1887

Chapter 44 : Microbial Metal Cycling in Aquatic Environments

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Microbial Metal Cycling in Aquatic Environments , Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815882/9781555813796_Chap44-1.gif /docserver/preview/fulltext/10.1128/9781555815882/9781555813796_Chap44-2.gif

Abstract:

This chapter focuses on microbial metal redox metabolism, with an emphasis on iron (Fe) and manganese (Mn) cycling in the water column and surface sediments. It deals exclusively with metal cycling in circumneutral pH environments. The majority of the Fe and Mn that enters aquatic systems comes in the form of insoluble oxides (Fe and Mn) and silicate phases (Fe only; Mn-rich silicates are uncommon), which are produced during weathering of rock-forming silicate minerals (e.g., olivines, pyroxenes, and amphiboles) in the terrestrial environment and transported to coastal marine environments and lakes by rivers and streams. Although insoluble oxide phases are by far the most abundant forms of Fe(III) and Mn(IV) in neutral-pH aquatic environments, several recent studies suggested that small but significant quantities of soluble Fe(III) exist in circumneutral sediment pore fluids. A review by Emerson provides an overview of the history of research on circum-neutral bacterial Fe(II) oxidation as well as the physiology and systematics of Fe(II)-oxidizing bacteria (FeOB). In light of the foregoing analysis of the role of microbes in the oxidative side of the Fe and Mn cycles in aquatic environments, it is clear that Fe and Mn redox cycling is an example of microbial syntrophy analogous to the well-known syntrophic relationships among N- and S-oxidizing and -reducing microorganisms in natural systems. Both the water column and sediment chemical profiles illustrate several key aspects of the Fe-Mn redox cycling systems in aquatic environments.

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44

Key Concept Ranking

Bacteria and Archaea
0.43636662
Environmental Microbiology
0.43636662
Restriction Fragment Length Polymorphism
0.42510906
Denaturing Gradient Gel Electrophoresis
0.42176172
0.43636662
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Schematic representation of the cycling of metals in aquatic ecosystems. Note that when the water column is well-oxygenated, metal redox cycling is localized at the sediment-water interface. Modified from Fig. 1 in reference with permission of Routledge/Taylor & Francis Group LLC.

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Pathways of Fe and Mn oxidation and reduction in circumneutral-pH aquatic environments. Modified from Fig. 8.4 in reference with permission of the publisher.

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Depth profiles of dissolved Fe(II) and Mn(II), particulate Fe(III) and Mn(IV), and other constituents in a stratified lake (Paul Lake, Mich.). Particulate Fe(III) and Mn(IV) may include small amounts of sorbed Fe(II) and/or Mn(II). Dashed lines indicate approximate boundaries across which metal redox cycling takes place. Redrawn from Fig. 1 in reference and Fig. 1 and 7 in reference with permission of the publishers.

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4
FIGURE 4

Depth profiles of aqueous and solid-phase Fe, Mn, and other constituents and rates of Fe(III) reduction (FeR), sulfate reduction (SR), and methanogenesis (MG) in the sediments of a freshwater wetland (Talladega National Forest) (top panels) and a shallow coastal embayment (Aarhus Bay, Denmark) (bottom panels). The Mn(IV) values shown in panels C and G may include small amounts of sorbed or precipitated Mn(II). Data are redrawn from Fig. 1 in reference , Fig. 2 in reference , Fig. 3 in reference , Fig. 2 , 4, and 6 in reference , Fig. 2 in reference , and Fig. 3 in reference with permission of the publishers.

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5
FIGURE 5

Fe(III) oxide morphologies produced by O-dependent FeOB activity. (A) Stalk-like structures characteristic of spp. from a freshwater spring rich in Fe(II); (B) sheath structures of Fe(III) oxides, also from a freshwater spring; (C) filamentous Fe(III) oxides from a marine hydrothermal vent. In all cases, the structures are composed of amorphous ferrihydrite-like minerals that dissolve readily in ammonium oxalate. Although these structures were all formed by FeOB, the bacteria are not visible unless stained with a fluorescent dye. Bar = 10 µm.

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555815882.ch44
1. Aguilar, C.,, and K. H. Nealson. 1994. Manganese reduction in Oneida Lake, New York—estimates of spatial and temporal manganese flux. Can. J. Fish. Aquat. Sci. 51:185196.
2. Aller, R. C. 1990. Bioturbation and manganese cycling in hemipelagic sediments. Phil. Trans. R. Soc. London A 331:5168.
3. Aller, R. C.,, and P. D. Rude. 1988. Complete oxidation of solid phase sulfides by manganese and bacteria in anoxic marine sediments. Geochim. Cosmochim. Acta 52:751765.
4. Amann, R. I.,, L. Krumholz, and, D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762770.
5. Amann, R. I.,, J. Stromley,, R. Devereux,, R. Key, and, D. A. Stahl. 1992. Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl. Environ. Microbiol. 58:614623.
6. Anderson, R. T.,, J. N. Rooney-Varga,, C. V. Gaw, and, D. R. Lovley. 1998. Anaerobic benzene oxidation in the Fe(III) reduction zone of petroleum-contaminated aquifers. Environ. Sci. Technol. 32:12221229.
7. Anderson, R. T.,, H. A. Vrionis,, I. Ortiz-Bernad,, C. T. Resch,, P. E. Long,, R. Dayvault,, K. Karp,, S. Marutzky,, D. R. Metzler,, A. Peacock,, D. C. White,, M. Lowe, and, D. R. Lovley. 2003. Stimulating in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl. Environ. Microbiol. 69:58845891.
8. Arnold, R. G.,, M. R. Hoffmann,, T. J. DiChristina, and, F. W. Picardal. 1990. Regulation of dissimilatory Fe(III) reduction activity in Shewanella putrefaciens. Appl. Environ. Microbiol. 56:28112817.
9. Bak, F.,, and N. Pfenning. 1991. Sulfate-reducing bacteria in littoral sediment of Lake Konstanz. FEMS Microbiol. Ecol. 85:4352.
10. Barbeau, K.,, E. L. Rue,, K. W. Bruland, and, A. Butler. 2001. Photochemical cycling of iron in the surface ocean mediated by microbial iron(III)-binding ligands. Nature 413:409413.
11. Belzile, N.,, Y. W. Chen, and, R. R. Xu. 2000. Early diagenetic behaviour of selenium in freshwater sediments. Appl. Geochem. 15:14391454.
12. Benz, M.,, A. Brune, and, B. Schink. 1998. Anaerobic and aerobic oxidation of ferrous iron at neutral pH by chemoheterotrophic nitrate-reducing bacteria. Arch. Microbiol. 169:159165.
13. Bond, D. R.,, T. Mester,, C. L. Nesbo,, A. V. Izquierdo-Lopez,, F. L. Collart, and, D. R. Lovley. 2005. Characterization of citrate synthase from Geobacter sulfurreducens and evidence for a family of citrate synthases similar to those of eukaryotes throughout the Geobacteraceae. Appl. Environ. Microbiol. 71:38583865.
14. Bostick, B. C.,, S. Fendorf, and, B. A. Manning. 2003. Arsenite adsorption on galena (PbS) and sphalerite (ZnS). Geochim. Cosmochim. Acta 67:895907.
15. Braker, G.,, J. Z. Zhou,, L. Y. Wu,, A. H. Devol, and, J. M. Tiedje. 2000. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest marine sediment communities. Appl. Environ. Microbiol. 66:20962104.
16. Brendel, P. J.,, and G. W. Luther. 1995. Development of a gold amalgam voltammetric microelectrode for the determination of dissolved Fe, Mn, O2, and S(II) in porewaters of marine and freshwater sediments. Environ. Sci. Technol. 29:751761.
17. Buffle, J.,, and R. R. DeVitre (ed.). 1994. Chemical and Biological Regulation of Aquatic Systems. Lewis, Boca Raton, Fla.
18. Buffle, J.,, and G. Horvai. 2000. In Situ Monitoring of Aquatic Systems. John Wiley & Sons, New York, N.Y.
19. Buffle, J.,, and W. Stumm. 1994. General chemistry of aquatic systems, p. 1–43. In J. Buffle and, R. R. DeVitre (ed.), Chemical and Biological Regulation of Aquatic Systems. Lewis, Boca Raton, Fla.
20. Burdige, D. J. 1993. The biogeochemistry of manganese and iron reduction in marine sediments. Earth Sci. Rev. 35:249284.
21. Burdige, D. J.,, and P. E. Kepkay. 1983. Determination of bacterial manganese oxidation rates in sediments using an in situ dialysis technique. 1. Laboratory studies. Geochim. Cosmochim. Acta 47:19071916.
22. Burke, I. T.,, C. Boothman,, J. R. Lloyd,, R. J. G. Mortimer,, F. R. Livens, and, K. Morris. 2005. Effects of progressive anoxia on the solubility of technetium in sediments. Environ. Sci. Technol. 39:41094116.
23. Caccavo, F.,, D. J. Lonergan,, D. R. Lovley,, M. Davis,, J. F. Stolz, and, M. J. McInerney. 1994. Geobacter sulfur-reducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl. Environ. Microbiol. 60:37523759.
24. Canfield, D. E.,, and D. J. DesMarais. 1993. Biogeochemical cycles of carbon, sulfur, and free oxygen in a microbial mat. Geochim. Cosmochim. Acta 57:39713984.
25. Canfield, D. E.,, B. B. Jorgensen,, H. Fossing,, R. Glud,, J. Gundersen,, N. B. Ramsing,, B. Thamdrup,, J. W. Hansen,, L. P. Neilsen, and, P. O. J. Hall. 1993. Pathways of organic carbon oxidation in three continental margin sediments. Mar. Geol. 113:2740.
26. Canfield, D. E.,, and B. Thamdrup. 1994. The production of 34S-depleted sulfide during bacterial disproportionation of elemental sulfur. Science 266:19731975.
27. Canfield, D. E.,, B. Thamdrup, and, J. W. Hansen. 1993. The anaerobic degradation of organic matter in Danish coastal sediments: iron reduction, manganese reduction, and sulfate reduction. Geochim. Cosmochim. Acta 57:38673883.
28. Canfield, D. E.,, B. Thamdrup, and, E. Kristensen. 2005. Aquatic Geomicrobiology. Elsevier, San Diego, Calif.
29. Carey, E.,, and M. Taillefert. 2005. The role of soluble Fe(III) in the cycling of iron and sulfur in coastal marine sediments. Limnol. Oceanogr. 50:11291141.
30. Chandler, D. P.,, and A. E. Jarrell. 2004. Automated purification and suspension array detection of 16S rRNA from soil and sediment extracts by using tunable surface microparticles. Appl. Environ. Microbiol. 70:26212631.
31. Chandler, D. P.,, and A. E. Jarrell. 2005. Taking arrays from the lab to the field: trying to make sense of the unknown. BioTechniques 38:591600.
32. Chandler, D. P.,, A. E. Jarrell,, E. E. Roden,, J. Golova,, B. Chernov,, M. J. Schipma,, A. D. Peacock, and, P. E. Long. 2006. Suspension array analysis of 16S rRNA from Fe- and SO42–-reducing bacteria in uranium-contaminated sediments undergoing bioremediation. Appl. Environ. Microbiol. 72:46724687.
33. Chapelle, F. H. 2001. Ground-Water Microbiology and Geochemistry, 2nd ed. John Wiley & Sons, Inc., New York, N.Y.
34. Chapnick, S. D.,, W. S. Moore, and, K. H. Nealson. 1982. Microbially mediated manganese oxidation in a freshwater lake. Limnol. Oceanogr. 27:10041014.
35. Coates, J. D.,, and L. A. Achenbach. 2001. The biogeo-chemistry of aquifer systems, p. 719–727. In C. J. Hurst,, R. L. Crawford,, G. R. Knudsen,, M. J. McInerney, and, L. D. Stetzenbach (ed.), Manual of Environmental Microbiology, 2nd ed. ASM Press, Washington, D.C.
36. Coates, J. D.,, R. T. Anderson,, J. C. Woodward,, E. J. P. Phillips, and, D. R. Lovley. 1996. Anaerobic hydrocarbon degradation in petroleum-contaminated harbor sediments under sulfate-reducing and artificially imposed iron-reducing conditions. Environ. Sci. Technol. 30:27842789.
37. Cooper, D. C.,, A. L. Neal,, R. K. Kukkadapu,, D. Brewe,, A. Coby, and, F. W. Picardal. 2005. Effects of sediment iron mineral composition on microbially mediated changes in divalent metal speciation: importance of ferrihydrite. Geochim. Cosmochim. Acta 69:17391754.
38. Cooper, D. C.,, F. Picardal,, J. Rivera, and, C. Talbot. 2000. Zinc immobilization and magnetite formation via ferric oxide reduction by Shewanella putrefaciens 200. Environ. Sci. Technol. 34:100106.
39. Cornell, R. M.,, and U. Schwertmann. 1996. The Iron Oxides. VCH Verlagsgesellschaft mbH, Weinheim, Germany.
40. Croal, L. R.,, J. A. Gralnick,, D. Malasarn, and, D. K. Newman. 2004. The genetics of geochemistry. Annu. Rev. Genet. 38:175202.
41. Croal, L. R.,, C. M. Johnson,, B. L. Beard, and, D. K. Newman. 2003. Iron isotope fractionation by anoxygenic Fe(II)-phototrophic bacteria. Geochim. Cosmochim. Acta 68:12271242.
42. Cummings, D. E.,, O. L. Snoeyenbos-West,, D. T. Newby,, A. M. Niggemyer,, D. R. Lovley,, L. A. Achenbach, and, R. F. Rosenzweig. 2003. Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses. Microb. Ecol. 46:257269.
43. Davies, S. H. R.,, and J. J. Morgan. 1989. Manganese(II) oxidation kinetics on metal oxide surfaces. J. Colloid Interface Sci. 129:6377.
44. Davison, W.,, G. W. Grime,, J. A. W. Morgan, and, K. Clarke. 1991. Distribution of dissolved iron in sediment pore waters at submillimetre resolution. Nature 353:323325.
45. Davison, W.,, and G. Seed. 1983. The kinetics of the oxidation of ferrous iron in synthetic and natural waters. Geochim. Cosmochim. Acta 47:6779.
46. Davison, W.,, and H. Zhang. 1994. In situ speciation measurements of trace components in natural waters using thin-film gels. Nature 367:546548.
47. DiChristina, T. J. 1992. Effects of nitrate on dissimilatory iron reduction by Shewanella putrefaciens 200. J. Bacteriol. 174:18911896.
48. DiChristina, T. J.,, J. K. Fredrickson, and, J. M. Zachara. 2005. Enzymology of electron transport: energy generation with geochemical consequences, p. 27–52. In J. F. Banfield,, J. Cervini-Silva, and, K. H. Nealson (ed.), Molecular Geomicrobiology, vol. 59. Mineralogical Society of America, Washington, D.C.
49. Diem, D.,, and W. Stumm. 1984. Is dissolved Mn2+ being oxidized by O2 in absence of Mn-bacteria or surface catalysts? Geochim. Cosmochim. Acta 48:15711573.
50. Donahoe, R. J.,, and C. X. Liu. 1998. Pore water geochemistry near the sediment-water interface of a zoned, freshwater wetland in the southeastern United States. Environ. Geol. 33:143153.
51. Dowdle, P. R.,, A. M. Laverman, and, R. S. Oremland. 1996. Bacterial dissimilatory reduction of arsenic(V) to arsenic(III) in anoxic sediments. Appl. Environ. Microbiol. 62:16641669.
52. Dowdle, P. R.,, and R. S. Oremland. 1998. Microbial oxidation of elemental selenium in soil slurries and bacterial cultures. Environ. Sci. Technol. 32:37493755.
53. Duce, R. A.,, and N. W. Tindale. 1991. Atmospheric transport of iron and its deposition in the ocean. Limnol. Oceanogr. 36:17151726.
54. Edwards, K. J.,, D. R. Rogers,, C. O. Wirsen, and, T. M. McCollom. 2003. Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing chemolithoautotrophic α- and γ-Proteobacteria from the deep sea. Appl. Environ. Microbiol. 69:29062913.
55. Ehrenberg, C. G. 1836. Vorlage mettheilungen ueber das wirklige vorkommen fossiler infusorien und ihre grosse verbreitung. Poggendorfs Ann. Phys. Chem. 38:213227.
56. Ehrenreich, A.,, and F. Widdel. 1994. Anaerobic oxidation of ferrous iron by purple bacteria, a new type of phototrophic metabolism. Appl. Environ. Microbiol. 60:45174526.
57. Ehrlich, H. L. 1995. Geomicrobiology. Marcel Dekker, Inc., New York, N.Y.
58. Ehrlich, H. L. 2002. Geomicrobiology, 4th ed. Marcel Dekker, New York, N,Y.
59. Ehrlich, H. L. 2000. Ocean manganese nodules: biogenesis and bioleaching possibilities. Miner. Metallurg. Proc. 17:121128.
60. Emerson, D. 2004. Introduction to special issue on microbial Fe(II) oxidation at neutral pH. Geomicrobiol. J. 21:369.
61. Emerson, D. 2000. Microbial oxidation of Fe(II) and Mn(II) at circumneutral pH, p. 31–52. In D. R. Lovley (ed.), Environmental Microbe-Metal Interactions. ASM Press, Washington, D.C.
62. Emerson, D.,, and M. M. Floyd. 2005. Enrichment and isolation of iron-oxidizing bacteria at neutral pH. Methods Enzymol. 397:112130.
63. Emerson, D.,, and C. Moyer. 1997. Isolation and characterization of novel lithotrophic iron-oxidizing bacteria that grow at circumneutral pH. Appl. Environ. Microbiol. 63:47844792.
64. Emerson, D.,, and C. Moyer. 2002. Neutrophilic Feoxidizing bacteria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition. Appl. Environ. Microbiol. 68:30853093.
65. Emerson, D.,, and N. P. Revsbech. 1994. Investigation of an iron-oxidizing microbial mat community located near Aarhus, Denmark: field studies. Appl. Environ. Microbiol. 60:40224031.
66. Emerson, D.,, and N. P. Revsbech. 1994. Investigation of an iron-oxidizing microbial mat community located near Aarhus, Denmark: laboratory studies. Appl. Environ. Microbiol. 60:40324038.
67. Emerson, D.,, and J. V. Weiss. 2004. Bacterial iron oxidation in circumneutral freshwater habitats: findings from the field and the laboratory. Geomicrobiol. J. 21:405414.
68. Emerson, D.,, J. V. Weiss, and, J. P. Megonigal. 1999. Iron-oxidizing bacteria are associated with ferric hydroxide precipitates (Fe plaque) on the roots of wetland plants. Appl. Environ. Microbiol. 65:27582761.
69. Emerson, S.,, S. Kalhorn,, L. Jacobs,, B. M. Tebo,, K. H. Nealson, and, R. A. Rosson. 1982. Environmental oxidation rate of manganese(II): bacterial catalysis. Geochim. Cosmochim. Acta 46:10731079.
70. Finneran, K. T.,, M. E. Housewright, and, D. R. Lovley. 2002. Multiple influences of nitrate on uranium solubility during bioremediation of uranium-contaminated subsurface sediments. Environ. Microbiol. 4:510516.
71. Fleming, E. J.,, E. E. Mack,, P. G. Green, and, D. C. Nelson. 2006. Mercury methylation from unexpected sources: molyb-date-inhibited freshwater sediments and an iron-reducing bacterium. Appl. Environ. Microbiol. 72:457464.
72. Ford, T.,, and R. Mitchell. 1992. Microbial transport of toxic metals, p. 83–101. In R. Mitchell (ed.), Environmental Microbiology. Wiley-Liss, New York, N.Y.
73. Friedrich, M. W. 2005. Methyl-coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane-oxidizing Archaea. Methods Enzymol. 397:428442.
74. Froelich, P. N.,, G. P. Klinkhammer,, M. L. Bender,, N. A. Luedtke,, G. R. Heath,, D. Cullen,, P. Dauphin,, D. Hammond,, B. Hartman, and, V. Maynard. 1979. Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic: suboxic diagenesis. Geochim. Cosmochim. Acta 43:10751090.
75. Gadd, G. M. 1993. Microbial formation and transformation of organometallic and organometalloid compounds. FEMS Microbiol. Rev. 11:297316.
76. Ghiorse, W. C. 1984. Biology of iron- and manganese-depositing bacteria. Annu. Rev. Microbiol. 38:515550.
77. Ghiorse, W. C. 1994. Iron and manganese oxidation and reduction, p. 1079–1096. In J. M. Bigham (ed.), Methods of Soil Analysis, part 2. Microbiological and Biochemical Properties. Soil Science Society of America, Madison, Wis.
78. Gibney, B.,, and K. Neusslin. Arsenic sequestration by nitrate respiring microbes in urban lake sediments. Submitted for publication.
79. Gibson, G. R.,, R. J. Parkes, and, R. A. Herbert. 1987. Evaluation of viable counting procedures for the enumeration of sulfate-reducing bacteria in estuarine sediments. J. Microbiol. Methods 7:201210.
80. Glud, R. N.,, J. K. Gundersen,, B. B. Jorgensen,, N. P. Revsbech, and, H. D. Schulz. 1994. Diffusive and total oxygen-uptake of deep-sea sediments in the Eastern South-Atlantic Ocean: in situ and laboratory measurements. Deep-Sea Res. I 41:17671788.
81. Glud, R. N.,, J. K. Gundersen,, N. P. Revsbech, and, B. B. Jorgensen. 1994. Effects on the benthic diffusive boundary layer imposed by microelectrodes. Limnol. Oceanogr. 39:462467.
82. Gorby, Y. A.,, F. Caccavo, and, H. Bolton. 1998. Microbial reduction of cobaltIIIEDTA in the presence and absence of manganese(IV) oxide. Environ. Sci. Technol. 32:244250.
83. Gorby, Y. A.,, and D. R. Lovley. 1991. Electron transport in the dissimilatory iron reducer, GS-15. Appl. Environ. Microbiol. 57:867870.
84. Habicht, K. S.,, and D. E. Canfield. 2001. Isotope fractionation by sulfate-reducing natural populations and the isotopic composition of sulfide in marine sediments. Geology 29:555558.
85. Haese, R. R. 2000. The reactivity of iron, p. 233–261. In H. D. Schulz and, M. Zabel (ed.), Marine Geochemistry. Springer, New York, N.Y.
86. Hansen, J. W.,, B. Thamdrup, and, B. B. Jorgensen. 2000. Anoxic incubation of sediment in gas-tight plastic bags: a method for biogeochemical process studies. Mar. Ecol. Prog. Ser. 208:273282.
87. Harder, E. C. 1919. Iron-depositing bacteria and thier geologic relations. U. S. Geol. Surv. Prof. Pap. 113:789.
88. Heising, S.,, L. Richter,, W. Ludwig, and, B. Schink. 1999. Chlorobium ferrooxidans sp. nov., a phototrophic green sulfur bacterium that oxidizes ferrous iron in coculture with a “Geospirillum” sp. strain. Arch. Microbiol. 172:116124.
89. Heising, S.,, and B. Schink. 1998. Phototrophic oxidation of ferrous iron by a Rhodomicrobium vannielii strain. Microbiology (Reading) 144:22632269.
90. Hering, J. G.,, and W. Stumm. 1990. Oxidative and reductive dissolution of minerals, p. 427–464. In M. F. Hochella and, A. F. White (ed.), Mineral-Water Interface Geochemistry, vol. 23. Mineralogical Society of America, Washington, D.C.
91. Hines, M. E.,, J. Faganeli, and, R. Planinc. 1997. Sedimentary anaerobic microbial biogeochemistry in the Gulf of Trieste, northern Adriatic Sea: influences of bottom water oxygen depletion. Biogeochemistry 39:6586.
92. Holland, H. D.,, and J. F. Kasting. 1992. The environment of the archaean Earth, p. 21–24. In J. W. Schopf and, C. Klein (ed.), The Proterozoic Biosphere: an Interdisciplinary Study. Cambridge University Press, Cambridge, United Kingdom.
93. Holmes, D. E.,, K. T. Finneran,, R. A. O’Neil, and, D. R. Lovley. 2002. Enrichment of members of the family Geobacteraceae associated with the stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments. Appl. Environ. Microbiol. 68:23002306.
94. Holmes, D. E.,, K. P. Nevin, and, D. R. Lovley. 2004. In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl. Environ. Microbiol. 70:72517259.
95. Holmes, D. E.,, K. P. Nevin,, R. A. O’Neil,, J. E. Ward,, L. A. Adams,, T. L. Woodard,, H. A. Vrionis, and, D. R. Lovley. 2005. Potential for quantifying expression of the Geobacteraceae citrate synthase gene to assess the activity of Geobacteraceae in the subsurface and on current-harvesting electrodes. Appl. Environ. Microbiol. 71:68706877.
96. Hungate, R. E. 1969. A roll tube method for cultivation of strict anaerobes. Methods Microbiol. 3B:117132.
97. Islam, F. S.,, A. G. Gault,, C. Boothman,, D. A. Polya,, J. M. Charnock,, D. Chatterjee, and, J. R. Lloyd. 2004. Role of metal-reducing bacteria in arsenic release from Bengal delta sediments. Nature 430:6871.
98. Jiao, Y. Y. Q.,, A. Kappler,, L. R. Croal, and, D. K. Newman. 2005. Isolation and characterization of a genetically tractable photo autotrophic Fe(II)-oxidizing bacterium, Rhodopseudomonas palustris strain TIE-1. Appl. Environ. Microbiol. 71:44874496.
99. Johnson, C. M.,, and B. L. Beard. 2005. Biogeochemical cycling of iron isotopes. Science 309:10251027.
100. Johnson, C. M.,, B. L. Beard,, E. E. Roden,, D. K. Newman, and, K. H. Nealson. 2004. Isotopic constraints on biogeochemical cycling of Fe, p. 359–408. In C. M. Johnson,, B. L. Beard, and, F. Albarède (ed.), Reviews in Mineralogy and Geochemistry, vol. 55. Geochemistry of Non-Traditional Stable Isotopes. Mineralogical Society of America, Washington, D.C.
101. Johnson, D.,, B. Chiswell, and, K. Ohalloran. 1995. Microorganisms and manganese cycling in a seasonally stratified freshwater dam. Water Res. 29:27392745.
102. Jones, J. G. 1983. A note on the isolation and enumeration of bacteria which deposit and reduce ferric iron. J. Appl. Bacteriol. 54:305310.
103. Jorgensen, B. B. 1989. Biogeochemistry of chemoautotrophic bacteria, p. 117–146. In H. G. Schlegel and, B. Bowien (ed.), Biochemistry of Autotrophic Bacteria. Science Tech Publishers, Madison, Wis.
104. 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. 1:1128.
105. Kashefi, K.,, D. E. Holmes,, A. L. Reysenbach, and, D. R. Lovley. 2002. Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov. Appl. Environ. Microbiol. 68:17351742.
106. Kepkay, P. E. 1985. Kinetics of microbial manganese oxidation and trace-metal binding in sediments—results from an in situ dialysis technique. Limnol. Oceanogr. 30:713726.
107. Kepkay, P. E. 1985. Microbial manganese oxidation and nitrification in relation to the occurrence of macrophyte roots in a lacustrine sediment. Hydrobiologia 128:135142.
108. Klinkhammer, G. P. 1980. Early diagenesis in sediments from the eastern equatorial Pacific. II. Pore water metal results. Earth Planet. Sci. Lett. 49:81101.
109. Konhauser, K. O.,, T. Hamade,, R. Raiswell,, R. C. Morris,, F. G. Ferris,, G. Southam, and, D. E. Canfield. 2002. Could bacteria have formed the Precambrian banded iron formations? Geology 30:10791082.
110. Konhauser, K. O.,, D. K. Newman, and, A. Kappler. 2005. The potential significance of microbial Fe(III) reduction during deposition of Precambrian banded iron formations. Geobiology 3:167177.
111. Koretsky, C. M.,, C. M. Moore,, K. L. Lowe,, C. Meile,, T. J. Dichristina, and, P. Van Cappellen. 2003. Seasonal oscillation of microbial iron and sulfate reduction in salt-marsh sediments (Sapelo Island, GA, USA). Biogeo-chemistry 64:179203.
112. Koretsky, C. M.,, P. Van Cappellen,, T. J. DiChristina,, J. E. Kostka,, K. L. Lowe,, C. M. Moore,, A. N. Roychoudhury, and, E. Viollier. 2005. Salt marsh pore water geochemistry does not correlate with microbial community structure. Estuar. Coast. Shelf Sci. 62:233251.
113. Kostka, J. E.,, B. Gribsholt,, E. Petrie,, D. Dalton,, H. Skelton, and, E. Kristensen. 2002. The rates and pathways of carbon oxidation in bioturbated saltmarsh sediments. Limnol. Oceanogr. 2002:230240.
114. Kostka, J. E.,, E. Haefele,, R. Vieweger, and, J. W. Stucki. 1999. Respiration and dissolution of iron(III)-containing clay minerals by bacteria. Environ. Sci. Technol. 33:31273133.
115. Kostka, J. E.,, and G. W. Luther III. 1994. Partitioning and speciation of solid phase iron in saltmarsh sediments. Geochim. Cosmochim. Acta 58:17011710.
116. Kostka, J. E.,, G. W. Luther, and, K. H. Nealson. 1995. Chemical and biological reduction of Mn(III)-pyrophosphate complexes: potential importance of dissolved Mn(III) as an environmental oxidant. Geochim. Cosmochim. Acta 59:885894.
117. Kostka, J. E.,, and K. N. Nealson. 1998. Isolation, cultivation, and characterization of iron- and manganese-reducing bacteria, p. 58–78. In R. S. Burlage,, R. Atlas,, D. Stahl,, G. Geesey, and, G. Sayler (ed.), Techniques in Microbial Ecology. Oxford University Press, Oxford, United Kingdom.
118. Kostka, J. E.,, A. Roychoudhury, and, P. VanCappellen. 2002. Rates and controls of anaerobic microbial respiration across spatial and temporal gradients in saltmarsh sediments. Biogeochemistry 60:4976.
119. Kostka, J. E.,, B. Thamdrup,, R. N. Glud, and, D. E. Canfield. 1999. Rates and pathways of carbon oxidation in permanently cold arctic sediments. Mar. Ecol. Prog. Ser. 180:721.
120. Kucera, S.,, and R. S. Wolfe. 1957. A selective enrichment method for Gallionella ferruginea. J. Bacteriol. 74:344349.
121. Lack, J. G.,, S. K. Chaudhuri,, R. Chakraborty,, L. A. Achenbach, and, J. D. Coates. 2002. Anaerobic biooxidation of Fe(II) by Dechlorosoma suillum. Microb. Ecol. 43:424431.
122. Lack, J. G.,, S. K. Chaudhuri,, S. D. Kelly,, K. M. Kemner,, S. M. O’Connor, and, J. D. Coates. 2002. Immobilization of radionuclides and heavy metals through anaerobic bio-oxidation of Fe(II). Appl. Environ. Microbiol. 68:27042710.
123. Landa, E. R.,, E. J. P. Phillips, and, D. R. Lovley. 1991. Release of 226Ra from uranium mill tailings by microbial Fe(III) reduction. Appl. Geochem. 6:647652.
124. Larocque, A. C. L.,, and P. E. Rasmussen. 1998. An overview of trace metals in the environment, from mobilization to remediation. Environ. Geol. 33:8591.
125. Lee, B. G.,, and N. S. Fisher. 1993. Microbially mediated cobalt oxidation in seawater revealed by radiotracer experiments. Limnol. Oceanogr. 38:15931602.
126. Lee, Y.,, and B. M. Tebo. 1994. Cobalt(II) oxidation by the marine manganese(II)-oxidizing Bacillus sp. strain SG-1. Appl. Environ. Microbiol. 60:29492957.
127. Lienemann, C. P.,, M. Taillefert,, D. Perret, and, J. F. Gaillard. 1997. Association of cobalt and manganese in aquatic systems: chemical and microscopic evidence. Geochim. Cosmochim. Acta 61:14371446.
128. Lin, W. C.,, M. V. Coppi, and, D. R. Lovley. 2004. Geobacter sulfurreducens can grow with oxygen as a terminal electron acceptor. Appl. Environ. Microbiol. 70:25252528.
129. Lloyd, J. R. 2003. Microbial reduction of metals and radionuclides. FEMS Microbiol. Rev. 27:411425.
130. Lovley, D. R. 1991. Dissimilatory Fe(III) and Mn(IV) reduction. Microbiol. Rev. 55:259287.
131. Lovley, D. R. 1993. Dissimilatory metal reduction. Annu. Rev. Microbiol. 47:263290.
132. Lovley, D. R. 1987. Organic matter mineralization with the reduction of ferric iron: a review. Geomicrobiol. J. 5:375399.
133. Lovley, D. R.,, S. J. Giovannoni,, D. C. White,, J. E. Champine,, E. J. P. Phillips,, Y. A. Gorby, and, S. Goodwin. 1993. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch. Microbiol. 159:336344.
134. Lovley, D. R.,, D. E. Holmes, and, K. P. Nevin. 2004. Dissimilatory Fe(III) and Mn(IV) reduction. Adv. Microb. Physiol. 49:219286.
135. Lovley, D. R.,, and E. J. P. Phillips. 1986. Availability of ferric iron for microbial reduction in bottom sediments of the freshwater tidal Potomac River. Appl. Environ. Microbiol. 52:751757.
136. Lovley, D. R.,, and E. J. P. Phillips. 1991. Enzymatic versus nonenzymatic mechanisms for Fe(III) reduction in aquatic sediments. Environ. Sci. Technol. 25:10621067.
137. Lovley, D. R.,, and E. J. P. Phillips. 1988. Manganese inhibition of microbial iron reduction in anaerobic sediments. Geomicrobiol. J. 6:145155.
138. Lovley, D. R.,, and E. J. P. Phillips. 1994. Novel processes for anaerobic sulfate production from elemental sulfur by sulfate-reducing bacteria. Appl. Environ. Microbiol. 60:23942399.
139. Lovley, D. R.,, and E. J. P. Phillips. 1987. Rapid assay for microbially reducible ferric iron in aquatic sediments. Appl. Environ. Microbiol. 53:15361540.
140. Lovley, D. R.,, E. J. P. Phillips,, Y. A. Gorby, and, E. R. Landa. 1991. Microbial reduction of uranium. Nature 350:413416.
141. Lovley, D. R.,, E. E. Roden,, E. J. P. Phillips, and, J. C. Woodward. 1993. Enzymatic iron and uranium reduction by sulfate-reducing bacteria. Mar. Geol. 113:4153.
142. Lowe, K. L.,, T. J. Dichristina,, A. N. Roychoudhury, and, P. V. Cappellen. 2000. Microbiological and geo-chemical characterization of microbial Fe(III) reduction in salt marsh sediments. Geomicrobiol. J. 17:163176.
143. Luther, G. W.,, D. B. Nuzzio, and, J. F. Wu. 1994. Speciation of manganese in Chesapeake Bay waters by voltammetric methods. Anal. Chim. Acta 284:473480.
144. Luther, G. W.,, P. A. Shellenbarger, and, P. J. Brendel. 1996. Dissolved organic Fe(III) and Fe(II) complexes in salt marsh porewaters. Geochim. Cosmochim. Acta 60:951960.
145. Madigan, M. T.,, and J. M. Martinko. 2006. Brock Biology of Microorganisms, 11th ed. Prentice Hall, Upper Saddle River, N.J.
146. Malasarn, D.,, C. W. Saltikov,, K. M. Campbell,, J. M. Santini,, J. G. Hering, and, D. K. Newman. 2004. arrA is a reliable marker for As(V) respiration. Science 306:455.
147. Mandernack, K. W.,, and B. M. Tebo. 1993. Manganese scavenging and oxidation at hydrothermal vents and in vent plumes. Geochim. Cosmochim. Acta 57:39073923.
148. Megonigal, J. P.,, M. E. Hines, and, P. T. Visscher. 2004. Anaerobic metabolism: linkages to trace gases and aerobic processes, p. 317–424. In W. H. Schlesinger (ed.), Biogeochemistry. Elsevier-Pergamon, Oxford, United Kingdom.
149. Millero, F. J.,, S. Sotolongo, and, M. Izaguirre. 1987. The oxidation kinetics of Fe(II) in seawater. Geochim. Cosmochim. Acta 51:793801.
150. Miyajima, T. 1992. Biological manganese oxidation in a lake. 1. Occurrence and distribution of Metallogenium sp and its kinetic properties. Arch. Hydrobiol. 124:317335.
151. Miyajima, T. 1992. Biological manganese oxidation in a lake. 2. A thermodynamic consideration of the habitat utilization of Metallogenium sp. Arch. Hydrobiol. 124:411426.
152. Moffett, J. W.,, and J. Ho. 1996. Oxidation of cobalt and manganese in seawater via a common microbially catalyzed pathway. Geochim. Cosmochim. Acta 60:34153424.
153. Munch, J. C.,, and J. C. G. Ottow. 1983. Reductive transformation mechanism of ferric oxides in hydromorphic soils. Ecol. Bull. 35:383394.
154. Murray, J. W.,, and P. G. Brewer. 1977. Mechanism of removal of manganese, iron, and other trace metals from seawater, p. 291–325. In G. P. Glasby (ed.), Marine Manganese Deposits. Elsevier, Amsterdam, The Netherlands.
155. Murray, J. W.,, L. A. Codispoti, and, G. E. Friedrich. 1995. Oxidation-reduction environments—the suboxic zone in the Black Sea. Adv. Chem. Ser. 244:157176.
156. Nealson, K. H.,, and D. Saffarini. 1994. Iron and manganese in anaerobic respiration: environmental significance, physiology, and regulation. Annu. Rev. Microbiol. 48:311343.
157. Neretin, L. N.,, C. Pohl,, G. Jost,, T. Leipe, and, F. Pollehne. 2003. Manganese cycling in the Gotland Deep, Baltic Sea. Mar. Chem. 82:125143.
158. Neubauer, S. C.,, D. Emerson, and, J. P. Megonigal. 2002. Life at the energetic edge: kinetics of circumneutral iron oxidation by lithotrophic iron-oxidizing bacteria isolated from the wetland-plant rhizosphere. Appl. Environ. Microbiol. 68:39883995.
159. Neubauer, S. C.,, D. Emerson, and, J. P. Megonigal. Microbial oxidation and reduction of iron in the root zone and mobility of heavy metals. In A. Violante,, P. M. Huang, and, G. Stotzky (ed.), Biophysico-Chemical Processes of Heavy Metals and Metalloids in Soil Environments, in press. John Wiley & Sons, Hoboken, N.J.
160. Neubauer, S. C.,, K. Givler,, S. K. Valentine, and, J. P. Megonigal. 2005. Seasonal patterns and plant-mediated controls of subsurface wetland biogeochemistry. Ecology 86:33343344.
161. Nevin, K. P.,, and D. R. Lovley. 2002. Mechanisms of Fe(III) oxide reduction in sedimentary environments. Geomicrobiol. J. 19:141159.
162. Nogales, B.,, K. N. Timmis,, D. B. Nedwell, and, A. M. Osborn. 2002. Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA. Appl. Environ. Microbiol. 68:50175025.
163. Northup, D. E.,, S. M. Barns,, L. E. Yu,, M. N. Spilde,, R. T. Schelble,, K. E. Dano,, L. J. Crossey,, C. A. Connolly,, P. J. Boston,, D. O. Natvig, and, C. N. Dahm. 2003. Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider caves. Environ. Microbiol. 5:10711086.
164. Oremland, R. S.,, and D. G. Capone. 1988. Use of specific inhibitors in biogeochemistry and microbial ecology. Adv. Microb. Ecol. 10:285383.
165. Oremland, R. S.,, and J. Stolz. 2000. Dissimilatory reduction of selenate and arsenate in nature, p. 199–224. In D. R. Lovley (ed.), Environmental Microbe-Metal Interactions. ASM Press, Washington, D.C.
166. Oremland, R. S.,, and J. F. Stolz. 2005. Arsenic, microbes and contaminated aquifers. Trends Microbiol. 13:4549.
167. Oremland, R. S.,, and J. F. Stolz. 2003. The ecology of arsenic. Science 300:939943.
168. Ortiz-Bernad, I.,, R. T. Anderson,, H. A. Vrionis, and, D. R. Lovley. 2004. Vanadium respiration by Geobacter metallireducens: novel strategy for in situ removal of vanadium from groundwater. Appl. Environ. Microbiol. 70:30913095.
169. Parker, D. L.,, G. Sposito, and, B. M. Tebo. 2004. Manganese(III) binding to a pyoverdine siderophore produced by a manganese(II)-oxidizing bacterium. Geochim. Cosmochim. Acta 68:48094820.
170. Phillips, E. J. P.,, and D. R. Lovley. 1987. Determination of Fe(III) and Fe(II) in oxalate extracts of sediments. Soil Sci. Soc. Am. J. 51:938941.
171. Phillips, E. J. P.,, D. R. Lovley, and, E. E. Roden. 1993. Composition of non-microbially reducible Fe(III) in aquatic sediments. Appl. Environ. Microbiol. 59:27272729.
172. Ponnamperuma, F. N. 1972. The chemistry of submerged soils. Adv. Agron. 24:2996.
173. Post, J. E. 1999. Manganese oxide minerals: crystal structures and economic and environmental significance. Proc. Natl. Acad. Sci. USA 96:34473454.
174. Postma, D. 1985. Concentration of Mn and separation from Fe in sediments. I. Kinetics and stoichiometry of the reaction between birnessite and dissolved Fe(II) at 10oC. Geochim. Cosmochim. Acta 49:10231033.
175. Poulton, S. W.,, and R. Raiswell. 2002. The low-temperature geochemical cycle of iron: from continental fluxes to marine sediment deposition. Am. J. Sci. 302:774805.
176. Purdy, K. J.,, M. A. Munson,, T. Cresswell-Maynard,, D. B. Nedwell, and, T. M. Embley. 2003. Use of 16S rRNA-targeted oligonucleotide probes to investigate function and phylogeny of sulphate-reducing bacteria and methanogenic archaea in a UK estuary. FEMS Microbiol. Ecol. 44:361371.
177. Ramsing, N. R.,, H. Fossing,, T. G. Ferdelman,, F. Andersen, and, B. Thamdrup. 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. 62:13911404.
178. Raskin, L.,, J. M. Stromley,, B. Rittmann, and, D. A. Stahil. 1994. Group-specific 16S rRNA hybidization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60:12321240.
179. Ratering, S.,, and S. Schnell. 2000. Localization of iron-reducing activity in paddy soil by profile studies. Biogeochemistry 48:341365.
180. Rentz, J. A.,, C. Kraiya,, G. W. Luther, and, D. Emerson. 2005. Iron cycle in a neutrophilic iron seep. Astrobiology 5:292.
181. Revsbech, N. P. 1989. An oxygen microelectrode with guard cathode. Limnol. Oceanogr. 34:472476.
182. Rhine, E. D.,, E. Garcia-Dominguez,, C. D. Phelps, and, L. Y. Young. 2005. Environmental microbes can speciate and cycle arsenic. Environ. Sci. Technol. 39:95699573.
183. Rittle, K. A.,, J. I. Drever, and, P. J. S. Colberg. 1995. Precipitation of arsenic during bacterial sulfate reduction. Geomicrobiol. J. 13:111.
184. Roden, E. E. 2005. Unpublished data.
185. Roden, E. E.,, M. R. Leonardo, and, F. G. Ferris. 2002. Immobilization of strontium during iron biomineralization coupled to dissimilatory hydrous ferric oxide reduction. Geochim. Cosmochim. Acta 66:28232839.
186. Roden, E. E.,, and D. R. Lovley. 1993. Evaluation of 55Fe as a tracer of Fe(III) reduction in aquatic sediments. Geomicrobiol. J. 11:4956.
187. Roden, E. E.,, D. Sobolev,, B. Glazer, and, G. W. Luther. 2004. Potential for microscale bacterial Fe redox cycling at the aerobic-anaerobic interface. Geomicrobiol. J. 21:379391.
188. Roden, E. E.,, and R. G. Wetzel. 2002. Kinetics of microbial Fe(III) oxide reduction in freshwater wetland sediments. Limnol. Oceanogr. 47:198211.
189. Roden, E. E.,, and R. G. Wetzel. 1996. Organic carbon oxidation and suppression of methane production by microbial Fe(III) oxide reduction in vegetated and unvegetated freshwater wetland sediments. Limnol. Oceanogr. 41:17331748.
190. Rodrigo, M. A.,, E. Vicente, and, M. R. Miracle. 2000. The role of light and concentration gradients in the vertical stratification and seasonal development of phototrophic bacteria in a meromictic lake. Arch. Hydrobiol. 148:533548.
191. Rogers, D. R.,, C. M. Santelli, and, K. J. Edwards. 2003. Geomicrobiology of deep-sea deposits; estimating community diversity from low-temperature seafloor rocks and minerals. Geobiology 1:109118.
192. Röling, W. F. M.,, B. M. van Breukelen,, M. Braster,, B. Lin, and, H. W. van Verseveld. 2001. Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer. Appl. Environ. Microbiol. 67:46194629.
193. Rooney-Varga, J. N.,, R. T. Anderson,, J. L. Fraga,, D. Ringelberg, and, D. R. Lovley. 1999. Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl. Environ. Microbiol. 65:30563063.
194. Rosson, R. A.,, B. M. Tebo, and, K. H. Nealson. 1984. Use of poisons in determination of microbial manganese binding rates in seawater. Appl. Environ. Microbiol. 47:740745.
195. Schippers, A.,, and B. B. Jorgensen. 2001. Biogeochemistry of pyrite and iron sulfide oxidation in marine sediments. Geochim. Cosmochim. Acta 66:8592.
196. Schippers, A.,, L. N. Neretin,, G. Lavik,, T. Leipe, and, F. Pollehne. 2005. Manganese(II) oxidation driven by lateral oxygen intrusions in the western Black Sea. Geochim. Cosmochim. Acta 69:22412252.
197. Schwertmann, U. 1964. Differenzierung der Eisenoxide des Bodens durch Extraktion mit Ammoniumoxalatlosung. Z. Pflanzenernaehr. Dueng. Bodenkd. 105:194202.
198. Senko, J. M.,, Y. Mohamed,, T. A. Dewers, and, L. R. Krumholz. 2005. Role for Fe(III) minerals in nitrate-dependent microbial U(IV) oxidation. Environ. Sci. Technol. 39:25292536.
199. Senn, D. B.,, and H. F. Hemond. 2002. Nitrate controls on iron and arsenic in an urban lake. Science 296:23732376.
200. Shelobolina, E. S.,, R. R. Anderson,, Y. N. Vodyanitskii,, A. M. Sivtsov,, R. Yuretich, and, D. R. Lovley. 2004. Importance of clay size minerals for Fe(III) respiration in a petroleum-contaminated aquifer. Geobiology 2:6776.
201. Shelobolina, E. S.,, C. Gaw-VanPraagh, and, D. R. Lovley. 2003. Use of ferric and ferrous iron containing minerals for respiration by Desulfitobacterium frappieri. Geomicrobiol. J. 20:143156.
202. Shelobolina, E. S.,, S. M. Pickering, and, D. R. Lovley. 2005. Fe-cycle bacteria from industrial clays mined in Georgia, USA. Clays Clay Min. 53:580586.
203. Shiller, A. M.,, and T. H. Stephens. 2005. Microbial manganese oxidation in the lower Mississippi River: methods and evidence. Geomicrobiol. J. 22:117125.
204. Siering, P. L.,, and W. C. Ghiorse. 1997. Development and application of 16S rRNA-targeted probes for detection of iron- and manganese-oxidizing sheathed bacteria in environmental samples. Appl. Environ. Microbiol. 63:644651.
205. Siering, P. L.,, and W. C. Ghiorse. 1997. PCR detection of a putative manganese oxidation gene (mofA) in environmental samples and assessment of mofA gene homology among diverse manganese-oxidizing bacteria. Geomicrobiol. J. 14:109125.
206. Sigg, L. 1994. Regulation of trace elements in lakes: the role of sedimentation, p. 177–197. In J. Buffle and, R. R. DeVitre (ed.), Chemical and Biological Regulation of Aquatic Systems. Lewis, Boca Raton, Fla.
207. Silver, S. 1997. The bacterial view of the periodic table: specific functions for all elements, p. 345–360. In J. F. Banfield and, K. H. Nealson (ed.), Geomicrobiology: Interactions between Microbes and Minerals, vol. 35. Mineralogical Society of America, Washington, D.C.
208. Singer, P. C.,, and W. Stumm. 1972. Acid mine drainage—the rate limiting step. Science 167:11211123.
209. Snoeyenbos-West, O. L.,, K. P. Nevin,, R. T. Anderson, and, D. R. Lovley. 2000. Enrichment of Geobacter species in response to stimulation of Fe(III) reduction in sandy aquifer sediments. Microb. Ecol. 39:153167.
210. Sobolev, D.,, and E. Roden. 2004. Characterization of a neutrophilic, chemolithoautotrophic Fe(II)-oxidizing β-Proteobacterium from freshwater wetland sediments. Geomicrobiol. J. 21:110.
211. Sobolev, D.,, and E. E. Roden. 2002. Evidence for rapid microscale bacterial redox cycling of iron in circumneutral environments. Antonie Leeuwenhoek 181:587597.
212. Sobolev, D.,, and E. E. Roden. 2001. Suboxic deposition of ferric iron by bacteria in opposing gradients of Fe(II) and oxygen at circumneutral pH. Appl. Environ. Microbiol. 67:13281334.
213. Sorensen, J. 1982. Reduction of ferric iron in anaerobic, marine sediment and interaction with reduction of nitrate and sulfate. Appl. Environ. Microbiol. 43:319324.
214. Spilde, M. N.,, D. E. Northup,, P. J. Boston,, R. T. Schelble,, K. E. Dano,, L. J. Crossey, and, C. N. Dahm. 2005. Geomicrobiology of cave ferromanganese deposits: a field and laboratory investigation. Geomicrobiol. J. 22:99116.
215. Stein, L. Y.,, G. Jones,, B. Alexander,, K. Elmund,, C. Wright-Jones, and, K. H. Nealson. 2002. Intriguing microbial diversity associated with metal-rich particles from a freshwater reservoir. FEMS Microbiol. Ecol. 42:431440.
216. Stein, L. Y.,, M. T. LaDuc,, T. J. Grundl, and, K. H. Nealson. 2001. Bacterial and archael populations associated with freshwater ferromanganous micronodules and sediments. Environ. Microbiol. 3:1018.
217. Stone, A. T.,, and J. J. Morgan. 1987. Reductive dissolution of metal oxides, p. 221–254. In W. Stumm (ed.), Aquatic Surface Chemistry. John Wiley & Sons, New York, N.Y.
218. Stookey, L. L. 1970. Ferrozine—a new spectrophotometric reagent for iron. Anal. Chem. 42:779781.
219. Straub, K. L.,, M. Benz,, B. Schink, and, F. Widdel. 1996. Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Appl. Environ. Microbiol. 62:14581460.
220. Straub, K. L.,, and B. E. E. Buchholz-Cleven. 1998. Enumeration and detection of anaerobic ferrous-iron-oxidizing, nitrate-reducing bacteria from diverse European sediments. Appl. Environ. Microbiol. 64:48464856.
221. Straub, K. L.,, F. A. Rainey, and, F. Widdel. 1999. Rhodovulum iodosum sp. nov, and Rhodovulum robiginosum sp. nov., two new marine phototrophic ferrous-iron-oxidizing purple bacteria. Int. J. Syst. Evol. Microbiol. 49:729735.
222. Straub, K. L.,, W. A. Schonhuber,, B. E. E. Buchholz-Cleven, and, B. Schink. 2004. Diversity of ferrous iron-oxidizing, nitrate-reducing bacteria and their involvement in oxygen-independent iron cycling. Geomicrobiol. J. 21:371378.
223. Stults, J. R.,, O. Snoeyenbos-West,, B. Methe,, D. R. Lovley, and, D. P. Chandler. 2001. Application of the 5′ fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments. Appl. Environ. Microbiol. 67:27812789.
224. Stumm, W.,, and J. J. Morgan. 1996. Aquatic Chemistry, 2nd ed. John Wiley & Sons, Inc., New York, N.Y.
225. Stumm, W.,, and B. Sulzberger. 1992. The cycling of iron in natural environments: considerations based on laboratory studies of heterogeneous redox processes. Geochim. Cosmochim. Acta 56:32333257.
226. Sunda, W. G. 2000. Trace metal-phytoplankton interactions in aquatic systems, p. 79–107. In D. R. Lovley (ed.), Environmental Micorbe-Metal Interactions. ASM Press, Washington, D.C.
227. Sunda, W. G.,, and D. J. Kieber. 1994. Oxidation of humic substances by manganese oxides yields low-molecular-weight organic substrates. Nature 367:6264.
228. Sundby, B.,, L. G. Anderson,, P. O. J. Hall,, A. Iverfeldt,, M. M. Rutgersvanderloeff, and, S. F. G. Westerlund. 1986. The effect of oxygen on release and uptake of cobalt, manganese, iron and phosphate at the sediment-water interface. Geochim. Cosmochim. Acta 50:12811288.
229. Suter, D.,, C. Siffert,, B. Sulzberger, and, W. Stumm. 1988. Catalytic dissolution of iron(III) (hydr)oxides by oxalic acid in the presence of Fe(II). Naturwissenschaften 75:571573.
230. Taillefert, M.,, B. J. MacGregor,, J. F. Gaillard,, C. P. Lienemann,, D. Perret, and, D. A. Stahl. 2002. Evidence for a dynamic cycle between Mn and Co in the water column of a stratified lake. Environ. Sci. Technol. 36:468476.
231. Taylor, G. T.,, M. Iabichella,, T. Y. Ho,, M. I. Scranton,, R. C. Thunell,, F. Muller-Karger, and, R. Varela. 2001. Chemoautotrophy in the redox transition zone of the Cariaco Basin: a significant midwater source of organic carbon production. Limnol. Oceanogr. 2001:148163.
232. Teasdale, P. R.,, S. Hayward, and, W. Davison. 1999. In situ, high-resolution measurement of dissolved sulfide using diffusive gradients in thin films with computer-imaging densitometry. Anal. Chem. 71:21862191.
233. Tebo, B. M. 1991. Manganese(II) oxidation in the suboxic zone of the Black Sea. Deep-Sea Res. 38:S883S905.
234. Tebo, B. M.,, J. R. Bargar,, B. G. Clement,, G. J. Dick,, K. J. Murray,, D. Parker,, R. Verity, and, S. M. Webb. 2004. Biogenic manganese oxides: properties and mechanisms of formation. Annu. Rev. Earth Planet. Sci. 32:287328.
235. Tebo, B. M.,, and L. M. He. 1999. Microbially mediated oxidation precipitation reactions, p. 393–414. In D. L. Sparks and, T. J. Grundl (ed.), Mineral-Water Interfacial Reactions. American Chemical Society, Washington, D.C.
236. Tebo, B. M.,, H. A. Johnson,, J. K. McCarthy, and, A. S. Templeton. 2005. Geomicrobiology of manganese(II) oxidation. Trends Microbiol. 13:421428.
237. Tebo, B. M.,, K. H. Nealson,, S. Emerson, and, L. Jacobs. 1984. Microbial mediation of Mn(II) and Co(II) precipitation at the O2/H2S interfaces in two anoxic fjords. Limnol. Oceanogr. 29:12471258.
238. Templeton, A. S.,, H. Staudigel, and, B. M. Tebo. 2005. Diverse Mn(II)-oxidizing bacteria isolated from submarine basalts at Loihi Seamount. Geomicrobiol. J. 22:127139.
239. Thamdrup, B. 2000. Bacterial manganese and iron reduction in aquatic sediments. Adv. Microb. Ecol. 16:4184.
240. Thamdrup, B.,, and D. E. Canfield. 2000. Benthic respiration in aquatic sediments, p. 86–103. In O. E. Sala,, R. B. Jackson,, H. A. Mooney, and, R. W. Howarth (ed.), Methods in Ecosystem Science. Springer, New York, N.Y.
241. Thamdrup, B.,, and D. E. Canfield. 1996. Pathways of carbon oxidation in continental margin sediments off central Chile. Limnol. Oceanogr. 41:16291650.
242. Thamdrup, B.,, K. Finster,, J. W. Hansen, and, F. Bak. 1993. Bacterial disproportionation of elemental sulfur coupled to chemical reduction of iron or manganese. Appl. Environ. Microbiol. 59:101108.
243. Thamdrup, B.,, H. Fossing, and, B. B. Jorgensen. 1994. Manganese, iron, and sulfur cycling in a coastal marine sediment, Aarhus Bay, Denmark. Geochim. Cosmochim. Acta 58:51155129.
244. Thamdrup, B.,, R. N. Glud, and, J. W. Hansen. 1994. Manganese oxidation and in situ manganese fluxes from a coastal sediment. Geochim. Cosmochim. Acta 58:25632570.
245. Thamdrup, B.,, R. Rossello-Mora, and, R. Amann. 2000. Microbial manganese and sulfate reduction in Black Sea shelf sediments. Appl. Environ. Microbiol. 66:28882897.
246. Thomsen, U.,, B. Thamdrup,, D. A. Stahl, and, D. E. Canfield. 2004. Pathways of organic carbon oxidation in a deep lacustrine sediment, Lake Michigan. Limnol. Oceanogr. 49:20462057.
247. Thorseth, I. H.,, T. Torsvik,, V. Torsvik,, F. L. Daae,, R. Pedersen, and, K.-S. Party. 2001. Diversity of life in ocean floor basalt. Earth Planet. Sci. Lett. 194:3137.
248. vanBreemen, N. 1988. Effects of seasonal redox processes involving iron on the chemistry of periodically reduced soils, p. 797–809. In J. W. Stucki,, B. A. Goodman, and, U. Schwertmann (ed.), Iron in Soils and Clay Minerals. D. Reidel Publishing Co., Boston, Mass.
249. vanBreemen, N. 1988. Long-term chemical, mineralogical and morphological effects of iron-redox processes in periodically flooded soils, p. 811–823. In J. W. Stucki,, B. A. Goodman, and, U. Schwertmann (ed.), Iron in Soils and Clay Minerals. D. Reidel Publishing Co., Boston, Mass.
250. VanCappellen, P.,, E. Viollier, and, A. Roychoudhury. 1998. Biogeochemical cycles of manganese and iron at the oxic-anoxic transition of a stratified marine basin (Orca Basin, Gulf of Mexico). Environ. Sci. Technol. 32:29312939.
251. VanCappellen, P.,, and Y. Wang. 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. 296:197243.
252. VanCappellen, P.,, and Y. Wang. 1995. Metal cycling in surface sediments: modeling the interplay of transport and reaction, p. 21–64. In H. E. Allen (ed.), Metal Contaminated Aquatic Sediments. Ann Arbor Press, Chelsea, Mich.
253. Vester, F.,, and K. Invorsen. 1998. Improved most-probable-number method to detect sulfate-reducing bacteria with natural media and a radiotracer. Appl. Environ. Microbiol. 64:17001707.
254. Villalobos, M.,, and B. M. Tebo. 2005. Introduction: advances in the geomicrobiology and biogeochemistry of manganese and iron oxidation. Geomicrobiol. J. 22:7778.
255. Viollier, E.,, C. Rabouille,, S. E. Apitz,, E. Breuer,, G. Chaillou,, K. Dedieu,, Y. Furukawa,, C. Grenz,, P. Hall,, F. Janssen,, J. L. Morford,, J. C. Poggiale,, S. Roberts,, T. Shimmield,, M. Taillefert,, A. Tengberg,, F. Wenzhofer, and, U. Witte. 2003. Benthic biogeochemistry: state of the art technologies and guidelines for the future of in situ survey. J. Exp. Mar. Biol. Ecol. 285:531.
256. Wagner, M.,, A. Loy,, M. Klein,, N. Lee,, N. B. Ramsing,, D. A. Stahl, and, M. W. Friedrich. 2005. Functional marker genes for identification of sulfate-reducing prokaryotes. Methods Enzymol. 397:469489.
257. Waite, T. D. 1988. Photochemical effects on the mobility and fate of heavy metals in the aquatic environment. Environ. Technol. Lett. 9:977982.
258. Walker, J. C. G. 1984. Suboxic diagenesis in banded iron formations. Nature 309:340342.
259. Wallmann, K.,, K. Hennies,, I. Konig,, W. Petersen, and, H. D. Knauth. 1993. New procedure for determining reactive Fe(III) and Fe(II) minerals in sediments. Limnol. Oceanogr. 38:18031812.
260. Wan, J.,, T. K. Tokunaga,, E. Brodie,, Z. Wang,, Z. Zheng,, D. Herman,, T. C. Hazen,, M. K. Firestone, and, S. R. Sutton. 2005. Reoxidation of bioreduced uranium under reducing conditions. Environ. Sci. Technol. 39:61626169.
261. Wang, Y. T. 2000. Microbial reduction of chromate, p. 225–235. In D. R. Lovley (ed.), Environmental Microbe-Metal Interactions. ASM Press, Washington, D.C.
262. Ward, B. B.,, and G. D. O’Mullan. 2005. Community level analysis: genetic and biogeochemical approaches to investigate community composition and function in aerobic ammonia oxidation. Methods Enzymol. 397:395413.
263. Warner, K. A.,, E. E. Roden, and, J. C. Bonzongo. 2003. Microbial mercury transformations in anoxic freshwater sediments under iron-reducing and other electron-accepting conditions. Environ. Sci. Technol. 37:21592165.
264. Webb, S. M.,, G. J. Dick,, J. R. Bargar, and, B. M. Tebo. 2005. Evidence for the presence of Mn(III) intermediates in the bacterial oxidation of Mn(II). Proc. Natl. Acad. Sci. USA 102:55585563.
265. Weber, K. A.,, P. F. Churchill,, M. M. Urrutia,, R. K. Kukkadapu, and, E. E. Roden. 2006. Anaerobic redox cycling of iron by freshwater sediment microorganisms. Environ. Microbiol. 8:100113.
266. Weber, K. A.,, F. W. Picardal, and, E. E. Roden. 2001. Microbially-catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds. Environ. Sci. Technol. 35:16441650.
267. Weber, K. A.,, J. Pollock,, K. A. Cole,, S. M. O’Connor,, L. A. Achenbach, and, J. D. Coates. 2006. Anaerobic nitrate-dependent iron(II) bio-oxidation by a novel lithoautotrophic betaproteobacterium, strain 2002. Appl. Environ. Microbiol. 72:686694.
268. Wedepohl, K. H. 1995. The composition of the continental-crust. Geochim. Cosmochim. Acta 59:12171232.
269. Weiss, J. V.,, D. Emerson,, S. M. Backer, and, J. P. Megonigal. 2003. Enumeration of Fe(II)-oxidizing and Fe(III)-reducing bacteria in the root zone of wetland plants: implications for a rhizosphere iron cycle. Biogeo-chemistry 64:7796.
270. Weiss, J. V.,, D. Emerson, and, J. P. Megonigal. 2005. Rhizosphere iron(III) deposition and reduction in a Juncus effusus L.-dominated wetland. Soil. Sci. Soc. Am. J. 69:18611870.
271. Weiss, J. V.,, D. Emerson, and, P. Megonigal. 2004. The role of geochemical composition on the microbial reduction potential of Fe(III) pools in wetlands: comparison of the rhizosphere and bulk soil. FEMS Microbiol. Ecol. 48:89100.
272. Widdel, F.,, S. Schnell,, S. Heising,, A. Ehrenreich,, B. Assmus, and, B. Schink. 1993. Ferrous iron oxidation by anoxygenic phototrophic bacteria. Nature 362:834835.
273. Wielinga, B.,, M. M. Mizuba,, C. M. Hansel, and, S. Fendorf. 2001. Iron promoted reduction of chromate by dissimilatory iron-reducing bacteria. Environ. Sci. Technol. 35:522527.
274. Wilson, K. H.,, W. J. Wilson,, J. L. Radosevich,, T. Z. DeSantis,, V. S. Viswanathan,, T. A. Kuczmarski, and, G. L. Andersen. 2002. High-density microarray of small-subunit ribosomal DNA probes. Appl. Environ. Microbiol. 68:25352541.
275. Zachara, J. M.,, J. K. Fredrickson,, S. C. Smith, and, P. L. Gassman. 2001. Solubilization of Fe(III) oxide-bound trace metals by a dissimilatory Fe(III) reducing bacterium. Geochim. Cosmochim. Acta 65:7593.
276. Zobrist, J.,, P. R. Dowdle,, J. A. Davis, and, R. S. Oremland. 2000. Mobilization of arsenite by dissimila-tory reduction of adsorbed arsenate. Environ. Sci. Technol. 34:47474753.
277. Zopfi, J.,, T. G. Ferdelman,, B. B. Jorgensen,, A. Teske, and, B. Thamdrup. 2001. Influence of water column dynamics on sulfide oxidation and other major biogeochemical processes in the chemocline of Mariager Fjord (Denmark). Mar. Chem. 74:2951.

Tables

Generic image for table
TABLE 1

Overview of metal biochemistry in aquatic environments

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44
Generic image for table
TABLE 2

Summary of reactions associated with Fe and Mn redox cycling in natural water and sediments

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44
Generic image for table
TABLE 3

Studies which have enumerated the abundance of culturable Fe- and Mn-reducing and -oxidizing microorganisms in aquatic environments

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44
Generic image for table
TABLE 4

Molecular biological studies of metal-reducing and metal-oxidizing microorganisms in aquatic environments

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44
Generic image for table
TABLE 5

Overview of connections between Fe and Mn redox transformations and the behaviors of other metals or metalloid elements in aquatic systems

Citation: Roden E, Emerson D. 2007. Microbial Metal Cycling in Aquatic Environments , p 540-562. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch44

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error