Definition
The biological processes that modify unconsolidated sediment after initial deposition and burial.
Overview
Throughout the sediment column, up to the temperature threshold of life, microbial activity plays an integral role in diagenesis . It is widely recognized that through their various chemoheterotrophic pathways, microorganisms are ultimately responsible for the conversion of organic carbon to CO2 and CH4 at temperatures <100oC. Some aerobic bacteria use hydrolytic enzymes to break down complex molecules into simple monomers such as sugars, amino acids, and fatty acids that they can then utilize, while most anaerobes are restricted to simple organic compounds (e.g., acetate, lactate, H2) that are the by-products of fermentation (Lovley and Chapelle, 1995). Typically, the more labile materials (e.g., proteins, carbohydrates) are degraded in near-surface sediments on time scales of days to years, and more refractory materials (e.g., lipids) are broken down deeper in the...
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Bibliography
Aller, R. C., 1980. Quantifying solute distributions in the bioturbated zone of marine sediments by defining an average microenvironment. Geochimica et Cosmochimica Acta, 44, 1955–1965.
Aller, R. C., 1990. Bioturbation and manganese cycling in hemipelagic sediments. Philosophical Transactions of the Royal Society of London, 331, 51–68.
Bender, B., and Heggie, D. T., 1984. Fate of organic carbon reaching the deep sea: a status report. Geochimica et Cosmochimica Acta, 48, 977–986.
Berner, R. A., 1982. Burial of organic carbon and pyrite sulphur in the modern ocean: its geochemical and environmental significance. American Journal of Science, 282, 451–473.
Berner, R. A., and Raiswell, R., 1983. Burial of organic carbon and pyrite sulfur in sediments over Phanerozoic time: a new theory. Geochimica et Cosmochimica Acta, 47, 855–862.
Berner, R. A., and Westrich, J. T., 1985. Bioturbation and the early diagenesis of carbon and sulphur. American Journal of Science, 285, 193–206.
Blackburn, T. H., and Blackburn, N. D., 1993. Coupling of cycles and global significance of sediment diagenesis. Marine Geology, 113, 101–110.
Burdige, D. J., 1993. The biogeochemistry of manganese and iron reduction in marine sediments. Earth-Science Reviews, 35, 249–284.
Canfield, D. E., 1993. Organic matter oxidation in marine sediments. In Wollast, R., Chou, L., and Mackenzie, F. (eds.), Interactions of C, N, P and S Biogeochemical Cycles and Global Change. Berlin: Springer, pp. 333–363.
Canfield, D. E., Raiswell, R., and Bottrell, S., 1992. The reactivity of sedimentary iron minerals toward sulfide. American Journal of Science, 292, 659–683.
Chapelle, F. H., and Lovley, D. R., 1992. Competitive exclusion of sulfate reduction by Fe(III)-reducing bacteria: a mechanism for producing discrete zones of high-iron ground water. Ground Water, 30, 29–36.
Coleman, M. L., 1985. Geochemistry of diagenetic non-silicate minerals. Kinetic considerations. Philosophical Transactions of the Royal Society of London, 315, 39–56.
Devol, A. H., 1991. Direct measurement of nitrogen gas fluxes from continental shelf sediments. Nature, 349, 319–321.
D’Hondt, S., Rutherford, S., and Spivack, A. J., 2002. Metabolic activity of subsurface life in deep-sea sediments. Science, 295, 2067–2070.
diChristina, T. J., 1992. Effects of nitrate and nitrite on dissimilatory iron reduction by Shewanella putrefaciens 200. Journal of Bacteriology, 174, 1891–1896.
Emerson, S., and Hedges, J. I., 1988. Processes controlling the organic carbon content of open ocean sediments. Paleooceanograpghy, 3, 621–634.
Froelich, P. N. 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.
Hammond, D. E., Fuller, C., Harmon, D., Hartman, B., Korosec, M., Miller, L. G., Rea, R., Warren, S., Berelson, W., and Hager, S. W., 1985. Benthic fluxes in San Francisco Bay. Hydrobiologia, 129, 69–90.
Hansen, J. I., Henriksen, K., and Blackburn, T. H., 1981. Seasonal distribution of nitrifying bacteria and rates of nitrification in coastal marine sediments. Microbial Ecology, 7, 297–304.
Hedges, J. I., Clark, W. A., and Cowie, G. L., 1988. Fluxes and reactivities of organic matter in a coastal marine bay. Limnology and Oceanography, 33, 1137–1152.
Jones, J. G., 1985. Microbes and microbial processes in sediments. Philosophical Transactions of the Royal Society of London, 315, 3–17.
Jørgensen, B. B., 1982. Mineralization of organic matter in the seabed – the role of sulfate reduction. Nature, 296, 643–645.
Jørgensen, B. B., 1990. A thiosulphate shunt in the sulfur cycle of marine sediments. Science, 249, 152–154.
Konhauser, K. O., 2007. Introduction to Geomicrobiology. Oxford: Blackwell Publishing.
Krom, M. D., and Berner, R. A., 1980. Adsorption of phosphate in anoxic marine sediments. Limnology and Oceanography, 25, 797–806.
Leang, C., Adams, L. A., Chin, K. J., Nevin, K. P., Methé, B. A., Webster, J., Sharma, M. L., and Lovley, D. R., 2005. Adaptation to disruption of the electron transfer pathway for Fe(III) reduction in Geobacter sulfurreducens. Journal of Bacteriology, 187, 5918–5926.
Lee, C., 1992. Controls on organic carbon preservation: the use of stratified water bodies to compare intrinsic rates of decomposition in oxic and anoxic systems. Geochimica et Cosmochimica Acta, 56, 3323–3335.
Lovley, D. R., and Chapelle, F. H., 1995. Deep subsurface microbial processes. Reviews of Geophysics, 33, 365–381.
Lovley, D. R., and Goodwin, S., 1988. Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments. Geochimica et Cosmochimica Acta, 52, 2993–3003.
Lovley, D. R., and Klug, M. J., 1986. Model for the distribution of sulfate reduction and methanogenesis in freshwater sediments. Geochimica et Cosmochimica Acta, 50, 11–18.
Lovley, D. R., and Phillips, E. J. P., 1986. Organic matter mineralization with reduction of ferric iron in anaerobic sediments. Applied and Environmental Microbiology, 51, 683–689.
Lovley, D. R., and Phillips, E. J. P., 1987. Competitive mechanisms for inhibition of sulphate reduction and methane production in the zone of ferric iron reduction in sediments. Applied and Environmental Microbiology, 53, 2636–2641.
Lovley, D. R., and Phillips, E. J. P., 1988. Manganese inhibition of microbial iron reduction in anaerobic sediments. Geomicrobiology Journal, 6, 145–155.
Lovley, D. R., Dwyer, D. F., and Klug, M. J., 1982. Kinetic analysis of competition between sulfate reducers and methanogens for hydrogen in sediments. Applied and Environmental Microbiology, 43, 1373–1379.
Lovley, D. R., Holmes, D. E., and Nevin, K. P., 2004. Dissimilatory Fe(III) and Mn(IV) reduction. Advances in Microbial Physiology, 49, 219–286.
Luther, G. W., III, Sundby, B., Lewis, B. L., Brendel, P. J., and Silverberg, N., 1997. Interactions of manganese with the nitrogen cycle. Alternative pathways to dinitrogen. Geochimica et Cosmochimica Acta, 61, 4043–4052.
Martens, C. S., and Berner, R. A., 1974. Methane production in the interstitial waters of sulfate-depleted sediments. Science, 185, 1167–1169.
Martens, C. S., and Klump, J. V., 1984. Biogeochemical cycling in an organic-rich coastal marine basin. 4. An organic carbon budget for sediments dominated by sulfate reduction and methanogenesis. Geochimica et Cosmochimica Acta, 48, 1987–2004.
Mortimer, R. J. G., Davey, J. T., Krom, M. D., Watson, P. G., Frickers, P. E., and Clifton, R. J., 1999. The effect of macrofauna on pore-water profiles and nutrient fluxes in the intertidal zone of the Humber Estuary. Estuarine, Coastal and Shelf Science, 48, 683–699.
Murray, J. W., and Grundmanis, V., 1980. Oxygen consumption in pelagic marine sediments. Science, 209, 1527–1530.
Myers, K. H., and Nealson, K. H., 1988. Microbial reduction of manganese oxides: interactions with iron and sulfur. Geochimica et Cosmochimica Acta, 52, 2727–2732.
Nevin, K. P., and Lovely, D. R., 2002. Mechanisms for accessing insoluble Fe(III) oxide during dissimilatory Fe(III) reduction by Geothrix fermentans. Applied and Environmental Microbiology, 68, 2294–2299.
Over, D. J., 1990. Trace metals in burrow walls and sediments, Georgia Bight, USA. Ichnos, 1, 31–41.
Thamdrup, B., and Dalsgaard, T., 2002. Production of N2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments. Applied and Environmental Microbiology, 68, 1312–1318.
Van Cappellen, P., and Gaillard, J. F., 1996. Biogeochemical dynamics in aquatic sediments. In Lichtner, P. C., Steefel, C. I.,and Oelkers, E. H. (eds.), Reactive Transport in Porous Media. Reviews in Mineralogy. Washington: Mineralogical Society of America, Vol. 34, pp. 335–376.
Westrich, J. T., and Berner, R. A., 1984. The role of sedimentary organic matter in bacterial sulphate reduction: the G model tested. Limnology and Oceanography, 29, 236–249.
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Konhauser, K.O., Gingras, M.K., Kappler, A. (2011). Sediment Diagenesis – Biologically Controlled. In: Reitner, J., Thiel, V. (eds) Encyclopedia of Geobiology. Encyclopedia of Earth Sciences Series. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-9212-1_179
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DOI: https://doi.org/10.1007/978-1-4020-9212-1_179
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