Scanning Hard X-ray Microscopy Imaging Modalities for Geobiological Samples

References

• Abbey B.. 2013. From grain boundaries to single defects: A review of coherent methods for materials imaging in the X-ray sciences. JOM-J Min Met Mat S 65:11831201.
   Web of Science ®Google Scholar
• Als-Nielsen J, McMorrow D. 2011. Elements of Modern X-ray Physics, 2nd ed. Chichester, West Sussex: Wiley & Sons, Ltd. p1–421.
   Google Scholar
• Beckers M., Senkbeil T., Gorniak T., Reese M., Giewekemeyer K., Gleber S-C, Salditt T., Rosenhahn A.. 2011. Chemical contrast in soft X-ray ptychography. Phys Rev Lett 107:208101.
   PubMed Web of Science ®Google Scholar
• Benzerara K., Menguy N., Obst M., Stolarski J., Mazur M., Tylisczak T., G E., Meibom A. 2011. Study of the crystallographic architecture of corals at the nanoscale by scanning transmission X-ray microscopy and transmission electron microscopy. Ultramicroscopy 111:1268–1275.
   PubMed Web of Science ®Google Scholar
• Bilderback DH, Elleaume P., Weckert E. 2005. Review of third and next generation synchrotron light sources. J Phys B: Atom Mol Opt Phys 38:S773–S797.
   Web of Science ®Google Scholar
• Chapman HN, Nugent KA. 2010. Coherent lensless X-ray imaging. Nat Photonics 4:833–839.
   Web of Science ®Google Scholar
• Cosmidis J., Benzerara K. 2014. Soft X-ray scanning transmission spectromicroscopy. In: DiMasi E., Gower LB., editors. Biomineralization Sourcebook: Characterization of Biominerals and Biomimetic Materials, 1st ed. New York: CRC Press Taylor & Francis Group, p115–134.
   Google Scholar
• Dahl C., Prange A. 2006. Bacterial sulfur globules: occurrence, structure and metabolism. In: Shively JM, editor. Inclusions in Prokaryotes: Microbial Monographs. Berlin: Springer, p21–51.
   Google Scholar
• Dierolf M., Menzel A., Thibault P., Schneider P., Kewish CM, Wepf R., Bunk O., Pfeiffer F. 2010. Ptychographic X-ray computed tomography at the nanoscale. Nature 467:436–439.
   PubMed Web of Science ®Google Scholar
• Fallon SJ, McCulloch MT, Guilderson TP. 2005. Interpreting environmental signals from the coralline sponge Astrosclera willeyana. In: Schöne BR, Surge D, editors. Looking back over Skeletal Diaries - High-resolution Environmental Reconstructions from Accretionary Hard Parts of Aquatic Organisms. Palaeogeogr Palaeocl 228:58–69.
   Google Scholar
• Färber G., Keller W., Kratky C., Jaun B., Pfaltz A., Spinner C., Kobelt A., Eschenmoser A. 1991. Coenzyme F430 from methanogenic bacteria: Complete assignment of configuration based on an X-ray analysis of 12,13-diepi-F430-pentamethyl ester and on NMR-spectroscopy. Helv Chim Acta 74:697–716.
   Web of Science ®Google Scholar
• Giewekemeyer K., Beckers M., Gorniak T., Grunze M., Salditt T., Rosenhahn A. 2011. Ptychographic coherent X-ray diffractive imaging in the water window. Opt Express 19:1037–1050.
   PubMed Web of Science ®Google Scholar
• Giewekemeyer K., Thibault P., Kalbfleisch S., Beerlink A., Kewish CM, Dierolf M., Pfeiffer F., Salditt T. 2010. Quantitative biological imaging by ptychographic X-ray diffraction microscopy. P Natl Acad Sci USA 107:529–534.
   PubMed Web of Science ®Google Scholar
• Hallam SJ, Girguis PR, Preston CM, Richardson PM, DeLong EF. 2003. Identification of methyl coenzyme M reductase A (mcrA) Genes associated with methane-oxidizing archaea. Appl Environ Microb 69:5483–5491.
   PubMed Web of Science ®Google Scholar
• Hallam SJ, Putnam N., Preston CM, Detter JC, Rokhsar D., Richardson PM, DeLong EF. 2004. Reverse methanogenesis: Testing the hypothesis with environmental genomics. Science 305:1457–1462.
   PubMed Web of Science ®Google Scholar
• Heim C, Quéric N-V, Ionescu D, Simon K, Thiel V. 2014. Chemolithotrophic microbial mats in an open pond in the continental subsurface – implications for microbial biosignatures. In: Wiese F., Reich M., Arp G., editors. “Göttingen Contributions to Geosciences”, vol. 70, “Spongy, slimy, cosy & more”. Göttingen, Germany: Universitätsverlag Göttingen, p99–112.
   Google Scholar
• Heller C., Hoppert M., Reitner J. 2008. Immunological localization of coenzyme M reductase in anaerobic methane-oxidizing archaea of ANME 1 and ANME 2 type. Geomicrobiol J 25:149–156.
   Web of Science ®Google Scholar
• Henke BL, Gullikson EM, Davis JC. 1993. X-ray Interactions: Photoabsorption, Scattering, Transmission, and Reflection at E = 50-30,000 eV, Z = 1-92. Atom Data Nucl Data Tables 54:181342.
   Web of Science ®Google Scholar
• Hentunen TA, Harkonen PL, Vaananen HK. 2000. Carbonic anhydrases in calcified tissues. In: Chegwidden WR, Carter ND, Edwards YH, editors. The Carbonic Anhydrases: New Horizons, vol. Basel, Switzerland: 90. Basel, Switzerland, p491–497.
   Google Scholar
• Hitchcock A., Tyliszczak T., Obst M., Swerhone G., Lawrence J. 2010. Improving sensitivity in soft X-ray STXM Using low energy X-ray fluorescence. Microsc Microanal 16:924–925.
   Google Scholar
• Hoffmann F., Janussen D., Dröse W., Arp G., Reitner J. 2003. Histological investigation of organisms with hard skeletons: a case study of siliceous sponges. Biotech Histochem 78:191–199.
   PubMed Web of Science ®Google Scholar
• Hoppe W. 1969a. Beugung im inhomogenen Primärstrahlwellenfeld. I. Prinzip einer Phasenmessung von Elektronenbeungungsinterferenzen. Acta Crystallogr A 25:495–501.
   Web of Science ®Google Scholar
• Hoppe W. 1969b. Beugung im inhomogenen Primärstrahlwellenfeld. III. Amplituden- und Phasenbestimmung bei unperiodischen Objekten. Acta Crystallogr A 25:508–514.
   Web of Science ®Google Scholar
• Hoppe W., Strube G. 1969. Beugung in inhomogenen Primärstrahlenwellenfeld. II. Lichtoptische Analogieversuche zur Phasenmessung von Gitterinterferenzen. Acta Crystallogr A 25:502–507.
   Web of Science ®Google Scholar
• Hoppe R., Reinhardt J., Hofmann G., Patommel J., Grunwaldt J-D, Damsgaard CD, Wellenreuther G., Falkenberg G., Schroer CG. 2013. High-resolution chemical imaging of gold nanoparticles using hard X-ray ptychography. Appl Phys Lett 102:203104.
   Web of Science ®Google Scholar
• Jackson DJ, Macis L., Reitner J., Degnan BM, Wörheide G. 2007. Sponge paleogenomics reveals an ancient role for carbonic anhydrase in skeletogenesis. Science 316:1893–1895.
   PubMed Web of Science ®Google Scholar
• Kirz J., Jacobsen C., Howells M. 1995. Soft X-ray microscopes and their biological applications. Q Rev Biophys 28:33–130.
   PubMed Web of Science ®Google Scholar
• Kneip S., McGuffey C., Martins JL, Martins SF, Bellei C., Chvykov V., Dollar F., Fonseca R., Huntington C., Kalintchenko G., Maksimchuk A., Mangles SPD, Matsuoka T., Nagel SR, Palmer CAJ, Schreiber J., Phuoc KT, Thomas AGR, Yanovsky V., Silva LO, Krushelnick K., Najmudin Z. 2010. Bright spatially coherent synchrotron X-rays from a table-top source. Nat Phys 6:980–983.
   Web of Science ®Google Scholar
• Kraft P., Bergamaschi A., Broennimann C., Dinapoli R., Eikenberry EF, Henrich B., Johnson I., Mozzanica A., Schleputz CM, Willmott PR, Schmitt B. 2009. Performance of single-photon-counting PILATUS detector modules. J Synchrotron Radiat 16:368–375.
   PubMed Web of Science ®Google Scholar
• Krüger M., Meyerdierks A., Glöckner FO, Amann R., Widdel F., Kube M., Reinhardt R., Kahnt J., Böcher R., Thauer RK, Shima S. 2003. A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426:878–881.
   PubMed Web of Science ®Google Scholar
• Larabell CA, Nugent KA. 2010. Imaging cellular architecture with X-rays. Curr Opin Struc Biol 20:623–631.
   PubMed Web of Science ®Google Scholar
• Lima E., Diaz A., Guizar-Sicairos M., Gorelick S., Pernot P., Schleier T., Menzel A. 2013. Cryo-scanning X-ray diffraction microscopy of frozen-hydrated yeast. J Microsc 249:1–7.
   Web of Science ®Google Scholar
• Lister JJ. 1900. Astrosclera willeyana, the type of a new family of sponges. Zool Results 4:461–482.
   Google Scholar
• Llopart X., Campbell M., Dinapoli R., San Segundo D, Pernigotti E. 2002. Medipix2: A 64k pixel readout chip with55μ, square elements working in single photon counting mode. IEEE T Nucl Sci 49:2279–2283.
   Web of Science ®Google Scholar
• Maiden AM, Rodenburg JM. 2009. An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109:1256–1262.
   PubMed Web of Science ®Google Scholar
• Maiden A., Morrison G., Kaulich B., Gianoncelli A., Rodenburg J. 2013. Soft X-ray spectromicroscopy using ptychography with randomly phased illumination. Nat Commun 4:1669.
   PubMed Web of Science ®Google Scholar
• Maki J. 2013. Bacterial intracellular sulfur globules: Structure and function. J Mol Microbiol Biotechnol 23:270–280.
   PubMed Web of Science ®Google Scholar
• Meyerdierks A., Kube M., Kostadinov I., Teeling H., Glöckner FO, Reinhardt R., Amann R. 2010. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ Microbiol 12:422–439.
   PubMed Web of Science ®Google Scholar
• Miao J., Charalambous P., Kirz J., Sayre D. 1999. Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens. Nature 400:342–344.
   Web of Science ®Google Scholar
• Miao JW, Sandberg RL, Song CY. 2012. Coherent X-ray Diffraction imaging. IEEE J Select Top Quant 18:399–410.
   Web of Science ®Google Scholar
• Michaelis W., Seifert R., Nauhaus K., Treude T., Thiel V., Blumenberg M., Knittel K., Gieseke A., Peterknecht K., Pape T., Boetius A., Amann R., Jørgensen B B, Widdel F., Peckmann J., Pimenov NV, Gulin MB. 2002. Microbial reefs in the Black sea fueled by anaerobic oxidation of methane. Science 297:1013–1015.
   PubMed Web of Science ®Google Scholar
• Miot J., Benzerara K., Morin G., Bernard S., Beyssac O., Larquet E., Kappler A., Guyot F. 2009. Transformation of vivianite by anaerobic nitrate-reducing iron-oxidizing bacteria. Geobiol 7:373–384.
   PubMed Web of Science ®Google Scholar
• Morrison G., Eaton W., Barrett R., Charalambous P. 2003. STXM imaging with a configured detector. J Phys IV 104:547–550.
   Google Scholar
• Morrison G., Niemann B. 1998. Differential phase contrast x-ray microscopy. In: Thieme, J., Schmahl, G., Rudolph, D., Umbach, E., editors. X-ray microscopy and spectromicroscopy: status report from the Fifth International Conference, Würzburg, August 19–23, 1996, Part I. Springer Berlin Heidelberg:85–94.
   Google Scholar
• Nauhaus K., Treude T., Boetius A., Krüger M. 2005. Environmental regulation of the anaerobic oxidation of methane: a comparison of ANME-I and ANME-II communities. Environ Microbiol 7:98–106.
   PubMed Web of Science ®Google Scholar
• Nielsen PH, De Muro MA, Nielsen JL. 2000. Studies on the in situ physiology of Thiothrix spp. present in activated sludge. Environ Microbiol 2:389–398.
   PubMed Web of Science ®Google Scholar
• Obst M., Schmid G. 2014. 3D chemical mapping: Application of scanning transmission (Soft) X-ray microscopy (STXM) in combination with angle-scan tomography in bio-, geo-, and environmental sciences. In: Kuo J., editor. Electron Microscopy Methods in Molecular Biology, Vol. 1117, 3rd ed. New York: Springer Science+Business Media, p757–781.
   Google Scholar
• Obst M., Wang J., Hitchcock AP. 2009. Soft X-ray spectro-tomography study of cyanobacterial biomineral nucleation. Geobiol 7:577–591.
   PubMed Web of Science ®Google Scholar
• Ohradanova A., Vullo D., Pastorekova S., Pastorek J., Jackson DJ, Wörheide G., Supuran CT. 2012. Anion inhibition studies of an α-carbonic anhydrase from the living fossil Astrosclera willeyana. Bioorg Med Chem Lett 22:1314–1316.
   PubMed Web of Science ®Google Scholar
• Pfaltz A., Jaun B., Fassler A., Eschenmoser A., Jaenchen R., Gilles HH, Diekert G., Thauer RK. 1982. Zur Kenntnis des Faktors F430 aus methanogenen Bakterien: Struktur des porphinoiden Ligandsystems. Helv Chim Acta 65:828–865.
   Web of Science ®Google Scholar
• Ponchut C., Clément J., Rigal J-M, Papillon E., Vallerga J., LaMarra D., Mikulec B. 2007. Photon-counting X-ray imaging at kilohertz frame rates. In: Bisogni MG, Rosso V, editors. Proceedings of the 8th International Workshop on Radiation Imaging Detectors, Pisa Italy July 2006. Nucl Instrum Meth A: Accelerators, Spectrometers, Detectors and Associated Equipment 576:109–112.
   Google Scholar
• Ponchut C., Rigal JM, Clément J., Papillon E., Homs A., Petitdemange S. 2011. MAXIPIX, a fast readout photon-counting X-ray area detector for synchrotron applications. J Instrum 6:C01069.
   Web of Science ®Google Scholar
• Pósfai M, Buseck PR, Bazylinsky DA, Frankel RB. 1998. Iron sulfides from magnetotactic bacteria: structure, composition, and phase transitions. Am Mineral 83:1469–1481.
   Web of Science ®Google Scholar
• Reitner J. 1992. Coralline Spongien - Der Versuch einer phylo-genetisch-taxonomischen Analyse. Berl geowiss Abh E 1:1–352.
   Google Scholar
• Reitner J., Peckmann J., Blumenberg M., Michaelis W., Reimer A., Thiel V. 2005a. Concretionary methane-seep carbonates and associated microbial communities in Black Sea sediments. In: Peckmann J, Goedert JL, editors. Geobiology of Ancient and Modern Methane-Seeps - Geobiology of Ancient and Modern Methane-Seeps, Palaeogeogr Palaeocl Vol. 227, Amsterdam: Elsevier, p18–30.
   Google Scholar
• Reitner J., Peckmann J., Reimer A., Schumann G., Thiel V. 2005b. Methane-derived carbonate build-ups and associated microbial communities at cold seeps on the lower Crimean shelf (Black Sea). Facies 51:66–79.
   Web of Science ®Google Scholar
• Rodenburg J. 2008. Ptychography and related diffractive imaging methods. In: Hawkes, editor. Adv Imag Elect Phys, Vol. 150, Amsterdam: Elsevier, p87–184.
   Google Scholar
• Rodenburg JM, Hurst AC, Cullis AG, Dobson BR, Pfeiffer F., Bunk O., David C., Jefimovs K., Johnson I. 2007. Hard-X-ray lensless imaging of extended objects. Phys Rev Lett 98:034801.
   PubMed Web of Science ®Google Scholar
• Russell T. 1990. X-ray and neutron reflectivity for the investigation of polymers. Mater Sci Rep 5:171–271.
   Google Scholar
• Sakdinawat A., Attwood D. 2010. Nanoscale X-ray imaging. Nat Photon 4:840–848.
   Web of Science ®Google Scholar
• Scheller S., Goenrich M., Boecher R., Thauer RK, Jaun B. 2010. The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane. Nature 465:606–608.
   PubMed Web of Science ®Google Scholar
• Schlenvoigt H-P, Haupt K., Debus A., Budde F., Jackel O., Pfotenhauer S., Schwoerer H., Rohwer E., Gallacher JG, Brunetti E., Shanks RP, Wiggins SM, Jaroszynski DA. 2008. A compact synchrotron radiation source driven by a laser-plasma Wakefield accelerator. Nat Phys 4:130–133.
   Web of Science ®Google Scholar
• Schroer CG, Kurapova O., Patommel J., Boye P., Feldkamp J., Lengeler B., Burghammer M., Riekel C., Vincze L., van der Hart A., Kuchler M. 2005. Hard X-ray nanoprobe based on refractive X-ray lenses. Appl Phys Lett 87:124103.
   Web of Science ®Google Scholar
• Schropp A., Boye P., Feldkamp JM, Hoppe R., Patommel J., Samberg D., Stephan S., Giewekemeyer K., Wilke RN, Salditt T., Gulden J., Mancuso AP, Vartanyants IA, Weckert E., Schoder S., Burghammer M., Schroer CG. 2010. Hard X-ray nanobeam characterization by coherent diffraction microscopy. Appl Phys Lett 96:091102.
   Web of Science ®Google Scholar
• Schropp A., Hoppe R., Meier V., Patommel J., Seiboth F., Lee HJ, Nagler B., Galtier EC, Arnold B., Zastrau U., Hastings JB, Nilsson D., Uhlen F., Vogt U., Hertz HM, Schroer CG. 2013. Full spatial characterization of a nanofocused X-ray free-electron laser beam by ptychographic imaging. Sci Rep 3:1633.
   PubMed Web of Science ®Google Scholar
• Schropp A., Hoppe R., Patommel J., Samberg D., Seiboth F., Stephan S., Wellenreuther G., Falkenberg G., Schroer CG. 2012. Hard X-ray scanning microscopy with coherent radiation: Beyond the resolution of conventional X-ray microscopes. Appl Phys Lett 100:253112.
   Web of Science ®Google Scholar
• Shima S., Krueger M., Weinert T., Demmer U., Kahnt J., Thauer RK, Ermler U. 2012. Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically. Nature 481:98–101.
   Web of Science ®Google Scholar
• Skerman VBD, Dementjeva G., Carey BJ. 1957. Intracellular Deposition of Sulfur by Sphaerotilus Natans. J Bacteriol 73(4): 504–512.
   PubMed Web of Science ®Google Scholar
• Solé V., Papillon E., Cotte M., Walter P., Susini J. 2007. A multiplatform code for the analysis of energy-dispersive X-ray fluorescence spectra. Spectrochim Acta B: Atom Spectrosc 62:63–68.
   Web of Science ®Google Scholar
• Takahashi Y., Suzuki A., Zettsu N., Kohmura Y., Yamauchi K., Ishikawa T. 2011a. Multiscale element mapping of buried structures by ptychographic X-ray diffraction microscopy using anomalous scattering. Appl Phys Lett 99:131905.
   Web of Science ®Google Scholar
• Takahashi Y., Suzuki A., Zettsu N., Kohmura Y., Senba Y., Ohashi H., Yamauchi K., Ishikawa T. 2011b. Towards high-resolution ptychographic X-ray diffraction microscopy. Phys Rev B 83:214109.
   Web of Science ®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. Annu Rev Earth Pl Sci 37:367–391.
   Web of Science ®Google Scholar
• Thauer RK. 1998. Biochemistry of methanogenesis: A tribute to Marjory Stephenson. Microbiology 144:2377–2406.
   PubMed Web of Science ®Google Scholar
• Thauer RK, Kaster A-K, Goenrich M., Schick M., Hiromoto T., Shima S. 2010. Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage. Annu Rev Biochem 79:507–536.
   PubMed Web of Science ®Google Scholar
• Thauer RK, Shima S. 2008. Methane as fuel for anaerobic microorganisms. Ann NY Acad Sci 1125:158–170.
   PubMed Web of Science ®Google Scholar
• Thibault P., Dierolf M., Bunk O., Menzel A., Pfeiffer F. 2009a. Probe retrieval in ptychographic coherent diffractive imaging. Ultramicroscopy 109:338–343.
   PubMed Web of Science ®Google Scholar
• Thibault P., Dierolf M., Menzel A., Bunk O., David C., Pfeiffer F. 2008. High-resolution scanning X-ray diffraction microscopy. Science 321:379–382.
   PubMed Web of Science ®Google Scholar
• Thibault P., Dierolf M., Kewish C M, Menzel A., Bunk O., Pfeiffer F. 2009b. Contrast mechanisms in scanning transmission X-ray microscopy. Phys Rev A 80:043813.
   Web of Science ®Google Scholar
• Vine DJ, Pelliccia D., Holzner C., Baines SB, Berry A., McNulty I., Vogt S., Peele AG, Nugent KA. 2012. Simultaneous X-ray fluorescence and ptychographic microscopy of Cyclotella meneghiniana. Opt Express 20:18287–18296.
   PubMed Web of Science ®Google Scholar
• Wilke RN, Priebe M., Bartels M., Giewekemeyer K., Diaz A., Karvinen P., Salditt T. 2012. Hard X-ray imaging of bacterial cells: nano-diffraction and ptychographic reconstruction. Optics Expr 20:19232–19254.
   PubMed Web of Science ®Google Scholar
• Wilke RN, Vassholz M., Salditt T. 2013. Semi-transparent central stop in high-resolution X-ray ptychography using Kirkpatrick-Baez focusing. Acta Crystallogr A 69:490–497.
   Web of Science ®Google Scholar
• Wörheide G. 1998. The reef cave dwelling ultraconservative coralline demosponge Astrosclera willeyana Lister 1900 from the Indo-Pacific. Facies 38:1–88.
   Web of Science ®Google Scholar
• Wrede C., Heller C., Reitner J., Hoppert M. 2008. Correlative light/electron microscopy for the investigation of microbial mats from Black Sea cold seeps. J Microbiol Meth 73:85–91.
   PubMed Web of Science ®Google Scholar
• Wrede C., Kokoschka S., Dreier A., Heller C., Reitner J., Hoppert M. 2013a. Deposition of biogenic iron minerals in a methane oxidizing microbial mat. Archaea, ID 102972.
   Google Scholar
• Wrede C., Krukenberg V., Dreier A., Reitner J., Heller C., Hoppert M. 2013b. Detection of metabolic key enzymes of methane turnover processes in cold seep microbial biofilms. Geomicrobiol J 30:214–227.
   Web of Science ®Google Scholar