The goal of this specific research task is to develop proxy tracers that mimic contaminant movement to better understand and predict contaminant fate and transport in karst aquifers. Hydrogel tracer beads are transported as a separate phase than water and can used as a proxy tracer to mimic the transport of non-aqueous phase liquids (NAPL). They can be constructed with different densities, sizes & chemical attributes. This poster describes the creation and optimization of the beads and the field testing of buoyant beads, including sampling, tracer analysis, and quantitative analysis. The buoyant beads are transported ahead of the dissolved solutes, suggesting that light NAPL (LNAPL) transport in karst may occur faster than predicted from traditional tracing techniques. The hydrogel beads were successful in illustrating this enhanced transport.

Over the past two decades, numerous studies have produced high quality information on the rates at which bacteria can reduce metal oxides. The prototypical study--such as the one depicted to the right--focuses on only a few of the myriad variables affecting the rate. This approach allows for effective dissection of the mechanisms underlying DMRB activity, but, it also produces disjoint information that must be synthesized if we hope to predict the behavior of bacteria at the systems level.

Plutonium has a long half-life (2.4 x 104 years) and is of concern because of its chemical and radiological toxicity, high-energy alpha radioactive decay. A full understanding of its speciation and interactions with environmental processes is required in order to predict, contain, or remediate contaminated sites. Under aerobic conditions Pu is sparingly soluble, existing primarily in its tetravalent oxidation state. To the extent that pentavalent and hexavalent complexes and small colloidal species form they will increase the solubility and resultant mobility from contamination sources. There is evidence that in both marine environments and brines substantial fractions of the plutonium in solution is present as hexavalent plutonyl, PuO2 2+.

Physicochemical and microbiological processes taking place at environmental interfaces influence natural processes as well as the transport and fate of environmental contaminants, the remediation of toxic chemicals, and the sequestration of anthropogenic CO2. A team of scientists and engineers has been assembled to develop and apply new experimental and computational techniques to expand our knowledge of environmental kinetics. We are also training a cohort of talented and diverse students to work on these complex problems at multiple length scales and to compile and synthesize the kinetic data. Development of the human resources capable of translating molecular-scale information into parameters that are applicable in real world, field-scale problems of environmental kinetics is a major and relatively unique objective of the Institute's efforts. The EMSI team is a partnership among 10 faculty at The Pennsylvania State University (funded by the National Science Foundation Divisions of Chemistry and Earth Sciences), one faculty member at Juniata College, one faculty member at the University of Florida, and four researchers drawn from Los Alamos National Laboratory, Pacific Northwest National Laboratory, and Lawrence Berkeley National Laboratory (funded by the Department of Energy Division of Environmental Remediation Sciences). Interactions among the applied and academic scientists drives research approaches …

Desulfovibrio vulgaris is an anaerobic sulfate-reducing bacterium capable of facilitating the removal of toxic metals such as uranium from contaminated sites via reduction. As such, it is essential to understand the intricate regulatory cascades involved in how D. vulgaris and its relatives respond to stressors in such sites. One approach is the identification and analysis of small non-coding RNAs (sRNAs); molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion and therefore provide an immediate regulatory response. To identify sRNAs in D. vulgaris, a bacterium that does not possess an annotated hfq gene, RNA was pooled from stationary and exponential phases, nitrate exposure, and biofilm conditions. The subsequent RNA was size fractionated, modified, and converted to cDNA for high throughput transcriptomic deep sequencing. A computational approach to identify sRNAs via the alignment of seven separate Desulfovibrio genomes was also performed. From the deep sequencing analysis, 2,296 reads between 20 and 250 nt were identified with expression above genome background. Analysis of those reads limited the number of candidates to ~;;87 intergenic, while ~;;140 appeared to be antisense to annotated open reading frames (ORFs). Further BLAST analysis of the intergenic …

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Our goal is to use isotopic measurements to understand how contaminants are introduced to and stored in the vadose zone, and what processes control migration from the vadose zone to groundwater and then to surface water. We have been using the Hanford Site in south-central Washington as our field laboratory, and our investigations are often stimulated by observations made as part of the groundwater monitoring program and vadose zone characterization activities. Understanding the transport of contaminants at Hanford is difficult due to the presence of multiple potential sources within small areas, the long history of activities, the range of disposal methods, and the continuing evolution of the hydrological system. Observations often do not conform to simple models, and cannot be adequately understood with standard characterization approaches, even though the characterization activities are quite extensive. One of our objectives is to test the value of adding isotopic techniques to the characterization program, which has the immediate potential benefit of addressing specific remediation issues, but more importantly, it allows us to study fundamental processes at the scale and in the medium where they need to be understood. Here we focus on two recent studies at the waste management area (WMA) T-TX-TY, which …

Biodiversity and its responses to environmental changes is a central issue in ecology, and for society. Almost all microbial biodiversity researches focus on species richness and abundance but ignore the interactions among different microbial species/populations. However, determining the interactions and their relationships to environmental changes in microbial communities is a grand challenge, primarily due to the lack of information on the network structure among different microbial species/populations. Here, a novel random matrix theory (RMT)-based conceptual framework for identifying functional ecological gene networks (fEGNs) is developed with the high throughput functional gene array hybridization data from the grassland microbial communities in a long-term FACE (Free Air CO2 Enrichment) experiment. Both fEGNs under elevated CO2 (eCO2) and ambient CO2 (aCO2) possessed general characteristics of many complex systems such as scale-free, small-world, modular and hierarchical. However, the topological structure of the fEGNs is distinctly different between eCO2 and aCO2, suggesting that eCO2 dramatically altered the interactions among different microbial functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen dynamics, and plant productivity, indicating the potential importance of network interactions in ecosystem functioning. Elucidating network interactions in microbial communities and their responses to environmental changes are …

Reconstruction of transcriptional regulatory networks is one of the major challenges facing the bioinformatics community in view of constantly growing number of complete genomes. The comparative genomics approach has been successfully used for the analysis of the transcriptional regulation of many metabolic systems in various bacteria taxa. The key step in this approach is given a position weight matrix, find an optimal threshold for the search of potential binding sites in genomes. In our previous work we proposed an approach for automatic selection of TFBS score threshold coupled with inference of regulon content. In this study we developed two modifications of this approach providing two additional levels of sensitivity.

The Environmental Molecular Sciences laboratory (EMSL) is a national scientific user facility operated by the Pacific Northwest National Laboratory (PNNL) for the U.S. Department of Energy's Office of Biological and Environmental Research. Located in Richland, Washington, EMSL offers researchers a comprehensive array of cutting-edge capabilities unmatched anywhere else in the world and access to the expertise of over 300 resident users--all at one location. EMSL's resources are available on a peer-reviewed proposal basis and are offered at no cost if research results are shared in the open literature. Researchers are encouraged to submit a proposal centered around one of EMSL's four Science Themes, which represent growing areas of research: (1) Geochemistry/Biogeochemistry and Subsurface Science; (2) Atmospheric Aerosol Chemistry; (3) Biological Interactions and Dynamics; and (4) Science of Interfacial Phenomena. To learn more about EMSL, visit www.emsl.pnl.gov.

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Mycobacterium tuberculosis is a dangerous Actinobacteria infecting nearly one third of the human population. It becomes dormant and phenotypically drug resistant in response to stresses. An important feature of the M. tuberculosis pathogenesis is the prevalence of latent infection without disease, making understanding of the mechanisms used by the bacteria to exist in this state and to switch to metabolically active infectious form a vital problem to consider. M. tuberculosis dormancy is regulated by the three-component regulatory system of two kinases (DosT and DevS) and transcriprional regulator (DevR). DevR activates transcription of a set of genes, which allow the bacteria to survive long periods of anaerobiosis, and may be important for long-term survival within the host during latent infection. The DevR-regulon is studied experimentally in M. tuberculosis and few other phylogenetically close Mycobacteria spp. As many other two-component systems, the devRS operon is autoregulated. However, the mechanism of the dormancy is not completely clear even for these bacteria and there is no data describing the dormancy regulons in other species.

The global atmospheric concentration of CO2 has increased by more than 30percent since the industrial revolution. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been well studied, its influences on belowground microbial communities are poorly understood and controversial. In this study, we showed a significant change in the structure and functional potential of soil microbial communities at eCO2 in a grassland ecosystem, the BioCON (Biodiversity, CO2 and Nitrogen) experimental site (http://www.biocon.umn.edu/) using a comprehensive functional gene array, GeoChip 3.0, which contains about 28,0000 probes and covers approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles as well as other functional processes. GeoChip data indicated that the functional structure of microbial communities was markedly different between ambient CO2 (aCO2) and eCO2 by detrended correspondence analysis (DCA) of all 5001 detected functional gene probes although no significant differences were detected in the overall microbial diversity. A further analysis of 1503 detected functional genes involved in C, N, P, and S cycles showed that a considerable portion (39percent) of them were only detected under either aCO2 (14percent) or eCO2 (25percent), indicating that the functional characteristics of the microbial …

Oxy-fired or low-nitrogen combustion is a technology that will facilitate CO2 capture while also reducing NOx formation and which offers the opportunity for near-zero emissions coal combustion via either the retrofit of existing power plants, or the design of new power plants. Because of the opportunity to improve the environmental performance of the existing coal fired fleet (currently approximately 800 GW of capacity in the US alone) and the potential for converting these plants from air-blown to oxy-fired burners, NETL’s Office of Research & Development is focusing its attention on the impact of retrofitting existing plants on the service life of the materials of construction

Due to increasing atmospheric CO2 concentrations causing the global energy and environmental crises, geological sequestration of carbon dioxide is now being actively considered as an attractive option to mitigate greenhouse gas emissions. One of the important strategies is to use deep unminable coal seams, for those generally contain significant quantities of coal bed methane that can be recovered by CO2 injection through enhanced coal bed natural gas production, as a method to safely store CO2. It has been well known that the adsorbing CO2 molecules introduce structural deformation, such as distortion, shrinkage, or swelling, of the adsorbent of coal organic matrix. The accurate investigations of CO2 sorption capacity as well as of adsorption behavior need to be performed under the conditions that coals deform. The U.S. Department of Energy-National Energy Technology Laboratory and Regional University Alliance are conducting carbon dioxide sorption isotherm experiments by using manometric analysis method for estimation of CO2 sorption capacity of various coal samples and are constructing a gravimetric apparatus which has a visual window cell. The gravimetric apparatus improves the accuracy of carbon dioxide sorption capacity and provides feasibility for the observation of structural deformation of coal sample while carbon dioxide molecules interact with coal …

This poster describes the Changes in Microbial Community Structure During Biostimulation for Uranium Reduction at Different Levels of Resolution

The overall goal of this project is to develop and test a thermodynamic network model for predicting the effects of substrate additions and environmental perturbations on microbial growth, community composition and system geochemistry. The hypothesis is that a thermodynamic analysis of the energy-yielding growth reactions performed by defined groups of microorganisms can be used to make quantitative and testable predictions of the change in microbial community composition that will occur when a substrate is added to the subsurface or when environmental conditions change.

Environmental nanoparticles are often poorly-crystalline or metastable structures, whose kinetics of formation and growth are poorly understood. Further, the sorption or growth of nanoparticles on mineral surfaces may control the mineral surface's reactivity and modify its ability to influence contaminant transport. Due to the characteristic length scale, a holistic understanding of the nucleation mechanisms and kinetics of nanoparticle formation on mineral surfaces is difficult to achieve with traditional methodology. In this work, our intent is to determine the molecular nature of nucleation on surfaces, the kinetics of surface nucleation and growth, and the effect of crystal surface topology using new synchrotron-based techniques. We have approached these objectives by: (1) combining state-of-the-art crystal-truncation rod diffraction (CTR) and grazing incidence x-ray absorption fine structure spectroscopy (GIXAS) techniques to investigate the three-dimensional molecular-scale geometry of silicate monomer sorption on the r-plane of hematite; and (2) developing a new grazing-incidence small angle x-ray scattering (GISAXS) setup at SSRL (0.08 nm{sup -1} < q < 8 nm{sup -1}) to explore the initial development of environmental nanoparticles on various mineral surfaces. This study also includes complementary techniques such as atomic force microscopy (AFM), bulk SAXS, dynamic light scattering (DLS), XRD, and TEM.

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in this study, we carried out large-scale comparative genomics analysis of regulatory interactions in Desulfovibrio vulgaris and 12 related genomes from Desulfovibrionales order using our recently developed web server RegPredict (http://regpredict.lbl.gov). An overall reference collection of 26 Desulfovibrionales regulogs can be accessed through RegPrecise database (http://regpredict.lbl.gov).

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Diversity and spatial patterns in plant and animal communities are well documented as a positive-power law of a taxa-area relationship (TAR). At present little is known whether this also applies to soil microbial communities and whether long-term fertilization has an influence on the underlying microbial diversity. To test the effects of long-term fertilization on above-ground botanical diversity and below-ground microbial diversity, a nested sampling approach on Park Grass plots (12d& 11/2c) of Rothamsted Reseach in United Kingdom, both at ~;; pH 5 but with plant diversities of between 42 and 13 respectively were used. GeoChip 3.0, covering approximately 57, 000 gene sequences of 292 gene families involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation, was used to determine the gene area relationships for both functional and phylogenetic groups and the relationship to plant diversity. Our analysis indicated that the microbial communities were separated by different plant diversity based on DCA. The soil microbial diversity was in accord with plant diversity. Soil microbial community exhibited different z value with different plant diversity, z = 0.0449 with higher plant diversity and z = 0.0583 with lower plant diversity (P< 0.0001). These results suggest that …

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