Skip to main content
SpringerLink
Log in

Microbiological Controls on Geochemical Kinetics 1: Fundamentals and Case Study on Microbial Fe(III) Oxide Reduction

  • Chapter
Kinetics of Water-Rock Interaction

The pervasive influence of microorganisms (abbreviated hereafter as “morgs”; see Table 8.1 for a list of abbreviations) on the geochemistry of low-temperature environments is well-recognized and has been the subject of voluminous experimental and observational research (Banfield and Nealson, 1997; Brezonik, 1994; Canfield et al., 2005; Chapelle, 2001; Ehrlich, 2002; Lovley, 2000b). Many of the foundational insights into the role of morgs as agents of geochemical reaction can be traced to basic discoveries in microbiology which took place in the 19th and early 20th centuries. Perhaps the most important contribution of all was Louis Pasteur’s definitive demonstration that decomposition of OM does not proceed in the absence of living morgs (Pasteur, 1860). Though not made in the context of geochemistry, his decisive defeat of the theory of spontaneous generation was a key step toward recognizing the role of microbial life as a direct agent of chemical transformation in natural, medical, and industrial settings. A long series of discoveries followed in which the participation of morgs in various aspects of elemental cycling and mineral transformation was revealed, many in the context of soil and aquatic microbiology (Clarke, 1985; Ehrlich, 2002; Gorham, 1991). These early discoveries, together with developments in the fields of general microbiology and biochemistry (e.g., as embodied in Kluyver (1957)’s synthesis of unity and diversity in microbial metabolism) laid the groundwork for our current understanding of microbial metabolism based on principles of biochemical energetics (thermodynamics) and enzymatic reaction kinetics.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Albrechtsen H. J., Heron G., and Christensen T. H. (1995) Limiting factors for microbial Fe(III)-reduction in a landfill leachate polluted aquifer (Vejen, Denmark). FEMS Microbiol. Ecol. 16, 233-247.

    Google Scholar 

  • Amirbahman A., Schonenberger R., Johnson C. A., and Sigg L. (1998) Aqueous-and solid-phase biogeochemistry of a calcareous aquifer system downgradient from a municipal solid waste landfill (Winterthur, Switzerland). Environ. Sci. Technol. 32, 1933-1940.

    Google Scholar 

  • Anderson R. T., Rooney-Varga J. N., Gaw C. V., and Lovley D. R. (1998) Anaerobic benzene oxidation in the Fe(III) reduction zone of petroleum-contaminated aquifers. Environ. Sci. Technol. 32, 1222-1229.

    Google Scholar 

  • Arnold R. G., DiChristina T. J., and Hoffman M. R. (1988) Reductive dissolution of Fe(III) oxides by Pseudomonas sp. 200. Biotechnol. Bioengin. 32, 1081-1096.

    Google Scholar 

  • Bader F. B. (1982) Kinetics of double-substrate limited growth. In Microbial Population Dynamics (ed. M. J. Bazin), pp. 1-32. CRC Press, Boca Raton, FL.

    Google Scholar 

  • Bae W. and Rittmann B. E. (1995) A structured model of dual-limitation kinetics. Biotechnol. Bioengin. 49, 683-689.

    Google Scholar 

  • Bak F. and Pfenning N. (1991) Sulfate-reducing bacteria in littoral sediment of Lake Konstanz. FEMS Microbiol. Ecol. 85, 43-52.

    Google Scholar 

  • Banfield J. F. and Nealson K. H. (1997) Geomicrobiology: Interactions Between Microbes and Minerals, Vol. 35. Mineralogical Society of America.

    Google Scholar 

  • Banfield J. F., Cervini-Silva J., and Nealson K. H. (2005a) Molecular Geomicrobiology, Vol. 59. Mineralogical Society of America.

    Google Scholar 

  • Banfield J. F., Tyson G. W., Allen E. A., and Whitaker R. J. (2005b) The search for a molecular-level understanding of processes that underpin Earth’s bio-geochemical cycles. In Molecular Geomicrobiology, Vol. 59 (ed. J. F. Ban-field, J. Cervini-Silva, and K. H. Nealson), pp. 1-7. Mineralogical Society of America.

    Google Scholar 

  • Banwart S. A. and Thornton S. F. (2003) The geochemistry and hydrology of groundwater bioremediation by natural attenuation. In Bioremediation: A Critical Review (ed. I. M. Head, I. Singleton, and Milner), pp. 93-138. Horizon Scientific, Norfolk, UK.

    Google Scholar 

  • Barns S. M. and Nierzwicki-Bauer S. (1997) Microbial diversity in modern sub-surface, ocean, surface environments. In Geomicrobiology: Interactions Between Microbes and Minerals, Vol. 35 (ed. J. F. Banfield and K. H. Nealson), pp. 35-79. Mineralogical Society of America.

    Google Scholar 

  • Bazylinski D. A. and Moskowitz B. M. (1997) Microbial biomineralization of magnetic iron minerals: Microbiology, magnetism, and environmental signifi-cance. In Geomicrobiology: Interactions Between Microbes and Minerals, Vol. 35 (ed. J. F. Banfield and K. H. Nealson), pp. 181-223. Mineralogical Society of America.

    Google Scholar 

  • Bazylinski D. A. and Frankel R. B. (2000) Biologically controlled mineralization of magnetic iron minerals by magnetotactic bacteria. In Environmental MicrobeMetal Interactions (ed. D. R. Lovley). ASM Press, Washington, DC.

    Google Scholar 

  • Berner R. A. (1964) An idealized model of dissolved sulfate in recent sediments. Geochim. Cosmochim. Acta 28, 1497-1503.

    Google Scholar 

  • Berner R. A. (1977) Stoichiometric models for nutrient regeneration in anoxic sediments. Limnol. Oceanogr. 22, 781-786.

    Google Scholar 

  • Berner R. A. (1980) Early Diagenesis: A Theoretical Approach. Princeton University Press, Princeton, NJ.

    Google Scholar 

  • Berner R. A. (1981) Authigenic mineral formation resulting from organic matter decomposition in modern sediments. Fortschr. Mineral. 59, 117-135.

    Google Scholar 

  • Berner R. A. (1982) Burial of organic carbon and pyrite sulfur in the modern ocean: Its geochemical and environmental significance. Am. J. Sci. 282, 451-473.

    Google Scholar 

  • Berner R. A. (1989) Biogeochemical cycles of carbon and sulfur and their effect on atmospheric oxygen over phanerozoic time. Global Planet. Change 75, 97-122.

    Google Scholar 

  • Beveridge T. J. (1989) Role of cellular design in bacterial metal accumulation and mineralization. Annu. Rev. Microbiol. 43, 147-171.

    Google Scholar 

  • Bevington P. R. and Robinson D. K. (1992) Data Reduction and Error Analysis for the Physical Sciences. McGraw Hill, New York.

    Google Scholar 

  • Blackman F. F. (1905) Optima and limiting factors. Ann. Botany 19, 281-295.

    Google Scholar 

  • Bond D. R. and Lovley D. R. (2002) Reduction of Fe(III) by methanogens in the presence and absence of extracellular quinones. Environ. Microbiol. 4, 115-124.

    Google Scholar 

  • Bonneville S., Behrends T., VanCappellen P., Hyacinthe C., and Roling W. F. M. (2006) Reduction of Fe(III) colloids by Shewanella putrefaciens: A kinetic model. Geochim. Cosmochim. Acta 70, 5842-5854.

    Google Scholar 

  • Borrok D. and Fein J. B. (2004) Distribution of protons and Cd between bacterial surfaces and dissolved humic substances determined through chemical equilibrium modeling. Geochim. Cosmochim. Acta 68, 3043-3052.

    Google Scholar 

  • Boudreau B. P. and Westrich J. T. (1984) The dependence of bacterial sulfate reduction on sulfate concentration in marine sediments. Geochim. Cosmochim. Acta 48,2503-2516.

    Google Scholar 

  • Boudreau B. P. and Ruddick B. R. (1991) On a reactive continuum representation of organic matter diagenesis. Am. J. Sci. 291, 507-538.

    Google Scholar 

  • Boudreau B. P. (1992) A kinetic model for microbic organic-matter decomposition in marine sediments. FEMS Microb. Ecol. 102, 1-14.

    Google Scholar 

  • Boudreau B. P. (1996) A numerical-method-of-lines code for carbon and nutrient diagenesis in aquatic sediments. Comput. Geosci. 22, 479-496.

    Google Scholar 

  • Boudreau B. P. (1997) Diagenetic Models and Their Implementation. Springer, Berlin.

    Google Scholar 

  • Brezonik P. L. (1994) Chemical Kinetics and Process Dynamics in Aquatic Systems. Lewis Publishers, Boca Raton, FL.

    Google Scholar 

  • Burdige D. J. (1991) The kinetics of organic matter mineralization in anoxic marine sediment. J. Mar. Res. 49, 727-761.

    Google Scholar 

  • Burgos W. D., Royer R. A., Fang Y., Yeh G. T., Fisher A. S., Jeon B. H., and Dempsey B. A. (2002) Theoretical and experimental considerations related to reaction-based modeling: A case study using iron(III) oxide bioreduction. Ge-omicrobiol. J. 19, 253-292.

    Google Scholar 

  • Burgos W. D., Fang Y., Royer R. A., Yeh G. T., Stone J. T., Jeon B. H., and Dempsey B. A. (2003) Reaction-based modeling of quinone-mediated bacterial iron(III) reduction. Geochim. Cosmochim. Acta 67, 2735-2748.

    Google Scholar 

  • Caccavo F., Schamberger P. C., Keiding K., and Nielsen P. H. (1997) Role of hy-drophobicity in adhesion of the dissimilatory Fe(III)-reducing bacterium She-wanella alga to amorphous Fe(III) oxide. Appl. Environ. Microbiol. 63, 3837-3843.

    Google Scholar 

  • Caccavo F. (1999) Protein-mediated adhesion of the dissimilatory Fe(III)-reducing bacterium Shewanella alga BrY to hydrous ferric oxide. Appl. Environ. Microbiol. 65, 5017-5022.

    Google Scholar 

  • Caccavo F. and Das A. (2002) Adhesion of dissimilatory Fe(III)-reducing bacteria to Fe(III) minerals. Geomicrobiol. J. 19, 161-177.

    Google Scholar 

  • Caccavo F., Jr, Frolund B., Van Ommen Kloeke F., and Nielsen P. (1996) Deflocculation of activated sludge by the dissimilatory Fe(III)-reducing bacterium Shewanella alga BrY. Appl. Environ. Microbiol. 62, 1487-1490.

    Google Scholar 

  • Canfield D. E. and DesMarais D. J. (1993) Biogeochemical cycles of carbon, sulfur, and free oxygen in a microbial mat. Geochim. Cosmochim. Acta 57, 3971-3984.

    Google Scholar 

  • Canfield D. E., Jorgensen B. B., Fossing H., Glud R., Gundersen J., Ramsing N. B., Thamdrup B., Hansen J. W., Neilsen L. P., and Hall P. O. J. (1993) Pathways of organic carbon oxidation in three continental margin sediments. Mar. Geol. 113, 27-40.

    Google Scholar 

  • Canfield D. E., Thamdrup B., and Kristensen E. (2005) Aquatic Geomicrobiology. Elsevier.

    Google Scholar 

  • Chao T. T. and Zhou L. (1983) Extraction techniques for selective dissolution of amorphous iron oxides from soils and sediments. Soil Sci. Soc. Am. J. 47, 225-232.

    Google Scholar 

  • 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 highiron ground water. Ground Water 30, 29-36.

    Google Scholar 

  • Chapelle F. H. (2001) Ground-water Microbiology and Geochemistry. John Wiley & Sons, New York.

    Google Scholar 

  • Childers S. E., Ciufo S., and Lovley D. R. (2002) Geobacter metallilreducens accesses insoluble Fe(III) oxide by chemotaxis. Nature 416, 767-769.

    Google Scholar 

  • Christensen D. (1984) Determination of substrates oxidized by sulfate reduction in intact cores of marine sediments. Limnol. Oceanogr. 29, 189-192.

    Google Scholar 

  • Clark W. M. (1960) Oxidation-Reduction Potentials of Organic Systems. The Williams and Wilkins Company, Baltimore, MD.

    Google Scholar 

  • Clarke P. H. (1985) The scientific study of bacteria, 1780-1980. In Bacteria in Nature, Vol. 1 (ed. E. R. Leadbetter and J. S. Poindexter), pp. 1-37. Plenum Press, New York.

    Google Scholar 

  • Cord-Ruwisch R., Seitz H. J., and Conrad R. (1988) The capacity of hy-drogenotrophic anaerobic bacteria to compete for traces of hydrogen depends on the redox potential of the terminal electron acceptor. Arch. Microbiol. 149, 350-357.

    Google Scholar 

  • Cornell R. M. and Schwertmann U. (1996) The Iron Oxides. VCH Verlagsgesellschaft mbH/VCH Publishers, Inc.

    Google Scholar 

  • Coughlin B. R. and Stone A. T. (1995) Nonreversible adsorption of divalent metal ions (Mn-II, Co-II, Ni-II, Cu-II and Pb-II) onto goethite: Effects of acidification, Fe-II addition, and picolinic acid addition. Environ. Sci. Technol. 29, 2445-2455.

    Google Scholar 

  • Cozzarelli I. M., Herman J. S., Baedecker M. J., and Fischer J. M. (1999) Geochemical heterogeneity of a gasoline-contaminated aquifer. J. Contam. Hydrol. 40,261-284.

    Google Scholar 

  • Cozzarelli I. M., Suflita J. M., Ulrich G. A., Harris S. H., Scholl M. A., Schlottmann J. L., and Christenson S. (2000) Geochemical and microbiological methods for evaluating anaerobic processes in an aquifer contaminated by landfill leachate. Environ. Sci. Technol. 34, 4025-4033.

    Google Scholar 

  • Crabtree B. and Nicholson B. (1988) Thermodyamics and metabolism. In Biochemical Thermodynamics (ed. M. Jones), pp. 347-395. Elsevier, Amsterdam.

    Google Scholar 

  • Crosby H. A., Johnson C. M., Roden E. E., and Beard B. L. (2005) Fe(II)-Fe(III) electron/atom exchange as a mechanism for Fe isotope fractionation during dissimilatory iron oxide reduction. Environ. Sci. Technol 39, 6698-6704.

    Google Scholar 

  • Curtis G. P. (2003) Comparison of approaches for simulating reactive solute transport involving organic degradation reactions by multiple terminal electron acceptors. Comput. Geosci. 29, 319-329.

    Google Scholar 

  • Das A. and Caccavo F. (2000) Dissimiliatory Fe(III) oxide reduction by Shewanella alga BrY requires adhesion. Curr. Microbiol. 40, 344-347.

    Google Scholar 

  • Das A. and Caccavo F. (2001) Adhesion of the dissimilatory Fe(III)-reducing bac-terium Shewanella alga BrY to crystalline Fe(III) oxides. Curr. Microbiol. 42, 151-154.

    Google Scholar 

  • Davis J. A. and Kent D. B. (1990) Surface complexation modeling in aqueous geochemistry. In Mineral-water interface geochemistry (ed. M. F. Hochella and A. F. White), pp. 177-260. Mineralogical Society of America.

    Google Scholar 

  • Davis J. A., Yabusaki S. B., Steefel C. I., Zachara J. M., Curtis G. P., Redden G. D., Criscenti L. J., and Honeyman B. D. (2004) Assessing conceptual models for subsurface reactive transport of inorganic contaminants. EOS 85, 449-455.

    Google Scholar 

  • Dhakar S. P. and Burdige D. J. (1996) A coupled, non-linear, steady state model for early diagenetic processes In pelagic sediments. AMJ 296, 296-330.

    Google Scholar 

  • DiChristina T. J., Fredrickson J. K., and Zachara J. M. (2005) Enzymology of electron transport: Energy generation with geochemical consequences. In Molecular Geomicrobiology, Vol. 59 (ed. J. F. Banfield, J. Cervini-Silva, and K. H. Nealson), pp. 27-52. Mineralogical Society of America.

    Google Scholar 

  • Dominik P. and Kaupenjohann M. (2004) Reduction of Fe(III) (Hydr)oxides with known thermodynamic stability by Geobacter metallireducens. Geomicrobiol. J. 21,287-295.

    Google Scholar 

  • Dzombak D. A. and Morel F. M. M. (1990) Surface Complexation Modeling: Hydrous Ferric Oxide. John Wiley & Sons, New York.

    Google Scholar 

  • Ehrlich H. L. (1999) Microbes as geologic agents: Their role in mineral formation. Geomicrobiol. J. 16, 135-153.

    Google Scholar 

  • Ehrlich H. L. (2002) Geomicrobiology. Marcel Dekker, New York.

    Google Scholar 

  • Fein J. B., Daughney C. J., Yee N., and Davis T. A. (1997) A chemical equilibrium model for metal adsorption onto bacterial surfaces. Geochim. Cosmochim. Acta 61,3319-3328.

    Google Scholar 

  • Fein J. B., Martin A. M., and Wightman P. G. (2001) Metal adsorption onto bacterial surfaces: Development of a predictive approach. Geochim. Cosmochim. Acta 65, 4267-4273.

    Google Scholar 

  • Fischer W. R. (1988) Microbiological reactions of iron in soils. In Iron in soils and clay minerals (ed. J. W. Stucki, B. A. Goodman, and U. Schwertmann), pp. 715-748. D. Reidel Publishing Co., Dordrecht.

    Google Scholar 

  • Frankel R. B. and Bazylinski D. A. (2003) Biologically induced mineralization by bacteria. In Biomineralization, Vol. 55 (ed. P. M. Dove, J. J. DeYoreo, and S. Weiner), pp. 95-114. Mineralogical Society of America.

    Google Scholar 

  • Gaillard J. F. and Rabouille C. (1992) Using Monod kinetics in geochemical models of organic carbon mineralization in deep-sea surficial sediments. In Deep-Sea Food Chains and the Global Carbon Cycle (ed. G. T. Rowe and V. Pariente), pp. 309-324. Kluwer Academic Publishing, Dordrecht.

    Google Scholar 

  • Geesey G. G., Neal A. L., Suci P. A., and Peyton B. M. (2002) A review of spectroscopic methods for characterizing microbial transformation of minerals. J. Microbiol. Meth. 51, 125-139.

    Google Scholar 

  • Ghiorse W. C. (1988) Microbial reduction of manganese and iron. In Biology of Anaerobic Microorganisms (ed. A. J. B. Zehnder), pp. 305-331. John Wiley & Sons.

    Google Scholar 

  • Gibson G. R., Parkes R. J., and Herbert R. A. (1987) Evaluation of viable counting procedures for the enumeration of sulfate-reducing bacteria in estuarine sediments. J. Microbiol. Meth. 7, 201-210.

    Google Scholar 

  • Glasauer S., Langley S., and Beveridge T. J. (2001) Sorption of Fe (hydr)oxides to the surface of Shewanella putrefaciens: Cell-bound fine-grained minerals are not always formed de novo. Appl. Environ. Microbiol. 67, 5544-5550.

    Google Scholar 

  • Gorby Y. A., Yanina S., McLean J. S., Rosso K. M., Moyles D., Dohnalkova A., Chang I. S., Kim B. H., Kim K. S., Culley D. E., Reed S. B., Romine M. F., Saffarini D. A., Hill E. A., Shi L., Elias D. A., Kennedy D. W., Pinchuk G., Watanabe K., Ishii S., Logan B., Nealson K. H., and Fredrickson J. K. (2006) Electrically conductive bacterial nanowires produced by Shewanella oneidensis MR-1 and other microorganisms. Proc. Nat. Acad. Sci. USA 103, 11358-11363.

    Google Scholar 

  • Gorham E. (1991) Biogeochemistry: Its origins and development. Biogeochemistry 13,199-239.

    Google Scholar 

  • Grantham M. C., Dove P. M., and DiChristina T. J. (1997) Microbially catalyzed dissolution of iron and aluminum oxyhydroxide mineral surface coatings. Geochim. Cosmochim. Acta 61, 4467-4477.

    Google Scholar 

  • Hacherl E. L., Kosson D. S., and Cowan R. M. (2003) A kinetic model for bacterial Fe(III) oxide reduction in batch cultures. Water Resour. Res. 39, Art. No. 1098.

    Google Scholar 

  • Haldane J. B. S. (1930) Enzymes. Longman Green and Co., London.

    Google Scholar 

  • Hansel C. M., Benner S. G., Neiss J., Dohnalkova A., Kukkadapu R. K., and Fendorf S. (2003) Secondary mineralization pathways induced by dissimilatory iron reduction of ferrihydrite under advective flow. Geochim. Cosmochim. Acta 67,2977-2992.

    Google Scholar 

  • Hansel C. M., Benner S. G., Nico P., and Fendorf S. (2004) Structural constraints of ferric (hydr)oxides on dissimilatory iron reduction and the fate of Fe(II). Geochim. Cosmochim. Acta 68, 3217-3229.

    Google Scholar 

  • Hem J. D. (1972) Chemical factors that influence the availability of iron and manganese in aqueous systems. Geol. Soc. Am. Bull. 83, 443-450.

    Google Scholar 

  • Hering J. G. and Stumm W. (1990) Oxidative and reductive dissolution of minerals. In Mineral-water interface geochemistry, Vol. 23 (ed. M. F. Hochella and A. F. White), pp. 427-464. Mineralogical Society of America.

    Google Scholar 

  • Hernandez M. E. and Newman D. K. (2001) Extracellular electron transfer. CMLS Cell Mol Life Sci 58, 1562-1571.

    Google Scholar 

  • Hernandez M. E., Kappler A., and Newman D. K. (2004) Phenazines and other redox active antibiotics promote microbial mineral reduction. Appl. Environ. Microbiol. 70, 921-928.

    Google Scholar 

  • Hines M. E., Faganeli J., and Planinc R. (1997) Sedimentary anaerobic microbial biogeochemistry in the Gulf of Trieste, northern Adriatic Sea: Influences of bottom water oxygen depletion. Biogeochemistry 39, 65-86.

    Google Scholar 

  • Ho C. Y. and Cord-Ruwisch R. (1996) A practical kinetic model that considers endproduct inhibition in anaerobic digestion processes by including the equilibrium constant. Biotechnol. Bioengin. 51, 597-604.

    Google Scholar 

  • Hoehler T. M., Alperin M. J., Albert D. B., and Martens C. S. (1998) Thermodynamic control on hydrogen concentrations in anoxic sediments. Geochim. Cosmochim. Acta 62, 1745-1756.

    Google Scholar 

  • Humphrey A. E. (1972) The kinetics of biosystems: A review. In Chemical Reac-tor Engineering, Vol. 109 (ed. R. F. Gould), pp. 630-650. American Chemical Society.

    Google Scholar 

  • Hunter K. S., Wang Y., and VanCappellen P. (1998) Kinetic modeling of microbially-driven redox chemistry of subsurface environments: Coupling transport, microbial metabolism and geochemistry. J. Hydrol. 209, 53-80.

    Google Scholar 

  • Icopini G. A., Anbar A. D., Ruebush S. S., Tien M., and Brantley S. L. (2004) Iron isotope fractionation during microbial reduction of iron: The importance of adsorption. Geology 32, 205-208.

    Google Scholar 

  • Jackson B. E. and McInerney M. J. (2002) Anaerobic microbial metabolism can proceed close to thermodynamic limits. Nature 415, 454-456.

    Google Scholar 

  • Jakobsen R., Albrechtsen H. J., Rasmussen M., Bay H., Bjerg P., and Christensen T. H. (1998) H2 concentrations in a landfill leachate plume (Grindsted, Denmark): In situ energetics of terminal electron acceptor processes. Environ. Sci. Technol. 32,2142-2148.

    Google Scholar 

  • Jakobsen R. and Postma D. (1999) Redox zoning, rates of sulfate reduction and interactions with Fe-reduction and methanogenesis in a shallow sandy aquifer, Romo, Denmark. Geochim. Cosmochim. Acta 63, 137-151.

    Google Scholar 

  • Jiang W., Saxena A., Song B., Ward B. B., Beveridge T. J., and Myneni S. C. B. (2004) Elucidation of functional groups on gram-positive and gram-negative bacterial surfaces using infrared spectroscopy. Langmuir 20, 11433-11442.

    Google Scholar 

  • Jin Q. and Bethke C. M. (2002) Kinetics of electron transfer through the respiratory chain. Biophys. J. 83, 1797-1808.

    Google Scholar 

  • Jin Q. and Bethke C. M. (2003) A new rate law describing microbial respiration. Appl. Environ. Microbiol. 69, 2340-2348.

    Google Scholar 

  • Jin Q. and Bethke C. M. (2005) Predicting the rate of microbial respiration in geochemical environments. Geochim. Cosmochim. Acta 69, 1133-1143.

    Google Scholar 

  • Jorgensen B. B. (1978) A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments I. Measurement with radiotracer techniques. Geomicrobiol. J. 1, 11-28.

    Google Scholar 

  • Keller M. and Zengler K. (2004) Tapping into microbial diversity. Nat. Rev. Micro. 2,141-150.

    Google Scholar 

  • Klump J. V. and Martens C. S. (1987) Biogeochemical cycling in an organic-rich coastal marine basin 5. Sedimentary nitrogen and phosphorus budgets based upon kinetic models, mass balances, and the stoichiometry of nutrient regeneration. Geochim. Cosmochim. Acta 51, 1161-1173.

    Google Scholar 

  • Klump J. V. and Martens C. S. (1989) The seasonality of nutrient regeneration in an organic-rich coastal sediment: Kinetic modeling of changing pore-water nutrient and sulfate distributions. Limnol. Oceanogr. 34, 559-577.

    Google Scholar 

  • Kluyver A. J. (1957) Unity and diversity in the metabolism of micro-organisms. In A.J. Kluyver: His Life and Work (ed. A. F. Kamp, J. W. M. LaRiviere, and W. Verhoeven), pp. 186-210. North-Holland, Amsterdam.

    Google Scholar 

  • Koch A. L. (1998) The Monod model and its alternatives. In Mathematical Modeling in Microbial Ecology (ed. A. L. Koch, J. A. Robinson, and G. A. Milliken). Chapman & Hall, London.

    Google Scholar 

  • Komeili A., Li Z., Newman D. K., and Jensen G. J. (2006) Magnetosomes are cell membrane invaginations organized by the actin-likeprotein MamK. Science 311, 242-245.

    Google Scholar 

  • Kostka J. E. and Nealson K. H. (1995) Dissolution and reduction of magnetite by bacteria. Environ. Sci. Technol. 29, 2535-2540.

    Google Scholar 

  • Kostka J. E., Thamdrup B., Glud R. N., and Canfield D. E. (1999) Rates and pathways of carbon oxidation in permanently cold arctic sediments. Mar. Ecol. Prog. Ser. 180, 7-21.

    Google Scholar 

  • Kostka J. E., Roychoudhury A., and VanCappellen P. (2002) Rates and controls of anaerobic microbial respiration across spatial and temporal gradients in saltmarsh sediments. Biogeochemistry 60, 49-76.

    Google Scholar 

  • Kraemer S. M. and Hering J. G. (1997) Influence of solution saturation state on the kinetics of ligand-controlled dissolution of oxide phases. Geochim. Cosmochim. Acta 61, 2855-2866.

    Google Scholar 

  • Laidler K. J. (1987) Chemical Kinetics. Harper & Row, New York.

    Google Scholar 

  • Larsen O. and Postma D. (2001) Kinetics of reductive bulk dissolution of lepi-docrocite, ferrihydrite, and goethite. Geochim. Cosmochim. Acta 65, 1367-1379.

    Google Scholar 

  • Lasaga A. C. and Kirkpatrick R. J. (1981) Kinetics of Geochemical Processes. In Reviews in Mineralogy and Geochemistry, Vol. 8 (ed. P. H. Ribbe), pp. 398. Mineralogical Society of America.

    Google Scholar 

  • Lasaga A. C. (1998) Kinetic Theory in the Earth Sciences. Princeton University Press, Princeton, NJ.

    Google Scholar 

  • Lerman A. (1979) Geochemical Processes - Water and Sediment Environments. John Wiley & Sons, New York.

    Google Scholar 

  • Lies D. P., Hernandez M. E., Kappler A., Mielke R. E., Gralnick J. A., and Newman D. K. (2005) Shewanella oneidensis MR-1 uses overlapping pathways for iron reduction at a distance and by direct contact under conditions relevant for biofilms. Appl. Environ. Microbiol. 71, 4414-4426.

    Google Scholar 

  • Liu C., Kota S., Zachara J. M., Fredrickson J. K., and Brinkman C. (2001a) Kinetic analysis of the bacterial reduction of goethite. Environ. Sci. Technol. 35, 2482-2490.

    Google Scholar 

  • Liu C., Zachara J. M., Gorby Y. A., Szecsody J. E., and Brown C. F. (2001b) Microbial reduction of Fe(III) and sorption/precipitation of Fe(II) on Shewanella putrefaciens strain CN32. Environ. Sci. Technol. 35, 1385-1393.

    Google Scholar 

  • Liu C., Gorby Y. A., Zachara J. M., Fredrickson J. K., and Brown C. F. (2002) Reduction kinetics of Fe(III), Co(III), U(VI), Cr(VI), Tc(VII) in cultures of dissimilatory metal reducing bacteria. Biotechnol. Bioengin. 80, 637-649.

    Google Scholar 

  • Lovley D. R. and Klug M. J. (1982) Intermediary metabolism of organic matter in the sediments of a eutrophic lake. Appl. Environ. Microbiol. 43, 552-560.

    Google Scholar 

  • Lovley D. R. (1985) Minimum threshold for hydrogen metabolism in methanogenic bacteria. Appl. Environ. Microbiol. 49, 1530-1531.

    Google Scholar 

  • Lovley D. R. and Klug M. J. (1986) Model for the distribution of sulfate reduction and methanogenesis in freshwater sediments. Geochim. Cosmochim. Acta 50,11-18.

    Google Scholar 

  • Lovley D. R. and Phillips E. J. P. (1986a) Availability of ferric iron for microbial reduction in bottom sediments of the freshwater tidal Potomac River. Appl. Environ. Microbiol. 52, 751-757.

    Google Scholar 

  • Lovley D. R. and Phillips E. J. P. (1986b) Organic matter mineralization with reduc-tion of ferric iron in anaerobic sediments. Appl. Environ. Microbiol. 51, 683-689.

    Google Scholar 

  • Lovley D. R. (1987) Organic matter mineralization with the reduction of ferric iron: A review. Geomicrobiol. J. 5, 375-399.

    Google Scholar 

  • Lovley D. R. and Phillips E. J. P. (1987) Rapid assay for microbially reducible ferric iron in aquatic sediments. Appl. Environ. Microbiol. 53, 1536-1540.

    Google Scholar 

  • Lovley D. R., Stolz J. F., Nord G. L., and Phillips E. J. P. (1987) Anaerobic produc-tion of magnetite by a dissimilatory iron-reducing microorganism. Nature 330, 252-254.

    Google Scholar 

  • Lovley D. R. and Goodwin S. (1988) Hydrogen concentrations as an indicator or the predominant terminal electron-accepting reactions in aquatic sediments. Geochim. Cosmochim. Acta 52, 2993-3003.

    Google Scholar 

  • Lovley D. R. and Phillips E. J. P. (1989) Requirement for a microbial consortium to completely oxidize glucose in Fe(III)-reducing sediments. Appl. Environ. Microbiol. 55, 3234-3236.

    Google Scholar 

  • Lovley D. R., Chapelle F. H., and Philips E. J. P. (1990) Fe(III)-reducing bacteria in deeply buried sediments of the Atlantic coastal plain. Geology 18, 954-957.

    Google Scholar 

  • Lovley D. R. (1991) Dissimilatory Fe(III) and Mn(IV) reduction. Microbiol. Rev. 55,259-287.

    Google Scholar 

  • Lovley D. R. and Phillips E. J. P. (1991) Enzymatic versus nonenzymatic mecha-nisms for Fe(III) reduction in aquatic sediments. Environ. Sci. Technol. 25, 1062-1067.

    Google Scholar 

  • Lovley D. R. (1992) Microbial oxidation of organic matter coupled to the reduc-tion of Fe(III) and Mn(IV) oxides. In Biomineralization processes of iron and manganese, Vol. 21 (ed. H. C. W. Skinner and R. W. Fitzpatrick), pp. 101-114. Catena Verlag.

    Google Scholar 

  • Lovley D. R. (1993) Dissimilatory metal reduction. Annu. Rev. Microbiol. 47, 263-290.

    Google Scholar 

  • Lovley D. R. and Chapelle F. H. (1998) A modeling approach to elucidating the distribution and rates of microbially catalyzed redox reactions in anoxic ground-water. In Mathematical Modeling in Microbial Ecology (ed. A. L. Koch, J. A. Robinson, and G. A. Milliken), pp. 196-209. Chapman & Hall, London.

    Google Scholar 

  • Lovley D. R. (2000a) Fe(III) and Mn(IV) reduction. In Environmental Metal-Microbe Interactions (ed. D. R. Lovley), pp. 3-30. ASM Press. Lovley D. R. (2000b) Environmental Metal-Microbe Interactions, pp. 395. ASM Press.

    Google Scholar 

  • Lovley D. R. (2002) Fe(III)-and Mn(IV)-reducing prokaryotes. In The Prokaryotes (ed. S. F. M. Dworkin, E. Rosenberg, K.H Schleifer, E. Stackebrandt), pp. [www document]. URL http://et.springer-ny.com:8080/prokPUB/index.htm. Springer-Verlag, Berlin.

  • Lovley D. R. (2004) Potential role of dissimilatory iron reduction in the early evolution of microbial respiration. In Origins, Evolution and Biodiversity of Microbial Life (ed. J. Seckbach), pp. 301-313. Kluwer, Dordrecht.

    Google Scholar 

  • Lovley D. R., Holmes D. E., and Nevin K. P. (2004) Dissimilatory Fe(III) and Mn(IV) Reduction. Adv. Microbiol. Physiol. 49, 219-286.

    Google Scholar 

  • Lowenstam H. A. (1981) Minerals formed by organisms. Science 211, 1126-1131.

    Google Scholar 

  • Lowenstam H. A. and Weiner S. (1989) On Biomineralization. Oxford University Press.

    Google Scholar 

  • Lower S. K., Hochella M. F., and Beveridge T. J. (2001) Bacterial recognition of mineral surfaces: Nanoscale interactions between Shewanella and α - FeOOH. Science 292, 1360-1363.

    Google Scholar 

  • Madigan M. T., Martinko J. M., and Parker J. (2000) Brock Biology of Microorganisms. Prentice-Hall, Englewood Cliffs, NJ.

    Google Scholar 

  • Madsen E. L. (2005) Identifying microorganisms responsible for ecologically sig-nificant biogeochemcial processes. Nat. Rev. Microbiol. 3, 439-446.

    Google Scholar 

  • Martens C. S. and Berner R. A. (1974) Methane production in the interstitial waters of sulfate depleted marine sediments. Science 185, 1167-1169.

    Google Scholar 

  • Maurer M. and Rittmann B. E. (2004) Formulation of the CBC-model for modelling the contaminants and footprints in natural attenuation of BTEX. Biodegradation 15,419-434.

    Google Scholar 

  • Methe B. A., Nelson K. E., Eisen J. A., Paulsen I. T., Nelson W., Heidelberg J. F., Wu D., Wu M., Ward N., Beanan M. J., Dodson R. J., Madupu R., Brinkac L. M., Daugherty S. C., DeBoy R. T., Durkin A. S., Gwinn M., Kolonay J. F., Sullivan S. A., Haft D. H., Selengut J., Davidsen T. M., Zafar N., White O., Tran B., Romero C., Forberger H. A., Weidman J., Khouri H., Feldblyum T. V., Utterback T. R., Van Aken S. E., Lovley D. R., and Fraser C. M. (2003) Genome of Geobac-ter sulfurreducens: Metal reduction in subsurface environments. Science 302, 1967-1969.

    Google Scholar 

  • Michaelis L. and Menten M. M. (1913) Die Kinetik der Invertingwirkung (The kinetics of invertase activity). Biochem. Z. 49, 333-369.

    Google Scholar 

  • Molz F. J., Widdowson M. A., and Benefield L. D. (1986) Simulation of microbial growth dynamics coupled to nutrient and oxygen transport in porous media. Water Resour. Res. 22, 1207-1216.

    Google Scholar 

  • Monod J. (1942) Recherches sur las croissance des culture bacteriennes (Research on the growth of bacterial cultures). Hermann et Cie.

    Google Scholar 

  • Monod J. (1949) The growth of bacterial cultures. Annu. Rev. Microbiol. 3, 371-394.

    Google Scholar 

  • Moskowitz B. M., Frankel R. B., Bazylinski D. A., Jannasch H. W., and Lovley D. R. (1989) A comparison of magnetite particles produced anaerobically by magnetotactic and dissimilatory iron-reducing bacteria. Geophys. Res. Lett. 16, 665-668.

    Google Scholar 

  • Munch J. C. and Ottow J. C. G. (1980) Preferential reduction of amorphous to crystalline iron oxides by bacterial activity. Soil Sci. 129, 15-21.

    Google Scholar 

  • Munch J. C. and Ottow J. C. G. (1983) Reductive transformation mechanism of ferric oxides in hydromorphic soils. Ecol. Bull. 35, 383-394.

    Google Scholar 

  • Nealson K. H. and Stahl D. A. (1997) Microorganisms and biogeochemical cycles: What can we learn from layered microbial communities? In Geomicrobiology: Interactions Between Microbes and Minerals, Vol. 35 (ed. J. F. Banfield and K. H. Nealson), pp. 5-34. Mineralogical Society of America.

    Google Scholar 

  • Nealson K. H., Ghiorse W. A., and Strauss E. (2001) Geobiology: Exploring the interface between the biosphere and the geosphere (A Report from the American Academy of Microbiology). American Academy of Microbiology, Washington, DC. (Available at: http://www.asm.org/Academy/index.asp?bid = 2132.)

  • Nevin K. P. and Lovley D. R. (2002) Mechanisms of Fe(III) oxide reduction in sedimentary environments. Geomicrobiol. J. 19, 141-159.

    Google Scholar 

  • Newman D. K. and Banfield J. F. (2002) Geomicrobiology: How molecular-scale interactions underpin biogeochemical systems. Science 296, 1071-1077.

    Google Scholar 

  • Oremland R. S., Capone D. G., Stolz J. F., and Fuhrman J. (2005) Whither or wither geomicrobiology in the era of ‘community metagenomics’. Nat. Rev. Microbiol. 3,572-578.

    Google Scholar 

  • Ottow J. C. G. (1968) Evaluation of iron-reducing bacteria in soil and the physiological mechanism of iron reduction in Aerobacter aerogenes. Z. Alig. Mikrobiol 8,441-443.

    Google Scholar 

  • Ottow J. C. G. (1971) Iron reduction and gley formation by nitrogen-fixing Clostridia. Oecologia 6, 164-175.

    Google Scholar 

  • Ottow J. C. G. and Glathe H. (1971) Isolation and identification of iron-reducing bacteria from gley soils. Soil Biol. Biochem. 3, 43-55.

    Google Scholar 

  • Pasteur L. (1860) Experiences relatives aux generations spontanees. Compt. Rend. Acad. Sci 50, 303-675.

    Google Scholar 

  • Penn R. L., Zhu C., Xu H., and Veblen D. R. (2001) Iron oxide coatings on sand grains from the Atlantic coastal plain: High-resolution transmission electron microscopy characterization. Geology 29, 843-846.

    Google Scholar 

  • Peters R. H. (1983) The Ecological Implications of Body Size. Cambridge University Press.

    Google Scholar 

  • Phillips E. J. P., Lovley D. R., and Roden E. E. (1993) Composition of nonmicrobially reducible Fe(III) in aquatic sediments. Appl. Environ. Microbiol. 59, 2727-2729.

    Google Scholar 

  • Ponnamperuma F. N. (1972) The chemistry of submerged soils. Adv. Agron. 24, 29-96.

    Google Scholar 

  • Postma D. (1993) The reactivity of iron oxides in sediments: A kinetic approach. Geochim. Cosmochim. Acta 57, 5027-5034.

    Google Scholar 

  • Postma D. and Jakobsen R. (1996) Redox zonation: Equilibrium constraints on the Fe(III)/S04-reduction interface. Geochim. Cosmochim. Acta 60, 3169-3175.

    Google Scholar 

  • Press W. H., Teukolsky S. A., Vetterling W. T., and Flannery B. P. (1992) Numerical Recipes in FORTRAN. Cambridge University Press.

    Google Scholar 

  • Ramsing N. R., Fossing H., Ferdelman T. G., Andersen F., and Thamdrup B. (1996) Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. Appl. Environ. Microbiol. 62, 1391-1404.

    Google Scholar 

  • Rawn J. D. (1983) Biochemistry. Harper and Row, New York.

    Google Scholar 

  • Reguera G., McCarthy K. D., Mehta T., Nicoll J. S., Tuominen M. T., and Lovley D. R. (2005) Extracellular electron transfer via microbial nanowires. Nature 435, 1098-1101.

    Google Scholar 

  • Revsbech N. P. and Jorgensen B. B. (1986) Microelectrodes: Their use in microbial ecology. In Advanced Microbial Ecology, Vol. 9 (ed. K. C. Marshall), pp. 293-352. Plenum Press, New York.

    Google Scholar 

  • Richardson D. J. (2000) Bacterial respiration: A flexible process for a changing environment. Microbiology 146, 551-571.

    Google Scholar 

  • Rickenberg H. V., Cohen G. N., Buttin G., and Monod J. (1956) La galactoside permease d’Escherichia coli. Ann. Inst. Pasteur 91, 829-857.

    Google Scholar 

  • Rittmann B. E. and VanBriesen J. M. (1996) Microbiological processes in reactive transport modeling. In Reactive Transport in Porous Media, Vol. 34 (ed. P. C. Lichtner, C. I. Steefel, and E. H. Oelkers), pp. 311-334. The Mineralogical Society of America.

    Google Scholar 

  • Rittmann B. E. and McCarty P. L. (2001) Environmental Biotechnology. McGrawHill, New York.

    Google Scholar 

  • Roden E. E. and Lovley D. R. (1993a) Evaluation of 55 Fe as a tracer of Fe(III) reduction in aquatic sediments. Geomicrobiol. J. 11, 49-56.

    Google Scholar 

  • Roden E. E. and Lovley D. R. (1993b) Dissimilatory Fe(III) reduction by the marine microorganism Desulfuromonas acetoxidans. Appl. Environ. Microbiol. 59, 734-742.

    Google Scholar 

  • Roden E. E. and Tuttle J. H. (1993) Inorganic sulfur turnover in oligohaline estuarine sediments. Biogeochemistry 22, 81-105.

    Google Scholar 

  • Roden E. E. and Tuttle J. H. (1996) Carbon cycling in mesohaline Chesapeake Bay sediments 2: Kinetics of particulate and dissolved organic carbon turnover. J. Mar. Sci. 54, 343-383.

    Google Scholar 

  • Roden E. E. and Wetzel R. G. (1996) Organic carbon oxidation and suppression of methane production by microbial Fe(III) oxide reduction in vegetated and unvegetated freshwater wetland sediments. Limnol. Oceanogr. 41, 1733-1748.

    Google Scholar 

  • Roden E. E. and Zachara J. M. (1996) Microbial reduction of crystalline iron(III) oxides: Influence of oxide surface area and potential for cell growth. Environ. Sci. Technol. 30, 1618-1628.

    Google Scholar 

  • Roden E. E. and Edmonds J. W. (1997) Phosphate mobilization in iron-rich anaerobic sediments: Microbial Fe(III) oxide reduction versus iron-sulfide formation. Arch. Hydrobiol. 139, 347-378.

    Google Scholar 

  • Roden E. E. and Urrutia M. M. (1999) Ferrous iron removal promotes microbial reduction of crystalline iron(III) oxides. Environ. Sci. Technol. 33, 1847-1853.

    Google Scholar 

  • Roden E. E., Urrutia M. M., and Mann C. J. (2000) Bacterial reductive dissolution of crystalline Fe(III) oxide in continuous-flow column reactors. Appl. Environ. Microbiol. 66, 1062-1065.

    Google Scholar 

  • Roden E. E., Leonardo M. R., and Ferris F. G. (2002) Immobilization of strontium during iron biomineralization coupled to dissimilatory hydrous ferric oxide reduction. Geochim. Cosmochim. Acta 66, 2823-2839.

    Google Scholar 

  • Roden E. E. and Urrutia M. M. (2002) Influence of biogenic Fe(II) on bacterial reduction of crystalline Fe(III) oxides. Geomicrobiol. J. 19, 209-251.

    Google Scholar 

  • Roden E. E. and Wetzel R. G. (2002) Kinetics of microbial Fe(III) oxide reduction in freshwater wetland sediments. Limnol. Oceanogr. 47, 198-211.

    Google Scholar 

  • Roden E. E. (2003a) Fe(III) oxide reactivity toward biological versus chemical reduction. Environ. Sci. Technol. 37, 1319-1324.

    Google Scholar 

  • Roden E. E. (2003b) Diversion of electron flow from methanogenesis to crystalline Fe(III) oxide reduction in acetate-limited cultures of wetland sediment microorganisms. Appl. Environ. Microbiol. 69, 5702-5706.

    Google Scholar 

  • Roden E. E. and Wetzel R. G. (2003) Competition between Fe(III)-reducing and methanogenic bacteria for acetate in iron-rich freshwater sediments. Microb. Ecol. 45, 252-258.

    Google Scholar 

  • Roden E. E. (2004) Analysis of long-term bacterial versus chemical Fe(III) oxide reduction kinetics. Geochim. Cosmochim. Acta 68, 3205-3216.

    Google Scholar 

  • Roden E. E. (2005) Unpublished data.

    Google Scholar 

  • Roden E. E. and Scheibe T. D. (2005) Conceptual and numerical model of uranium(VI) reductive immobilization in fractured subsurface sediments. Chemosphere 59, 617-628.

    Google Scholar 

  • Roden E. E. (2006) Geochemical and microbiological controls on dissimilatory iron reduction. C.R. Geosci. 338, 456-467.

    Google Scholar 

  • Roels J. A. (1983) Energetics and Kinetics in Biotechnology. Elsevier Biomedical Press, Amsterdam.

    Google Scholar 

  • Rooney-Varga J. N., Anderson R. T., Fraga J. L., Ringelberg D., and Lovley D. R. (1999) Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl. Environ. Microbiol. 65, 3056-3063.

    Google Scholar 

  • Ruebush S. S., Brantley S. L., and Tien M. (2006a) Reduction of soluble and in-soluble iron forms by membrane fractions of Shewanella oneidensis grown under aerobic and anaerobic conditions. Appl. Environ. Microbiol. 72, 2925-2935.

    Google Scholar 

  • Ruebush S. S., Icopini G. A., Brantley S. L., and Tien M. (2006b) In vitro reduction kinetics of mineral oxides by membrane fractions of Shewanella oneidensis MR-1. Geochim. Cosmochim. Acta 70, 56-70.

    Google Scholar 

  • Scheffel A., Gruska M., Faive D., Linaroudisn A., Graumann P. L., Plitzko J. M., and Schuler D. (2006) An acidic protein aligns magnetosomes along a filamentous structure in magnetotactic bacteria. Nature.

    Google Scholar 

  • Schink B. (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262-280.

    Google Scholar 

  • Schnoor J. L. (1996) Environmental Modeling. Wiley Interscience, New York.

    Google Scholar 

  • Schultze-Lam S., Fortin D., Davis B. S., and Beveridge T. J. (1996) Mineralization of bacterial surfaces. Chem. Geol. 132, 171-181.

    Google Scholar 

  • Snoeyenbos-West O. L., Nevin K. P., Anderson R. T., and Lovley D. R. (2000) Enrichment of Geobacter species in response to stimulation of Fe(III) reduction in sandy aquifer sediments. Microb. Ecol. 39, 153-167.

    Google Scholar 

  • Soetaert K., Herman P. M. J., and Middelburg J. J. (1996) A model of early diagenetic processes from the shelf to abyssal depths. Geochim. Cosmochim. Acta 60, 1019-1040.

    Google Scholar 

  • Sorensen J., Christensen D., and Jorgensen B. B. (1981) Volatile fatty acids and hydrogen as substrates for sulfate-reducing bacteria in anaerobic marine sediment. Appl. Environ. Microbiol. 42, 5-11.

    Google Scholar 

  • Sorensen J. (1982) Reduction of ferric iron in anaerobic, marine sediment and in-teraction with reduction of nitrate and sulfate. Appl. Environ. Microbiol. 43, 319-324.

    Google Scholar 

  • Southam G. (2000) Bacterial surface-mediated mineral formation. In Environmental Metal-Microbe Interactions (ed. D. R. Lovley), pp. 257-276. ASM Press, Washington.

    Google Scholar 

  • Sparks N. H. C., Mann S., Bazylinskio D. A., Lovley D. R., Jannasch H. W., and Frankel R. B. (1990) Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium. Earth Planet. Sci. Lett. 98, 14-22.

    Google Scholar 

  • Starkey R. L. and Halvorson H. O. (1927) Studies on the transformations of iron in nature. II. Concerning the importance of microorganisms in the solution and precipitation of iron. Soil Sci. 24, 381-402.

    Google Scholar 

  • Stone A. T. and Morgan J. J. (1987) Reductive dissolution of metal oxides. In Aquatic Surface Chemistry (ed. W. Stumm), pp. 221-254. John Wiley & Sons, New York.

    Google Scholar 

  • Stults J. R., Snoeyenbos-West O., Methe B., Lovley D. R., and Chandler D. P. (2001) Application of the 5′ fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments. Appl. Environ. Microbiol. 67, 2781-2789.

    Google Scholar 

  • Stumm W. (1990) Aquatic Chemical Kinetics: Reaction Rates of Processes in Natural Waters, pp. 545. Wiley-Interscience, New York.

    Google Scholar 

  • Stumm W. and Sulzberger B. (1992) The cycling of iron in natural environments: Considerations based on laboratory studies of heterogeneous redox processes. Geochim. Cosmochim. Acta 56, 3233-3257.

    Google Scholar 

  • Stumm W. and Morgan J. J. (1996) Aquatic Chemistry. John Wiley & Sons, New York.

    Google Scholar 

  • Sulzberger B., Suter D., Siffert C., Banwart S., and Stumm W. (1989) Dissolution of Fe(III) (hydr)oxides in natural waters; Laboratory assessment on the kinetics controlled by surface coordination. Mar. Chem. 28, 127-144.

    Google Scholar 

  • Suter D., Banwart S., and Stumm W. (1991) Dissolution of hydrous iron(III) oxides by reductive mechanisms. Langmuir 7, 809-813.

    Google Scholar 

  • Thamdrup B., Fossing H., and Jorgensen B. B. (1994) Manganese, iron, and sulfur cycling in a coastal marine sediment, Aarhus Bay, Denmark. Geochim. Cosmochim. Acta 58, 5115-5129.

    Google Scholar 

  • Thamdrup B. (2000) Bacterial manganese and iron reduction in aquatic sediments. Adv. Microb. Ecol. 16, 41-84.

    Google Scholar 

  • Tiedje J. M. (1988) Ecology of denitrification and dissimilatory nitrate reduction to ammonium. In Biology of Anaerobic Microorganisms (ed. A. J. B. Zehnder). John Wiley & Sons, New York.

    Google Scholar 

  • Truex M. J., Peyton B. M., Valentine N. B., and Gorby Y. A. (1997) Kinetics of U(VI) reduction by a dissimilatory Fe(III)-reducing bacterium under non-growth conditions. Biotech. Bioengin. 55, 490-496.

    Google Scholar 

  • Tuccillo M. E., Cozzarelli I. M., and Herman J. S. (1999) Iron reduction in the sediments of a hydrocarbon-contaminated aquifer. Appl. Geochem. 14, 655-667.

    Google Scholar 

  • Urrutia M. M., Roden E. E., Fredrickson J. K., and Zachara J. M. (1998) Microbial and geochemical controls on synthetic Fe(III) oxide reduction by Shewanella alga strain BrY. Geomicrobiol. J. 15, 269-291.

    Google Scholar 

  • Urrutia M. M., Roden E. E., and Zachara J. M. (1999) Influence of aqueous and solid-phase Fe(II) complexants on microbial reduction of crystalline Fe(III) oxides. Environ. Sci. Technol. 33, 4022-4028.

    Google Scholar 

  • vanBodegom P. M., Scholten J. C. M., and Stams A. J. M. (2004) Direct inhibition of methanogenesis by ferric iron. FEMS Microb. Ecol. 49, 261-268.

    Google Scholar 

  • VanCappellen P., Gaillard J., and Rabouille C. (1993) Biogeochemical transforma-tions in sediments: Kinetic models of early diagenesis. NATO ASI Series 1 4, 401-445.

    Google Scholar 

  • VanCappellen P. and Wang Y. (1995) Metal cycling in surface sediments: Modeling the interplay of transport and reaction. In Metal Contaminated Aquatic Sediments (ed. H. E. Allen), pp. 21-64. Ann Arbor Press, Chelsea, MI.

    Google Scholar 

  • VanCappellen P. and Gaillard J. F. (1996) Biogeochemical dynamics in aquatic sed-iments. In Reactive Transport in Porous Media, Vol. 34 (ed. P. C. Lichtner, C. I. Steefel, and E. H. Oelkers), pp. 335-376. The Mineralogical Society of America.

    Google Scholar 

  • VanCappellen P. and Wang Y. (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. Am. J. Sci. 296, 197-243.

    Google Scholar 

  • Vanderzee C., Roberts D. R., Rancourt D. G., and Slomp C. P. (2003) Nanogoethite is the dominant reactive oxyhydroxide phase in lake and marine sediments. Geology 31, 993-996.

    Google Scholar 

  • Vargas M., Kashefi K., Blunt-Harris E. L., and Lovley D. R. (1998) Microbiological evidence for Fe(III) reduction on early Earth. Nature 395.

    Google Scholar 

  • Vester F. and Invorsen K. (1998) Improved most-probable-number method to detect sulfate-reducing bacteria with natural media and a radiotracer. Appl. Environ. Microbiol. 64, 1700-1707.

    Google Scholar 

  • Visscher P. T., Reid R. P., Bebout B. M., Hoeft S. E., MacIntyre I. G., and Thompson J. A. (1998) Formation of lithified micritic laminae in modern marine stromato-lites (Bahamas): The role of sulfur cycling. Am. Min. 83, 1482-1493.

    Google Scholar 

  • Vroblesky D. A., Bradley P. M., and Chapelle F. H. (1997) Lack of correlation be-tween organic acid concentrations and predominant electron-accepting processes in a contaminated aquifer. Environ. Sci. Technol. 31, 1416-1418.

    Google Scholar 

  • Walker J. C. G. (1984) Suboxic diagenesis in banded iron formations. Nature 309, 340-342.

    Google Scholar 

  • Walker J. C. G. (1987) Was the archaean biosphere upside down? Nature 329, 710-712.

    Google Scholar 

  • Wallmann K., Hennies K., Konig I., Petersen W., and Knauth H. D. (1993) New procedure for determining reactive Fe(III) and Fe(II) minerals in sediments. Limnol. Oceanogr. 38, 1803-1812.

    Google Scholar 

  • Wang Y. and VanCappellen P. (1996) A multicomponent reactive transport model of early diagenesis: Application to redox cycling in coastal marine sediments. Geochim. Cosmochim. Acta 60, 2993-3014.

    Google Scholar 

  • Watson I. A., Oswald S. E., Mayer R. U., Wu Y., and Banwart S. A. (2003) Modeling kinetic processes controlling hydrogen and acetate concentrations in an aquiferderived microcosm. Environ. Sci. Technol. 37, 3910-3919.

    Google Scholar 

  • Weber K. A., Churchill P. F., Urrutia M. M., Kukkadapu R. K., and Roden E. E. (2006) Anaerobic redox cycling of iron by wetland sediment microorganisms. Environ. Microbiol. 8, 100-113.

    Google Scholar 

  • Weiner S. and Dove P. M. (2003) An overview of biomineralization processes and the problem of the vital effect. In Biomineralization, Vol. 54 (ed. P. M. Dove, J. J. DeYoreo, and S. Weiner), pp. 1-29. Mineralogical Society of America.

    Google Scholar 

  • Westall J. C. (1986) MICROQL I. A chemical equilibrium program in BASIC. Report 86-02, Department of Chemistry, Oregon State University, Corvalis, OR.

    Google Scholar 

  • Westrich J. T. and Berner R. A. (1984) The role of sedimentary organic matter in bacterial sulfate reduction: The G model tested. Limnol. Oceanogr. 29, 236-249.

    Google Scholar 

  • Widdowson M. A., Molz F. J., and Benefield L. D. (1988) A numerical transport model of oxygen-and nitrate-based respiration linked to substrate and nutrient availability in porous media. Water Resour. Res. 24, 1553-1565.

    Google Scholar 

  • Williams A. G. B. and Scherer M. M. (2004) Spectroscopic evidence for Fe(II)Fe(III) electron transfer at the iron oxide-water interface. Environ. Sci. Technol. 38,4782-4790.

    Google Scholar 

  • Wirtz K. A. (2003) Control of biogeochemical cycling by mobility and metabolic strategies of microbes in sediments: An integrated model study. FEMS Microb. Ecol. 46, 295-306.

    Google Scholar 

  • Woese C. R., Kandler O., and Wheelis M. L. (1990) Toward a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Nat. Acad. Sci. USA 87, 4576-4579.

    Google Scholar 

  • Yee N. and Fein J. (2001) Cd adsorption onto bacterial surfaces: A universal adsorption edge? Geochim. Cosmochim. Acta 65, 2037-2042.

    Google Scholar 

  • Zachara J. M., Kukkadapu R. K., Fredrickson J. K., Gorby Y. A., and Smith S. C. (2002) Biomineralization of poorly crystalline Fe(III) oxides by dissimilatory metal reducing bacteria (DMRB). Geomicrobiol. J. 19, 179-207.

    Google Scholar 

  • Zehnder A. J. B. and Stumm W. (1988) Geochemistry and biogeochemistry of anaerobic habitats. In Biology of Anaerobic Microorganisms (ed. A. J. B. Zehnder), pp. 1-38. John Wiley & Sons, New York.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Geology and Geophysics, University of Wisconsin, USA

    Eric E. Roden

Authors
  1. Eric E. Roden
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Earth and Environmental Systems Institute, The Pennsylvania State University, 2217 Earth-Engineering Science Building, University Park, PA, 16802, USA

    Susan L. Brantley

  2. Department of Geosciences and the Earth and Environmental Systems Institute, The Pennsylvania State University, 335 Deike Building, University Park, PA, 16802, USA

    James D. Kubicki

  3. U.S. Geological Survey, MS 420, 345 Middlefield Rd., Menlo Park, CA, 94025, USA

    Art F. White

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Roden, E. (2008). Microbiological Controls on Geochemical Kinetics 1: Fundamentals and Case Study on Microbial Fe(III) Oxide Reduction. In: Brantley, S., Kubicki, J., White, A. (eds) Kinetics of Water-Rock Interaction. Springer, New York, NY. https://doi.org/10.1007/978-0-387-73563-4_8

Download citation

Publish with us

Policies and ethics

Search

Navigation