Advanced Seminar in Geology and Geochemistry: Organic Geochemistry

Schauble, E. A. “Applying Stable Isotope Fractionation Theory to New Systems.” Reviews in Mineralogy and Geochemistry 55 (2004): 65-111.

Canfield, D. E. “Biogeochemistry of Sulfur Isotopes.” Reviews in Mineralogy and Geochemistry 43 (2001): 609-636.

Mangalo, M., R. U. Meckenstock, W. Stichler, and F. Einsiedl. “Stable Isotope Fractionation During Bacterial Sulfate Reduction is Controlled by Reoxidation of Intermediates.” Geochimica et Cosmochimica Acta 71 (2007): 4161-4171.

Johnston, D. T., J. Farquhar, and D. E. Canfield. “Sulfur Isotope Insights in to Microbial Sulfate Reduction: When Microbes Meet Models.” Geochimica et Cosmochimica Acta 71 (2007): 3929-3947.

Canfield, D. E., C. A. Olesen, and R. P. Cox. “Temperature and its Control of Isotope Fractionation by a Sulfate-reducing Bacterium.” Geochimica et Cosmochimica Acta 70 (2006): 548-561.

Bottcher, M. E., and B. Thamdrup. “Anaerobic Sulfide Oxidation and Stable Isotope Fractionation Associated with Bacterial Sulfur Disproportionation in the Presence of MnO2.” Geochimica et Cosmochimica Acta 65 (2001): 1573-1581.

Turchyn, A. V., and D. P. Schrag. “Oxygen Isotope Constraints on the Sulfur Cycle Over the Past 10 Million Years.” Science 303 (2004): 2004-2007.

Wortmann, U. G., B. Chernyavsky, S. M. Bernasconi, B. Brunner, M. E. Bottcher, and P. K. Swart. “Oxygen Isotope Biogeochemistry of Pore Water Sulfate in the Deep Biosphere: Dominance of Isotope Exchange Reactions with Ambient Water During Microbial Sulfate Reduction (ODP Site 1130).” Geochimica et Cosmochimica Acta 71 (2007): 4221-4232.

Turchyn, A. V., O. Sivan, and D. P. Schrag. “Oxygen Isotopic Composition of Sulfate in Deep Sea Pore Fluid: Evidence for Rapid Sulfur Cycling.” Geobiology 4 (2006): 191-201.

Canfield, D. E. “A New Model for Proterozoic Ocean Chemistry.” Nature 396 (1998): 450-453.

Logan, G. A., J. M. Hayes, G. B. Hieshima, and R. E. Summons. “Terminal Proterozoic Reorganization of Biogeochemical Cycles.” Nature 376 (1995): 53-56.

Riccardi, A. L., M. A. Arthur, and L. R. Kump. “Sulfur Isotopic Evidence for Chemocline Upward Excursions During the End-Permian Mass Extinction.” Geochimica Et Cosmochimica Acta 70 (2006): 5740-5752.

Riccardi, A., L. R. Kump, M. A. Arthur, and S. D’Hondt. “Carbon Isotopic Evidence for Chemocline Upward Excursions During the End-Permian Event.” Palaeogeography Palaeoclimatology Palaeoecology 248 (2007): 73-81.

Hotinski, R. M., K. L. Bice, L. R. Kump, R. G. Najjar, and M. A. Arthur. “Ocean Stagnation and End-Permian Anoxia.” Geology 29 (2001): 7-10.

Hotinski, R. M., L. R. Kump, and K. L. Bice. Comment on “Could the Late Permian Deep Ocean have been Anoxic?’’ by R. Zhang et al. Paleoceanography 17 (2002).

Kump, L. R., A. Pavlov, and M. A. Arthur. “Massive Release of Hydrogen Sulfide to the Surface Ocean and Atmosphere During Intervals of Oceanic Anoxia.” Geology 33 (2005): 397-400.

Anbar, A. D., G. L. Arnold, T. W. Lyons, and J. Barling. Response to comment on “Molybdenum Isotope Evidence for Widespread Anoxia in Mid-Proterozoic Oceans.” Science 309 (2005).

Anbar, A. D., and A. H. Knoll. “Proterozoic Ocean Chemistry and Evolution: A Bioinorganic Bridge?” Science 297 (2002): 1137-1142.

Arnold, G. L., A. D. Anbar, J. Barling, and T. W. Lyons. “Molybdenum Isotope Evidence for Widespread Anoxia in Mid-proterozoic Oceans.” Science 304 (2004): 87-90.

Johnston, D. T., B. A. Wing, J. Farquhar, A. J. Kaufman, H. Strauss, T. W. Lyons, L. C. Kah, and D. E. Canfield. “Active Microbial Sulfur Disproportionation in the Mesoproterozoic.” Science 310 (2005): 1477-1479.

Johnston, D. T., S. W. Poulton, P. W. Fralick, B. A. Wing, D. E. Canfield, and J. Farquhar. “Evolution of the Oceanic Sulfur Cycle at the End of the Paleoproterozoic.” Geochimica et Cosmochimica Acta 70 (2006): 5723-5739.

Holser, W. T., and I. R. Kaplan. “Isotope Geochemistry of Sedimentary Sulfates.” Chemical Geology 1 (1966): 93-135.

Garrels, R. M., and A. Lerman. “Phanerozoic Cycles of Sedimentary Carbon and Sulfur.” Proceedings of the National Academy of Sciences of the United States of America 78 (1981): 4652-4656.

Canfield, D. E. “The Evolution of the Earth Surface Sulfur Reservoir.” Am J Sci 304 (2004): 839-861.

Kurtz, A. C., L. R. Kump, M. A. Arthur, J. C. Zachos, and A. Paytan. “Early Cenozoic Decoupling of the Global Carbon and Sulfur Cycles.” Paleoceanography 18 (2003).

Berner, R. A. “GEOCARBSULF: A Combined Model for Phanerozoic Atmospheric O 2 and CO 2 .” Geochimica Et Cosmochimica Acta 70 (2006): 5653-5664.

Canfield, D. E., and A. Teske. “Late Proterozoic Rise in Atmospheric Oxygen Concentration Inferred from Phylogenetic and Sulphur-Isotope Studies.” Nature 382 (1996): 127-132.

Kah, L. C., T. W. Lyons, and T. D. Frank. “Low Marine Sulphate and Protracted Oxygenation of the Proterozoic Biosphere.” Nature 431 (2004): 834-838.

Turchyn, A. V., and D. P. Schrag. “Oxygen Isotope Constraints on the Sulfur Cycle Over the Past 10 Million Years.” Science 303 (2004): 2004-2007.

Wortmann, U. G., B. Chernyavsky, S. M. Bernasconi, B. Brunner, M. E. Bottcher, and P. K. Swart. “Oxygen Isotope Biogeochemistry of Pore Water Sulfate in the Deep Biosphere: Dominance of Isotope Exchange Reactions with Ambient Water During Microbial Sulfate Reduction (ODP Site 1130).” Geochimica et Cosmochimica Acta 71 (2007): 4221-4232.

Turchyn, A. V., O. Sivan, and D. P. Schrag. “Oxygen Isotopic Composition of Sulfate in Deep Sea Pore Fluid: Evidence for Rapid Sulfur Cycling.” Geobiology 4 (2006): 191-201.

Ohmoto, H., T. Kakegawa, and D. R. Lowe. “3.4-Billion-Year-Old Biogenic Pyrites from Barberton, South Africa; Sulfur Isotope Evidence.” Science 262 (1993): 555-557.

Shen, Y., R. Buick, and D. E. Canfield. “Isotopic Evidence for Microbial Sulphate Reduction in the Early Archaean Era.” Nature 410 (2001): 77-81.

Farquhar, J., J. Savarino, T. L. Jackson, and M. H. Thiemens. “Evidence of Atmospheric Sulphur in the Martian Regolith from Sulphur Isotopes in Meteorites.” Nature 404 (2000c): 50-52.

Farquhar, J., H. M. Bao, and M. Thiemens. “Atmospheric Influence of Earth’s Earliest Sulfur Cycle.” Science 289 (2000a): 756-758.

Ono, S., W. C. Shanks Iii, O. J. Rouxel, and D. Rumble. “S-33 Constraints on the Seawater Sulfate Contribution in Modern Seafloor Hydrothermal Vent Sulfides.” Geochimica et Cosmochimica Acta 71 (2000c): 1170-1182.

Ohmoto, H., and A. C. Lasaga. “Kinetics of Reactions Between Aqueous Sulfates and Sulfides in Hydrothermal Systems.” Geochimica et Cosmochimica Acta 46 (1982): 1727-1745.

Bach, W., and K. J. Edwards. “Iron and Sulfide Oxidation Within the Basaltic Ocean Crust: Implications for Chemolithoautotrophic Microbial Biomass Production.” Geochimica Et Cosmochimica Acta 67 (2003): 3871-3887.

D’hondt, S., B. B. Jorgensen, D. J. Miller, A. Batzke, R. Blake, B. A. Cragg, H. Cypionka, G. R. Dickens, T. Ferdelman, K. U. Hinrichs, N. G. Holm, R. Mitterer, A. Spivack, G. Z. Wang, B. Bekins, B. Engelen, K. Ford, G. Gettemy, S. D. Rutherford, H. Sass, C. G. Skilbeck, I. W. Aiello, G. Guerin, C. H. House, F. Inagaki, P. Meister, T. Naehr, S. Niitsuma, R. J. Parkes, A. Schippers, D. C. Smith, A. Teske, J. Wiegel, C. N. Padilla, and J. L. S. Acosta. “Distributions of Microbial Activities in Deep Subseafloor Sediments.” Science 306 (2004): 2216-2221.

Farquhar, J., J. Savarino, S. Airieau, and M. H. Thiemens. “Observation of Wavelength-Sensitive Mass-Independent Sulfur Isotope Effects During SO 2 Photolysis: Implications for the Early Atmosphere.” Journal of Geophysical Research 106 (2001): 1-11.

Ono, S., J. L. Eigenbrode, A. A. Pavlov, P., D. Rumble, J. F. Kasting, and K. H. Freeman. “New Insights in to Archean Sulfur Cycle from Mass-Independent Sulfur Isotope Records from the Hamersley Basin, Australia.” Earth and Planetary Science Letters 213 (2003): 15-30.

Pavlov, A. A., and J. F. Kasting. “Mass-Independent Fractionation of Sulfur Isotopes in Archean Sediments: Strong Evidence for an Anoxic Archean Atmosphere.” Astrobiology 2 (2002): 27-41.

Bekker, A., H. D. Holland, P. L. Wang, D. Rumble, H. J. Stein, J. L. Hannah, L. L. Coetzee, and N. J. Beukes. “Dating the Rise of Atmospheric Oxygen.” Nature 427 (2004): 117-20.

Ohmoto, H., Y. Watanabe, H. Ikemi, S. R. Poulson, and B. E. Taylor. “Sulphur Isotope Evidence for an Oxic Archaean Atmosphere.” Nature 442 (2006): 908-911.

Ono, S., N. J. Beukes, D. Rumble, and M. L. Fogel. “Early Evolution of Atmospheric Oxygen from Multiple-Sulfur and Carbon Isotope Records of the 2.9 Ga Mozaan Group of the Pongola Supergroup, Southern Africa.” South African Journal of Geology 109 (2006): 97-108.

Brimblecombe, P. “The Global Sulfur Cycle.” Treatise on Geochemistry 8 (2003): 645-682.

Ohmoto, H., and M. B. Goldhaber. “Sulfur and Carbon Isotopes.” In Geochemistry of Hydrothermal Ore Deposits . Edited by H. L. Barnes. New York: John Wiley & Sons, 1997. ISBN: 9780471571445.

Engel, M. H., and S. A. Macko, eds. Organic Geochemistry Principles and Applications . Springer; 1 edition, 1993. ISBN: 9780306443787.

Hayes, J. M. “Fractionation of the isotopes of carbon and hydrogen in biosynthetic processes.” In Stable Isotopic Geochemistry . Edited by J. W. Valley and D. R. Cole. Reviews in Mineralogy and Geochemistry 43 (2001): 225-278.

Peters, K. E., Walters, and J. M. Moldowan. The Biomarker Guide . Vols. 2. Cambridge, UK: Cambridge University Press, 2005. ISBN: 9780521781589, 9780521837620.

Fahy, E., et al. “A comprehensive classification system for lipids.” J Lipid Research 46 (2005): 839-861.

WEEK: 1 · READINGS: Allard, B., M.-N. Rager, and J. Templier. “Occurrence of high molecular weight lipids (C 80+ ) in the trilaminar outer cell walls of some freshwater microalgae. A reappraisal of algaenan structure.” Org Geochem 33 (2002): 789-801.

Derenne, S., and C. Largeau. “A review of some important families of refractory macromolecules: composition, origin and fate in soils and sediments.” Soil Science 166 (2001): 833-847.

Gelin, F., I. Boogers, A. A. M. Noordeloos, J. S. Sinninghe Damsté, R. Riegman, and J. W. de Leeuw. “Resistant biomacromolecules in marine microalgae of the classes Eustigmatophyceae and Chlorophyceae: geochemical implications.” Org Geochem 26, no. 11-12 (1997): 659-675.

Köster, J., J. K. Volkman, S.-B. Rullkötter, B. M., J. Rethmeier, and U. Fischer. “Mono-, di- and trimethyl-branched alkanes in cultures of the filamentous cyanobacterium Calothrix scopulorum.” Org Geochem 30 (1999): 1367-1379.

Rieley, G., J. W. Collister, B. Stern, and G. Eglinton. “Gas chromatography/isotope ratio mass spectrometry of leaf wax n-alkanes from plants of differing carbon dioxide metabolisms.” Rapid Communications in Mass Spectrometry 7 (1993): 488-491.

Tegelaar, E. W., J. W. de Leeuw, S. Derenne, and C. Largeau. “A reappraisal of kerogen formation.” Geochim Cosmochim Acta 53 (1989): 3103-3106.

WEEK: 2 · READINGS: Hayes, J. M. “Fractionation of the isotopes of carbon and hydrogen in biosynthetic processes.” In Stable Isotopic Geochemistry. Edited by J. W. Valley and D. R. Cole. Reviews in Mineralogy and Geochemistry 43 (2001): 225-278.

WEEK: 3 · READINGS: Kates, M. “Membrane lipids of Archaea.” In The Biochemistry of Archaea (Archaebacteria). Edited by M. Kates, K. D. J, and A. T. Matheson. Elsevier Science, 1993, pp. 261-295.

Sinninghe Damsté, J. S., W. I. C. Rijpstra, E. C. Hopmans, F. G. Prahl, S. G. Wakeham, and S. Schouten. “Distribution of membrane lipids of planktonic Crenarchaeota in the Arabian Sea.” Applied and Environmental Microbiology 68 (2002): 2997-3002.

Tornabene, T. G., T. A. Langworthy, G. Holzer, and V. Oro. “Squalenes, phytanes and other isoprenoids as major neutral lipids of methanogenic and thermoacidophilic archaebacteria.” J Mol Evol 13 (1979): 73-83.

Volkman, J. K., and J. R. Maxwell. “Acyclic isoprenoids as biological markers.” In Biological Markers and the Sedimentary Record. Edited by R. B. Johns. New York, NY: Elsevier, 1986, pp. 1-42.

Woese, C. R., O. Kandler, and M. L. Wheelis. “Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.” Proc Natl Acad Sci U.S.A. 87 (1990): 4576-4579.

Michaelis, W., R. Seifert, K. Nauhaus, T. Treude, V. Thiel, M. Blumenberg, K. Knittel, A. Gieseke, K. Peterknecht, T. Pape, A. Boetius, R. Amann, B. B. Jørgensen, F. Widdel, J. Peckmann, N. V. Pimenov, and M. B. Gulin. “Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane.” Science 297 (2002): 1013-1015.

Thiel, V., M. Blumenberg, T. Pape, R. Seifert, and W. Michaelis. “Unexpected occurrence of hopanoids at gas seeps in the Black Sea.” Org Geochem 34 (2003): 81-87.

Thiel, V., J. Peckmann, R. Seifert, P. Wehrung, J. Reitner, and W. Michaelis. “Highly isotopically depleted isoprenoids: molecular markers for ancient methane venting.” Geochim Cosmochim Acta 63, no. 23/24 (1999): 3959-3966.

McLafferty, F. W. Interpretation of Mass Spectra . New York, NY: WA Benjamin, 1967, chapters 1-4. ISBN: 9780805370478.

WEEK: 5 · READINGS: Anders, E. “Pre-biotic organic matter from comets and asteroids.” Nature 342 (1989): 255-257.

Bada, J. L., J. R. Cronin, M.-S. Ho, K. A. Kvenvolden, J. G. Lawless, S. L. Miller, J. Oro, and S. Steinberg. “On the reported optical activity of amino acids in the Murchison meteorite.” Nature 301 (1983): 494-497.

Cronin, J. R., and S. Pizzarello. “Enantiomeric excesses in meteoritic amino acids.” Science 275 (1997): 951-955.

Engel, M. H., and S. A. Macko. “Isotopic evidence for extraterrestrial non-racemic amino acids in the Murchison meteorite.” Nature 389 (1997): 265-268.

Pizzarello, S., and J. R. Cronin. “Non-racemic amino acids in the Murchison and Murray meteorites.” Geochim Cosmochim Acta 64 (2000): 329-338.

Sephton, M. A., and I. Gilmour. “Compound specific isotope analysis of the organic constituents in carbonaceous chondrites.” Mass Spectrometry Reviews 20 (2001): 111-120.

Eglinton, T. I., B. C. Benitez-Nelson, A. Pearson, A. P. McNichol, J. E. Bauer, and E. R. M. Druffel. “Variability in radiocarbon ages of individual organic compounds from marine sediments.” Science 277 (1997): 796-799.

WEEK: 6 · READINGS: Summons, R. E., and M. R. Walter. “Molecular fossils and microfossils of prokaryotes and protists from Proterozoic sediments.” Am J Sci 290-A (1990): 212-244.

WEEK: 8 · READINGS: Volkman, J. K. “Sterols and other triterpenoids: source specificity and evolution of biosynthetic pathways.” Organic Geochemistry 36 (2005): 139-159.

Xie, S., et al. “Two episodes of microbial change coupled with Permo/Triassic faunal mass extinction.” Nature 434 (2005): 494-497.

WEEK: 9 · READINGS: Xie, Shucheng, Richard D. Pancost, Hongfu Yin, Hongmei Wang, and Richard P. Evershed. “Two episodes of microbial change coupled with Permo/Triassic faunal mass extinction.” Nature 434 (March 24, 2005): 494-497.

Grice, Kliti, et al. “Photic Zone Euxinia During the Permian-Triassic Superanoxic Event.” Science 307, no. 5710 (February 4, 2005): 706-709.

Jin, Y. G., et al. “Pattern of Marine Mass Extinction Near the Permian-Triassic Boundary in South China” Science 289, no. 5478 (July 21, 2000): 432-436.

Knoll, A. H., R. K. Bambach, D. R. Canfield, and J. P. Grotzinger. “Comparative Earth History and Late Permian Mass Extinction.” Science 273, no. 5274 (July 26, 1996): 452-457.

WEEK: 12 · READINGS: Sinninghe Damsté, J. S., M. Strous, W. I. C. Rijpstra, E. C. Hopmans, J. A. J. Geenevasen, A. C. T. van Duin, L. A. van Niftrik, and M. S. M. Jetten. “Linearly concatenated cyclobutane lipids form a dense bacterial membrane.” Nature 419 (2002): 708-712.

Sinninghe Damsté, J. S., S. Schouten, and A. C. T. van Duin. “Isorenieratene derivatives in sediments: possible controls on their distribution.” Geochim Cosmochim Acta 65 (2001): 1557-1571.

Calver, Clive R., Lance P. Black, John L. Everard, and David B. Seymour. “U-Pb zircon age constraints on late Neoproterozoic glaciation in Tasmania.” Geology 32, no. 10 (2004): 893-896.

Hoffman, P. F., A. C. Maloof, and G. P. Halverson. “On the Syn-glacial Sedimentary Record of Snowball Earth: Tales of Three Ice-mass Types.” American Geophysical Union Spring Meeting, 2004. (Abstract #U21B-02.)

Kaufman, A. J., A. H. Knoll, and G. M. Narbonne. “Isotopes, ice ages, and terminal Proterozoic earth history.” Proceedings of the National Academy of Sciences 94 (1997): 6600-6605.

Kennedy, M. J., B. Runnegar, A. R. Prave, C. Hoffmann, and M. A. Arthur. “Two or four Neoproterozoic glaciations.” Geology 26 (1998): 1059-1063. (Special Report.)

WEEK: 13 · READINGS: Catling, D. C., and M. W. Claire. “How Earth’s atmosphere evolved to an oxic state: a status report.” Earth and Planetary Science Letters 237 (2005): 1-20.

Sreenivas, B., and T. Murakami. “Emerging views on the evolution of atmospheric oxygen during the Precambrian.” Journal of Mineralogical and Petrological Sciences 100 (2005): 184-201.

Kump, L. R., and W. E. Seyfried. “Hydrothermal Fe fluxes during the Precambrian: effect of low oceanic sulfate concentrations and low hydrostatic pressure on the compostion of black smokers.” Earth and Planetary Science Letters 235 (2005): 654-662.

Brocks, J. J., G. D. Love, R. E. Summons, A. H. Knoll, G. A. Logan, and S. A. Bowden. “Biomarker evidence for green and purple sulphur bacteria in a stratified Paleoproterozoic sea.” Nature 437 (2005): 866-870.

WEEK: 14 · READINGS: Seminar readings only.