Hostname: page-component-78c5997874-t5tsf Total loading time: 0 Render date: 2024-11-19T06:31:15.721Z Has data issue: false hasContentIssue false
  • English
  • Français

Synchrotron-Based Chemical Nano-Tomography of Microbial Cell-Mineral Aggregates in their Natural, Hydrated State

Published online by Cambridge University Press:  19 February 2014

Gregor Schmid ,
Fabian Zeitvogel ,
Likai Hao ,
Pablo Ingino ,
Wolfgang Kuerner ,
James J. Dynes ,
Chithra Karunakaran ,
Jian Wang ,
Yingshen Lu  and
Travis Ayers
...Show all authors
Gregor Schmid
Affiliation:
Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany
Fabian Zeitvogel
Affiliation:
Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany
Likai Hao
Affiliation:
Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany
Pablo Ingino
Affiliation:
Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany
Wolfgang Kuerner
Affiliation:
Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany
James J. Dynes
Affiliation:
Canadian Light Source Inc., Saskatoon, Canada
Chithra Karunakaran
Affiliation:
Canadian Light Source Inc., Saskatoon, Canada
Jian Wang
Affiliation:
Canadian Light Source Inc., Saskatoon, Canada
Yingshen Lu
Affiliation:
Canadian Light Source Inc., Saskatoon, Canada
Travis Ayers
Affiliation:
Luxel Corp., Friday Harbor, USA
Chuck Schietinger
Affiliation:
Luxel Corp., Friday Harbor, USA
Adam P. Hitchcock
Affiliation:
McMaster University, Hamilton, Canada
Martin Obst*
Affiliation:
Department of Geosciences, Center for Applied Geoscience, University of Tuebingen, Hoelderlinstr. 12, 72074 Tuebingen, Germany
*
*Corresponding author. [email protected]
Get access

Abstract

Chemical nano-tomography of microbial cells in their natural, hydrated state provides direct evidence of metabolic and chemical processes. Cells of the nitrate-reducing Acidovorax sp. strain BoFeN1 were cultured in the presence of ferrous iron. Bacterial reduction of nitrate causes precipitation of Fe(III)-(oxyhydr)oxides in the periplasm and in direct vicinity of the cells. Nanoliter aliquots of cell-suspension were injected into custom-designed sample holders wherein polyimide membranes collapse around the cells by capillary forces. The immobilized, hydrated cells were analyzed by synchrotron-based scanning transmission X-ray microscopy in combination with angle-scan tomography. This approach provides three-dimensional (3D) maps of the chemical species in the sample by employing their intrinsic near-edge X-ray absorption properties. The cells were scanned through the focus of a monochromatic soft X-ray beam at different, chemically specific X-ray energies to acquire projection images of their corresponding X-ray absorbance. Based on these images, chemical composition maps were then calculated. Acquiring projections at different tilt angles allowed for 3D reconstruction of the chemical composition. Our approach allows for 3D chemical mapping of hydrated samples and thus provides direct evidence for the localization of metabolic and chemical processes in situ.

Keywords

chemical tomographyhydratedbacteriaSTXMsoft X-rays3D
Type
Biological Applications
Information
Microscopy and Microanalysis , Volume 20 , Issue 2 , April 2014 , pp. 531 - 536
Copyright
© Microscopy Society of America 2014 

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

Bluhm, H., Andersson, K., Araki, T., Benzerara, K., Brown, G.E., Dynes, J.J., Ghosal, S., Gilles, M.K., Hansen, H.C., Hemminger, J.C., Hitchcock, A.P., Ketteler, G., Kilcoyne, A.L.D., Kneedler, E., Lawrence, J.R., Leppard, G.G., Majzlan, J., Mun, B.S., Myneni, S.C.B., Nilsson, A., Ogasawara, H., Ogletree, D.F., Pecher, K., Salmeron, M., Shuh, D.K., Tonner, B., Tyliszczak, T., Warwick, T. & Yoon, T.H. (2006). Soft X-ray microscopy and spectroscopy at the molecular environmental science beamline at the advanced light Source. J Electron Spectrosc 150(2–3), 86–104.Google Scholar
Chao, W., Fischer, P., Tyliszczak, T., Rekawa, S., Anderson, E. & Naulleau, P. (2012). Real space soft x-ray imaging at 10 nm spatial resolution. Opt Express 20(9), 9777–9783.Google Scholar
Dynes, J.J., Tyliszczak, T., Araki, T., Lawrence, J.R., Swerhone, G.D.W., Leppard, G.G. & Hitchcock, A.P. (2006). Speciation and quantitative mapping of metal species in microbial biofilms using scanning transmission X-ray microscopy. Environ Sci Technol 40(5), 1556–1565.CrossRefGoogle ScholarPubMed
Hanhan, S., Smith, A.M., Obst, M. & Hitchcock, A.P. (2009). Optimization of analysis of soft X-ray spectromicroscopy at the Ca 2p edge. J Electron Spectrosc 173(1), 44–49.Google Scholar
Henke, B.L., Gullikson, E.M. & Davis, J.C. (1993). X-ray interactions—Photoabsorption, scattering, transmission, and reflection at E=50-30,000 Ev, Z=1-92. Atom Data Nucl Data 54(2), 181–342.Google Scholar
Hitchcock, A.P. (2012). Soft X-ray imaging and spectromicroscopy. In Handbook of Nanoscopy, van Tendeloo, G., van Dyck, D. & Pennycook, S.J. (Eds.), pp. 745–791. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA.Google Scholar
Hitchcock, A.P. (2013). aXis2000 Is an IDL-Based Analytical Package. Available at http://unicorn.mcmaster.ca/aXis2000.html, free of charge for non-commercial use.Google Scholar
Hitchcock, A.P., Obst, M., Wang, J., Lu, Y.S. & Tyliszczak, T. (2012). Advances in the detection of as in environmental samples using low energy X-ray fluorescence in a scanning transmission X-ray microscope: Arsenic immobilization by an Fe(II)-oxidizing freshwater bacteria. Environ Sci Technol 46(5), 2821–2829.Google Scholar
Hunter, R.C., Hitchcock, A.P., Dynes, J.J., Obst, M. & Beveridge, T.J. (2008). Mapping the speciation of iron in Pseudomonas aeruginosa biofilms using scanning transmission X-ray microscopy. Environ Sci Technol 42(23), 8766–8772.Google Scholar
Johansson, G.A., Dynes, J.J., Hitchcock, A.P., Tyliszczak, T., Swerhone, G.D. & Lawrence, J.R. (2006). Chemically sensitive tomography at 50 nm spatial resolution using a soft X-ray scanning transmission X-ray microscope. Microsc Microanal 12(S02), 1412.Google Scholar
Johansson, G.A., Tyliszczak, T., Mitchell, G.E., Keefe, M.H. & Hitchcock, A.P. (2007). Three-dimensional chemical mapping by scanning transmission X-ray spectromicroscopy. J Synchrotron Radiat 14(Pt 5), 395–402.Google Scholar
Kappler, A., Schink, B. & Newman, D.K. (2005). Fe(III) mineral formation and cell encrustation by the nitrate-dependent Fe(II)-oxidizer strain BoFeN1. Geobiology 3(4), 235–245.Google Scholar
Kaznatcheev, K.V., Karunakaran, C., Lanke, U.D., Urquhart, S.G., Obst, M. & Hitchcock, A.P. (2007). Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results. Nucl Instrum Meth A 582(1), 96–99.Google Scholar
Kilcoyne, D., Ade, H., Attwood, D., Hitchcock, A., McKean, P., Mitchell, G., Monteiro, P., Tyliszczak, T. & Warwick, T. (2010). A new scanning transmission X-ray microscope at the ALS for operation up to 2500 eV. AIP Conf Proc 1234(1), 465–468.Google Scholar
Koprinarov, I.N., Hitchcock, A.P., McCrory, C.T. & Childs, R.F. (2002). Quantitative mapping of structured polymeric systems using singular value decomposition analysis of soft X-ray images. J Phys Chem B 106(21), 5358–5364.Google Scholar
Kremer, J.R., Mastronarde, D.N. & McIntosh, J.R. (1996). Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116(1), 71–76.Google Scholar
Midgley, P.A. & Weyland, M. (2003). 3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography. Ultramicroscopy 96(3–4), 413–431.Google Scholar
Miot, J., Benzerara, K., Morin, G., Kappler, A., Bernard, S., Obst, M., Ferard, C., Skouri-Panet, F., Guigner, J.M., Posth, N., Galvez, M., Brown, G.E. & Guyot, F. (2009). Iron biomineralization by anaerobic neutrophilic iron-oxidizing bacteria. Geochim Cosmochim Acta 73(3), 696–711.Google Scholar
Miot, J., Maclellan, K., Benzerara, K. & Boisset, N. (2011). Preservation of protein globules and peptidoglycan in the mineralized cell wall of nitrate-reducing, iron(II)-oxidizing bacteria: a cryo-electron microscopy study. Geobiology 9(6), 459–470.Google Scholar
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C. & Ferrin, T.E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. J Comput Chem 25(13), 1605–1612.Google Scholar
Schmid, G. & Obst, M. (2013). 3D chemical mapping: Application of scanning transmission (soft) X-ray microscopy (STXM) in combination with angle-scan tomography in bio-, geo- and environmental science. In Methods in Molecular Biology: Electron Microscopy, Kuo, J. (Ed.), pp. 757–781. Springer New York: Humana Press.Google Scholar
Stewart-Ornstein, J., Hitchcock, A.P., Cruz, D.H., Henklein, P., Overhage, J., Hilpert, K., Hale, J.D. & Hancock, R.E.W. (2007). Using intrinsic X-ray absorption spectral differences to identify and map peptides and proteins. J Phys Chem B 111(26), 7691–7699.Google Scholar
Thompson, A.C., Attwood, D., Gullikson, E., Howells, M., Kim, K.J., Kirz, J., Kortright, J., Lindau, I., Liu, Y., Pianetta, P., Robinson, A., Scofield, J., Underwood, J., Williams, G. & Winick, H. (2009). X-ray properties of the elements. In X-Ray Data Booklet, Thompson, A.C. (Ed.), pp. 1–53. Berkeley: Lawrence Berkeley National Laboratory.Google Scholar
Wang, J., Hitchcock, A.P., Karunakaran, C., Prange, A., Franz, B., Harkness, T., Lu, Y., Obst, M. & Hormes, J. (2011). 3D chemical and elemental imaging by STXM spectrotomography. In AIP Conference Proceedings 1365, McNulty, I., Eyberger, C. & Lai, B. (Eds.), pp. 215–218. New York: AIP Publishing.Google Scholar

Schmid Supplementary Material

Movie 1

Download Schmid Supplementary Material(Video)
Video 7.7 MB