Skip to main content Accessibility help
×
Hostname: page-component-76fb5796d-x4r87 Total loading time: 0 Render date: 2024-04-25T13:14:11.629Z Has data issue: false hasContentIssue false

Part IV - Spectroscopy

Published online by Cambridge University Press:  06 July 2019

Janice P. L. Kenney
Affiliation:
MacEwan University, Edmonton
Harish Veeramani
Affiliation:
Carleton University, Ottawa
Daniel S. Alessi
Affiliation:
University of Alberta
Get access

Summary

X-ray diffraction techniques provide information regarding the formation and alteration of mineral phases that is critical for assessing geomicrobial processes. Of particular interest is the use of powder X-ray diffraction (pXRD) to identify unknown solid-state materials, determine the particle size of nanoscale mineral phases, and refine structure characteristics, such as unit cell parameters and atomic positions. The goal of this chapter is to provide practical knowledge for the successful preparation of solid mineral samples, optimal data collection strategies, and analysis of diffractograms collected from pXRD experiments. Specific uses of pXRD techniques in geomicrobiology are discussed to demonstrate the importance of diffraction in advancing our understanding of microbial communities in geologic systems.

Type
Chapter
Information
Analytical Geomicrobiology
A Handbook of Instrumental Techniques
, pp. 213 - 338
Publisher: Cambridge University Press
Print publication year: 2019

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

9.6 References

Achal, V, Pan, X, Fu, Q and Zhang, D 2012, ‘Biomineralization based remediation of As(III) contaminated soil by Sporosarcina ginsengisoliJournal of Hazardous Materials, vol. 201–202, pp. 178184.Google Scholar
Alam, S, Patel, S and Bansal, AK 2010, ‘Effect of sample preparation method on quantification of polymorphs using PXRDPharmaceutical Development and Technology, vol. 15, no. 5, pp. 452459.Google Scholar
Altheimer, BD, Pagola, S, Zeller, M and Mehta, MA 2013, ‘Mechanochemical conversions between crystalline polymorphs of a complex organic solid’ Crystal Growth & Design, vol. 13, no. 8, pp. 34473453.Google Scholar
Baskar, S, Baskar, R, and Routh, J 2014, ‘Speleothems from Sahastradhara Caves in Siwalik Himalaya, India: Possible biogenic inputsGeomicrobiology Journal, vol. 31, no. 8, pp. 664681.CrossRefGoogle Scholar
Beazley, MJ, Martinez, RJ, Sobecky, PA, Webb, SM and Taillefert, M 2009, ‘Uranium biomineralization as a result of bacterial phosphatase activity: Insights from bacterial isolates from a contaminated subsurfaceGeomicrobiology Journal, vol. 26, pp. 431441.CrossRefGoogle Scholar
Bell, ATM, Coker, VS, Pearce, CI, et al. 2007, ‘Time-resolved synchrotron X-ray powder diffraction study of biogenic nanomagnetite’ Zeitschrift fuer Kristallographie. Supplement Issues, vol. 26, no. 2, pp. 423428.CrossRefGoogle Scholar
Benzerara, K, Morin, G, Yoon, TH, et al. 2008, ‘Nanoscale study of As biomineralization in an acid mine drainage systemGeochimica et Cosmochimica Acta, vol. 72, no. 16, pp. 39493963.CrossRefGoogle Scholar
Bertel, D, Peck, J, Quick, JQ and Senko, JM 2012, ‘Iron transformations induced by an acid-tolerant Desulfosporosinus speciesApplied and Environmental Microbiology, vol. 78, pp. 8188.Google Scholar
Bish, DL and Chipera, SJ 1989, ‘Comparison of a solid state Si detector to a conventional scintillation detector-monochromator system in X-ray powder diffraction analysisPowder Diffraction, vol. 4, pp. 137143.Google Scholar
Bish, DL and Post, JE (eds.) 1989, Modern Powder Diffraction, The Mineralogical Society of America, Washington, DC.Google Scholar
Bob He, B, Preckwinkel, U and Smith, KL 2000, ‘Fundamentals of two-dimensional X-ray diffraction (XRD)2Advances in X-ray Analysis, vol. 43, pp. 273280.Google Scholar
Brantner, J, Haake, ZJ, Burwick, JE, et al. 2014, ‘Depth-dependent geochemical and microbiological gradients in Fe(III) deposits resulting from coal mine-derived acid mine drainage’ Frontiers in Microbiology, vol. 5, pp. 115.Google Scholar
Brayner, R, Yepremain, C, Djediat, C, et al. 2009, ‘Photosynthetic microorganism-mediated synthesis of akaganeite (β-FeOOH) nanorodsLangmuir, vol. 25, no. 17, pp. 1006210067.Google Scholar
Coelho, A 2007, Topas Academic V4.1, Coelho Software, Brisbane.Google Scholar
Cosmidis, J, Benzerara, K, Morin, G, et al. 2014, ‘ Biomineralization of iron-phosphates in the water column of Lake Pavin (Massif Central, France)’ Geochimica et Cosmochimica Acta, vol. 126, pp. 7896.CrossRefGoogle Scholar
Das, R, Ali, ME and Abd Hamid, SB 2014, ‘Current applications of X-ray powder diffraction – a reviewReviews on Advanced Materials Science, vol. 38, pp. 95109.Google Scholar
Dick, GJ, Clement, BG, Webb, SM, et al. 2009, ‘Enzymatic microbial Mn(II) oxidation and Mn biooxide production in the Guaymas Basin deep-sea hydrothermal plume’ Geochimica et Cosmochimica Acta, vol. 73, no. 21, pp. 65176530.CrossRefGoogle Scholar
Dinnebier, RE and Billinge, SJL (eds.) 2008, Powder Diffraction Theory and Practice, Royal Society of Chemistry, Cambridge.Google Scholar
Downs, RT and Hall-Wallace, M 2003, ‘The American Mineralogist crystal structure databaseAmerican Mineralogist, vol. 88, no. 1, pp. 247250.Google Scholar
Fandeur, D, Juillot, F, Morin, G, et al. 2009, ‘XANES evidence for oxidation of Cr(III) to Cr(VI) by Mn-oxides in a lateritic regolith developed on serpentinized ultramafic rocks of New Caledonia’ Environmental Science & Technology, vol. 43, no. 19, pp. 73847390.Google Scholar
Fischer, A, Schmitz, M, Aichmayer, B, Fratzl, P and Faivre, D 2011, ‘Structural purity of magnetite nanoparticles in magnetotactic bacteriaJournal of the Royal Society Interface, vol. 8, pp. 10111018.CrossRefGoogle ScholarPubMed
Frierdich, AJ, Hasenmueller, EA and Catalano, JG 2011, ‘Composition and structure of nanocrystalline Fe and Mn oxide cave deposits: Implications for trace element mobility in karst systemsChemical Geology, vol. 284, no. 1, pp. 8296.Google Scholar
Ghashghaei, S and Emtiazi, G 2013, ‘Production of calcite nanocrystal by a urease-positive strain of Enterobacter ludwigii and study of its structure by SEM’ Current Microbiology, vol. 67, no. 4, pp. 406413.CrossRefGoogle ScholarPubMed
ICDD (2012), PDF-4+ 2012(Database), edited by Dr. Soorya Kabekkodu, International Centre for Diffraction Data, Newtown Square, PA.Google Scholar
Jackson, ML 1969 Soil Chemical Analysis – Advanced Course, Self-published, Madison.Google Scholar
Klein, C and Dutrow, B 2007 Manual of Mineral Science, 23rd edn., John Wiley & Sons, Inc., Hoboken.Google Scholar
Kukkadapu, RK, Zachara, JM, Smith, SC, Fredrickson, JK and Liu, CX, 2001, ‘Dissimilatory bacterial reduction of Al-substituted goethite in subsurface sediments’ Geochimica et Cosmochimica Acta, vol. 65, pp. 29132924.Google Scholar
Langsford, JI and Wilson, AJC 1978, ‘Scherrer after sixty years: A survey and some new results in the determination of crystallite size’ Journal of Applied Crystallography, vol. 11, pp. 102133.CrossRefGoogle Scholar
Larson, AC and Von Dreele, VB 2004, ‘General Structure Analysis System (GSAS)’ Los Alamos National Laboratory Report LAUR 86–748.Google Scholar
Lutterotti, L, Matthies, S and Wenk, HR 1999, ‘MAUD: A friendly Java program for material analysis using diffractionIUCr: Newsletter of the CPD, vol. 21, pp. 1415.Google Scholar
Maillot, F, Morin, G, Juillot, F, et al. 2013, ‘Structure and reactivity of As(III)- and As(V)-rich schwertmannites and amorphous ferric arsenate sulfate from the Carnoulès Acid Mine Drainage, France: Comparison with biotic and abiotic model compounds and implications for As remediationGeochimica et Cosmochimica Acta, vol. 104, pp. 310329.CrossRefGoogle Scholar
Materials Data 2002, Jade, Materials Data, Inc., Livermore, CA.Google Scholar
Monshi, A, Foroughi, MR and Monshi, MR 2012, ‘Modified Scherrer equation to estimate more accurately nano-crystallite size using XRD’ World Journal of Nano Science and Engineering, vol. 2, no. 3, pp. 154160.Google Scholar
Nesse, WD 2012, Introduction to Mineralogy, Oxford University Press, Oxford.Google Scholar
Obst, M, Dynes, JJ, Lawrence, JR, et al. 2009, ‘Precipitation of amorphous CaCO3 (aragonite-like) by cyanobacteria: A STXM study of the influence of EPS on the nucleation processGeochimica et Cosmochimica Acta, vol. 73, no. 14, pp. 41804198.CrossRefGoogle Scholar
Ona-Nguema, G, Carteret, C, Benali, O, et al. 2004, ‘Competitive formation of hydroxycarbonate green rust I vs hydroxysulphate green rust II in Shewanella putrefaciens cultures’ Geomicrobiology Journal, vol. 21, pp. 7990.CrossRefGoogle Scholar
O’Reilly, SE and Hochella, MF 2003, ‘Lead sorption efficiencies of natural and synthetic Mn and Fe-oxides’ Geochimica et Cosmochimica Acta, vol. 67, no. 23, pp. 44714487.Google Scholar
Pecharsky, VK and Zavalij, PY (eds.) 2005, Fundamentals of Powder Diffraction and Structural Characterization of Materials, Springer Science and Business Media, Inc., New York.Google Scholar
Peng, X, Chen, S and Xu, H 2013, ‘Formation of biogenic sheath-like Fe oxyhydroxides in a near-neutral pH hot spring: Implications for the origin of microfossils in high-temperature, Fe-rich environmentsJournal of Geophysical Research: Biogeosciences, vol. 118, pp. 13971413.CrossRefGoogle Scholar
Pesenti, H, Leoni, M, and Scardi, P 2008, ‘XRD line profile analysis of calcite powders produced by high energy millingZeitschrift fur Kristallographie, vol. 27, no. 27, pp. 143150.Google Scholar
Piepenbrock, A, Dippon, U, Porsch, K, Appel, E and Kappler, A 2011, ‘Dependence of microbial magnetite formation on humic substance and ferrihydrite concentrationsGeochimica et Cosmochimica Acta, vol. 75, pp. 68446858.Google Scholar
Pokroy, B, Quintana, JP, Caspi, EAN, Berner, A and Zolotoyabko, E 2004, ‘Anisotropic lattice distortions in biogenic aragoniteNature Materials, vol. 3, no. 12, pp. 900902.Google Scholar
Pokroy, B, Fitch, AN, Marin, F, Kapon, M, Adir, N and Zolotoyabko, E 2006, ‘Anisotropic lattice distortions in biogenic calcite induced by intra-crystalline organic moleculesJournal of Structural Biology, vol. 155, pp. 96103.Google Scholar
Roden, EE, Leonardo, MR, and Ferris, FG 2002, ‘Immobilization of strontium during iron biomineralization coupled to dissimilatory hydrous ferric oxide reductionGeochimica et Cosmochimica Acta. vol. 66, pp. 28232839.Google Scholar
Rodriguez-Carvajal, J 2001, ‘Recent developments of the program FULLPROFCommission on Powder Diffraction (IUCr) Newsletter, vol. 26, pp. 1219.Google Scholar
Ronholm, J, Schumann, D, Sapers, HM, et al. 2014, ‘A mineralogical characterization of biogenic calcium carbonates precipitated by heterotrophic bacteria isolated from cryophilic polar regionsGeobiology, vol. 12, no. 6, pp. 542556.Google Scholar
Rudolf, PR and Landes, BG 1994, ‘Two-dimensional X-ray diffraction and scattering of microcrystalline and polymeric materialsSpectroscopy, vol. 9, no. 6, pp. 2233.Google Scholar
Scherrer, P 1918, ‘Bestimmung der Grosse und der Inneren Struktur von Kolloidteilchen Mittels RontgenstrahlenNachrichten von der Gesellschaft der Wissenschaften, vol. 26, pp. 98100.Google Scholar
Sinha, A, Singh, A, Kumar, S, Khare, SK and Ramanan, A 2014, ‘Microbial mineralization of struvite: A promising process to overcome phosphate sequestering crisisWater Research, vol. 54, pp. 3343.Google Scholar
Sulyanov, SN, Popov, AN and Kheiker, DM 1994, ‘Using a two-dimensional detector for X-ray powder diffractometryJournal of Applied Crystallography, vol. 27, pp. 934942.Google Scholar
Tazaki, K, Rafiqul, IABM, Nagai, K, and Kurihara, T, 2003, ‘FeAs2 biomineralization on encrusted bacteria in hot springs: An ecological role of symbiotic bacteriaCanadian Journal of Earth Sciences, vol. 40, no. 11, pp. 17251738.Google Scholar
Thorpe, CL, Boothman, C, Lloyd, JR, et al. 2014, ‘The interactions of strontium and technetium with Fe(II) bearing biominerals: Implications for bioremediation of radioactively contaminated landApplied Geochemistry, vol. 40, pp. 135143.Google Scholar
Till, JL, Guyodo, Y, Lagroix, F, Ona-Guema, G, and Brest, J 2014, ‘Magnetic comparison of abiogenic and biogenic alteration products of lepidocrociteEarth and Planetary Science Letters, vol. 395, pp. 149158.Google Scholar
Toner, BM, Santelli, CM, Marcus, MA, et al. 2009, ‘Biogenic iron oxyhydroxide formation at mid-ocean ridge hydrothermal vents: Juan de Fuca Ridge’ Geochimica et Cosmochimica Acta, vol. 73, no. 2, pp. 388403.CrossRefGoogle Scholar
Verman, B and Kim, B 2004, ‘Analytical comparison of parallel beam and Bragg-Brentano diffractometer performances’ Materials Science Forum, vol. 443–444, pp. 167170.Google Scholar
Villalobos, M, Lanson, B, Manceau, A, Toner, B and Sposito, G 2006, ‘Structural model for the biogenic Mn oxide produced by Pseudomonas putidaAmerican Mineralogist, vol. 91, no. 4, pp. 489502.Google Scholar
Warren, LA, Maurice, PA, Parmar, N and Ferris, FG 2001, ‘Microbially mediated calcium carbonate precipitation: Implications for interpreting calcite precipitation and for solid-phase capture of inorganic contaminantsGeomicrobiology Journal, vol. 18, no. 1, pp. 93115.Google Scholar
Wenk, HR and Bulakh, A 2004, Minerals: Their Constitution and Origin, Cambridge University Press, Cambridge.Google Scholar
Wu, W, Li, B, Hu, J, et al. 2011, ‘Iron reduction and magnetite biomineralization mediated by a deep-sea iron-reducing bacterium Shewanella piezotolerans WP3’ Journal of Geophysical Research: Biogeosciences, vol. 116, no. G4.Google Scholar
Wyckoff, RWG 1963, Crystal Structures – Volume 1, Interscience Publishers, New York.Google Scholar
Yee, N, Shaw, S, Benning, LG and Nguyen, TH 2006, ‘The rate of ferrihydrite transformation to goethite via the Fe(II) pathway’ American Mineralogist, vol. 91, pp. 9296.Google Scholar
Young, RA (ed.) 2002, The Rietveld Method, Oxford University Press, Oxford.Google Scholar
Zachara, JM, Kukkadapu, RK, Fredrickson, JK, Gorby, YA and Smith, SC 2002, ‘Biomineralization of poorly crystalline Fe(III) oxides by dissimilatory metal reducing bacteria (DMRB)’ Geomicrobiology Journal, vol. 19, pp. 179207.Google Scholar
Zegeye, A, Ona-Nguema, G, Carteret, C, et al. 2005, ‘Formation of hydroxysulphate green rust 2 as a single iron (II-III) mineral in microbial cultureGeomicrobiology Journal, vol. 22, no. 7–8, pp. 389399.CrossRefGoogle Scholar

10.6 References

Bargar, J.R., Reitmeyer, R., Lenhart, J.J., Davis, J.A., 2000a. Characterization of U(VI)-carbonato ternary complexes on hematite: EXAFS and electrophoretic mobility measurements. Geochimica et Cosmochimica Acta, 64(16): 27372749.Google Scholar
Bargar, J.R., Tebo, B.M., Villinski, J.E., 2000b. In situ characterization of Mn(II) oxidation by spores of the marine Bacillus sp strain SG-1. Geochimica et Cosmochimica Acta, 64(16): 27752778.Google Scholar
Bergengren, J., 1920. On spectra of absorption of phosphorus by X-ray. Comptes Rendus Hebdomadaires Des Seances De L’Academie Des Sciences, 171: 624626.Google Scholar
Bernhard, G. et al., 2001. Uranyl(VI) carbonate complex formation: Validation of the Ca2UO2(CO3)(3)(aq.) species. Radiochimica Acta, 89(8): 511518.Google Scholar
Beyenal, H. et al., 2004. Uranium immobilization by sulfate-reducing biofilms. Environmental Science & Technology, 38(7): 20672074.Google Scholar
Booth, C.H., Bridges, F., 2005. Improved self-absorption correction for fluorescence measurements of extended X-ray absorption fine-structure. Physica Scripta, T115: 202204.Google Scholar
Boyanov, M.I. et al., 2011. Solution and microbial controls on the formation of reduced U(IV) species. Environmental Science & Technology, 45(19): 83368344.Google Scholar
Boyanov, M.I. et al., 2003. Adsorption of cadmium to Bacillus subtilis bacterial cell walls: A pH-dependent X-ray absorption fine structure spectroscopy study. Geochimica et Cosmochimica Acta, 67(18): 32993311.Google Scholar
Brinza, L. et al., 2014. Combining mu XANES and mu XRD mapping to analyse the heterogeneity in calcium carbonate granules excreted by the earthworm Lumbricus terrestris. Journal of Synchrotron Radiation, 21: 235241.Google Scholar
Brooks, S.C. et al., 2003. Inhibition of bacterial U(VI) reduction by calcium. Environmental Science & Technology, 37(9): 18501858.CrossRefGoogle ScholarPubMed
Brown, G.E., 1990. Spectroscopic Studies of Chemisorption Reaction Mechanisms at Oxide-Water Interfaces. In: Hochella, M.F., White, A.F. (Eds.), Mineral-Water Interface Geochemistry. Mineralogical Society of America, pp. 309364.CrossRefGoogle Scholar
Buchanan, B.B. et al., 1995. A XANES and EXAFS investigation of the speciation of selenite following bacterial metabolization. Inorganic Chemistry, 34(6): 16171619.Google Scholar
Bunker, G., 2010. Introduction to XAFS: A Practical Guide to X-ray Absorption Fine Structure Spectroscopy. Cambridge University Press, Cambridge.Google Scholar
Bunker, G., Stern, E.A., Blankenship, R.E., Parson, W.W., 1982. An x-ray absorption study of the iron site in bacterial photosynthetic reaction centers. Biophysical Journal, 37(2): 539551.Google Scholar
Carvalho-E-Silva, M.L. et al., 2003. Incorporation of Ni into natural goethite: An investigation by X-ray absorption spectroscopy. American Mineralogist, 88(5–6): 876882.Google Scholar
Catalano, J.G., Brown, G.E., 2005. Uranyl adsorption onto montmorillonite: Evaluation of binding sites and carbonate complexation. Geochimica et Cosmochimica Acta, 69(12): 29953005.Google Scholar
Charlet, L., Manceau, A., 1992. Insitu characterization of heavy-metal surface-reactions – the chromium case. International Journal of Environmental Analytical Chemistry, 46(1–3): 97108.Google Scholar
Charnock, J.M. et al., 2000. Structural investigations of the Cu-A centre of nitrous oxide reductase from Pseudomonas stutzeri by site-directed mutagenesis and X-ray absorption spectroscopy. European Journal of Biochemistry, 267(5): 13681381.Google Scholar
Delaney, J.S., Dyar, M.D., Sutton, S.R., Bajt, S., 1998. Redox ratios with relevant resolution: Solving an old problem by using the synchrotron microXANES probe. Geology, 26(2): 139142.Google Scholar
Denecke, M.A., Rothe, J., Dardenne, K., Lindqvist-Reis, P., 2003. Grazing incidence (GI) XAFS measurements of Hf(IV) and U(VI) sorption onto mineral surfaces. Physical Chemistry Chemical Physics, 5(5): 939946.Google Scholar
Dent, A.J., Ramsay, J.D.F., Swanton, S.W., 1992. An EXAFS study of uranyl-ion in solution and sorbed onto silica and montmorillonite clay colloids. Journal of Colloid and Interface Science, 150(1): 4560.Google Scholar
Eng, P.J., Rivers, M., Yang, B.X., Schildkamp, W., 1995. Micro-focusing 4 KeV to 65 KeV x-rays with bent Kirkpatrick-Baez mirrors. X-Ray Microbeam Technology and Applications, 2516: 4151.Google Scholar
Ertel, T.S., Bertagnolli, H., 1993. EXAFS investigations of air and moisture sensitive liquid compounds – development of an appropriate sample holder with variable sample thickness and temperature control. Nuclear Instruments & Methods in Physics Research Section B-Beam Interactions with Materials and Atoms, 73(2): 199202.Google Scholar
Etschmann, B.E. et al., 2014. Speciation mapping of environmental samples using XANES imaging. Environmental Chemistry, 11(3): 341350.Google Scholar
Fendorf, S., Eick, M.J., Grossl, P., Sparks, D.L., 1997. Arsenate and chromate retention mechanisms on goethite .1. Surface structure. Environmental Science & Technology, 31(2): 315320.Google Scholar
Fletcher, K.E. et al., 2010. U(VI) reduction to mononuclear U(IV) by Desulfitobacterium species. Environmental Science & Technology, 44(12): 47054709.Google Scholar
Foster, A.L., Brown, G.E., Tingle, T.N., Parks, G.A., 1998. Quantitative arsenic speciation in mine tailings using X-ray absorption spectroscopy. American Mineralogist, 83(5–6): 553568.Google Scholar
Francis, A.J., Dodge, C.J., Lu, F.L., Halada, G.P., Clayton, C.R., 1994. XPS and XANES studies of uranium reduction by Clostridium Sp. Environmental Science & Technology, 28(4): 636639.Google Scholar
Francis, A.J. et al., 2004. Uranium association with halophilic and non-halophilic bacteria and archaea. Radiochimica Acta, 92(8): 481488.Google Scholar
Frenkel, A.I., Kleifeld, O., Wasserman, S.R., Sagi, I., 2002. Phase speciation by extended x-ray absorption fine structure spectroscopy. Journal of Chemical Physics, 116(21): 94499456.Google Scholar
Glasauer, S. et al., 2007. Mixed-valence cytoplasmic iron granules are linked to anaerobic respiration. Applied and Environmental Microbiology, 73(3): 993996.CrossRefGoogle ScholarPubMed
Guine, V. et al., 2006. Zinc sorption to three gram-negative bacteria: Combined titration, modeling, and EXAFS study. Environmental Science & Technology, 40(6): 18061813.Google Scholar
Hattori, T. et al., 2009. The structure of monomeric and dimeric uranyl adsorption complexes on gibbsite: A combined DFT and EXAFS study. Geochimica et Cosmochimica Acta, 73(20): 59755988.Google Scholar
Hettiarachchi, G.M., Scheckel, K.G., Ryan, J.A., Sutton, S.R., Newville, M., 2006. mu-XANES and mu-XRF investigations of metal binding mechanisms in biosolids. Journal of Environmental Quality, 35(1): 342351.Google Scholar
Iida, A., Noma, T., 1993. Correction of the self-absorption effect in fluorescence x-ray-absorption fine-structure. Japanese Journal of Applied Physics Part 1-Regular Papers Short Notes & Review Papers, 32(6A): 28992902.Google Scholar
Ikeda, A. et al., 2007. Comparative study of uranyl(VI) and -(V) carbonato complexes in an aqueous solution. Inorganic Chemistry, 46(10): 42124219.Google Scholar
Ilton, E.S. et al., 2004. Heterogeneous reduction of uranyl by micas: Crystal chemical and solution controls. Geochimica et Cosmochimica Acta, 68(11): 24172435.Google Scholar
Jardine, P.M. et al., 1999. Fate and transport of hexavalent chromium in undisturbed heterogeneous soil. Environmental Science & Technology, 33(17): 29392944.Google Scholar
Kashiv, Y. et al., 2016. Imaging trace element distributions in single organelles and subcellular features. Scientific Reports, 6: 21437.Google Scholar
Kelly, S.D. et al., 2001. XAFS determination of the bacterial cell wall functional groups responsible for complexation of Cd and U as a function of pH. Journal of Synchrotron Radiation, 8: 946948.Google Scholar
Kelly, S.D., Hasterberg, D., Ravel, B., 2008. Analysis of Soils and Minerals Using X-ray Absorption Spectroscopy. In: Ulery, A.L., Drees, L.R. (Eds.), Methods of Soil Analysis, Part 5 -Mineralogical Methods. Soil Science Society of America, Madison, WI.Google Scholar
Kelly, S.D., Kemner, K.M., Brooks, S.C., 2007. X-ray absorption spectroscopy identifies calcium-uranyl-carbonate complexes at environmental concentrations. Geochimica et Cosmochimica Acta, 71(4): 821834.Google Scholar
Kelly, S.D. et al., 2003. Uranyl incorporation in natural calcite. Environmental Science & Technology, 37(7): 12841287.CrossRefGoogle Scholar
Kemner, K.M., Kelly, S.D., 2007. Synchrotron-based Techniques for Monitoring Metal Transformations. In: Hurst, C.J. et al. (Eds.), Manual of Environmental Microbiology. ASM Press, Washington, DC, pp. 11831194.Google Scholar
Kemner, K.M. et al., 2004. Elemental and redox analysis of single bacterial cells by X-ray microbeam analysis. Science, 306(5696): 686687.Google Scholar
Kim, C.S., Bloom, N.S., Rytuba, J.J., Brown, G.E., 2003. Mercury speciation by X-ray absorption fine structure spectroscopy and sequential chemical extractions: A comparison of speciation methods. Environmental Science & Technology, 37(22): 51025108.Google Scholar
Koningsberger, D.C., Prins, R., 1988. X-Ray Absorption: Principles, Applications, Techniques of EXAFS, SEXAFS and XANES. John Wiley and Sons, New York, NY.Google Scholar
Kwon, M.J. et al., 2014. Acid extraction overestimates the total Fe(II) in the presence of iron (hydr)oxide and sulfide minerals. Environmental Science & Technology Letters, 1(7): 310314.CrossRefGoogle Scholar
Lai, B. et al., 1992. Hard x-ray phase zone plate fabricated by lithographic techniques. Applied Physics Letters, 61(16): 18771879.Google Scholar
Latta, D.E., Kemner, K.M., Mishra, B., Boyanov, M.I., 2016. Effects of calcium and phosphate on uranium(IV) oxidation: Comparison between nanoparticulate uraninite and amorphous U-IV-phosphate. Geochimica et Cosmochimica Acta, 174: 122142.Google Scholar
Latta, D.E., Mishra, B., Cook, R.E., Kemner, K.M., Boyanov, M.I., 2014. Stable U(IV) complexes form at high-affinity mineral surface sites. Environmental Science & Technology, 48(3): 16831691.CrossRefGoogle ScholarPubMed
Li, W.-B. et al., 2014. Correction method for the self-absorption effects in fluorescence extended X-ray absorption fine structure on multilayer samples. Journal of Synchrotron Radiation, 21: 561567.Google Scholar
Lindahl, P.A. et al., 1984. Nickel and iron EXAFS of f-420-reducing hydrogenase from Methanobacterium thermoautotrophicum. Journal of the American Chemical Society, 106(10): 30623064.Google Scholar
Lytle, F.W., Sayers, D.E., Stern, E.A., 1975. Extended x-ray-absorption fine-structure technique. 2. Experimental practice and selected results. Physical Review B, 11(12): 48254835.CrossRefGoogle Scholar
Merroun, M.L. et al., 2005. Complexation of uranium by cells and S-layer sheets of Bacillus sphaericus JG-A12. Applied and Environmental Microbiology, 71(9): 55325543.Google Scholar
Michalowicz, A., Moscovici, J., Muller-Bouvet, D., Provost, K., 2009. MAX: Multiplatform Applications for XAFS. In: DiCicco, A., Filipponi, A. (Eds.), 14th International Conference on X-Ray Absorption Fine Structure. Journal of Physics Conference Series, 190: 012034.Google Scholar
Mitsunobu, S., Takahashi, Y., Terada, Y., Sakata, M., 2010. Antimony(V) incorporation into synthetic ferrihydrite, goethite, and natural iron oxyhydroxides. Environmental Science & Technology, 44(10): 37123718.Google Scholar
Moon, E.M., Peacock, C.L., 2011. Adsorption of Cu(II) to Bacillus subtilis: A pH-dependent EXAFS and thermodynamic modelling study. Geochimica et Cosmochimica Acta, 75(21): 67056719.Google Scholar
Nachtegaal, M., Sparks, D.L., 2003. Nickel sequestration in a kaolinite-humic acid complex. Environmental Science & Technology, 37(3): 529534.Google Scholar
O’Day, P.A., Brown, G.E., Parks, G.A., 1994. X-ray-absorption spectroscopy of cobalt(II) multinuclear surface complexes and surface precipitates on kaolinite. Journal of Colloid and Interface Science, 165(2): 269289.CrossRefGoogle Scholar
O’Loughlin, E.J., Kelly, S.D., Cook, R.E., Csencsits, R., Kemner, K.M., 2003. Reduction of uranium(VI) by mixed iron(II/iron(III) hydroxide (green rust): Formation of UO2 nanoparticles. Environmental Science & Technology, 37(4): 721727.Google Scholar
Paunesku, T., Vogt, S., Maser, J., Lai, B., Woloschak, G., 2006. X-ray fluorescence microprobe imaging in biology and medicine. Journal of Cellular Biochemistry, 99(6): 14891502.Google Scholar
Penner-Hahn, J.E., 2003. X-ray Absorption Spectroscopy, in: Comprehensive Coordination Chemistry II, pp. 159186.Google Scholar
Polette, L.A. et al., 2000. XAS and microscopy studies of the uptake and bio-transformation of copper in Larrea tridentata (creosote bush). Microchemical Journal, 65(3): 227236.Google Scholar
Pushie, M.J., Pickering, I.J., Korbas, M., Hackett, M.J., George, G.N., 2014. Elemental and chemically specific X-ray fluorescence imaging of biological systems. Chemical Reviews, 114(17): 84998541.Google Scholar
Ravel, B., Newville, M., 2005. ATHENA, ARTEMIS, HEPHAESTUS: Data analysis for X-ray absorption spectroscopy using IFEFFIT. Journal of Synchrotron Radiation, 12: 537541.Google Scholar
Ressler, T., 1998. WinXAS: A program for X-ray absorption spectroscopy data analysis under MS-Windows. Journal of Synchrotron Radiation, 5: 118122.Google Scholar
Ressler, T., Wienold, J., Jentoft, R.E., Neisius, T., 2002. Bulk structural investigation of the reduction of MoO3 with propene and the oxidation of MoO2 with oxygen. Journal of Catalysis, 210(1): 6783.Google Scholar
Rossberg, A., Reich, T., Bernhard, G., 2003. Complexation of uranium(VI) with protocatechuic acid – application of iterative transformation factor analysis to EXAFS spectroscopy. Analytical and Bioanalytical Chemistry, 376(5): 631638.Google Scholar
Rui, X. et al., 2013. Bioreduction of hydrogen uranyl phosphate: Mechanisms and U(IV) products. Environmental Science & Technology, 47(11): 56685678.Google Scholar
Sayers, D.E., Stern, E.A., Lytle, F.W., 1971. New technique for investigating noncrystalline structures: Fourier analysis of extended x-ray–absorption fine structure. Physical Review Letters, 27(18): 1204.Google Scholar
Scheinost, A.C. et al., 2008. X-ray absorption and photoelectron spectroscopy investigation of selenite reduction by Fe-II-bearing minerals. Journal of Contaminant Hydrology, 102(34): 228245.Google Scholar
Schulze, D.G., Bertsch, P.M., 1995. Synchrotron X-ray techniques in soil, plant, and environmental research. Advances in Agronomy, 55: 166.Google Scholar
Scott, R.A., 1985. Measurement of metal-ligand distances by EXAFS. Methods in Enzymology, 117: 414459.Google Scholar
Singer, D.M., Farges, F., Brown, G.E., 2009. Biogenic nanoparticulate UO2: Synthesis, characterization, and factors affecting surface reactivity. Geochimica et Cosmochimica Acta, 73(12): 35933611.Google Scholar
Stelling, O., 1925. Article with information on the connection between chemical constitution and K-x rays absorption spectra. IL.) Research on some phosphoric compounds. Zeitschrift Fur Physikalische Chemie –Stochiometrie Und Verwandtschaftslehre, 117(3/4): 161174.Google Scholar
Stern, E.A., 1974. Theory of extended x-ray-absorption fine-structure. Physical Review B, 10(8): 30273037.Google Scholar
Stern, E.A., Bunker, B.A., Heald, S.M., 1980. Many-body effects on extended x-ray absorption fine-structure amplitudes. Physical Review B, 21(12): 55215539.Google Scholar
Stern, E.A., Sayers, D.E., Lytle, F.W., 1975. Extended x-ray-absorption fine-structure technique. 3. Determination of physical parameters. Physical Review B, 11(12): 48364846.Google Scholar
Sylwester, E.R., Hudson, E.A., Allen, P.G., 2000. The structure of uranium (VI) sorption complexes on silica, alumina, and montmorillonite. Geochimica et Cosmochimica Acta, 64(14): 24312438.Google Scholar
Templeton, A., Knowles, E., 2009. Microbial transformations of minerals and metals: Recent advances in geomicrobiology derived from synchrotron-based x-ray spectroscopy and x-ray microscopy, Annual Review of Earth and Planetary Sciences, 37(1): 367391.Google Scholar
Templeton, A.S., Spormann, A.M., Brown, G.E., 2003. Speciation of Pb(II) sorbed by Burkholderia cepacia/goethite composites. Environmental Science & Technology, 37(10): 21662172.Google Scholar
Teo, B.K., 1986. EXAFS: Basic Principles and Data Analysis. Springer-Verlag, New York, NY.Google Scholar
Terzano, R. et al., 2010. Solving mercury (Hg) speciation in soil samples by synchrotron X-ray microspectroscopic techniques. Environmental Pollution, 158(8): 27022709.Google Scholar
Troger, L. et al., 1992. Full correction of the self-absorption in soft-fluorescence extended x-ray-absorption fine-structure. Physical Review B, 46(6): 32833289.Google Scholar
Vairavamurthy, A., Manowitz, B., Luther, G.W., Jeon, Y., 1993. Oxidation-state of sulfur in thiosulfate and implications for anaerobic energy-metabolism. Geochimica et Cosmochimica Acta, 57(7): 16191623.CrossRefGoogle Scholar
Veeramani, H. et al., 2011. Products of abiotic U(VI) reduction by biogenic magnetite and vivianite. Geochimica et Cosmochimica Acta, 75(9): 25122528.Google Scholar
Villalobos, M., Bargar, J., Sposito, G., 2005. Mechanisms of Pb(II) sorption on a biogenic manganese oxide. Environmental Science & Technology, 39(2): 569576.Google Scholar
Vodyanitskii, Y.N., 2013. Determination of the oxidation states of metals and metalloids: An analytical review. Eurasian Soil Science, 46(12): 11391149.Google Scholar
Vogt, S., Maser, J., Jacobsen, C., 2003. Data analysis for X-ray fluorescence imaging. Journal de Physique IV, 104: 617622.Google Scholar
Waite, T.D., Davis, J.A., Payne, T.E., Waychunas, G.A., Xu, N., 1994. Uranium(VI) adsorption to ferrihydrite – application of a surface complexation model. Geochimica et Cosmochimica Acta, 58(24): 54655478.Google Scholar
Waldo, G.S. et al., 1995. Formation of the ferritin iron mineral occurs in plastids – an x-ray-absorption spectroscopy study. Plant Physiology, 109(3): 797802.Google Scholar
Wasserman, S.R., Allen, P.G., Shuh, D.K., Bucher, J.J., Edelstein, N.M., 1999. EXAFS and principal component analysis: A new shell game. Journal of Synchrotron Radiation, 6: 284286.Google Scholar
Watson, J.H.P. et al., 2000. Structural and magnetic studies on heavy-metal-adsorbing iron sulphide nanoparticles produced by sulphate-reducing bacteria. Journal of Magnetism and Magnetic Materials, 214(1–2): 1330.Google Scholar
Watson, J.H.P., Ellwood, D.C., 2003. The removal of the pertechnetate ion and actinides from radioactive waste streams at Hanford, Washington, USA and Sellafield, Cumbria, UK: The role of iron-sulfide-containing adsorbent materials. Nuclear Engineering and Design, 226(3): 375385.Google Scholar
Webb, S.M., 2005. SIXpack: A graphical user interface for XAS analysis using IFEFFIT. Physica Scripta, T115: 10111014.Google Scholar
Williams, P.A. et al., 1999. The Cu-A domain of Thermus thermophilus ba(3)-type cytochrome c oxidase at 1.6 angstrom resolution. Nature Structural Biology, 6(6): 509516.Google Scholar
Yan, S., Boyanov, M.I., Mishra, B., Kemner, K.M., O’Loughlin, E.J., 2018. U(VI) reduction by biogenic and abiotic hydroxycarbonate green rusts: Impacts on U(IV) speciation and stability over time. Environmental Science & Technology, 52(8): 46014609.Google Scholar
Zachara, J.M. et al., 2004. Chromium speciation and mobility in a high level nuclear waste vadose zone plume. Geochimica et Cosmochimica Acta, 68(1): 1330.Google Scholar
Zachara, J.M. et al., 2007. Reduction of pertechnetate Tc(VII) by aqueous Fe(II) and the nature of solid phase redox products. Geochimica et Cosmochimica Acta, 71(9): 21372157.Google Scholar

11.4 References

Ahimou, F., Paquot, M., Jacques, P., Thonart, P. and Rouxhet, P. G. 2001. Influence of electrical properties on the evaluation of the surface hydrophobicity of Bacillus subtilis. J Microbiol Methods, 45, 119–26.Google Scholar
Beamson, G. and Briggs, D. 1992. High Resolution XPS of Organic Polymers: the Scienta ESCA300 Database, Chichester, UK, Wiley.Google Scholar
Beveridge, T. J. 2010. Bacterial Cells, Chichester, UK, Wiley.Google Scholar
Boonaert, C. J. and Rouxhet, P. G. 2000. Surface of lactic acid bacteria: relationships between chemical composition and physicochemical properties. Appl Environ Microbiol, 66, 2548–54.Google Scholar
Brierley, C. L. and Brierley, J. A. 2013. Progress in bioleaching: part B: applications of microbial processes by the minerals industries. Appl Microbiol Biotechnol, 97, 7543–52.Google Scholar
Briggs, D. and Grant, J. T. 2003. Surface Analysis by Auger and X-ray Photoelectron Spectroscopy, Trowbridge, UK, The Cromwell Press, IM Publications and SurfaceSpectra Limited.Google Scholar
Burger, K. 1978. Charge correction in XPS-ESCA – bulk solvent as internal standard in study of quick-frozen solutions. J Electron Spectros Relat Phenomena, 14, 405–10.Google Scholar
Burger, K. and Fluck, E. 1974. X-ray-photoelectron spectroscopy (ESCA) investigations in coordination chemistry .1. Solvation of SBCL5 studied in quick-frozen solutions. Inorg Nucl Chem Letters, 10, 171–7.Google Scholar
Burger, K., Fluck, E., Binder, H. and Varhelyi, C. 1975. X-ray photoelectron-spectroscopy (ESCA) investigations in coordination chemistry .2. Study of outer sphere coordination and hydrogen bridge formation in cobalt(III) and nickel(II) complexes. J Inorg Nucl Chem, 37, 5557.Google Scholar
Burger, K., Tschimarov, F. and Ebel, H. 1977. XPS-ESCA applied to quick-frozen solutions .1. Study of nitrogen-compounds in aqueous-solutions. Electron Spectros Relat Phenomena, 10, 461–5.Google Scholar
Busscher, H. J., Bialkowska-Hobrazanska, H., Reid, G., van der Kuijl-Booij, M. and van der Mei, H. C. 1994. Physicochemical characteristics of two pairs of coagulase-negative staphylococcal isolates with different plasmid profiles. Colloids Surf, B, 2, 7382.Google Scholar
Castner, D. G. and Ratner, B. D. 2002. Biomedical surface science: foundations to frontiers. Surf Sci, 500, 2860.Google Scholar
Clayton, C. R., Halada, G. P., Kearns, J. R., Gillow, J. B. and Francis, A. J. 1994. Spectroscopic study of sulfate reducing bacteria-metal ion interactions related to microbiologically influenced corrosion (MIC). ASTM Spec Tech Publ, 1232, 141–52.Google Scholar
Delcroix, M. F., Zuyderhoff, E. M., Genet, M. J. and Dupont-Gillain, C. C. 2012. Optimization of cryo-XPS analyses for the study of thin films of a block copolymer (PS-PEO). Surf Interface Anal, 44, 175–84.Google Scholar
Dufrêne, Y., Van der Wal, A., Norde, W. and Rouxhet, P. 1997. X-ray photoelectron spectroscopy analysis of whole cells and isolated cell walls of Gram-positive bacteria: comparison with biochemical analysis. J Bacteriol, 179, 1023–8.Google Scholar
Ellwood, D. C. and Tempest, D. W. 1972. Influence of culture pH on the content and composition of teichoic acids in the walls of Bacillus subtilis. J Gen Microbiol, 73, 395402.Google Scholar
Genet, M. J., Dupont-Gillain, C. C. and Rouxhet, P. G. 2008. XPS Analysis of Biosystems and Biomaterials, New York, Springer Science+Business Media.Google Scholar
Kalinowski, B. E., Liermann, L. J., Brantley, S. L., Barnes, A. and Pantano, C. G. 2000. X-ray photoelectron evidence for bacteria-enhanced dissolution of hornblende. Geochim Cosmochim Acta, 64, 1331–43.Google Scholar
Kang, C., Wu, P., Li, Y., et al. 2015. Understanding the role of clay minerals in the chromium(VI) bioremoval by Pseudomonas aeruginosa CCTCC AB93066 under growth condition: microscopic, spectroscopic and kinetic analysis. World J Microbiol Biotechnol, 31, 1765–79.Google Scholar
Kemper, M. A., Urrutia, M. M., Beveridge, T. J., Koch, A. L. and Doyle, R. J. 1993. Proton motive force may regulate cell wall-associated enzymes of Bacillus subtilis. J Bacteriol, 175, 5690–6.Google Scholar
Kern, T., Giffard, M., Hediger, S., et al. 2010. Dynamics characterization of fully hydrated bacterial cell walls by solid-state NMR: evidence for cooperative binding of metal ions. J Am Chem Soc, 132, 10911–19.CrossRefGoogle ScholarPubMed
Khoshkhoo, M., Dopson, M., Shchukarev, A. and Sandström, Å. 2014. Electrochemical simulation of redox potential development in bioleaching of a pyritic chalcopyrite concentrate. Hydrometallurgy, 144–145, 714.Google Scholar
Kolmakov, A., Dikin, D. A., Cote, L. J., et al. 2011. Graphene oxide windows for in situ environmental cell photoelectron spectroscopy. Nat Nanotechnol, 6, 651–7.Google Scholar
Krumbein, W. E. 1983. Microbial Geochemistry, Oxford, Blackwell Scientific Publications.Google Scholar
Leone, L., Ferri, D., Manfredi, C., et al. 2007. Modeling the acid-base properties of bacterial surfaces: a combined spectroscopic and potentiometric study of the Gram-positive bacterium Bacillus subtilis. Environ Sci Technol, 41, 6465–71.Google Scholar
Leone, L., Loring, J., Sjöberg, S., Persson, P. and Shchukarev, A. 2006. Surface characterization of the Gram-positive bacteria Bacillus subtilis – an XPS study. Surf Interface Anal, 38, 202–5.Google Scholar
Li, B., Pan, D., Zheng, J., et al. 2008. Microscopic investigations of the Cr(VI) uptake mechanism of living Ochrobactrum anthropi. Langmuir, 24, 9630–5.Google Scholar
Li, X., Ding, C., Liao, J., et al. 2017. Microbial reduction of uranium (VI) by Bacillus sp dwc-2: a macroscopic and spectroscopic study. J Environ Sci (China), 53, 915.Google Scholar
Lin, D. Q., Zhong, L. N. and Yao, S. J. 2006. Zeta potential as a diagnostic tool to evaluate the biomass electrostatic adhesion during ion-exchange expanded bed application. Biotechnol Bioeng, 95, 185–91.Google Scholar
Lukas, J., Sodhi, R. N. S. and Sefton, M. V. 1995. An XPS study of the surface reorientation of statistical methacrylate copolymers. J Colloid Interface Sci, 174, 421–7.Google Scholar
Mills, A. L. 1998. The role of bacteria in environmental geochemistry, in Mills, A.L. (ed.) The Environmental Geochemistry of Mineral Deposits, Part A: processes, Techniques, and Health Issues, Littleton, CO, USA: Society of Economic Geologists Inc., 125–32.Google Scholar
Mirimanoff, N. and Wilkinson, K. 2000. Regulation of Zn accumulation by a freshwater Gram-positive bacterium (Rhodococcus opacus). Environ Sci Technol, 34, 616–22.Google Scholar
Moulder, J. F., Stickle, W. F., Sobol, P. E. and Bomben, K. D. 1992. Handbook of X-ray Photoelectron Spectroscopy, Eden Prairie, Minnesota, USA, Perkin-Elmer Corporation Physical Electronics Division.Google Scholar
Naumkin, A. V., Kraut-Vass, A., Gaarenstroom, S. W. and Powell, C. J. 2012. NIST X-ray Photoelectron Spectroscopy Database, http://srdata.nist.gov/xps/, U.S. Secretary of Commerce on behalf of the United States of America.Google Scholar
Ojeda, J. J., Romero-Gonzalez, M. E., Bachmann, R. T., Edyvean, R. G. J. and Banwart, S. A. 2008. Characterization of the cell surface and cell wall chemistry of drinking water bacteria by combining XPS, FTIR spectroscopy, modeling, and potentiometric titrations. Langmuir, 24, 4032–40.Google Scholar
Olson, G. J., Brierley, J. A. and Brierley, C. L. 2003. Bioleaching review part B: progress in bioleaching: applications of microbial processes by the minerals industries. Appl Microbiol Biotechnol, 63, 249–57.Google Scholar
Ramstedt, M. 2004. Chemical processes at the water-manganite (gamma-MnOOH) interface, Umeå, Sweden, Umeå University, PhD Thesis.Google Scholar
Ramstedt, M., Leone, L., Persson, P. and Shchukarev, A. 2014. Cell wall composition of Bacillus subtilis changes as a function of pH and Zn²⁺ exposure: insights from cryo-XPS measurements. Langmuir, 30, 4367–74.Google Scholar
Ramstedt, M., Nakao, R., Wai, S., Uhlin, B. and Boily, J. 2011. Monitoring surface chemical changes in the bacterial cell wall – multivariate analysis of cryo-X-ray photoelectron spectroscopy data. J Biol Chem, 286, 12389–96.Google Scholar
Ramstedt, M., Norgren, C., Sheals, J., Shchukarev, A. and Sjoberg, S. 2004. Chemical speciation of N-(phosphonomethyl)glycine in solution and at mineral interfaces. Surf Interface Anal, 36, 1074–7.Google Scholar
Ramstedt, M. and Shchukarev, A. 2016. Analysis of bacterial cell surface chemical composition using cryogenic X-ray photoelectron spectroscopy. In: Hong, H.-J. (ed.) Bacterial Cell Wall Homeostasis: Methods and Protocols. New York, NY: Springer New York.Google Scholar
Ramstedt, M., Shchukarev, A. V. and Sjoberg, S. 2002. Characterization of hydrous manganite (gamma-MnOOH) surfaces – an XPS study. Surf Interface Anal, 34, 632–6.Google Scholar
Ratner, B. D. 1995. Advances in the analysis of surfaces of biomedical interest. Surf Interface Anal, 23, 521–8.Google Scholar
Ratner, B. D. and Castner, D. G. 2009. Chapter 3, in Electron Spectroscopy for Chemical Analysis, Wiley.Google Scholar
Ratner, B. D., Weathersby, P. K., Hoffman, A. S., Kelly, M. A. and Scharpen, L. H. 1978. Radiation-grafted hydrogels for biomaterial applications as studied by ESCA technique. J Appl Polym Sci, 22, 643–64.Google Scholar
Rouxhet, P. and Genet, M. 2011. XPS analysis of bio-organic systems. Surf Interface Anal, 43, 1453–70.Google Scholar
Salmeron, M. and Schlögl, R. 2008. Ambient pressure photoelectron spectroscopy: a new tool for surface science and nanotechnology. Surf Sci Rep, 63, 169–99.Google Scholar
Seidel, R., Thürmer, S. and Winter, B. 2011. Photoelectron spectroscopy meets aqueous solution: studies from a vacuum liquid microjet. J Phys Chem Lett, 2, 633–41.Google Scholar
Shchukarev, A. 2006a. XPS at solid-aqueous solution interface. Adv Colloid Interface Sci, 122, 149–57.Google Scholar
Shchukarev, A. 2006b. XPS at solid-solution interface: experimental approaches. Surf Interface Anal, 38, 682–5.Google Scholar
Shchukarev, A., Boily, J. F. and Felmy, A. R. 2007. XPS of fast-frozen hematite colloids in NaCl aqueous solutions: I. Evidence for the formation of multiple layers of hydrated sodium and chloride ions induced by the {001} basal plane. J Phys Chem C, 111, 18307–16.Google Scholar
Shchukarev, A. and Ramstedt, M. 2017. Cryo-XPS: probing intact interfaces in nature and life. Surf Interface Anal, 49, 349–56.Google Scholar
Shchukarev, A., Rosenquist, J. and Sjöberg, S. 2004. XPS study of the silica–water interface. J Electron Spectros Relat Phenomena, 137–140, 171–6.Google Scholar
Shchukarev, A. and Sjöberg, S. 2005. XPS with fast-frozen samples: a renewed approach to study the real mineral/solution interface. Surf Sci, 584, 106–12.Google Scholar
Shimizu, K., Shchukarev, A. and Boily, J. F. 2011. X-ray photoelectron spectroscopy of fast-frozen hematite colloids in aqueous solutions. 3. Stabilization of ammonium species by surface (hydr)oxo groups. J Phys Chem C, 115, 6796–801.Google Scholar
Skallberg, A., Brommesson, C. and Uvdal, K. 2017. Imaging XPS and photoemission electron microscopy; surface chemical mapping and blood cell visualization. Biointerphases, 12, 02C408.Google Scholar
Tebo, B. M., Bargar, J. R., Clement, B. G., et al. 2004. Biogenic manganese oxides: properties and mechanisms of formation. Annu Rev Earth Planet Sci, 32, 287328.Google Scholar
van der Mei, H., De Vries, J. and Busscher, H. 2000. X-ray photoelectron spectroscopy for the study of microbial cell surfaces. Surf Sci Rep, 39, 324.Google Scholar
Vollmer, W., Blanot, D. and De Pedro, M. A. 2008. Peptidoglycan structure and architecture. FEMS Microbiol Rev, 32, 149–67.Google Scholar
Winter, B. and Faubel, M. 2006. Photoemission from liquid aqueous solutions. Chem Rev, 106, 1176–211.Google Scholar
Yee, N. and Fein, J. 2001. Cd adsorption onto bacterial surfaces: A universal adsorption edge? Geochim et Cosmochim Acta, 65, 2037–42.Google Scholar
Yee, N. and Fein, J. 2003. Quantifying metal adsorption onto bacteria mixtures: a test and application of the surface complexation model. Geomicrobiol J, 20, 4360.Google Scholar
Young, K. D. 2010. Bacterial Cell Wall, Chichester, Wiley.Google Scholar

12.8 References

Alam, S.M., Cossio, M., Robinson, L., et al. (2016) Removal of organic acids from water using biochar and petroleum coke, Environmental Technology & Innovation, v. 6, pp. 141151.Google Scholar
Alessi, D.S., Lezama-Pacheco, J.S., Stubbs, J.E., et al. (2014) The product of microbial uranium reduction includes multiple species with U(IV)–phosphate coordination, Geochimica et Cosmochimica Acta, v. 131, pp. 115127.Google Scholar
Amarie, S., Keilmann, F., Zaslansky, P., Griesshaber, E. (2012) Nano-FTIR chemical mapping of minerals in biological materials, Proceedings of Microscopy & Microanalysis, v. 18, pp. 3233.Google Scholar
Baker, M.J., Trevisan, J., Bassan, P., et al. (2014) Using Fourier transform IR spectroscopy to analyze biological materials, Nature Protocols, v. 9, pp. 17711791.Google Scholar
Benning, L.G., Phoenix, V.R., Yee, N., Tobin, M.J. (2004) Molecular characterization of cyanobacterial silicification using synchrotron infrared micro-spectroscopy, Geochimica et Cosmochimica Acta, v. 68, p. 729.Google Scholar
Bertie, J.E, (2002) Optical Constants. In Handbook of Vibrational Spectroscopy (Eds. Chalmers, J.M., Griffiths, P.R.), John Wiley and Sons.Google Scholar
Bonhomme, S., Cuer, A., Delort, A-M., et al. (2003) Environmental biodegradation of polyethylene, Polymer Degradation and Stability, v 81, pp. 441452.Google Scholar
Borer, P., Hug, S.J., Sulzberger, B., Kraemer, S.M., Kretzschmar, R. (2009) ATR-FTIR spectroscopic study of the adsorption of desferrioxamine B and aerobactin to the surface of lepidocrocite (γ-FeOOH), Geochimica et Cosmochimica Acta, v. 73, pp. 46614672.Google Scholar
Carabante, I., Grahn, M., Holmgren, A., Kumpiene, J., Hedlund, J. (2009) Adsorption of As (V) on iron oxide nanoparticle films studied by in situ ATR-FTIR spectroscopy, Colloids and Surfaces A: Physicochemical and Engineering Aspects, v. 346, pp. 106113.Google Scholar
Chalmers, J.M., Griffiths, P.R. (2002) Handbook of Vibrational Spectroscopy (Eds. Chalmers, J.M.,Griffiths, P.R.), John Wiley and Sons.Google Scholar
Chan, K.L.A., Kazarian, S.G. (2007) Attenuated total reflection Fourier transform infrared imaging with variable angles of incidence: a three-dimensional profiling of heterogeneous materials, Applied Spectroscopy, v. 61, pp. 4854.Google Scholar
de Juan, A., Maeder, M., Hancewicz, T., Duponchel, L., Tauler, R. (2009), Chemometric Tools for Image Analysis. In Infrared and Raman Spectroscopic Imaging (Eds. Salzer, R., Siesler, HW), Ch. 2, 65–106, Wiley-VCH Verlag GmbH & Co. KGaA.Google Scholar
Driver, T., Bajhaiya, A.K., Allwood, J.W., et al. (2015), Metabolic responses of eukaryotic microalgae to environmental stress limit the ability of FT-IR spectroscopy for species identification, Algal Research, v. 11, pp. 148155.Google Scholar
Dziuba, B., Babuchowski, A., Nałęcz, D., Niklewicz, M. (2007) Identification of lactic acid bacteria using FTIR spectroscopy and cluster analysis, International Dairy Journal, v. 17, pp. 183189.Google Scholar
Eilers, P.H. (2004) Parametric time warping, Analytical Chemistry, v. 76 (2), pp. 404411.Google Scholar
Elzinga, E.J., Huang, J-H., Chorover, J., Kretzschmar, R. (2012) ATR-FTIR spectroscopy study of the influence of pH and contact time on the adhesion of Shewanella putrefaciens bacterial cells to the surface of hematite, Environmental Science & Technology, v. 46, pp. 1284812855.Google Scholar
Elzinga, E.J., Kretzschmar, R. (2013) In situ ATR-FTIR spectroscopic analysis of the co-adsorption of orthophosphate and Cd(II) onto hematite, Geochimica et Cosmochimica Acta, v. 117, pp. 5364.Google Scholar
Felten, J., Hall, H., Jaumot, J., et al. (2015) Vibrational spectroscopic image analysis of biological material using multivariate curve resolution-alternating least squares (MCR-ALS), Nature Protocols, v. 10, pp. 217240.Google Scholar
Gallé, T., Van Lagen, B., Kurtenbach, A., Bierl, R. (2004) An FTIR-DRIFT study on river sediment particle structure:  Implications for biofilm dynamics and pollutant binding, Environmental Science & Technology, v. 38, pp. 44964502.Google Scholar
Gillgren, T., Gorzsás, A. (2016) A one-pot set-up for real-time reaction monitoring by FTIR spectroscopy, Wood Science and Technology, v. 50, pp. 567580.Google Scholar
Gorzsás, A., Sundberg, B. (2014) Chemical Fingerprinting of Arabidopsis Using Fourier Transform Infrared (FT-IR) Spectroscopic Approaches. In Arabidopsis Protocols (Eds. Sanchez-Serrano, J.J., Salinas, J.), Humana Press.Google Scholar
Grahn, H.F., Geladi, P. (2007) Techniques and Applications of Hyperspectral Image Analysis (Eds. Grahn, H.F., Geladi, P.). John Wiley and Sons Ltd.Google Scholar
Griffiths, P.R. (2002) Introduction to Vibrational Spectroscopy. In Handbook of Vibrational Spectroscopy (Eds.Chalmers, J.M., Griffiths, P.R.), John Wiley and Sons.Google Scholar
Haberhauer, G., Rafferty, B., Strebl, F., Gerzabek, M.H. (1998) Comparison of the composition of forest soil litter derived from three different sites at various decompositional stages using FTIR spectroscopy, Geoderma, pp. 331342.Google Scholar
Hagvall, K., Persson, P., Karlsson, T. (2014) Spectroscopic characterization of the coordination chemistry and hydrolysis of gallium(III) in the presence of aquatic organic matter, Geochimica et Cosmochimica Acta, v. 146, pp. 7689.Google Scholar
Hagvall, K., Persson, P., Karlsson, T. (2015) Speciation of aluminum in soils and stream waters: the importance of organic matter, Chemical Geology, v. 417, pp. 3243.Google Scholar
Hamilton, M.L., Perston, B.B., Harland, P.W., et al. (2005) Grazing-angle fiber-optic IRRAS for in situ cleaning validation, Organic Process Research & Development, v. 9, pp. 337343.Google Scholar
Hazen, T.C., Dubinsky, E.A., DeSantis, T.Z., et al. (2010) Deep-sea oil plume enriches psychrophilic oil-degrading bacteria, Science, v. 330, p. 6001.Google Scholar
Holman, H-Y.N., Miles, R., Hao, Z., et al. (2009) Real-time chemical imaging of bacterial activity in biofilms using open-channel microfluidics and synchrotron FTIR spectromicroscopy, Analytical Chemistry, v. 81, pp. 85648570.Google Scholar
Holman, H-Y.N., Perry, D.L., Martin, M.C., et al. (1999) Real-time characterization of biogeochemical reduction of Cr(VI) on basalt surfaces by SR-FTIR imaging, Geomicrobiology Journal, v. 16, pp. 307324.Google Scholar
Huang, W., Liu, Z. (2013) Biosorption of Cd(II)/Pb(II) from aqueous solution by biosurfactant-producing bacteria: Isotherm kinetic characteristic and mechanism studies, Colloids and Surfaces B: Biointerfaces, v. 105, pp. 113119.Google Scholar
Jaumot, J., Gargallo, R., de Juan, A., Tauler, R. (2005) A graphical user-friendly interface for MCR-ALS: A new tool for multivariate curve resolution in MATLAB, Chemometrics and Intelligent Laboratory Systems, v. 76, pp. 101110.Google Scholar
Ji, J., Ge, Y., Balsam, W., Damuth, J.E., Chen, J. (2009) Rapid identification of dolomite using a Fourier Transform Infrared Spectrophotometer (FTIR): A fast method for identifying Heinrich events in IODP Site U1308, Marine Geology, v. 258, pp. 6068.Google Scholar
Jiang, W., Saxena, A., Song, B., et al. (2004) Elucidation of functional groups on Gram-positive and Gram-negative bacterial surfaces using infrared spectroscopy, Langmuir, v. 20, pp. 1143311442.Google Scholar
Johnston, C.P., Chrysochoou, M. (2012) Investigation of chromate coordination on ferrihydrite by in situ ATR-FTIR spectroscopy and theoretical frequency calculations, Environmental Science & Technology, v. 46, pp. 58515858.Google Scholar
Kamnev, A.A. (2008) FTIR spectroscopic studies of bacterial cellular responses to environmental factors, plant-bacterial interactions and signalling, Spectroscopy, v. 22, pp. 8395.Google Scholar
Kamnev, A.A., Tugarova, A.V., Antonyuk, L.P., et al. (2006) Instrumental analysis of bacterial cells using vibrational and emission Mossbauer spectroscopic techniques, Analytica Chimica Acta, v. 573–574, pp. 445452.Google Scholar
Kang, S-Y., Bremer, P.J., Kim, K-W., McQuillan, A.J. (2006) Monitoring metal ion binding in single-layer Pseudomonas aeruginosa biofilms using ATR−IR spectroscopy, Langmuir, v. 22, pp. 286291.Google Scholar
Kang, S., Xing, B. (2007) Adsorption of dicarboxylic acids by clay minerals as examined by in situ ATR-FTIR and ex situ DRIFT, Langmuir, v. 23, pp. 70247031.Google Scholar
Kenney, J.P.L., Ellis, T., Nicol, F.S., Porter, A., Weiss, D.J., (2018) The effect of bacterial growth phase and culture concentration on uranium removal from aqueous solution, Chemical Geology, v. 482, pp. 6171.Google Scholar
Kenney, J.P.L., Fein, J.B. (2011) Importance of extracellular polysaccharides in proton and Cd binding to bacteria: a comparative studyChemical Geology, v. 286 (3–4), pp. 109117.Google Scholar
Kong, J., Yu, S. (2007) Fourier transform infrared spectroscopic analysis of protein secondary structures,Acta Biochimica et Biophysica Sinica, v. 39, pp. 549559.Google Scholar
Krumina, L., Kenney, J.P.L., Loring, J., Persson, P. (2016) Desorption mechanisms of phosphate from iron oxide nanoparticle, Chemical Geology, v. 427, pp. 5464.Google Scholar
Kubicki, J.D., Itoh, M.J., Schroeter, L.M., Apitz, S.E. (1997) Bonding mechanisms of salicylic acid adsorbed onto illite clay:  An ATR−FTIR and molecular orbital study, Environmental Science & Technology, v. 31, pp. 11511156.Google Scholar
Lasch, P., Naumann, D. (2006) Spatial resolution in infrared microspectroscopic imaging of tissues, Biochimica Biophysica Acta, v. 1758, pp. 814829.Google Scholar
Leone, L. et al. (2007) Modeling the acid-base properties of bacterial surfaces: A combined spectroscopic and potentiometric study of the Gram-positive bacterium Bacillus subtilis. Environmental Science & Technology, v.41 (18), pp. 64656471.Google Scholar
Liu, Y.X., Alessi, D.S., Owttrim, G.W., et al. (2016) Cell surface properties of cyanobacterium Synechococcus: Influences of nitrogen source, growth phase and N:P ratios, Geochimica et Cosmochimica Acta, v 187, pp. 179194.Google Scholar
Loring, J.S., Sandström, M.H., Noren, K., Persson, P. (2009) Rethinking arsenate coordination at the surface of goethite, Chemistry – A European Journal, v. 15, pp. 50635072.Google Scholar
Madejová, J. (2003) FTIR techniques in clay mineral studies, Vibrational Spectroscopy, v. 31, pp. 110.Google Scholar
Manning, B.A., Goldberg, S. (1996) Modeling competitive adsorption of arsenate with phosphate and molybdate on oxide minerals, Science Society of America Journal, v. 60, pp. 121131.Google Scholar
Marcotte, L., Kegelaer, G., Sandt, C., Barbeau, J., LaXeur, M. (2007) An alternative infrared spectroscopy assay for the quantification of polysaccharides in bacterial samples, Analytical Biochemistry, v. 361, pp. 714.Google Scholar
Mariey, L., Signolle, J.P., Amiel, C., Travert, J. (2001) Discrimination, classification, identification of microorganisms using FTIR spectroscopy and chemometrics, Vibrational Spectroscopy, v. 26, pp. 151159.Google Scholar
Meyer-Jacob, C., Vogel, H., Boxberg, F., et al. (2014) Independent measurement of biogenic silica in sediments by FTIR spectroscopy and PLS regression, Journal of Paleolimnology, v.52, pp. 245255.Google Scholar
Mirabella, F.M. (1983) Strength of interaction and penetration of infrared radiation for polymer films in internal reflection spectroscopy, Journal of Polymer Science: Polymer Physics Edition, v. 21, pp. 24032417.Google Scholar
Mohorčič, M., Jerman, I., Zorko, M., et al. (2010) Surface with antimicrobial activity obtained through silane coating with covalently bound polymyxin B, Journal of Materials Science: Materials in Medicine, v. 21, p. 2775.Google Scholar
Movasaghi, Z., Rehman, S., ur Rehman, I. (2008) Fourier transform infrared (FTIR) spectroscopy of biological tissues, Applied Spectroscopy Reviews, v. 43, pp. 134179.Google Scholar
Noda, I., Ozaki, Y. (2005) Two-Dimensional Correlation Spectroscopy. In Applications in Vibrational and Optical Spectroscopy. John Wiley and Sons.Google Scholar
Ojeda, J.J., Romero-Gonzalez, M.E., Pouran, H.M., Banwart, S.A. (2008) In situ monitoring of the biofilm formation of Pseudomonas putida on hematite using flow-cell ATR-FTIR spectroscopy to investigate the formation of inner-sphere bonds between the bacteria and the mineral, Mineralogical Magazine, v. 72, pp. 101106.Google Scholar
Omoike, A., Chorover, J. (2004) Spectroscopic study of extracellular polymeric substances from Bacillus subtilis: Aqueous chemistry and adsorption effects, Biomacromolecules, v. 5, pp. 12191230.Google Scholar
Omoike, A., Chorover, J., Kwon, K.D., Kubicki, J.D. (2004) Adhesion of bacterial exopolymers to r-FeOOH: Inner-sphere complexation of phosphodiester groups, Langmuir, v. 20, pp. 1110811114.Google Scholar
Papageorgiou, S.K., Kouvelos, E.P., Favvas, E.P., et al. (2010) Metal–carboxylate interactions in metal–alginate complexes studied with FTIR spectroscopy, Carbohydrate Research, v. 345, pp. 469473.Google Scholar
Parikh, S.J., Chorover, J. (2006) ATR-FTIR spectroscopy reveals bond formation during bacterial adhesion to iron oxide, Langmuir, v 22, pp. 84928500.Google Scholar
Parikh, S.J., Mukome, F.N.D., Zhang, X. (2014) ATR-FTIR spectroscopic evidence for biomolecular phosphorus and carboxyl groups facilitating bacterial adhesion to iron oxides, Colloids and Surfaces B: Biointerfaces, v. 119, pp. 3846.Google Scholar
Peak, D., Ford, R.G., Sparks, D.L. (1999) An in situ ATR-FTIR investigation of sulfate bonding mechanisms on goethite, Journal of Colloid and Interface Science, v. 218, pp. 289299.Google Scholar
Pisapia, C., Jamme, F., Duponchel, L., Ménez, B. (2018) Tracking hidden organic carbon in rocks using chemometrics and hyperspectral imaging,Scientific Reports, v. 8, p. 2396.Google Scholar
Poggenburg, C., Mikutta, R., Schippers, A., Dohrmann, R., Guggenberger, G. (2018) Impact of natural organic matter coatings on the microbial reduction of iron oxides, Geochimica et Cosmochimica Acta, v. 224, pp. 223248.Google Scholar
Quilès, F., Humbert, F., Delille, A. (2010) Analysis of changes in attenuated total reflection FTIR fingerprints of Pseudomonas fluorescens from planktonic state to nascent biofilm state, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, v. 75, pp. 610616.Google Scholar
Reig, F.B., Adelantado, G.J.V., Moreno, M.C.M.M. (2002) FTIR quantitative analysis of calcium carbonate (calcite) and silica (quartz) mixtures using the constant ratio method. Application to geological samples, Talanta, v. 58, pp. 811821.Google Scholar
Rong, X., Huang, Q., He, X., et al. (2008) Interaction of Pseudomonas putida with kaolinite and montmorillonite: A combination study by equilibrium adsorption, ITC, SEM and FTIR, Colloids and Surfaces B: Biointerfaces, v. 64, pp. 4955.Google Scholar
Rosen, P., Persson, P. (2006) Fourier-transform infrared spectroscopy (FTIRS), a new method to infer past changes in tree-line position and TOC using lake sediment. Journal of Paleolimnology, v. 35, pp. 913923.Google Scholar
Rosen, P., Vogel, H., Cunningham, L., et al. (2010) Fourier transform infrared spectroscopy, a new method for rapid determination of total organic and inorganic carbon and biogenic silica concentration in lake sediments. Journal of Paleolimnology, v. 43 (2), pp. 247259.Google Scholar
Salzer, R., Siesler, H.W. (2009) Infrared and Raman Spectroscopic Imaging, Wiley-VCH Verlag GmbH & Co. KGaA.Google Scholar
Sar, P., Kazy, S.K, Asthana, R.K., Singh, S.P. (1999) Metal adsorption and desorption by lyophilized Pseudomonas aeruginosa, International Biodeterioration & Biodegradation, v. 44, pp. 101110.Google Scholar
Schmitt, J., Flemming, H.C. (1998) FTIR-spectroscopy in microbial and material analysis, International Biodeterioration & Biodegradation, v. 41, pp. 111.Google Scholar
Schmitt, J., Nivens, D., White, D.C., Flemming, H.C. (1995) Changes of biofilm properties in response to sorbed substances – an FTIR-ATR study, Water Science and Technology, v. 32, pp. 149155.Google Scholar
Shopska, M., Cherkezova-Zheleva, Z.P., Paneva, D.G., et al. (2013) Biogenic iron compounds: XRD, Mossbauer and FTIR study, Central European Journal of Chemistry, v. 11, pp. 215227.Google Scholar
Stenlund, H., Gorzsás, A., Persson, P., Sundberg, B., Trygg, J. (2008) Orthogonal projections to latent structures discriminant analysis modeling on in situ FT-IR spectral imaging of liver tissue for identifying sources of variability, Analytical Chemistry, 80 (18), pp. 68986906.Google Scholar
Suci, P.A., Mittelman, M.W., Yu, F.P., Geesey, G.G. (1994) Investigation of ciprofloxacin penetration into Pseudomonas aeruginosa biofilms, Antimicrobial Agents and Chemotherapy, v. 38, pp. 21252133.Google Scholar
Tapper, R. (1998) The use of biocides for the control of marine biofilms, PhD thesis, University of Portsmouth, UK.Google Scholar
Trygg, J., Wold, S. (2002) Orthogonal projections to latent structures (O-PLS), Journal of Chemometrics, v. 16, pp. 119128.Google Scholar
Ueshima, M., Ginn, R.R., Haack, E.A., Szymanowski, J.E.S., Fein, J.B., 2008. Cd adsorption onto Pseudomonas putida in the presence and absence of extracellular polymeric substances. Geochimica et Cosmochimica Acta, v. 24, pp. 58855895.Google Scholar
ur Rehman, I., Movasaghi, Z., Rehman, S. (2013) Vibrational Spectroscopy for Tissue Analysis. Series in Medical Physics and Biomedical Engineering, CRC Press.Google Scholar
Vaculíková, L., Plevová, E. (2005) Identification of clay minerals and micas in sedimentary rocks, Acta Geodynamica et Geomaterialia, v. 2, pp. 167175.Google Scholar
Vogel, H., Rosén, P., Wagner, B., Melles, M., Persson, P. (2008) Fourier transform infrared spectroscopy, a new cost-effective tool for quantitative analysis of biogeochemical properties in long sediment records, Journal of Paleolimnology, v. 40, pp. 689702.Google Scholar
Wang, H., Hollywood, K., Jarvis, R.M., Lloyd, J.R., Goodacre, R. (2010) Phenotypic characterisation of Shewanella oneidensis MR-1 under aerobic and anaerobic growth conditions by using Fourier transform infrared spectroscopy and high-performance liquid chromatography analyses, Applied and Environmental Microbiology, v. 76, pp. 62666276.Google Scholar
Wei, X., Fang, L., Cai, P., et al. (2011) Influence of extracellular polymeric substances (EPS) on Cd adsorption by bacteria, Environmental Pollution, v. 159, pp. 13691374.Google Scholar
Yao, J-W., Xiao, Y., Lin, F. (2012) The effect of various pH, ionic strength and temperature on papain hydrolysis of salivary film, European Journal of Oral Sciences, v. 120, pp. 140146.Google Scholar
Yoon, T.H., Johnson, S.B., Musgrave, C.B., Brown Jr, G.E., (2004) Adsorption of organic matter at mineral/water interfaces: I. ATR-FTIR spectroscopic and quantum chemical study of oxalate adsorbed at boehmite/water and corundum/water interfaces, Geochimica et Cosmochimica Acta, v. 68, pp. 45054518.Google Scholar

13.6 References

Bernal, J. D., Dasgupta, D. R. and Mackay, A. L. 1959. The oxides and hydroxides of iron and their structural inter-relationships. Clay Minerals Bulletin, 4, 15.Google Scholar
Brown, A. R., Wincott, P. L., Laverne, J. A., et al. 2014. The impact of γ radiation on the bioavailability of Fe(III) minerals for microbial respiration. Environmental Science & Technology, 48, 1067210680.Google Scholar
Byrne, J. M., Coker, V. S., Cespedes, E., et al. 2014. Biosynthesis of zinc substituted magnetite nanoparticles with enhanced magnetic properties. Advanced Functional Materials, 24, 25182529.Google Scholar
Byrne, J. M., Coker, V. S., Moise, S., et al. 2013. Controlled cobalt doping in biogenic magnetite nanoparticles. Journal of the Royal Society Interface, 10, 20130134.Google Scholar
Byrne, J. M., Klueglein, N., Pearce, C., et al. 2015. Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria. Science, 347, 14731476.Google Scholar
Byrne, J. M., Telling, N. D., Coker, V. S., et al. 2011. Control of nanoparticle size, reactivity and magnetic properties during the bioproduction of magnetite by Geobacter sulfurreducens. Nanotechnology, 22, 455709.Google Scholar
Chadwick, J., Jones, D. H., Thomas, M. F., Tatlock, G. J. and Devenish, R. W. 1986. A Mössbauer study of ferrihydrite and aluminium substituted ferrihydrites. Journal of Magnetism and Magnetic Materials, 61, 88100.Google Scholar
Chaudhuri, S. K., Lack, J. G. and Coates, J. D. 2001. Biogenic magnetite formation through anaerobic biooxidation of Fe(II). Applied and Environmental Microbiology, 67, 28442848.Google Scholar
Chen, C., Kukkadapu, R. and Sparks, D. L. 2015. Influence of coprecipitated organic matter on Fe2+(aq)-catalyzed transformation of ferrihydrite: Implications for carbon dynamics. Environmental Science & Technology, 49, 1092710936.Google Scholar
Cornell, R. M. and Schwertmann, U. 2003. The Iron Oxides: Structure, Properties, Reactions, Occurrences and Uses, Weinheim, Germany, Wiley-VCH.Google Scholar
Cutting, R. S., Coker, V. S., Fellowes, J. W., Lloyd, J. R. and Vaughan, D. J. 2009. Mineralogical and morphological constraints on the reduction of Fe(III) minerals by Geobacter sulfurreducens. Geochimica et Cosmochimica Acta, 73, 40044022.Google Scholar
Cuttler, A., Man, V., Cranshaw, T. and Longworth, G. 1990. A Mössbauer study of green rust precipitates: I. Preparations from sulphate solutions. Clay Minerals, 25, 289301.Google Scholar
De Grave, E. and Van Alboom, A. 1991. Evaluation of ferrous and ferric Mössbauer fractions. Physics and Chemistry of Minerals, 18, 337342.Google Scholar
Dippon, U., Pantke, C., Porsch, K., Larese-Casanova, P. and Kappler, A. 2012. Potential function of added minerals as nucleation sites and effect of humic substances on mineral formation by the nitrate-reducing Fe(II)-oxidizing strain Acidovorax sp. BoFeN1. Environmental Science & Technology, 46, 65566565.Google Scholar
Dippon, U., Schmidt, C., Behrens, S. and Kappler, A. 2015. Secondary mineral formation during ferrihydrite reduction by Shewanella oneidensis MR-1 depends on incubation vessel orientation and resulting gradients of cells, Fe2+ and Fe3+ minerals. Geomicrobiology Journal, 32, 868877.Google Scholar
Dong, H., Fredrickson, J. K., Kennedy, D. W., et al. 2000. Mineral transformations associated with the microbial reduction of magnetite. Chemical Geology, 169, 299318.Google Scholar
Drits, V., Sakharov, B., Salyn, A. and Manceau, A. 1993. Structural model for ferrihydrite. Clay Minerals, 28, 185207.Google Scholar
Dyar, M. D., Agresti, D. G., Schaefer, M. W., Grant, C. A. and Sklute, E. C. 2006. Mössbauer spectroscopy of earth and planetary materials. Annual Review of Earth and Planetary Sciences, 34, 83125.CrossRefGoogle Scholar
Eickhoff, M., Obst, M., Schröder, C., et al. 2014. Nickel partitioning in biogenic and abiogenic ferrihydrite: The influence of silica and implications for ancient environments. Geochimica et Cosmochimica Acta, 140, 6579.Google Scholar
Ericsson, T., Krishnamurthy, A. and Srivastava, B. K. 1986. Morin-transition in Ti-substituted hematite: A Mössbauer study. Physica Scripta, 33, 88.Google Scholar
Forester, D. W. and Koon, N. C. 1969. Mössbauer investigation of metamagnetic FeCO3. Journal of Applied Physics, 40, 13161317.Google Scholar
Forsyth, J. B., Johnson, C. E. and Wilkinson, C. 1970. The magnetic structure of vivianite, Fe3(PO4)2.8H2O. Journal of Physics C: Solid State Physics, 3, 1127.Google Scholar
Fortin, D., Leppard, G. G. and Tessier, A. 1993. Characteristics of lacustrine diagenetic iron oxyhydroxides. Geochimica et Cosmochimica Acta, 57, 43914404.Google Scholar
Frankel, R. B., Papaefthymiou, G. C., Blakemore, R. P. and O’Brien, W. 1983. Fe3O4 precipitation in magnetotactic bacteria. Biochimica et Biophysica Acta (BBA) – Molecular Cell Research, 763, 147159.Google Scholar
Fysh, S. and Clark, P. 1982. Aluminous hematite: A Mössbauer study. Physics and Chemistry of Minerals, 8, 257267.Google Scholar
Génin, J.-M. R., Bourrié, G., Trolard, F., et al. 1998. Thermodynamic equilibria in aqueous suspensions of synthetic and natural Fe(II)−Fe(III) green Rusts:  Occurrences of the mineral in hydromorphic soils. Environmental Science & Technology, 32, 10581068.Google Scholar
Gonser, U. and Grant, R. W. 1967. Determination of spin directions and electric field gradient axes in vivianite by polarized recoil-free γ-rays. Physica Status Solidi (B), 21, 331342.Google Scholar
Gorski, C. A., Handler, R. M., Beard, B. L., et al. 2012. Fe atom exchange between aqueous Fe2+ and magnetite. Environmental Science & Technology, 46, 1239912407.Google Scholar
Gorski, C. A. and Scherer, M. M. 2010. Determination of nanoparticulate magnetite stoichiometry by Mössbauer spectroscopy, acidic dissolution, and powder X-ray diffraction: A critical review. American Mineralogist, 95, 10171026.Google Scholar
Greenwood, N. N. and Gibb, T. C. 1971. Mössbauer Spectroscopy, London, Chapman and Hall Ltd.Google Scholar
Gütlich, P., Bill, E. and Trautwein, A. X. 2010. Mössbauer Spectroscopy and Transition Metal Chemistry: Fundamentals and Applications, Berlin Heidelberg, Springer Science & Business Media.Google Scholar
Gütlich, P., Schröder, C. and Schünemann, V. 2012. Mössbauer spectroscopy—an indispensable tool in solid state research. Spectroscopy Europe, 24, 21.Google Scholar
Handler, R. M., Beard, B. L., Johnson, C. M. and Scherer, M. M. 2009. Atom exchange between aqueous Fe(II) and goethite: An Fe isotope tracer study. Environmental Science & Technology, 43, 11021107.Google Scholar
Hirt, A. M., Lanci, L., Dobson, J., Weidler, P. and Gehring, A. U. 2002. Low-temperature magnetic properties of lepidocrocite. Journal of Geophysical Research: Solid Earth, 107, EPM 5–1-EPM 5–9.Google Scholar
Hohmann, C., Winkler, E., Morin, G. and Kappler, A. 2010. Anaerobic Fe(II)-oxidizing bacteria show As resistance and immobilize As during Fe(III) mineral precipitation. Environmental Science & Technology, 44, 94101.Google Scholar
Housley, R. M., Gonser, U. and Grant, R. W. 1968. Mössbauer determination of the Debye-Waller factor in single-crystal absorbers. Physical Review Letters, 20, 12791282.Google Scholar
Klein, C. 2005. Some Precambrian banded iron-formations (BIFs) from around the world: Their age, geologic setting, mineralogy, metamorphism, geochemistry, and origins. American Mineralogist, 90, 14731499.Google Scholar
Klingelhöfer, G., Morris, R. V., Bernhardt, B., et al. 2003. Athena MIMOS II Mössbauer spectrometer investigation. Journal of Geophysical Research: Planets, 108, 8067.Google Scholar
Klingelhöfer, G., Morris, R. V., Bernhardt, B., et al. 2004. Jarosite and hematite at Meridiani Planum from Opportunity’s Mössbauer spectrometer. Science, 306, 17401745.Google Scholar
Klingelhöfer, G., Morris, R. V., De Souza, P. A., Jr., Rodionov, D. and Schröder, C. 2006. Two earth years of Mössbauer studies of the surface of Mars with MIMOS II. Hyperfine Interactions, 170, 169177.Google Scholar
Klueglein, N. and Kappler, A. 2012. Abiotic oxidation of Fe(II) by reactive nitrogen species in cultures of the nitrate-reducing Fe(II) oxidizer Acidovorax sp. BoFeN1 – questioning the existence of enzymatic Fe(II) oxidation. Geobiology, 11, 396.Google Scholar
Kündig, W., Bömmel, H., Constabaris, G. and Lindquist, R. H. 1966. Some properties of supported small a-Fe2O3 particles determined with the Mössbauer effect. Physical Review, 142, 327333.Google Scholar
Kündig, W. and Steven Hargrove, R. 1969. Electron hopping in magnetite. Solid State Communications, 7, 223227.Google Scholar
Lagarec, K. and Rancourt, D. G. 1997. Extended Voigt-based analytic lineshape method for determining N-dimensional correlated hyperfine parameter distributions in Mössbauer spectroscopy. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 129, 266280.Google Scholar
Larese-Casanova, P., Haderlein, S. B. and Kappler, A. 2010. Biomineralization of lepidocrocite and goethite by nitrate-reducing Fe(II)-oxidizing bacteria: Effect of pH, bicarbonate, phosphate, and humic acids. Geochimica et Cosmochimica Acta, 74, 37213734.Google Scholar
Larese-Casanova, P. and Scherer, M. M. 2007. Fe(II) sorption on hematite:  New insights based on spectroscopic measurements. Environmental Science & Technology, 41, 471477.Google Scholar
Latta, D. E., Boyanov, M. I., Kemner, K. M., et al. 2012. Abiotic reduction of uranium by Fe(II) in soil. Applied Geochemistry, 27, 15121524.Google Scholar
Markovski, C., Byrne, J. M., Lalla, E., et al. 2017. Abiotic versus biotic iron mineral transformation studied by a miniaturized backscattering Mössbauer spectrometer (MIMOS II), X-ray diffraction and Raman spectroscopy. Icarus, 296, 4958.Google Scholar
Michel, F. M., Ehm, L., Antao, S. M., et al. 2007. The structure of ferrihydrite, a nanocrystalline material. Science, 316, 17261729.Google Scholar
Mikutta, C., Mikutta, R., Bonneville, S., et al. 2008. Synthetic coprecipitates of exopolysaccharides and ferrihydrite. Part I: Characterization. Geochimica et Cosmochimica Acta, 72, 11111127.Google Scholar
Miot, J. and Etique, M. 2016. Formation and Transformation of Iron-Bearing Minerals by Iron(II)-Oxidizing and Iron(III)-Reducing Bacteria. In Iron Oxides, ed. Faivre, D., Weinheim, Germany, Wiley-VCH Verlag GmbH & Co. KGaA.Google Scholar
Miot, J., Li, J., Benzerara, K., et al. 2014. Formation of single domain magnetite by green rust oxidation promoted by microbial anaerobic nitrate-dependent iron oxidation. Geochimica et Cosmochimica Acta, 139, 327343.Google Scholar
Morice, J. A., Rees, L. V. C. and Rickard, D. T. 1969. Mössbauer studies of iron sulphides. Journal of Inorganic and Nuclear Chemistry, 31, 37973802.Google Scholar
Mossbauer, R. L. 1958. Kernresonanzfluoreszenz von gammastrahlung in Ir-191. Zeitschrift Fur Physik, 151, 124143.Google Scholar
Murad, E. 1988. The Mössbauer spectrum of “well”-crystallized ferrihydrite. Journal of Magnetism and Magnetic Materials, 74, 153157.Google Scholar
Murad, E. 2010. Mössbauer spectroscopy of clays, soils and their mineral constituents. Clay Minerals, 45, 413430.Google Scholar
Murad, E. and Cashion, J. 2004. Mössbauer Spectroscopy of Environmental Materials and their Industrial Utilization, USA, Kluwer Academic Publishers.Google Scholar
Murad, E. and Schwertmann, U. 1986. Influence of Al substitution and crystal size on the room-temperature Mössbauer spectrum of hematite. Clays and Clay Minerals, 34, 16.Google Scholar
Nitzsche, K. S., Lan, V. M., Trang, P. T. K., et al. 2015. Arsenic removal from drinking water by a household sand filter in Vietnam – Effect of filter usage practices on arsenic removal efficiency and microbiological water quality. Science of the Total Environment, 502, 526536.Google Scholar
O’Loughlin, E. J.,Larese-Casanova, P.,Scherer, M. and Cook, R. 2007. Green rust formation from the bioreduction of γ–FeOOH (lepidocrocite): Comparison of several Shewanella species. Geomicrobiology Journal, 24, 211230.Google Scholar
Pankhurst, Q. and Pollard, R. 1992. Structural and magnetic properties of ferrihydrite. Clays and Clay Minerals, 40, 268272.Google Scholar
Pantke, C., Obst, M., Benzerara, K., et al. 2012. Green rust formation during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1. Environmental Science & Technology, 46, 14391446.Google Scholar
Prescher, C., McCammon, C. and Dubrovinsky, L. 2012. MossA: A program for analyzing energy-domain Mossbauer spectra from conventional and synchrotron sources. Journal of Applied Crystallography, 45, 329331.Google Scholar
Rancourt, D., McDonald, A., Lalonde, A. and Ping, J. 1993. Mössbauer absorber thicknesses for accurate site populations in Fe-bearing minerals. American Mineralogist, 78, 17.Google Scholar
Rancourt, D. G. and Ping, J. Y. 1991. Voigt-based methods for arbitrary-shape static hyperfine parameter distributions in Mössbauer spectroscopy. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 58, 8597.Google Scholar
Roden, E. E. and Zachara, J. M. 1996. Microbial reduction of crystalline iron(iii) oxides:  Influence of oxide surface area and potential for cell growth. Environmental Science & Technology, 30, 16181628.Google Scholar
Sawicki, J. and Brown, D. 1998. Investigation of microbial–mineral interactions by Mössbauer spectroscopy. Hyperfine Interactions, 117, 371382.Google Scholar
Srivastava, C. M., Shringi, S. N. and Babu, M. V. 1981. Mössbauer study of the low-temperature phase of magnetite. Physica Status Solidi (A), 65, 731735.Google Scholar
Stookey, L. L. 1970. Ferrozine – a new spectrophotometric reagent for iron. Analytical Chemistry, 42, 779781.Google Scholar
Swanner, E. D., Wu, W., Schoenberg, R., et al. 2015. Fractionation of Fe isotopes during Fe (II) oxidation by a marine photoferrotroph is controlled by the formation of organic Fe-complexes and colloidal Fe fractions. Geochimica et Cosmochimica Acta, 165, 4461.Google Scholar
ThomasArrigo, L. K., Mikutta, C., Byrne, J., et al. 2014. Iron and arsenic speciation and distribution in organic flocs from streambeds of an arsenic-enriched peatland. Environmental Science & Technology, 48, 1321813228.Google Scholar
van der Zee, C., Roberts, D. R., Rancourt, D. G. and Slomp, C. P. 2003. Nanogoethite is the dominant reactive oxyhydroxide phase in lake and marine sediments. Geology, 31, 993996.Google Scholar
Vandenberghe, R. E., De Grave, E., De Bakker, P. M. A., Krs, M. and Hus, J. J. 1992. Mössbauer effect study of natural greigite. Hyperfine Interactions, 68, 319322.Google Scholar
Vollrath, S., Behrends, T., Koch, C. B. and Cappellen, P. V. 2013. Effects of temperature on rates and mineral products of microbial Fe(II) oxidation by Leptothrix cholodnii at microaerobic conditions. Geochimica et Cosmochimica Acta, 108, 107124.Google Scholar
Wan, M., Schröder, C. and Peiffer, S. 2017. Fe(III):S(-II) concentration ratio controls the pathway and the kinetics of pyrite formation during sulfidation of ferric hydroxides. Geochimica et Cosmochimica Acta, 217, 334348.Google Scholar
Williams, A. G. B. and Scherer, M. M. 2004. Spectroscopic evidence for Fe(II)−Fe(III) electron transfer at the iron oxide−water interface. Environmental Science & Technology, 38, 47824790.Google Scholar
Žák, T. and Jirásková, Y. 2006. CONFIT: Mössbauer spectra fitting program. Surface and Interface Analysis, 38, 710714.Google Scholar
Zegeye, A., Abdelmoula, M., Usman, M., Hanna, K. and Ruby, C. 2011. In situ monitoring of lepidocrocite bioreduction and magnetite formation by reflection Mössbauer spectroscopy. American Mineralogist, 96, 14101413.Google Scholar
Ziganshin, A. M., Ziganshina, E. E., Byrne, J., et al. 2015. Fe(III) mineral reduction followed by partial dissolution and reactive oxygen species generation during 2,4,6-trinitrotoluene transformation by the aerobic yeast Yarrowia lipolytica. AMB Express, 5(8), 112.Google Scholar

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×