BER Research Highlights

Search Date: December 13, 2017

11 Records match the search term(s):


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