Detection and phylogenetic identification of labeled prokaryotic cells on mineral surfaces using Scanning X-ray Microscopy

Chemical Geology

Volumn 240, Issue 1-2, 2007, Pages 182-192

  Ménez, Bénédicte ^a   Rommevaux Jestin, Céline ^a   Salomé, Murielle ^b   Wang, Yuheng ^a   Philippot, Pascal ^a   Bonneville, Alain ^a   Gérard, Emmanuelle ^a,c  

^a SCHLUMBERGER   (France)

^b EUROPEAN SYNCHROTRON RADIATION FACILITY   (France)

^c UNIVERSITÉ PARIS SUD   (France)

Author keywords

Fluorescent in situ hybridization; Immunodetection; Mineralized environment; Prokaryotic cells; Synchrotron radiation; X ray microscopy

Indexed keywords

DEPOSITION; DETECTION METHOD; GEOMICROBIOLOGY; MICROBIAL COMMUNITY; MICROSCOPY; MINERAL; PHYLOGENY; PROKARYOTE;

PROKARYOTA;

EID: 34247229054     PISSN: 00092541     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemgeo.2007.02.009     Document Type: Article

References (30)

1. Amann R., Glöckner F.O., and Neef A. Modern methods in subsurface microbiology: in situ identification of microorganisms with nucleic acid probes. FEMS Microbiol. Rev. 20 (1997) 191-200
2. Amend J.P., and Teske A. Expanding frontiers in deep subsurface microbiology. Palaeogeogr. Palaeoclimatol. Palaeoecol. 219 (2005) 131-155
3. Benzerara K., Yoon T.H., Menguy N., Tyliszczak T., and Brown J.G.E. Nanoscale environments associated with bioweathering of a Mg-Fe-pyroxene. Proc. Natl. Acad. Sci. U. S. A. 102 4 (2005) 979-982
4. Benzerara K., Yoon T.H., Tyliszczak T., Constantz B., Spormann A.M., and Brown J.G.E. Scanning transmission X-ray microscopy study of microbial calcification. Geobiology 2 (2005) 249-259
5. Bohic S., Simionovici A., Snigirev A., Ortega R., Devès G., Heymann D., et al. Synchrotron hard x-ray microprobe: fluorescence imaging of single cells. Appl. Phys. Lett. 78 22 (2001) 3544-3546
6. Di Fabrizio E., Cojoc D., Cabrini S., Altissimo M., Kaulich B., Wilhein T., et al. Phase and intensity control through diffractive optical elements in X-ray microscopy. J. Electron Spectrosc. Relat. Phenom. 144-147 (2005) 957-961
7. Foriel J., Philippot P., Susini J., Dumas P., Somogyi A., Salomé M., et al. High-resolution imaging of sulfur oxidation states, trace elements, and organic molecules distribution in individual microfossils and contemporary microbial filaments. Geochim. Cosmochim. Acta 68 7 (2004) 1561-1569
8. Fredrickson J.K., and Onstott T.C. Biogeochemical and geological significance of subsurface microbiology. In: Fredrickson J.K., and Fletcher M. (Eds). Subsurface Microbiology and Biogeochemistry, New York (2001) 3-37
9. Geesey G.G., Neal A.L., Suci P.A., and Peyton B.M. A review of spectroscopic methods for characterizing microbial transformations of minerals. J. Microbiol. Methods 51 (2002) 125-139
10. Gérard E., Guyot F., Philippot P., and Lopez-Garcia P. Fluorescence in situ hybridisation coupled to ultra small immunogold detection to identify prokaryotic cells using transmission and scanning electron microscopy. J. Microbiol. Methods 63 (2005) 20-28
11. Jamin N., Dumas P., Moncuits J., Fridman W.H., Teillaud J.L., Lawrence Carr G., et al. Highly resolved chemical imaging of living cells by using synchrotron infrared microspectrometry. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 4837-4840
12. Kaulich B., Polack F., Neuhäusler U., Susini J., Di Fabrizio E., and Wilhein T. Diffracting aperture based differential phase contrast for scanning X-ray microscopy. Opt. Express 10 20 (2002) 1111-1117
13. Kemner K.M., Kelly S.D., Lai B., Maser J., O'Loughlin E.J., Sholto-Douglas D., et al. Elemental and redox analysis of single bacterial cells by X-ray microbeam analysis. Science 306 (2004) 686-687
14. Kieft T.L., and Phelps T.J. Life in the slow lane. In: Amy P.S., and Haldeman D.L. (Eds). The Microbiology of the Terrestrial Subsurface (1997), CRC Press, Boca Raton, FL 137-164
15. Krumholz L. Microbial communities in the deep subsurface. Hydrogeol. J. 8 (2000) 4-10
16. Larabell C.A., and Le Gros M.A. X-ray tomography generates 3-D reconstructions of the yeast, Saccharomyces cerevisiae, at 60-nm resolution. Mol. Biol. Cell 15 3 (2004) 957-962
17. Lemelle L., Salomé M., Fialin M., Simionovici A., and Gillet P. In situ identification and X-ray imaging of microorganisms distribution on the Tatahouine meteorite. Spectrochim. Acta B 59 (2004) 1703-1710
18. Loy A., Horn M., and Wagner M. ProbeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res. 31 (2003) 514-516
19. Magnuson T.S., Neal A.L., and Geesey G.G. Combining in situ reverse transcriptase polymerase chain reaction, optical microscopy, and X-ray photoelectron spectroscopy to investigate mineral surface-associated microbial activities. Microb. Ecol. 48 4 (2004) 578-588
20. Miao J., Hodgson K.O., Ishikawa T., Larabell C.A., LeGros M.A., and Nishino Y. Imaging whole Escherichia coli bacteria by using single-particle X-ray diffraction. Proc. Natl. Acad. Sci. U. S. A. 100 1 (2003) 110-112
21. Ortega R., Bohic S., Tucoulou R., Somogyi A., and Devès G. Microchemical element imaging of yeast and human cells using synchrotron X-ray microprobe with Kirkpatrick-Baez optics. Anal. Chem. 76 2 (2004) 309-314
22. Parkes R.J., and Wellsbury P. Deep biospheres. In: Bull A.T. (Ed). Microbial Diversity and Bioprospecting (2004), ASM Press, Washington, D. C. 120-129
23. Pedersen K. Exploration of deep intraterrestrial microbial life: current perspectives. FEMS Microbiol. Lett. 185 (2000) 9-16
24. Susini J., Salomé M., Fayard B., Ortega R., and Kaulich B. The scanning X-ray microprobe at the ESRF X-ray microscopy beamline. Surf. Rev. Lett. 9 1 (2002) 203-211
25. Twining B., Baines S.B., Fisher N.S., Maser J., Vogt S., Jacobsen C., et al. Quantifying trace elements in individual aquatic protist cells with a Synchrotron X-ray Fluorescence microprobe. Anal. Chem. 75 (2003) 3806-3816
26. Ueki T., Takemoto K., Fayard B., Salomé M., Yamamoto A., Kihara H., et al. Scanning X-ray microscopy of living and freeze-dried blood cells in two vanadium-rich Ascidian species, Phallusia mammillata and Ascidia sydneiensis samea. Zool. Sci. 19 (2002) 27-35
27. Vekemans B., Janssens K., Vincze L., Adams F., and Van Espen P. Analysis of X-ray spectra by iterative least squares (AXIL): new developments. X-Ray Spectrom. 23 6 (1994) 278-285
28. Whitman W.B., Coleman D.C., and Wiebe W.J. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. U. S. A. 95 12 (1998) 6578-6583
29. Wilhein T., Kaulich B., Di Fabrizio E., Romanato F., Cabrini S., and Susini J. Differential interference contrast X-ray microscopy with submicron resolution. Appl. Phys. Lett. 78 14 (2001) 2082-2084
30. Wilkins S.W., Gureyev T.E., Gao D., Pogany A., and Stevenson A.W. Phase-contrast imaging using polychromatic hard X-rays. Nature 384 (1996) 335-338