Garrison Sposito

Characterization of the manganese oxide produced by Pseudomonas putida strain MnB1

Manganese oxides form typically in natural aqueous environments via Mn(II) oxidation catalyzed by microorganisms, primarily bacteria, but little is known about the structure of the incipient solid-phase products. The Mn oxide produced by a Pseudomonas species representative of soils and freshwaters was characterized as to composition, average Mn oxidation number, and N2 specific surface area. Electron microscopy, X-ray diffraction, and X-ray absorption near edge structure spectroscopy were applied to complement the physicochemical data with morphological and structural information. A series of synthetic Mn oxides also was analyzed by the same methods to gain better comparative understanding of the structure of the biogenic oxide. The latter was found to be a poorly crystalline layer type Mn(IV) oxide with hexagonal symmetry, significant negative structural charge arising from cation vacancies, and a relatively small number of randomly stacked octahedral sheets per particle. Its properties were comparable to those of δ-MnO2 (vernadite) and a poorly crystalline hexagonal birnessite (“acid birnessite”) synthesized by reduction of permanganate with HCl, but they were very different from those of crystalline triclinic birnessite. Overall, the structure and composition of the Mn oxide produced by P. putida were similar to what has been reported for other freshly precipitated Mn oxides in natural weathering environments, yielding further support to the predominance of biological oxidation as the pathway for Mn oxide formation. Despite variations in the degree of sheet stacking and Mn(III) content, all poorly crystalline oxides studied showed hexagonal symmetry. Thus, there is a need to distinguish layer type Mn oxides with structures similar to those of natural birnessites from the synthetic triclinic variety. We propose designating the unit cell symmetry as an addition to the current nomenclature for these minerals.

Monte Carlo simulation of interlayer molecular structure in swelling clay minerals; 1, Methodology

Monte Carlo (MC) simulations of molecular structure in the interlayers of 2:1 Na-saturated clay minerals were performed to address several important simulation methodological issues. Investigation was focused on monolayer hydrates of the clay minerals because these systems provide a severe test of the quality and sensitivity of MC interlayer simulations. Comparisons were made between two leading models of the water-water interaction in condensed phases, and the sensitivity of the simulations to the size or shape of the periodically-repeated simulation cell was determined. The results indicated that model potential functions permitting significant deviations from the molecular environment in bulk liquid water are superior to those calibrated to mimic the bulk water structure closely. Increasing the simulation cell size or altering its shape from a rectangular 21.12 Å × 18.28 Å × 6.54 Å cell (about eight clay mineral unit cells) had no significant effect on the calculated interlayer properties.

Structural model for the biogenic Mn oxide produced by Pseudomonas putida

Abstract X-ray diffraction (XRD) and Mn K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy were combined to elaborate a structural model for phyllomanganates (layer-type Mn oxides) lacking 3D ordering (turbostratic stacking). These techniques were applied to a sample produced by a common soil and freshwater bacterium (Pseudomonas putida), and to two synthetic analogs, δ-MnO2 and acid birnessite, obtained by the reduction of potassium permanganate with MnCl2 and HCl, respectively. To interpret the diffraction and spectroscopic data, we applied an XRD simulation technique utilized previously for well-crystallized birnessite varieties, complementing this approach with single-scattering-path simulations of the Mn K-edge EXAFS spectra. Our structural analyses revealed that all three Mn oxides have an hexagonal layer symmetry with layers comprising edgesharing Mn4+O6 octahedra and cation vacancies, but no layer Mn3+O6 octahedra. The proportion of cation vacancies in the layers ranged from 6 to 17%, these vacancies being charge-compensated in the interlayer by protons, alkali metals, and Mn atoms, in amounts that vary with the phyllomanganate species and synthesis medium. Both vacancies and interlayer Mn were most abundant in the biogenic oxide. The diffracting crystallites contained three to six randomly stacked layers and have coherent scattering domains of 19.42 Å in the c* direction, and of 60.85 Å in the a-b plane. Thus, the Mn oxides investigated here are nanoparticles that bear significant permanent structural charge resulting from cation layer vacancies and variable surface charge from unsaturated O atoms at layer edges.

Redox properties of standard humic acids

Humic acid (HA) participates in a variety of electron transfer reactions, but its fundamental redox properties, such as formal electrode potential and oxidation capacity, are not well characterized. Specific functionalities in HA, such as semiquinone free radicals, have been hypothesized to participate in redox reactions; however, few supportive data exist. To address these issues, three standard humic acids (Suwannee River, soil, and peat) were titrated at pH 5 and 7 with I2 as an oxidant under an inert Ar atmosphere at 25°C. The formal electrode potential of the three HA samples at pH 5 was 0.778±0.017 V, decreasing with pH by −20.0±3.2 mV per pH unit. The oxidation capacity of HA (moles of HA charge per unit mass transferred to a strong oxidant) ranged from 1.09 to 6.5 molc kg−1 at pH 5 and from 3.3 to 11.5 molc kg−1 at pH 7. The increasing order of oxidation capacity for the humic acids was: soil HA<peat HA<Suwannee River HA. A positive correlation between oxidation capacity and the stable free radical content of HA was found, but the latter property could account for only a tiny fraction of the observed moles of electrons transferred between HA and the I2 oxidant. Based on these results and those of previous research, a hypothesis for abiotic electron transfer reactions of HA involving complexed Fe(III) as a mediator was proposed.

Scale Dependence and Scale Invariance in Hydrology

List of contributors Preface 1. Scale analyses for land-surface hydrology Eric F. Wood 2. Hillslopes, channels, and landscape scale William E. Dietrich and David R. Montgomery 3. Scaling in river networks Andrea Rinaldo and Ignacio Rodriguez-Iturbe 4. Spatial variability and scale invariance in hydrologic regionalization Vijay K. Gupta and Edward C. Waymire 5. An emerging technology for scaling field soil-water behavior Donald R. Nielson, Jan W. Hopmans and Klaus Reichardt 6. Scaling invariance and the Richards equation Garrison Sposito 7. Scaling of the Richards equation and its application to watershed modeling R. Haverkamp, J.-Y. Parlange, R. Cuenca, P. J. Ross and T. S. Steenhuis 8. Scale issues of heterogeneity in vadose-zone hydrology T.-C. J. Yeh 9. Stochastic modeling of scale-dependent macrodispersion in the vadose zone David Russo 10. Dilution of nonreactive solutes in heterogeneous porous media Vivek Kapoor and Peter Kitanidis 11. Analysis of scale effects in large-scale solute-transport models Roger Beckie 12. Scale effects in fluid flow through fractured geologic media Paul A. Hsieh 13. Correlation, flow, and transport in multiscale permeability fields Shlomo P. Neuman and Vittorio Di Federico 14. Conditional simulation of geologic media with evolving scales of heterogeneity Yoram Rubin and Alberto Bellin Index.

SIDEROPHORE-PROMOTED DISSOLUTION OF HEMATITE

Siderophores are highly Fe( III)-specific bidentate ligands excreted by aerobic and facultative anaerobic microorganisms to facilitate Fe uptake in oxic environments. These compounds are thought to influence mineral weathering and the biogeochemical cycling of Fe, but quantitative information concerning this possible influence is nonexistent. Preparative quantities of a soil bacterium siderophore were extracted and purified for use in batch dissolution experiments performed with synthetic hematite particles suspended in 1 mmol dm−3 NaNO3 at pH 3 under exclusion of light. The initial siderophore concentration used, 0.24 mmol dm−3 was representative of microniche environments. Soluble Fe per unit mass of hematite was linear with time over an observational period between 2 and 24 h, leading to an area-based dissolution rate of 10−8 mol m−2 h−1 . Comparative dissolution experiments, performed with oxalate and ascorbate ligands at the 2–3 mmol dm−3 initial concentration typical of soil environments (otherwise identical conditions to the siderophore experiments), led to dissolution rates of 5 X 10−8 mol m−2 h−1 , in agreement with literature values. The comparability of dissolution rates for a soil bacterium siderophore and two terrestrial organic ligands, despite an order-of-magnitude difference in their initial concentrations, suggests that siderophores may indeed figure significantly in Fe(Ill) -mineral weathering reactions under natural conditions.

MONTE CARLO SIMULATION OF INTERLAYER MOLECULAR STRUCTURE IN SWELLING CLAY MINERALS. 2. MONOLAYER HYDRATES

Monte Carlo (MC) simulations of interlayer molecular structure in monolayer hydrates of Nasaturated Wyoming-type montmorillonites and vermiculite were performed. Detailed comparison of the stimulation results with experimental diffraction and thermodynamic data for these clay-water systems indicated good semiquantitative to quantitative agreement. The MC simulations revealed that, in the monolayer hydrate, interlayer water molecules tend to increase their occupation of the midplane as layer charge increases. As the percentage of tetrahedral layer charge increases, water molecules are induced to interact with the siloxane surface O atoms through hydrogen bonding and Na+ counter-ions are induced to form inner-sphere surface complexes. These results suggest the need for careful diffraction experiments on a series of monolayer hydrates of montmorillonite whose layer charge and tetrahedral isomorphic substitution charge vary systematically.

Steady-state dissolution kinetics of goethite in the presence of desferrioxamine B and oxalate ligands: implications for the microbial acquisition of iron

This paper reports an investigation of the effects of a trihydroxamate siderophore, desferrioxamine B (DFO-B), and a common biological ligand, oxalate, on the steady-state dissolution of goethite at pH 5 and 25 °C. The main goal of our study was to quantify the adsorption of the ligands and the dissolution of goethite they promote in a two-ligand system. In systems with one ligand only, the adsorption of oxalate and DFO-B each followed an L-type isotherm. The surface excess of oxalate was approximately 40 mmol kg−1 at solution concentrations above 80 μM, whereas the surface excess of DFO-B was only 1.2 mmol kg−1 at 80 μM solution concentration. In the two-ligand systems, oxalate decreased DFO-B adsorption quite significantly, but not vice versa. For example, in solutions containing 40 μM DFO-B and 40 μM oxalate, 30% of the DFO-B adsorbed in the absence of oxalate was displaced. The mass-normalized dissolution rate of goethite in the presence of DFO-B alone increased as the surface excess of the ligand increased, suggesting a ligand-promoted dissolution mechanism. In systems containing oxalate only, mass-normalized goethite dissolution rates were very low at concentrations below 200 μM, despite maximal adsorption of the ligand. At higher oxalate concentrations (up to 8 mM), the steady-state dissolution rate continued to increase, even though the surface excess of adsorbed ligand was essentially constant. Chemical affinity calculations and dissolution experiments with variation of the reactor flow rate showed that far-from-equilibrium conditions did not obtain in systems containing oxalate at concentrations below 5 mM. The dissolution rate in the presence of DFO-B at solution concentrations between 1 and 80 μM was approximately doubled when oxalate was also present at 40 μM solution concentration. The dissolution rate in the presence of oxalate at solution concentrations between 0 and 200 μM was increased by more than an order of magnitude when DFO-B was also present at 40 μM solution concentration. Chemical affinity calculations showed that, in systems containing DFO-B, goethite dissolution was always under far-from-equilibrium conditions, irrespective of the presence of oxalate. These results were described quantitatively by a model rate law containing a term proportional to the surface excess of DFO-B and a term proportional to that of oxalate, with both surface excesses being determined in the two-ligand system. The pseudo first-order rate coefficient in the DFO-B term has the same value as measured for goethite dissolution in the presence of DFO-B only, while the rate coefficient in the oxalate term must be measured in the two-ligand system, since it is only in this system that far-from-equilibrium conditions obtain. These latter conditions do not exist in the system containing oxalate only, but they do exist in the DFO-B/oxalate system because the siderophore is able to remove Fe(III) from all Fe–oxalate complexes rapidly, leaving the uncomplexed oxalate ligand in solution free to react again with the goethite surface. This synergy observed in the two-ligand system implies that the production of modest quantities of siderophore in the presence of very low concentrations of oxalate would be an extremely effective mechanism for the microbially induced release of Fe from goethite.

On the mechanism of specific phosphate adsorption by hydroxylated mineral surfaces: A review

Abstract The mechanism of specific phosphate adsorption by hydroxy‐lated mineral surfaces comprises two aspects: the phosphate‐hydroxyl surface reaction and the configuration of the adsorbed phosphate ion. Evidence pointing to ligand exchange as the mechanism of the phosphate‐surface hydroxyl reaction include kinetics of adsorption and desorption; hydroxyl ion release; infrared spectroscopy, and stereochemical calculations. Data pertaining to the coordination of adsorbed phosphate on hydroxy‐lated mineral surfaces have not been conclusive overall. Isotopic exchange experiments and studies of desorption kinetics do not provide definitive information on surface coordination. Measurements of hydroxyl ion release and crystallographic calculations provide support for the existence of both monodentate and bidentate surface complexes of phosphate ions. Infrared spectroscopic investigations suggest a binuclear complex on dried, phosphated goethite. However, these studies cannot be extrapolated automatically to so...

On the surface complexation model of the oxide-aqueous solution interface

Abstract The recent chemical models that describe oxide-aqueous solution reactions in terms of surface complexes are examined. It is shown that chemical thermodynamics can give a self-contained description of these reactions without hypotheses concerning the molecular structure of the interfacial region. Surface complexation models that combine concepts of coordination chemistry with those in electrical double-layer theory are attempts at molecular theory to account for the observed thermodynamic behavior of surface species. These models can be interpreted as applications of a statistical mechanical van der Waals model, according to which charged surface species interact mutually through a mean electric field created by themselves. The van der Waals model shows that the electrical double-layer parameters which appear in expressions for conditional equilibrium constants in surface complexation models represent contributions of the mean electric field to the rational activity coefficients of surface species.