Molecular characterization of cyanobacterial silicification using synchrotron infrared micro-spectroscopy

Geochimica et Cosmochimica Acta

Volumn 68, Issue 4, 2004, Pages 729-741

  Benning, Liane G ^a   Phoenix, V R ^b   Yee, N ^a   Tobin, M J ^c  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b UNIVERSITY OF TORONTO   (Canada)

^c DARESBURY LABORATORY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYANOBACTERIUM; GEOMICROBIOLOGY; INFRARED SPECTROSCOPY; SILICIFICATION; THERMAL WATER;

EID: 1342289974     PISSN: 00167037     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0016-7037(03)00489-7     Document Type: Article

References (103)

1. Awramik S.M.The oldest records of photosynthesis Photosyn. Res 33 1992 75-89
2. Benning L.G.Phoenix V.Yee N.Tobin M.J.Konhauser K.O.Mountain B.W.Molecular characterization of cyanobacterial cells during silicification: A synchrotron-based infrared study: Geochem. Earth Surf 6 2002 259-263
3. Benning L.G.Phoenix V.Yee N.Konhauser K.O.The dynamics of cyanobacterial silicification: An infrared micro-spectroscopic investigation Geochim. Cosmochim. Acta 67 2003 0000-0000
4. Bertoluzza A.Fagano C.Morelli M.A.Gottardi V.Guglielni M.J.Raman and infrared spectra on silica gel evolving toward glass J. Non-Cryst. Solids 48 1982 117-128
5. Beveridge T.J.Murray R.G.E.Sites of metal deposition in the cell wall of Bacillus subtilis J. Bacteriol 141 1980 876-887
6. Brandenburg K.Seydel U.Fourier transform infrared spectroscopy of cell surface polysaccharides Mantsch H.H. Chapman D. Infrared Spectroscopy of Biomolecules 1996 203-238 Wiley-LissNew York
7. Brock T.D.Madigan M.T.Martinko J.M.Parker J. Biology of Microorganisms 7th ed 994 Prentice Hall, Englewood CliffsNJ
8. Cady S.L.Paleobiology of the Archean Adv. Appl. Microbiol 50 2001 3-35
9. Carr G.L.High-resolution microspectroscopy and sub-nanosecond time-resolved spectroscopy with the synchrotron infrared source Vib. Spectrosc 191 1999 53-60
10. Carr G.L.Resolution limit for infrared microspectroscopy explored with synchrotron radiation Rev. Sci. Instrum 723 2001 1613-1619
11. Carroll S.Mroczek E.Alai M.Ebert M.Amorphous silica precipitation (60 to 120 degrees C): Comparison of laboratory and field rates Geochim. Cosmochim. Acta 62 1998 1379-1396
12. Chiriboga L.Yee H.Diem M.Infrared spectroscopy of human cells and tissue. Part VI: A comparative study of histopathology and infrared microspectroscopy of normal, cirrhotic, and cancerous liver tissue Appl. Spectrosc 541 2000 1-8
13. Choo-Smith L.Q.Maquelin K.van Vreeswijk T.Bruining H.A.Puppels G.J.Thi N.Kirschner C.Naumann D.Ami D.Villa A.M.Orsini F.Doglia S.M.Lamfarraj H.Sockalingum G.D.Investigating microbial (micro)colony heterogeneity by vibrational spectroscopy Appl. Environ. Microbiol 674 2001 1461-1469
14. Daughney C.J.Fein J.B.Yee N.A comparison of the thermodynamics of metal adsorption onto two common bacteria Chem. Geol 144 1998 161-176
15. Diem M. Introduction to Modern Vibrational Spectrscopy 1993 Wiley InterscienceNew York
16. Diem M.Boydston-White S.Chiriboga L.Infrared spectroscopy of cells and tissues: Shining light onto a novel subject Appl. Spectrosc 534 1999 148A-161A
17. Dove P.M.Crerar D.A.Kinetics of quartz dissolution in electrolyte-using a hydrothermal mixed flow reactor Geochim. Cosmochim. Acta 54 1990 955-969
18. Drews G.Weckesser J.Function, structure and composition of cell walls and external layers Carr N.G. Whitton B.A. The Biology of Cyanobacteria 1982 333-357 Blackwell Scientific PublicationsOxford, UK
19. Dudman W.F.The role of surface polysaccharides in natural environments Sutherland I. Surface Carbohydrates of the Prokaryotic Cell 1977 357-414 Academic PressLondon
20. Farmer V.C.The infrared spectra of minerals Min. Soc. Mon 4 1974 360-370
21. Fay P.The blue-greens (cyanophyta-cyanobacteria) Studies in Biology/Institute of Biology 160 1983 Edward Arnold LtdLondon
22. Fein J.B.Scott S.Rivera N.The effect of Fe on Si adsorption by Bacillus subtilis cell walls: Insights into non-metabolic bacterial precipitation of silicate minerals: Chem. Geol 182 2002 265-273
23. Ferris F.G.Beveridge T.J.Fyfe W.S.Iron-silica crystallite nucleation by bacteria in a geothermal sediment Nature 320 1986 609-611
24. Ferris F.G.Fyfe W.S.Beveridge T.J.Metallic ion binding by bacillus subtilis-Implications for the fossilization of microorganisms Geology 16 1988 149-152
25. Fortin D.Ferris F.G.Beveridge T.J.Surface mediated mineral development by bacteria Banfield J.F. Nealson K.H. Geomicrobiology: Interactions Between Microbes and Minerals 1997 Mineralogical Society of AmericaWashington DC
26. Fournier R.O.The behaviour of silica in hydrothermal solutions Berger B.R. Bethke P.M. Geology and Geochemistry of Epithermal Systems 2 1985 45-61 Soc. Econ. Geol
27. Giordano M.Kansiz M.Heraud P.Beardall J.Wood B.McNaughton D.Fourier transform infrared spectroscopy as a novel tool to investigate changes in intracellular macromolecular pools in the marine microalga Chaetoceros muellerii (Bacillariophyceae) J. Phycol 37 2001 271-279
28. 18O systems Bull. Chem. Soc. Jpn 44 1971 33-37
29. Henley R.W.Truesdell A.H.Barton P.B.Whitney J.A.Fluid-mineral equilibria in hydrothermal systems Rev. Econ. Geol. 1 1984 Soc. Econ. Geol
30. Hoiczyk E.Structural and biochemical analysis of the sheath of Phormidium uncinatum J Bacteriol 1805 1998 3923-3932
31. Holman H.-Y.N.Perry D.L.Martin M.C.Lamble G.M.McKinney W.R.Hunter- Cevera J.C.Real-time characterization of biogeochemical reduction of Cr(VI) on basalt surfaces by SR-FTIR imaging Geomicrobiol. J 164 1999 307-324
32. Holman H.-Y.N.Goth-Goldstein R.Martin M.C.Russell M.L.Mckinney W.R.Low-dose responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin in single living human cells measured by synchrotron infrared spectromicroscopy Environ. Sci. Technol 34 2000 2513-2517
33. Holman H.-Y.N.Martin M.C.Blakely E.A.Bjornstad K.McKinney W.R.IR spectroscopic characteristics of cell cycle and cell death probed by synchrotron radiation based Fourier transform IR spectromicroscopy Biopolymers 576 2000 329-335
34. Holman H.-Y.N.Nieman K.Sorensen D.L.Miller C.D.Martin M.C.Borch T.McKinney W.R.Sims R.C.Catalysis of PAH biodegradation by humic acid shown in synchrotron infrared studies Environ. Sci. Technol 366 2002 1276-1280
35. Iler R.K. The Chemistry of Silica 1981 Plenum PressNew York
36. Jamin N.Dumas P.Moncuit J.Fridman W.Teillaud J.Carr G.L.Williams G.P.Highly resolved chemical imaging of living cells by using synchrotron infrared microspectrometry Proc. Natl. Acad. Sci. U. S. A 95,9 1998 4837-4840
37. Jamin N.Dumas P.Moncuit J.Fridman W.Teillaud J.Carr G.L.Williams G.P.Chemical imaging of nucleic acids, proteins and lipids of a single living cell. Application of synchrotron infrared microspectrometry in cell biology Cell. Mol. Biol 441 1998 9-13
38. Jones B.Renaut R.W.Rosen M.R.Stromatolites forming in acidic hot-spring waters, North Island, New Zealand Palaios 15 2000 450-475
39. Jones B.Renaut R.W.Rosen M.R.Taphonomy of silicified filamentous microbes in modern geothermal sinters-Implications for identification Palaios 16 2001 580-592
40. Kansiz M.Heraud P.Wood B.Burden F.Beardall J.McNaughton D.Fourier transform infrared microspectroscopy and chemometrics as a tool for the discrimination of cyanobacterial strains Phytochemistry 52 1999 407-417
41. Keller R.J. Sigma Library of FT-IR Spectra 1986 Sigma Chemical CompanySt. Louis, MO
42. Kloprogge J.T.Frost R.L.Hickey L.Infrared emmision spectroscopic study of the dehydroxylation of some hectorites Thermochim. Acta 345 2000 145-156
43. Konhauser K.O.Ferris F.G.Diversity of iron and silica precipitation by microbial mats hydrothermal waters, Iceland: Implications for Precambrian iron formations Geology 24 1996 323-326
44. Konhauser K.O.Phoenix V.R.Bottrell S.H.Adams D.G.Head I.M.Microbial- silica interactions in Icelandic hot spring sinter: Possible analogues for some Precambrian siliceous stromatolites Sedimentology 48 2001 415-433
45. Krumbein W.E. Microbial Geochemistry 1983 Blackwell Scientific PublicationsOxford, UK
46. Landmesser H.Kosslick H.Storek W.Fricke R.Interior surface hydroxyl groups in ordered mesoporous silicates Solid State Ionics 271 1997 101-103
47. Lasch P.Boese M.Pacifico A.Diem M.A FT-IR spectroscopic investigations of single cells on the subcellular level Vib. Spectrosc 281 2002 147-157
48. Lazarev A.N. Vibrational Spectra and Structure of Silicates 1972 Consultants BureauNew York
49. LeVine S.M.Wetzel D.L.Chemical analysis of multiple sclerosis lesions by FT-IR microspectroscopy Free Rad. Biol. Med 251 1998 33-41
50. Lewis R.N.McElhaney R.N.Fourier transform infrared spectroscopy in the study of hydrated lipids and lipid bilayer membranes Mantsch H.H. Chapman D. In Infrared Spectroscopy of Biomolecules 1996 159-202 John WileyChichester, UK
51. Lippencot E.R.van Valkenburg A.Weir C.E.Bunting E.N.Infrared studies of polymorphs of silica and germania J. Res. Nat. Bur. Stand 61 1958 61-70
52. Liquier J.Taillandier E.Infrared spectroscopy of nucleic acids Mantsch H.H. Chapman D. In Infrared Spectroscopy of Biomolecules 1996 131-158 John WileyChichester, UK
53. Lowenstam H.A.Minerals formed by organisms Science 211 1981 1126-1131
54. Martin M.C.Tsvetkova N.M.Crowe J.H.McKinney W.R.Negligible sample heating from synchrotron infrared beam Appl. Spectrosc 552 2001 111-113
55. Martin M.C.Holman H.-Y.McKinney W.R.First performance results for a new continuum IR microscope ALS IR News 7 2002
56. McMillan P.F.Hofmeister A.M.Infrared and Raman spectroscopy In Rev. Mineral 18 1988 99-160
57. Messerschmidt R.G.Minimizing optical nonlinearities in infrared microspectroscopy Humecki H.J. Practical Guide to Infrared Microspectroscopy 3 1995 Marcel DekkerNew York
58. Miller L.M.Carlson C.S.Carr G.L.Chance M.R.A method for examining the chemical basis for bone disease: Synchrotron infrared microspectroscopy Cell. Mol. Biol 441 1998 117-127
59. Miller L.M.Tague J.R.Thomas J.Development and biomedical applications of fluorescence-assisted synchrotron infrared micro-spectroscopy Vib.Spectrosc 281 2002 159-165
60. Moenke H. [in German] Mineralspektren II 1966 Akademie VerlagBerlin, Germany
61. Mountain B.W.Benning L.G.Boerema J.Biomineralization in New Zealand geothermal areas: Rates of growth and trace metal incorporation Geochem. Earth Surf 6 2002 276-282
62. Mukherjee J.Sol-gel processes in glass science and technology J. Non-Cryst. Solids 42 1980 477-488
63. Nakamoto K. Infrared and Raman Spectra of Inorganic and Coordination Compounds 1986 John WileyNew York
64. Naumann D.FT-IR and FT-Raman spectroscopy in medical microbiology Carmona P. Navarro R. Hernanz A. Spectroscopy of Biological Molecules: Modern Trends 1997 433-434 Kluwer, Dordrechtthe Netherlands
65. Naumann D.Infrared spectroscopy in microbiology Meyers R.A. Encyclopedia of Analytical Chemistry 2000 102-131
66. Naumann D.Helm D.Labischinski H.Microbiological characterizations by FT-IR spectroscopy Nature 351 1991 81-82
67. Naumann D.Schultz C.Helm D.What can infrared spectroscopy tell us about the structure and composition of intact bacterial cells? Mantsch H.H. Chapman D. Infrared Spectroscopy of Biomolecules 1996 279-310 Wiley-LissNew York
68. Nelson W.H. Modern Techniques for Rapid Microbiological Analysis 1991 VCHNew York
69. Padmaja P.Anilkumar G.M.Mukundan P.Aruldhas G.Warrier K.G.K.Characterization of stoichiometric sol-gel mullite by fourier transform infrared spectroscopy Int. J. Inorg. Mat 3 2001 693-698
70. Panick G.Winter R.Pressure-induced unfolding/refolding of ribonuclease A: Static and kinetic Fourier transform infrared spectroscopy study Biochemistry 397 2000 1862-1869
71. Parker F.S. Applications of Infrared, Raman, and Resonance Raman Spectroscopy in Biochemistry 1983 Plenum PressNew York
72. Perry C.C.Biogenic silica Mann S. Webb J. Williams R.J.P. Biomineralisation, Chemical and Biological Perspectives 1989 233-256 VCHWeinheim
73. Phoenix V.R. Microbial-Biomineral Interactions and Their Significance for the Formation of Chemical Sediments 2001 University of Leeds Ph.D. dissertation
74. Phoenix V.R.Adams D.G.Konhauser K.O.Cyanobacterial viability during hydrothermal biomineralization Chem. Geol 169 2000 329-338
75. Phoenix V.R.Konhauser K.O.Adams D.G.Bottrell S.H.Role of biomineralization as an ultraviolet shield: Implications for Archean life Geology 29 2001 823-826
76. Phoenix V.R.Martinez R.E.Konhauser K.O.Ferris F.G.Characterization and implications of the cell surface reactivity of the cyanobacteria Calothrix sp. (strain KC97) Appl. Environ. Microbiol 68 2002 4827-4834
77. Phoenix V. R., Konhauser K. O. and Ferris F. G. (in press) Experimental study of iron and silica immobilization by bacteria in mixed Fe-Si systems: Implications for microbial silicification in hot-springs.
78. Pouchard C.J. Aldrich Library of FT-IR Spectra 2 1985 Aldrich Chemical Company IncMilwaukee, WI
79. Reffner J.A.Martoglio P.A.Williams G.P.FTIR microscopical analysis with synchrotron radiation: The microscope optics and system performance Rev. Sci. Instr 66 1995 1298
80. Rimstidt J.D.Barnes H.L.The kinetics of silica-water reactions Geochim. Cosmochim. Acta 44 1980 1683-1699
81. Ringwald S.C.Pemberton J.E.Adsorption interactions of aromatics and heretoaromatics with hydrated and dehydrated silica surfaces by Raman and FTIR spectroscopies Environ. Sci. Technol 34 2000 259-265
82. Schultz C.Naumann D.In vivo study of the state of order of the membranes of gram-negative bacteria by Fourier-transform infrared spectroscopy (FT-IR) FEBS Lett 294 1991 43-46
83. Schultze-Lam S.Ferris F.G.Konhauser K.O.Wiese R.G.In situ silicification of an Icelandic hot spring microbial mat: Implications for microfossil formation Can. J. Earth Sci 32 1995 2021-2026
84. Schuster K.C.Metrens F.Gapes J.R.FTIR spectroscopy applied to bacterial cells as a novel method for monitoring complex biotechnological processes Vib. Spectrosc 19 1999 467-477
85. Scott C.Fletcher R.L.Bremer G.B.Observations of the mechanisms of attachment of some marine fouling blue-green algae Biofouling 10 1996 161-173
86. Shi L.Carmichael W.W.Miller I.Immunogold localization of hepatotoxins in cyanobacterial cells Arch. Microbiol 163 1995 7-15
87. Sigee D.C.Dean A.Levado E.Tobin M.J.Fourier-transform infrared spectroscopy of Pediastrum duplex: Characterization of micro-population isolated from a eutrophic lake Eur. J. Phycol 37 2002 19-26
88. Socrates G. Infrared and Raman Characteristic Group Frequencies: Tables and Charts 3rd ed 2001 John WileyChichester, UK
89. Stuart B.Ando D.J. Biological Applications of Infrared Spectroscopy 1997 John WileyChichester, UK
90. Tobin M.J.Chesters M.A.Pearson M.Griffin N.R.Fisher S.E.Ruzicka B.Synchrotron IR microspectroscopy of malignant tissue Proc. SPIE Int. Soc. Opt. Eng., Soc. Phot-Opt. Instr. Eng 3775 1999 96-103
91. Tripp C. P. and Hair M. (1991) Reaction of chloromethylsilanes with silica: A low-frequency infrared study. Langmuir 7, 923-927.
92. Urrutia M.M.Beveridge T.J.Formation of fine-grained metal and silicate precipitates on a bacterial surface (Bacillus subtilis) Chem. Geol 116 1994 261-280
93. Walter M.R.Bauld J.Brock T.D.Siliceous algal and bacterial stromatolites in hot spring and geyser effluents of Yellowstone National Park Science 178 1972 402-405
94. Ward D.M.Ferris M.J.Nold S.C.Bateson M.M.A natural view of microbial biodiversity within hot spring cyanobacterial mat communities Microbiol. Mol. Biol. Rev 62 1998 1353-1370
95. Weckesser J.Hofmann K.Jürgens U.J.Whitton B.A.Raffelsberger B.Isolation and chemical analysis of the sheaths of the filamentous cyanobacteria Calothrix parienta and C. scopulorum J. Gen. Microbiol 134 1988 629-634
96. Westall F.Boni L.Guerzoni E.The experimental silicification of microorganisms Palaeontology 38 1995 495-528
97. Wetzel D.L.Levine S.M.Imaging molecular chemistry with infrared microscopy Science 285 1999 1224-1225
98. Williams D.H.Fleming I. Spectroscopic Methods in Organic Chemistry 5th ed 1996 McGraw-Hill International LtdLondon
99. Wilson W.W.Wade M.M.Holman S.C.Champlin F.R.Status of methods for assessing bacterial cell surface charge properties based on zeta potential measurements J. Microbiol. Meth 43 2001 153-164
100. Wong P.T.T.Wong R.H.Caputo T.A.Godwin T.A.Rigas B.Infrared- spectroscopy if exfoliated human cervical cells-Evidence of extensive structural changes during carcinogenesis Proc. Natl. Acad. Sci. U. S. A 88 1991 10988-10992
101. Yee N.Phoenix V.R.Konhauser K.O.Benning L.G.Ferris F.G.The effect of cyanobacteria on Si precipitation kinetics at neutral pH: Implications for bacterial silicification in geothermal hot springs Chem. Geol 99 2003 83-90
102. 2; etude comparative des reseaux vitreux Adv. Mol. Spectrosc 3 1962 1071-1083
103. Zeroual W.Manfait M.Choisy C.FT-IR spectroscopy study of perturbations induced by antibiotic on bacteria Pathol. Biol 434 1995 300-305