Visualising Fe speciation diversity in ocean particulate samples by micro X-ray absorption near-edge spectroscopy

This paper is not subject to U.S. copyright. The definitive version was published in Environmental Chemistry 11 (2014): 10-17, doi:10.1071/EN13075.It is a well known truism that natural materials are inhomogeneous, so analysing them on a point-by-point basis can generate a large volume of data, from which it becomes challenging to extract understanding. In this paper, we show an example in which particles taken from the ocean in two different regions (the Western Subarctic Pacific and the Australian sector of the Southern Ocean, south of Tasmania) are studied by Fe K-edge micro X-ray absorption near-edge spectroscopy (μXANES). The resulting set of data consists of 209 spectra from the Western Subarctic Pacific and 126 from the Southern Ocean. We show the use of principal components analysis with an interactive projection visualisation tool to reduce the complexity of the data to something manageable. The Western Subarctic Pacific particles were grouped into four main populations, each of which was characterised by spectra consistent with mixtures of 1–3 minerals: (1) Fe3+ oxyhydroxides + Fe3+ clays + Fe2+ phyllosilicates, (2) Fe3+ clays, (3) mixed-valence phyllosilicates and (4) magnetite + Fe3+ clays + Fe2+ silicates, listed in order of abundance. The Southern Ocean particles break into three clusters: (1) Fe3+-bearing clays + Fe3+ oxyhydroxides, (2) Fe2+ silicates + Fe3+ oxyhydroxides and (3) Fe3+ oxides + Fe3+-bearing clays + Fe2+ silicates, in abundance order. Although there was some overlap between the two regions, this analysis shows that the particulate Fe mineral assemblage is distinct between the Western Subarctic Pacific and the Southern Ocean, with potential implications for the bioavailability of particulate Fe in these two iron-limited regions. We then discuss possible advances in the methods, including automatic methods for characterising the structure of the data.The operations of the Advanced Light Source at Lawrence Berkeley National Laboratory are supported by the Director, Office of Science, Office of Basic Energy Sciences, US Department of Energy under contract number DE-AC02-05CH11231. Collection of samples for the VERTIGO project was supported by the US National Science Foundation Program in Chemical Oceanography to Ken Buesseler and the US Department of Energy, Office of Science, Biological and Environmental Research Program to Jim Bishop. The SAZ-SENSE project was supported by the Australian Government Cooperative Research Centres Programme. Collection of spectroscopic data by PJL was supported through the WHOI Postdoctoral Scholar Program, WHOI Independent Study Award and NSF Chemical Oceanography

Analyzer Free Linear Dichroic Ptychography

Linear-dichroism is an important tool to characterize the transmission matrix and determine the crystal or orbital orientation in a material. In order to gain high resolution mapping of the transmission properties of such materials, we introduce the linear-dichroism scattering model in ptychographic imaging, and then develop an efficient two-stage reconstruction algorithm. Using proposed algorithm, the dichroic transmission matrix without an analyzer can be recovered by using ptychography measurements with as few as three different polarization angles, with the help of an empty region to remove phase ambiguities.Comment: 12 pages, 7 figure

Phase imaging and the lever-sample tilt angle in dynamic atomic force microscopy

The phase shift in amplitude-controlled dynamic atomic force microscopy (AFM) is shown to depend on the cantilever-sample tilt angle. For a silicon sample and tip the phase shift changes by nearly 15º for a change in tilt angle of 15º. This contribution to the phase results from the oscillating tip\u27s motion parallel to the surface, which contributes to the overall energy dissipation. It occurs even when the measurements are carried out in the attractive regime. An off-axis dynamic AFM model incorporating van der Waals attraction and a thin viscous damping layer near the surface successfully describes the observed phase shifts. This effect must be considered to interpret phase images quantitatively. © 2004 American Institute of Physics

Localization and speciation of Zn in mycorrihizd roots by μSXRF and μEXAFS.

Mycorrhizae are symbiotic associations between soil fungi and plant roots, which enhance mineral nutrition for the plant, and might play an important role in metals acquisition and accumulation. The processes allowing metals mobilization in the soil, absorption by the root and/or the fungus, transfer or bioaccumulation are still poorly understood. However, the properties of mycorrhizal fungi could be used for phytoremediation, a soft technique using plants for the clean-up of metal polluted soils. In this work, mycorrhized roots of tomato plants grown in a Zn-contaminated soil were investigated. The distribution of metals and the speciation of Zn were studied at the micron scale using micro synchrotron-based X-ray fluorescence (μSXRF) and micro X-ray absorption spectroscopy (μEXAFS). Zn associated to the root was Zn malate and/or Zn citrate, and Zn associated to the fungus was Zn phyllosilicate. This study illustrates the great potential of X-ray microbeams for the study of biological samples containing various amounts of metals

Material Anisotropy Revealed by Phase Contrast in Intermittent Contact Atomic Force Microscopy

Phase contrast in intermittent-contact atomic force microscopy (AFM) reveals in-plane structural and mechanical properties of polymer monolayers. This is surprising, because measurements of nanoscale in-plane properties typically require contact mode microscopies. Our measurements are possible because the tip oscillates not just perpendicular but also parallel to the sample surface along the long axis of the cantilever. This lateral tip displacement is virtually universal in AFM, implying that any oscillating-tip AFM technique is sensitive to in-plane material properties

Selenium Biotransformations in an Engineered Aquatic Ecosystem for Bioremediation of Agricultural Wastewater via Brine Shrimp Production

An engineered aquatic ecosystem was specifically designed to bioremediate selenium (Se), occurring as oxidized inorganic selenate from hypersalinized agricultural drainage water while producing brine shrimp enriched in organic Se and omega-3 and omega-6 fatty acids for use in value added nutraceutical food supplements. Selenate was successfully bioremediated by microalgal metabolism into organic Se (seleno-amino acids) and partially removed via gaseous volatile Se formation. Furthermore, filterfeeding brine shrimp that accumulated this organic Se were removed by net harvest. Thriving in this engineered pond system, brine shrimp (Artemia franciscana Kellogg) and brine fly (Ephydridae sp.) have major ecological relevance as important food sources for large populations of waterfowl, breeding, and migratory shore birds. This aquatic ecosystem was an ideal model for study because it mimics trophic interactions in a Se polluted wetland. Inorganic selenate in drainage water was metabolized differently in microalgae, bacteria, and diatoms where it was accumulated and reduced into various inorganic forms (selenite, selenide, or elemental Se) or partially incorporated into organic Se mainly as selenomethionine. Brine shrimp and brine fly larva then bioaccumulated Se from ingesting aquatic microorganisms and further metabolized Se predominately into organic Se forms. Importantly, adult brine flies, which hatched from aquatic larva, bioaccumulated the highest Se concentrations of all organisms tested

Formation of Zn–Ca phyllomanganate nanoparticles in grass roots

International audienceIt is now well established that a number of terrestrial and aquatic microorganisms have the capacity to oxidize and precipitate Mn as phyllomanganate. However, this biomineralization has never been shown to occur in plant tissues, nor has the structure of a natural Mn(IV) biooxide been characterized in detail. We show that the graminaceous plant Festuca rubra (red fescue) produces a Zn-rich phyllomanganate with constant Zn:Mn and Ca:Mn atomic ratios (0.46 and 0.38, respectively) when grown on a contaminated sediment. This new phase is so far the Zn-richest manganate known to form in nature (chalcophanite has a Zn:Mn ratio of 0.33) and has no synthetic equivalent. Visual examination of root fragments under a microscope shows black precipitates about ten to several tens of microns in size, and their imaging with backscattered and secondary electrons demonstrates that they are located in the root epidermis. In situ measurements by Mn and Zn K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy and X-ray diffraction (XRD) with a micro-focused beam can be quantitatively described by a single-phase model consisting of Mn(IV) octahedral layers with 22% vacant sites capped with tetrahedral and octahedral Zn in proportions of 3:1. The layer charge deficit is also partly balanced by interlayer Mn and Ca. Diffracting crystallites have a domain radius of 33 Å in the ab plane and contain only 1.2 layers (not, vert, similar8.6 Å) on average. Since this biogenic Mn oxide consists mostly of isolated layers, basal 00l reflections are essentially absent despite its lamellar structure. Individual Mn layers are probably held together in the Mn–Zn precipitates by stabilizing organic molecules. Zinc biomineralization by plants likely is a defense mechanism against toxicity induced by excess concentrations of this metal in the rhizosphere