Effect of Water Chemistry and Hydrodynamics on Nitrogen Transformation Activity and Microbial Community Functional Potential in Hyporheic Zone Sediment Columns.

Hyporheic zones (HZ) are active biogeochemical regions where groundwater and surface water mix. N transformations in HZ sediments were investigated in columns with a focus on understanding how the dynamic changes in groundwater and surface water mixing affect microbial community and its biogeochemical function with respect to N transformations. The results indicated that denitrification, DNRA, and nitrification rates and products changed quickly in response to changes in water and sediment chemistry, fluid residence time, and groundwater-surface water exchange. These changes were accompanied by the zonation of denitrification functional genes along a 30 cm advective flow path after a total of 6 days' elution of synthetic groundwater with fluid residence time >9.8 h. The shift of microbial functional potential toward denitrification was correlated with rapid NO3- reduction collectively affected by NO3- concentration and fluid residence time, and was resistant to short-term groundwater-surface water exchange on a daily basis. The results implied that variations in microbial functional potential and associated biogeochemical reactions in the HZ may occur at space scales where steep concentration gradients present along the flow path and the variations would respond to dynamic HZ water exchange over different time periods common to natural and managed riverine systems.

Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals.

The mineral-respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decaheme cytochromes, MtrC and MtrA, brought together inside a transmembrane porin, MtrB, to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system containing a pool of internalized electron carriers was used to investigate how the topology of the MtrCAB complex relates to its ability to transport electrons across a lipid bilayer to externally located Fe(III) oxides. With MtrA facing the interior and MtrC exposed on the outer surface of the phospholipid bilayer, the established in vivo orientation, electron transfer from the interior electron carrier pool through MtrCAB to solid-phase Fe(III) oxides was demonstrated. The rates were 10(3) times higher than those reported for reduction of goethite, hematite, and lepidocrocite by S. oneidensis, and the order of the reaction rates was consistent with those observed in S. oneidensis cultures. In contrast, established rates for single turnover reactions between purified MtrC and Fe(III) oxides were 10(3) times lower. By providing a continuous flow of electrons, the proteoliposome experiments demonstrate that conduction through MtrCAB directly to Fe(III) oxides is sufficient to support in vivo, anaerobic, solid-phase iron respiration.

Effect of subgrid heterogeneity on scaling geochemical and biogeochemical reactions: a case of U(VI) desorption.

The effect of subgrid heterogeneity in sediment properties on the rate of uranyl[U(VI)] desorption was investigated using a sediment collected from the U.S. Department of Energy Hanford site. The sediment was sieved into 7 grain size fractions that each exhibited different U(VI) desorption properties. Six columns were assembled using the sediment with its grain size fractions arranged in different spatial configurations to mimic subgrid heterogeneity in reactive transport properties. The apparent rate of U(VI) desorption varied significantly in the columns. Those columns with sediment structures leading to preferential transport had much lower rates of U(VI) desorption than those with relatively homogeneous transport. Modeling analysis indicated that the U(VI) desorption model and parameters characterized from well-mixed reactors significantly overpredicted the measured U(VI) desorption in the columns with preferential transport. A dual domain model, which operationally separates reactive transport properties into two subgrid domains, improved the predictions significantly. A similar effect of subgrid heterogeneity, albeit to a lesser degree, was observed for denitrification, which also occurred in the columns. The results imply that subgrid heterogeneity is an important consideration in extrapolating reaction rates from the laboratory to field.

Investigation of U(VI) adsorption in quartz-chlorite mineral mixtures.

A batch and cryogenic laser-induced time-resolved luminescence spectroscopy investigation of U(VI) adsorbed on quartz-chlorite mixtures with variable mass ratios have been performed under field-relevant uranium concentrations (5×10(-7) M and 5×10(-6) M) in pH 8.1 synthetic groundwater. The U(VI) adsorption Kd values steadily increased as the mass fraction of chlorite increased, indicating preferential sorption to chlorite. For all mineral mixtures, U(VI) adsorption Kd values were lower than that calculated from the assumption of component additivity possibly caused by surface modifications stemming from chlorite dissolution; The largest deviation occurred when the mass fractions of the two minerals were equal. U(VI) adsorbed on quartz and chlorite displayed characteristic individual luminescence spectra that were not affected by mineral mixing. The spectra of U(VI) adsorbed within the mixtures could be simulated by one surface U(VI) species on quartz and two on chlorite. The luminescence intensity decreased in a nonlinear manner as the adsorbed U(VI) concentration increased with increasing chlorite mass fraction-likely due to ill-defined luminescence quenching by both structural Fe/Cr in chlorite, and trace amounts of solubilized and reprecipitated Fe/Cr in the aqueous phase. However, the fractional spectral intensities of U(VI) adsorbed on quartz and chlorite followed the same trend of fractional adsorbed U(VI) concentration in each mineral phase with approximate linear correlations, offering a method to estimate of U(VI) concentration distribution between the mineral components with luminescence spectroscopy.

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 ß-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.

Electron transport at the microbe-mineral interface: a synthesis of current research challenges.

Many bacterial and archaeal species can couple growth to the respiratory reduction or oxidation of insoluble mineral oxides of transition metals. These solid substrates are abundant electron sinks and sources for life on Earth, but, since they are insoluble in water, they cannot enter the bacterial cells. So, to exploit these electron sinks and sources, specific respiratory electron-transfer mechanisms must overcome the physical limitations associated with electron transfer between a microbe and extracellular metal oxides. Recent microbiological, geochemical, biochemical, spectroscopic and structural work is beginning to shed light on the molecular mechanism and impacts of electron transfer at the microbe-mineral interface from a nanometre to kilometre scale. The research field is attracting attention in applied quarters from those with interests in nanowires, microbial fuel cells, bioremediation and microbial cell factories.

Mtr extracellular electron-transfer pathways in Fe(III)-reducing or Fe(II)-oxidizing bacteria: a genomic perspective.

Originally discovered in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 (MR-1), key components of the Mtr (i.e. metal-reducing) pathway exist in all strains of metal-reducing Shewanella characterized. The protein components identified to date for the Mtr pathway of MR-1 include four multihaem c-Cyts (c-type cytochromes), CymA, MtrA, MtrC and OmcA, and a porin-like outer membrane protein MtrB. They are strategically positioned along the width of the MR-1 cell envelope to mediate electron transfer from the quinone/quinol pool in the inner membrane to Fe(III)-containing minerals external to the bacterial cells. A survey of microbial genomes has identified homologues of the Mtr pathway in other dissimilatory Fe(III)-reducing bacteria, including Aeromonas hydrophila, Ferrimonas balearica and Rhodoferax ferrireducens, and in the Fe(II)-oxidizing bacteria Dechloromonas aromatica RCB, Gallionella capsiferriformans ES-2 and Sideroxydans lithotrophicus ES-1. The apparent widespread distribution of Mtr pathways in both Fe(III)-reducing and Fe(II)-oxidizing bacteria suggests a bidirectional electron transfer role, and emphasizes the importance of this type of extracellular electron-transfer pathway in microbial redox transformation of iron. The organizational and electron-transfer characteristics of the Mtr pathways may be shared by other pathways used by micro-organisms for exchanging electrons with their extracellular environments.

Analysis of structural MtrC models based on homology with the crystal structure of MtrF.

The outer-membrane decahaem cytochrome MtrC is part of the transmembrane MtrCAB complex required for mineral respiration by Shewanella oneidensis. MtrC has significant sequence similarity to the paralogous decahaem cytochrome MtrF, which has been structurally solved through X-ray crystallography. This now allows for homology-based models of MtrC to be generated. The structure of these MtrC homology models contain ten bis-histidine-co-ordinated c-type haems arranged in a staggered cross through a four-domain structure. This model is consistent with current spectroscopic data and shows that the areas around haem 5 and haem 10, at the termini of an octahaem chain, are likely to have functions similar to those of the corresponding haems in MtrF. The electrostatic surfaces around haem 7, close to the ß-barrels, are different in MtrF and MtrC, indicating that these haems may have different potentials and interact with substrates differently.

Molecular structure and free energy landscape for electron transport in the decahaem cytochrome MtrF.

The free energy profile for electron flow through the bacterial decahaem cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help to validate the method and results, because differences in the profiles can be related to differences in the charged amino acids local to specific haem groups. First estimates of reorganization free energies λ yield a range consistent with expectations for partially solvent-exposed cofactors, and reveal an activation energy range surmountable for electron flow. Future work will aim at increasing the accuracy of λ with polarizable forcefield dynamics and quantum chemical energy gap calculations, as well as quantum chemical computation of electronic coupling matrix elements.

The roles of CymA in support of the respiratory flexibility of Shewanella oneidensis MR-1.

Shewanella species are isolated from the oxic/anoxic regions of seawater and aquatic sediments where redox conditions fluctuate in time and space. Colonization of these environments is by virtue of flexible respiratory chains, many of which are notable for the ability to reduce extracellular substrates including the Fe(III) and Mn(IV) contained in oxide and phyllosilicate minerals. Shewanella oneidensis MR-1 serves as a model organism to consider the biochemical basis of this flexibility. In the present paper, we summarize the various systems that serve to branch the respiratory chain of S. oneidensis MR-1 in order that electrons from quinol oxidation can be delivered the various terminal electron acceptors able to support aerobic and anaerobic growth. This serves to highlight several unanswered questions relating to the regulation of respiratory electron transport in Shewanella and the central role(s) of the tetrahaem-containing quinol dehydrogenase CymA in that process.

Development of a proteoliposome model to probe transmembrane electron-transfer reactions.

The mineral-respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decahaem cytochromes brought together inside a transmembrane porin to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system has been developed that contains Methyl Viologen as an internalized electron carrier and valinomycin as a membrane-associated cation exchanger. These proteoliposomes can be used as a model system to investigate MtrCAB function.

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 site's 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.

Redox reactions of reduced flavin mononucleotide (FMN), riboflavin (RBF), and anthraquinone-2,6-disulfonate (AQDS) with ferrihydrite and lepidocrocite.

Flavins are secreted by the dissimilatory iron-reducing bacterium Shewanella and can function as endogenous electron transfer mediators. To assess the potential importance of flavins in Fe(III) bioreduction, we investigated the redox reaction kinetics of reduced flavin mononucleotide (i.e., FMNH(2)) and reduced riboflavin (i.e., RBFH(2)) with ferrihydrite and lepidocrocite. The organic reductants rapidly reduced and dissolved ferrihydrite and lepidocrocite in the pH range 4-8. The rate constant k for 2-line ferrihydrite reductive dissolution by FMNH(2) was 87.5 ± 3.5 M(-1)·s(-1) at pH 7.0 in batch reactors, and k was similar for RBFH(2). For lepidocrocite, k was 500 ± 61 M(-1)·s(-1) for FMNH(2) and 236 ± 22 M(-1)·s(-1) for RBFH(2). The surface area normalized initial reaction rates (r(a)) were between 0.08 and 77 µmol·m(-2)·s(-1) for various conditions in stopped-flow experiments. Initial rates (r(o)) were first-order with respect to iron(III) oxide concentration, and r(a) increased with decreasing pH. Poorly crystalline 2-line ferrihydrite yielded the highest r(a), followed by more crystalline 6-line ferrihydrite and crystalline lepidocrocite. Compared to a previous whole-cell study with Shewanella oneidensis strain MR-1, our findings suggest that the reduction of electron transfer mediators by the Mtr (i.e., metal-reducing) pathway coupled to lactate oxidation is rate limiting, rather than heterogeneous electron transfer to the iron(III) oxide.

Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions.

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both X-ray microprobe and X-ray absorption spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively reduced in the presence of an electron shuttle (AQDS), and Fe(II) ions adsorbed onto the precipitated mineral surface without inducing any structural change. In the absence of Fe(III), U(VI) was effectively reduced by the microbial population to insoluble U(IV), which was precipitated in discrete regions associated with biomass. In the presence of Fe(III) phases, however, both U(IV) and U(VI) could be detected associated with biomass, suggesting reoxidation of U(IV) by localized Fe(III) phases. These results demonstrate the importance of the spatial localization of biomass and redox active metals, and illustrate the key effects of pore-scale processes on contaminant fate and reactive transport.

Characterization of an electron conduit between bacteria and the extracellular environment.

A number of species of Gram-negative bacteria can use insoluble minerals of Fe(III) and Mn(IV) as extracellular respiratory electron acceptors. In some species of Shewanella, deca-heme electron transfer proteins lie at the extracellular face of the outer membrane (OM), where they can interact with insoluble substrates. To reduce extracellular substrates, these redox proteins must be charged by the inner membrane/periplasmic electron transfer system. Here, we present a spectro-potentiometric characterization of a trans-OM icosa-heme complex, MtrCAB, and demonstrate its capacity to move electrons across a lipid bilayer after incorporation into proteoliposomes. We also show that a stable MtrAB subcomplex can assemble in the absence of MtrC; an MtrBC subcomplex is not assembled in the absence of MtrA; and MtrA is only associated to the membrane in cells when MtrB is present. We propose a model for the modular organization of the MtrCAB complex in which MtrC is an extracellular element that mediates electron transfer to extracellular substrates and MtrB is a trans-OM spanning beta-barrel protein that serves as a sheath, within which MtrA and MtrC exchange electrons. We have identified the MtrAB module in a range of bacterial phyla, suggesting that it is widely used in electron exchange with the extracellular environment.

Identification and characterization of UndAHRCR-6, an outer membrane endecaheme c-type cytochrome of Shewanella sp. strain HRCR-6.

UndA(HRCR-6) was identified from the metal-reducing bacterium Shewanella sp. strain HRCR-6. Both in vivo and in vitro characterization results indicate that UndA(HRCR-6) is an outer membrane endecaheme c-type cytochrome and probably has a key functional role in the extracellular reduction of iron [Fe(III)] oxides and uranium [U(VI)] by Shewanella sp. HRCR-6.

Purification and characterization of the [NiFe]-hydrogenase of Shewanella oneidensis MR-1.

Shewanella oneidensis MR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H(2)ase) that has been implicated in H(2) production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H(2)ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H(2)ase were cloned and then expressed in an MR-1 mutant without hyaB and hydA genes. Expression of recombinant MR-1 [NiFe]-H(2)ase in trans restored the mutant's ability to produce H(2) at 37% of that for the wild type. Following purification, MR-1 [NiFe]-H(2)ase coupled H(2) oxidation to reduction of Tc(VII)O(4)(-) and methyl viologen. Change of the buffers used affected MR-1 [NiFe]-H(2)ase-mediated reduction of Tc(VII)O(4)(-) but not methyl viologen. Under the conditions tested, all Tc(VII)O(4)(-) used was reduced in Tris buffer, while in HEPES buffer, only 20% of Tc(VII)O(4)(-) was reduced. The reduced products were soluble in Tris buffer but insoluble in HEPES buffer. Transmission electron microscopy analysis revealed that Tc precipitates reduced in HEPES buffer were aggregates of crystallites with diameters of ∼5 nm. Measurements with X-ray absorption near-edge spectroscopy revealed that the reduction products were a mixture of Tc(IV) and Tc(V) in Tris buffer but only Tc(IV) in HEPES buffer. Measurements with extended X-ray adsorption fine structure showed that while the Tc bonding environment in Tris buffer could not be determined, the Tc(IV) product in HEPES buffer was very similar to Tc(IV)O(2)·nH(2)O, which was also the product of Tc(VII)O(4)(-) reduction by MR-1 cells. These results shows for the first time that MR-1 [NiFe]-H(2)ase catalyzes Tc(VII)O(4)(-) reduction directly by coupling to H(2) oxidation.

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.

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 + UO2²âº + 2CO3²â» = >SOUO2(CO3HCO3)²â», provided the best fit to experimental data for each sediment sample resulting in a range of conditional equilibrium constants (logK(c)) 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 logK(c) values. Using this approach, logK(c) 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 logK(c) 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.