Geochemistry and microbiology of tropical serpentine soils in the Santa Elena Ophiolite, a landscape-biogeographical approach.

The Santa Elena Ophiolite is a well-studied ultramafic system in Costa Rica mainly comprised of peridotites. Here, tropical climatic conditions promote active laterite formation processes, but the biogeochemistry of the resulting serpentine soils is still poorly understood. The aim of this study was to characterize the soil geochemical composition and microbial community of contrasting landscapes in the area, as the foundation to start exploring the biogeochemistry of metals occurring there. The soils were confirmed as Ni-rich serpentine soils but differed depending on their geographical location within the ophiolite area, showing three serpentine soil types. Weathering processes resulted in mountain soils rich in trace metals such as cobalt, manganese and nickel. The lowlands showed geochemical variations despite sharing similar landscapes: the inner ophiolite lowland soils were more like the surrounding mountain soils rather than the north lowland soils at the border of the ophiolite area, and within the same riparian basin, concentrations of trace metals were higher downstream towards the mangrove area. Microbial community composition reflected the differences in geochemical composition of soils and revealed potential geomicrobiological inputs to local metal biogeochemistry: iron redox cycling bacteria were more abundant in the mountain soils, while more manganese-oxidizing bacteria were found in the lowlands, with the highest relative abundance in the mangrove areas. The fundamental ecological associations recorded in the serpentine soils of the Santa Elena Peninsula, and its potential as a serpentinization endemism hotspot, demonstrate that is a model site to study the biogeochemistry, geomicrobiology and ecology of tropical serpentine areas.

Biosynthesis and Characterization of Copper Nanoparticles Using Shewanella oneidensis: Application for Click Chemistry.

Copper nanoparticles (Cu-NPs) have a wide range of applications as heterogeneous catalysts. In this study, a novel green biosynthesis route for producing Cu-NPs using the metal-reducing bacterium, Shewanella oneidensis is demonstrated. Thin section transmission electron microscopy shows that the Cu-NPs are predominantly intracellular and present in a typical size range of 20-40 nm. Serial block-face scanning electron microscopy demonstrates the Cu-NPs are well-dispersed across the 3D structure of the cells. X-ray absorption near-edge spectroscopy and extended X-ray absorption fine-structure spectroscopy analysis show the nanoparticles are Cu(0), however, atomic resolution images and electron energy loss spectroscopy suggest partial oxidation of the surface layer to Cu2 O upon exposure to air. The catalytic activity of the Cu-NPs is demonstrated in an archetypal "click chemistry" reaction, generating good yields during azide-alkyne cycloadditions, most likely catalyzed by the Cu(I) surface layer of the nanoparticles. Furthermore, cytochrome deletion mutants suggest a novel metal reduction system is involved in enzymatic Cu(II) reduction and Cu-NP synthesis, which is not dependent on the Mtr pathway commonly used to reduce other high oxidation state metals in this bacterium. This work demonstrates a novel, simple, green biosynthesis method for producing efficient copper nanoparticle catalysts.

Redox Interactions of Tc(VII), U(VI), and Np(V) with Microbially Reduced Biotite and Chlorite.

Technetium, uranium, and neptunium are contaminants that cause concern at nuclear facilities due to their long half-life, environmental mobility, and radiotoxicity. Here we investigate the impact of microbial reduction of Fe(III) in biotite and chlorite and the role that this has in enhancing mineral reactivity toward soluble TcO4(-), UO2(2+), and NpO2(+). When reacted with unaltered biotite and chlorite, significant sorption of U(VI) occurred in low carbonate (0.2 mM) buffer, while U(VI), Tc(VII), and Np(V) showed low reactivity in high carbonate (30 mM) buffer. On reaction with the microbially reduced minerals, all radionuclides were removed from solution with U(VI) reactivity influenced by carbonate. Analysis by X-ray absorption spectroscopy (XAS) confirmed reductive precipitation to poorly soluble U(IV) in low carbonate conditions and both Tc(VII) and Np(V) in high carbonate buffer were also fully reduced to poorly soluble Tc(IV) and Np(IV) phases. U(VI) reduction was inhibited under high carbonate conditions. Furthermore, EXAFS analysis suggested that in the reaction products, Tc(IV) was associated with Fe, Np(IV) formed nanoparticulate NpO2, and U(IV) formed nanoparticulate UO2 in chlorite and was associated with silica in biotite. Overall, microbial reduction of the Fe(III) associated with biotite and chlorite primed the minerals for reductive scavenging of radionuclides: this has clear implications for the fate of radionuclides in the environment.

Biogenic nano-magnetite and nano-zero valent iron treatment of alkaline Cr(VI) leachate and chromite ore processing residue.

Highly reactive nano-scale biogenic magnetite (BnM), synthesized by the Fe(III)-reducing bacterium Geobacter sulfurreducens, was tested for the potential to remediate alkaline Cr(VI) contaminated waters associated with chromite ore processing residue (COPR). The performance of this biomaterial, targeting aqueous Cr(VI) removal, was compared to a synthetic alternative, nano-scale zero valent iron (nZVI). Samples of highly contaminated alkaline groundwater and COPR solid waste were obtained from a contaminated site in Glasgow, UK. During batch reactivity tests, Cr(VI) removal from groundwater was inhibited by ∼25% (BnM) and ∼50% (nZVI) when compared to the treatment of less chemically complex model pH 12 Cr(VI) solutions. In both the model Cr(VI) solutions and contaminated groundwater experiments the surface of the nanoparticles became passivated, preventing complete coupling of their available electrons to Cr(VI) reduction. To investigate this process, the surfaces of the reacted samples were analyzed by TEM-EDX, XAS and XPS, confirming Cr(VI) reduction to the less soluble Cr(III) on the nanoparticle surface. In groundwater reacted samples the presence of Ca, Si and S was also noted on the surface of the nanoparticles, and is likely responsible for earlier onset of passivation. Treatment of the solid COPR material in contact with water, by addition of increasing weight % of the nanoparticles, resulted in a decrease in aqueous Cr(VI) concentrations to below detection limits, via the addition of ⩾5% w/w BnM or ⩾1% w/w nZVI. XANES analysis of the Cr K edge, showed that the % Cr(VI) in the COPR dropped from 26% to a minimum of 4-7% by the addition of 5% w/w BnM or 2% w/w nZVI, with higher additions unable to reduce the remaining Cr(VI). The treated materials exhibited minimal re-mobilization of soluble Cr(VI) by re-equilibration with atmospheric oxygen, with the bulk of the Cr remaining in the solid fraction. Both nanoparticles exhibited a considerable capacity for the remediation of COPR related Cr(VI) contamination, with the synthetic nZVI demonstrating greater reactivity than the BnM. However, the biosynthesized BnM was also capable of significant Cr(VI) reduction and demonstrated a greater efficiency for the coupling of its electrons towards Cr(VI) reduction than the nZVI.

Redox interactions between Cr(VI) and Fe(II) in bioreduced biotite and chlorite.

Contamination of the environment with Cr as chromate (Cr(VI)) from industrial activities is of significant concern as Cr(VI) is a known carcinogen, and is mobile in the subsurface. The capacity of Fe(II)-containing phyllosilicates including biotite and chlorite to alter the speciation, and thus the mobility, of redox-sensitive contaminants including Cr(VI) is of great interest since these minerals are common in soils and sediments. Here, the capacity of bacteria, ubiquitous in the surface and near-surface environment, to reduce Fe(III) in phyllosilicate minerals and, thus, alter their redox reactivity was investigated in two-step anaerobic batch experiments. The model Fe(III)-reducing bacterium Geobacter sulfurreducens was used to reduce Fe(III) in the minerals, leading to a significant transformation of structural Fe(III) to Fe(II) of 0.16 mmol/g (∼ 40%) in biotite and 0.15 mmol/g (∼ 20%) in chlorite. The unaltered minerals could not remove Cr(VI) from solution despite containing a larger excess of Fe(II) than would be required to reduce all the added Cr(VI), unless they were supplied in a very high concentration (a 1:10 solid to solution ratio). By contrast, even at very low concentrations, the addition of bioreduced biotite and chlorite caused removal of Cr(VI) from solution, and surface and near surface X-ray absorption spectroscopy confirmed that this immobilization was through reductive transformation to Cr(III). We provide empirical evidence that the amount of Fe(II) generated by microbial Fe(III) reduction is sufficient to reduce the Cr(VI) removed and, in the absence of reduction by the unaltered minerals, suggest that only the microbially reduced fraction of the iron in the minerals is redox-active against the Cr(VI).

Microbial reduction of arsenic-doped schwertmannite by Geobacter sulfurreducens.

The fate of As(V) during microbial reduction by Geobacter sulfurreducens of Fe(III) in synthetic arsenic-bearing schwertmannites has been investigated. During incubation at pH7, the rate of biological Fe(III) reduction increased with increasing initial arsenic concentration. From schwertmannites with a relatively low arsenic content (<0.3 wt %), only magnetite was formed as a result of dissimilatory iron reduction. However, bioreduction of schwertmannites with higher initial arsenic concentrations (>0.79 wt %) resulted in the formation of goethite. At no stage during the bioreduction process did the concentration of arsenic in solution exceed 120 µgL(1), even for a schwertmannite with an initial arsenic content of 4.13 wt %. This suggests that the majority of the arsenic is retained in the biominerals or by sorption at the surfaces of newly formed nanoparticles. Subtle differences in the As K-edge XANES spectra obtained from biotransformation products are clearly related to the initial arsenic content of the schwertmannite starting materials. For products obtained from schwertmannites with higher initial As concentrations, one dominant population of As(V) species bonded to only two Fe atoms was evident. By contrast, schwertmannites with relatively low arsenic concentrations gave biotransformation products in which two distinctly different populations of As(V) persisted. The first is the dominant population described above, the second is a minority population characterized by As(V) bonded to four Fe atoms. Both XAS and XMCD evidence suggest that the latter form of arsenic is that taken into the tetrahedral sites of the magnetite. We conclude that the majority population of As(V) is sorbed to the surface of the biotransformation products, whereas the minority population comprises As(V) incorporated into the tetrahedral sites of the biomagnetite. This suggests that microbial reduction of highly bioavailable As(V)-bearing Fe(III) mineral does not necessarily result in the mobilization of the arsenic.

Microbial engineering of nanoheterostructures: biological synthesis of a magnetically recoverable palladium nanocatalyst.

Precious metals supported on ferrimagnetic particles have a diverse range of uses in catalysis. However, fabrication using synthetic methods results in potentially high environmental and economic costs. Here we show a novel biotechnological route for the synthesis of a heterogeneous catalyst consisting of reactive palladium nanoparticles arrayed on a nanoscale biomagnetite support. The magnetic support was synthesized at ambient temperature by the Fe(III)-reducing bacterium, Geobacter sulfurreducens , and facilitated ease of recovery of the catalyst with superior performance due to reduced agglomeration (versus conventional colloidal Pd nanoparticles). Surface arrays of palladium nanoparticles were deposited on the nanomagnetite using a simple one-step method without the need to modify the biomineral surface, most likely due to an organic coating priming the surface for Pd adsorption, which was produced by the bacterial culture during the formation of the nanoparticles. A combination of EXAFS and XPS showed the Pd nanoparticles on the magnetite to be predominantly metallic in nature. The Pd(0)-biomagnetite was tested for catalytic activity in the Heck reaction coupling iodobenzene to ethyl acrylate or styrene. Rates of reaction were equal to or superior to those obtained with an equimolar amount of a commercial colloidal palladium catalyst, and near complete conversion to ethyl cinnamate or stilbene was achieved within 90 and 180 min, respectively.

Optimizing Cr(VI) and Tc(VII) remediation through nanoscale biomineral engineering.

The influence of Fe(III) starting material on the ability of magnetically recoverable biogenic magnetites produced by Geobacter sulfurreducens to retain metal oxyanion contaminants has been investigated. The reduction/removal of aqueous Cr(VI) was used to probe the reactivity of the biomagnetites. Nanomagnetites produced by the bacterial reduction of schwertmannite powder were more efficient at reducing Cr(VI) than either ferrihydrite "gel"-derived biomagnetite or commercial nanoscale Fe(3)O(4). Examination of post-exposure magnetite surfaces indicated both Cr(III) and Cr(VI) were present. X-ray magnetic circular dichroism (XMCD) studies at the Fe L(2,3)-edge showed that the amount of Fe(III) "gained" by Cr(VI) reduction could not be entirely accounted for by "lost" Fe(II). Cr L(2,3)-edge XMCD spectra found Cr(III) replaced approximately 14%-20% of octahedral Fe in both biogenic magnetites, producing a layer resembling CrFe(2)O(4). However, schwertmannite-derived biomagnetite was associated with approximately twice as much Cr as ferrihydrite-derived magnetite. Column studies using a gamma-camera to image a (99)mTc(VII) radiotracer were performed to visualize the relative performances of biogenic magnetites at removing aqueous metal oxyanion contaminants. Again, schwertmannite-derived biomagnetite proved capable of retaining more (approximately 20%) (99)mTc(VII) than ferrihydrite-derived biomagnetite, confirming that the production of biomagnetite can be fine-tuned for efficient environmental remediation through careful selection of the Fe(III) mineral substrate supplied to Fe(III)-reducing bacteria.

Investigating different mechanisms for biogenic selenite transformations: Geobacter sulfurreducens, Shewanella oneidensis and Veillonella atypica.

The metal-reducing bacteria Geobacter sulfurreducens, Shewanella oneidensis and Veillonella atypica, use different mechanisms to transform toxic, bioavailable sodium selenite to less toxic, non-mobile elemental selenium and then to selenide in anaerobic environments, offering the potential for in situ and ex situ bioremediation of contaminated soils, sediments, industrial effluents, and agricultural drainage waters. The products of these reductive transformations depend on both the organism involved and the reduction conditions employed, in terms of electron donor and exogenous extracellular redox mediator. The intermediary phase involves the precipitation of elemental selenium nanospheres and the potential role of proteins in the formation of these structures is discussed. The bionanomineral phases produced during these transformations, including both elemental selenium nanospheres and metal selenide nanoparticles, have catalytic, semiconducting and light-emitting properties, which may have unique applications in the realm of nanophotonics. This research offers the potential to combine remediation of contaminants with the development of environmentally friendly manufacturing pathways for novel bionanominerals.

Aerobic microbial manufacture of nanoscale selenium: exploiting nature's bio-nanomineralization potential.

The potential of the environment to yield organisms that can produce functional bionanominerals is demonstrated by selenium-tolerant, aerobic bacteria isolated from a seleniferous rhizosphere soil. An isolate, NS3, was identified as a Bacillus species (EU573774.1) based on morphological and 16S rRNA characterization. This strain reduced Se(IV) under aerobic conditions to produce amorphous alpha Se(0) nanospheres. A room-temperature washing treatment was then employed to remove the biomass and resulted in the production of clusters of hexagonal Se(0) nano-rods. The Se(0) nanominerals were analyzed using electron microscopy and X-ray diffraction techniques. This Bacillus isolate has the potential to be used both in the neutralizing of toxic Se(IV) anions in the environment and in the environmentally friendly manufacture of nanomaterials.

Harnessing the extracellular bacterial production of nanoscale cobalt ferrite with exploitable magnetic properties.

Nanoscale ferrimagnetic particles have a diverse range of uses from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of monodisperse nanoparticles with well-controlled size, composition, and magnetic properties. To fabricate these materials purely using synthetic methods is costly in both environmental and economical terms. However, metal-reducing microorganisms offer an untapped resource to produce these materials. Here, the Fe(III)-reducing bacterium Geobacter sulfurreducens is used to synthesize magnetic iron oxide nanoparticles. A combination of electron microscopy, soft X-ray spectroscopy, and magnetometry techniques was employed to show that this method of biosynthesis results in high yields of crystalline nanoparticles with a narrow size distribution and magnetic properties equal to the best chemically synthesized materials. In particular, it is demonstrated here that cobalt ferrite (CoFe(2)O(4)) nanoparticles with low temperature coercivity approaching 8 kOe and an effective anisotropy constant of ∼10(6) erg cm(-3) can be manufactured through this biotechnological route. The dramatic enhancement in the magnetic properties of the nanoparticles by the introduction of high quantities of Co into the spinel structure represents a significant advance over previous biomineralization studies in this area using magnetotactic bacteria. The successful production of nanoparticulate ferrites achieved in this study at high yields could open up the way for the scaled-up industrial manufacture of nanoparticles using environmentally benign methodologies.

Microbial manufacture of chalcogenide-based nanoparticles via the reduction of selenite using Veillonella atypica: an in situ EXAFS study.

The ability of metal-reducing bacteria to produce nanoparticles, and their precursors, can be harnessed for the biological manufacture of fluorescent, semiconducting nanomaterials. The anaerobic bacterium Veillonella atypica can reduce selenium oxyanions to form nanospheres of elemental selenium. These selenium nanospheres are then further reduced by the bacterium to form reactive selenide which could be precipitated with a suitable metal cation to produce nanoscale chalcogenide precipitates, such as zinc selenide, with optical and semiconducting properties. The whole cells used hydrogen as the electron donor for selenite reduction and an enhancement of the reduction rate was observed with the addition of a redox mediator (anthraquinone disulfonic acid). A novel synchrotron-based in situ time-resolved x-ray absorption spectroscopy technique was used, in conjunction with ion chromatography and inductively coupled plasma-atomic emission spectroscopy, to study the mechanisms and kinetics of the microbial reduction of selenite to selenide. The products of this biotransformation were also assessed using electron microscopy, energy-dispersive spectroscopy, x-ray diffraction and fluorescence spectroscopy. This process offers the potential to prepare chalcogenide-based nanocrystals, for application in optoelectronic devices and biological labelling, from more environmentally benign precursors than those used in conventional organometallic synthesis.

X-ray absorption spectroscopy studies of reactions of technetium, uranium and neptunium with mackinawite.

Technetium, uranium and neptunium may all occur in the environment in more than one oxidation state (IV or VII, IV or VI and IV or V respectively). The surface of mackinawite, the first-formed iron sulfide phase in anoxic conditions, can promote redox changes so a series of laboratory experiments were carried out to explore the interactions of Tc, U and Np with this mineral. The products of reaction were characterised using X-ray absorption spectroscopy. Technetium, added as TcO4(-), is reduced to oxidation state IV and forms a TcS(2)-like species. On oxidation of the mackinawite in air to form goethite, Tc remains in oxidation state IV but in an oxide, rather than a sulfide environment. At low concentrations, uranium forms uranyl surface complexes on oxidised regions of the mackinawite surface but at higher concentrations, the uranium promotes surface oxidation and forms a mixed oxidation state oxide phase. Neptunium is reduced to oxidation IV and forms a surface complex with surface sulfide ions. The remainder of the Np coordination sphere is filled with water molecules or hydroxide ions.

Treatment of radioactive wastes: an X-ray absorption spectroscopy study of the reaction of technetium with green rust.

Technetium is a long-lived product of nuclear fission that readily forms the soluble pertechnetate anion [TcO(4)](-). Green rusts (layered hydrous oxides containing both Fe(II) and Fe(III) and with interlayer sulfate or carbonate anions) concentrate >99.8% of 99Tc, present as [TcO(4)](-), from aqueous solution, even in the presence of high concentrations of NaNO(3), a common constituent of radioactive waste streams. The mechanism of removal from solution is apparently reduction and formation of strong Tc(IV) surface complexes. X-ray absorption spectroscopy shows that [TcO(4)](-) is indeed reduced by reaction with both sulfate- and carbonate-form green rusts and is found in a TcO(2)-like environment. On contact with air, the green rusts oxidize to poorly crystalline goethite but the Tc environment is unchanged. There is no increase in Tc solubility associated with oxidation of the host green rust. This behavior suggests that green rusts may be useful in the treatment of Tc-containing waste streams, in groundwater cleanup, and in restricting Tc migration from repositories.

An X-ray absorption spectroscopy study of neptunium(V) reactions with Mackinawite (FeS).

Neptunium is a transuranium element, produced in tonne quantities in nuclear reactors. Because it has access to a range of oxidation states, neptunium may undergo redox transformations in the environment and these can have far-reaching effects on its environmental mobility. Here, the reaction of NpO2+ (the soluble and thermodynamically stable neptunium species in oxic systems) with microcrystalline mackinawite is studied. Uptake of neptunium from solution is relatively low (approximately 10% of the total initially present in solution) and independent of initial solution concentration over the range 0.27-2.74 mM and of equilibration time. X-ray absorption spectroscopy (XAS) of the solid sulfide samples indicates nearest neighbor oxygen atoms at distances around 2.25-2.26 A, sulfur atoms at around 2.61-2.64 A, and two more distant shells fitted with iron, at 3.91-3.95 A and 4.15-4.16 A. These observations suggest that on interaction with the sulfide surface reduction of Np(V) to Np(IV) occurs, accompanied by loss of axial oxygen atoms. Neptunium coordinates directly to surface sulfide atoms, in contrast to the behavior previously observed for uranium under similar conditions. These results demonstrate the importance and variability of the speciation of redox sensitive actinides under anoxic conditions.