Abstract
Geochemical cycles on Earth follow the basic laws of thermodynamics and proceed towards a state of maximal entropy and the most stable mineral phases. Redox reactions between oxidants such as atmospheric oxygen or manganese oxide and reductants such as ammonium or sulfide may proceed by chemical reaction, but they are most often accelerated by many orders of magnitude through enzymatic catalysis in living organisms. Throughout Earth’s history, prokaryotic physiology has evolved towards a versatile use of chemical energy available from this multitude of potential reactions. Biology, thereby, to a large extent regulates the rate at which the elements are cycled in the environment and affects where and in which chemical form the elements accumulate. By coupling very specifically certain reactions through their energy metabolism, the organisms also direct the pathways of transformation and the ways in which the element cycles are coupled.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Alperin, M.J. and Reeburgh, W.S., 1985. Inhibition Experiments on Anaerobic Methane Oxidation. Applied and Environmental Microbiology, 50: 940–945.
Arnosti, C, 1996. A new method for measuring polysaccharide hydrolysis rates in marine environments. Organic Geochemistry, 25: 105–115.
Bak, F. and Cypionka, H., 1987. A novel type of energy metabolism involving fermentation of inorganic sulphur compounds. Nature, 326: 891–892.
Benz, M., Brune, A. and Schink, B., 1998. Anaerobic and aerobic oxidation of ferrous iron and neutral pH by chemoheterotrophic nitrate-reduction bacteria. Arch. Microbiology, 169: 159–165.
Berelson, W.M., Hammond, D.E., Smith, K.L. Jr; Jahnke, R.A., Devol, A.H., Hinge, K.R., Rowe, G.T. and Sayles, F. (eds), 1987. In situ benthic flux measurement devices: bottom lander technology. MTS Journal, 21: 26–32.
Berner, R.A., 1980. Early diagenesis: A theoretical approach. Princton Univ. Press, Princton, NY, 241 pp.
Boetius, A. and Lochte, K., 1996. Effect of organic enrichments on hydrolytic potentials and growth of bacteria in deep-sea sediments. Marine Ecology Progress Series, 140: 239–250.
Boetius, A. and Damm, E., 1998. Benthic oxygen uptake, hydrolytic potentials and microbial biomass at the Arctic continental slope. Deep-Sea Research I, 45: 239–275.
Borowski, W.S., Paull, C.K. and Ussier, W., 1996. Marine pore-water sulfate profiles indicate in situ methane flux from underlying gas hydrate. Geology, 24: 655–658.
Boudreau, B.P., 1988. Mass-transport constraints on the growth of discoidal ferromanganese nodules. American Journal of Science, 288: 777–797.
Boudreau, B.P., 1997. Diagenetic models and their impletation: modelling transport and reactions in aquatic sediments. Springer, Berlin, Heidelberg, NY, 414 pp.
Canfield, D.E., 1993. Organic matter oxidation in marine sediments. In: Wollast, R., Mackenzie, F.T. and Chou, L. (eds), Interactions of C, N, P and S biogeochemical cycles. NATO ASI Series, 14. Springer, Berlin, Heidelberg, NY, pp. 333–363.
Canfield, D.E., Jorgensen B.B., Fossing, H., Glud, R.N., Gundersen, J., Ramsing, N.B., Thamdrup, B., Hansen, J.W., Nielsen, L.P. and Hall, P.O.J., 1993b. Pathways of organic carbon oxidation in three continental margin sediments. Marine Geology, 113: 27–40.
Canfield, D.E. and Teske, A., 1996. Late Proterozoic rise in atmospheric oxygen concentration inferred from phylogenetic and sulphur-isotope studies. Nature, 382: 127–132.
Christensen, D., 1984. Determination of substrates oxidized by sulfate reduction in intact cores of marine sediments. Limnology and Oceanography, 29: 189–192.
Chrost, R.J., 1991. Microbial enzymes in aquatic environments. Springer, Berlin, Heidelberg, NY, 317 pp.
Coleman, M.L., Hedrick, D.B., Lovley, D.R., White, D.C. and Pye, K., 1993. Reduction of Fe(III) in sediments by sulphate-reducing bacteria. Nature, 361: 436–438.
Conrad, R., Schink, B. and Phelps, T.J., 1986. Thermodynamics of H2-consuming and H2-producing metabolic reactions in diverse methanogenic environments under in situ conditions. FEMS Microbiology Ecology, 38: 353–360.
Cypionka, H., 1994. Novel matabolic capacities of sulfate-reducing bacteria, and their activities in microbial mats. In: Stal, L.J. and Caumette, P.(eds), Microbial mats, NATO ASI Series, 35, Springer, Berlin, Heidelberg, NY, pp. 367–376.
Dannenberg, S., Kroder, M., Dilling, W. and Cypionka, H., 1992. Oxidation of H2, organic compounds and inorganic sulfur compounds coupled to reduction of 02 or nitrate by sulfate-reducing bacteria. Archives of Microbiology, 158: 93–99.
Ehrenreich, A. and Widdel, F., 1994. Anaerobic oxidation of ferrous iron by purple bacteria, a new type of prototrophic metabolism. Applied and Environmental Microbiology, 60: 4517–4526.
Ehrlich, H.L., 1996. Geomicrobiology. Marcel Dekker, NY, 719 pp.
Fenchel, T.M. and Jorgensen, B.B., 1977. Detritus food chains of aquatic ecosystems: The role of bacteria. In: Alexander, M. (ed), Advances in Microbial Ecology, 1, Plenum Press, NY, pp. 1–58.
Fenchel, T., King, G.M. and Blackburn, T.H., 1998. Bacterial biogeochemistry: The ecophysiology of mineral cycling. Academic Press, London, 307 pp.
Fossing, H. and Jorgensen, B.B., 1989. Measurement of bacterial sulfate reduction in sediments: evaluation of a single-step chromium reduction method. Biogeochemistry, 8: 205–222.
Fossing, H. and Jorgensen, B.B., 1990. Isotope exchange reactions with radiolabeled sulfur compounds in anoxic seawater. Biogeochemistry, 9: 223–245.
Fossing, H., Thode-Andersen, S. and Jorgensen, B.B., 1992. Sulfur isotope exchange between 35S-labeled inorganic sulfur compounds in anoxic marine sediments. Marine Chemistry, 38: 117–132.
Fossing, H., Gallardo, V.A., Jorgensen, B.B., Hiittel, M., Nielsen, L.P., Schulz, H., Canfield, D.E., Forster, S., Glud, R.N., Gundersen, J.K., Kiifer, J., Ramsing, N.B., Teske, A., Thamdrup, B. and Ulloa, O., 1995. Concentration and transport of nitrate by the mat-forming sulphur bacterium Thioploca. Nature, 374: 713–715.
Fossing, H., 1995. 35S-radiolabeling to probe biogeochemical cycling of sulfur. In:. Vairavamurthy, M.A and. Schoonen, M.A.A (eds), Geochemical transformations of sedimentary sulfur. ACS Symposium Series, 612, American Chemical Society, Washington, DC, pp. 348–364.
Froelich, P.N., Klinkhammer, G.P., Bender, M.L., Luedtke, N.A., Heath, G.R., Cullen, D., Dauphin, P., Hammond, D., Hartman, B. and Maynard, V., 1979. Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic: suboxic diagenesis. Geochimica et Cosmochimica Acta, 43: 1075–1088.
Glud, R.N., Gundersen, J.K., Jorgensen, B.B., Revsbech, N.P. and Schulz, H.D., 1994. Diffusive and total oxygen uptake of deep-sea sediments in the eastern South Atlantic Ocean: in situ and laboratory measurements. Deep-Sea Research, 41: 1767–1788.
Greeff, O., Glud, R.N., Gundersen, J., Holby, O. and Jorgensen, B.B., in press. A benthic lander for tracer studies in the sea bed: in situ measurements of sulfate reduction. Continental Shelf Research.
Gundersen, J.K. and Jorgensen, B.B., 1990. Microstructure of diffusive boundary layer and the oxygen uptake of the sea floor. Nature, 345: 604–607.
Gundersen, J.K., Glud, R.N. and Jorgensen, B.B., 1995. Oxygen turnover of the sea floor (in Danish). Marine research from the danisch environmental agency, 57, Danish Ministry of Environment and Energy, Copenhagen, 155 pp.
Hedges, J.I., 1978. The formation and clay mineral reactions of melanoidins. Geochimica Cosmochimica Acta, 42: 69–76.
Henrichs, S.M. and Reeburgh, W.S., 1987. Anaerobic mineralization of marine sediment organic matter: rates and the role of anaerobic processes in the oceanic carbon economy. Geomicrobiological Journal, 5: 191–237.
Henrichs, S.M., 1992. Early diagenesis of organic matter in marine sediments: progress and perplexity. Marine Chemistry, 39: 119–149.
Henriksen, K., 1980. Measurement of in situ rates of nitrification in sediment. Microbial Ecology, 6: 329–337.
Hoehler, T.M., Alperin, M.J., Albert, D.B. and Martens, C.S., 1994. Field and laboratory studies of methane oxidation in an anoxic marine sediment: Evidence for a methanogen-sulfate reducer consortium. Global Biogeochemical Cycles, 8: 451–463.
Hoehler, T.M., Alperin, M.J., Albert, D.B. and Martens, C.S., 1998. Thermodynamic control on hydrogen concentrations in anoxic sediments. Geochimic et Cosmochimica Acta, 62: 1745–1756.
Huettel, M., Ziebis, W., Forster, S. and Luther, G.W., 1998.Advective transport affecting metal and nutrient distributions and interfacial fluxes in permeable sediments. Geochimica et Cosmochimica Acta, 62: 613–631.
Isaksen, M.F. and Jorgensen, B.B., 1996. Adaptation of psychrophilic and psychrotrophic sulfate-reducing bacteria to permanently cold marine environments. Applied and Environmental Microbiology, 62: 408–414.
Iversen, N. and Jorgensen, B.B., 1985. Anaerobic methane oxidation rates at the sulfate-methane transition in marine sediments from Kattegat and Skagerrak (Denmark). Limnology and Oceanography, 30: 944–955.
Jorgensen, B.B., 1978. A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments. I. Measurement with radiotracer techniques. Geomicrobiology Journal, 1: 11–27.
Jorgensen, B.B., 1982. Mineralization of organic matter in the sea bed-the role of sulphate reduction. Nature, 296: 643–645.
Jorgensen, B.B., 1987. Ecology of the sulphur cycle: Oxidative pathways in sediments. In: Cole, J.A. and Ferguson, S. (eds), The nitrogen and sulphur cycles. Society for General Microbiology Symposium, 42, Cambridge University Press, pp. 31–63.
Jorgensen, B.B., 1990. A thiosulfate shunt in the sulfur cycle of marine sediments. Science, 249: 152–154.
Jorgensen, B.B. and Bak, R, 1991. Pathways and microbiology of thiosulfate transformation and sulfate reduction in a marine sediment (Kattegat, Denmark). Applied and Environmental Microbiology, 57: 847–856.
Jorgensen, B.B., Isaksen, M.F. and Jannasch, H.W., 1992. Bacterial sulfate reduction above 100°C in deep-sea hy-drothermal vent sediments. Science, 258: 1756–1757.
Jorgensen, B.B., 1996. The micro-world of marine bacteria (in German). Naturwissenschaften, 82: 269–278.
Jorgensen, B.B., in press. Microbial life in the diffusive boundery layer. In: Boudreau, B.P. and Jorgensen, B.B. (eds), The benethic boundary layer: transport processes and biogeochemistry. Oxford University Press, Oxford.
Karp-Boss, L., Boss, E. and Jumars, P.A., 1996. Nutrient fluxes to planktonic osmotrophs in the presence of fluid motion. Oceanographic Marine Biology Annual Reviews, 34: 71–107.
Keil, R.G., Montlucon, Prahl, EG. and Hedges, J.I., 1994b. Sorptive preperation of labile organic matter in marine sediments. Nature, 370: 549–552.
Kelly, D.P., 1982. Biochemistry of the chemolithotrophic oxidation of inorganic sulphur. Philosophic Transactions of the Royal Society of London, 298: 499–528.
King, G.M., 1983. Sulfate reduction in Georgia salt marsh soils: An evaluation of pyrite formation by use of 35S and 55Fe tracers. Limnology and Oceanography, 28: 987–995.
Klinkhammer, G.P., 1980. Early diagenesis in sediments from the eastern equatorial Pacific, II. Pore water metal results. Earth and Planetary Science Letters, 49: 81–101.
Koch, A.L., 1990. Diffusion, the crucial process in many aspects of the biology of bacteria. In: Marshall, K.C. (ed), Advances in microbial ecology, 11, Plenum, NY, pp. 37–70.
Koch, A.L., 1996. What size should a bacterium be? A question of scale. Annual Reviews of Microbiology, 50: 317–348.
Krekeler, D. and Cypionka, H., 1995. The preferred electron acceptor of Desulfovibrio desulfuricans CSN. FEMS Microbiology Ecology, 17: 271–278.
Kiihl, M. and Revsbech, N.P., in press. Microsensors for studies of interfacial biogeochemical processes. In: Boudreau, B.P. and Jorgensen, B.B. (eds), The benthic boundary layer: transport processes and biogeochemistry. Oxford University Press, Oxford.
Llobet-Brossa, E., Rosello-Mora, R. and Ammann, R., 1998. Microbial community composition of Wadden Sea sediments as revealed by fluorescent in situ hybridization. Applied and Environmental Microbiology, 64: 2691–2696.
Lochte, K. and Turley, CM., 1988. Bacteria and cyanobacteria associated with phytodetritus in the deep sea. Nature, 333: 67–69.
Madigan, M.T., Martinko, J.M. and Parker, J., 1997. Biology of microorganisms. Prentice Hall, London, 986 pp.
Nielsen, L.P., 1992. Denitrification in sediment determined from nitrogen isotope pairing. FEMS Microbiology Ecology, 86: 357–362.
Niewohner, C, Hensen, C, Kasten, S., Zabel, M. and Schulz, H.D., 1998. Deep sulfate reduction completely mediated by anaerobic methane oxidation in sediments of the upwelling area off Namibia. Geochimica et Cosmochimica Acta, 62: 455–464.
Oremland, R.S. and Polcin, S., 1982. Methanogenesis and sulfate reduction: Competitive and noncompetetive substrates in estuarine sediments. Applied and Environmental Microbiology, 44: 1270–1276.
Oremland, R.S., Marsh, L.M. and Polcin, S., 1982. Methane production and simultaneous sulphate reduction in anoxic saltmarsh sediments. Nature, 296: 143–145.
Oremland, R.S. and Capone, D.G., 1988. Use of „specific“ inhibitors in biogeochemistry and microbial ecology. In: Marshall, K.C. (ed), Advances in microbial ecology, 10, Plenum Press, NY, pp. 285–383.
Parkes, J.R., Cragg, B.A., Bale, S.J., Getliff, J.M., Goodman, K., Rochell, P.A., Fry, J.C., Weightman, A.J. and Harvey, S.M., 1994. Deep bacterial biosphere in Pacific Ocean sediments. Nature, 371: 410–413.
Postgate, J.R., 1979. The sulfate-reduction bacteria. Cambridge University Press, Cambridge, 208 pp.
Rabus, F., Fukui, M., Wilkes, H. and Widdel, R, 1996. Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Applied and Environmental Microbiology, 62: 3605–3613.
Redfield, A.C., 1958. The biological control of chemical factors in the environment. Am. Scientist, 46: 206–222.
Reeburgh, W.S., 1969. Observations of gases in Chesapeake Bay sediments. Limnology and Oceanography, 14: 368–375.
Reimers, C.E., 1987. An in situ microprofiling instrument for measuring interfacial pore water gradients: methods and oxygen profiles from the North Pacific Ocean. Deep-Sea Research, 34: 2019–2035.
Revsbech, N.R, Nielsen, L.R, Christensen, RB. and Sorensen, J., 1988. Combined oxygen and nitrous oxide microsensor for denitrification studies. Applied and Environmental Microbiology, 54: 2245–2249.
Roden, E.E. and Lovley, D.R., 1993. Evaluation of 55Fe as a tracer of Fe(III) reduction in aquatic sediments. Geomicrobiological Journal, 11: 49–56.
Rueter, P., Rabus, R., Wilkes, H., Aeckersberg, F., Rainey, F.A., Jannasch, H.W. and Widdel, F., 1994. Anaerobic oxidation of hydrocarbons in crude oil by new types of sulphate-reducing bacteria. Nature, 372: 455–458.
Sagemann, J., Jorgensen, B.B. and Greeff, O., 1998. Temperature dependence and rates of sulfate reduction in cold sediments of Svalbard, Arctic Ocean. Geomicrobiological Journal, 15: 83–98.
Sansone, F.J., Andrews, C.C. and Okamoto, M.Y., 1987. Adsorption of short-chain organic acids onto nearshore marine sediments. Geochimica et Cosmochimica Acta, 51: 1889–1896.
Santschi, PH., Anderson R.F., Fleisher, M.Q. and Bowles, W., 1991. Measurements of diffusive sublayer thicknesses in the ocean by alabaster dissolution, and their implications for the measurements of benthic fluxes. Journal of Geophysical Research, 96: 10.641–10.657.
Schopf, J.W. and Klein, C. (eds), 1992. The proterozoic biosphere. Cambridge University Press, Cambridge, 1348 pp.
Schulz, H.D., Dahmke, A., Schinzel, U., Wallmann, K. and Zabel, M., 1994. Early diagenetic processes, fluxes and reaction rates in sediments of the South Atlantic. Geochimica et Cosmochimica Acta, 58: 2041–2060.
Smith, K.L.Jr., Clifford, C.H. Eliason, A.h., Walden, B., Rowe, G.T. and Teal, J.M., 1976. A free vehicle for measuring benthic community metabolism. Limnology and Oceanography, 21: 164–170.
Sorensen, J., 1978. Denitrification rates in a marine sediment as measured by the acetylene inhibition technique. Applied and Environmental Microbiology, 35: 301–305.
Sorensen, J., Christensen, D. and Jorgensen, B.B., 1981. Volatile fatty acids and hydrogen as substrates for sulfate-reducing bacteria in anaerobic marine sediment. Applied and Environmental Microbiology, 42: 5–11.
Stetter, K.O., Huber, R., Blochl, E., Knurr, M., Eden, R.D., Fielder, M., Cash, H. and Vance, I., 1993. Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature, 365: 743–745.
Stetter, K.O., 1996. Hyperthermophilic procaryotes. FEMS Microbiology Revue, 18: 149–158.
Straub, K.L., Benz, M., Schink, B. and Widdel, F., 1996. Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Applied and Environmental Microbiology, 62: 1458–1460.
Straub, K.L. and Buchholz-Cleven, B.E.E., 1998. Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse European sediments. Applied and Environmental Microbiology, 64: 4846–4856.
Suess, E., 1980. Particulate organic carbon flux in the oceans-surface productivity and oxygen utilization. Nature, 288: 260–263.
Tegelaar, E.W., de Leeuw, J.W., Derenne, S. and Largeau, C, 1989. A reappraisal of kerogen formation. Geochimica et Cosmochimica Acta, 53: 3103–3106.
Tengberg, A., de Bovee, F., Hall, P, Berelson, W., Chadwick, D., Ciceri, G., Crassous, P., Devol, A., Emerson, s., Gage, J., Glud, R., Graziottin, F., Gundersen, J., Hammond, D., Helder, W., Hinga, K., Holby, O., Jahnke, R., Khripounoff, A., Lieberman, S., Nuppenau, V., Pfannkuche, O., Reimers, C, Rowe, G., Sahami, A., Sayles, F., Schurter, M., Smallman, D., Wehrli, B. and de Wilde, P., 1995. Benthic chamber and profiling landers in oceanography — A review of design, technical solutions and function. Progress in Oceanography, 35: 253–292.
Thamdrup, B., Finster, K., Hansen, J.W. and Bak, E, 1993. Bacterial disproportionation of elemental sulfur coupled to chemical reduction of iron or manganese. Applied and Environmental Microbiology, 59: 101–108.
Thamdrup, B., Fossing, H. and Jorgensen, B.B., 1994. Manganese, iron, and sulfur cycling in a coastal marine sediment, Aarhus Bay, Denmark. Geochimica et Cosmochimica Acta, 58: 5115–5129.
Thauer, R.K., Jungermann, K. and Decker, K., 1977. Energy conservation in chemotrophic anaerobic bacteria. Bacterial Reviews, 41: 100–180.
Thomsen, L., Jahmlich, S., Graf, G., Friedrichs, M., Wanner, S. and Springer, B., 1996. An instrument for aggregate studies in the benthic boundary layer. Marine Geology, 135: 153–157.
Vetter, Y.A., Deming, J.W., Jumars, P.A. and Kriegerbrockett, B.B., 1998. A predictive model of bacterial foraging by means of freely released extracellular enzymes. Microbiology Ecology, 36: 75–92.
Weiss, M.S., Abele, U., Weckesser, J., Welte, W. und Schulz, G.E., 1991. Molecular architecture and electrostatic properties of a bacterial porin. Science, 254: 1627–1630.
Wellsbury, P., Goodman, K., Barth, T., Cragg, B.A., Barnes, S.P. and Parkes R.J., 1997. Deep marine biosphere fuelled by increasing organic matter availability during burial and heating. Nature, 388: 573–576.
Westrich, J.T. and Berner, R.A., 1984. The role of sedimentary organic matter in bacterial sulfate reduction: The Gmodel tested. Limnology and Oceanography, 29: 236–249.
Widdel, E, 1988. Microbiology and ecology of sulfate-and sulfur-reduction bacteria. In: Zehnder, A.J.B. (ed). Biology of anaerobic microorganisms. Wiley & Sons, NY, 469–585 pp.
Widdel, F., Schnell, S., Heising, S., Ehrenreich, A., Assmus, B. and Schink, B., 1993. Ferrous iron oxidation by anoxygenic phototrophic bacteria. Nature, 362: 834–836.
Yayanos, A.A., 1986. Evolutional and ecological implications of the properties of deep-sea barophilic bacteria. Proc. Natl. Acad. Sci., 83: 9542–9546.
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2000 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Jørgensen, B.B. (2000). Bacteria and Marine Biogeochemistry. In: Schulz, H.D., Zabel, M. (eds) Marine Geochemistry. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-04242-7_5
Download citation
DOI: https://doi.org/10.1007/978-3-662-04242-7_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-662-04244-1
Online ISBN: 978-3-662-04242-7
eBook Packages: Springer Book Archive