The reduction of uranium by sulfate-reducing bacteria in the terrestrial subsurface and a pure culture bacterium.

The microbial reduction of uranium was investigated in a contaminated aquifer and with a pure culture model organism, Desulfovibrio vulgaris Hildenborough. The concentrations of Fe(III), U(VI), nitrate and sulfate were highly variable within the aquifer, with the latter anion being quantitatively more important than the other potential electron acceptors. While this degree of heterogeneity made it difficult to discern the predominant electron accepting processes that impact U-reduction rates, several trends were notable. Nitrate inhibited the reduction of the other electron acceptors, and once it was biologically removed, the reduction of Fe(III), U(VI), and sulfate occurred concomitantly. The simultaneous loss the latter electron acceptors can be partially explained with the model sulfate reducing bacterium. In D. vulgaris, Fe(III) inhibited U-reduction while U(VI) interfered with sulfate loss from organic electron donors. However, during H2-mediated sulfate-reduction, Fe(III) impeded U-reduction, but only slowed sulfidogenesis, implicating separate electron transfer pathways. Hence, when H2 served as an electron donor, U(VI) and sulfate could be reduced concomitantly. A second trend noted during field investigations was that the presence of clays inhibited sulfate- but not Fe(III)- or U(VI)-reduction. In sandy sediments, reduction rates for the former two activities showed a positive correlation with their respective acceptor concentrations. This relationship may also be partially explained by the pure culture investigation. With lactate as the donor, 2 mM U(VI) inhibited the reduction of 2 mM sulfate, suggesting preferential electron flow to uranium. However, sulfidogenesis was only slowed in the presence of 2 mM U(VI) when 20 mM sulfate was used. In the presence of U(VI), high sulfate concentrations may be required to overcome this inhibitory effect on sulfate-reduction. During field investigations it was also found that a considerable amount of the total oxidized uranium present in sedimentary systems was complexed U(VI). When assessing remediative efforts, this pool should also be measured since only soluble U(VI) and U(IV) are routinely quantified, and the complexed pool will most likely be grouped with U(IV), thus underestimating the total U(VI) pool size. Through the development of a new procedure, this fraction of the total uranium pool can be measured without interfering with the quantitation of soluble U(VI) and U(IV). By tracking all three pools during microbial U-reduction, it could be shown that the complexed U(VI) is not initially bioavailable, but appears to solubilize as soluble U(VI) becomes reduced. Hence it is only when both U(VI) pools are reduced can migration into water bodies be considered negligible

Trajectory Optimization Methods for Robotic Cells Considering Energy Efficiency and Collisions

In production robots are moved at maximum speed whenever possible in order to achieve the shortest overall cycle time. This can lead to individual waiting times, especially in interlinked production processes. These waiting times offer opportunities for optimization. Due to high energy prices and political efforts, energy efficiency has become the focus of trajectory optimization in recent years. Robot cells with a common intermediate circuit offer the possibility of energy exchange across individual axes or robots. By adapting the robot trajectories, the total power consumption of a robotic cell on the grid side can be significantly reduced. This paper focuses on trajectory optimization, whereby a detailed collision detection of individual robots is included within the analysis. It is shown that with collision detection energy optimization for cramped robot cells becomes possible and the losses in efficiency compared to the optimization without it are minute

Analysis of strain IRB-1 as a potential candidate for uranium bioremediation in an extreme environment [abstract]

Abstract only availableSoap Lake, a halo-alkaline meromictic lake, in central Washington State is host to a variety of microorganisms capable of growth in these extreme conditions. These microorganisms have been shown to play a central role in geochemical cycling of the lake. In particular, an isolate designated strain IRB-1, a sulfur- and iron-reducing obligately anaerobic bacterium, exhibits qualities that may be beneficial for bioremediation in highly alkaline and saline environments found in contaminated industrial sites and some water systems. Strain IRB-1 was cultivated in batch cultures under anaerobic conditions in a medium that simulated site geochemistry. The original cultures were grow at a pH of 9.5, 1.2M NaCl, 60mM lactate, and 2mM Fe(III)-citrate as an electron acceptor. In all cultures growth was observed through increased protein biomass and reduction of Fe(III) over time. Scanning electron microscopy was used to analyze planktonic and biofilm cultures of IRB-1. The electron micrographs depicted the presence of extracellular appendages extending into the substrate and creating cell to cell connections. The original medium was modified by altering the terminal electron acceptor to 50mM of either sulfate, sulfite, thiosulfate, or elemental sulfur to determine the metabolic flexibility of the organism. Growth was observed only in cultures containing sulfur and thiosulfate and was confirmed over the span of several subcultures. We infer from the ability of IRB-1 to reduce Fe(III), thiosulfate, and sulfur that it may also have the ability to reduce heavy metals, specifically U(VI). Experiments are currently underway to determine the capacity of IRB-1 to grow in the presence of and/or reduce 2mM U(VI) as the sole terminal electron acceptor. Should this bacterium have the capability to reduce U(VI) and other heavy metals, it would become a candidate for bioremediation efforts in saline and highly alkaline environments where organisms traditionally employed for bioremediation can not be used.Department of Energy Genomics: Genomes to Life Progra

Draft Genome Sequence for Desulfovibrio africanus Strain PCS.

Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated from sediment from Paleta Creek, San Diego, CA. Strain PCS is capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is predicted to produce methylmercury. We present the D. africanus PCS genome sequence

Conversion of Glycerol to 1,3-propanediol under Haloalkaline Conditions

A method of producing 1,3-propanediol. The method comprises fermenting a haloalkaliphilic species of Halanaerobium with a source of glycerol into 1,3-propanediol, at a pH of greater than about 10 and at a salt concentration of greater than about 5% w/v. Furthermore, with supplementation of vitamin B12, the yield of 1,3-propanediol to glycerol can be increased

Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum.

The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45

A Streamlined Strategy for Biohydrogen Production with Halanaerobium hydrogeniformans, an Alkaliphilic Bacterium

Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, lignocellulosic biohydrogen production remains inefficient with pretreatments that are heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium hydrogeniformans, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. hydrogeniformans ferments a variety of 5- and 6-carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen, acetate, and formate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources

Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

Hypothetical (HyP) and conserved HyP genes account for >30% of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved HyP (9.5%) along with 887 HyP genes (24.4%). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 HyP and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC–MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. One thousand two hundred and twelve of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations

Development of a Model, Metal-reducing Microbial Community for a System Biology Level Assessment of Desulfovibrio vulgaris as part of a Community

One of the largest experimental gaps is between the simplicity of pure cultures and the complexity of open environmental systems, particularly in metal-contaminated areas. These microbial communities form ecosystem foundations, drive biogeochemical processes, and are relevant for biotechnology and bioremediation. A model, metal-reducing microbial community was constructed as either syntrophic or competitive to study microbial cell to cell interactions, cell signaling and competition for resources. The microbial community was comprised of the metal-reducing Desulfovibrio vulgaris Hildenborough and Geobacter sulfurreducens PCA. Additionally, Methanococcus maripaludis S2 was added to study complete carbon reduction and maintain a low hydrogen partial pressure for syntrophism to occur. Further, considerable work has been published on D. vulgaris and the D. vulgaris/ Mc. maripaludis co-culture both with and without stress. We are extending this work by conducting the same stress conditions on the model community. Additionally, this comprehensive investigation includes physiological and metabolic analyses as well as specially designed mRNA microarrays with the genes for all three organisms on one slide so as to follow gene expression changes in the various cultivation conditions as well as being comparable to the co- and individual cultures. Further, state-of -the-art comprehensive AMT tag proteomics allows for these comparisons at the protein level for a systems biology assessment of a model, metal-reducing microbial community. Preliminary data revealed that lactate oxidation by D. vulgaris was sufficient to support both G. sulfurreducens and M. maripaludis via the excretion of H2 and acetate. Fumarate was utilized by G. sulfurreducens and reduced to succinate since neither of the other two organisms can reduce fumarate. Methane was quantified, suggesting acetate and H2 concentrations were sufficient for M. maripaludis. Steady state community cultivation will allow for a comprehensive, system biology level analysis of a metal-reducing microbial community