Microbial anaerobic Fe(II) oxidation at neutral pH produces poorly soluble Fe(III) which is expected to bind to cell surfaces causing cell encrustation and potentially impeding cell metabolism. The challenge for Fe(II)-oxidizing prokaryotes therefore is to avoid encrustation with Fe(III). Using different microscopic techniques we tracked Fe(III) minerals at the cell surface and within cells of phylogenetically distinct phototrophic and nitrate-reducing Fe(II)-oxidizing bacteria. While some strains successfully prevented encrustation others precipitated Fe(III) minerals at the cell surface and in the periplasm. Our results indicate differences in the cellular mechanisms of Fe(II) oxidation, transport of Fe(II)/Fe(III) ions, and Fe(III) mineral precipitation.

Scanning Electron Microscopy (SEM) has long been the standard in imaging the sub-micrometer surface ultrastructure of both hard and soft materials. In the case of biological samples, it has provided great insights into their physical architecture. However, three of the fundamental challenges in the SEM imaging of soft materials are that of limited imaging resolution at high magnification, charging caused by the insulating properties of most biological samples and the loss of subtle surface features by heavy metal coating. These challenges have recently been overcome with the development of the Helium Ion Microscope (HIM), which boasts advances in charge reduction, minimized sample damage, high surface contrast without the need for metal coating, increased depth of field, and 5 angstrom imaging resolution. We demonstrate the advantages of HIM for imaging biological surfaces as well as compare and contrast the effects of sample preparation techniques and their consequences on sub-nanometer ultrastructure.

The formation of cell-(iron)mineral aggregates as a consequence of bacterial iron oxidation is an environmentally widespread process with a number of implications for processes such as sorption and coprecipitation of contaminants and nutrients. Whereas the overall appearance of such aggregates is easily accessible using 2-D microscopy techniques, the 3-D and internal structure remain obscure. In this study, we examined the 3-D structure of cell-(iron)mineral aggregates formed during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1 using a combination of advanced 3-D microscopy techniques. We obtained 3-D structural and chemical information on different cellular encrustation patterns at high spatial resolution (4-200 nm, depending on the method): more specifically, (1) cells free of iron minerals, (2) periplasm filled with iron minerals, (3) spike- or platelet-shaped iron mineral structures, (4) bulky structures on the cell surface, (5) extracellular iron mineral shell structures, (6) cells with iron mineral filled cytoplasm, and (7) agglomerations of extracellular globular structures. In addition to structural information, chemical nanotomography suggests a dominant role of extracellular polymeric substances (EPS) in controlling the formation of cell-(iron)mineral aggregates. Furthermore, samples in their hydrated state showed cell-(iron)mineral aggregates in pristine conditions free of preparation (i.e., drying/dehydration) artifacts. All these results were obtained using 3-D microscopy techniques such as focused ion beam (FIB)/scanning electron microscopy (SEM) tomography, transmission electron microscopy (TEM) tomography, scanning transmission (soft) X-ray microscopy (STXM) tomography, and confocal laser scanning microscopy (CLSM). It turned out that, due to the various different contrast mechanisms of the individual approaches, and due to the required sample preparation steps, only the combination of these techniques was able to provide a comprehensive understanding of structure and composition of the various Fe-precipitates and their association with bacterial cells and EPS.

By scanning with a 30 keV focused He ion beam (He-FIB) across YBa2Cu3O7 (YBCO) thin film microbridges, we create Josephson barriers with critical current density jc adjustable by irradiation dose D. The dependence jc(D) yields an exponential decay. At 4.2 K, a transition from flux-flow to Josephson behavior occurs when jc decreases below ≈ 2 MA/cm 2 . The Josephson junctions exhibit current-voltage characteristics (IVCs) that are well described by the resistively and capacitively shunted junction model, without excess current for characteristic voltages Vc 1 mV. Devices on MgO and LSAT substrates show non-hysteretic IVCs, while devices on SrTiO3 show a small hysteresis. For all junctions an approximate scaling Vc ∝ j 1/2 c is found. He-FIB irradiation with high dose produces barriers with jc = 0 and high resistances of 10 kΩ . . . 1 GΩ. This provides the possibility to write highly resistive walls or areas into YBCO using a He-FIB. Transmission electron microscopy reveals an amorphous phase within the walls, whereas for lower doses the YBCO stays crystalline. We have also "drawn" superconducting quantum interference devices (SQUIDs) by using a He-FIB for definition of the SQUID hole and the junctions. The SQUIDs show high performance, with flux noise < 500 nΦ0/Hz 1/2 in the thermal white noise limit for a device with 19 pH inductance.

The structure of brine films in grain boundaries of halite has been the subject of much controversy over the past 20 years; although a number of innovative methods have been developed to study these structures, much is still unknown and fundamental information is missing. In this study, we investigated different methods of plungefreezing to vitrify the brine fill of grain boundaries for natural salt polycrystal. This was followed by a preliminary study of the 3D morphology of a vitrified grain boundary in a natural rock salt sample with a focused ion beam (FIB) excavation system. We have shown that brine-filled grain boundaries in rock salt can be efficiently well frozen when dimensions are less than about 1 mm. Coupled with an ion beam tool, cryo-SEM allows 3D observation of the well-frozen grain boundaries in large volumes and high resolution. Initial results of brine-filled natural halite grain boundaries show non-faceted crystal-brine interfaces and unexpectedly low dihedral angles at room temperature and pressure.