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.     

The effect of species diversity on metal adsorption onto bacteria

In this study, we measure proton, Pb, and Cd adsorption onto the bacteria Deinococcus radiodurans, Thermus thermophilus, Acidiphlium angustum, Flavobacterium aquatile, and Flavobacterium hibernum, and we calculate the thermodynamic stability constants for the important surface complexes. These bacterial species represent a wide genetic diversity of bacteria, and they occupy a wide range of habitats. All of the species, except for A. angustum, exhibit similar proton and metal uptake. The only species tested that exhibits significantly different protonation behavior is A. angustum, an acidophile that grows at significantly lower pH than the other species of this study. We demonstrate that a single, metal-specific, surface complexation model can be used to reasonably account for the acid/base and metal adsorption behaviors of each species. We use a four discrete site non-electrostatic model to describe the protonation of the bacterial functional groups, with averaged pK_a values of 3.1 ± 0.3, 4.8 ± 0.2, 6.7 ± 0.1, and 9.2 ± 0.3, and site concentrations of (1.0 ± 0.17) × 10⁻⁴, (9.0 ± 3.0) × 10⁻⁵, (4.6 ± 1.8) × 10⁻⁵, and (6.1 ± 2.3) × 10⁻⁵ mol of sites per gram wet mass of bacteria, respectively. Adsorption of Cd and Pb onto the bacteria can be accounted for by the formation of complexes with each of the bacterial surface sites. The average log stability constants for Cd complexes with Sites 1-4 are 2.4 ± 0.4, 3.2 ± 0.1, 4.4 ± 0.1, and 5.3 ± 0.1, respectively. The average log stability constants for Pb complexes with Sites 1-4 are 3.3 ± 0.2, 4.5 ± 0.3, 6.5 ± 0.1, and 7.9 ± 0.5, respectively. This study demonstrates that a wide range of bacteria exhibit similar proton and metal adsorption behaviors, and that a single set of averaged acidity constants, site concentrations, and stability constants for metal-bacterial surface complexes yields a reasonable model for the adsorption behavior of many of these species. The differences in adsorption behavior that we observed for A. angustum demonstrate that genetic differences do exist between the cell wall functional group chemistries of some bacterial species, and that significant exceptions to the typical bacterial adsorption behavior do exist.     

Zinc sorption to biogenic hexagonal-birnessite particles within a hydrated bacterial biofilm

Biofilm-embedded Mn oxides exert important controls on trace metal cycling in aquatic and soil environments. The speciation and mobility of Zn in particular has been linked to Mn oxides found in streams, wetlands, soils, and aquifers. We investigated the mechanisms of Zn sorption to a biogenic Mn oxide within a biofilm produced by model soil and freshwater Mn^II-oxidizing bacteria Pseudomonas putida. The biogenic Mn oxide is a c-disordered birnessite with hexagonal layer symmetry. Zinc adsorption isotherm and Zn and Mn K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy experiments were conducted at pH 6.9 to characterize Zn sorption to this biogenic Mn oxide, and to determine whether the bioorganic components of the biofilm affect metal sorption properties. The EXAFS data were analyzed by spectral fitting, principal component analysis, and linear least-squares fitting with reference spectra. Zinc speciation was found to change as Zn loading to the biosorbent [bacterial cells, extracellular polymeric substances (EPS), and biogenic Mn oxide] increased. At low Zn loading (0.13 ± 0.04 mol Zn kg⁻¹ biosorbent), Zn was sorbed to crystallographically well-defined sites on the biogenic oxide layers in tetrahedral coordination to structural O atoms. The fit to the EXAFS spectrum was consistent with Zn sorption above and below the Mn^IV vacancy sites of the oxide layers. As Zn loading increased to 0.72 ± 0.04 mol Zn kg⁻¹ biosorbent, Zn was also detected in octahedral coordination to these sites. Overall, our results indicate that the biofilm did not intervene in Zn sorption by the Mn-oxide because sorption to the organic material was observed only after all Mn vacancy sites were capped by Zn. The organic functional groups present in the biofilm contributed significantly to Zn removal from solution when Zn concentrations exceeded the sorption capacity of the biooxide. At the highest Zn loading studied, 1.50 ± 0.36 mol Zn kg⁻¹ biosorbent, the proportion of total Zn sorption attributed to bioorganic material was 38 mol%. The maximum Zn loading to the biogenic oxide that we observed was 4.1 mol Zn kg⁻¹ biogenic Mn oxide, corresponding to 0.37 ± 0.02 mol Zn mol⁻¹ Mn. This loading is in excellent agreement with previous estimates of the content of cation vacancies in the biogenic oxide. The results of this study improve our knowledge of Zn speciation in natural systems and are consistent with those of Zn speciation in mineral soil fractions and ferromanganese nodules where the Mn oxides present are possibly biogenic.     

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.     

Complexation of cadmium to sulfur and oxygen functional groups in an organic soil

Cadmium (Cd) is a toxic trace element and due to human activities soils and waters are contaminated by Cd both on a local and global scale. It is widely accepted that chemical interactions with functional groups of natural organic matter (NOM) is vital for the bioavailability and mobility of trace elements. In this study the binding strength of cadmium (Cd) to soil organic matter (SOM) was determined in an organic (49% organic C) soil as a function of reaction time, pH and Cd concentration. In experiments conducted at native Cd concentrations in soil (0.23 μg g⁻¹ dry soil), halides (Cl, Br) were used as competing ligands to functional groups in SOM. The concentration of Cd in the aqueous phase was determined by isotope-dilution (ID) inductively-coupled-plasma-mass-spectrometry (ICP-MS), and the activity of Cd²⁺ was calculated from the well-established Cd-halide constants. At higher Cd loading (500-54,000 μg g⁻¹), the Cd²⁺ activity was directly determined by an ion-selective electrode (ISE). On the basis of results from extended X-ray absorption fine structure (EXAFS) spectroscopy, a model with one thiolate group (RS⁻) was used to describe the complexation (Cd²⁺ + RS⁻ ? CdSR⁺; log K_CdSR) at native Cd concentrations. The concentration of thiols (RSH; 0.047 mol kg⁻¹ C) was independently determined by X-ray absorption near-edge structure (XANES) spectroscopy. Log K_CdSR values of 11.2-11.6 (pK_a for RSH = 9.96), determined in the pH range 3.1-4.6, compare favorably with stability constants for the association between Cd and well-defined thiolates like glutathione. In the concentration range 500-54,000 μg Cd g⁻¹, a model consisting of one thiolate and one carboxylate (RCOO⁻) gave the best fit to data, indicating an increasing role for RCOOH groups as RSH groups become saturated. The determined log K_CdOOCR of 3.2 (Cd²⁺ +  RCOO⁻ ? CdOOCR⁺; log K_CdOOCR; pK_a for RCOOH = 4.5) is in accordance with stability constants determined for the association between Cd and well-defined carboxylates. Given a concentration of reduced sulfur groups of 0.2% or higher in NOM, we conclude that the complexation to organic RSH groups may control the speciation of Cd in soils, and most likely also in surface waters, with a total concentration less than 5 mg Cd g⁻¹ organic C.     

Cd adsorption onto Anoxybacillus flavithermus: Surface complexation modeling and spectroscopic investigations

Several recent studies have applied surface complexation theory to model metal adsorption behaviour onto mesophilic bacteria. However, no investigations have used this approach to characterise metal adsorption by thermophilic bacteria. In this study, we perform batch adsorption experiments to quantify cadmium adsorption onto the thermophile Anoxybacillus flavithermus. Surface complexation models (incorporating the Donnan electrostatic model) are developed to determine stability constants corresponding to specific adsorption reactions. Adsorption reactions and stoichiometries are constrained using spectroscopic techniques (XANES, EXAFS, and ATR-FTIR). The results indicate that the Cd adsorption behaviour of A. flavithermus is similar to that of other mesophilic bacteria. At high bacteria-to-Cd ratios, Cd adsorption occurs by formation of a 1:1 complex with deprotonated cell wall carboxyl functional groups. At lower bacteria-to-Cd ratios, a second adsorption mechanism occurs at pH > 7, which may correspond to the formation of a Cd-phosphoryl, CdOH-carboxyl, or CdOH-phosphoryl surface complex. X-ray absorption spectroscopic investigations confirm the formation of the 1:1 Cd-carboxyl surface complex, but due to the bacteria-to-Cd ratio used in these experiments, other complexation mechanism(s) could not be unequivocally resolved by the spectroscopic data.     

Seawater temperature proxies based on DSr, DMg, and DU from culture experiments using the branching coral Porites cylindrica

In order to investigate the incorporation of Sr, Mg, and U into coral skeletons and its temperature dependency, we performed a culture experiment in which specimens of the branching coral (Porites cylindrica) were grown for 1 month at three seawater temperatures (22, 26, and 30 °C). The results of this study showed that the linear extension rate of P. cylindrica has little effect on the skeletal Sr/Ca, Mg/Ca, and U/Ca ratios. The following temperature equations were derived: Sr/Ca (mmol/mol) = 10.214(±0.229) − 0.0642(±0.00897) × T (°C) (r² = 0.59, p < 0.05); Mg/Ca (mmol/mol) = 1.973(±0.302) + 0.1002(±0.0118) × T (°C) (r² = 0.67, p < 0.05); and U/Ca (μmol/mol) = 1.488(±0.0484) − 0.0212(±0.00189) × T (°C) (r² = 0.78, p < 0.05). We calculated the distribution coefficient (D) of Sr, Mg, and U relative to seawater temperature and compared the results with previous data from massive Porites corals. The seawater temperature proxies based on D calibrations of P. cylindrica established in this study are generally similar to those for massive Porites corals, despite a difference in the slope of D_U calibration. The calibration sensitivity of D_Sr, D_Mg, and D_U to seawater temperature change during the experiment was 0.64%/°C, 1.93%/°C, and 1.97%/°C, respectively. These results suggest that the skeletal Sr/Ca ratio (and possibly the Mg/Ca and/or U/Ca ratio) of the branching coral P. cylindrica can be used as a potential paleothermometer.     

Uranium-series dating and growth characteristics of the deep-sea scleractinian coral: Enallopsammia rostrata from the Equatorial Pacific

The deep-sea coral, Enallopsammia rostrata, a member of the Dendrophylliidae family, is a major structure-forming species that creates massive dendroid colonies, up to 1 m wide and 0.5 m tall. Living colonies of E. rostrata have been collected using the PISCES submersibles from three locations from 480 to 788 m water depth in the Line Islands (∼160°W) in the Equatorial Pacific. We have applied to these colonies a high sensitivity, low blank technique to determine U-series ages in small quantities (70 ± 15 mg) of modern and near modern calcareous skeletons using MC-ICP-MS (Multi-collector Inductively Coupled Plasma Mass Spectrometer). The application of this method to living slow-growing colonies from a range of sites as well as the observations of axial growth patterns in thin sections of their skeletons offer the first expanded and well constrained data on longevity, growth pattern and mean growth rates in E. rostrata. Absolute dated specimens indicate life spans of colonies ranging from 209 ± 8 yrs to 605 ± 7 yrs with radial growth rates from 0.012 to 0.072 mm yr⁻¹ and vertical extension rates from 0.6 to 1.9 mm yr⁻¹. The linear growth rates reported here are lower than those reported for other deep-sea scleractinian corals (Lophelia pertusa and Madrepora oculata). The U-series dating indicates that the growth ring patterns of E. rostrata are not consistent with annual periodicity emphasizing the importance of absolute radiometric dating methods to constrain growth rates. Slow accretion and extreme longevity make this species and its habitat especially vulnerable to disturbances and impacts from human activities. This dating method combined with observation of growth patterns opens up new perspectives in the field of deep-sea corals since it can provide quantitative estimates of growth rates and longevity of deep-sea corals in general.     

Use of biomarkers indices in a sediment core to evaluate potential pollution sources in a subtropical reservoir in Brazil

The presence of PAHs, n-alkanes, pristane, and phytanes in core sediment from the Vossoroca reservoir (Parana, southern Brazil) was investigated. The total concentration of the 16 PAHs varied from 15.5 to 1646 μg kg⁻¹. Naphthalene was present in all layers (3.34–74.0 μg kg⁻¹). The most abundant and dominant n-alkanes were n-C₁₅ and n-C₃₆, with average concentrations of 198.1 ± 46.8 and 522.9 ± 167.7 μg kg⁻¹, respectively. Lighter n-alkanes were distributed more evenly through the layers and showed less variation, specially n-C₉, n-C₁₂, and n-C₁₈, with average concentrations of 14.6 ± 3.0, 31.6 ± 1.9, and 95.0 ± 5.2 μg kg⁻¹, respectively; heavier n-alkanes were more unevenly distributed.     

Fractionation of carbon isotopes in biosynthesis of fatty acids by a piezophilic bacterium Moritella japonica strain DSK1

We examined stable carbon isotope fractionation in biosynthesis of fatty acids of a piezophilic bacterium Moritella japonica strain DSK1. The bacterium was grown to stationary phase at pressures of 0.1, 10, 20, and 50 MPa in media prepared using sterile-filtered natural seawater supplied with glucose as the sole carbon source. Strain DSK1 synthesized typical bacterial fatty acids (C_14-19 saturated, monounsaturated, and cyclopropane fatty acids) as well as long-chain polyunsaturated fatty acids (PUFA) (20:6ω3). Bacterial cell biomass and individual fatty acids exhibited consistent pressure-dependent carbon isotope fractionations relative to glucose. The observed Δδ_FA-glucose (−1.0‰ to −11.9‰) at 0.1 MPa was comparable to or slightly higher than fractionations reported in surface bacteria. However, bulk biomass and fatty acids became more depleted in ¹³C with pressure. Average carbon isotope fractionation (Δδ_FA-glucose) at high pressures was much higher than that for surface bacteria: −15.7‰, −15.3‰, and −18.3‰ at 10, 20, and 50 MPa, respectively. PUFA were more ¹³C depleted than saturated and monounsaturated fatty acids at all pressures. The observed isotope effects may be ascribed to the kinetics of enzymatic reactions that are affected by hydrostatic pressure and to biosynthetic pathways that are different for short-chain and long-chain fatty acids. A simple quantitative calculation suggests that in situ piezophilic bacterial contribution of polyunsaturated fatty acids to marine sediments is nearly two orders of magnitude higher than that of marine phytoplankton and that the carbon isotope imprint of piezophilic bacteria can override that of surface phytoplankton. Our results have important implications for marine biogeochemistry. Depleted fatty acids reported in marine sediments and the water column may be derived simply from piezophilic bacteria resynthesis of organic matter, not from bacterial utilization of a ¹³C-depleted carbon source (i.e., methane). The interpretation of carbon isotope signatures of marine lipids must be based on principles derived from piezophilic bacteria.     

Joint determination of K decay constants and Ar∗/K for the Fish Canyon sanidine standard, and improved accuracy for Ar/Ar geochronology

⁴⁰Ar/³⁹Ar and K-Ar geochronology have long suffered from large systematic errors arising from imprecise K and Ar isotopic data for standards and imprecisely determined decay constants for the branched decay of ⁴⁰K by electron capture and β⁻ emission. This study presents a statistical optimization approach allowing constraints from ⁴⁰K activity data, K-Ar isotopic data, and pairs of ²³⁸U-²⁰⁶Pb and ⁴⁰Ar/³⁹Ar data for rigorously selected rocks to be used as inputs for estimating the partial decay constants (λ_ε and λ_β) of ⁴⁰K and the ⁴⁰Ar∗/⁴⁰K ratio (κ_FCs) of the widely used Fish Canyon sanidine (FCs) standard. This yields values of κ_FCs = (1.6418 ± 0.0045) × 10⁻³, λ_ε = (0.5755 ± 0.0016) × 10⁻¹⁰ a⁻¹ and λ_β = (4.9737 ± 0.0093) × 10⁻¹⁰ a⁻¹. These results improve uncertainties in the decay constants by a factor of >4 relative to values derived from activity data alone. Uncertainties in these variables determined by our approach are moderately to highly correlated (cov(κ_FCs, λ_ε) = 7.1889 × 10⁻¹⁹, cov(κ_FCs, λ_β) = −7.1390 × 10⁻¹⁹, cov(λ_ε, λ_β) = −3.4497 × 10⁻²⁶) and one must take account of the covariances in error propagation by either linear or Monte Carlo methods. ⁴⁰Ar/³⁹Ar age errors estimated from these results are significantly reduced relative to previous calibrations. Also, age errors are smaller for a comparable level of isotopic measurement precision than those produced by the ²³⁸U/²⁰⁶Pb system, because the ⁴⁰Ar/³⁹Ar system is now jointly calibrated by both the ⁴⁰K and ²³⁸U decay constants, and because λ_ε(⁴⁰K) < λ(²³⁸U). Based on this new calibration, the age of the widely used Fish Canyon sanidine standard is 28.305 ± 0.036 Ma. The increased accuracy of ⁴⁰Ar/³⁹Ar ages is now adequate to provide meaningful validation of high-precision U/Pb or astronomical tuning ages in cases where closed system behavior of K and Ar can be established.     

Copper isotope fractionation during its interaction with soil and aquatic microorganisms and metal oxy(hydr)oxides: Possible structural control

This work is aimed at quantifying the main environmental factors controlling isotope fractionation of Cu during its adsorption from aqueous solutions onto common organic (bacteria, algae) and inorganic (oxy(hydr)oxide) surfaces. Adsorption of Cu on aerobic rhizospheric (Pseudomonas aureofaciens CNMN PsB-03) and phototrophic aquatic (Rhodobacter sp. f-7bl, Gloeocapsa sp. f-6gl) bacteria, uptake of Cu by marine (Skeletonema costatum) and freshwater (Navicula minima, Achnanthidium minutissimum and Melosira varians) diatoms, and Cu adsorption onto goethite (FeOOH) and gibbsite (AlOOH) were studied using a batch reaction as a function of pH, copper concentration in solution and time of exposure. Stable isotopes of copper in selected filtrates were measured using Neptune multicollector ICP-MS. Irreversible incorporation of Cu in cultured diatom cells at pH 7.5-8.0 did not produce any isotopic shift between the cell and solution (Δ^65/63Cu(solid-solution)) within ±0.2‰. Accordingly, no systematic variation was observed during Cu adsorption on anoxygenic phototrophic bacteria (Rhodobacter sp.), cyanobacteria (Gloeocapsa sp.) or soil aerobic exopolysaccharide (EPS)-producing bacteria (P. aureofaciens) in circumneutral pH (4-6.5) and various exposure times (3 min to 48 h): Δ⁶⁵Cu(solid-solution) = 0.0 ± 0.4‰. In contrast, when Cu was adsorbed at pH 1.8-3.5 on the cell surface of soil the bacterium P. aureofacienshaving abundant or poor EPS depending on medium composition, yielded a significant enrichment of the cell surface in the light isotope (Δ⁶⁵Cu (solid-solution) = −1.2 ± 0.5‰). Inorganic reactions of Cu adsorption at pH 4-6 produced the opposite isotopic offset: enrichment of the oxy(hydr)oxide surface in the heavy isotope with Δ⁶⁵Cu(solid-solution) equals 1.0 ± 0.25‰ and 0.78 ± 0.2‰ for gibbsite and goethite, respectively. The last result corroborates the recent works of Mathur et al. [Mathur R., Ruiz J., Titley S., Liermann L., Buss H. and Brantley S. (2005) Cu isotopic fractionation in the supergene environment with and without bacteria. Geochim. Cosmochim. Acta69, 5233-5246] and Balistrieri et al. [Balistrieri L. S., Borrok D. M., Wanty R. B. and Ridley W. I. (2008) Fractionation of Cu and Zn isotopes during adsorption onto amorhous Fe(III) oxyhydroxide: experimental mixing of acid rock drainage and ambient river water. Geochim. Cosmochim. Acta72, 311-328] who reported heavy Cu isotope enrichment onto amorphous ferric oxyhydroxide and on metal hydroxide precipitates on the external membranes of Fe-oxidizing bacteria, respectively.Although measured isotopic fractionation does not correlate with the relative thermodynamic stability of surface complexes, it can be related to their structures as found with available EXAFS data. Indeed, strong, bidentate, inner-sphere complexes presented by tetrahedrally coordinated Cu on metal oxide surfaces are likely to result in enrichment of the heavy isotope on the surface compared to aqueous solution. The outer-sphere, monodentate complex, which is likely to form between Cu²⁺ and surface phosphoryl groups of bacteria in acidic solutions, has a higher number of neighbors and longer bond distances compared to inner-sphere bidentate complexes with carboxyl groups formed on bacterial and diatom surfaces in circumneutral solutions. As a result, in acidic solution, light isotopes become more enriched on bacterial surfaces (as opposed to the surrounding aqueous medium) than they do in neutral solution.Overall, the results of the present study demonstrate important isotopic fractionation of copper in both organic and inorganic systems and provide a firm basis for using Cu isotopes for tracing metal transport in earth-surface aquatic systems. It follows that both adsorption on oxides in a wide range of pH values and adsorption on bacteria in acidic solutions are capable of producing a significant (up to 2.5-3‰ (±0.1-0.15‰)) isotopic offset. At the same time, Cu interaction with common soil and aquatic bacteria, as well as marine and freshwater diatoms, at 4 < pH < 8 yields an isotopic shift of only ±0.2-0.3‰, which is not related to Cu concentration in solution, surface loading, the duration of the experiment, or the type of aquatic microorganisms.     

Coordination of Cd ions in the internal pore system of zeolite-X: A combined EXAFS and isotopic exchange study

The effect of prolonged contact time (up to 130 days) on the immobilization of Cd by sorption to calcium exchanged zeolite-X (CaX), under environmentally relevant conditions, was studied using both isotopic exchange and extended X-ray absorption fine structure spectroscopy (EXAFS). Sorption and isotopic exchange measurements revealed time-dependent Cd sorption and indicated the movement of Cd²⁺ ions into less accessible sites due to ageing. EXAFS suggested progressive fixation of Cd in the double six-ring (D6R) unit of the CaX structure. Proportional allocation of the apparent Cd-Si bond distance to two ‘end-members’, across all contact times, indicated that the bond distance for labile Cd was 3.41 Å and for non-labile (or fixed) Cd was 3.47 Å.     

Mechanisms of nickel sorption by a bacteriogenic birnessite

A synergistic experimental-computational approach was used to study the molecular-scale mechanisms of Ni sorption at varying loadings and at pH 6-8 on the biogenic hexagonal birnessite produced by Pseudomonas putida GB-1. We found that Ni is scavenged effectively by bacterial biomass-birnessite assemblages. At surface excess values below 0.18 mol Ni kg⁻¹ sorbent (0.13 mol Ni mol⁻¹ Mn), the biomass component of the sorbent did not interfere with Ni sorption on mineral sites. Extended X-ray absorption fine structure (EXAFS) spectra showed two dominant coordination environments: Ni bound as a triple-corner-sharing (Ni-TCS) complex at vacancy sites and Ni incorporated (Ni-inc) into the MnO₂ sheet, with the latter form of Ni favored at high sorptive concentrations and decreased proton activity. In parallel to our spectral analysis, first-principles geometry optimizations based on density functional theory (DFT) were performed to investigate the structure of Ni surface complexes at vacancy sites. Excellent agreement was achieved between EXAFS- and DFT-derived structural parameters for Ni-TCS and Ni-inc. Reaction-path calculations revealed a pH-dependent energy barrier associated with the transition from Ni-TCS to Ni-inc. Our results are consistent with the rate-limited incorporation of Ni at vacancy sites in our sorption samples, but near-equilibrium state of Ni in birnessite phases found in nodule samples. This study thus provides direct and quantitative evidence of the factors governing the occurrence of Ni adsorption versus Ni incorporation in biogenic hexagonal birnessite, a key mineral in the terrestrial manganese cycle.     

Bioreduction of hematite nanoparticles by the dissimilatory iron reducing bacterium Shewanella oneidensis MR-1

We examined the reduction of different size hematite (α-Fe₂O₃) nanoparticles (average diameter of 11, 12, 30, 43, and 99 nm) by the dissimilatory iron reducing bacteria (DIRB), Shewanella oneidensis MR-1, to determine how S. oneidensis MR-1 may utilize these environmentally relevant solid-phase electron acceptors. The surface-area-normalized-bacterial Fe(III) reduction rate for the larger nanoparticles (99 nm) was one order of magnitude higher than the rate observed for the smallest nanoparticles (11 nm). The Fe(III) reduction rates for the 12, 30, and 43 nm nanoparticles fell between these two extremes. Whole-cell TEM images showed that the mode of Fe₂O₃ nanoparticle attachment to bacterial cells was different for the aggregated, pseudo-hexagonal/irregular and platey 11, 12, and 99 nm nanoparticles compared to the non-aggregated 30 and 43 nm rhombohedral nanoparticles. Due to differences in aggregation, the 11, 12, and 99 nm nanoparticles exhibited less cell contact and less cell coverage than did the 30 and 43 nm nanoparticles. We hypothesize that S. oneidensis MR-1 employs both indirect and direct mechanisms of electron transfer to Fe(III)-oxide nanoparticles and that the bioreduction mechanisms employed and Fe(III) reduction rates depend on the nanoparticles’ aggregation state, size, shape and exposed crystal faces.     

Solubility of cyclooctasulfur in pure water and sea water at different temperatures

The solubility of cyclooctasulfur in water and sea water at various temperatures in the range between 4 and 80 °C was determined. Cyclooctasulfur in equilibrium with rhombic sulfur reacted with hot acidic aqueous potassium cyanide to form thiocyanate anion which was measured by anion chromatography. Sulfur solubility in pure water was found to increase with temperature by more than 78 times: from 6.1 nM S₈ at 4 °C to 478 nM S₈ at 80 °C. The following thermodynamic values for solubilisation of S₈ in water were calculated from the experimental data: K° = 3.01 ± 1.04 × 10⁻⁸, ΔG_r° = 42.93 ± 0.73 kJ mol⁻¹, ΔH_r° = 47.4 ± 3.6 kJmol⁻¹, ΔS_r° = 15.0 ± 11.7 J mol⁻¹ K⁻¹). Solubility of cyclooctasulfur in sea water was found to be 61 ± 13% of the solubility in pure water regardless of the temperature.     

Interindividual variability and ontogenetic effects on Mg and Sr incorporation in the planktonic foraminifer Globigerinoides sacculifer

In order to investigate the interindividual and ontogenetic effects on Mg and Sr incorporation, magnesium/calcium (Mg/Ca) and strontium/calcium (Sr/Ca) ratios of cultured planktonic foraminifera have been determined. Specimens of Globigerinoides sacculifer were grown under controlled physical and chemical seawater conditions in the laboratory. By using this approach, we minimised the effect of potential environmental variability on Mg/Ca and Sr/Ca ratios. Whereas temperature is the overriding control of Mg/Ca ratios, the interindividual variability observed in the Mg/Ca values contributes 2-3 °C to the apparent temperature variance. Interindividual variability in Sr/Ca ratios is much smaller than that observed in Mg/Ca values. The variability due to ontogeny corresponds to −0.43 mmol/mol of Mg/Ca ratio per chamber added. This translates into an apparent decrease of ∼1 °C in Mg/Ca-based temperature per ontogenetic (chamber) stage. No significant ontogenetic effect is observed on Sr incorporation. We conclude that the presence of a significant ontogenetic effect on Mg incorporation can potentially offset Mg/Ca-based temperature reconstructions. We propose two new empirical Mg/Ca-temperature equation based on Mg/Ca measurements of the last four ontogenetic (chamber) stages and whole foraminiferal test: Mg/Ca = (0.55(±0.03) − 0.0002(±4 × 10⁻⁵) MSD) e^0.089T and, Mg/Ca = (0.55(±0.03) − 0.0001(±2 × 10⁻⁵) MSD) e^0.089T, respectively, where MSD corresponds to the maximum shell diameter of the individual.     

Magnetite biomineralization induced by Shewanella oneidensis

Shewanella oneidensis is a dissimilatory iron reducing bacterium capable of inducing the extracellular precipitation of magnetite. This precipitation requires a combination of passive and active mechanisms. Precipitation occurs as a consequence of active production of Fe²⁺_(aq) when bacteria utilize ferrihydrite as a terminal electron acceptor, and the pH rise probably due to the bacterial metabolism of amino acids. As for passive mechanisms, the localized concentration of Fe²⁺_(aq) and Fe³⁺_(aq) at the net negatively charged cell wall, cell structures and/or cell debris induces a local rise of supersaturation of the system with respect to magnetite, triggering the precipitation of such a phase.These biologically induced magnetites are morphologically identical to those formed inorganically in free-drift experiments (closed system; 25 °C, 1 atm total pressure), both from aqueous solutions containing Fe(ClO₄)₂, FeCl₃, NaHCO₃, NaCO₃ and NaOH, and also from sterile culture medium added with FeCl₂. However, organic material becomes incorporated in substantial amounts into the crystal structure of S. oneidensis-induced magnetites, modifying such a structure compared to that of inorganic magnetites. This structural change and the presence of organic matter are detected by Raman and FT-IR spectroscopic analyses and may be used as a biomarker to recognize the biogenic origin of natural magnetites.     

Iron and magnesium isotopic compositions of peridotite xenoliths from Eastern China

We present high-precision measurements of Mg and Fe isotopic compositions of olivine, orthopyroxene (opx), and clinopyroxene (cpx) for 18 lherzolite xenoliths from east central China and provide the first combined Fe and Mg isotopic study of the upper mantle. δ⁵⁶Fe in olivines varies from 0.18‰ to −0.22‰ with an average of −0.01 ± 0.18‰ (2SD, n = 18), opx from 0.24‰ to −0.22‰ with an average of 0.04 ± 0.20‰, and cpx from 0.24‰ to −0.16‰ with an average of 0.10 ± 0.19‰. δ²⁶Mg of olivines varies from −0.25‰ to −0.42‰ with an average of −0.34 ± 0.10‰ (2SD, n = 18), opx from −0.19‰ to −0.34‰ with an average of −0.25 ± 0.10‰, and cpx from −0.09‰ to −0.43‰ with an average of −0.24 ± 0.18‰. Although current precision (∼±0.06‰ for δ⁵⁶Fe; ±0.10‰ for δ²⁶Mg, 2SD) limits the ability to analytically distinguish inter-mineral isotopic fractionations, systematic behavior of inter-mineral fractionation for both Fe and Mg is statistically observed: Δ⁵⁶Fe_ol-cpx = −0.10 ± 0.12‰ (2SD, n = 18); Δ⁵⁶Fe_ol-opx = −0.05 ± 0.11‰; Δ²⁶Mg_ol-opx = −0.09 ± 0.12‰; Δ²⁶Mg_ol-cpx = −0.10 ± 0.15‰. Fe and Mg isotopic composition of bulk rocks were calculated based on the modes of olivine, opx, and cpx. The average δ⁵⁶Fe of peridotites in this study is 0.01 ± 0.17‰ (2SD, n = 18), similar to the values of chondrites but slightly lower than mid-ocean ridge basalts (MORB) and oceanic island basalts (OIB). The average δ²⁶Mg is −0.30 ± 0.09‰, indistinguishable from chondrites, MORB, and OIB. Our data support the conclusion that the bulk silicate Earth (BSE) has chondritic δ⁵⁶Fe and δ²⁶Mg.The origin of inter-mineral fractionations of Fe and Mg isotopic ratios remains debated. δ⁵⁶Fe between the main peridotite minerals shows positive linear correlations with slopes within error of unity, strongly suggesting intra-sample mineral-mineral Fe and Mg isotopic equilibrium. Because inter-mineral isotopic equilibrium should be reached earlier than major element equilibrium via chemical diffusion at mantle temperatures, Fe and Mg isotope ratios of coexisting minerals could be useful tools for justifying mineral thermometry and barometry on the basis of chemical equilibrium between minerals. Although most peridotites in this study exhibit a narrow range in δ⁵⁶Fe, the larger deviations from average δ⁵⁶Fe for three samples likely indicate changes due to metasomatic processes. Two samples show heavy δ⁵⁶Fe relative to the average and they also have high La/Yb and total Fe content, consistent with metasomatic reaction between peridotite and Fe-rich and isotopically heavy melt. The other sample has light δ⁵⁶Fe and slightly heavy δ²⁶Mg, which may reflect Fe-Mg inter-diffusion between peridotite and percolating melt.     

Speciation and thermodynamic properties for cobalt chloride complexes in hydrothermal fluids at 35-440 °C and 600 bar: An in-situ XAS study

Aqueous Co(II) chloride complexes play a crucial role in cobalt transport and deposition in ore-forming hydrothermal systems, ore processing plants, and in the corrosion of special Co-bearing alloys. Reactive transport modelling of cobalt in hydrothermal fluids relies on the availability of thermodynamic properties for Co complexes over a wide range of temperature, pressure and salinity. Synchrotron X-ray absorption spectroscopy was used to determine the speciation of cobalt(II) in 0-6 m chloride solutions at temperatures between 35 and 440 °C at a constant pressure of 600 bar. Qualitative analysis of XANES spectra shows that octahedral species predominate in solution at 35 °C, while tetrahedral species become increasingly important with increasing temperature. Ab initio XANES calculations and EXAFS analyses suggest that in high temperature solutions the main species at high salinity (Cl:Co >> 2) is CoCl₄²⁻, while a lower order tetrahedral complex, most likely CoCl₂(H₂O)_2(aq), predominates at low salinity (Cl:Co ratios ∼2). EXAFS analyses further revealed the bonding distances for the octahedral Co(H₂O)₆²⁺ (^octCo-O = 2.075(19) Å), tetrahedral CoCl₄²⁻ (^tetCo-Cl = 2.252(19) Å) and tetrahedral CoCl₂(H₂O)_2(aq) (^tetCo-O = 2.038(54) Å and ^tetCo-Cl = 2.210(56) Å). An analysis of the Co(II) speciation in sodium bromide solutions shows a similar trend, with tetrahedral bromide complexes becoming predominant at higher temperature/salinity than in the chloride system. EXAFS analysis confirms that the limiting complex at high bromide concentration at high temperature is CoBr₄²⁻. Finally, XANES spectra were used to derive the thermodynamic properties for the CoCl₄²⁻ and CoCl₂(H₂O)_2(aq) complexes, enabling thermodynamic modelling of cobalt transport in hydrothermal fluids. Solubility calculations show that tetrahedral CoCl₄²⁻ is responsible for transport of cobalt in hydrothermal solutions with moderate chloride concentration (∼2 m NaCl) at temperatures of 250 °C and higher, and both cooling and dilution processes can cause deposition of cobalt from hydrothermal fluids.