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1 - Geomicrobiology: relative roles of bacteria and fungi as geomicrobial agents

Published online by Cambridge University Press:  10 December 2009

By
Henry L. Ehrlich
Edited by
Geoffrey Michael Gadd
Henry L. Ehrlich
Affiliation:
Biology Department Rensselaer Polytechnic Institute, 110 8th St Troy, NY 12180, USA
Geoffrey Michael Gadd
Affiliation:
University of Dundee
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Summary

Introduction

The following definition of geomicrobiology will provide a proper context for the discussion in this essay. Geomicrobiology is a study of the role that microbes have played in the geologic past from the time of their first appearance on the planet Earth about 4 eons ago to the present, and the role they are playing today and are likely to play in the future in some of the processes that are of fundamental importance to geology. The discussion will be restricted to current geomicrobial activities because being able to observe them directly, we know most about them. Geomicrobial activities in the geologic past have been deduced from the detection in the geologic record of (1) microbial fossils that morphologically resemble present-day microorganisms of geologic significance and (2) relevant biomarkers. Past geomicrobial activities have also been inferred from present-day geomicrobial activities that occur under conditions similar to those presumed to have existed in the geologic past. Molecular phylogeny is providing information that supports inferences about ancient geomicrobial activity.

Geomicrobial agents

Phylogenetic distribution

Although geomicrobial agents that are presently recognized include members of the domains Bacteria (Eubacteria) and Archaea in the Prokaryota and members of Algae, Protozoa and Fungi in the Eukaryota, the following discussion will emphasize mainly geomicrobial activities of members of the Bacteria, Archaea and Fungi.

Geomicrobial activities

Types of geomicrobial activities

Geomicrobial activities play a role in (1) mineral formation, (2) mineral degradation, (3) the cycling of organic and inorganic matter, (4) chemical and isotopic fractionation and (5) fossil-fuel genesis and degradation.

Type
Chapter
Information
Fungi in Biogeochemical Cycles , pp. 1 - 27
Publisher: Cambridge University Press
Print publication year: 2006

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References

Ahmadjian, V. (1967). The Lichen Symbiosis. Waltham, MA: Blaidsell.Google Scholar
Atlas, R. M. (1984). Petroleum Microbiology. New York: McGraw-Hill.Google Scholar
Baker, K. H. & Herson, D. S. (1994). Microbiology and biodegradation. In Bioremediation, ed. Baker, K. H. & Herson, D. S.. New York: McGraw-Hill, pp. 9–60.Google Scholar
Barker, H. A. (1940). Studies upon the methane fermentation. IV. The isolation and culture of Methanobacterium omelianskii. Antonie van Leeuwenhoek, 6, 201–20.CrossRefGoogle Scholar
Barker, W. W. & Banfield, J. F. (1996). Biologically versus inorganically mediated weathering reactions: relationships between minerals and extracellular microbial polymers in lithobiontic communities and minerals. Chemical Geology, 132, 55–69.CrossRefGoogle Scholar
Bazylinski, D. A. & Frankel, R. B. (2000). Biologically controlled mineralization of magnetotactic iron minerals by magnetotactic bacteria. In Environmental Microbe-Metal Interactions, ed. Lovley, D. R.. Washington, DC: ASM Press, pp. 109–44.CrossRefGoogle Scholar
Blake, R. II & Johnson, D. B. (2000). Phylogenetic and biochemical diversity among acidophilic bacteria that respire on iron. In Environmental Microbe-Metal Interactions, ed. Lovley, D. R.. Washington, DC: ASM Press, pp. 53–78.CrossRefGoogle Scholar
Brierley, J. A., Wan, R. Y., Hill, D. L. & Logan, T. C. (1995). Biooxidation-heap pretreatment technology for processing lower grade refractory gold ores. In Biohydrometallurgical Processing, Vol. 1, ed. Vargas, T., Jerez, C. A., Wiertz, J. V. & Toledo, H.. Santiago: University of Chile, pp. 253–62.Google Scholar
Bryant, M. P., Wolin, E. A., Wolin, M. J. & Wolfe, R. S. (1967). Methanobacillus omelianskii, a symbiotic association of two species of bacteria. Archiv für Mikrobiologie, 59, 20–31.CrossRefGoogle Scholar
Burggraf, S., Jannasch, H. W., Nicolaus, B. & Stetter, K. O. (1990). Archeoglobus profundus sp. nov. represents a new species within the sulfate-reducing archaebacteria. Systematic and Applied Microbiology, 13, 24–8.CrossRefGoogle Scholar
Burgstaller, W. & Schinner, F. (1993). Leaching of metals with fungi. Journal of Biotechnology, 27, 91–116.CrossRefGoogle Scholar
Coleman, M. L., Hedrick, D. B., Lovley, D. R., White, D. C. & Pye, K. (1993). Reduction of Fe(III) in sediments by sulfate reducing bacteria. Nature, 361, 436–8.CrossRefGoogle Scholar
de Vrind-de Jong, E. W. & de Vrind, J. P. M. (1997). Algal deposition of carbonates and silicates. In Reviews in Mineralogy, Vol. 35. Geomicrobiology: Interactions Between Microbes and Minerals, ed. Banfield, J. F. & Nealson, K. H.. Washington, DC: Mineralogical Society of America, pp. 267–307.Google Scholar
Ehrlich, H. L. (1980). Bacterial leaching of manganese ores. In Biogeochemistry of Ancient and Modern Environments, ed. Trudinger, P. A., Walter, M. R. & Ralph, B. J.. Canberra: Australian Academy of Science, pp. 609–14.Google Scholar
Ehrlich, H. L. (1993a). Electron transfer from acetate to the surface of MnO2 particles by a marine bacterium. Journal of Industrial Microbiology, 12, 121–8.CrossRefGoogle Scholar
Ehrlich, H. L. (1993b). A possible mechanism for the transfer of reducing power to insoluble mineral oxide in bacterial respiration. In Biohydrometallurgical Technologies, Vol. II, ed. Torma, A. E., Apel, M. L. & Brierley, C. L.. Warrendale, PA: The Minerals, Metals & Materials Society, pp. 415–22.Google Scholar
Ehrlich, H. L. (1999). Microbes as geologic agents: their role in mineral formation. Geomicrobiology Journal, 16, 135–53.CrossRefGoogle Scholar
Ehrlich, H. L. (2002a). Geomicrobiology, 4th edn. New York: Marcel Dekker.Google Scholar
Ehrlich, H. L. (2002b). How microbes mobilize metals in ores: a review of current understandings and proposals for further research. Minerals and Metallurgical Processing, 19, 220–4.Google Scholar
Ehrlich, H. L. & Fox, S. I. (1967). Copper sulfide precipitation by yeasts from acid mine-waters. Applied Microbiology, 15, 135–9.Google ScholarPubMed
Ehrlich, H. L. & Wickert, L. M. (1997). Bacterial action on bauxites in columns fed with full-strength and dilute sucrose-mineral salts medium. In Biotechnology and the Mining Environment, ed. Lortie, L., Bédard, P. & Gould, W. D.. Proceedings of 13th Annual General Meeting Biominet SP 97–1, CANMET, Natural Resources, Canada, Ottawa, Canada, pp. 73–89.Google Scholar
Ehrlich, H. L., Yang, S. H. & Mainwaring, J. D. Jr. (1973). Bacteriology of manganese nodules. VI. Fate of copper, nickel, cobalt and iron during bacterial and chemical reduction of the manganese(IV). Zeitschrift für Allgemeine Mikrobiologie, 13, 39–48.CrossRefGoogle Scholar
Ehrlich, H. L., Ingle, J. L. & Salerno, J. C. (1991). Iron and manganese oxidizing bacteria. In Variations in Autotrophic Life, ed. Shively, J. M. & Barton, L. L.. London: Academic Press, pp. 147–70.Google Scholar
Ehrlich, H. L., Wickert, L. M., Noteboom, D. & Doucet, J. (1995). Weathering of bauxite by heterotrophic bacteria. In Biohydrometallurgical Processing, Vol. 1, ed. Vargas, T., Jerez, C. A., Wiertz, J. V. & Toledo, H., Santiago: University of Chile, pp. 395–403.Google Scholar
Emerson, D. (2000). Microbial oxidation of Fe(II) and Mn(II) at circumneutral pH. In Environmental Microbe-Metal Interactions, ed. Lovley, D. R.. Washington, DC: ASM Press, pp. 31–52.CrossRefGoogle Scholar
Fox, S. I. (1967). Bacterial oxidation of simple copper sulfides. Unpublished Ph.D. thesis, Rensselaer Polytechnic Institute, Troy, NY.
Friedmann, E. I. (1982). Endolithic microorganisms in the Antarctic cold desert. Science, 215, 1045–53.CrossRefGoogle ScholarPubMed
Friedmann, E. I. & Ocampo, R. (1984). Endolithic microorganisms in extreme dry environments: Analysis of a lithobiontic microbial habitat. In Current Perspectives in Microbial Ecology, ed. Klug, M. J. & Reddy, C. A.. Proceedings of the Third International Symposium on Microbial Ecology. Washington, DC: American Society of Microbiology, pp. 177–85.Google Scholar
Ghiorse, W. C. & Ehrlich, H. L. (1976). Electron transport components of the MnO2 reductase system and the location of the terminal reductase in a marine bacillus. Applied and Environmental Microbiology, 31, 977–85.Google Scholar
Grossman, M. J., Lee, M. K., Prince, R. C.et al. (2001). Deep desulfurization of extensively hydrodesulfurized middle distillate oil by Rhodococcus sp. strain ECRD-1. Applied and Environmental Microbiology, 67, 1949–52.CrossRefGoogle ScholarPubMed
Guay, R. & Silver, M. (1975). Thiobacillus acidophilus sp. nov. Isolation and some physiological characteristics. Canadian Journal of Microbiology, 21, 281–8.CrossRefGoogle ScholarPubMed
Hale, M. E. Jr. (1967). The Biology of Lichens. London, UK: Edward Arnold.Google Scholar
Harrison, A. P. Jr. (1981). Acidiphilium cryptum gen. nov., heterotrophic bacterium from acidic mineral environments. International Journal of Systematic Bacteriology, 31, 327–32.CrossRefGoogle Scholar
Harrison, A. P. Jr. (1984). The acidophilic thiobacilli and other acidophilic bacteria that share their habitat. Annual Review of Microbiology, 38, 265–92.CrossRefGoogle ScholarPubMed
Hartmannova, V. & Kuhr, I. (1974). Copper leaching by lower fungi. Rudy, 22, 234–8.Google Scholar
Huber, R., Sacher, M., Vollman, A., Huber, H. & Rose, D. (2000). Respiration of arsenate and selenate by hyperthermophilic Archaea. Systematic and Applied Microbiology, 23, 305–14.CrossRefGoogle ScholarPubMed
Ivanov, M. V. (1968). Microbiological Processes in the Formation of Sulfur Deposits. Israel Program for Scientific Translations. US Department of Agriculture and National Science Foundation, Washington, DC.Google Scholar
Johnson, D. B., Ghauri, M. A. & Said, M. F. (1993). Isolation and characterization of an acidophilic, heterotrophic bacterium capable of oxidizing ferrous iron. Applied and Environmental Microbiology, 58, 1423–8.Google Scholar
Lazaroff, N., Melanson, L., Lewis, E., Santoro, N. & Pueschel, C. (1985). Scanning electron microscopy and infrared spectroscopy of iron sediment formed by Thiobacillus ferrooxidans. Geomicrobiology Journal, 4, 231–68.CrossRefGoogle Scholar
Livesey-Goldblatt, E., Norman, P. & Livesey-Goldblatt, D. R. (1983). Gold recovery from arsenopyrite/pyrite ore by bacterial leaching and cyanidation. In Recent Progress in Biohydrometallurgy, ed. Rossi, G. & Torma, A. E.. Iglesias, Italy: Associazione Mineraria Sarda, pp. 627–41.Google Scholar
Lovley, D. R. (1991). Dissimilatory Fe(III) and Mn(IV) reduction. Microbiological Reviews, 55, 259–87.Google ScholarPubMed
Lovley, D. R. (2000). Fe(III) and Mn(IV) reduction. In Environmental Microbe-Metal Interactions, ed. Lovley, D. R.. Washington, DC: ASM Press, pp. 3–30.CrossRefGoogle Scholar
Lovley, D. R. & Phillips, E. J. P. (1988). Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Applied and Environmental Microbiology, 54, 1472–80.Google ScholarPubMed
Lovley, D. R., Stolz, J. F., Nord, G. L. & Phillips, E. J. P. (1987). Anaerobic production of magnetite by dissimilatory iron-reducing microorganisms. Nature, 330, 252–4.CrossRefGoogle Scholar
Macaskie, L. E., Dean, A. C. R., Cheetham, A. K., Jakema, R. J. B. & Skarnulis, A. J. (1987). Cadmium accumulation by a Citrobacter sp.: the chemical nature of the accumulated metal precipitate and its location on the bacterial cells. Journal of General Microbiology, 133, 539–44.Google Scholar
Macaskie, L. E., Empson, R. M., Cheetham, A. K., Grey, C. P. & Skarnulis, A. J. (1992). Uranium bioaccumulation by a Citrobacter sp. as a result of enzymatically mediated growth of polycrystalline HUO2PO4. Science, 257, 782–4.CrossRefGoogle Scholar
McConnaughey, T. (1991). Calcification in Chara carollina: CO2 hydroxylation generates protons for bicarbonate assimilation. Limnology and Oceanography, 36, 619–28.CrossRefGoogle Scholar
Macy, J. M., Nunan, K., Hagen, K. D.et al. (1996). Chrysogenes arsenatis gen. nov, spec. nov., a new arsenate-respiring bacterium isolated from gold mine wastewater. International Journal of Systematic Bacteriology, 46, 1153–7.CrossRefGoogle Scholar
Mandernack, K. W., Post, J. & Tebo, B. M. (1995). Manganese mineral formation by bacterial spores of a marine Bacillus sp., strain SG-1: evidence for the direct oxidation of Mn(II) to Mn(IV). Geochimica et Cosmochimica Acta, 59, 4393–408.CrossRefGoogle Scholar
Myers, C. R. & Myers, J. M. (1992). Localization of cytochromes in the outer membrane of anaerobically grown Shewanella putrefaciens MR-1. Journal of Bacteriology, 174, 3429–38.CrossRefGoogle ScholarPubMed
Nielsen, A. M. & Beck, J. V. (1972). Chalcocite oxidation and coupled carbon dioxide fixation by Thiobacillus ferrooxidans. Science, 175, 1124–6.CrossRefGoogle ScholarPubMed
Oremland, R. S., Hoeft, S. E., Santini, J. M.et al. (2002a). Anaerobic oxidation of arsenite in Mono Lake water by a facultative arsenite oxidizing chemoautotroph, strain MLHE-1. Applied and Environmental Microbiology, 68, 4795–802.CrossRefGoogle Scholar
Oremland, R. S., Newman, D. K., Kail, B. W. & Stolz, J. F. (2002b). Bacterial respiration of arsenate and its significance in the environment. In Environmental Chemistry of Arsenic, ed. Frankenberger, W. T.. New York: Marcel Dekker, pp. 273–95.Google Scholar
Oremland, R. S., Stolz, J. F. & Hollibaugh, J. T. (2004). The microbial arsenic cycle in Mono Lake, California. FEMS Microbiology Ecology, 48, 15–27.CrossRefGoogle ScholarPubMed
Orphan, V. J., Hinrichs, K.-U., Ussler, W. IIIet al. (2001). Comparative analysis of methane oxidizing Archaea and sulfate-reducing bacteria in anoxic marine sediments. Applied and Environmental Microbiology, 67, 1922–34.CrossRefGoogle ScholarPubMed
Pye, K. (1984). SEM analysis of siderite cements in interstitial marsh sediments, Norfolk, England. Marine Geology, 56, 1–12.CrossRefGoogle Scholar
Pye, K., Dickson, A. D., Schiavon, N., Coleman, M. L. & Cox, M. (1990). Formation of siderite-Mg-calcite-iron sulfide concentrations in intertidal marsh and sandflat sediments, north Norfolk, England. Sedimentology, 37, 325–43.CrossRefGoogle Scholar
Stetter, K. O., Laurer, G., Thomm, M. & Neuner, A. (1987). Isolation of extremely thermophilic sulfate reducers: evidence for a novel branch of archaebacteria. Science, 236, 822–4.CrossRefGoogle ScholarPubMed
Stolz, J. F. & Oremland, R. S. (1999). Bacterial respiration of arsenic and selenium. FEMS Microbiology Reviews, 23, 615–27.CrossRefGoogle ScholarPubMed
Stone, A. T. (1987). Microbial metabolites and the reductive dissolution of manganese oxides: Oxalate and pyruvate. Geochimica et Cosmochimica Acta, 51, 153–7.CrossRefGoogle Scholar
Straub, K. L., Benz, M., Schink, B. & Widdel, F. (1996). Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Applied and Environmental Microbiology, 62, 1458–60.Google ScholarPubMed
Sullivan, J. D. (1930). Chemistry of leaching chalcocite. Tech. Paper 473. US Department of Commerce, Bureau of Mines, Washington, DC.Google Scholar
Thompson, J. B., Ferris, F. G. & Smith, D. A. (1990). Geomicrobiology and sedimentology of the mixolimnion and chemocline of Fayetteville Green Lake, New York. Palaios, 5, 52–75.CrossRefGoogle Scholar
Trudinger, P. A., Swaine, D. J. & Skyring, G. W. (1979). Biogeochemical cycling of elements – general considerations. In Biogeochemical Cycling of Mineral-Forming Elements, eds. Trudinger, P. A. & Swaine, D. J.. Amsterdam: Elsevier, pp. 1–27.Google Scholar
Ende, F. P. & Gemerden, H. (1993). Sulfide oxidation under oxygen limitation by a Thiobacillus thioparus isolated from a marine microbial mat. FEMS Microbiology Ecology, 13, 69–78.CrossRefGoogle Scholar
Welch, S. A. & Vandevivere, P. (1995). Effect of microbial and other naturally occurring polymers on mineral dissolution. Geomicrobiology Journal, 12, 227–38.CrossRefGoogle Scholar
Wenberg, G. M., Erbisch, F. H. & Violon, M. (1971). Leaching of copper by fungi. Transactions of the Society of Minerals Engineering AIME, 250, 207–12.Google Scholar
Widdel, F. & Pfennig, N. (1977). A new anaerobic, sporing, acetate-oxidizing sulfate-reducing bacterium, Desulfotomaculum (emend.) acetoxidans. Archives of Microbiology, 112, 119–22.CrossRefGoogle ScholarPubMed
Widdel, F., Schnell, S., Heising, S.et al. (1993). Ferrous oxidation by anoxygenic phototrophic bacteria. Nature, 362, 834–6.CrossRefGoogle Scholar
Yarzábal, A., Brasseur, G., Ratouchniak, J.et al. (2002). The high-molecular-weight cytochrome c Cyc2 of Acidithiobacillus ferrooxidans is an outer membrane protein. Journal of Bacteriology, 184, 313–17.CrossRefGoogle ScholarPubMed
Zavarzin, G. A. (1972). Heterotrophic satellite of Thiobacillus ferrooxidans. Mikrobiologiya, 41, 369–70.Google Scholar

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