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Microbial dissolution of clay minerals as a source of iron and silica in marine sediments

Nature Geoscience volume 2, pages 221–225 (2009)Cite this article

Abstract

Interactions between microbes and minerals have the potential to contribute significantly to the global cycles of various elements, and serve as a link between the geosphere and life. In particular, the microbially mediated cycle of iron within marine sediments is closely tied to the carbon cycle. The dissolved iron that serves as a nutrient is thought to be primarily drawn from well-known pools of highly reactive, bioavailable iron and iron complexes. Iron contained within the crystal lattice of clay minerals, the most abundant materials found at the Earth’s surface, is not thought to be part of this pool. Here we analyse the mineral composition of Middle-Cambrian-aged mudstones from the western United States. We find intergrown mineral aggregates of quartz, pyrite and calcite. On the basis of mineral phase relationships and temperatures of crystallization derived from stable isotopes of oxygen, we infer that mineral dissolution driven by microbes released iron and silica to the surrounding sediment pore waters, and led to the subsequent precipitation of the observed minerals. The microbial extraction of structurally coordinated Fe3+ from clay minerals after their deposition in marine sediments may liberate a fraction of iron previously considered unavailable, and may be important in iron and silica cycling in marine sediments.

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Figure 1: Mineral aggregates.
Figure 2: Petrographic and SEM micrographs of mineral by-products of microbial respiration of Fe3+ from clay minerals, Wheeler Formation.

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References

  1. Lowenstam, H. A. On Biomineralization (Oxford Univ. Press, 1989).

    Google Scholar 

  2. Ehrlich, H. L. How microbes influence mineral growth and dissolution. Chem. Geol. 132, 5–9 (1996).

    Article  Google Scholar 

  3. Kostka, J. E., Stucki, J. W., Nealson, K. H. & Wu, J. Reduction of structural Fe(III) in smectite by a pure culture of Shewanella putrefaciens strain MR-1. Clays Clay Minerals 44, 522–529 (1996).

    Article  Google Scholar 

  4. Stucki, J. W. & Kostka, J. E. Microbial reduction of iron in smectite. Comptes Rendus Geosci. 338, 468–475 (2006).

    Google Scholar 

  5. Kim, J., Dong, H. L., Seabaugh, J., Newell, S. W. & Eberl, D. D. Role of microbes in the smectite-to-illite reaction. Science 303, 830–832 (2004).

    Article  Google Scholar 

  6. Buesseler, K. O., Andrews, J. E., Pike, S. M. & Charette, M. A. The effects of iron fertilization on carbon sequestration in the Southern Ocean. Science 304, 414–417 (2004).

    Article  Google Scholar 

  7. Nealson, K. H. & Saffarini, D. Iron and manganese in anaerobic respiration: Environmental significance, physiology, and regulation. Annu. Rev. Microbiol. 48, 311–343 (1994).

    Article  Google Scholar 

  8. Canfield, D. E. et al. Pathways of organic carbon oxidation in three continental margin sediments. Mar. Geol. 113, 27–40 (1993).

    Article  Google Scholar 

  9. Garrels, R. M. & Mackenzie, F. T. Evolution of Sedimentary Rocks Ch. 7 (W. W. Norton & Co, 1971).

    Google Scholar 

  10. Potter, P. E., Maynard, J. B. & Pedro, J. D. Mud And Mudstones: Introduction and Overview (Springer, 2005).

    Google Scholar 

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

    Google Scholar 

  12. Lyle, M. The brown–green color transition in marine sediments: A marker of the Fe(III)–Fe (II) redox boundary. Limnol. Oceanogr. 28, 1026–1033 (1983).

    Article  Google Scholar 

  13. Konig, I., Drodt, M., Suess, E. & Trautwein, A. X. Iron reduction through the tan-green colour transition in deep-sea sediments. Geochim. Cosmochim. Acta 61, 1679–1683 (1997).

    Article  Google Scholar 

  14. Leslie, B. W., Hammond, D. E., Berelson, W. M. & Lund, S. P. Diagenesis in anoxic sediments from the California continental borderland and its influence on iron, sulfur, and magnetite behaviour. J. Geophys. Res. 95, 4453–4470 (1990).

    Article  Google Scholar 

  15. Kostka, J. E. & Luther, G. W. Seasonal cycling of Fe in saltmarsh sediments. Biogeochemistry 29, 159–181 (1995).

    Article  Google Scholar 

  16. Canfield, D. E., Thamdrup, B. & Kristensen, E. Advances in marine biology. Aquatic Geomicrobiol. 48, 272–277 (2005).

    Google Scholar 

  17. Hower, J., Eslinger, E. V., Hower, M. E. & Perry, E. A. Mechanism of burial metamorphism of argillaceous sediment; 1, Mineralogical and chemical evidence. Geol. Soc. Am. Bull. 87, 725–737 (1976).

    Article  Google Scholar 

  18. Perry, E. & Hower, J. Burial diagenesis in Gulf Coast pelitic sediments. Clays Clay Minerals 18, 165–177 (1970).

    Article  Google Scholar 

  19. Freed, R. L. & Peacor, D. R. Geopressured shale and sealing effect of smectite to illite transition. Aapg Bull. Am. Assoc. Petrol. Geol. 73, 1223–1232 (1989).

    Google Scholar 

  20. Pollard, C. O. Semi-displacive mechanism for diagenetic alteration of mont-morillonite layers to illite layers. Geol. Soc. Am. Spec. Papers 134, 79–96 (1971).

    Article  Google Scholar 

  21. Drits, V. A., Sakharov, B. A., Lindgreen, H. & Salyn, A. Sequential structure transformation of illite-smectite-vermiculite during diagenesis of Upper Jurassic shales from the North Sea and Denmark. Clay Minerals 32, 351–371 (1997).

    Article  Google Scholar 

  22. Eslinger, E., Highsmith, P., Albers, D. & Demayo, B. Role of iron reduction in the conversion of smectite to illite in bentonites in the Disturbed Belt, Montana. Clays Clay Minerals 27, 327–338 (1979).

    Article  Google Scholar 

  23. Nadeau, P. H., Wilson, M. J., McHardy, W. J. & Tait, J. M. The conversion of smectite to illite during diagenesis: Evidence from some illitic clays from bentonites and sandstones. Mineral. Mag. 49, 393–400 (1985).

    Article  Google Scholar 

  24. Nadeau, P. H. & Bain, D. C. Composition of some smectites and diagenetic illitic clays and implications for their origin. Clays Clay Minerals 34, 455–464 (1986).

    Article  Google Scholar 

  25. Kostka, J. E., Dalton, D. D., Skelton, H., Dollhopf, S. & Stucki, J. W. Growth of iron(III)-reducing bacteria on clay minerals as the sole electron acceptor and comparison of growth yields on a variety of oxidized iron forms. Appl. Environ. Microbiol. 68, 6256–6262 (2002).

    Article  Google Scholar 

  26. Dong, H. L., Kostka, J. E. & Kim, J. Microscopic evidence for microbial dissolution of smectite. Clays Clay Minerals 51, 502–512 (2003).

    Article  Google Scholar 

  27. Lee, K., Kostka, J. E. & Stucki, J. W. Comparisons of structural Fe reduction in smectites by bacteria and dithionite: An infrared spectroscopic study. Clays Clay Minerals 54, 195–208 (2006).

    Article  Google Scholar 

  28. Kostka, J. E., Haefele, E., Viehweger, R. & Stucki, J. W. Respiration and dissolution of iron(III) containing clay minerals by bacteria. Environ. Sci. Tech. 33, 3127–3133 (1999).

    Article  Google Scholar 

  29. Zhang, G. X., Kim, J. W., Dong, H. L. & Sommer, A. J. Microbial effects in promoting the smectite to illite reaction: Role of organic matter intercalated in the interlayer. Am. Mineral. 92, 1401–1410 (2007).

    Article  Google Scholar 

  30. Li, Y. L. et al. Iron reduction and alteration of nontronite NAu-2 by a sulphate-reducing bacterium. Geochim. Cosmochim. Acta 68, 3251–3260 (2004).

    Article  Google Scholar 

  31. O’Reilly, S. E., Watkins, J. & Furukawa, Y. Secondary mineral formation associated with respiration of nontronite, NAu-1 by iron reducing bacteria. Geochem. Trans. 6, 67–76 (2005).

    Article  Google Scholar 

  32. Peacor, D. R. Diagenesis and low grade metamorphism of shales and slates. Rev. Mineral. 27, 335–380 (1992).

    Google Scholar 

  33. Tolmacheva, T. J., Danelian, T. & Popov, L. E. Evidence for 15 m.y. of continuous deep-sea biogenic siliceous sedimentation in early Paleozoic oceans. Geology 29, 755–758 (2001).

    Article  Google Scholar 

  34. Gaines, R. R. & Droser, M. L. New approaches to understanding the mechanics of Burgess Shale-type deposits: From the micrometre-scale to the global picture. Sedim. Record 3, 4–8 (2005).

    Article  Google Scholar 

  35. Rees, M. N. A fault-controlled trough through a carbonate platform; the Middle Cambrian House Range Embayment. Geol. Soc. Am. Bull. 97, 1054–1069 (1986).

    Article  Google Scholar 

  36. Totten, M. W. & Blatt, H. Alterations in the non-clay-mineral fraction of pelitic rocks across the diagenetic to low-grade metamorphic transition, Ouachita Mountains, Oklahoma and Arkansas. J. Sedim. Petrol. 63, 899–908 (1993).

    Google Scholar 

  37. Hendry, J. P., Pearson, M. J., Trewin, N. H. & Fallick, A. E. Jurassic septarian concretions from NW Scotland record interdependent bacterial, physical and chemical processes of marine mudrock diagenesis. Sedimentology 53, 537–565 (2006).

    Article  Google Scholar 

  38. Knauth, L. P. & Epstein, S. Hydrogen and oxygen isotope ratios in nodular and bedded cherts. Geochim. Cosmochim. Acta 40, 1095–1108 (1976).

    Article  Google Scholar 

  39. Clayton, R. N., Mayeda, T. K. & O’Neil, J. R. Oxygen isotope exchange between quartz and water. J. Geophys. Res. 77, 3057–3067 (1972).

    Article  Google Scholar 

  40. Wallmann, K. The geological water cycle and the evolution of marine delta O-18 values. Geochim. Cosmochim. Acta 65, 2469–2485 (2001).

    Article  Google Scholar 

  41. Veizer, J. et al. Oxygen isotope evolution of Phanerozoic seawater. Palaeogeogr. Palaeoclimatol. Palaeoecol. 132, 159–172 (1997).

    Article  Google Scholar 

  42. Jaffres, J. B. D., Shields, G. A. & Wallmann, K. The oxygen isotope evolution of seawater: A critical review of a long-standing controversy and an improved geological water cycle model for the past 3.4 billion years. Earth Sci. Rev. 83, 83–122 (2007).

    Article  Google Scholar 

  43. Canfield, D. E., Raiswell, R. & Bottrell, S. The reactivity of sedimentary iron minerals toward sulfide. Am. J. Sci. 292, 659–683 (1992).

    Article  Google Scholar 

  44. Favre, F., Stucki, J. W. & Boivin, P. Redox properties of structural Fe in ferruginous smectite. A discussion of the standard potential and its environmental implications. Clays Clay Minerals 54, 466–472 (2006).

    Article  Google Scholar 

  45. Akob, D. M. et al. Functional diversity and electron donor dependence of microbial populations capable of U(VI) reduction in radionuclide-contaminated subsurface sediments. Appl. Environ. Microbiol. 74, 3159–3170 (2008).

    Article  Google Scholar 

  46. Tung, H. C., Price, P. B., Bramall, N. E. & Vrdoljak, G. Microorganisms metabolizing on clay grains in 3-km-deep Greenland basal ice. Astrobiology 6, 69–86 (2006).

    Article  Google Scholar 

  47. Matheney, R. K. & Knauth, L. P. New isotopic temperature estimates for early silica diagenesis in bedded cherts. Geology 21, 519–522 (1993).

    Article  Google Scholar 

  48. Schieber, J., Krinsley, D. & Riciputi, L. Diagenetic origin of quartz silt in mudstones and implications for silica cycling. Nature 406, 981–985 (2000).

    Article  Google Scholar 

  49. Pevear, D. R. Illite and hydrocarbon exploration. Proc. Natl Acad. Sci. USA 96, 3440–3446 (1999).

    Article  Google Scholar 

  50. Pollastro, R. M. Considerations and applications of the illite/smectite geothermometer in hydrocarbon-bearing rocks of Miocene to Mississippian age. Clays Clay Minerals 41, 119–133 (1993).

    Article  Google Scholar 

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Acknowledgements

We thank J. Kostka and K. Nealson for beneficial comments that improved the manuscript greatly. We thank D. Hammond, M. Prokopenko and T. Bristow for helpful discussions, E.Crane for use of laboratory facilities, T. Algeo for X-ray fluorescence analyses and D. Haley and D. Tanenbaum for assistance with SEM and R. Halford and C. Kneale. This is contribution number 1 in the framework of Project CoSLAP. This work was supported by NSF EAR-0518732 to R.R.G.

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  1. Geology Department, Pomona College, Claremont, California 91711, USA

    John S. Vorhies & Robert R. Gaines

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  1. John S. Vorhies
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J.S.V. and R.R.G. participated in field work, laboratory analyses, data interpretation and writing of the manuscript.

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Correspondence to Robert R. Gaines.

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Vorhies, J., Gaines, R. Microbial dissolution of clay minerals as a source of iron and silica in marine sediments. Nature Geosci 2, 221–225 (2009). https://doi.org/10.1038/ngeo441

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