Environmental Property of Mineralogy

Peking UniversityScedule:17-18 March 2003, Vemue: Kanazawa, Japan, Kanazawa Citymonde Hotel, Project Leader : Hayakawa, Kazuichi, Symposium Secretariat: XO kamata, Naoto, Edited by:Kamata, Naoto

Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients

There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator

Natural Extracellular Electron Transfer Between Semiconducting Minerals and Electroactive Bacterial Communities Occurred on the Rock Varnish

Rock varnish is a thin coating enriched with manganese (Mn) and iron (Fe) oxides. The mineral composition and formation of rock varnish elicit considerable attention from geologists and microbiologists. However, limited research has been devoted to the semiconducting properties of these Fe/Mn oxides in varnish and relatively little attention is paid to the mineral–microbe interaction under sunlight. In this study, the mineral composition and the bacterial communities on varnish from the Gobi Desert in Xinjiang, China were analyzed. Results of principal components analysis and t-test indicated that more electroactive genera such as Acinetobacter, Staphylococcus, Dietzia, and Pseudomonas gathered on varnish bacterial communities than on substrate rock and surrounding soils. We then explored the culture of varnish, substrate and soil samples in media and the extracellular electron transfer (EET) between bacterial communities and mineral electrodes under light/dark conditions for the first time. Orthogonal electrochemical experiments demonstrated that the most remarkable photocurrent density of 6.1 ± 0.4 μA/cm2 was observed between varnish electrode and varnish microflora. Finally, based on Raman and 16S rRNA gene–sequencing results, coculture system of birnessite and Pseudomonas (the major Mn oxide and a common electroactive bacterium in varnish) was established to study underlying mechanism. A steadily growing photocurrent (205 μA at 100 h) under light was observed with a stable birnessite after 110 h. However, only 47 μA was generated in the dark control and birnessite was reduced to Mn2+ in 13 h, suggesting that birnessite helped deliver electrons instead of serving as an electron acceptor under light. Our study demonstrated that electroactive bacterial communities were positively correlated with Fe/Mn semiconducting minerals in varnish, and diversified EET process occurred on varnish under sunlight. Overall, these phenomena may influence bacterial–community structure in natural environments over time

The Behavior of Water in Orthoclase Crystal and Its Implications for Feldspar Alteration

The phenomenon of feldspar alteration that occurs in the interior of feldspar crystals remains poorly understood. We observed experimentally that water can go into orthoclase crystals under pressures of up to 600 MPa at room temperature. With increasing pressure, the FTIR spectra of colorless orthoclase show a sharp increase in integral absorbance from 1.50 cm−1 to 14.54 cm−1 and normalized integral absorbance from 120 cm−2 to 1570 cm−2; the pink orthoclase saturates quickly with no significant change in either the integral absorbance or normalized integral absorbance. The different responses to the pressure between colorless orthoclase and pink orthoclase might be related to the K content in the structure. Moreover, FTIR spectra at atmospheric pressure collected in different crystallography directions show different absorbance intensities, which illustrates the characteristic of preferred crystallographic orientations. These results reveal that H2O molecules can occur as structural constituents entering the crystallographic channels of alkali feldspar crystals, preferentially along (001) orientation. These findings provide clues into the mechanism of feldspar alteration occurring in the interior of feldspar crystals, as well as the formation of micropores and microstructure in feldspar minerals. This study also provides important insights into the behavior of water molecules in nominally anhydrous minerals in the upper crust of the Earth

Chemical Composition and Crystal Structure of Kenoargentotetrahedrite-(Fe), Ag6Cu4Fe2Sb4S12, from the Bajiazi Pb-Zn Deposit, Liaoning, China

Kenoargentotetrahedrite-(Fe) is observed as greenish-grey anhedral grains, 50–150 μm in size, in association with galena, sphalerite and chalcopyrite in the Bajiazi Pb-Zn deposit of magmatic-hydrothermal type, Liaoning, China. The empirical formula from electron microprobe analyses is Ag5.50Cu4.17Fe1.75Zn0.31Sb3.96As0.04S12.08, corresponding to the ideal formula Ag6Cu4Fe2Sb4S12. The crystal structure of kenoargentotetrahedrite-(Fe) has been determined and refined by single-crystal X-ray diffraction with R1 = 0.0192 for 1866 (404 unique) reflections. It is cubic, space group I4¯3m with unit cell parameters a = 10.4928(2) Å, V = 1155.26(7) Å3 and Z = 2. The structure of kenoargentotetrahedrite-(Fe) is characterized by a poor occupancy of 0.05 of the octahedral S(2) site with the S(2)-M(2) bonding length of 1.9994(8) Å. The six Ag atoms at M(2) around S(2) form an octahedron cluster (Ag6)4+ with the valence state of +4 and Ag-Ag distance of 2.8276(1) Å. The structure is identical to that by Rozhdestvenskaya et al., being composed of a collapsed sodalite-like framework of corner-connected M(1)S4 tetrahedron forming cages containing M(2)6-octahedron cluster, encircled by four SbS3 trigonal pyramids. It is related to the tetrahedrite group minerals with the existence of the (Ag6)4+ cluster replacing the S(2)-centered Ag6 octahedron according to the substitution mechanism 6M(2)Ag+ + S(2)S2−=M(2)(Ag6)4+ + S(2) S

Natural Hematite as a Low-Cost and Earth-Abundant Cathode Material for Performance Improvement of Microbial Fuel Cells

Developing cheap electrocatalysts for cathodic oxygen reduction in neutral medium is a key factor for practical applications of microbial fuel cells (MFCs). Natural hematite was investigated as a low-cost cathode to improve the performance of microbial fuel cells (MFCs). With hematite-coated cathode, the cell current density stabilized at 330.66 ± 3.1 mA·m−2 (with a 1000 Ω load) over 10 days under near-neutral conditions. The maximum power density of MFC with hematite cathode reached to 144.4 ± 7.5 mW·m−2, which was 2.2 times that of with graphite cathode (64.8 ± 5.2 mW·m−2). X-ray diffraction (XRD), Raman, electrode potential analysis, and cyclic voltammetry (CV) revealed that hematite maintained the electrode activities due to the stable existence of Fe(II)/Fe(III) in mineral structure. Electrochemical impedance spectroscopy (EIS) results indicated that the cathodic electron transfer dynamics was significantly improved by using hematite to lower the cathodic overpotential. Therefore, this low-cost and earth-abundant natural mineral is promised as an effective cathode material with potential large-field applications of MFCs in future

Chemical Composition and Crystal Structure of Kenoargentotetrahedrite-(Fe), Ag₆Cu₄Fe₂Sb₄S₁₂, from the Bajiazi Pb-Zn Deposit, Liaoning, China

Kenoargentotetrahedrite-(Fe) is observed as greenish-grey anhedral grains, 50–150 μm in size, in association with galena, sphalerite and chalcopyrite in the Bajiazi Pb-Zn deposit of magmatic-hydrothermal type, Liaoning, China. The empirical formula from electron microprobe analyses is Ag5.50Cu4.17Fe1.75Zn0.31Sb3.96As0.04S12.08, corresponding to the ideal formula Ag6Cu4Fe2Sb4S12. The crystal structure of kenoargentotetrahedrite-(Fe) has been determined and refined by single-crystal X-ray diffraction with R1 = 0.0192 for 1866 (404 unique) reflections. It is cubic, space group I4¯3m with unit cell parameters a = 10.4928(2) Å, V = 1155.26(7) Å3 and Z = 2. The structure of kenoargentotetrahedrite-(Fe) is characterized by a poor occupancy of 0.05 of the octahedral S(2) site with the S(2)-M(2) bonding length of 1.9994(8) Å. The six Ag atoms at M(2) around S(2) form an octahedron cluster (Ag6)4+ with the valence state of +4 and Ag-Ag distance of 2.8276(1) Å. The structure is identical to that by Rozhdestvenskaya et al., being composed of a collapsed sodalite-like framework of corner-connected M(1)S4 tetrahedron forming cages containing M(2)6-octahedron cluster, encircled by four SbS3 trigonal pyramids. It is related to the tetrahedrite group minerals with the existence of the (Ag6)4+ cluster replacing the S(2)-centered Ag6 octahedron according to the substitution mechanism 6M(2)Ag+ + S(2)S2−=M(2)(Ag6)4+ + S(2) S

The Fine Characterization and Potential Photocatalytic Effect of Semiconducting Metal Minerals in Danxia Landforms

The Danxia landform is representative of the Cretaceous continental red sediment. The careful identification and potential environmental effects of minerals in Danxia red beds have yet to be clearly reported. In this work, reddish sandstone samples were collected from Lang Mountain Danxia landform in Xinning, Hunan province, China, and their mineral phases, element distribution, microstructure, and the spatial relationship of different minerals were investigated using polarizing optical microscope, environmental scanning electron microscopy, energy-dispersive X-ray analysis, electron probe microanalysis, micro-Raman spectra, micro- X-ray diffraction, X-ray fluorescence spectroscopy, and high-resolution transmission electron microscopy. The results revealed that iron oxide (mainly hematite) and titanium oxide (mainly anatase) were the dominant minerals in Danxia red layers. Microcrystalline hematite was suggested as being the coloring mineral. Anatase, reported here for the first time in Danxia red beds, constituted the content of titanium in the red layer (0.17⁻0.57%) and was present in a significantly higher amount than the adjacent limestone formation (0.13%). Over 95% of Fe/Ti oxides served as a cementation agent along the framework of coarse-grain minerals (quartz and feldspar). The hematite and anatase were visible-light-responsive semiconductors, with a band gap of 2.01 eV and 3.05 eV, respectively. Photoelectrochemical experiments were performed on synthetic hematite, anatase, and their coupled material. The inactive hematite displayed an enhanced 23-fold photocurrent at 0.8 V (vs. Ag/AgCl) when coupled with anatase. Furthermore, in a photodegradation experiment using methyl orange dye under simulated sunlight, the coupled material showed decolorizing efficiency 2.4 times that of hematite. The anatase, therefore, prominently improved the photocatalytic activities of hematite. It is proposed that these semiconducting minerals in red beds produce oxygen reactive species and have significant environmental effects, which is of great importance