John M. Zachara

Structure of a bacterial cell surface decaheme electron conduit

Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along “nanowire” appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split β-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface.

The ‘porin–cytochrome’ model for microbe-to-mineral electron transfer

Many species of bacteria can couple anaerobic growth to the respiratory reduction of insoluble minerals containing Fe(III) or Mn(III/IV). It has been suggested that in Shewanella species electrons cross the outer membrane to extracellular substrates via ‘porin–cytochrome’ electron transport modules. The molecular structure of an outer‐membrane extracellular‐facing deca‐haem terminus for such a module has recently been resolved. It is debated how, once outside the cells, electrons are transferred from outer‐membrane cytochromes to insoluble electron sinks. This may occur directly or by assemblies of cytochromes, perhaps functioning as ‘nanowires’, or via electron shuttles. Here we review recent work in this field and explore whether it allows for unification of the electron transport mechanisms supporting extracellular mineral respiration in Shewanella that may extend into other genera of Gram‐negative bacteria.

Effect of Grain Size on Uranium(VI) Surface Complexation Kinetics and Adsorption Additivity

The contribution of variable grain sizes to uranium adsorption/desorption was studied using a sediment from the US DOE Hanford site. The sediment was wet sieved into four size fractions: coarse sand (1-2 mm), medium sand (0.2-1 mm), fine sand (0.053-0.2 mm), and clay/silt fraction (<0.053 mm). For each size fraction and their composite (sediment), batch and flow-cell experiments were performed to determine uranium adsorption isotherms and kinetic uranium adsorption and subsequent desorption. The results showed that uranium adsorption isotherms and adsorption/desorption kinetics were size specific, reflecting the effects of size-specific adsorption site concentration and kinetic rate constants. The larger-size fraction had a larger mass percentage in the sediment but with a smaller adsorption site concentration and generally a slower uranium adsorption/desorption rate. The same equilibrium surface complexation reaction and reaction constant could describe uranium adsorption isotherms for all size fractions and the composite after accounting for the effect of adsorption site concentration. Mass-weighted, linear additivity was observed for both uranium adsorption isotherms and adsorption/desorption kinetics in the composite. One important implication of this study is that grain-size distribution may be used to estimate uranium adsorption site and adsorption/desorption kinetic rates in heterogeneous sediments from a common location.

Competitive reduction of pertechnetate (99TcO4-) by dissimilatory metal reducing bacteria and biogenic Fe(II).

The fate of pertechnetate ((99)Tc(VII)O(4)(-)) during bioreduction was investigated in the presence of 2-line ferrihydrite (Fh) and various dissimilatory metal reducing bacteria (DMRB) (Geobacter, Anaeromyxobacter, Shewanella) in comparison with TcO(4)(-) bioreduction in the absence of Fh. In the presence of Fh, Tc was present primarily as a fine-grained Tc(IV)/Fe precipitate that was distinct from the Tc(IV)O(2)·nH(2)O solids produced by direct biological Tc(VII) reduction. Aqueous Tc concentrations (<0.2 μm) in the bioreduced Fh suspensions (1.7 to 3.2 × 10(-9) mol L(-1)) were over 1 order of magnitude lower than when TcO(4)(-) was biologically reduced in the absence of Fh (4.0 × 10(-8) to 1.0 × 10(-7) mol L(-1)). EXAFS analyses of the bioreduced Fh-Tc products were consistent with variable chain length Tc-O octahedra bonded to Fe-O octahedra associated with the surface of the residual or secondary Fe(III) oxide. In contrast, biogenic TcO(2)·nH(2)O had significantly more Tc-Tc second neighbors and a distinct long-range order consistent with small particle polymers of TcO(2). In Fe-rich subsurface sediments, the reduction of Tc(VII) by Fe(II) may predominate over direct microbial pathways, potentially leading to lower concentrations of aqueous (99)Tc(IV).

Quantifying differences in the impact of variable chemistry on equilibrium Uranium(VI) adsorption properties of aquifer sediments.

Uranium adsorption–desorption on sediment samples collected from the Hanford 300-Area, Richland, WA varied extensively over a range of field-relevant chemical conditions, complicating assessment of possible differences in equilibrium adsorption properties. Adsorption equilibrium was achieved in 500–1000 h although dissolved uranium concentrations increased over thousands of hours owing to changes in aqueous chemical composition driven by sediment-water reactions. A nonelectrostatic surface complexation reaction, >SOH + UO22+ + 2CO32- = >SOUO2(CO3HCO3)2–, provided the best fit to experimental data for each sediment sample resulting in a range of conditional equilibrium constants (logKc) from 21.49 to 21.76. Potential differences in uranium adsorption properties could be assessed in plots based on the generalized mass-action expressions yielding linear trends displaced vertically by differences in logKc values. Using this approach, logKc values for seven sediment samples were not significantly different. However, a significant difference in adsorption properties between one sediment sample and the fines (<0.063 mm) of another could be demonstrated despite the fines requiring a different reaction stoichiometry. Estimates of logKc uncertainty were improved by capturing all data points within experimental errors. The mass-action expression plots demonstrate that applying models outside the range of conditions used in model calibration greatly increases potential errors.

Multispecies diffusion models: A study of uranyl species diffusion

[1]xa0Rigorous numerical description of multispecies diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication in imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multispecies diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multispecies diffusion. Numerical simulations found that a diffusion model with a single, common diffusion coefficient for all species was sufficient to describe multispecies U(VI) diffusion under a steady state condition of major chemical composition, but not under transient chemical conditions. Simulations revealed that for multispecies U(VI) diffusion under transient chemical conditions, a fully coupled diffusion model could be well approximated by a component-based diffusion model when the diffusion coefficient for each chemical component was properly selected. The component-based diffusion model considers the difference in diffusion coefficients between chemical components, but not between the species within each chemical component. This treatment significantly enhanced computational efficiency at the expense of minor charge conservation. The charge balance in the component-based diffusion model can be enforced, if necessary, by adding a secondary migration term resulting from model simplification. The effect of ion activity coefficient gradients on multispecies diffusion is also discussed. The diffusion models were applied to describe U(VI) diffusive mass transfer in intragranular domains in two sediments collected from U.S. Department of Energys Hanford 300A, where intragranular diffusion is a rate-limiting process controlling U(VI) adsorption and desorption. The grain-scale reactive diffusion model was able to describe U(VI) adsorption/desorption kinetics that had been previously described using a semiempirical, multirate model. Compared with the multirate model, the diffusion models have the advantage to provide spatiotemporal speciation evolution within the diffusion domains.

Three-dimensional Bayesian geostatistical aquifer characterization at the Hanford 300 Area using tracer test data

[1]xa0Tracer tests performed under natural or forced gradient flow conditions can provide useful information for characterizing subsurface properties, through monitoring, modeling, and interpretation of the tracer plume migration in an aquifer. Nonreactive tracer experiments were conducted at the Hanford 300 Area, along with constant-rate injection tests and electromagnetic borehole flowmeter tests. A Bayesian data assimilation technique, the method of anchored distributions (MAD) (Rubin et al., 2010), was applied to assimilate the experimental tracer test data with the other types of data and to infer the three-dimensional heterogeneous structure of the hydraulic conductivity in the saturated zone of the Hanford formation.In this study, the Bayesian prior information on the underlying random hydraulic conductivity field was obtained from previous field characterization efforts using constant-rate injection and borehole flowmeter test data. The posterior distribution of the conductivity field was obtained by further conditioning the field on the temporal moments of tracer breakthrough curves at various observation wells. MAD was implemented with the massively parallel three-dimensional flow and transport code PFLOTRAN to cope with the highly transient flow boundary conditions at the site and to meet the computational demands of MAD. A synthetic study proved that the proposed method could effectively invert tracer test data to capture the essential spatial heterogeneity of the three-dimensional hydraulic conductivity field. Application of MAD to actual field tracer data at the Hanford 300 Area demonstrates that inverting for spatial heterogeneity of hydraulic conductivity under transient flow conditions is challenging and more work is needed.

Quantitative 3-D elemental mapping by LA-ICP-MS of a basaltic clast from the hanford 300 area, Washington, USA

Laser ablation with inductively coupled plasma-mass spectrometry (LA-ICP-MS) was used to measure elemental concentrations at the 100-μm scale in a 3-dimensional manner within a basaltic clast sample collected from the Hanford 300 Area in south-central Washington State, United States. A calibration method was developed to quantify the LA-ICP-MS signal response using a constant-sum mass fraction of eight major elements; the method produced reasonable concentration measurements for both major and trace elements when compared to a standard basalt sample with known concentrations. 3-Dimensional maps (stacked 2-D contour layers, each representing 2100 μm × 2100 μm) show relatively uniform concentration with depth for intrinsic elements such as Si, Na, and Sr. However, U and Cu accumulation were observed near the sample surface, consistent with the sites release history of these contaminants. U and Cu show substantial heterogeneity in their concentration distributions within horizontal slices, while the intrinsic elements are essentially uniformly distributed. From these measured U concentrations and published grain size distributions, gravel and cobbles were estimated to contain about 1% of the contaminant U, implicating the coarse fraction as a long-term release source.

Transient groundwater chemistry near a river: Effects on U(VI) transport in laboratory column experiments

[1]xa0In the 300 Area of a U(VI)-contaminated aquifer at Hanford, Washington, USA, inorganic carbon and major cations, which have large impacts on U(VI) transport, change on an hourly and seasonal basis near the Columbia River. Batch and column experiments were conducted to investigate the factors controlling U(VI) adsorption/desorption by changing chemical conditions over time. Low alkalinity and low Ca concentrations (Columbia River water) enhanced adsorption and reduced aqueous concentrations. Conversely, high alkalinity and high Ca concentrations (Hanford groundwater) reduced adsorption and increased aqueous concentrations of U(VI). An equilibrium surface complexation model calibrated using laboratory batch experiments accounted for the decrease in U(VI) adsorption observed with increasing (bi)carbonate concentrations and other aqueous chemical conditions. In the column experiment, alternating pulses of river and groundwater caused swings in aqueous U(VI) concentration. A multispecies multirate surface complexation reactive transport model simulated most of the major U(VI) changes in two column experiments. The modeling results also indicated that U(VI) transport in the studied sediment could be simulated by using a single kinetic rate without loss of accuracy in the simulations. Moreover, the capability of the model to predict U(VI) transport in Hanford groundwater under transient chemical conditions depends significantly on the knowledge of real-time change of local groundwater chemistry.

Characterization of the intragranular water regime within subsurface sediments: Pore volume, surface area, and mass transfer limitations

[1]xa0Although “intragranular” pore space within grain aggregates, grain fractures, and mineral surface coatings may contain a relatively small fraction of the total porosity within a porous medium, it often contains a significant fraction of the reactive surface area, and can thus strongly affect the transport of sorbing solutes. In this work, we demonstrate a batch experiment procedure using tritiated water as a high-resolution diffusive tracer to characterize the intragranular pore space. The method was tested using uranium-contaminated sediments from the vadose and capillary fringe zones beneath the former 300A process ponds at the Hanford site (Washington). Sediments were contacted with tracers in artificial groundwater, followed by a replacement of bulk solution with tracer-free groundwater and the monitoring of tracer release. From these data, intragranular pore volumes were calculated and mass transfer rates were quantified using a multirate first-order mass transfer model. Tritium-hydrogen exchange on surface hydroxyls was accounted for by conducting additional tracer experiments on sediment that was vacuum dried after reaction. The complementary (“wet” and “dry”) techniques allowed for the simultaneous determination of intragranular porosity and surface area using tritium. The Hanford 300A samples exhibited intragranular pore volumes of ∼1% of the solid volume and intragranular surface areas of ∼20%–35% of the total surface area. Analogous experiments using bromide ion as a tracer yielded very different results, suggesting very little penetration of bromide into the intragranular porosity.