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Author: Dianne K. Newman
The effects of human activities on the environment pale by comparison with the effects of unicellular microorganisms.
Contributions from anthropogenic sources generally dominate the discussion on global change. And yet, although human activities have unquestionably left their mark on the environment, when averaged over geologic time, their importance pales in comparison with changes that have been effected by the activities of unicellular microorganisms (e.g., Bacteria, Archaea, and single-celled Eucarya). Not only does the number of microorganisms on Earth significantly exceed the number of humans (Whitman et al., 1998), microorganisms, unlike humans, are also found everywhere, are remarkably efficient at catalyzing a wide range of chemical reactions through their metabolisms, and have been around for billions of years.
Microbial metabolisms have brought about many changes in the Earth’s environment. Microorganisms have altered the chemistry of the atmosphere via oxygenic photosynthesis, nitrogen fixation, and carbon sequestration. They have modified the composition of oceans, rivers, and pore fluids by controling mineral weathering rates or by inducing mineral precipitation. They have changed the speciation of metals and metalloids in water, soils, and sediments by releasing complexing agents and/or by enzymatically catalyzing redox reactions. And they have shaped the physical world by binding sediments, precipitating ore deposits, and weathering rocks (Newman and Banfield, 2002).
Respiratory metabolisms have impacted mineral formation and/or dissolution. The thought of respiring a mineral may seem suffocating, but bacteria have been doing it for billions of years. Respiration is fundamentally the process of making energy available by transferring electrons from an electron donor to an electron acceptor. Typically, the transfer occurs down a respiratory chain embedded in the cell membrane; specific molecules hand off electrons from one end to the other. In the process, they generate a potential across the membrane that can be harnessed to do work (i.e., to store chemical energy in the form of ATP) (Mitchell, 1961). For respiration to succeed, a terminal electron acceptor, such as oxygen, must be available to receive the electrons. Before the evolution of oxygen in the atmosphere, microorganisms had to respire with alternative electron acceptors.
Most of the terminal electron acceptors used by bacteria for respiration, such as oxygen, nitrate, and sulfate, are soluble. This means they can make their way to the cell to receive electrons from the membrane-bound molecules of the respiratory chain. The real question is how bacteria transfer electrons to solids like hematite (a?Fe2O3) and goethite (a?FeOOH). Because these minerals are effectively insoluble under environmentally relevant conditions, simple dissolution and diffusion of ferric iron to the cell cannot be the answer (ferric iron is the constituent of the mineral that receives electrons). Therefore, bacteria must have other strategies for transferring electrons to minerals during respiration. The question is, what are they?
Several mechanisms have been proposed. Some have suggested that bacteria solubilize the minerals by producing chelators. Although the addition of synthetic chelators has been shown to stimulate microbial electron transfer to iron minerals, no evidence has been found that bacteria use this mechanism in respiration. Another suggestion is that they may use soluble shuttles, such as organic compounds with quinone moieties, to transfer electrons from the cell to the mineral. These shuttles may be exogenous substances, or they may be substances produced by the organisms themselves (Lovley et al, 1998; Newman and Kolter, 2000).
Another mechanism, possibly the dominant one, is that bacteria transfer electrons directly from the cell surface to the mineral after a regulated search and attachment process. A variety of biomolecules (including cytochromes, quinones, and dehydrogenases) have been identified as part of this electron-transfer pathway (Schr?der et al., 2003). Several of these biomolecules are located on the outer membrane of the cell and presumably make contact with the mineral directly (Lower et al., 2001). Given that the initial rate and long-term extent of electron transfer is correlated with their surface area and the concentration of reactive sites, this seems like a reasonable explanation (Zachara et al., 1998). Yet the nature of the electron-transfer event remains obscure and is a subject of active research.
Putting Mineral Respiration to Work
Despite uncertainties about the molecular mechanisms of mineral respiration, environmental microbiologists and engineers have been putting it to work for more than two decades. The best example is bioremediation; microbial metabolisms based on mineral respiration have been used to clean up organic and/or inorganic contaminants in groundwater.
In the late 1980s, researchers at the U.S. Geological Survey observed that the oxidation of aromatic hydrocarbons (e.g., benzene, xylenes, and toluene) in contaminated shallow aquifers was associated with the depletion of Fe(III) oxides from contaminated sediments and the accumulation of dissolved Fe(II) over time (Lovley et al., 1989). Hypothesizing that Fe(III)-respiring microorganisms may have been responsible for this phenomenon, Derek Lovley and his coworkers showed that the oxidation of added toluene to CO2 was dependent on active microbial metabolism. They went on to demonstrate that Geobacter metallireducens strain GS-15, an Fe(III)-respiring bacterium, could oxidize a variety of aromatic compounds. Two decades later, members of the Geobacteraceae family have been observed to account for a significant portion of the microbial population in contaminated sediments (Snoeyenbos-West et al., 2000), and the U.S. Department of Energy (DOE) is actively investing in research to get a better understanding of and to stimulate Fe(III) respiration for bioremediation (DOE, 2003a).
In addition to coupling the oxidation of organic contaminants to the reduction of Fe(III), microbial activity can be of value for the bioremediation of inorganic contaminants, uranium (U) and technetium (Tc), for example, two abundant radioactive metals that contaminate the subsurface environments at some DOE sites. Fe(III)-respiring bacteria have been shown to enzymatically reduce highly soluble U(VI) carbonate complexes and Tc(VII)O4- to the insoluble tetravalent phases, UO2 and TcO2 (Lloyd, 2003). The theory is that if organisms with this capacity are stimulated in situ, toxic inorganic compounds may be precipitated from groundwater and immobilized in the subsurface (Barkay and Schaefer, 2001).
Although the long-term efficacy of this approach is still a subject of debate, encouraging preliminary field studies show that a significant percentage of soluble U can be removed rapidly from groundwater by stimulating the indigenous microbial population (Finneran et al., 2002). Similarly, hexavalent chrominum [Cr(VI)] is a strong, highly mobile carcinogen that forms an insoluble Cr(III) precipitate when reduced. Efforts are currently under way at the Hanford DOE site to determine whether stimulation of the indigenous microbial population with lactate (a carbon source) can enhance Cr immobilization (DOE, 2003b).
Besides removing toxic inorganic compounds from groundwater, microbial respiratory metabolisms also have the potential to generate electricity. In a recently reported example, members of the family Geobacteraceae were shown to grow by oxidizing organics with a graphite electrode as the sole electron acceptor (Bond et al., 2002). When fuel cells consisting of anodes embedded in the sediment connected to cathodes positioned in the overlying seawater were deployed in two coastal marine environments (a salt marsh near Tuckerton, New Jersey, and the Yaquina Bay Estuary near Newport, Oregon), oxidation of both organic and inorganic electron donors in the sediment supported power generation (Tender et al., 2002). Although much work remains to be done before we can understand how microbial communities catalyze electron-transfer reactions to the anode, this process has the potential to sustain long-term power generation from marine sediments.
Lest microbial respiratory metabolisms be considered uniformly beneficial, it is important to point out that mineral respiration does not always improve water quality. A tragic example of this can be seen today in Bangladesh, where thousands of people are dying from drinking arsenic-contaminated well water. It is now widely believed that microbial respiratory activities are contributing to this problem by mobilizing arsenic in the groundwater (Harvey et al., 2002). Although the details have not yet been determined, evidence points to the reductive dissolution of iron arsenate minerals as a likely mechanism (Oremland and Stolz, 2003).
Microbial respiratory metabolisms based on minerals are fascinating from a purely scientific standpoint because of what they can teach us about electron-transfer reactions. They are also of great interest to environmental engineers seeking novel ways to remediate contaminated environments and/or to generate electricity. How organisms evolved the capacity to transfer electrons to mineral surfaces is not well understood but merits further investigation. It is possible that horizontal gene transfer has accelerated the distribution of this capability in both time and space; if so, this mechanism could be exploited in the future to deliver useful genetic material to targeted microbial populations.
I would like to thank the Clare Boothe Luce Foundation, the Packard Foundation, and the Office of Naval Research for providing generous research support.
Barkay, T., and J. Schaefer. 2001. Metal and radionuclide bioremediation: issues, considerations and potentials. Current Opinion in Microbiology 4(3): 318-323.
Bond, D.R., D.E. Holmes, L.M. Tender, and D.R. Lovley. 2002. Electrode-reducing microorganisms that harvest energy from marine sediments. Science 295(5554): 483-485.
DOE (U.S. Department of Energy). 2003a. Natural and Accelerated Bioremediation (NABIR) Program. Available online at: http://www.lbl.gov/NABIR/.
DOE. 2003b. NABIR Research Program. Available online at: http://www.lbl.gov/NABIR/researchprogram/awards/em_ projects0 2.html#hazen.
Finneran, K.T., R.T. Anderson, K.P. Nevin, and D.R. Lovley. 2002. Potential for bioremediation of uranium-contaminated aquifers with microbial U(VI) reduction. Soil and Sediment Contamination 11(3): 339-357.
Harvey, C.F., C.H. Swartz, A.B.M. Badruzzaman, N. Keon-Blute, W. Yu, M.A. Ali, J. Jay, R. Beckie, V. Niedan, D. Brabander, P.M. Oates, K.N. Ashfaque, S. Islam, H.F. Hemond, and M.F. Ahmed. 2002. Arsenic mobility and groundwater extraction in Bangladesh. Science 298(5598): 1602-1606.
Lloyd, J.R. 2003. Microbial reduction of metals and radionuclides. FEMS Microbiology Reviews 27 (2-3): 411-425.
Lovley, D.R., M.J. Baedecker, D.J. Lonergan, I.M. Cozzarelli, E.J.P. Phillips, and D.I. Siegel. 1989. Oxidation of aromatic contaminants coupled to microbial iron reduction. Nature 339(6222): 297-299.
Lovley, D.R., J.D. Coates, E.L. Blunt-Harris, E.J.P. Phillips, and J.C. Woodward. 1998. Humic substances as electron acceptors for microbial respiration. Nature 382(6564): 445-448.
Lower, S.K., M.F. Hochella, Jr., and T.J. Beveridge. 2001. Bacterial recognition of mineral surfaces: nanoscale interactions between Shewanella and a-FeOOH. Science 292(5520): 1360-1363.
Mitchell, P. 1961. Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature 191: 144-148.
Newman, D.K., and J.F. Banfield. 2002. Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems. Science 296(5570): 1071-1077.
Newman, D.K., and R. Kolter. 2000. A role for excreted quinines in extracellular electron transfer. Nature 405(6782): 94-97.
Oremland, R.S., and J.F. Stolz. 2003. The ecology of arsenic. Science 300(5621): 939-944.
Schr?der, I., E. Johnson, and S. de Vries. 2003. Microbial ferric iron reductases. FEMS Microbiology Reviews 27(2-3): 427-447.
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. Microbial Ecology 39(2): 153-167.
Tender, L.M., C.E. Reimers, H.A. Stecher III, D.E. Holmes, D.R. Bond, D.A. Lowy, K. Pilobello, S.J. Fertig, and D.R. Lovley. 2002. Harnessing microbially generated power on the seafloor. Nature Biotechnology 20(8): 821-825.
Whitman, W.B., D.C. Coleman, and W.J. Wiebe. 1998. Prokaryotes: the unseen majority. Proceedings of the National Academy of Sciences 95(12): 6578-6583.
Zachara, J.M., J.K. Fredrickson, S-M. Li, D.W. Kennedy, S.C. Smith, and P.L. Gassman. 1998. Bacterial reduction of crystalline Fe3+ oxides in single phase suspensions and subsurface materials. American Mineralogist 83(11-12, Part 2): 1426-1443.