Physica Scripta. Vol. T115, 888–890, 2005 EXAFS, XANES and In-Situ SR-XRD Characterization of Biogenic Manganese Oxides Produced in SeaWater J. R. Bargar 1 , S. M. Webb 1* and B. M. Tebo 2 1 Stanford Synchrotron Radiation Laboratory, Menlo Park, CA, 94025, USA 2 Scripps Institute of Oceanography, University of San Diego, La Jolla, CA 92093, USA Received June 26, 2003; accepted in revised form November 4, 2003 pacs number: 61.10.−i Abstract Natural manganese oxide nanoparticles and grain coatings are ubiquitous in the environment and profoundly impact the quality of sediments via their ability to degrade and sequester contaminants. These oxides are believed to form dominantly via oxidation of Mn(II) by marine and freshwater bacteria and have extremely high sorptive capacities for heavy metals. We have used XANES, EXAFS, and synchrotron (SR)-XRD techniques to study biogenic manganese oxides produced by spores of the marine Bacillus sp., strain SG-1 in sea water as a function of reaction time under fully in-situ conditions. The primary biogenic product is a nanocrystalline solid with an oxidation state and layered phyllomanganate local structure similar to that in -MnO 2 . XRD data show the biooxides to have a phyllomanganate 10 Å basal plane spacing, suggesting the interlayer is hydrated and contains calcium. Fits to EXAFS spectra suggest the octahedral layers of the biooxides to be relatively flat (out-of-plane bend <10 ◦ ) and to have relatively low octahedral layer Mn site vacancies (12 to 14%). These results suggest that aqueous Ca 2+ is inserted into the biogenic oxide structure after completion of the enzymatic oxidation process. The biooxides observed in this study may be the most abundant manganese oxide phase suspended in the oxic and sub-oxic zones of the oceanic water column. 1. Introduction Bacterially generated Mn oxides are ubiquitous in natural waters as reactive nanoparticles and grain coatings and have profound impacts on contaminant degradation, nutrient cycling, and carbon cycling in the environment. They have high sorptive capacities for metal ions, can degrade toxic organic contaminants, including aromatic hydrocarbons, and oxidize a variety of inorganics, e.g., Cr(III), Co(II), and hydrogen sulfide. Sequestration of dissolved heavy metals during Mn oxide biogenesis is believed to be a key mechanism for attenuation of contaminants in polluted waters. The most important pathway for environmental Mn oxidation is believed to be catalytic oxidation of Mn(II) by freshwater and marine bacteria [1–3]. Understanding the chemical mechanism(s) by which this process occurs is therefore crucial to understanding the cycling of essential and toxic trace constituents in the environment. In spite of their importance, relatively little is known about the mechanisms and products of bacterial Mn oxide biogenesis. Our overarching goals are to define the mechanisms of bacterial Mn(II) oxidation and the structures, compositions, and reactivity of the resulting biooxides. In addition, manganese oxides are important reactive components of the oceanic water column, and we seek their identities and properties. We have previously investigated the products of bacterial Mn(II) oxidation in 50 mM NaCl solutions [4–6]. This work indicated that the primary biogenic oxidation product is a poorly crystalline phyllomanganate oxide with local structure and oxidation state * e-mail: bargar@ssrl.slac.stanford.edu similar to -MnO 2 . We extend this work here to investigate how these reactions proceed in sea water (SW), which contains relatively high concentrations of dissolved magnesium (60 mM) and calcium (10 mM). Both solutes can react with manganese to form tunnel-structured manganese oxides such as todorokite. We seek to investigate whether such phases are created during bacterial Mn(II) oxidation, and to discern the implications for bacterial Mn(II) oxidation mechanisms. 2. Methods SG-1 spores were incubated in 10 M Mn(II) (added as MnCl 2 ·4H 2 O) in filtered (0.2 m pore diameter) sea water (SW) obtained from the Scripps Pier. Experiments were started by adding approximately 1.3 × 10 10 spores to each incubation vessel resulting in 2.2 × 10 6 spores · mL −1 . The sampling times for the experiment ranged from 6 to 80 hours. For each time point the entire sample was harvested by settling and centrifugation (4 ◦ C). Samples were stored at −20 ◦ C in about 10 mL of their original medium until analysis. Mn K-edge XAS spectra were collected at room temperature from wet homogeneous spore-biooxide samples in rigid thermoplastic sample holders at SSRL beamline 4-3, which was equipped with a Si(220) monochromator and harmonic rejection mirror set at a 9keV cut-off energy. Data were collected in transmission geometry to eliminate spectral distortion from self absorption, which is unavoidable and substantial in fluorescence data. Spectra were background subtracted and splined using the SIXPack software [7]. Linear combination fitting and EXAFS fitting were also performed with SIXPack. Energy was allowed to float by up to 0.15 eV during fits. In comparison, the energy difference between birnessite and -MnO 2 is about 0.4eV. Model compound spectra were fit as unknowns, the results of which were fit with a linear regression to obtain the following:1-sigma error estimates: +/−1.7% for Mn(II), +/−2.6% for Mn(III) oxides, and +/− 2.9% for Mn(IV) oxides. These estimates are substantially larger than the ESDs obtained from individual fits (which typically had values of ∼0.5%). Phase and amplitude files for the EXAFS fitting were created with FEFF7 [8]. Mn EXAFS were fit using a model based on a layered phyllomanganate structure [6], which follows the concept used previously by Ressler et al. [9] and explicitly accounts for splitting of the Mn-O and Mn-Mn distances in the structure due to Jahn-Teller distortions, angular deviations from planar sheets (particularly important with Mn-Mn multiple scattering), aqueous and spore- bound Mn(II), Mn bound to the surfaces of Mn oxides, and vacancies present in the manganese octahedral layer. This model has been tested on relevant model spectra (birnessite, -MnO 2 , and Physica Scripta T115 C  Physica Scripta 2005