J. Thieme

X-ray tomography of a microhabitat of bacteria and other soil colloids with sub-100 nm resolution.

Visualization of the spatial arrangement of bacteria and other colloids permits to describe relevant soil parameters like porosity or nutrient storage capacity. Major advantages of X-ray microscopy for these investigations are the much higher spatial resolution compared to visible light microscopy and its ability to study colloidal structures directly in aqueous media. To obtain information about the three-dimensional structure of the microhabitats formed by bacteria and other soil colloids, tomography based on X-ray microscopy images with about 45 nm resolution was performed. Tomographic reconstructions presented in this paper clearly reveal the spatial arrangement of bacteria and other soil colloids which cannot be obtained from two-dimensional projections. The results show that X-ray nanotomography is a very powerful tool for examining the three-dimensional structure of flocs of colloidal particles.

STXM and NanoSIMS Investigations on EPS Fractions before and after Adsorption to Goethite

Extracellular polymeric substances (EPS) are expected to be an important source for the formation of mineral-organic associations in soil. Because such formations affect the composition of mobile and immobile organic matter as well as the reactivity of minerals, we investigated the composition of EPS before and after adsorption to goethite. Raman measurements on EPS extracted from Bacillus subtilis distinguished four fractions rich in proteins, polysaccharides, lipids, or lipids and proteins. Scanning transmission X-ray microscopy identified three different EPS-fractions that varied in their composition in proteins, nonaromatic proteins, and polysaccharides. Reaction of EPS with goethite led to a preferential adsorption of lipids and proteins. The organic coverage was heterogeneous, consisting of ~100 × 200 nm large patches of either lipid-rich or protein-rich material. Nanoscale secondary ion mass spectrometry showed a strong S enrichment in aggregates of ~400 nm in the goethite adsorbed EPS. From our simplified model system, we learned that only a small portion (<10%) of EPS was immobilized via adsorption to goethite. This fraction formed a coating of subμm spaced protein-rich and lipid-rich domains, i.e., of two materials which will strongly differ in their reactive sites. This will finally affect further adsorption, the particle mobility and eventually also colloidal stability.

The Geochemical Effects of Microbial Humic Substances Reduction

As part of a study on microbial redox alteration of humic substances we investigated the potential effect of this metabolism on the fate of heavy metals and hydrocarbons as a result of conformational alteration of the humic molecular structure due to microbial reduction. Our studies indicate that the microbial reduction of humic acids (HA) results in significant morphological and geochemical alterations. X-ray microscopy analysis indicate that the conformational structure of the humic colloids is altered as a result of the redox change. In the reduced state, the HA appeared as small dense particles, on reoxidation, large loose aggregates were formed. In addition, spectrofluorometric studies indicated that the binding capacity of the HA for naphthalene was decreased by 10% when the HA was reduced. Similarly, the reduced HA yielded higher surface tension values at all concentrations tested which is indicative of a more hydrophilic and less hydrophobic solute. On reoxidation, the surface tension values reverted back to values similar to those obtained for the untreated oxidized HA. These data indicate that the hydrophobicity of the HA is altered on biological reduction of the HA and that this alteration is reversible. In contrast the reduced HA demonstrated a 15% higher affinity for heavy metals such as divalent cobalt than the oxidized HA. In addition to increasing the binding capacity of HA for heavy metals, the reduction of the HA also decreased the bioavailability and toxicity of bound heavy metals such as chromium. When incubated in the presence of Cr(III) and HA, cells of Escherichia coli grew much more rapidly in the presence of the reduced HA suggesting that the higher metal binding capacity of the reduced humic substances resulted in a removal of the Cr(III) from solution and hence reduced its bioavailability and toxicity. These studies demonstrate that HA redox state and reduction of humic acids by microorganisms can have a significant effect on the molecular morphology and binding constants of HA for heavy metals and hydrocarbons and also directly affects the bioavailability of these compounds in the environment. Geochemische Effekte der mikrobiellen Huminstoffreduktion In der vorliegenden Studie sollte untersucht werden, ob die mikrobielle Huminstoffreduktion morphologische und geochemische Veranderungen der Huminstoffe zur Folge hat, die sich auch auf ihr Bindungsvermogen gegenuber Schwermetallen oder Kohlenwasserstoffen auswirken. Mittels Rontgenmikroskopie wurde gezeigt, dass sich die Konformation kolloidaler Huminsauren (HA) in Abhangigkeit vom Redox-Zustand verandert. Im reduzierten Zustand liegen die HA als kleine, dichte Partikel vor, nach Wiederherstellen des oxidierten Zustandes bilden sie grose, lockere Aggregate. Die Oberflachenspannung wassriger Systeme mit reduzierten HA war fur alle untersuchten Konzentrationen hoher als im Falle oxidierter HA, was auf starker hydrophile Eigenschaften bei den reduzierten HA hindeutet. Nach Wiederherstellung des oxidierten Zustandes ergaben sich dieselben niedrigen Werte fur die Oberflachenspannung wie fur Systeme mit unbehandelten, oxidierten HA. Daraus lasst sich schliesen, dass der hydrophobe Charakter der HA sich durch die mikrobielle Reduktion verandert und dass diese Anderung reversibel ist. Fluoreszenzspektroskopische Untersuchungen ergaben, dass bei HA im reduzierten Zustand die Bindungskapazitat fur Naphthalin um 10% vermindert ist. Gegenuber Schwermetallen wie Cobalt(II) hingegen zeigten die HA im reduzierten Zustand eine um 15% hohere Affinitat als in oxidierter Form. Im Falle des Chroms fuhrte die Reduktion der HA zu einem starker detoxifizierenden Effekt auf dieses Schwermetall: In Gegenwart von Cr(III) und HA inkubiert, wuchsen Escherichia coli in Gegenwart reduzierter HA schneller als in Gegenwart oxidierter HA, was darauf hindeutet, dass aufgrund ihrer hoheren Bindungskapazitat reduzierte HA das Cr(III) aus der Losung entfernen und somit seine Bioverfugbarkeit einschranken. Die vorgestellten Untersuchungen zeigen am Beispiel von Huminsauren, dass die mikrobielle Veranderung des Redox-Zustandes bei Huminstoffen zu Anderungen von Morphologie und Bindungsvermogen gegenuber Kohlenwasserstoffen und Schwermetallen fuhren kann, die fur Transport, Festlegung und vor allem die Bioverfugbarkeit in der Umwelt von Wichtigkeit sind.

Morphological quantification of hierarchical geomaterials by X-ray nano-CT bridges the gap from nano to micro length scales

Abstract Morphological quantification of the complex structure of hierarchical geomaterials is of great relevance for Earth science and environmental engineering, among others. To date, methods that quantify the 3D morphology on length scales ranging from a few tens of nanometers to several hundred nanometers have had limited success. We demonstrate, for the first time, that it is possible to go beyond visualization and to extract quantitative morphological information from X-ray images in the aforementioned length scales. As examples, two different hierarchical geomaterials exhibiting complex porous structures ranging from nanometer to macroscopic scale are studied: a flocculated clay water suspension and two hydrated cement pastes. We show that from a single projection image it is possible to perform a direct computation of the ultra-small angle-scattering spectra. The predictions matched very well the experimental data obtained by the best ultra-small angle-scattering experimental setups as observed for the cement paste. In this context, we demonstrate that the structure of flocculated clay suspension exhibit two well-distinct regimes of aggregation, a dense mass fractal aggregation at short distance and a more open structure at large distance, which can be generated by a 3D reaction limited cluster-cluster aggregation process. For the first time, a high-resolution 3D image of fibrillar cement paste cluster was obtained from limited angle nanotomography.

X-ray spectromicroscopy in soil and environmental sciences

X-ray microscopy is capable of imaging particles in the nanometer size range directly with sub-micrometer spatial resolution and can be combined with high spectral resolution for spectromicroscopy studies. Two types of microscopes are common in X-ray microscopy: the transmission X-ray microscope and the scanning transmission X-ray microscope; their set-ups are explained in this paper. While the former takes high-resolution images from an object with exposure times of seconds or faster, the latter is very well suited as an analytical instrument for spectromicroscopy. The morphology of clusters or particles from soil and sediment samples has been visualized using a transmission X-ray microscope. Images are shown from a cryo-tomography experiment based on X-ray microscopy images to obtain information about the three-dimensional structure of clusters of humic substances. The analysis of a stack of images taken with a scanning transmission X-ray microscope to combine morphology and chemistry within a soil sample is shown. X-ray fluorescence is a method ideally applicable to the study of elemental distributions and binding states of elements even on a trace level using X-ray energies above 1 keV.

Thermally driven shape instabilities of Nb/Cu multilayer structures: instability of Nb/Cu multilayers

The disintegration of Nb layers in Nb/Cu multilayers during heat treatments was investigated by means of X-ray diffraction (XRD), transmission electron microscopy (TEM), and X-ray microscopy (XRM). Spherically shaped Nb particles were observed after a heat treatment at 870 K for 3 h. The growth velocity of the Nb particles depends strongly on the initial interface roughness and the Nb layer thickness. The XRM investigations indicate a process of self-assembly, leading to a non-statistical distribution of the particles. Measurements of the superconducting properties of both annealed and non-annealed samples, confirm the microstructural observations.

Control of sulfidogenesis through bio‐oxidation of H2S coupled to (per)chlorate reduction

We investigated H2S attenuation by dissimilatory perchlorate-reducing bacteria (DPRB). All DPRB tested oxidized H2S coupled to (per)chlorate reduction without sustaining growth. H2S was preferentially utilized over organic electron donors resulting in an enriched (34S)-elemental sulfur product. Electron microscopy revealed elemental sulfur production in the cytoplasm and on the cell surface of the DPRB Azospira suillum. Based on our results, we propose a novel hybrid enzymatic-abiotic mechanism for H2S oxidation similar to that recently proposed for nitrate-dependent Fe(II) oxidation. The results of this study have implications for the control of biosouring and biocorrosion in a range of industrial environments.

X-ray spectromicroscopy with the scanning transmission X-ray microscope at BESSY II

Using the scanning transmission X-ray microscope at BESSY II, colloidal structures from a Chernozem soil have been studied with a spatial resolution around 60 nm and a spectral resolution of 1,700 at the K-absorption edge of carbon. Elemental mapping has been used to determine the distribution of organic matter within the colloidal structures. Spectra have been extracted from image stacks to obtain information about the chemical state. For the analysis of the latter, principal component analysis and cluster analysis have been applied. It was possible, for example, to discriminate clay particles against organic components.

Diffraction optics for X-ray imaging

Diffraction optics for X-ray imaging are being used, for example, for X-ray microscopy experiments. In this paper the fabrication of high resolution zone plates and condenser zone plates is discussed. The fabrication techniques described include electron beam lithography, UV laser lithography, and pattern transfer by reactive ion etching. Zone plates with outermost zone widths down to 19 nm have been built.

Stereo soft X‐ray microscopy and elemental mapping of haematite and clay suspensions

The combination of high‐resolution chemically sensitive soft X‐ray microscopy with stereo imaging and processing techniques presented here forms a novel tool for the investigation of aqueous colloidal systems. Information about the spatial distribution within the sample is provided with small calculation effort processing just a pair of stereo micrographs. Thus, the extension towards investigation of dynamical behaviour is possible on the part of the experiment as well as of the processing.