James J. Dynes

Advanced imaging techniques for assessment of structure, composition and function in biofilm systems

Scientific imaging represents an important and accepted research tool for the analysis and understanding of complex natural systems. Apart from traditional microscopic techniques such as light and electron microscopy, new advanced techniques have been established including laser scanning microscopy (LSM), magnetic resonance imaging (MRI) and scanning transmission X-ray microscopy (STXM). These new techniques allow in situ analysis of the structure, composition, processes and dynamics of microbial communities. The three techniques open up quantitative analytical imaging possibilities that were, until a few years ago, impossible. The microscopic techniques represent powerful tools for examination of mixed environmental microbial communities usually encountered in the form of aggregates and films. As a consequence, LSM, MRI and STXM are being used in order to study complex microbial biofilm systems. This mini review provides a short outline of the more recent applications with the intention to stimulate new research and imaging approaches in microbiology.

Properties of Fe-organic matter associations via coprecipitation versus adsorption.

The association of organic matter (OM) with minerals is recognized as the most important stabilization mechanism for soil organic matter. This study compared the properties of Fe-OM complexes formed from adsorption (reaction of OM to postsynthesis ferrihydrite) versus coprecipitation (formation of Fe solids in the presence of OM). Coprecipitates and adsorption complexes were synthesized using dissolved organic matter (DOM) extracts from a forest little layer at varying molar C/Fe ratios of 0.3-25.0. Sample properties were studied by N2 gas adsorption, XRD, FTIR, Fe EXAFS, and STXM-NEXAFS techniques. Coprecipitation resulted in much higher maximum C contents (∼130 mg g(-1) C difference) in the solid products than adsorption, which may be related to the formation of precipitated insoluble Fe(III)-organic complexes at high C/Fe ratios in the coprecipitates as revealed by Fe EXAFS analysis. Coprecipitation led to a complete blockage of mineral surface sites and pores with ≥177 mg g(-1) C and molar C/Fe ratios ≥2.8 in the solid products. FTIR and STXM-NEXAFS showed that the coprecipitated OM was similar in composition to the adsorbed OM. An enrichment of aromatic C was observed at low C/Fe ratios. Association of carboxyl functional groups with Fe was shown with FTIR and STXM-NEXAFS analysis. STXM-NEXAFS analysis showed a continuous C distribution on minerals. Desorption of the coprecipitated OM was less than that of the adsorbed OM at comparable C/Fe ratios. These results are helpful to understand C and Fe cycling in the natural environments with periodically fluctuating redox conditions, where coprecipitation can occur.

Soft X-ray spectromicroscopy of nickel sorption in a natural river biofilm

Scanning transmission X-ray microscopy (STXM) at the C 1s, O 1s, Ni 2p, Ca 2p, Mn 2p, Fe 2p, Mg 1s, Al 1s and Si 1s edges was used to study Ni sorption in a complex natural river biofilm. The 10-week grown river biofilm was exposed to 10 mg L(-1) Ni(2+) (as NiCl(2)) for 24 h. The region of the biofilm examined was dominated by filamentous structures, which were interpreted as the discarded sheaths of filamentous bacteria, as well as a sparse distribution of rod-shaped bacteria. The region also contained discrete particles with spectra similar to those of muscovite, SiO(2) and CaCO(3). The Ni(II) ions were selectively adsorbed by the sheaths of the filamentous bacteria. The sheaths were observed to be metal rich with significant amounts of Ca, Fe and Mn, along with the Ni. In addition, the sheaths had a large silicate content but little organic material. The metal content of the rod-shaped bacterial cells was much lower. The Fe on the sheath was mainly in the Fe(III) oxidation state. Mn was found in II, III and IV oxidation states. The Ni was likely sorbed to Mn-Fe minerals on the sheath. These STXM results have probed nano-scale biogeochemistry associated with bacterial species in a complex, natural biofilm community. They have implications for selective Ni contamination of the food chain and for developing bioremediation strategies.

Soft X-ray Spectromicroscopy Study of Mineral-Organic Matter Associations in Pasture Soil Clay Fractions

There is a growing acceptance that associations with soil minerals may be the most important overarching stabilization mechanism for soil organic matter. However, direct investigation of organo-mineral associations has been hampered by a lack of methods that can simultaneously characterize organic matter (OM) and soil minerals. In this study, STXM-NEXAFS spectroscopy at the C 1s, Ca 2p, Fe 2p, Al 1s, and Si 1s edges was used to investigate C associations with Ca, Fe, Al, and Si species in soil clay fractions from an upland pasture hillslope. Bulk techniques including C and N NEXAFS, Fe K-edge EXAFS spectroscopy, and XRD were applied to provide additional information. Results demonstrated that C was associated with Ca, Fe, Al, and Si with no separate phase in soil clay particles. In soil clay particles, the pervasive C forms were aromatic C, carboxyl C, and polysaccharides with the relative abundance of carboxyl C and polysaccharides varying spatially at the submicrometer scale. Only limited regions in the soil clay particles had aliphatic C. Good C-Ca spatial correlations were found for soil clay particles with no CaCO3, suggesting a strong role of Ca in organo-mineral assemblage formation. Fe EXAFS showed that about 50% of the total Fe in soils was contained in Fe oxides, whereas Fe-bearing aluminosilicates (vermiculite and Illite) accounted for another 50%. Fe oxides in the soil were mainly crystalline goethite and hematite, with lesser amounts of poorly crystalline ferrihydrite. XRD revealed that soil clay aluminosilicates were hydroxy-interlayered vermiculite, Illite, and kaolinite. C showed similar correlation with Fe to Al and Si, implying a similar association of Fe oxides and aluminosilicates with organic matter in organo-mineral associations. These direct microscopic determinations can help improve understanding of organo-mineral interactions in soils.

Investigation at the nanometre scale on the corrosion mechanisms of archaeological ferrous artefacts by STXM

For the first time, corrosion products of a 450 year old archaeological iron nail were investigated at the nanometer level using STXM. NEXAFS acquisitions at the Fe L-edge were performed on a thin film taken of the metal–corrosion products including the interface. Comparison with Fe L-edge reference spectra gathered on maghemite (Fe2O3), magnetite (Fe3O4), siderite (FeCO3), chukanovite (Fe2(OH)2CO3) and metallic iron (Fe) showed the presence of an interfacial layer of about 100 nm at the metal–corrosion product interface consisting of maghemite and magnetite. Further from this interface, corrosion products are mainly constituted of Fe-carbonates, as well as smaller quantities of iron oxides, probably maghemite. These results support the hypothesis of the presence of a nanolayer controlling the corrosion processes at the metal–corrosion product interface, proposed during former studies at the macroscopic and microscopic levels. They also bring important new insights for the prediction of very long term corrosion of steels, especially into the fields of cultural heritage conservation and storage of nuclear wastes.

Effect of inorganic and organic ligands on the sorption/desorption of arsenate on/from Al-Mg and Fe-Mg layered double hydroxides.

This paper describes the sorption of arsenate on Al-Mg and Fe-Mg layered double hydroxides as affected by pH and varying concentrations of inorganic and organic ligands, and the effect of residence time on the desorption of arsenate by ligands. The capacity of ligands to inhibit the fixation of arsenate followed the sequence: nitrate<nitrite<sulphate<selenite<tartrate<oxalate≪phosphate on Al-Mg-LDH and nitrate<sulphate≈nitrite<tartrate<oxalate<selenite≪ phosphate on Fe-Mg-LDH. The inhibition of arsenate sorption increased by increasing the initial ligand concentration and was greater on Al-Mg-LDH than on Fe-Mg-LDH. The longer the arsenate residence time on the LDH surfaces the less effective the competing ligands were in desorbing arsenate from sorbents. A greater percentage of arsenate was removed by phosphate from Al-Mg-LDH than from Fe-Mg-LDH, due to the higher affinity of arsenate for iron than aluminum.

Theory-driven design of high-valence metal sites for water oxidation confirmed using in situ soft X-ray absorption

The efficiency with which renewable fuels and feedstocks are synthesized from electrical sources is limited at present by the sluggish oxygen evolution reaction (OER) in pH-neutral media. We took the view that generating transition-metal sites with high valence at low applied bias should improve the activity of neutral OER catalysts. Here, using density functional theory, we find that the formation energy of desired Ni4+ sites is systematically modulated by incorporating judicious combinations of Co, Fe and non-metal P. We therefore synthesized NiCoFeP oxyhydroxides and probed their oxidation kinetics with in situ soft X-ray absorption spectroscopy (sXAS). In situ sXAS studies of neutral-pH OER catalysts indicate ready promotion of Ni4+ under low overpotential conditions. The NiCoFeP catalyst outperforms IrO2 and retains its performance following 100 h of operation. We showcase NiCoFeP in a membrane-free CO2 electroreduction system that achieves a 1.99 V cell voltage at 10 mA cm-2, reducing CO2 into CO and oxidizing H2O to O2 with a 64% electricity-to-chemical-fuel efficiency.

Soft X-ray induced photoreduction of organic Cu(II) compounds probed by X-ray absorption near-edge (XANES) spectroscopy.

Photoreduction is a major obstacle for using the X-ray absorption near-edge structure (XANES) fingerprint to perform metal speciation at the molecular level in biological and environmental samples, especially for metalloproteins. In this study, soft X-ray induced photoreduction was observed in organic Cu(II) compounds during XANES measurements in a third-generation synchrotron source. Next Cu L(3)-edge, O K-edge, and C K-edge XANES spectroscopy, together with the scanning transmission X-ray microscopy (STXM), were used to probe the specific radiation damage processes of Cu acetate with similar local structures to Cu metalloproteins. Breakup of the Cu-Cu bond was hypothesized for the initial photoreduction of Cu acetate. The following radiation damage of Cu acetate produced CuO and an organic Cu(I) compound with a C═C bond, and the further photoreduction of the resulting CuO to Cu metal was also demonstrated. Our results indicated the importance of consideration of photoreduction during soft XANES measurements for the solid state compounds with high valence metals. Reducing the radiation dose to ~0.1 MGy effectively prevented the photoreduction of organic Cu(II) compounds during these measurements. This proposed radiation damage mechanism in Cu acetate may be generally useful in explaining the photoreduction process in Cu metalloproteins.

Speciation and distribution of copper in a mining soil using multiple synchrotron-based bulk and microscopic techniques

Molecular-level understanding of soil Cu speciation and distribution assists in management of Cu contamination in mining sites. In this study, one soil sample, collected from a mining site contaminated since 1950s, was characterized complementarily by multiple synchrotron-based bulk and spatially resolved techniques for the speciation and distribution of Cu as well as other related elements (Fe, Ca, Mn, K, Al, and Si). Bulk X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopy revealed that soil Cu was predominantly associated with Fe oxides instead of soil organic matter. This agreed with the closest association of Cu to Fe by microscopic X-ray fluorescence (U-XRF) and scanning transmission X-ray microscopy (STXM) nanoanalysis, along with the non-occurrence of photoreduction of soil Cu(II) by quick Cu L3,2-edge XANES spectroscopy (Q-XANES) which often occurs when Cu organic complexes are present. Furthermore, bulk-EXAFS and STXM-coupled Fe L3,2-edge nano-XANES analysis revealed soil Cu adsorbed primarily to Fe(III) oxides by inner-sphere complexation. Additionally, Cu K-edge μ-XANES, L3,2-edge bulk-XANES, and successive Q-XANES results identified the presence of Cu2S rather than radiation-damage artifacts dominant in certain microsites of the mining soil. This study demonstrates the great benefits in use of multiple combined synchrotron-based techniques for comprehensive understanding of Cu speciation in heterogeneous soil matrix, which facilitates our prediction of Cu reactivity and environmental fate in the mining site.

Phosphatation of Zeolite H‐ZSM‐5: A Combined Microscopy and Spectroscopy Study

A variety of phosphated zeolite H-ZSM-5 samples are investigated by using a combination of Fourier transfer infrared (FTIR) spectroscopy, single pulse (27)Al, (29)Si, (31)P, (1)H-(31)P cross polarization (CP), (27)Al-(31)P CP, and (27)Al 3Q magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy, scanning transmission X-ray microscopy (STXM) and N2 physisorption. This approach leads to insights into the physicochemical processes that take place during phosphatation. Direct phosphatation of H-ZSM-5 promotes zeolite aggregation, as phosphorus does not penetrate deep into the zeolite material and is mostly found on and close to the outer surface of the zeolite, acting as a glue. Phosphatation of pre-steamed H-ZSM-5 gives rise to the formation of a crystalline tridymite AlPO4 phase, which is found in the mesopores of dealuminated H-ZSM-5. Framework aluminum species interacting with phosphorus are not affected by hydrothermal treatment. Dealuminated H-ZSM-5, containing AlPO4 , retains relatively more framework Al atoms and acid sites during hydrothermal treatment than directly phosphated H-ZSM-5.