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News - 2011

• 9-30-11 PCR Amplification-Independent Detection of Active Microbial Communities. Detection of microbial communities often relies on the amplification of nucleic acid sequences (DNA or RNA) extracted from environmental samples. Amplification using the polymerase chain reaction (PCR) is known to be subject to variety of biases and can skew detection results for organisms in low abundance. To circumvent the potential for PCR bias, researchers at Lawrence Berkeley National Laboratory (LBNL) have devised a method for direct detection of nucleic acids using the PhyloChip microarray without the need for PCR-amplification and demonstrate the utility of this technique to detect the active members of microbial communities in environmental samples. Using the PhyloChip, a microarray tool developed at LBNL, the team tested the analysis technique first on a mock microbial community in the laboratory then on environmental samples collected from several diverse sources including a chromium-contaminated aquifer, a tropical forest soil and secondary sewage. By analyzing both the DNA and RNA signatures directly within the samples the team was able to rapidly measure the active portion of the total microbial population. The ease of use of the PhyloChip coupled with new techniques to directly detect both ribosomal DNA and RNA provides a rapid way to measure the active microbial population within an individual sample thereby improving the ability to understand changes in microbial community composition and function catalyzing a variety of environmental processes. Reference:  DeAngelis, K.M., Wu, C.H., Beller, H.R., Brodie, E.L., Chakraborty, R., DeSantis, T.Z., Fortney, J.L., Hazen, T.C., Osman, S.R., Singer, M.E., Tom, L.M., Andersen, G.L. (2011) PCR Amplification-Independent Methods for Detection of Microbial Communities by the High-Density Microarray PhyloChip. Appl. Environ. Microbiol. Vol. 77(18): 6313-6322.
• 09-15-11 Conductive Pili Reduce Toxic Uranium. Metal-reducing microorganisms are known to respire radionuclide contaminants such as uranium as part of their central metabolism despite uranium’s known toxic effects. Conductive pili extruded outside the cell membrane serve as electron conduits linking central metabolism occurring inside the cell to the reduction of uranium outside the cell. The exterior appendages allow the cell to “breathe” uranium extracellularly thereby avoiding many of the toxic effects that uranium can have on intracellular metabolism. Researchers from Michigan State University, publishing in the Proceedings of the National Academy of Science, provide a plausible mechanism to explain how such a toxic radionuclide can be utilized for such a vital metabolic process. Metal-reducing bacteria produce conductive pili, long filaments, on the cell exterior enabling the cell to funnel electrons produced from central metabolism to the exterior of the cell during the process of electron transport. As a consequence, redox-active metals such as soluble uranium are reduced at the pili surface, forming solid phase precipitates that accumulate on or near the pili surface. The overall result is that toxic uranium is used as an electron acceptor for central metabolism (i.e. cellular respiration) without ever having to enter the cell interior thereby avoiding many of the toxic effects of uranium. The mechanism helps to explain field observations of stimulated uranium reduction by metal-reducing microorganisms in uranium-contaminated groundwater and provides mechanistic details to help advance a predictive understanding of microbial activity in the environment. Reference:  Cologgi, DL, Lampa-Pastirk, S, Speers, AM, Kelly, SD, Reguera, G., (2011), Extracellular reduction of uranium via Geobacter’s conductive pili as a protective cellular mechanism, PNAS 108(37):15248-15252, doi10.1073/pnas.1108616108
• 07-27-11 Microbial Appendages Exhibit Metallic-like Conductivity. Recent reports from several groups indicate that anaerobic microorganisms commonly found in subsurface environments respire metal-containing minerals and radionuclide contaminants via pili appendages, known as “nanowires,” on the cell surface that facilitate electron transport from central metabolism inside the cell to electron acceptors on the outside of the cell. Critical to the understanding of this proposed process is a demonstration of a plausible electron transport mechanism in “nanowires” that are composed of electrically insulating protein. New results from a team led by the University of Massachusetts show that microbially produced pili composed of naturally occurring amino acids (i.e protein) exhibit metallic-like conductivity in the absence of cytochromes and in fact function as “nanowires”, a finding that could have far-reaching biotechnological and bioelectronic implications. Researchers evaluating the metabolic properties of subsurface microorganisms more typically known for their ability to immobilize contaminant metals and radionuclides could manipulate biofilms grown in microbial fuel cells and show that electrical conductance could be “tuned” depending on the expression of specific genes associated with pili (“nanowire”) production. Furthermore, X-ray diffraction and electrical studies of purified “nanowire” filaments sheared from the microorganisms 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 π –orbital overlap and charge delocalization. The data helps to explain how these microorganisms respire solid minerals and radionuclide contaminants in anaerobic subsurface environments but also has far-reaching implications for nanomaterial biodesign and biotechnology.  Reference:  Malvankar, NS, Vargas, M., Nevin, KP, Franks, AE, Leang, C., Kim, B., Inoue, K., Mester, T., Covalla, SF, Johnson, JP, Rotello, VM, Tuominen, MT, Lovley, DR. (2011), “Tunable metallic-like conductivity in microbial nanowire networks”, Nature Nanotechnology, Volume: 6   Issue: 9   Pages: 573-579   DOI: 10.1038/NNANO.2011.119   Published: SEP 2011

• 04-19-11 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, AR, Moore, DA, Rosso, KM, Qafoku, O, Rai, D, Buck, EC and Ilton, ES. (2011) Heterogeneous Reduction of PuO2 with Fe(II): Importance of the Fe(III) Reaction Product. Environ. Sci. Technol. Article ASAP Publication Date (Web): April 6, 2011.

• 3-14-11 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 the Lawrence Berkeley National Laboratory, the 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, Tennessee, 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, MB, E Gasperikova, S Finsterle, D Watson, G Baker and SS 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.

• 3-3-11 Limiting Technetium Mobility in Groundwater. Technetium-99 (Tc-99) is a product of legacy nuclear fuel reprocessing operations at DOE sites such as Hanford and is a major risk driver when detected in groundwater due to its mobility and very long half-life. Understanding the factors that limit Tc-99 mobility in natural systems is of interest to better define the risk posed by this radionuclide in the environment. A team of scientists from the Pacific Northwest National Laboratory has found that several species of microorganisms can increase the amount of reduced iron associated with iron-containing minerals found in the subsurface as part of their metabolic processes. This reduced iron reacts with and significantly reduces the mobility of Tc-99 by converting it from a soluble form to an insoluble form. Using electron microscopy, X-ray absorption spectroscopy, microcapillary X-ray diffraction and other techniques made available through the Environmental Molecular Sciences Laboratory (EMSL) and the Advanced Photon Source (APS), both DOE scientific user facilities, the team found that Tc-99 was much less soluble when it came in contact with microbially-generated reduced iron minerals than when reduced by microorganisms enzymatically. This research suggest that reduced iron, particularly when associated with mineral phases, can serve as an effective reductant for soluble Tc-99, lowering concentrations to levels that approach the regulatory limit. The research provides a basis for a conceptual approach for limiting the movement of Tc-99 in groundwater at DOE sites. Support for this research was provided through PNNL’s Subsurface Biogeochemical Research Scientific Focus Area.
  Reference:  Plymale, AE, JK Fredrickson, JM Zachara, AC Dohnalkova, SM Heald, DA Moore, DW Kennedy, MJ Marshall, C Wang, CT Resch and P Nachimuthu. 2011.  Environ. Sci & Tech.  45: 951-957.

• 3-3-11 Predicting Microbial Interactions using Genome-Scale Models. Advances in genome sequencing and the capability to capture this information in the form of genome-scale metabolic models have enabled the ability to predict microbial interactions. An analysis of two microorganisms known to compete in situ during tests of uranium bioremediation predicts how life strategies and growth rates for each microorganism are altered by the presence of substrates and nutrient availability and the implications of these interactions on uranium bioremediation strategies. The model helps explain observational data and shows how genome-scale modeling can be used to predict the competitive metabolic interactions of microorganisms in an environmental setting and/or optimize bioremediation strategies. Researchers from the University of Massachusetts and the University of Toronto working with metabolic models developed from the genome sequences of two metal-reducing microorganisms (Rhodoferax and Geobacter) known to be 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 to the subsurface 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 to 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., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R. Lovley, DR 2011.  The ISME Journal.  5: 305-316.

• 2-24-11 A New Method to Attenuate U(VI) Mobility in Acidic Waste Plumes Using Humic Acids. Acidic uranium (U) groundwater plumes have resulted from acid-extraction of plutonium during the Cold War and from U mining and milling operations. Currently a sustainable remediation method is not yet available. A team of scientists from the Lawrence Berkeley National Laboratory (LBNL) are exploring the use of humic acids (HA) to immobilize U in groundwater under acidic conditions. The laboratory investigations show that by treating acidic groundwater (pH below 5.0) with humic acid that U can adsorb onto aquifer sediments rapidly, strongly and practically irreversibly. Using historically contaminated sediments from the DOE’s Savannah River Site, column leaching experiments show that upon humic acid-treatment, 99% of the contaminant U was immobilized at pH < 4.5 under site groundwater flow rates (120 and 12 m/year), indicating 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 to the subsurface.
  Reference: Jiamin Wan, Wenming Dong, and Tetsu K. Tokunaga, “Method to Attenuate U(VI) Mobility in Acidic Waste Plumes Using Humic Acids,” Environmental Science & Technology, February 14, 2011, DOI: 10.1021/es103864t.

• 2-23-11 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 LLNL 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, BA, Z Dai, M Zavarin, P Zhao and AB Kersting. 2011. “Stabilization of Plutonium Nano-colloids by Epitaxial Distortion on Mineral Surfaces.” ES&T.  DOI 10.1021/es1033487.

• 1-10-11 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. Proc. Natl. Acad. Sci. USA. 108, doi:10.1073/pnas.1008747108. January 10, 2011 .