Adsorption of Cu(II) to Bacillus subtilis: A pH-dependent EXAFS and thermodynamic modelling study

Bacteria are very efficient sorbents of trace metals, and their abundance in a wide variety of natural aqueous systems means biosorption plays an important role in the biogeochemical cycling of many elements. We measured the adsorption of Cu(II) to Bacillus subtilis as a function of pH and surface loading. Adsorption edge and XAS experiments were performed at high bacteria-to-metal ratio, analogous to Cu uptake in natural geologic and aqueous environments. We report significant Cu adsorption to B. subtilis across the entire pH range studied (pH ∼2-7), with adsorption increasing with pH to a maximum at pH ∼6. We determine directly for the first time that Cu adsorbs to B. subtilis as a (CuO₅H_n)ⁿ⁻⁸ monodentate, inner-sphere surface complex involving carboxyl surface functional groups. This Cu-carboxyl complex is able to account for the observed Cu adsorption across the entire pH range studied. Having determined the molecular adsorption mechanism of Cu to B. subtilis, we have developed a new thermodynamic surface complexation model for Cu adsorption that is informed by and consistent with EXAFS results. We model the surface electrostatics using the 1pK basic Stern approximation. We fit our adsorption data to the formation of a monodentate, inner-sphere RCOOCu⁺ surface complex. In agreement with previous studies, this work indicates that in order to accurately predict the fate and mobility of Cu in complex biogeochemical systems, we must incorporate the formation of Cu-bacteria surface complexes in reactive transport models. To this end, this work recommends log K RCOOCu⁺ = 7.13 for geologic and aqueous systems with generally high B. subtilis-to-metal ratio.     

X-ray absorption fine structure determination of pH-dependent U-bacterial cell wall interactions

X-ray absorption fine structure (XAFS) measurements was used at the U L3-edge to directly determine the pH dependence of the cell wall functional groups responsible for the absorption of aqueous UO₂²⁺ to Bacillus subtilis from pH 1.67 to 4.80. Surface complexation modeling can be used to predict metal distributions in water-rock systems, and it has been used to quantify bacterial adsorption of metal cations. However, successful application of these models requires a detailed knowledge not only of the type of bacterial surface site involved in metal adsorption/desorption, but also of the binding geometry. Previous acid-base titrations of B. subtilis cells suggested that three surface functional group types are important on the cell wall; these groups have been postulated to correspond to carboxyl, phosphoryl, and hydroxyl sites. When the U(VI) adsorption to B. subtilis is measured, observed is a significant pH-independent absorption at low pH values (<3.0), ascribed to an interaction between the uranyl cation and a neutrally charged phosphoryl group on the cell wall. The present study provides independent quantitative constraints on the types of sites involved in uranyl binding to B. subtilis from pH 1.67 to 4.80. The XAFS results indicate that at extremely low pH (pH 1.67) UO₂²⁺ binds exclusively to phosphoryl functional groups on the cell wall, with an average distance between the U atom and the P atom of 3.64 ± 0.01 Å. This U-P distance indicates an inner-sphere complex with an oxygen atom shared between the UO₂²⁺ and the phosphoryl ligand. The P signal at extremely low pH value is consistent with the UO₂²⁺ binding to a protonated phosphoryl group, as previously ascribed. With increasing pH (3.22 and 4.80), UO₂²⁺ binds increasingly to bacterial surface carboxyl functional groups, with an average distance between the U atom and the C atom of 2.89 ± 0.02 Å. This U-C distance indicates an inner-sphere complex with two oxygen atoms shared between the UO₂²⁺ and the carboxyl ligand. The results of this XAFS study confirm the uranyl-bacterial surface speciation model.     

High- and low-affinity binding sites for Cd on the bacterial cell walls of Bacillus subtilis and Shewanella oneidensis

Bulk Cd adsorption isotherm experiments, thermodynamic equilibrium modeling, and Cd K edge EXAFS were used to constrain the mechanisms of proton and Cd adsorption to bacterial cells of the commonly occurring Gram-positive and Gram-negative bacteria, Bacillus subtilis and Shewanella oneidensis, respectively. Potentiometric titrations were used to characterize the functional group reactivity of the S. oneidensis cells, and we model the titration data using the same type of non-electrostatic surface complexation approach as was applied to titrations of B. subtilis suspensions by Fein et al. (2005). Similar to the results for B. subtilis, the S. oneidensis cells exhibit buffering behavior from approximately pH 3-9 that requires the presence of four distinct sites, with pK_a values of 3.3 ± 0.2, 4.8 ± 0.2, 6.7 ± 0.4, and 9.4 ± 0.5, and site concentrations of 8.9(±2.6) × 10⁻⁵, 1.3(±0.2) × 10⁻⁴, 5.9(±3.3) × 10⁻⁵, and 1.1(±0.6) × 10⁻⁴ moles/g bacteria (wet mass), respectively. The bulk Cd isotherm adsorption data for both species, conducted at pH 5.9 as a function of Cd concentration at a fixed biomass concentration, were best modeled by reactions with a Cd:site stoichiometry of 1:1. EXAFS data were collected for both bacterial species as a function of Cd concentration at pH 5.9 and 10 g/L bacteria. The EXAFS results show that the same types of binding sites are responsible for Cd sorption to both bacterial species at all Cd loadings tested (1-200 ppm). Carboxyl sites are responsible for the binding at intermediate Cd loadings. Phosphoryl ligands are more important than carboxyl ligands for Cd binding at high Cd loadings. For the lowest Cd loadings studied here, a sulfhydryl site was found to dominate the bound Cd budgets for both species, in addition to the carboxyl and phosphoryl sites that dominate the higher loadings. The EXAFS results suggest that both Gram-positive and Gram-negative bacterial cell walls have a low concentration of very high-affinity sulfhydryl sites which become masked by the more abundant carboxyl and phosphoryl sites at higher metal:bacteria ratios. This study demonstrates that metal loading plays a vital role in determining the important metal-binding reactions that occur on bacterial cell walls, and that high affinity, low-density sites can be revealed by spectroscopy of biomass samples. Such sites may control the fate and transport of metals in realistic geologic settings, where metal concentrations are low.     

Adsorption to goethite of extracellular polymeric substances from Bacillus subtilis

Extracellular polymeric substances (EPS) are heterogeneous biopolymers produced by Gram-negative and Gram-positive bacterial cells. Adsorption of EPS to minerals can alter the substrata physico-chemistry and influence initial bacterial adhesion processes via conditioning film formation, but the effects of solution chemistry on uptake of EPS remain poorly understood. In this study, the adsorption to goethite (α-FeOOH) of EPS isolated from the early stationary growth-phase culture of Bacillus subtilis was investigated as a function of pH and ionic strength (I) in NaCl background electrolyte using batch studies coupled with Fourier transform infrared spectroscopy and size-exclusion high-performance liquid chromatography. Proteins, particularly those of higher molar mass, and phosphorylated macromolecules were adsorbed preferentially. Increasing solution I (1-100 mM NaCl) or pH (3.0-9.0) resulted in a decrease in the mass of EPS adsorbed. Batch studies and diffuse reflectance infrared Fourier transform spectra are consistent with ligand exchange of EPS phosphate groups for surface hydroxyls at Fe metal centers. The data indicate that both electrostatic and chemical bonding interactions contribute to selective fractionation of the EPS solution. Proteins and phosphate groups in phosphodiester bridges of nucleic acids likely play an important role in conditioning film formation at Fe oxide surfaces.     

Enthalpies and entropies of proton and cadmium adsorption onto Bacillus subtilis bacterial cells from calorimetric measurements

We used titration calorimetry to measure the bulk heats of proton and Cd adsorption onto a common Gram positive soil bacterium Bacillus subtilis at 25.0 °C. Using the 4-site non-electrostatic model of Fein et al. [Fein, J.B., Boily, J.-F., Yee, N., Gorman-Lewis, D., Turner, B.F., 2005. Potentiometric titrations of Bacillus subtilis cells to low pH and a comparison of modeling approaches. Geochim. Cosmochim. Acta69 (5), 1123-1132.] to describe the bacterial surface reactivity to protons, our bulk enthalpy measurements can be used to determine the following site-specific enthalpies of proton adsorption for Sites 1-4, respectively: −3.5 ± 0.2, −4.2 ± 0.2, −15.4 ± 0.9, and −35 ± 2 kJ/mol, and these values yield the following third law entropies of proton adsorption onto Sites 1-4, respectively: +51 ± 4, +78 ± 4, +79 ± 5, and +60 ± 20 J/mol K. An alternative data analysis using a 2-site Langmuir-Freundlich model to describe proton binding to the bacterial surface (Fein et al., 2005) resulted in the following site-specific enthalpies of proton adsorption for Sites 1 and 2, respectively: −3.6 ± 0.2 and −35.1 ± 0.3 kJ/mol. The thermodynamic values for Sites 1-3 for the non-electrostatic model and Site 1 of the Langmuir-Freundlich model of proton adsorption onto the bacterial surface are similar to those associated with multifunctional organic acid anions, such as citrate, suggesting that the protonation state of a bacterial surface site can influence the energetics of protonation of neighboring sites. Our bulk Cd enthalpy data, interpreted using the 2-site non-electrostatic Cd adsorption model of Borrok et al. [Borrok, D., Fein, J.B., Tischler, M., O’Loughlin, E., Meyer, H., Liss, M., Kemner, K.M., 2004b. The effect of acidic solutions and growth conditions on the adsorptive properties of bacterial surfaces. Chem. Geol.209 (1-2), 107-119.] to account for Cd adsorption onto B. subtilis, yield the following site-specific enthalpies of Cd adsorption onto bacterial surface Sites 2 and 3, respectively: −0.2 ± 0.4 and +14.4 ± 0.9 kJ/mol, and the following third law entropies of Cd adsorption onto Sites 2 and 3, respectively: +57 ± 4 and +128 ± 5 J/mol K. The calculated enthalpies of Cd adsorption are typical of those associated with Cd complexation with anionic oxygen ligands, and the entropies are indicative of inner sphere complexation by multiple ligands. The experimental approach described in this study not only yields constraints on the molecular-scale mechanisms involved in proton and Cd adsorption reactions, but also provides new thermodynamic data that enable quantitative estimates of the temperature dependence of proton and Cd adsorption reactions.     

Experimental study of neptunyl adsorption onto Bacillus subtilis

The subsurface mobility of Np is difficult to predict in part due to uncertainties associated with its sorption behavior in geologic systems. In this study, we measured Np adsorption onto a common gram-positive soil bacterium, Bacillus subtilis. We performed batch adsorption experiments with Np(V) solutions as a function of pH, from 2.5 to 8, as a function of total Np concentration from 1.29 × 10⁻⁵ M to 2.57 × 10⁻⁴ M, and as a function of ionic strength from 0.001 to 0.5 M NaClO₄. Under most pH conditions, Np adsorption is reversible and exhibits an inverse relationship with ionic strength, with adsorption increasing with increasing pH. At low pH in the 0.1 M ionic strength systems, we observed irreversible adsorption, which is consistent with reduction of Np(V) to Np(IV). We model the adsorption reaction using a nonelectrostatic surface complexation approach to yield ionic strength dependent NpO₂⁺-bacterial surface stability constants. The data require two bacterial surface complexation reactions to account for the observed adsorption behavior: R-L₁⁻ + NpO₂⁺ ↔ R-L₁-NpO₂^° and R-L₂⁻ + NpO₂⁺ ↔ R-L₂-NpO₂^°, where R represents the bacterium to which each functional group is attached, and L₁ and L₂ represent the first and second of four discrete site types on the bacterial surface. Stability constants (log K values) for the L₁ and L₂ reactions in the 0.001 M system are 2.3 ± 0.3 and 2.3 ± 0.2, and in the 0.1 M system the values are 1.7 ± 0.2 and 1.6 ± 0.2, respectively. The calculated neptunyl-bacterial surface stability constants are not consistent with values predicted using the linear free energy correlation approach from Fein et al. (2001), suggesting that possible unfavorable steric interactions and the low charge of NpO₂⁺ affects Np-bacterial adsorption.     

Antimony speciation in saline hydrothermal fluids: A combined X-ray absorption fine structure spectroscopy and solubility study

Solubility of senarmontite (Sb₂O₃, cubic) in pure water and NaCl-HCl aqueous solutions, and local atomic structure around antimony in these fluids were characterized using in situ X-ray absorption fine structure (XAFS) spectroscopy at temperatures to 450 °C and pressures to 600 bars. These experiments were performed using a new X-ray cell which allows simultaneous measurement of the absolute concentration of the absorbing element in the fluid, and atomic environment around the absorber. Results show that aqueous Sb(III) speciation is dominated by the complex in pure water, mixed Sb-hydroxide-chloride complexes in acidic NaCl-HCl solutions (2 m NaCl-0.1 m HCl), and by Sb-chloride species in concentrated HCl solutions (3.5 m HCl). Interatomic Sb-O and Sb-Cl distances in these complexes range from 1.96 to 1.97 Å and from 2.37 to 2.47 Å, respectively. These structural data, together with senarmontite solubility determined from XAFS spectra, were complemented by batch-reactor measurements of senarmontite and stibnite (Sb₂S₃, rhombic) solubilities over a wide range of HCl and NaCl concentrations from 300 to 400 °C. Analysis of the whole dataset shows that Sb(III) speciation in high-temperature moderately acid (pH > 2-3) Cl-rich fluids is dominated by mixed hydroxy-chloride species like Sb(OH)₂Cl° and Sb(OH)₃Cl⁻, but other species containing two or three Cl atoms appear at higher acidities and moderate temperatures (?300 °C). Calculations using stability constants retrieved in this study indicate that mixed hydroxy-chloride complexes control antimony transport in saline high-temperature ore fluids at acidic conditions. Such species allow for a more effective Sb partitioning into the vapor phase during boiling and vapor-brine separation processes occurring in magmatic-hydrothermal systems. Antimony hydroxy-chloride complexes are however minor in the neutral low- to moderate-temperature solutions (?250-300 °C) typical of Sb deposits formation; the antimony speciation in these systems is dominated by Sb(OH)₃ and potentially Sb-sulfide species.     

Potentiometric titrations of Bacillus subtilis cells to low pH and a comparison of modeling approaches

To provide constraints on the speciation of bacterial surface functional groups, we have conducted potentiometric titrations using the gram-positive aerobic species Bacillus subtilis, covering the pH range 2.1 to 9.8. Titration experiments were conducted using an auto-titrator assembly, with the bacteria suspended in fixed ionic strength (0.01 to 0.3 M) NaClO₄ solutions. We observed significant adsorption of protons over the entire pH range of this study, including to the lowest pH values examined, indicating that proton saturation of the cell wall did not occur under any of the conditions of the experiments. Ionic strength, over the range studied here, did not have a significant effect on the observed buffering behavior relative to experimental uncertainty. Electrophoretic mobility measurements indicate that the cell wall is negatively charged, even under the lowest pH conditions studied. These experimental results necessitate a definition of the zero proton condition such that the total proton concentration at the pH of suspension is offset to account for the negative bacterial surface charge that tends towards neutrality at pH <2.The buffering intensity of the bacterial suspensions reveals a wide spread of apparent pKa values. This spread was modeled using three significantly different approaches: a Non-Electrostatic Model, a Constant Capacitance Model, and a Langmuir-Freundlich Model. The approaches differ in the manner in which they treat the surface electric field effects, and in whether they treat the proton-active sites as discrete functional groups or as continuous distributions of related sites. Each type of model tested, however, provides an excellent fit to the experimental data, indicating that titration data alone are insufficient for characterizing the molecular-scale reactions that occur on the bacterial surface. Spectroscopic data on the molecular-scale properties of the bacterial surface are required to differentiate between the underlying mechanisms of proton adsorption inherent in these models. The applicability and underlying conceptual foundation of each model is discussed in the context of our current knowledge of the structure of bacterial cell walls.     

An X-ray absorption spectroscopy study of Cd binding onto bacterial consortia

In this study, we use extended X-ray absorption fine structure (EXAFS) spectroscopy measurements to examine the atomic environment of Cd bound onto two experimental bacterial consortia: one grown from river water, and one grown from a manufacturing gas plant site. The experiments were conducted as a function of pH and demonstrate that the complex mixtures of bacteria, containing both Gram-positive and Gram-negative species, yield relatively simple EXAFS spectra, a result which indicates that only a limited number of functional group types contribute to Cd binding for each bacterial consortium. The EXAFS spectra indicate that the average Cd binding environment in the river water consortium varies significantly with pH, but the manufacturing gas plant consortium exhibits a Cd binding environment that remains relatively constant over the pH range examined. The EXAFS data for the river water consortium were modeled using carboxyl, phosphoryl and sulfhydryl sites. However, only carboxyl and phosphoryl sites were required to model the manufacturing gas plant consortium data under similar experimental conditions. This is the first EXAFS study to identify and quantify the relative importance of metal binding sites in bacterial consortia. Although our results indicate differences in the binding environments of the two consortia, the data suggest that there are broad similarities in the binding environments present on a wide range of bacterial cell walls.     

An X-ray absorption fine structure and nuclear magnetic resonance spectroscopy study of gallium-silica complexes in aqueous solution

The influence of aqueous silica on gallium(III) hydrolysis in dilute (2 × 10⁻⁴ ≤ m_Ga ≤ 5 × 10⁻³) and moderately concentrated (0.02 ≤ m_Ga ≤ 0.3) aqueous solutions was studied at ambient temperature, using high resolution X-ray absorption fine structure (XAFS) and nuclear magnetic resonance (NMR) spectroscopies, respectively. Results show that, in Si-free acidic solutions (pH < 3), Ga is hexa-coordinated with oxygens of H₂O molecules and/or OH groups in the first coordination sphere of the metal. With increasing pH, these hydroxyl groups are progressively replaced by bridging oxygens (-O-), and polymerized Ga-hydroxide complexes form via Ga-O-Ga chemical bonds. In the 2.5-3.5 pH range, both XAFS and NMR spectra are consistent with the dominant presence of the Ga₁₃ Keggin polycation, which has the same local structure as A1₁₃. Under basic pH (pH > 8), Ga exhibits a tetrahedral coordination, corresponding to Ga(OH)₄⁻ species, in agreement with previous NMR and potentiometric studies. Major changes in Ga hydrolysis have been detected in the presence of aqueous silica. Ga is tetra-coordinated, both in basic and acid (i.e., at pH > 2.7) Si-bearing solutions (0.01 ≤ m_Si ≤ 0.2), and forms stable gallium-silicate complexes. In these species, Ga binds via bridging oxygen to 2 ± 1 silicons, with an average Ga-Si distance of 3.16 ± 0.05 Å, and to 2 ± 1 silicons, with an average Ga-Si distance of 3.39 ± 0.03 Å. These two sets of Ga-Si distances imply the formation of two types of Ga-silicate aqueous complex, cyclic Ga-Si_2-3 species (formed by the substitution of Si in its tri-, tetra- or hexa-cyclic polymers by Ga atoms), and chainlike GaSi_2-4 species (similar to those found for A1), respectively. The increase in the number of Si neighbors (a measure of the complex concentration and stability), in alkaline media, with increasing SiO₂(aq) content and decreasing pH is similar to that for A1-Si complexes found in neutral to basic solutions. At very acid pH and moderate silica concentrations, the presence of another type of Ga-Si complex, in which Ga remains hexa-coordinated and binds to the silicon tetrahedra via the GaO₆ octahedron corners, has also been detected. These species are similar to those found for Al³⁺ in acid solutions. Thus, as for aluminum, silicic acid greatly hampers Ga hydrolysis and enhances Ga mobility in natural waters via the formation of gallium-silicate complexes.     

Iron (III)-silica interactions in aqueous solution: insights from X-ray absorption fine structure spectroscopy

The influence of aqueous silica on the hydrolysis of iron(III) nitrate and chloride salts in dilute aqueous solutions (m_Fe ∼ 0.01 mol/kg) was studied at ambient temperature using X-ray absorption fine structure (XAFS) spectroscopy at the Fe K-edge. Results show that in Si-free iron nitrate and chloride solutions at acid pH (pH < 2.5), Fe is hexa-coordinated with 6 oxygens of H₂O- and/or OH-groups in the first coordination sphere of the metal, at an Fe-O distance of 2.00 ± 0.01 Å. With increasing pH (2.7 < pH < 13), these groups are rapidly replaced by bridging hydroxyls (-OH-) or oxygens (-O-), and polymerized Fe hydroxide complexes form via Fe-(O/OH)-Fe bonds. In these polymers, the first atomic shell of iron represents a distorted octahedron with six O/OH groups and Fe-O distances ranging from 1.92 to 2.07 Å. The Fe octahedra are linked together by their edges (Fe-Fe distance 2.92-3.12 Å) and corners (Fe-Fe distance ∼3.47 ± 0.03 Å). The Fe-Fe coordination numbers (N_edge = 1-2; N_corner = 0.5-0.7) are consistent with the dominant presence of iron dimers, trimers and tetramers at pH 2.5 to 2.9, and of higher-polymerized species at pH > 3.At pH > 2.5 in the presence of aqueous silica, important changes in Fe(III) hydrolysis are detected. In 0.05-m Si solutions (pH ∼ 2.7-3.0), the corner linkages between Fe octahedra in the polymeric complexes disappear, and the Fe-Fe distances corresponding to the edge linkages slightly increase (Fe-Fe_edge ∼ 3.12-3.14 Å). The presence of 1 to 2 silicons at 3.18 ± 0.03 Å is detected in the second atomic shell around iron. At basic pH (∼12.7), similar structural changes are observed for the iron second shell. The Fe-Si and Fe-Fe distances and coordination numbers derived in this study are consistent with (1) Fe-Si complex stoichiometries Fe₂Si_1-2 and Fe₃Si_2-3 at pH < 3; (2) structures composed of Fe-Fe dimers and trimers sharing one or two edges of FeO₆-octahedra; and (3) silicon tetrahedra linked to two neighboring Fe octahedra via corners. At higher Si concentration (0.16 m, polymerized silica solution) and pH ∼ 3, the signal of the Fe second shell vanishes indicating the destruction of the Fe-Fe bonds and the formation of different Fe-Si linkages. Moreover, ∼20 mol.% of Fe is found to be tetrahedrally coordinated with oxygens in the first coordination shell (R_Fe-O = 1.84 Å). This new finding implies that Fe may partially substitute for Si in the tetrahedral network of the silica polymers in Si-rich solutions.The results of this study demonstrate that aqueous silica can significantly inhibit iron polymerization and solid-phase formation, and thus increase the stability and mobility of Fe(III) in natural waters. The silica “poisoning” of the free corner sites of iron-hydroxide colloids should reduce the adsorption and incorporation of trace elements by these colloids in Si-rich natural waters.     

Antimony(III) complexing with O-bearing organic ligands in aqueous solution: An X-ray absorption fine structure spectroscopy and solubility study

The stability and structure of aqueous complexes formed by trivalent antimony (Sb^III) with carboxylic acids (acetic, adipic, malonic, lactic, oxalic, tartaric, and citric acid), phenols (catechol), and amino acids (glycine) having O- and N-functional groups (carboxyl, alcoholic hydroxyl, phenolic hydroxyl and amine) typical of natural organic matter, were determined at 20 and 60 °C from solubility and X-ray absorption fine structure (XAFS) spectroscopy measurements. In organic-free aqueous solutions and in the presence of acetic, adipic, malonic acids and glycine, both spectroscopic and solubility data are consistent with the dominant formation of Sb^III hydroxide species, , at strongly acid, acid-to-neutral and basic pH, respectively, demonstrating negligible complexing with mono-functional organic ligands (acetic) or those having non adjacent carboxylic groups (adipic, malonic). In contrast, in the presence of poly-functional carboxylic and hydroxy-carboxylic acids and catechol, Sb^III forms stable 1:1 and 1:2 complexes with the studied organic ligands over a wide pH range typical of natural waters (3 < pH < 9). XAFS spectroscopy measurements show that in these species the central Sb^III atom has a distorted pseudo-trigonal pyramidal geometry composed of the lone pair of 5s² electrons of Sb and four oxygen atoms from two adjacent functional groups of the ligand (OC-OH and/or COH), forming a five-membered bidendate chelate cycle. Stability constants for these species, generated from Sb₂O₃ (rhomb.) solubility experiments, were used to model Sb complexing with natural humic acids possessing the same functional groups as those investigated in this study. Our predictions show that in an aqueous solution of pH between 2 and 10, containing 1 μg/L of Sb and 5 mg/L of dissolved organic carbon (DOC), up to 35% of total dissolved Sb binds to aqueous organic matter via carboxylic and hydroxy-carboxylic groups. This amount of complexed Sb for typical natural DOC concentrations is in agreement with that estimated from dialysis experiments performed with commercial humic acid in our work and those available in the literature for a range of standardized IHSS humic acids. Our results imply that a significant part of Sb is likely to be bound with humic acids via hydroxy-carboxylic moieties, in the form of bidendate complexes. However, following the strong chemical affinity of Sb^III for reduced sulfur, some undefined fraction of Sb^III might also be bound to the minor thiol-bearing moieties of humic acids; further studies are required to check this hypothesis.     

Neoformation of Ni phyllosilicate upon Ni uptake on montmorillonite: A kinetics study by powder and polarized extended X-ray absorption fine structure spectroscopy

Wet chemistry kinetics and powder and polarized extended X-ray absorption fine structure (EXAFS and P-EXAFS) spectroscopy were combined to investigate the mechanism of Ni uptake on montmorillonite, at pH 8, high ionic strength (0.2 M Ca(NO₃)₂), initial Ni concentration of 660 μM, and solid concentration of 5.3 g/L. Approximately 20% of Ni sorbed within the first 24 h; thereafter, the Ni uptake rate slowed, and 12% of the initial Ni concentration remained in solution after 206 d of reaction time. Powder EXAFS spectra collected on wet pastes at 1, 14, 90, and 206 d showed the presence of Ni-Ni pairs at ∼3.08 Å in an amount that gradually increased with time. Results were interpreted by the nucleation of a Ni phase having either an α-Ni-hydroxide- or a Ni-phyllosilicate-like local structure. The latter possibility was confirmed by recording P-EXAFS spectra of a highly textured, self-supporting montmorillonite film prepared in the same conditions as the wet samples and equilibrated for 14 d. The orientation distribution of the c*-axes of individual clay particles off the film plane, as measured by quantitative texture analysis, was 32.8° full width at half maximum, and this value was used to correct from texture effect the effective numbers of Ni and Si nearest neighbors determined by P-EXAFS. Ni atoms were found to be surrounded by 2.6 ± 0.5 Ni atoms at 3.08 Å in the in-plane direction and by 4.2 ± 0.5 Si atoms at 3.26 Å in the out-of-plane direction. These structural parameters, but also the orientation and angular dependence of the Ni and Si shells, strongly support the formation of a Ni phyllosilicate having its layers parallel to the montmorillonite layers. The neoformation of a phyllosilicate on metal uptake on montmorillonite, documented herein for the first time, has important geochemical implications because this dioctahedral smectite is overwhelmingly present in the environment. The resulting sequestration of sorbed trace metals in sparingly soluble phyllosilicate structure may durably decrease their migration and bioavailability at the Earth’s surface and near surface.     

Stabilization of extracellular polymeric substances (Bacillus subtilis) by adsorption to and coprecipitation with Al forms

Extracellular polymeric substances (EPS) are continuously produced by bacteria during their growth and metabolism. In soils, EPS are bound to cell surfaces, associated with biofilms, or released into solution where they can react with other solutes and soil particle surfaces. If such reaction results in a decrease in EPS bioaccessibility, it may contribute to stabilization of microbial-derived organic carbon (OC) in soil. Here we examined: (i) the chemical fractionation of EPS produced by a common Gram positive soil bacterial strain (Bacillus subtilis) during reaction with dissolved and colloidal Al species and (ii) the resulting stabilization against desorption and microbial decay by the respective coprecipitation (with dissolved Al) and adsorption (with Al(OH)_3(am)) processes. Coprecipitates and adsorption complexes obtained following EPS-Al reaction as a function of pH and ionic strength were characterized by Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). The stability of adsorbed and coprecipitated EPS against biodegradation was assessed by mineralization experiments for 1100 h. Up to 60% of the initial 100 mg/L EPS-C was adsorbed at the highest initial molar Al:C ratio (1.86), but this still resulted only in a moderate OC mass fraction in the solid phase (17 mg/g Al(OH)_3(am)). In contrast, while coprecipitation by Al was less efficient in removing EPS from solution (maximum values of 33% at molar Al:C ratios of 0.1-0.2), the OC mass fraction in the solid product was substantially larger than that in adsorption complexes. Organic P compounds were preferentially bound during both adsorption and coprecipitation. Data are consistent with strong ligand exchange of EPS phosphoryl groups during adsorption to Al(OH)_3(am), whereas for coprecipitation weaker sorption mechanisms are also involved. X-ray photoelectron analyses indicate an intimate mixing of EPS with Al in the coprecipitates, which is not observed in the case of EPS adsorption complexes. The incubation experiments showed that both processes result in overall stabilization of EPS against microbial decay. Stabilization of adsorbed or coprecipitated EPS increased with increasing molar Al:C ratio and biodegradation was correlated with EPS desorption, implying that detachment of EPS from surface sites is a prerequisite for microbial utilization. Results indicate that the mechanisms transferring EPS into Al-organic associations may significantly affect the composition and stability of biomolecular C, N and P in soils. The observed efficient stabilization of EPS might explain the strong microbial character of organic matter in subsoils.     

An X-ray absorption spectroscopy study of the structure and reversibility of copper adsorbed to montmorillonite clay

X-ray absorption spectroscopy (XAS) and adsorption-desorption measurements have been performed to assess the relationship between the structure and reversibility of copper complexes on montmorillonite clay. By varying the solution pH and background electrolyte concentration, the adsorption of copper on either the edge sites or permanent charge sites of montmorillonite was controlled. This allowed the structure and reversibility of copper complexes on each of these site types to be assessed independently of each other. XAS analysis of copper adsorbed on the permanent charge sites indicated outer-sphere surface complexes, with these complexes showing sorption reversibility. For copper complexes formed on the edge sites of montmorillonite, XAS data confirmed the presence of monomer and dimer copper surface complexes. Sorption irreversibility at edge sites was noted at copper coverages less than 20 μmoles/g clay at pH=4.2 and at coverages greater than 50 μmoles/g clay at pH=6.8. At pH=6.8, higher Cu-Cu coordination numbers indicated the copper sorption irreversibility may be due, in part, to the formation of dimer surface complexes. The coordination numbers at pH=4.2 indicated the irreversibility could be due to the formation of dimers or due to formation of surface complexes on high energy edge sites.     

Structure of heavy metal sorbed birnessite. Part III: Results from powder and polarized extended X-ray absorption fine structure spectroscopy

The local structures of divalent Zn, Cu, and Pb sorbed on the phyllomanganate birnessite (Bi) have been studied by powder and polarized extended X-ray absorption fine structure (EXAFS) spectroscopy. Metal-sorbed birnessites (MeBi) were prepared at different surface coverages by equilibrating at pH 4 a Na-exchanged buserite (NaBu) suspension with the desired aqueous metal. Me/Mn atomic ratios were varied from 0.2% to 12.8% in ZnBi and 0.1 to 5.8% in PbBi. The ratio was equal to 15.6% in CuBi. All cations sorbed in interlayers on well-defined crystallographic sites, without evidence for sorption on layer edges or surface precipitation. Zn sorbed on the face of vacant layer octahedral sites (□), and shared three layer oxygens (O_layer) with three-layer Mn atoms (Mn_layer), thereby forming a tridentate corner-sharing (TC) interlayer complex (Zn-3O_layer-□-3Mn_layer). ^TCZn complexes replace interlayer Mn²⁺ (Mn_inter²⁺) and protons. ^TCZn and ^TCMn_inter³⁺ together balance the layer charge deficit originating from Mn_layer⁴⁺ vacancies, which amounts to 0.67 charge per total Mn according to the structural formula of hexagonal birnessite (HBi) at pH 4. At low surface coverage, zinc is tetrahedrally coordinated to three O_layer and one water molecule (^[IV]TC complex: (H₂O)-^[IV]Zn-3O_layer). At high loading, zinc is predominantly octahedrally coordinated to three O_layer and to three interlayer water molecules (^[VI]TC complex: 3(H₂O)-^[VI]Zn-3O_layer), as in chalcophanite (^[VI]ZnMn₃⁴⁺O₇·3H₂O). Sorbed Zn induces the translation of octahedral layers from −a/3 to +a/3, and this new stacking mode allows strong H bonds to form between the ^[IV]Zn complex on one side of the interlayer and oxygen atoms of the next Mn layer (O_next): O_next…(H₂O)-^[IV]Zn-3O_layer. Empirical bond valence calculations show that O_layer and O_next are strongly undersaturated, and that ^[IV]Zn provides better local charge compensation than ^[VI]Zn. The strong undersaturation of O_layer and O_next results not only from Mn_layer⁴⁺ vacancies, but also from Mn³⁺ for Mn⁴⁺ layer substitutions amounting to 0.11 charge per total Mn in HBi. As a consequence, ^[IV]Zn,Mn_layer³⁺, and Mn_next³⁺ form three-dimensional (3D) domains, which coexist with chalcophanite-like particles detected by electron diffraction. Cu²⁺ forms a Jahn-Teller distorted ^[VI]TC interlayer complex formed of two oxygen atoms and two water molecules in the equatorial plane, and one oxygen and one water molecule in the axial direction. Sorbed Pb²⁺ is not oxidized to Pb⁴⁺ and forms predominantly ^[VI]TC interlayer complexes. EXAFS spectroscopy is also consistent with the formation of tridentate edge-sharing (^[VI]TE) interlayer complexes (Pb-3O_layer-3Mn), as in quenselite (Pb²⁺Mn³⁺O₂OH). Although metal cations mainly sorb to vacant sites in birnessite, similar to Zn in chalcophanite, EXAFS spectra of MeBi systematically have a noticeably reduced amplitude. This higher short-range structural disorder of interlayer Me species primarily originates from the presence of Mn_layer³⁺, which is responsible for the formation of less abundant interlayer complexes, such as ^[IV]Zn TC in ZnBi and ^[VI]Pb TE in PbBi.     

胶质芽孢杆菌3027对钙基蒙脱石的矿物结构影响

粘土矿物在地球表层分布广泛,与微生物的交互作用十分常见。微生物能否通过除还原Fe(Ⅲ)之外的其他途径影响贫铁蒙脱石的结构与物相,成为粘土矿物与微生物交互作用的新问题。本研究选取胶质芽孢杆菌Bacillus mucilaginosus 3027与钙基蒙脱石在35℃、常压条件下进行交互作用实验,考察胶质芽孢杆菌生命活动对蒙脱石晶体结构的影响。实验定期取样进行pH值与体系总蛋白含量测试,并利用显微傅里叶变换红外光谱(micro-FTIR)、同步辐射X射线近边吸收结构(XANES)、X射线衍射(XRD)和扫描电镜(SEM)对最终产物进行矿物学表征。实验结果显示,胶质芽孢杆菌在蒙脱石矿物悬浊液中生长,代谢分泌大量有机酸导致体系pH值降低,使蒙脱石中Si元素溶出,并造成蒙脱石晶体结构中硅氧四面体对称性、O—H振动等发生变化,Fe配位八面体对称性下降,矿物表面出现边缘卷曲现象。在微生物作用后的矿物样品中,探测到新形成的α-石英物相,可能与微生物的活动密切相关。     

Surface complexation and precipitate geometry for aqueous Zn(II) sorption on ferrihydrite I: X-ray absorption extended fine structure spectroscopy analysis

“Two-line” ferrihydrite samples precipitated and then exposed to a range of aqueous Zn solutions (10⁻⁵ to 10⁻³ M), and also coprecipitated in similar Zn solutions (pH 6.5), have been examined by Zn and Fe K-edge X-ray absorption spectroscopy. Typical Zn complexes on the surface have Zn-O distances of 1.97(.02) Å and coordination numbers of about 4.0(0.5), consistent with tetrahedral oxygen coordination. This contrasts with Zn-O distances of 2.11(.02) Å and coordination numbers of 6 to 7 in the aqueous Zn solutions used in sample preparation. X-ray absorption extended fine structure spectroscopy (EXAFS) fits to the second shell of cation neighbors indicate as many as 4 Zn-Fe neighbors at 3.44(.04) Å in coprecipitated samples, and about two Zn-Fe neighbors at the same distance in adsorption samples. In both sets of samples, the fitted coordination number of second shell cations decreases as sorption density increases, indicating changes in the number and type of available complexing sites or the onset of competitive precipitation processes. Comparison of our results with the possible geometries for surface complexes and precipitates suggests that the Zn sorption complexes are inner sphere and at lowest adsorption densities are bidentate, sharing apical oxygens with adjacent edge-sharing Fe(O,OH)₆ octahedra. Coprecipitation samples have complexes with similar geometry, but these are polydentate, sharing apices with more than two adjacent edge-sharing Fe(O,OH)₆ polyhedra. The results are inconsistent with Zn entering the ferrihydrite structure (i.e., solid solution formation) or formation of other Zn-Fe precipitates. The fitted Zn-Fe coordination numbers drop with increasing Zn density with a minimum of about 0.8(.2) at Zn/(Zn + Fe) of 0.08 or more. This change appears to be attributable to the onset of precipitation of zinc hydroxide polymers with mainly tetrahedral Zn coordination. At the highest loadings studied, the nature of the complexes changes further, and a second type of precipitate forms. This has a structure based on a brucite layer topology, with mainly octahedral Zn coordination. Amorphous zinc hydroxide samples prepared for comparison had a closely similar local structure. Analysis of the Fe K-edge EXAFS is consistent with surface complexation reactions and surface precipitation at high Zn loadings with little or no Fe-Zn solid solution formation. The formation of Zn-containing precipitates at solution conditions two or more orders of magnitude below their solubility limit is compared with other sorption and spectroscopic studies that describe similar behavior.     

X-ray absorption spectroscopy study on the effect of hydroxybenzoic acids on the formation and structure of ferrihydrite

Organic ligands are known to interfere with the polymerization of Fe(III), but the extent of interference has not been systematically studied as a function of structural ligand properties. This study examines how the number and position of phenol groups in hydroxybenzoic acids affect both ferrihydrite formation and its local (<5 Å) Fe coordination. To this end, acid Fe(III) nitrate solutions were neutralized up to pH 6.0 in the presence of 4-hydroxybenzoic acid (4HB), 2,4-dihydroxybenzoic acid (2,4DHB), and the hydroquinone 3,4-dihydroxybenzoic acid (3,4DHB). The initial molar ligand/Fe ratios ranged from 0 to 0.6. The precipitates were dialyzed, lyophilized, and subsequently studied by X-ray absorption spectroscopy and synchrotron X-ray diffraction. The solids contained up to 32 wt.% organic C (4HB ∼ 2,4DHB < 3,4DHB). Only precipitates formed in 3,4DHB solutions comprised considerable amounts of Fe(II) (Fe(II)/Fe_tot ≤ 6 mol%), implying the abiotic mineralization of the catechol-group bearing ligand during Fe(III) hydrolysis under oxic conditions. Hydroxybenzoic acids decreased ferrihydrite formation in the order 4HB ∼ 2,4DHB ? 3,4DHB, which documents that phenol group position rather than the number of phenol groups controls the ligand’s interaction with Fe(III). The coordination numbers of edge- and double corner-sharing Fe in the precipitates decreased by up to 100%. Linear combination fitting (LCF) of Fe K-edge X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectra revealed that this decrease was due to increasing amounts of organic Fe(III) complexes in the precipitates. Although EXAFS derived coordination numbers of Fe in ferrihydrite remained constant within error, all organic ligands decreased the coherently scattering domain (CSD) size of ferrihydrite as indicated by synchrotron X-ray diffraction analysis (4HB < 2,4DHB ? 3,4DHB). With decreasing particle size of ferrihydrite its Fe(O,OH)₆ octahedra became progressively distorted as evidenced by an increasing loss of centrosymmetry of the Fe sites. Pre-edge peak analysis of the Fe K-edge XANES spectra in conjunction with LCF results implied that ferrihydrite contains on an average 13 ± 3% tetrahedral Fe(III), which is in very good agreement with the revised single-phase structural model of ferrihydrite (Michel, F. M., Barron, V., Torrent, J., Morales, M. P. et al. (2010) Ordered ferrimagnetic form of ferrihydrite reveals links among structure, composition, and magnetism. Proc. Natl. Acad. Sci. USA107, 2787-2792). The results suggest that hydroxybenzoic acid moieties of natural organic matter (NOM) effectively suppress ferrihydrite precipitation as they kinetically control the availability of inorganic Fe(III) species for nucleation and/or polymerization reactions. As a consequence, NOM can trigger the formation of small ferrihydrite nanoparticles with increased structural strain. These factors may eventually enhance the biogeochemical reactivity of ferrihydrite formed in NOM-rich environments. This study highlights the role of hydroquinone structures of NOM for Fe complexation, polymerization, and redox speciation.     

Experimental study of germanium adsorption on goethite and germanium coprecipitation with iron hydroxide: X-ray absorption fine structure and macroscopic characterization

Adsorption of germanium on goethite was studied at 25 °C in batch reactors as a function of pH (1-12), germanium concentration in solution (10⁻⁷ to 0.002 M) and solid/solution ratio (1.8-17 g/L). The maximal surface site density determined via Ge adsorption experiments at pH from 6 to 10 is equal to 2.5 ± 0.1 μmol/m². The percentage of adsorbed Ge increases with pH at pH < 9, reaches a maximum at pH ∼ 9 and slightly decreases when pH is further increased to 11. These results allowed generation of a 2-pK Surface Complexation Model (SCM) which implies a constant capacitance of the electric double layer and postulates the presence of two Ge complexes, and , at the goethite-solution interface. Coprecipitation of Ge with iron oxy(hydr)oxides formed during Fe(II) oxidation by atmospheric oxygen or by Fe(III) hydrolysis in neutral solutions led to high Ge incorporations in solid with maximal Ge/Fe molar ratio close to 0.5. The molar Ge/Fe ratio in precipitated solid is proportional to that in the initial solution according to the equation (Ge/Fe)_solid = k × (Ge/Fe)_solution with 0.7 ? k ? 1.0. The structure of adsorbed and coprecipitated Ge complexes was further characterized using XAFS spectroscopy. In agreement with previous data on oxyanions adsorption on goethite, bi-dentate bi-nuclear surface complexes composed of tetrahedrally coordinated Ge attached to the corners of two adjacent Fe octahedra represent the dominant contribution to the EXAFS signal. Coprecipitated samples with Ge/Fe molar ratios >0.1, and samples not aged in solution (<1 day) having intermediate Ge/Fe ratios (0.01-0.1) show 4 ± 0.3 oxygen atoms at 1.76 ± 0.01 Å around Ge. Samples less concentrated in Ge (0.001 < Ge/Fe < 0.10) and aged longer times in solution (up to 280 days) exhibit a splitting of the first atomic shell with Ge in both tetrahedral (R = 1.77 ± 0.02 Å) and octahedral (R = 1.92 ± 0.03 Å) coordination with oxygen. In these samples, octahedrally coordinated Ge accounts for up to ∼20% of the total Ge. For the least concentrated samples (Ge/Fe < 0.001-0.0001) containing lepidocrocite, 30-50% of total co-precipitated germanium substitutes for Fe in octahedral sites with the next-nearest environment dominated by edge-sharing GeO₆-FeO₆ linkages (R_Ge-Fe ∼ 3.06 Å). It follows from the results of our study that the largest structural change of Ge (from tetrahedral to octahedral environment) occurs during its coprecipitation with Fe hydroxide at Ge/Fe molar ratio ?0.0001. These conditions are likely to be met in many superficial aquatic environments at the contact of anoxic groundwaters with surficial oxygenated solutions. Adsorption and coprecipitation of Ge with solid Fe oxy(hydr)oxides and organo-mineral colloids and its consequence for Ge/Si fractionation and Ge geochemical cycle are discussed.