X-ray Diffraction Techniques

doi:10.1017/9781107707399.009

9 - X-ray Diffraction Techniques

from Part IV - Spectroscopy

Published online by Cambridge University Press: 06 July 2019

Daniel K. Unruh and

Tori Z. Forbes

Edited by

Janice P. L. Kenney ,

Harish Veeramani and

Daniel S. Alessi

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

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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.

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Type: Chapter
Information: Analytical Geomicrobiology
A Handbook of Instrumental Techniques
, pp. 215 - 237

DOI: https://doi.org/10.1017/9781107707399.009 [Opens in a new window]

Publisher: Cambridge University Press

Print publication year: 2019

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References

9.6 References

Achal, V, Pan, X, Fu, Q and Zhang, D 2012, ‘Biomineralization based remediation of As(III) contaminated soil by Sporosarcina ginsengisoli’ Journal of Hazardous Materials, vol. 201–202, pp. 178–184.Google Scholar

Alam, S, Patel, S and Bansal, AK 2010, ‘Effect of sample preparation method on quantification of polymorphs using PXRD’ Pharmaceutical Development and Technology, vol. 15, no. 5, pp. 452–459.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. 3447–3453.Google Scholar

Baskar, S, Baskar, R, and Routh, J 2014, ‘Speleothems from Sahastradhara Caves in Siwalik Himalaya, India: Possible biogenic inputs’ Geomicrobiology Journal, vol. 31, no. 8, pp. 664–681.Google 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 subsurface’ Geomicrobiology Journal, vol. 26, pp. 431–441.Google 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. 423–428.Google Scholar

Benzerara, K, Morin, G, Yoon, TH, et al. 2008, ‘Nanoscale study of As biomineralization in an acid mine drainage system’ Geochimica et Cosmochimica Acta, vol. 72, no. 16, pp. 3949–3963.Google Scholar

Bertel, D, Peck, J, Quick, JQ and Senko, JM 2012, ‘Iron transformations induced by an acid-tolerant Desulfosporosinus species’ Applied and Environmental Microbiology, vol. 78, pp. 81–88.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 analysis’ Powder Diffraction, vol. 4, pp. 137–143.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)2’ Advances in X-ray Analysis, vol. 43, pp. 273–280.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. 1–15.Google Scholar

Brayner, R, Yepremain, C, Djediat, C, et al. 2009, ‘Photosynthetic microorganism-mediated synthesis of akaganeite (β-FeOOH) nanorods’ Langmuir, vol. 25, no. 17, pp. 10062–10067.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. 78–96.CrossRef Google Scholar

Das, R, Ali, ME and Abd Hamid, SB 2014, ‘Current applications of X-ray powder diffraction – a review’ Reviews on Advanced Materials Science, vol. 38, pp. 95–109.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. 6517–6530.Google 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 database’ American Mineralogist, vol. 88, no. 1, pp. 247–250.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. 7384–7390.Google Scholar

Fischer, A, Schmitz, M, Aichmayer, B, Fratzl, P and Faivre, D 2011, ‘Structural purity of magnetite nanoparticles in magnetotactic bacteria’ Journal of the Royal Society Interface, vol. 8, pp. 1011–1018.Google Scholar

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 systems’ Chemical Geology, vol. 284, no. 1, pp. 82–96.CrossRef 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. 406–413.Google Scholar

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. 2913–2924.CrossRef 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. 102–133.Google 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 diffraction’ IUCr: Newsletter of the CPD, vol. 21, pp. 14–15.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 remediation’ Geochimica et Cosmochimica Acta, vol. 104, pp. 310–329.CrossRef Google 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. 154–160.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 process’ Geochimica et Cosmochimica Acta, vol. 73, no. 14, pp. 4180–4198.CrossRef Google 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. 79–90.CrossRef Google 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. 4471–4487.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 environments’ Journal of Geophysical Research: Biogeosciences, vol. 118, pp. 1397–1413.Google Scholar

Pesenti, H, Leoni, M, and Scardi, P 2008, ‘XRD line profile analysis of calcite powders produced by high energy milling’ Zeitschrift fur Kristallographie, vol. 27, no. 27, pp. 143–150.Google Scholar

Piepenbrock, A, Dippon, U, Porsch, K, Appel, E and Kappler, A 2011, ‘Dependence of microbial magnetite formation on humic substance and ferrihydrite concentrations’ Geochimica et Cosmochimica Acta, vol. 75, pp. 6844–6858.Google Scholar

Pokroy, B, Quintana, JP, Caspi, EAN, Berner, A and Zolotoyabko, E 2004, ‘Anisotropic lattice distortions in biogenic aragonite’ Nature Materials, vol. 3, no. 12, pp. 900–902.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 molecules’ Journal of Structural Biology, vol. 155, pp. 96–103.Google Scholar

Roden, EE, Leonardo, MR, and Ferris, FG 2002, ‘Immobilization of strontium during iron biomineralization coupled to dissimilatory hydrous ferric oxide reduction’ Geochimica et Cosmochimica Acta. vol. 66, pp. 2823–2839.Google Scholar

Rodriguez-Carvajal, J 2001, ‘Recent developments of the program FULLPROF’ Commission on Powder Diffraction (IUCr) Newsletter, vol. 26, pp. 12–19.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 regions’ Geobiology, vol. 12, no. 6, pp. 542–556.Google Scholar

Rudolf, PR and Landes, BG 1994, ‘Two-dimensional X-ray diffraction and scattering of microcrystalline and polymeric materials’ Spectroscopy, vol. 9, no. 6, pp. 22–33.Google Scholar

Scherrer, P 1918, ‘Bestimmung der Grosse und der Inneren Struktur von Kolloidteilchen Mittels Rontgenstrahlen’ Nachrichten von der Gesellschaft der Wissenschaften, vol. 26, pp. 98–100.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 crisis’ Water Research, vol. 54, pp. 33–43.CrossRef Google Scholar PubMed

Sulyanov, SN, Popov, AN and Kheiker, DM 1994, ‘Using a two-dimensional detector for X-ray powder diffractometry’ Journal of Applied Crystallography, vol. 27, pp. 934–942.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 bacteria’ Canadian Journal of Earth Sciences, vol. 40, no. 11, pp. 1725–1738.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 land’ Applied Geochemistry, vol. 40, pp. 135–143.Google Scholar

Till, JL, Guyodo, Y, Lagroix, F, Ona-Guema, G, and Brest, J 2014, ‘Magnetic comparison of abiogenic and biogenic alteration products of lepidocrocite’ Earth and Planetary Science Letters, vol. 395, pp. 149–158.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. 388–403.Google Scholar

Verman, B and Kim, B 2004, ‘Analytical comparison of parallel beam and Bragg-Brentano diffractometer performances’ Materials Science Forum, vol. 443–444, pp. 167–170.Google Scholar

Villalobos, M, Lanson, B, Manceau, A, Toner, B and Sposito, G 2006, ‘Structural model for the biogenic Mn oxide produced by Pseudomonas putida’ American Mineralogist, vol. 91, no. 4, pp. 489–502.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 contaminants’ Geomicrobiology Journal, vol. 18, no. 1, pp. 93–115.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. 92–96.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. 179–207.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 culture’ Geomicrobiology Journal, vol. 22, no. 7–8, pp. 389–399.Google Scholar

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