Hiromi Konishi

Importance of c-Type Cytochromes for U(VI) Reduction by Geobacter Sulfurreducens

BackgroundIn order to study the mechanism of U(VI) reduction, the effect of deleting c-type cytochrome genes on the capacity of Geobacter sulfurreducens to reduce U(VI) with acetate serving as the electron donor was investigated.ResultsThe ability of several c-type cytochrome deficient mutants to reduce U(VI) was lower than that of the wild type strain. Elimination of two confirmed outer membrane cytochromes and two putative outer membrane cytochromes significantly decreased (ca. 50–60%) the ability of G. sulfurreducens to reduce U(VI). Involvement in U(VI) reduction did not appear to be a general property of outer membrane cytochromes, as elimination of two other confirmed outer membrane cytochromes, OmcB and OmcC, had very little impact on U(VI) reduction. Among the periplasmic cytochromes, only MacA, proposed to transfer electrons from the inner membrane to the periplasm, appeared to play a significant role in U(VI) reduction. A subpopulation of both wild type and U(VI) reduction-impaired cells, 24–30%, accumulated amorphous uranium in the periplasm. Comparison of uranium-accumulating cells demonstrated a similar amount of periplasmic uranium accumulation in U(VI) reduction-impaired and wild type G. sulfurreducens. Assessment of the ability of the various suspensions to reduce Fe(III) revealed no correlation between the impact of cytochrome deletion on U(VI) reduction and reduction of Fe(III) hydroxide and chelated Fe(III).ConclusionThis study indicates that c-type cytochromes are involved in U(VI) reduction by Geobacter sulfurreducens. The data provide new evidence for extracellular uranium reduction by G. sulfurreducens but do not rule out the possibility of periplasmic uranium reduction. Occurrence of U(VI) reduction at the cell surface is supported by the significant impact of elimination of outer membrane cytochromes on U(VI) reduction and the lack of correlation between periplasmic uranium accumulation and the capacity for uranium reduction. Periplasmic uranium accumulation may reflect the ability of uranium to penetrate the outer membrane rather than the occurrence of enzymatic U(VI) reduction. Elimination of cytochromes rarely had a similar impact on both Fe(III) and U(VI) reduction, suggesting that there are differences in the routes of electron transfer to U(VI) and Fe(III). Further studies are required to clarify the pathways leading to U(VI) reduction in G. sulfurreducens.

Seafloor bioalteration of sulfide minerals: Results from in situ incubation studies

We present results of incubation studies conducted at low temperatures (∼4°C) in the vicinity of a seafloor hydrothermal vent system. We reacted Fe-, S-, Cu-, and Zn-bearing minerals including pyrite, marcasite, chalcopyrite, sphalerite, elemental sulfur, and a portion of a natural chimney sulfide structure for 2 months at the Main Endeavour Segment of the Juan de Fuca Ridge in the Pacific Ocean. Our study utilizes Fluorescent In Situ Hybridizations (FISH), Scanning and Transmission Electron Microscopy (SEM, TEM), and light microscopic analysis. The surfaces of these minerals are solely colonized by Bacteria and not by Archaea. Colonization densities vary over an order of magnitude with the following sequence: elemental sulfur > chimney sulfide > marcasite > pyrite > sphalerite > chalcopyrite, and correspond well with the abiotic oxidation kinetics of these materials, excepting elemental sulfur, which is both the least reactive to oxidizing species and the most heavily colonized. Colonization densities also correspond with apparent degree of reaction (dissolution pitting + accumulation of secondary alteration products). Heavy accumulations of secondary Fe oxides on Fe-bearing minerals, most notably on the chimney sulfide, form in situ as the result of mineral dissolution and the activity of neutrophilic Fe-oxidizing bacteria. Results suggest that mineral-oxidizing bacteria play a prominent role in weathering of seafloor sulfide deposits, and that microbial utilization of mineral substrates contributes to biomass production in seafloor hydrothermal environments.

Polysaccharide-catalyzed nucleation and growth of disordered dolomite: A potential precursor of sedimentary dolomite

Abstract The origin of dolomite is a long-standing enigma in sedimentary geology. It has been proposed that microorganisms, especially anaerobic microorganisms, can overcome kinetic barriers to facilitate dolomite precipitation, although their specific role in dolomite formation is still unclear. Our experimental results demonstrate that disordered dolomite can be synthesized at room temperature abiotically from solutions containing polysaccharides such as carboxymethyl cellulose or agar. We propose that when dissolved in solution, polysaccharides can be strongly adsorbed on Ca-Mg carbonate surfaces through hydrogen bonding. The adsorbed polysaccharides may help weaken the chemical bonding between surface Mg2+ ions and water molecules, which can lower the energy barrier to the desolvation of surface Mg2+-water complexes, enhance Mg2+ incorporation into the precipitating carbonate, and thereby promote disordered dolomite formation. In natural environments, it is possible that polysaccharides produced by microorganisms, e.g., extracellular polysaccharides, may play a key role in promoting disordered dolomite nucleation and crystallization. In marine sediments, the accumulated dissolved carbohydrates produced from organic matter degradation during early diagenesis may also serve as catalysts for disordered dolomite formation.

A relationship between d104 value and composition in the calcite-disordered dolomite solid-solution series

Abstract X-ray diffraction has been widely used in analyzing Ca-Mg carbonates. Compositions of biogenic and inorganic (Ca,Mg)CO3 crystals are often calculated by comparing their d104 values with published empirical curves. However, previous studies suggested that these curves do not apply to very high-Mg calcite and disordered dolomite. Based on synthesized high-Mg calcite and disordered dolomite, a new empirical curve between values of magnesian calcite d104 and MgCO3 content in the calcite-disordered dolomite solid-solution series is constructed. This new curve is consistent with the significant cell parameter changes accompanying the Mg-Ca cation disorder in dolomite, and it can help the characterization of the MgCO3 content of both natural and synthetic magnesian calcite and disordered dolomite, especially for the mineral mixtures that are not suitable for other analysis methods.

Testing the cation-hydration effect on the crystallization of Ca–Mg–CO3 systems

Significance Magnesium-bearing carbonate minerals play critical roles in the health and function of the Earth system because they constitute a significant fraction of lithosphere carbon reservoir and build skeletal structures for the majority of marine invertebrate organisms. Despite wide occurrence, high-Mg and sole-Mg phases such as dolomite ([Ca,Mg]CO3) and magnesite (MgCO3) prove virtually impossible to be crystallized under ambient conditions. It has long been believed that Mg2+ hydration is the cause for such a geological mystery. Here, we probe this hypothesis by investigating Ca–Mg–CO3 precipitation in the absence of water and find direct proof suggesting the existence of a more intrinsic crystallization barrier. These findings provide a perspective augmenting our understanding in carbonate mineralogy, biomineralization, and mineral-carbonation processes. Dolomite and magnesite are simple anhydrous calcium and/or magnesium carbonate minerals occurring mostly at Earth surfaces. However, laboratory synthesis of neither species at ambient temperature and pressure conditions has been proven practically possible, and the lack of success was assumed to be related to the strong solvation shells of magnesium ions in aqueous media. Here, we report the synthesis of MgCO3 and MgxCa(1−x)CO3 (0 < x < 1) solid phases at ambient conditions in the absence of water. Experiments were carried out in dry organic solvent, and the results showed that, although anhydrous phases were readily precipitated in the water-free environment, the precipitates’ crystallinity was highly dependent on the Mg molar percentage content in the solution. In specific, magnesian calcite dominated in low [Mg2+]/[Ca2+] solutions but gave way to exclusive formation of amorphous MgxCa(1−x)CO3 and MgCO3 in high-[Mg2+]/[Ca2+] and pure-Mg solutions. At conditions of [Mg2+]/[Ca2+] = 1, both nanocrystals of Ca-rich protodolomite and amorphous phase of Mg-rich MgxCa(1−x)CO3 were formed. These findings exposed a previously unrecognized intrinsic barrier for Mg2+ and CO32− to develop long-range orders at ambient conditions and suggested that the long-held belief of cation-hydration inhibition on dolomite and magnesite mineralization needed to be reevaluated. Our study provides significant insight into the long-standing “dolomite problem” in geochemistry and mineralogy and may promote a better understanding of the fundamental chemistry in biomineralization and mineral-carbonation processes.

Rapid control of phase growth by nanoparticles

Effective control of phase growth under harsh conditions (such as high temperature, highly conductive liquids or high growth rate), where surfactants are unstable or ineffective, is still a long-standing challenge. Here we show a general approach for rapid control of diffusional growth through nanoparticle self-assembly on the fast-growing phase during cooling. After phase nucleation, the nanoparticles spontaneously assemble, within a few milliseconds, as a thin coating on the growing phase to block/limit diffusion, resulting in a uniformly dispersed phase orders of magnitude smaller than samples without nanoparticles. The effectiveness of this approach is demonstrated in both inorganic (immiscible alloy and eutectic alloy) and organic materials. Our approach overcomes the microstructure refinement limit set by the fast phase growth during cooling and breaks the inherent limitations of surfactants for growth control. Considering the growing availability of numerous types and sizes of nanoparticles, the nanoparticle-enabled growth control will find broad applications.

Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite

ABSTRACT Microorganisms are known to participate in the weathering of primary phyllosilicate minerals through the production of organic ligands and acids and through the uptake of products of weathering. Here we show that the lithotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458–1460, 1996) can grow via oxidation of structural Fe(II) in biotite, a Fe(II)-rich trioctahedral mica found in granitic rocks. Oxidation of silt/clay-sized biotite particles was detected by a decrease in extractable Fe(II) content and simultaneous nitrate reduction. Mössbauer spectroscopy confirmed structural Fe(II) oxidation. Approximately 1.5 × 107 cells were produced per μmol of Fe(II) oxidized, in agreement with previous estimates of the growth yield of lithoautotrophic circumneutral-pH Fe(II)-oxidizing bacteria. Microbial oxidation of structural Fe(II) resulted in biotite alterations similar to those found in nature, including a decrease in the unit cell b dimension toward dioctahedral levels and Fe and K release. Structural Fe(II) oxidation may involve either direct enzymatic oxidation, followed by solid-state mineral transformation, or indirect oxidation as a result of the formation of aqueous Fe, followed by electron transfer from Fe(II) in the mineral to Fe(III) in solution. Although it is not possible to distinguish between these two mechanisms with available data, the complete absence of aqueous Fe in oxidation experiments favors the former alternative. The demonstration of microbial oxidation of structural Fe(II) suggests that microorganisms are directly responsible for the initial step in the weathering of biotite in granitic aquifers and the plant rhizosphere.

Perovskite hollow cubes: morphological control, three-dimensional twinning and intensely enhanced photoluminescence

Hollow sub-micrometer sized cubes of perovskite CaTiO3 with twinned and textured orthorhombic (pseudocubic) nanodomains in three dimensions are prepared via a facile solvothermal route from calcium nitrate and titanium n-butoxide in poly(ethylene glycol) solvent.

Mechanical Properties and Microstructure of Mg∕SiC Nanocomposites Fabricated by Ultrasonic Cavitation Based Nanomanufacturing

Magnesium, the lightest structural metal, is of significance to improve energy efficiency in various applications. Mg/SiC nanocomposites were successfully fabricated by ultrasonic cavitation based dispersion of SiC nanoparticles in Mg melts. As compared to pure magnesium, the mechanical properties including tensile strength and yield strength of the MglSiC nanocomposites were improved significantly, while the good ductility of pure Mg was retained. The grain size of the pure magnesium was refined significantly when SiC nanoparticles were dispersed in the Mg matrix. In the microstructure of MglSiC nanocomposites, while there were still some SiC microclusters, most of the SiC nanoparticles were dispersed very well. Transmission electron microscopy study of the interface between SiC nanoparticles and magnesium matrix indicates that SiC nanoparticles bond well with Mg without forming an intermediate phase.

Silician magnetite from the Dales Gorge Member of the Brockman Iron Formation, Hamersley Group, Western Australia

Abstract We report silician magnetite from banded iron formation (BIF) in the Dales Gorge Member of the Brockman Iron Formation, Hamersley Group, Western Australia. Magnetite mesobands typically consisting of individual ~100 μm microlaminae are revealed to be composed of silician magnetite overgrowths on magnetite. Silician magnetite overgrowths contain from 1 to 3 wt% SiO2, whereas (low-Si) magnetite domains contain less than 1 wt% SiO2. Silicon solid solution is present in the magnetite crystal lattice as determined by in situ micro-X-ray diffraction and high-resolution transmission electron microscopy. Three textures are distinguished in magnetite mesobands: (1) magnetite sub-microlaminae with silician magnetite overgrowths, (2) recrystallized magnetite fragments with silician magnetite overgrowths, and (3) a complex intergrowth of magnetite and silician magnetite. All three textures are found in magnetite mesobands from the BIF4-5 and BIF12-16 macrobands of the Dales Gorge type-section drill core DDH-47A from Wittenoom, Western Australia. Magnetite domains contain numerous submicrometer-to-micrometer inclusions of quartz, carbonate, stilpnomelane, and apatite, whereas silician magnetite overgrowths are devoid of mineral inclusions. The presence of mineral inclusions in magnetite indicates the BIF oxide precipitate was not chemically pure iron oxyhydroxide/oxide. Magnetite domains display textures formed during soft sediment deformation that are the earliest and best preserved relict sedimentary structures in this BIF. Silician magnetite is the dominant iron oxide in the Dales Gorge BIF and is present in many other sub-greenschist facies BIFs worldwide. We suggest the former presence of organic matter creates reducing conditions necessary to stabilize silician magnetite. Thus, silician magnetite is a potential biosignature in BIFs.