Scanning Transmission X-ray Microscopy Analysis Research Articles

Direct evidence from STXM analysis of enhanced oxygen storage capacity in ceria through the addition of Cu and Mg: Correlation of HT-WGS reaction performance

Here, scanning transmission X-ray microscopy (STXM) analysis was utilized to directly present visual evidence of changes in oxygen storage capacity (OSC) when small amounts of an additive were incorporated into CeO2. Specifically, the chemical map measured by STXM analysis differentiated between Cu-rich and Ce-rich areas to derive the proportion of Ce3+. Additionally, we found that the dispersion of Cu significantly influenced the formation of OSC. The findings were applied to the high-temperature water–gas shift reaction for producing high-purity hydrogen from waste-derived syngas, establishing a correlation with catalyst performance. Consequently, the CCM75 (Ce/Mg = 75/25) catalyst demonstrated the highest Cu dispersion and OSC values (6.9 %, 800.3 μmolO/gcat), and it also showed the highest CO conversion (79 % at 450 °C) and stability (−7.7 % at 450 °C after 50 h), attributed to the significant presence of active Cu. This study confirms previously reported interactions between Cu and CeO2 and uncovers the significant roles of Cu and Mg in this catalysis system, providing new understanding of the mechanisms that facilitate OSC improvement.

Oxalic acid enhances bioremediation of Cr(VI) contaminated soil using Penicillium oxalicum SL2

Oxalic acid is the most abundant low molecular weight organic acid (LMWOA) in many environments and offers enormous prospects for treating Cr(VI) contamination. In this study, laboratory batch experiments were conducted to estimate the roles of oxalic acid in Cr(VI) removal by Penicillium oxalicum SL2. Oxalic acid changed the initial pH and provided a suitable condition for the growth of strain SL2 when the penicillium was applied to bioremediation of Cr(VI) contamination in alkaline soil. Gompertz model analysis indicated that initial pH affected the lag time of the growth curve of strain SL2. Scanning electron microscopy and scanning transmission X-ray microscopy analysis showed strain SL2 sufficiently contacted with contaminated soil and reduced Cr(VI) to Cr(III) in the hyphae. The results suggested that oxalic acid could enhance the bioremediation efficiency of strain SL2 though improving chromium bioleaching from the contaminated soil and strengthening Cr(VI) removal in the leaching solution. This study provided oxalic acid as a green reagent for stimulating Cr(VI) removal by strain SL2 and would expand knowledge on the roles of LMWOA in Cr(VI) bioremediation.

Nano-silica particles synergistically IgE-mediated mast cell activation exacerbating allergic inflammation in mice.

BackgroundAllergic respiratory diseases have increased dramatically due to air pollution over the past few decades. However, studies are limited on the effects of inorganic components and particulate matter with different particle sizes in smog on allergic diseases, and the possible molecular mechanism of inducing allergies has not been thoroughly studied.MethodsFour common mineral elements with different particle sizes in smog particles were selected, including Al2O3, TiO2, Fe2O3, and SiO2. We studied the relationship and molecular mechanism of smog particle composition, particle size, and allergic reactions using mast cells, immunoglobulin E (IgE)-mediated passive cutaneous anaphylaxis (PCA) model, and an ovalbumin (OVA)-induced asthmatic mouse model in vitro and in vivo, combined with transmission electron microscopy, scanning transmission X-ray microscopy analysis, and transcriptome sequencing.ResultsOnly 20 nm SiO2 particles significantly increased β-hexosaminidase release, based on dinitrophenol (DNP)-human serum albumin (HSA) stimulation, from IgE-sensitized mast cells, while other particles did not. Meanwhile, the PCA model showed that Evan’s blue extravasation in mice was increased after treatment with nano-SiO2 particles. Nano-SiO2 particles exposure in the asthmatic mouse model caused an enhancement of allergic airway inflammation as manifested by OVA-specific serum IgE, airway hyperresponsiveness, lung inflammation injury, mucous cell metaplasia, cytokine expression, mast cell activation, and histamine secretion, which were significantly increased. Nano-SiO2 particles exposure did not affect the expression of FcϵRI or the ability of mast cells to bind IgE but synergistically activated mast cells by enhancing the mitogen-activated protein kinase (MAPK) signaling pathway, especially the phosphorylation levels of the extracellular signal-regulated kinase (ERK)1/2. The ERK inhibitors showed a significant inhibitory effect in reducing β-hexosaminidase release.ConclusionOur results indicated that nano-SiO2 particles stimulation might synergistically activate IgE-sensitized mast cells by enhancing the MAPK signaling pathway and that nano-SiO2 particles exposure could exacerbate allergic inflammation. Our experimental results provide useful information for preventing and treating allergic diseases.

Anaerobic Microscopic Analysis of Ferrous Saponite and Its Sensitivity to Oxidation by Earth’s Air: Lessons Learned for Analysis of Returned Samples from Mars and Carbonaceous Asteroids

Ferrous saponite is a secondary mineral that can be used to reveal the redox state of past aqueous environments on Mars. In mineralogical analyses for ferrous saponite formed in laboratory simulations or contained in future returned samples from Mars, its oxidation by the Earth’s air could be problematic due to the high redox sensitivity. Here, we performed micro X-ray diffraction and scanning transmission X-ray microscopy analyses for a single particle of synthesized ferrous saponite without any exposure to air. The sample was reanalyzed after air exposure for 10–18 h to assess the adequacy of our anoxic preparation/measurement methods and the impacts of air on the sample. We found that the crystal structures agreed with ferrous saponite, both before and after air exposure; however, ferrous iron in saponite was partially oxidized, at least until 0.1–1 μm from the surface, after air exposure at the submicron scale, forming micro-vein-like Fe(III)-rich features. Together with our results of infrared spectroscopy of ferrous saponite, we showed that oxidation of octahedral iron occurred rapidly and heterogeneously, even in a short time of air exposure without any structural rearrangement. Since ferrous saponite is expected to exist on carbonaceous asteroids and icy dwarf planets, our methodology is also applicable to mineralogical studies of samples returned from these bodies.

Molecular Sorption Mechanisms of Cr(III) to Organo-Ferrihydrite Coprecipitates Using Synchrotron-Based EXAFS and STXM Techniques.

Ubiquitous organo-ferrihydrite coprecipitates (OFC) significantly affect the mobility and availability of Cr in soil through sorption, but the underlying sorption mechanisms remain unclear at the molecular level. Due to the potential formation of OFC in agricultural soils with returned crop straws, we synthesized OFC with rice/rape straw-derived carbon (C) sources and different loadings. The molecular sorption mechanisms of Cr(III) to the synthesized OFC under different conditions were investigated by Cr K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy and scanning transmission X-ray microscopy (STXM). Cr(III) sorption by OFC decreased with increasing C loading and decreasing pH, regardless of C sources. Moreover, inhibition of Cr(III) sorption to OFC with high C loading occurred when ionic strength (IS) increased, suggesting the presence of outer-sphere complexed Cr(III). EXAFS analysis revealed that more Cr(III) were bound to ferrihydrite of the OFC at a relatively high pH, and organically bound Cr(III) enhanced when increasing C loading and decreasing IS. STXM analysis strongly suggested that C loading reduced Cr(III) sorption through blocking the binding sites on the ferrihydrite, which overwhelmed Cr(III) retention by the direct binding of Cr(III) to carboxyl of the particulate organic matter (OM) and OM coated on the Fh fractions of the OFC. These findings facilitated the comprehensive understanding of the sorption mechanisms of Cr(III) to OFC at the molecular level, which will assist the prediction of Cr(III) mobility in soils, particularly for Cr(III)-contaminated agricultural soils with the application of crop straws.

Lignans in Knotwood of Norway Spruce: Localisation with Soft X-ray Microscopy and Scanning Transmission Electron Microscopy with Energy Dispersive X-ray Spectroscopy

Lignans are bioactive compounds that are especially abundant in the Norway spruce (Picea abies L. Karst.) knotwood. By combining a variety of chromatographic, spectroscopic and imaging techniques, we were able to quantify, qualify and localise the easily extractable lignans in the xylem tissue. The knotwood samples contained 15 different lignans according to the gas chromatography-mass spectrometry analysis. They comprised 16% of the knotwood dry weight and 82% of the acetone extract. The main lignans were found to be hydroxymatairesinols HMR1 and HMR2. Cryosectioned and resin-embedded ultrathin sections of the knotwood were analysed with scanning transmission X-ray microscopy (STXM). Cryosectioning was found to retain only lignan residues inside the cell lumina. In the resin-embedded samples, lignan was interpreted to be unevenly distributed inside the cell lumina, and partially confined in deposits which were either readily present in the lumina or formed when OsO4 used in staining reacted with the lignans. Furthermore, the multi-technique characterisation enabled us to obtain information on the chemical composition of the structural components of knotwood. A simple spectral analysis of the STXM data gave consistent results with the gas chromatographic methods about the relative amounts of cell wall components (lignin and polysaccharides). The STXM analysis also indicated that a torus of a bordered pit contained aromatic compounds, possibly lignin.

Microanalysis of silica-based adsorbent for effective recovery of radioactive elements

ABSTRACTFor effective recovery of radioactive elements by adsorbents using polymer-immobilized silica (SiO2-P) supports, the microstructure of SiO2-P particles impregnated with octyl(phenyl)-N, N-diisobutylcarbamoylmethylphosphine oxide as extractants and their change with the crosslinking degree of polymer (CDP) were investigated using scanning transmission X-ray microscopy (STXM) and extended X-ray absorption fine structures (EXAFS) analyses; further, their relation with adsorption/elution behavior was discussed. The results of STXM analysis suggested that the polymer is distributed within several hundred nanometers of the pore surface, and its distributions are spread by the increase of CDP. In addition, the capture of impurity molecules such as H2O by polymers with high CDP was indicated. EXAFS analyses showed that the local structure around adsorbed europium ions is similar irrespective of the CDP. The adsorption/elution tests demonstrated that a higher CDP inhibited the elution of adsorbed europium ions from the adsorbent.

Synergistic desalination of potash brine-impacted groundwater using a dual adsorbent

The impact of saline mining effluent has been a significant environmental concern. Natural and modified clay-mineral adsorbents have been receiving increasing attention for salinity reduction of brine-impacted water, especially for natural resource extraction sites and surrounding environments. In this study, a dual-adsorbent treatment based on the sequential application of calcined layered double hydroxide (CLDH) and acid-treated zeolite was developed, evaluated and characterized for the desalination of potash brine-impacted groundwater. Potash brine produced by conventional potash mining in Saskatchewan (Canada) contains a large amount of Na+, K+ and Cl−. The CLDH and acid-treated clinoptilolite zeolites were combined to sequentially remove Cl− and Na+. A series of batch adsorption experiments were conducted for synthetic saline water and potash brine-spiked groundwater using various combinations of adsorbents: natural zeolites (NZ) or acid-treated zeolites (AZ) with or without the CLDH pretreatment. The experiment revealed that the Na+ removal percentage was synergistically increased by the dechlorination pretreatment using CLDH, and further improved by AZ. The CLDH-AZ dual adsorbent achieved a Langmuir Na+ adsorption capacity of 24.4mg/g, a significant improvement over conventional approaches to zeolite-based desalination. Using the brine-impacted groundwater with a high sodium adsorption ratio (SAR) of 13.3±0.1, the CLDH-AZ dual adsorbent decreased the concentrations of Na+, K+, and Cl− by 87, 97, and 87%, respectively (below drinking water standards). It also exhibited the additional advantages of neutralizing the effluent pH and decreasing the hardness, SAR, and total dissolved sulfur concentration. This study addresses the removal mechanisms, which are associated with the structural memory effect, dealumination, protonic exchanges, and zeolite porosity changes. Synchrotron-based scanning transmission X-ray microscopy analyses provided visual evidence of sodium adsorption sites (SiONa and AlONa) associated with dealumination in the acid-treated zeolites. This study is the first report that demonstrates the synergy of the CLDH-AZ dual adsorbent treatment for potash brine-impacted water.

Unfolding the Anatase-to-Rutile Phase Transition in TiO2 Nanotubes Using X-ray Spectroscopy and Spectromicroscopy

This work reports a study of the anatase-to-rutile phase transition (ART) in a highly ordered TiO2 nanotube (NT) specimen fabricated using an electrochemical process followed by thermal annealing at 750 °C (NT750). Two-dimensional X-ray absorption near-edge structure–X-ray excited optical luminescence spectroscopy reveals the hierarchically two-layered structure of NT750 by resolving the surface anatase luminescence and bulk rutile optical emission. Scanning transmission X-ray microscopy analysis of a sliced NT750 lamella spatially differentiates the top nanotubular anatase structure from the denser rutile bottom layer with a gradual ART interface layer. On the basis of these results together with the known behavior of size and anisotropy dependence of ART in TiO2 nanocrystal, we propose the “bottom-up” mechanism for ART in anodic TiO2 NTs. This result is particularly relevant to the fundamental understanding of phase transition in nanostructures as well as the fabrication of desired TiO2 NT mixed-phase c...

Iron mineralogy across the oxycline of a lignite mine lake

Iron-rich pelagic aggregates of microbial origin named “iron snow” are formed in the water column of some acidic lignite mine lakes. We investigated the evolution of Fe mineralogy across the oxycline of the Lusatian lake 77, Germany at two sampling sites differing by their pH and mixing profiles. The central basin (CB) of this lake shows a dimictic water regime with a non-permanent anoxic deep layer and a homogeneous acidic pH all over the water column (pH3). In contrast, the northern basin (NB) is meromictic with a permanently anoxic bottom layer and a pH increase from pH3 in the mixolimnion (superficial part of the lake) to pH5.5 in the monimolimnion (anoxic bottom layer). Fe minerals above and below the oxycline were identified using X-ray Absorption Spectroscopy (XAS) at the Fe K-edge and further characterized down to the atomic scale by High Resolution Transmission Electron Microscopy (HRTEM) and Scanning Transmission Electron Microscopy (STEM) coupled to Energy Dispersive X-ray Spectroscopy (EDXS). We explored local Fe redox state and C speciation using Scanning Transmission X-ray Microscopy (STXM) at the Fe L2,3-edges and C K-edge. Schwertmannite [Fe8O8(OH)8-2x(SO4)x] identified as the sole Fe mineral in CB, was polycrystalline, consisting in the aggregation of nanodomains of 2–3nm each one exhibiting the crystal structure of schwertmannite. In contrast, schwertmannite was partly (40%) converted to aluminous ferrihydrite when reaching the oxycline in NB. This mineralogical transformation was most probably due to a combination of abiotic and microbial anaerobic processes promoting pH increase and release of Fe(II) (e.g. via heterotrophic Fe(III) reduction) that induce the catalytic hydrolysis of schwertmannite to ferrihydrite. Mineral products were stabilized in the monimolimnion by the adsorption of aluminum, silicate and organic matter. Noteworthy, local Fe redox state heterogeneities were observed, with a few areas enriched in Fe(II) as evidenced by STXM analyses at the Fe L2,3-edges. These local redox heterogeneities could arise from microbial activity (e.g. Fe(III) and/or sulfate reduction). All these results provide an in-depth mineralogical overview of iron phases forming in lake 77 as a basis for future investigations of microbial vs. abiotic parameters controlling their stability and transformation.

Composition analysis of a polymer electrolyte membrane fuel cell microporous layer using scanning transmission X-ray microscopy and near edge X-ray absorption fine structure analysis

The novel application of scanning transmission X-ray microscopy (STXM) to the microporous layer (MPL) of a polymer electrolyte membrane fuel cell is investigated. A spatially resolved chemical component distribution map is obtained for the MPL of a commercially available SGL 25 BC sample. This is achieved with near edge X-ray absorption fine structure spectroscopic analysis. Prior to analysis the sample is embedded in non-reactive epoxy and ultra-microtomed to a thickness of 100 nm. Polytetrafluoroethylene (PTFE), carbon particle agglomerates, and supporting epoxy resin distributions are identified and reconstructed for a scanning area of 6 μm × 6 μm. It is observed that the spatial distribution of PTFE is strongly correlated to the carbon particle agglomerations. Additionally, agglomerate structures of PTFE are identified, possibly indicating the presence of a unique mesostructure in the MPL. STXM analysis is presented as a useful technique for the investigation of chemical species distributions in the MPL.

Microscopic characterization of the bacterial cell envelope of Planococcus halocryophilus Or1 during subzero growth at −15 °C

Microbial psychrophiles continue to expand our understanding of the adaptations required to thrive in cold environments. Planococcus halocryophilus strain Or1, a gram-positive, aerobic bacterial isolate from a Canadian high Arctic permafrost active layer, divides at temperatures as low as −15 °C and high salinity of 18 % NaCl. Initial studies of P. halocryophilus Or1 identified that under subzero conditions the cell envelope changed in appearance and composition. Our goal was to further analyze these features using scanning and transmission electron microscopy (SEM, TEM), confocal laser scanning microscopy (CLSM), and scanning transmission X-ray microscopy (STXM), which showed progressive changes in cell envelope composition during growth from optimal (25 °C) down to subzero (−15 °C) temperatures. S/TEM and CLSM illustrate that growth at −15 °C coincides with increasing hydrophobicity and distinct extracellular encrustations closely associated with the cell wall. STXM analyses resolved differences in cell composition with temperature, favoring higher amounts of protein and polysaccharide at higher temperatures compared to cells grown at −15 °C that were characterized by a cell envelope comprised of 20 % calcium carbonate, 50 % peptidoglycan, and 29 % choline. Analyses of the sequenced genome found the presence of several copies of carbonic anhydrase, a protein responsible for mineralization of calcium carbonate, and transcriptomic analyses revealed increased expression of a single copy at −15 °C along with the synthesis of peptidoglycan. The unique cell features of P. halocryophilus Or1 grown at −15 °C demonstrate unusual physiology that expands our understanding of psychrophilic adaptations and provides an example of microbially mediated calcium carbonate precipitation at subzero temperatures.

Direct and up-close views of plant cell walls show a leading role for lignin-modifying enzymes on ensuing xylanases.

BackgroundA key barrier that limits the full potential of biological processes to create new, sustainable materials and fuels from plant fibre is limited enzyme accessibility to polysaccharides and lignin that characterize lignocellulose networks. Moreover, the heterogeneity of lignocellulosic substrates means that different enzyme combinations might be required for efficient transformation of different plant resources. Analytical techniques with high chemical sensitivity and spatial resolution that permit direct characterization of solid samples could help overcome these challenges by allowing direct visualization of enzyme action within plant fibre, thereby identify barriers to enzyme action.ResultsIn the current study, the high spatial resolution (about 30 nm) of scanning transmission X-ray microscopy (STXM), and the detection sensitivity (ppm) of time-of-flight secondary ion mass spectrometry (ToF-SIMS), were harnessed for the first time to investigate the progression of laccase, cellulase and xylanase activities through wood samples, and to evaluate complementary action between lignin-modifying and polysaccharide-degrading enzymes. In particular, complementary insights from the STXM and ToF-SIMS analyses revealed the key role of laccase in promoting xylanase activity throughout and between plant cell walls.ConclusionsThe spatial resolution of STXM clearly revealed time-dependent progression and spatial distribution of laccase and xylanase activities, whereas ToF-SIMS analyses confirmed that laccase promoted protein penetration into fibre samples, leading to an overall increase in polysaccharide degradation. Spectromicroscopic visualizations of plant cell wall chemistry allowed simultaneous tracking of changes to lignin and polysaccharide contents, which provides new possibilities for investigating the complementary roles of lignin-modifying and carbohydrate-active enzymes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-014-0176-9) contains supplementary material, which is available to authorized users.

Characterization of Ca-phosphate biological materials by scanning transmission X-ray microscopy (STXM) at the Ca L2,3-, P L2,3- and C K-edges

Several naturally occurring biological materials, including bones and teeth, pathological calcifications, microbial mineral deposits formed in marine phosphogenesis areas, as well as bio-inspired cements used for bone and tooth repair are composed of Ca-phosphates. These materials are usually identified and characterized using bulk-scale analytical tools such as X-ray diffraction, Fourier transform infrared spectroscopy or nuclear magnetic resonance. However, there is a need for imaging techniques that provide information on the spatial distribution and chemical composition of the Ca-phosphate phases at the micrometer- and nanometer scales. Such analyses provide insightful indications on how the materials may have formed, e.g. through transient precursor phases that eventually remain spatially separated from the mature phase. Here, we present scanning transmission X-ray microscopy (STXM) analyses of Ca-phosphate reference compounds, showing the feasibility of fingerprinting Ca-phosphate-based materials. We calibrate methods to determine important parameters of Ca-phosphate phases, such as their Ca/P ratio and carbonate content at the ∼25nm scale, using X-ray absorption near-edge spectra at the C K-, Ca L2,3- and P L2,3-edges. As an illustrative case study, we also perform STXM analyses on hydroxyapatite precipitates formed in a dense fibrillar collagen matrix. This study paves the way for future research on Ca-phosphate biomineralization processes down to the scale of a few tens of nanometers.

Microscopic and spectroscopic analyses of chlorhexidine tolerance in Delftia acidovorans biofilms.

The physicochemical responses of Delftia acidovorans biofilms exposed to the commonly used antimicrobial chlorhexidine (CHX) were examined in this study. A CHX-sensitive mutant (MIC, 1.0 μg ml(-1)) was derived from a CHX-tolerant (MIC, 15.0 μg ml(-1)) D. acidovorans parent strain using transposon mutagenesis. D. acidovorans mutant (MT51) and wild-type (WT15) strain biofilms were cultivated in flow cells and then treated with CHX at sub-MIC and inhibitory concentrations and examined by confocal laser scanning microscopy (CLSM), scanning transmission X-ray microscopy (STXM), and infrared (IR) spectroscopy. Specific morphological, structural, and chemical compositional differences between the CHX-treated and -untreated biofilms of both strains were observed. Apart from architectural differences, CLSM revealed a negative effect of CHX on biofilm thickness in the CHX-sensitive MT51 biofilms relative to those of the WT15 strain. STXM analyses showed that the WT15 biofilms contained two morphochemical cell variants, whereas only one type was detected in the MT51 biofilms. The cells in the MT51 biofilms bioaccumulated CHX to a similar extent as one of the cell types found in the WT15 biofilms, whereas the other cell type in the WT15 biofilms did not bioaccumulate CHX. STXM and IR spectral analyses revealed that CHX-sensitive MT51 cells accumulated the highest levels of CHX. Pretreating biofilms with EDTA promoted the accumulation of CHX in all cells. Thus, it is suggested that a subpopulation of cells that do not accumulate CHX appear to be responsible for greater CHX resistance in D. acidovorans WT15 biofilm in conjunction with the possible involvement of bacterial membrane stability.

Microscopy evidence of bacterial microfossils in phosphorite crusts of the Peruvian shelf: Implications for phosphogenesis mechanisms

Phosphorites are sedimentary formations enriched in Ca-phosphate minerals. The precipitation of these minerals is thought to be partly mediated by the activity of microorganisms. The vast majority of studies on phosphorites have focused on a petrological and geochemical characterization of these rocks. However, detailed descriptions are needed at the sub-micrometer scale at which crucial information can be retrieved about traces of past or modern microbial activities. Here, scanning electron microscopy (SEM) analyses of a recent phosphorite crust from the upwelling-style phosphogenesis area off Peru revealed that it contained a great number of rod-like and coccus-like shaped micrometer-sized (~1.1μm and 0.5μm, respectively) objects, referred to as biomorphs. Some of these biomorphs were filled with carbonate fluoroapatite (CFA, a calcium-phosphate phase common in phosphorites); some were empty; some were surrounded by one or two layers of pyrite. Transmission electron microscopy (TEM) and energy dispersive X-ray spectrometry (EDXS) analyses were performed on focused ion beam (FIB) milled ultrathin foils to characterize the texture of CFA and pyrite in these biomorphs at the few nanometer scale. Non-pyritized phosphatic biomorphs were surrounded by a thin (5–15nm thick) rim appearing as a void on TEM images. Bundles of CFA crystals sharing the same crystallographic orientations (aligned along their c-axis) were found in the interior of some biomorphs. Pyrite formed a thick (~35–115nm) layer with closely packed crystals surrounding the pyritized biomorphs, whereas pyrite crystals at distance from the biomorphs were smaller and distributed more sparsely. Scanning transmission X-ray microscopy (STXM) analyses performed at the C K-edge provided maps of organic and inorganic carbon in the samples. Inorganic C, mainly present as carbonate groups in the CFA lattice, was homogeneously distributed, whereas organic C was concentrated in the rims of the phosphatic biomorphs. Finally, STXM analyses at the Fe L2,3-edges together with TEM-EDXS analyses, revealed that some pyritized biomorphs experienced partial oxidation. The mineralogical features of these phosphatic biomorphs are very similar to those formed by bacteria having precipitated phosphate minerals intra- and extracellularly in laboratory experiments. Similarly, pyritized biomorphs resemble bacteria encrusted by pyrite. We therefore interpret phosphatic and pyritized biomorphs present in the Peruvian phosphorite crust as microorganisms fossilized near the boundary of zones of sulfate reduction. The implications of these observations are then discussed in the light of the different possible and non-exclusive microbially-driven phosphogenesis mechanisms that have been proposed in the past: (i) Organic matter mineralization, in particular mediated by iron reducing bacteria and/or sulfate-reducing bacteria (SRB), (ii) reduction of iron-(oxyhydr)oxides by iron-reducing bacteria and/or SRB, and (iii) polyphosphate metabolism in sulfide-oxidizing bacteria, possibly associated with SRB.

Synchrotron radiation based STXM analysis and micro-XRF mapping of differential expression of extracellular thiol groups by Acidithiobacillus ferrooxidans grown on Fe2 + and S0

The differential expression of extracellular thiol groups by Acidithiobacillus ferrooxidans grown on substrates Fe2+ and S0 was investigated by using synchrotron radiation based scanning transmission X-ray microscopy (STXM) imaging and microbeam X-ray fluorescence (μ-XRF) mapping. The extracellular thiol groups (SH) were first alkylated by iodoacetic acid forming Protein-SCH2COOH and then the P-SCH2COOH was marked by calcium ions forming P-SCH2COOCa. The STXM imaging and μ-XRF mapping of SH were based on analysis of SCH2COO-bonded Ca2+. The results indicated that the thiol group content of A. ferrooxidans grown on S0 is 3.88 times to that on Fe2+. Combined with selective labeling of SH by Ca2+, the STXM imaging and μ-XRF mapping provided an in situ and rapid analysis of differential expression of extracellular thiol groups.

Structural stability of coprecipitated natural organic matter and ferric iron under reducing conditions

The objective was to assess the interaction of Fe coprecipitated with dissolved organic matter (DOM) and its effect on Fe (hydr)oxide crystallinity and DOM retention under abiotic reducing conditions. A Fe-based coagulant was reacted with DOM from an agricultural drain and the resulting precipitate (floc) was exposed to S(-II) and Fe(II). Solution concentrations of Fe(II/III) and DOM were monitored, floc crystallinity was determined using X-ray diffraction, and the composition and distribution of functional groups were assessed using scanning transmission X-ray microscopy (STXM) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. Results indicate coprecipitation of Fe(III) with DOM forms a non-crystalline floc that withstands crystallization regardless of change in pH, Fe:DOM ratio and type of reductant added. There was no evidence that exposure to reducing conditions led to release of DOM from the floc, indicating that coprecipitation with complex natural DOM in aquatic environments may stabilize Fe (hydr)oxides against crystallization upon reaction with reduced species and lead to long term sequestration of the DOM. STXM analysis identified spatially distinct regions with remarkable functional group purity, contrary to the model of DOM as a relatively uniform complex polymer lacking identifiable organic compounds. Polysaccharide-like OM was strongly and directly correlated with the presence of Fe but showed different Fe binding strength depending on the presence of carboxylic acid functional groups, whereas amide and aromatic functional groups were inversely correlated with Fe content.

Extracellular Iron Biomineralization by Photoautotrophic Iron-Oxidizing Bacteria

Iron oxidation at neutral pH by the phototrophic anaerobic iron-oxidizing bacterium Rhodobacter sp. strain SW2 leads to the formation of iron-rich minerals. These minerals consist mainly of nano-goethite (alpha-FeOOH), which precipitates exclusively outside cells, mostly on polymer fibers emerging from the cells. Scanning transmission X-ray microscopy analyses performed at the C K-edge suggest that these fibers are composed of a mixture of lipids and polysaccharides or of lipopolysaccharides. The iron and the organic carbon contents of these fibers are linearly correlated at the 25-nm scale, which in addition to their texture suggests that these fibers act as a template for mineral precipitation, followed by limited crystal growth. Moreover, we evidence a gradient of the iron oxidation state along the mineralized fibers at the submicrometer scale. Fe minerals on these fibers contain a higher proportion of Fe(III) at cell contact, and the proportion of Fe(II) increases at a distance from the cells. All together, these results demonstrate the primordial role of organic polymers in iron biomineralization and provide first evidence for the existence of a redox gradient around these nonencrusting, Fe-oxidizing bacteria.

Classification of multiple types of organic carbon composition in atmospheric particles by scanning transmission X-ray microscopy analysis

A scanning transmission X-ray microscope at the Lawrence Berkeley National Laboratory is used to measure organic functional group abundance and morphology of atmospheric aerosols. We present a summary of spectra, sizes, and shapes observed in 595 particles that were collected and analyzed between 2000 and 2006. These particles ranged between 0.1 and 12 μm and represent aerosols found in a large range of geographical areas, altitudes, and times. They include samples from seven different field campaigns: PELTI, ACE-ASIA, DYCOMS II, Princeton, MILAGRO (urban), MILAGRO (C-130), and INTEX-B. At least 14 different classes of organic particles show different types of spectroscopic signatures. Different particle types are found within the same region while the same particle types are also found in different geographical domains. Particles chemically resembling black carbon, humic-like aerosols, pine ultisol, and secondary or processed aerosol have been identified from functional group abundance and comparison of spectra with those published in the literature.