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Volume 26 Issue 5
Oct 2015
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Hong Ye, Tao Yang, Guorong Zhu, Shaoyong Jiang. An object-oriented diagnostic model for the quantification of porewater geochemistry in marine sediments. Journal of Earth Science, 2015, 26(5): 648-660. doi: 10.1007/s12583-015-0586-z
Citation: Hong Ye, Tao Yang, Guorong Zhu, Shaoyong Jiang. An object-oriented diagnostic model for the quantification of porewater geochemistry in marine sediments. Journal of Earth Science, 2015, 26(5): 648-660. doi: 10.1007/s12583-015-0586-z

An object-oriented diagnostic model for the quantification of porewater geochemistry in marine sediments

doi: 10.1007/s12583-015-0586-z
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  • Corresponding author: Tao Yang, yangtao@nju.edu.cn
  • Received Date: 25 Jan 2015
  • Accepted Date: 01 Jun 2015
  • Publish Date: 01 Oct 2015
  • The reaction-transport model is widely used to identify and quantify dissolved chemical species in sediment porewaters. In this paper, a modularized code framework of diagenetic model was proposed as a diagnostic tool to fit the porewater profiles in marine sediments. Based on the conservation principle of the finite volume method, we combined the discretized diagenetic equations with various geochemical reactions, including but not limited to methanogenesis, sulfate reduction, etc.. The code was organized in object-oriented FORTRAN and verified with literature parameters, which proved its robustness and effectiveness. Finally, three different sites (IODP Expedition 311 Site U1327, UBGH2-1_1, ODP Leg204 Site 1245) are exemplified as case studies.

     

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  • Arndt, S., Jørgensen, B. B., LaRowe, D. E., et al., 2013. Quantifying the Degradation of Organic Matter in Marine Sediments: A Review and Synthesis. Earth-Science Reviews, 123: 53–86. doi: 10.1016/j.earscirev.2013.02.008
    Bear, J., 1972. Dynamics of Fluids In Porous Media. Elsevier, New York. 764 http://www.sciencedirect.com/science/article/pii/0013795273900471
    Berg, P., Rysgaard, S., Thamdrup, B., 2003. Dynamic Modeling of Early Diagenesis and Nutrient Cycling: A Case Study in an Artic Marine Sediment. American Journal of Science, 303(10): 905–955. doi: 10.2475/ajs.303.10.905
    Berner, R. A., 1964. An Idealized Model of Dissolved Sulfate Distribution in Recent Sediments. Geochimica et Cosmochimica Acta, 28(9): 1497–1503. doi: 10.1016/0016-7037(64)90164-4
    Berner, R. A., 1980. Early Diagenesis: A Theoretical Approach. Princeton University Press, Princeton. 241 http://www.researchgate.net/publication/340371877_Early_Diagenesis_A_Theoretical_Approach
    Bhatnagar, G., Chapman, W. G., Dickens, G. R., et al., 2007. Generalization of Gas Hydrate Distribution and Saturation in Marine Sediments by Scaling of Thermodynamic and Transport Processes. American Journal of Science, 307(6): 861–900. doi: 10.2475/06.2007.01
    Boetius, A., Ravenschlag, K., Schubert, C. J., et al., 2000. A Marine Microbial Consortium Apparently Mediating Anaerobic Oxidation of Methane. Nature, 407(6804): 623–626. doi: 10.1038/35036572
    Borowski, W. S., Paull, C. K., William Ussler Ⅲ, 1999. Global and Local Variations of Interstitial Sulfate Gradients in Deep-Water, Continental Margin Sediments: Sensitivity to Underlying Methane and Gas Hydrates. Marine Geology, 159. doi: 10.1016/S0025-3227(99)00004-3
    Boudreau, B. P., 1984. On the Equivalence of Nonlocal and Radial-Diffusion Models for Porewater Irrigation. Journal of Marine Research, 42: 731–735. DOI: 10.1357/002224084788505924
    Boudreau, B. P., 1996. A Method-of-Lines Code for Carbon and Nutrient Diagenesis in Aquatic Sediments. Computers & Geosciences, 22(5): 479–496. doi: 10.1016/0098-3004(95)00115-8
    Boudreau, B. P., 1997. Diagenetic Models and Their Implementation. Springer, Berlin
    Boudreau, B. P., Ruddick, B. R., 1991. On a Reactive Continuum Representation of Organic Matter Diagenesis. American Journal of Science, 291: 507–538. doi: 10.2475/ajs.291.5.507
    Boudreau, B. P., Westrich, J. T., 1984. The Dependence of Bacterial Sulfate Reduction on Sulfate Concentration in Marine Sediments. Geochimica et Cosmochimica Acta, 48(12): 2503–2516. doi: 10.1016/0016-7037(84)90301-6
    Burdige, D. J., 2006. Geochemistry of Marine Sediments. Princeton University Press, Princeton
    Chatterjee, S., Dickens, G. R., Bhatnagar, G., et al., 2011. Pore Water Sulfate, Alkalinity, and Carbon Isotope Profiles in Shallow Sediment above Marine Gas Hydrate Systems: A Numerical Modeling Perspective. Journal of Geophysical Research, 116(B9): 2156–2202 doi: 10.1029/2011JB008290
    Conrad, R., 2005. Quantification of Methanogenic Pathways Using Stable Carbon Isotopic Signatures: A Review and a Proposal. Organic Geochemistry, 36(5): 739–752. doi: 10.1016/j.orggeochem.2004.09.006
    Conrad, R., 2009. The Global Methane Cycle: Recent Advances in Understanding the Microbial Processes Involved. Environmental Microbiology Reports, 1(5): 285–292. doi: 10.1111/j.1758-2229.2009.00038.x
    Dale, A. W., Aguilera, D. R., Regnier, P., et al., 2008. Seasonal Dynamics of the depth and Rate of Anaerobic Oxidation of Methane in Aarhus Bay (Denmark) Sediments. Journal of Marine Research, 66(1): 127–155. doi: 10.1357/002224008784815775
    Dale, A. W., Regnier, P., Van Cappellen, P., 2006. Bioenergetic Controls on Anaerobic Oxidation of Methane (AOM) in Coastal Marine Sediments: A Theoretical Analysis. American Journal of Science, 306(4): 246–294. doi: 10.2475/ajs.306.4.246
    Davie, M. K., Buffett, B. A., 2001. A Numerical Model for the Formation of Gas Hydrate below the Seafloor. Journal of Geophysical Research, 106(B1): 497–514. doi: 10.1029/2000JB900363
    Duan, Z., Mao, S., 2006. A Thermodynamic Model for Calculating Methane Solubility, Density and Gas Phase Composition of Methane-Bearing Aqueous Fluids from 273 to 523 K and from 1 to 2 000 bar. Geochimica et Cosmochimica Acta, 70(13): 3369–3386. doi: 10.1016/j.gca.2006.03.018
    Emerson, S., Hedges, J., 2008. Chemical Oceanography and the Marine Carbon Cycle: Cambridge University Press, Cambridge, 462
    Emerson, S., Jahnke, R., Heggie, D., 1984. Sediment-Water Exchange in Shallow Water Estuarine Sediments. Journal of Marine Research, 42: 709–730. doi: 10.1357/002224084788505942
    Expedition 311 Scientists, 2006a. Expedition 311 Summary. In: Riedel, M., Collett, T. S., Malone, M. J., and the Expedition 311 Scientists, eds., Proc. IODP, 311: Washington, DC
    Expedition 311 Scientists, 2006b. Site U1327. In: Riedel, M., Collett, T. S., Malone, M. J., and the Expedition 311 Scientists, eds., Proc. IODP, 311: Washington, DC
    Froelich, P. N., Klinkhammer, G. P., Bender, M. L., et al., 1979. Early Oxidation of Organic Matter in Pelagic Sediments of the Eastern Equatorial Atlantic Suboxic Diagenesis. Geochimica et Cosmochimica Acta, 43: 1075–1090. doi: 10.1016/0016-7037(79)90095-4
    Higgins, J. A., Fischer, W. W., Schrag, D. P., 2009. Oxygenation of the Ocean and Sediments: Consequences for the Seafloor Carbonate Factory. Earth and Planetary Science Letters, 284(1): 25–33. doi: 10.1016/j.epsl.2009.03.039
    Inskeep, W. P., Bloom, P. R., 1985. An Evaluation of Rate Equations for Calcite Precipitation Kinetics at pCO2 less than 0.01 atm and pH Greater than 8. Geochimica et Cosmochimica Acta, 49(10): 2165–2180. doi: 10.1016/0016-7037(85)90074-2
    Jakobsen, R., Cold, L., 2007. Geochemistry at the Sulfate Reduction-Methanogenesis Transition Zone in an Anoxic Aquifer—A Partial Equilibrium Interpretation using 2D Reactive Transport Modeling. Geochimica et Cosmochimica Acta, 71(8): 1949–1966. doi: 10.1016/j.gca.2007.01.013
    Jørgensen, B. B., Parkes, R. J., 2010. Role of Sulfate Reduction and Methane Production by Organic Carbon Degradation in Eutrophic Fjord Sediments (Limfjorden, Denmark). Limnol. Oceanogr. 55(3): 1338–1352. doi: 10.4319/lo.2010.55.3.1338
    Kastner, M., Sample, J. C., Whiticar, M. J., et al., 1995. Geochemical Evidence for Fluid Flow and Diagenesis at the Cascadia Convergent Margin. Proceedings of the Ocean Drilling Program, Scientific Results, 146, No. Pt 1.
    Kim, J. H., Torres, M. E., Hong, W. L., et al., 2013. Pore Fluid Chemistry from the Second Gas Hydrate Drilling Expedition in the Ulleung Basin (UBGH2): Source, Mechanisms and Consequences of Fluid Freshening in the Central Part of the Ulleung Basin, East Sea. Marine and Petroleum Geology, 47: 99–112. doi: 10.1016/j.marpetgeo.2012.12.011
    Luff, R., Wallmann, K., 2003. Fluid Flow, Methane Fluxes, Carbonate Precipitation and Biogeochemical Turnover in Gas Hydrate-Bearing Sediments at Hydrate Ridge, Cascadia Margin: Numerical Modeling and Mass Balances. Geochimica et Cosmochimica Acta, 67(18): 3403–3421. doi: 10.1016/S0016-7037(03)00127-3
    Meister, P., Liu, B., Ferdelman, T. G., et al., 2013. Control of Sulphate and Methane Distributions in Marine Sediments by Organic Matter Reactivity. Geochimica et Cosmochimica Acta, 104: 183–193. doi: 10.1016/j.gca.2012.11.011
    Meysman, F. J., Middelburg, J. J., Herman, P. M., et al., 2003. Reactive Transport in Surface Sediments. Ⅱ. Media: An Object-Oriented Problem-Solving Environment for Early Diagenesis. Computers & Geosciences, 29(3): 301–318. doi: 10.1016/S0098-3004(03)00007-4
    Middelburg, J. J., 1989. A Simple Rate Model for Organic Matter Decomposition in Marine Sediments. Geochimica et Cosmochimica Acta, 53(7): 1577–1581. doi: 10.1016/0016-7037(89)90239-1
    Parkhurst, D. L., Appelo, C. A. J., 2013. Description of Input and Examples for PHREEQC Version 3—A Computer Program for Speciation, Batch-Reaction, One-Dimensional Transport, and Inverse Geochemical Calculations: U. S. Geological Survey Techniques and Methods. Book 6, 497
    Reeburgh, W. S., 1976. Methane Consumption in Cariaco Trench Waters and Sediments. Earth and Planetary Science Letters, 28(3): 337–344. doi: 10.1016/0012-821X(76)90195-3
    Reeburgh, W. S., 2007. Oceanic Methane Biogeochemistry. Chemical Reviews, 107(2): 486–513 doi: 10.1021/cr050362v
    Regnier, P., Dale, A. W., Arndt, S., et al., 2011. Quantitative Analysis of Anaerobic Oxidation of Methane (AOM) in Marine Sediments: A Modeling Perspective. Earth-Science Reviews, 106(1–2): 105–130. doi: 10.1016/j.earscirev.2011.01.002
    Regnier, P., Dale, A. W., Pallud, C., et al., 2005. Incorporating Geomicrobial Processes in Reactive Transport Models of Subsurface Environments. In: Nützmann., G., Viotti, P., Aagaard, P., eds., Reactive Transport in Soil and Groundwater. Springer, Berlin Heidelberg. 109–125
    Reid, J. 2003. The New Features of Fortran, ISO/IEC JTC1/SC22/WG5N1579. http://j3-fortran.org/doc/WG5/N1551-N1600/N1579.pdf
    Richter, F. M., Liang, Y., 1993. The Rate and Consequences of Sr Diagenesis in Deep-Sea Carbonates. Earth and Planetary Science Letters, 117(3): 553–565. doi: 10.1016/0012-821X(93)90102-F
    Ridgwell, A., Hargreaves, J. C., Edwards, N. R., et al., 2007. Marine Geochemical Data Assimilation in an Efficient Earth System Model of Global Biogeochemical Cycling. Biogeosciences, 4(1): 87–104. doi: 10.5194/bg-4-87-2007
    Rudnicki, M. D., Elderfield, H., Mottl, M. J., 2001. Pore Fluid Advection and Reaction in Sediments of the Eastern Flank, Juan de Fuca Ridge, 48N. Earth and Planetary Science Letters, 187: 173–189. doi: 10.1016/S0012-821X(99)00191-0
    Ryu, B. J., Collett, T. S., Riedel, M., et al., 2013. Scientific Results of the Second Gas Hydrate Drilling Expedition in the Ulleung Basin (UBGH2). Marine and Petroleum Geology, 47: 1–20. doi: 10.1016/j.marpetgeo.2013.07.007
    Saltelli, A., Ratto, M., Tarantola, S., et al., 2005. Sensitivity Analysis for Chemical Models. Chemical Reviews, 105(7): 2811–2828 doi: 10.1021/cr040659d
    Schultz, H. D., Zabel, M., 2006. Marine Geochemistry (2ed. ). Springer, Berlin. 593
    Shipboard Scientific Party, 2003. Site 1245. In: Tréhu, A. M., Bohrmann, G., Rack, F. R., et al., Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program), 1–131
    Thullner, M., Regnier, P., Van Cappellen, P., 2007. Modeling Microbially Induced Carbon Degradation in Redox-Stratified Subsurface Environments: Concepts and Open Questions. Geomicrobiology Journal, 24(3–4): 139–155. doi: 10.1080/01490450701459275
    Torres, M. E., McManus, J., Hammond, D. E., et al., 2002. Fluid and Chemical Fluxes in and out of Sediments Hosting Methane Hydrate Deposits on Hydrate Ridge, OR, Ⅰ: Hydrological Provinces. Earth and Planetary Science Letters, 201. doi: 10.1016/S0012-821X(02)00733-1
    Treude, T., Boetius, A., Knittel, K., et al., 2003. Anaerobic Oxidation of Methane above Gas Hydrates at Hydrate Ridge, NE Pacific Ocean. Marine Ecology Progress Series, 264: 1–14. doi: 10.3354/meps264001
    Turchyn, A. V., DePaolo, D. J., 2011. Calcium Isotope Evidence for Suppression of Carbonate Dissolution in Carbonate-Bearing Organic-Rich Sediments. Geochimica et Cosmochimica Acta, 75(22): 7081–7098. doi: 10.1016/j.gca.2011.09.014
    Van Cappellen, P., Wang, Y. F., 1996. Cycling of Iron and Manganese in Surface Sediments: A General Theory for the Coupled Transport and Reaction of Carbon, Oxygen, Nitrogen, Sulfur, Iron, and Manganese. American Journal of Science, 296(3): 197–243. doi: 10.2475/ajs.296.3.197
    Versteeg, H. K., Malalasekera, W., 2007. An Introduction to Computational Fluid Dynamics: The Finite Volume Method: Pearson Education Limited.
    Wegener, G., Boetius, A., 2009. An Experimental Study on Short-Term Changes in the Anaerobic Oxidation of Methane in Response to Varying Methane and Sulfate Fluxes. Biogeosciences, 6: 867–876. doi: 10.5194/bg-6-867-2009
    Wortmann, U. G., Chernyavsky, B. M., 2011. The Significance of Isotope Specific Diffusion Coefficients for Reaction-Transport Models of Sulfate Reduction in Marine Sediments. Geochimica et Cosmochimica Acta, 75(11): 3046–3056. doi: 10.1016/j.gca.2011.03.007
    Yang, T., Jiang, S., Ge, L., et al., 2013. Geochemistry of Pore Waters from HQ-1PC of the Qiongdongnan Basin, Northern South China Sea, and Its Implications for Gas Hydrate Exploration. Science China Earth Sciences, 56(4): 521–529. DOI: 10.1007/s11430-012-4560-7
    Zatsepin, O. Y., Buffett, B. A., 1997. Phase Equilibrium of Gas Hydrate: Implications for the Formation of Hydrate in the Deep Sea Floor. Geophysical Research Letters, 24 (13): 1567–1570. DOI: 10.1029/97GL01599
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