Advertisement

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

  • Eric E. Roden

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.

Keywords

Oxide Reduction Reductive Dissolution Microbial Reduction Wetland Sediment Magnetotactic Bacterium 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. Bae W. and Rittmann B. E. (1995) A structured model of dual-limitation kinetics. Biotechnol. Bioengin. 49, 683-689.Google Scholar
  7. Bak F. and Pfenning N. (1991) Sulfate-reducing bacteria in littoral sediment of Lake Konstanz. FEMS Microbiol. Ecol. 85, 43-52.Google Scholar
  8. Banfield J. F. and Nealson K. H. (1997) Geomicrobiology: Interactions Between Microbes and Minerals, Vol. 35. Mineralogical Society of America.Google Scholar
  9. Banfield J. F., Cervini-Silva J., and Nealson K. H. (2005a) Molecular Geomicrobiology, Vol. 59. Mineralogical Society of America.Google Scholar
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. Berner R. A. (1964) An idealized model of dissolved sulfate in recent sediments. Geochim. Cosmochim. Acta 28, 1497-1503.Google Scholar
  16. Berner R. A. (1977) Stoichiometric models for nutrient regeneration in anoxic sediments. Limnol. Oceanogr. 22, 781-786.Google Scholar
  17. Berner R. A. (1980) Early Diagenesis: A Theoretical Approach. Princeton University Press, Princeton, NJ.Google Scholar
  18. Berner R. A. (1981) Authigenic mineral formation resulting from organic matter decomposition in modern sediments. Fortschr. Mineral. 59, 117-135.Google Scholar
  19. 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
  20. 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
  21. Beveridge T. J. (1989) Role of cellular design in bacterial metal accumulation and mineralization. Annu. Rev. Microbiol. 43, 147-171.Google Scholar
  22. Bevington P. R. and Robinson D. K. (1992) Data Reduction and Error Analysis for the Physical Sciences. McGraw Hill, New York.Google Scholar
  23. Blackman F. F. (1905) Optima and limiting factors. Ann. Botany 19, 281-295.Google Scholar
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. Boudreau B. P. (1992) A kinetic model for microbic organic-matter decomposition in marine sediments. FEMS Microb. Ecol. 102, 1-14.Google Scholar
  30. 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
  31. Boudreau B. P. (1997) Diagenetic Models and Their Implementation. Springer, Berlin.Google Scholar
  32. Brezonik P. L. (1994) Chemical Kinetics and Process Dynamics in Aquatic Systems. Lewis Publishers, Boca Raton, FL.Google Scholar
  33. Burdige D. J. (1991) The kinetics of organic matter mineralization in anoxic marine sediment. J. Mar. Res. 49, 727-761.Google Scholar
  34. 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
  35. 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
  36. 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
  37. 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
  38. Caccavo F. and Das A. (2002) Adhesion of dissimilatory Fe(III)-reducing bacteria to Fe(III) minerals. Geomicrobiol. J. 19, 161-177.Google Scholar
  39. 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
  40. 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
  41. 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
  42. Canfield D. E., Thamdrup B., and Kristensen E. (2005) Aquatic Geomicrobiology. Elsevier.Google Scholar
  43. 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
  44. 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
  45. Chapelle F. H. (2001) Ground-water Microbiology and Geochemistry. John Wiley & Sons, New York.Google Scholar
  46. 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
  47. Christensen D. (1984) Determination of substrates oxidized by sulfate reduction in intact cores of marine sediments. Limnol. Oceanogr. 29, 189-192.Google Scholar
  48. Clark W. M. (1960) Oxidation-Reduction Potentials of Organic Systems. The Williams and Wilkins Company, Baltimore, MD.Google Scholar
  49. 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
  50. 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
  51. Cornell R. M. and Schwertmann U. (1996) The Iron Oxides. VCH Verlagsgesellschaft mbH/VCH Publishers, Inc.Google Scholar
  52. 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
  53. 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
  54. 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
  55. Crabtree B. and Nicholson B. (1988) Thermodyamics and metabolism. In Biochemical Thermodynamics (ed. M. Jones), pp. 347-395. Elsevier, Amsterdam.Google Scholar
  56. 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
  57. 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
  58. Das A. and Caccavo F. (2000) Dissimiliatory Fe(III) oxide reduction by Shewanella alga BrY requires adhesion. Curr. Microbiol. 40, 344-347.Google Scholar
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. Dzombak D. A. and Morel F. M. M. (1990) Surface Complexation Modeling: Hydrous Ferric Oxide. John Wiley & Sons, New York.Google Scholar
  66. Ehrlich H. L. (1999) Microbes as geologic agents: Their role in mineral formation. Geomicrobiol. J. 16, 135-153.Google Scholar
  67. Ehrlich H. L. (2002) Geomicrobiology. Marcel Dekker, New York.Google Scholar
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. Gorham E. (1991) Biogeochemistry: Its origins and development. Biogeochemistry 13,199-239.Google Scholar
  79. 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
  80. 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
  81. Haldane J. B. S. (1930) Enzymes. Longman Green and Co., London.Google Scholar
  82. 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
  83. 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
  84. 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
  85. 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
  86. Hernandez M. E. and Newman D. K. (2001) Extracellular electron transfer. CMLS Cell Mol Life Sci 58, 1562-1571.Google Scholar
  87. 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
  88. 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
  89. 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
  90. 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
  91. 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
  92. 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
  93. 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
  94. Jackson B. E. and McInerney M. J. (2002) Anaerobic microbial metabolism can proceed close to thermodynamic limits. Nature 415, 454-456.Google Scholar
  95. 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
  96. 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
  97. 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
  98. Jin Q. and Bethke C. M. (2002) Kinetics of electron transfer through the respiratory chain. Biophys. J. 83, 1797-1808.Google Scholar
  99. Jin Q. and Bethke C. M. (2003) A new rate law describing microbial respiration. Appl. Environ. Microbiol. 69, 2340-2348.Google Scholar
  100. Jin Q. and Bethke C. M. (2005) Predicting the rate of microbial respiration in geochemical environments. Geochim. Cosmochim. Acta 69, 1133-1143.Google Scholar
  101. 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
  102. Keller M. and Zengler K. (2004) Tapping into microbial diversity. Nat. Rev. Micro. 2,141-150.Google Scholar
  103. 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
  104. 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
  105. 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
  106. 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
  107. 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
  108. Kostka J. E. and Nealson K. H. (1995) Dissolution and reduction of magnetite by bacteria. Environ. Sci. Technol. 29, 2535-2540.Google Scholar
  109. 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
  110. 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
  111. 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
  112. Laidler K. J. (1987) Chemical Kinetics. Harper & Row, New York.Google Scholar
  113. 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
  114. 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
  115. Lasaga A. C. (1998) Kinetic Theory in the Earth Sciences. Princeton University Press, Princeton, NJ.Google Scholar
  116. Lerman A. (1979) Geochemical Processes - Water and Sediment Environments. John Wiley & Sons, New York.Google Scholar
  117. 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
  118. 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
  119. 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
  120. 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
  121. 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
  122. Lovley D. R. (1985) Minimum threshold for hydrogen metabolism in methanogenic bacteria. Appl. Environ. Microbiol. 49, 1530-1531.Google Scholar
  123. 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
  124. 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
  125. 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
  126. Lovley D. R. (1987) Organic matter mineralization with the reduction of ferric iron: A review. Geomicrobiol. J. 5, 375-399.Google Scholar
  127. 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
  128. 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
  129. 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
  130. 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
  131. 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
  132. Lovley D. R. (1991) Dissimilatory Fe(III) and Mn(IV) reduction. Microbiol. Rev. 55,259-287.Google Scholar
  133. 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
  134. 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
  135. Lovley D. R. (1993) Dissimilatory metal reduction. Annu. Rev. Microbiol. 47, 263-290.Google Scholar
  136. 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
  137. 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
  138. 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.
  139. 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
  140. 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
  141. Lowenstam H. A. (1981) Minerals formed by organisms. Science 211, 1126-1131.Google Scholar
  142. Lowenstam H. A. and Weiner S. (1989) On Biomineralization. Oxford University Press.Google Scholar
  143. 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
  144. Madigan M. T., Martinko J. M., and Parker J. (2000) Brock Biology of Microorganisms. Prentice-Hall, Englewood Cliffs, NJ.Google Scholar
  145. Madsen E. L. (2005) Identifying microorganisms responsible for ecologically sig-nificant biogeochemcial processes. Nat. Rev. Microbiol. 3, 439-446.Google Scholar
  146. 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
  147. 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
  148. 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
  149. Michaelis L. and Menten M. M. (1913) Die Kinetik der Invertingwirkung (The kinetics of invertase activity). Biochem. Z. 49, 333-369.Google Scholar
  150. 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
  151. Monod J. (1942) Recherches sur las croissance des culture bacteriennes (Research on the growth of bacterial cultures). Hermann et Cie.Google Scholar
  152. Monod J. (1949) The growth of bacterial cultures. Annu. Rev. Microbiol. 3, 371-394.Google Scholar
  153. 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
  154. 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
  155. 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
  156. 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
  157. 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.)
  158. Nevin K. P. and Lovley D. R. (2002) Mechanisms of Fe(III) oxide reduction in sedimentary environments. Geomicrobiol. J. 19, 141-159.Google Scholar
  159. Newman D. K. and Banfield J. F. (2002) Geomicrobiology: How molecular-scale interactions underpin biogeochemical systems. Science 296, 1071-1077.Google Scholar
  160. 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
  161. 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
  162. Ottow J. C. G. (1971) Iron reduction and gley formation by nitrogen-fixing Clostridia. Oecologia 6, 164-175.Google Scholar
  163. 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
  164. Pasteur L. (1860) Experiences relatives aux generations spontanees. Compt. Rend. Acad. Sci 50, 303-675.Google Scholar
  165. 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
  166. Peters R. H. (1983) The Ecological Implications of Body Size. Cambridge University Press.Google Scholar
  167. 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
  168. Ponnamperuma F. N. (1972) The chemistry of submerged soils. Adv. Agron. 24, 29-96.Google Scholar
  169. Postma D. (1993) The reactivity of iron oxides in sediments: A kinetic approach. Geochim. Cosmochim. Acta 57, 5027-5034.Google Scholar
  170. 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
  171. Press W. H., Teukolsky S. A., Vetterling W. T., and Flannery B. P. (1992) Numerical Recipes in FORTRAN. Cambridge University Press.Google Scholar
  172. 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
  173. Rawn J. D. (1983) Biochemistry. Harper and Row, New York.Google Scholar
  174. 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
  175. 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
  176. Richardson D. J. (2000) Bacterial respiration: A flexible process for a changing environment. Microbiology 146, 551-571.Google Scholar
  177. 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
  178. 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
  179. Rittmann B. E. and McCarty P. L. (2001) Environmental Biotechnology. McGrawHill, New York.Google Scholar
  180. 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
  181. 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
  182. Roden E. E. and Tuttle J. H. (1993) Inorganic sulfur turnover in oligohaline estuarine sediments. Biogeochemistry 22, 81-105.Google Scholar
  183. 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
  184. 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
  185. 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
  186. 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
  187. 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
  188. 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
  189. 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
  190. 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
  191. 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
  192. Roden E. E. (2003a) Fe(III) oxide reactivity toward biological versus chemical reduction. Environ. Sci. Technol. 37, 1319-1324.Google Scholar
  193. 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
  194. 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
  195. Roden E. E. (2004) Analysis of long-term bacterial versus chemical Fe(III) oxide reduction kinetics. Geochim. Cosmochim. Acta 68, 3205-3216.Google Scholar
  196. Roden E. E. (2005) Unpublished data.Google Scholar
  197. 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
  198. Roden E. E. (2006) Geochemical and microbiological controls on dissimilatory iron reduction. C.R. Geosci. 338, 456-467.Google Scholar
  199. Roels J. A. (1983) Energetics and Kinetics in Biotechnology. Elsevier Biomedical Press, Amsterdam.Google Scholar
  200. 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
  201. 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
  202. 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
  203. 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
  204. Schink B. (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262-280.Google Scholar
  205. Schnoor J. L. (1996) Environmental Modeling. Wiley Interscience, New York.Google Scholar
  206. Schultze-Lam S., Fortin D., Davis B. S., and Beveridge T. J. (1996) Mineralization of bacterial surfaces. Chem. Geol. 132, 171-181.Google Scholar
  207. 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
  208. 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
  209. 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
  210. 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
  211. 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
  212. 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
  213. 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
  214. 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
  215. 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
  216. Stumm W. (1990) Aquatic Chemical Kinetics: Reaction Rates of Processes in Natural Waters, pp. 545. Wiley-Interscience, New York.Google Scholar
  217. 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
  218. Stumm W. and Morgan J. J. (1996) Aquatic Chemistry. John Wiley & Sons, New York.Google Scholar
  219. 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
  220. Suter D., Banwart S., and Stumm W. (1991) Dissolution of hydrous iron(III) oxides by reductive mechanisms. Langmuir 7, 809-813.Google Scholar
  221. 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
  222. Thamdrup B. (2000) Bacterial manganese and iron reduction in aquatic sediments. Adv. Microb. Ecol. 16, 41-84.Google Scholar
  223. 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
  224. 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
  225. 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
  226. 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
  227. 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
  228. 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
  229. 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
  230. 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
  231. 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
  232. 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
  233. 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
  234. 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
  235. 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
  236. 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
  237. 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
  238. Walker J. C. G. (1984) Suboxic diagenesis in banded iron formations. Nature 309, 340-342.Google Scholar
  239. Walker J. C. G. (1987) Was the archaean biosphere upside down? Nature 329, 710-712.Google Scholar
  240. 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
  241. 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
  242. 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
  243. 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
  244. 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
  245. 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
  246. 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
  247. 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
  248. 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
  249. 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
  250. 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
  251. Yee N. and Fein J. (2001) Cd adsorption onto bacterial surfaces: A universal adsorption edge? Geochim. Cosmochim. Acta 65, 2037-2042.Google Scholar
  252. 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
  253. 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

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Eric E. Roden
    • 1
  1. 1.Department of Geology and GeophysicsUniversity of WisconsinUSA

Personalised recommendations