyn Faison, SC-75, 3-0042
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


May 29, 2002

NABIR-Sponsored Bioremediation Research Featured at Microbiology Meeting

Research supported by the Office of Science NABIR (Natural and Accelerated Bioremediation Research) program dominated environmental microbiology poster sessions at the 2002 annual Meeting of the American Society for Microbiology, May 19-23, in Salt Lake City. Two full poster sessions were devoted to microbial treatment of soils contaminated with metals and/or radionuclides; another, more general session concentrated on microbial activity in the subsurface. Projects funded through NABIR's Biotransformation and Biogeochemical Dynamics elements comprised half of the work presented (25 of 51 metal bioremediation posters, and 6 of 12 biogeochemistry posters). These NABIR investigators' additional work was included in general sessions on soil or subsurface microbiology. The strong presence of NABIR-funded work at this premier microbiology meeting (organized by the largest life-science society in the US) contributes to DOE's position as a leader in basic microbiological and environmental research.

Contact: Brendlyn Faison, SC-74, 3-0042
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


May 08, 2002

NABIR Supported Research on Metal-Oxide Sensing Microorganism Yields Surprise Finding

Contact: Anna Palmisano, SC-74, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


March 27, 2002

Fifth Annual DOE Natural and Accelerated Bioremediation Research (NABIR) Program Grantee/Contractor Meeting

The fifth annual NABIR grantee/contractor meeting was held in Warrenton, Virginia, on March 17-20, 2002. Over 150 attendees participated including bioremediation researchers, Office of Science (SC) and Office of Environmental Management (EM) program managers, and other agency representatives. A highlight of the meeting was a roundtable organized by Caroline Purdy (EM-54) on connecting NABIR science to EM customer needs. Representatives from sites at Fernald, Oak Ridge, Savannah River, Los Alamos, and Idaho discussed metal and radionuclide contamination in the subsurface at their sites. The NABIR program supports research on biotechnology to immobilize radionuclides and metals in subsurface environments to reduce risk to humans and the environment. Extraordinary progress has been made in understanding the complex subsurface environment at the NABIR Field Research Center on the Oak Ridge Reservation.

Contact: Anna Palmisano, SC-74, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


March 13, 2002

Minority Researcher, Trained With NABIR Support, Publishes in Key Scientific Journals

One of the Natural and Accelerated Bioremediation Research (NABIR) Program's most visible success stories is Dr. James Scott. Scott, an African-American microbiologist, originally worked as an undergraduate technician on a NABIR-funded project with Dr. Kenneth Nealson, then at the University of Wisconsin-Milwaukee. Nealson encouraged Scott to continue the project for his PhD thesis. His thesis research, published in the Journal of Bacteriology and the journal Applied Environmental Microbiology, was on the metabolism of a one-carbon compound (formate) by the soil bacterium Shewanella, which displays differing activities in the presence and absence of oxygen (as in subsurface environments). In the absence of oxygen, Shewanella metabolizes, and precipitates uranium or other metals. The organism is now studied by several NABIR researchers and could serve as a basis for bioremediation of soils and sediments at DOE sites contaminated with these materials. Scott's latest publication, describing formate metabolism and survival by Shewanella at very high pressure or within ice, recently appeared in the highly respected journal Science. The results, widely reported on national news, suggest that Shewanella may play a quantitatively important role in precipitating uranium and other metals in deep soils, sediments, and other geological formations. Dr. Scott is a highly visible example of DOE's efforts to expand and diversify the U.S. scientific workforce. BER's support has been integral to his professional success, and has contributed to NABIR's success by describing the physiology of an organism that may be critical to the development of bioremediation strategies to immobilize metal and radionuclide contaminants in subsurface environments at DOE sites.

Contact: Brendlyn Faison, SC-74, 3-0042
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


January 30, 2002

The World and I Highlights BER Microbial Genome Program

The January 2002 issue of The World and I prominently features results from the DOE Biological and Environmental Research (BER) Microbial Genome Program in a major article titled "Great Expectations of Small Genomes" by staff writer Dinshaw Dadachanji, and boldly notes that "Ongoing efforts to sequence the DNA of various microorganisms are fueled by the promise that the information gained will boost advances in such areas as medicine, energy production, environmental cleanup, and industrial processes." The focus of BER's Natural and Accelerated Bioremediation Research (NABIR) program includes microbial bioremediation as a particular emphasis and the majority of the microbes sequenced under the sponsorship of the Microbial Genome program have demonstrated relevance to bioremediation, energy production, and global climate processes. The article further notes that "Shewanella oneidensis, a bacterium that can grow in water and soil, can consume toxic organic wastes and precipitate certain heavy metals--including radioactive uranium--from solution. This ability could be used to trap and remove uranium from a contaminated stream." BER-supported researchers at the DOE Oak Ridge National Laboratory are now placing hundreds of its DNA segments on microarrays to find genes that might be useful for environmental remediation.

Contact: Dan Drell, SC-72, 3-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


January 23, 2002

NABIR Researcher Publishes Biogeochemistry Finding in Science

Terry Beveridge (Department of Microbiology, University of Guelph; Ontario, Canada) and coworkers have published a paper in the January 4, 2002, issue of Science (295:117-119) on "intracellular iron minerals in a dissimilatory iron-reducing bacterium [DIRB]." The paper describes the controlled formation of minerals--by naturally occurring, indigenous bacteria--in subsurface soils and sediments. Beveridge, et al., study bacteria that have been strongly implicated in the immobilization of contaminating metals and radionuclides in soil environments. Contaminants precipitated by these organisms include but are not limited to uranium, technetium, and chromium. Immobilization of such contaminants via precipitation in soils reduces their concentration in groundwater and transport into surface waters. These latter contaminants are widespread throughout the DOE complex and are the target of the Biological and Environmental Research's (BER) Natural and Accelerated Bioremediation Research (NABIR) program. NABIR supports several projects that examine the fundamental biology and geochemistry associated with the activity of DIRB's at DOE sites. The published work contributes to the development of new strategies for the cleanup of hazardous and/or radioactive waste deposited in soils as a legacy of nuclear weapons production activities.

Contact: Brendlyn Faison, SC-74, 3-0042
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


January 02, 2002

NABIR Researcher Featured on Environmental News Network Website

Dr. Judy Wall, a researcher in the Natural and Accelerated Bioremediation Research (NABIR) Program, was featured on the Environmental News Network (ENN) website on November 26, 2001. ENN is one of the most popular websites on environmental sciencesfor the general public. Dr. Wall is a professor of biochemistry at the University of Missouri-Columbia. The article described her research on the bacterium Desulfovibrio desulfuricans to determine its potential for bioremediation of sites contaminated by uranium. This particular bacterium is widely distributed in soils and sediments, and it obtains its energy by adding electrons onto other compounds. By adding electrons onto U(VI), a soluble and toxic form of uranium, D. desulfuricans can chemically reduce uranium to U(IV), a less soluble and less toxic form. Dr. Wall is examining the bacterial genes that are responsible for controlling the flow of electrons to U(VI). By determining the genetic pathways, she can begin to examine regulatory and environmental factors that might enhance its use in bioremediation. Dr. Wall is also collaborating with researchers at the Los Alamos National Laboratory to identify and characterize the bacterial proteins that are involved in providing electrons to U(VI). The researchers hope to increase the bacterium's affinity for uranium and thus its efficiency in bioremediation.

Contact: Anna Palmisano, SC-74, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


December 05, 2001

NABIR Researcher Invited to Present at Three International Meetings (Austria, Japan, Germany)

Mary Neu, Los Alamos National Laboratory, described her work on the biological chelation and reduction of plutonium (Pu) in subsurface soil environments at 1) the Eighth International Conference on the Migration of Radionuclides in the Geosphere in Austria, 2) the Actinides-2001 Conference in Japan, and 3) the Gotenburg University in Germany. Her work is critical to understanding the fate of radionuclides released to soil environments, and to the development of new biotechnologies to migrate radionuclides at DOE sites. Her research is receiving much deserved national and international professional recognition. She has been invited to speak at a new Gordon Conference on Environmental Bioinorganic Chemistry (to be held in New Hampshire), and to organize a session for the 23rd Rare Earth Conference (to be held in California). She has also initiated a collaboration with the European Centre d'Energie Atomique.

Contact: Brendlyn Faison, SC-74, 3-0042
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


August 01, 2001

NABIR Researchers Report Uptake of Plutonium by Common Soil Microorganisms

Researchers in BER's Natural and Accelerated Bioremediation Research (NABIR) Program reported in the June 8 edition of the journal Environmental Science & Technology that commonly occurring microorganisms can take up the radionuclide plutonium (Pu). Dr. Mary Neu and her co-workers at LANL studied Microbacterium flavescens, a relatively common soil microbe that takes up iron as a nutrient by producing siderophores. Siderophores are agents that bind and transport iron into the cell. The researchers found that the microbe can use the same type of siderophores that transport iron as a mechanism to take up and accumulate Pu. While other researchers have previously reported sorption of some forms of Pu to the surfaces of cells, Neu's work is the first to show unequivocal transport into the cell and to elucidate the mechanism for that transport. Because iron is an essential nutrient for life, iron siderophores are common in bacteria, fungi and even plants, suggesting a major pathway for removal of plutonium from the aqueous phase. The effects of microbes and microbially produced siderophores on plutonium are significant not only for the prediction of the long term fate of such toxics in the environment, but also for the development of novel technologies for bioremediation of plutonium and other actinide elements through removal from the aqueous phase and immobilization in microbial biomass.

Contact: Anna Palmisano, SC-74, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


June 06, 2001

Natural and Accelerated Bioremediation Research (NABIR) Findings Published in Science.

In the May 18, 2001, issue of the journal Science, NABIR researcher Dr. Terry Beveridge of the University of Guelph, Canada, and collaborators at the Virginia Polytechnic Institute and State University published a paper entitled "Bacterial recognition of mineral surfaces: Nanoscale interactions between Shewanella and alpha-FeOOH." Shewanella oneidensis is a bacterium that can "respire" iron (oxy)hydroxide minerals, as well as metals such as chromium and uranium, in the absence of oxygen. Little is known about how bacteria might use a solid mineral substrate for respiration because of the difficulty in observing molecular level processes at the microbe-mineral interface. The researchers used a novel approach to examine the binding of metal reductases in the outer membrane of the bacterium to the mineral surface. Atomic force microscopy measured the binding strength between the bacterium and the mineral surface in the presence and absence of oxygen. Nanomechanical measurements showed an affinity between Shewanella and the iron containing mineral, goethite. This affinity was not measurable in the presence of oxygen or with minerals that were not respired. Molecular modeling suggested that an iron reductase protein in the outer membrane of the bacterium reduced the iron present in goethite as part of the respiratory process. This study is the first to measure microbe-mineral interactions at a nanoscale, and opens the possibility of combining nanoscale measurements with molecular genetics and mineralogy to identify all components of electron transfer in metal and radionuclide reduction during bacterial respiration.

Contact: Anna Palmisano, SC-74, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


June 06, 2001

Natural and Accelerated Bioremediation Research (NABIR) Highlighted at the American Society of Microbiology.

NABIR investigators had a major impact on the annual meeting of the American Society of Microbiology which was attended by over 15,000 scientists. NABIR research was presented in 12 invited talks and over 50 additional scientific papers. NABIR researchers reported their findings in two sessions on "Bioreduction of Metals and Bioremediation of Metal-Contaminated Soils," as well as at sessions on "Subsurface Microbiology," "Anaerobic Respiration," "Molecular Microbiology Ecology," and "Gene Expression in the Environment." Dr. Gil Geesey, a NABIR investigator from Montana State University, won the most prestigious award in environmental microbiology, the 2001 Procter & Gamble Applied and Environmental Microbiology Award. Dr. Geesey was recognized for his research on bacterial-surface interactions, and he presented a lecture entitled "Surfaces: Catalysts of diverse bacterial cell behavior." Other highlights include a report by Dr. James Fredrickson of Pacific Northwest National Laboratory that the highly radiation-resistant bacterium Deinoccoccus radiodurans is endemic to subsurface soils beneath radioactive waste storage tanks at the Hanford reservation, making this microbe especially promising for in situ bioremediation approaches. Dr. Derek Lovley from the University of Massachusetts reported that during active metal reduction, subsurface microbial communities are dominated by metal- and radionuclide-reducing bacteria called Geobacter. Genomes of both Geobacter and Deinococcus have been sequenced by the BER Microbial Genome Program, and researchers are using this information to better understand the potential of these bacteria for bioremediation of metals and radionuclides at DOE sites.

Contact: Anna Palmisano, SC-74, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


March 21, 2001

Fourth Annual DOE Natural and Accelerated Bioremediation Research (NABIR) Program Grantee/Contractor Meeting.

The fourth annual NABIR grantee/contractor meeting was held in Warrenton, VA, on March 11-14, 2001. The nearly 140 attendees included bioremediation researchers, BER program managers, and EM managers and staff. In a keynote address, Dr. Gerald Boyd, Deputy Assistant Secretary of Science and Technology for Environmental Management, emphasized the importance of NABIR research to finding solutions to legacy wastes of radionuclides and metals at DOE sites. EM representatives from headquarters and field operations participated in a roundtable organized by Paul Bayer (SC-74) on connecting NABIR research to EM customer needs. A scientific highlight of the NABIR meeting was a session on the use of data from BER's Microbial Genome Program by NABIR researchers. Genomic data have provided new insights into the physiology and ecology of radionuclide-reducing microorganisms, such as Geobacter and Desulfovibrio, and radiation-resistant microbes, such as Deinococcus. Special sessions were also devoted to new field research projects at the NABIR field research site at ORNL, NABIR research at Uranium Mill Tailing Remedial Action sites, and on Bioremediation and its Societal Implications and Concerns. A "town hall" style session was held as part of ongoing strategic planning for the NABIR program. NABIR researchers agreed that the program's focus on immobilization of metals and radionuclides in the subsurface is appropriate, and that communication of NABIR results to regulators and stakeholders was critical to the acceptance of this approach.

Contact: Anna Palmisano, SC-74, 3-9963 and John Houghton, SC-74, 3-8288
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


February 28, 2001

Field-portable Immunoassay Developed to Measure Uranium.

Uranium is a common legacy waste contaminant at DOE sites. Because it can occur in several chemical forms, it is difficult to quantify the total at a site and differentiate between the uranium compounds. As part of the Natural and Accelerated Bioremediation Research (NABIR) program, Dr. Diane Blake of Tulane University has developed a sensor that can be used to identify the type of uranium compounds and quantify the uranium in the field. The sensor involves the use of monoclonal antibodies. These antibodies were joined with a fluorescent dye to allow quantification. The method was found to have a 10-1000 fold greater sensitivity when compared to more traditional approaches. Monoclonal antibodies have also been developed that recognize cadmium, cobalt, or lead. Dr. Blake's NABIR research has been accepted for publication in the journals Analytical Chimica Acta, ImmunoAssays, and Biosensors and Bioelectronics. A prototype instrument has been developed in collaboration with Sapidyne Instruments, Inc. that is approximately the size of a "Palm Pilot" and allows an easy interface to a PC.

Contact: Anna Palmisano, SC-74, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


February 28, 2001

Research at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) on Transition Metal Oxides Contributes to Greater Understanding of Mineral Surface Interactions with Contaminants.

For the first time, EMSL scientist Scott Chambers and postdoctoral associate Tim Droubay have determined the difference in electron energy levels (crystal field splitting) at the surface of three well-defined single crystals of different iron oxides: I-Fe2O3(0001), y-Fe2O3(001), and Fe3O4(001). Until this work, the actual energy difference at the surface of any transition metal oxide was not known. Knowing the differences between surface and bulk crystal field strength is important for obtaining a fundamental understanding of the reactivity of oxide and mineral surfaces. In turn, this fundamental understanding of specific mineral surface-site reactivities substantially improves reactive transport models of contaminants in geologic systems, and allows more effective remediation schemes to be devised. The EMSL molecular beam epitaxy (MBE) system was used to prepare the crystals, and high-energy-resolution x-ray photoemission, synchrotron radiation x-ray absorption spectroscopy, and first-principles atomic multiplet theory were used to analyze the samples. This work was funded by EMSP and will be submitted for publication in Physical Review B.

Contact: Paul Bayer, SC-74, 3-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


December 14, 2000

Natural and Accelerated Bioremediation Research (NABIR) Supported Research on Microbe-Metal Interactions is Published in Science:

Research on the formation of zinc sulfides by biofilms of sulfate reducing bacteria was published in the December 1, 2000, issue of the journal, Science, and featured on the cover photo. Contributing to this article was Dr. Kenneth Kemner, a researcher in the NABIR program and winner of a Presidential Young Investigator Award. Working at the Advanced Photon Source at Argonne National Laboratory, Kemner used a finely focused high-energy X-ray beam to document that zinc sulfides as well as small quantities of other toxic ions, arsenic and selenium, were extracted from groundwater and concentrated in naturally occurring biofilms. The biofilms, found deep in an abandoned mine, are heavily populated with bacteria which convert zinc and sulfate (or sulfuric acid) from groundwater into insoluble zinc sulfides. The interdisciplinary research team was led by Dr. Jill Banfield, a geomicrobiologist at the University of Wisconsin. The results of this study show how microbes can reduce metal concentrations in groundwater and suggest microbially mediated routes for the formation of some low temperature ore deposits of zinc sulfides. Understanding such microbe-metal interactions is critical to developing new methods to remediate Department of Energy sites contaminated with metals and radionuclides.

Contact: Anna Palmisano, SC-74, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)