Skip to main content Accessibility help
×
Hostname: page-component-8448b6f56d-tj2md Total loading time: 0 Render date: 2024-04-25T06:54:36.980Z Has data issue: false hasContentIssue false

9 - Anaerobic respiration

Published online by Cambridge University Press:  05 September 2012

Byung Hong Kim
Affiliation:
Korea Institute of Science and Technology, Seoul
Geoffrey Michael Gadd
Affiliation:
University of Dundee
Get access

Summary

In the previous chapter, respiration was defined as an energy conservation process achieved through electron transport phosphorylation (ETP) using externally supplied electron acceptors. Electron acceptors used in anaerobic respiration include oxidized sulfur and nitrogen compounds, metal ions, organic halogens and carbon dioxide. Other oxidized compounds reduced under anaerobic conditions include iodate, (per)chlorate, and phosphate. There is evidence to suggest that these compounds are used as electron acceptors in anaerobic ecosystems but there are some exceptions. ATP synthesis mechanisms dependent on a proton motive force are known in some fermentative bacteria. These include Na+-dependent decarboxylation, fumarate reduction and product/proton symport, as described earlier (Section 5.8.6). Sulfidogenesis and methanogenesis are described as fermentations in some cases since a small amount of energy is conserved in these anaerobic processes. However, in these processes ATP is generated mainly through the proton motive force and they can therefore be classified as anaerobic respiration.

Many ecosystems become anaerobic when oxygen consumption is greater than its supply. Even under anaerobic conditions, natural organic compounds are continuously recycled. Anaerobic respiratory microbes convert organic materials to carbon dioxide and methane under anaerobic conditions in conjunction with fermentative microbes.

Energy is required for all forms of life. At any given conditions, those organisms utilizing energy sources more efficiently will become dominant over the others. Among the anaerobic respiratory prokaryotes, denitrifiers conserve more energy than other groups. For this reason sulfidogenesis and methanogenesis are inhibited in the presence of nitrate, and sulfate inhibits methanogenesis.

Type
Chapter
Information
Publisher: Cambridge University Press
Print publication year: 2008

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Croal, L. R., Gralnick, J. A., Malasarn, D. & Newman, D. K. (2004). The genetics of geochemistry. Annual Review of Genetics 38, 175–202.CrossRefGoogle ScholarPubMed
Ehrlich, H. L. (2002). Geomicrobiology. New York: Marcel Dekker.Google Scholar
Gal'chenko, V. F. (2004). On the problem of anaerobic methane oxidation. Microbiology-Moscow 73, 599–608.CrossRefGoogle Scholar
Strous, M. & Jetten, M. S. M. (2004). Anaerobic oxidation of methane and ammonium. Annual Review of Microbiology 58, 99–117.CrossRefGoogle ScholarPubMed
Teske, A. P. (2005). The deep subsurface biosphere is alive and well. Trends in Microbiology 13, 402–404.CrossRefGoogle ScholarPubMed
Warren, L. A. & Kauffman, M. E. (2003). Geoscience: microbial geoengineers. Science 299, 1027–1029.CrossRefGoogle ScholarPubMed
Baker, S. C., Ferguson, S. J., Ludwig, B., Page, M. D., Richter, O. M. H. & Spanning, R. J. M. (1998). Molecular genetics of the genus Paracoccus: metabolically versatile bacteria with bioenergetic flexibility. Microbiology and Molecular Biology Reviews 62, 1046–1078.Google ScholarPubMed
Blasco, F., Guigliarelli, B., Magalon, A., Asso, M., Giordano, G. & Rothery, R. A. (2001). The coordination and function of the redox centres of the membrane-bound nitrate reductases. Cellular and Molecular Life Sciences 58, 179–193.CrossRefGoogle ScholarPubMed
Cabello, P., Roldan, M. D. & Moreno-Vivian, C. (2004). Nitrate reduction and the nitrogen cycle in archaea. Microbiology-UK 150, 3527–3546.CrossRefGoogle ScholarPubMed
Cole, J. A. (1996). Nitrate reduction to ammonia by enteric bacteria: redundancy, or a strategy for survival during oxygen starvation?FEMS Microbiology Letters 136, 1–11.CrossRefGoogle ScholarPubMed
Ferguson, S. J. (1994). Denitrification and its control. Antonie van Leeuwenhoek 66, 89–110.CrossRefGoogle ScholarPubMed
Fritz, G., Einsle, O., Rudolf, M., Schiffer, A. & Kroneck, P. M. H. (2005). Key bacterial multi-centered metal enzymes involved in nitrate and sulfate respiration. Journal of Molecular Microbiology and Biotechnology 10, 223–233.CrossRefGoogle ScholarPubMed
Gregory, K. B., Bond, D. R. & Lovley, D. R. (2004). Graphite electrodes as electron donors for anaerobic respiration. Environmental Microbiology 6, 596–604.CrossRefGoogle ScholarPubMed
Hendriks, J., Oubrie, A., Castresana, J., Urbani, A., Gemeinhardt, S. & Saraste, M. (2000). Nitric oxide reductases in bacteria. Biochimica et Biophysica Acta – Bioenergetics 1459, 266–273.CrossRefGoogle ScholarPubMed
Jetten, M. S. M., Logemann, S., Muyzer, G., Robertson, L. A., Devries, S., Loosdrecht, M. C. M. & Kuenen, J. G. (1997). Novel principles in the microbial conversion of nitrogen compounds. Antonie van Leeuwenhoek 71, 75–93.CrossRefGoogle ScholarPubMed
Jetten, M. S. M., Strous, M., Pas-Schoonen, K. T., Schalk, J., Dongen, U., Graaf, A. A., Logemann, S., Muyzer, G., Loosdrecht, M. C. M., & Kuenen, J. G. (1999). The anaerobic oxidation of ammonium. FEMS Microbiology Reviews 22, 421–437.CrossRefGoogle Scholar
Moura, I., Bursakov, S., Costa, C. & Moura, J. J. G. (1997). Nitrate and nitrite utilization in sulfate-reducing bacteria. Anaerobe 3, 279–290.CrossRefGoogle ScholarPubMed
Park, H. I., Kim, J. S., Kim, D. K., Choi, Y. J. & Pak, D. (2006). Nitrate-reducing bacterial community in a biofilm-electrode reactor. Enzyme and Microbial Technology 39, 453–458.CrossRefGoogle Scholar
Philippot, L. (2002). Denitrifying genes in bacterial and archaeal genomes. Biochimica et Biophysica Acta – Gene Structure and Expression 1577, 355–376.CrossRefGoogle ScholarPubMed
Philippot, L. (2005). Denitrification in pathogenic bacteria: for better or worse?Trends in Microbiology 13, 191–192.CrossRefGoogle ScholarPubMed
Philippot, L. & Hojberg, O. (1999). Dissimilatory nitrate reductases in bacteria. Biochimica et Biophysica Acta – Gene Structure and Expression 1446, 1–23.CrossRefGoogle ScholarPubMed
Potter, L., Angove, H., Richardson, D. & Cole, J. (2001). Nitrate reduction in the periplasm of Gram-negative bacteria. Advances in Microbial Physiology 45, 51–86.CrossRefGoogle ScholarPubMed
Richardson, D. J. & Watmough, N. J. (1999). Inorganic nitrogen metabolism in bacteria. Current Opinion in Chemical Biology 3, 207–219.CrossRefGoogle ScholarPubMed
Simon, J. (2002). Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiology Reviews 26, 285–309.CrossRefGoogle ScholarPubMed
Stouthamer, A. H., Deboer, A. P. N., Vanderoost, J. & Vanspanning, R. J. M. (1997). Emerging principles of inorganic nitrogen metabolism in Paracoccus denitrificans and related bacteria. Antonie van Leeuwenhoek 71, 33–41.CrossRefGoogle ScholarPubMed
Takaya, N. (2002). Dissimilatory nitrate reduction metabolisms and their control in fungi. Journal of Bioscience and Bioengineering 94, 506–510.CrossRefGoogle ScholarPubMed
Niftrik, L. A., Fuerst, J. A., Damste, J. S. S., Kuenen, J. G., Jetten, M. S. M. & Strous, M. (2004). The anammoxosome: an intracytoplasmic compartment in anammox bacteria. FEMS Microbiology Letters 233, 7–13.CrossRefGoogle ScholarPubMed
Ward, B. B. (2003). Significance of anaerobic ammonium oxidation in the ocean. Trends in Microbiology 11, 408–410.CrossRefGoogle ScholarPubMed
Zumft, W. G. (2005). Biogenesis of the bacterial respiratory CuA, Cu-S enzyme nitrous oxide reductase. Journal of Molecular Microbiology and Biotechnology 10, 154–166.CrossRefGoogle ScholarPubMed
Zumft, W. G. & Kroneck, P. M. H. (2006). Respiratory transformation of nitrous oxide (N2O) to dinitrogen by bacteria and archaea. Advances in Microbial Physiology 52, 107–227.CrossRefGoogle Scholar
Barkay, T. & Schaefer, J. (2001). Metal and radionuclide bioremediation: issues, considerations and potentials. Current Opinion in Microbiology 4, 318–323.CrossRefGoogle ScholarPubMed
Carmona, M. & Diaz, E. (2005). Iron-reducing bacteria unravel novel strategies for the anaerobic catabolism of aromatic compounds. Molecular Microbiology 58, 1210–1215.CrossRefGoogle ScholarPubMed
Cervantes, C., Campos-Garcia, J., Devars, S., Gutierrez-Corona, F., Loza-Tavera, H., Torres-Guzman, J. C. & Moreno-Sanchez, R. (2001). Interactions of chromium with microorganisms and plants. FEMS Microbiology Reviews 25, 335–347.CrossRefGoogle ScholarPubMed
Chang, I. S., Moon, H., Bretschger, O., Jang, J. K., Park, H. I., Nealson, K. H. & Kim, B. H. (2006). Electrochemically active bacteria (EAB) and mediator-less microbial fuel cells. Journal of Microbiology and Biotechnology 16, 163–177.Google Scholar
Kim, B. H., Kim, H. J., Hyun, M. S. & Park, D. H. (1999). Direct electrode reaction of an Fe(III)-reducing bacterium, Shewanella putrefaciens. Journal of Microbiology and Biotechnology 9, 127–131.Google Scholar
Kim, B. H., Park, H. S., Kim, H. J., Kim, G. T., Chang, I. S., Lee, J. & Phung, N. T. (2004). Enrichment of microbial community generating electricity using a fuel-cell-type electrochemical cell. Applied Microbiology and Biotechnology 63, 672–681.CrossRefGoogle ScholarPubMed
Landa, E. R. (2005). Microbial biogeochemistry of uranium mill tailings. Advances in Applied Microbiology 57, 113–130.CrossRefGoogle ScholarPubMed
Lee, A. K. & Newman, D. K. (2003). Microbial iron respiration: impacts on corrosion processes. Applied Microbiology and Biotechnology 62, 134–139.CrossRefGoogle ScholarPubMed
Lloyd, J. R. (2003). Microbial reduction of metals and radionuclides. FEMS Microbiology Reviews 27, 411–425.CrossRefGoogle ScholarPubMed
Lovley, D. R., Holmes, D. E. & Nevin, K. P. (2004). Dissimilatory Fe(III) and Mn(IV) reduction. Advances in Microbial Physiology 49, 219–286.CrossRefGoogle ScholarPubMed
Messens, J. & Silver, S. (2006). Arsenate reduction: thiol cascade chemistry with convergent evolution. Journal of Molecular Biology 362, 1–17.CrossRefGoogle ScholarPubMed
Mukhopadhyay, R., Rosen, B. P., Phung, L. T. & Silver, S. (2002). Microbial arsenic: from geocycles to genes and enzymes. FEMS Microbiology Reviews 26, 311–325.CrossRefGoogle ScholarPubMed
Nealson, K. & Cox, B. (2002). Microbial metal-ion reduction and Mars: extraterrestrial expectations?Current Opinion in Microbiology 5, 296–300.CrossRefGoogle ScholarPubMed
Newman, D. K. (2001). Microbiology: how bacteria respire minerals. Science 292, 1312–1313.CrossRefGoogle ScholarPubMed
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
Schroder, I., Johnson, E. & Vries, S. (2003). Microbial ferric iron reductases. FEMS Microbiology Reviews 27, 427–447.CrossRefGoogle ScholarPubMed
Slobodkin, A. (2005). Thermophilic microbial metal reduction. Microbiology-Moscow 74, 501–514.CrossRefGoogle ScholarPubMed
Stolz, J. F., Basu, P., Santini, J. M. & Oremland, R. S. (2006). Arsenic and selenium in microbial metabolism. Annual Review of Microbiology 60, 107–130.CrossRefGoogle ScholarPubMed
Valls, M. & Lorenzo, V. (2002). Exploiting the genetic and biochemical capacities of bacteria for the remediation of heavy metal pollution. FEMS Microbiology Reviews 26, 327–338.CrossRefGoogle ScholarPubMed
Wall, J. D. & Krumholz, L. R. (2006). Uranium reduction. Annual Review of Microbiology 60, 149–166.CrossRefGoogle ScholarPubMed
Weber, K. A., Achenbach, L. A. & Coates, J. D. (2006). Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction. Nature Reviews Microbiology 4, 752–764.CrossRefGoogle Scholar
Wilkins, M., Livens, F., Vaughan, D. & Lloyd, J. (2006). The impact of Fe(III)-reducing bacteria on uranium mobility. Biogeochemistry 78, 125–150.CrossRefGoogle Scholar
Angell, P. (1999). Understanding microbially influenced corrosion as biofilm- mediated changes in surface chemistry. Current Opinion in Biotechnology 10, 269–272.CrossRefGoogle ScholarPubMed
Castro, H. F., Williams, N. H. & Ogram, A. (2000). Phylogeny of sulfate-reducing bacteria. FEMS Microbiology Ecology 31, 1–9.Google ScholarPubMed
Colwell, F. S., Onstott, T. C., Delwiche, M. E., Chandler, D., Fredrickson, J. K., Yao, Q. J., McKinley, J. P., Boone, D., Griffiths, R., Phelps, T. J., Ringelberg, D., White, D. C., LaFreniere, L., Balkwill, D., Lehman, R. M., Konisky, J. & Long, P. E. (1997). Microorganisms from deep, high temperature sandstones: constraints on microbial colonization. FEMS Microbiology Reviews 20, 425–435.CrossRefGoogle Scholar
Cypionka, H. (2000). Oxygen respiration by Desulfovibrio species. Annual Review of Microbiology 54, 827–848.CrossRefGoogle ScholarPubMed
Hansen, T. A. (1994). Metabolism of sulfate-reducing prokaryotes. Antonie van Leeuwenhoek 66, 165–185.CrossRefGoogle ScholarPubMed
Hedderich, R., Klimmek, O., Kroger, A., Dirmeier, R., Keller, M. & Stetter, K. O. (1999). Anaerobic respiration with elemental sulfur and with disulfides. FEMS Microbiology Reviews 22, 353–381.CrossRefGoogle Scholar
Hockin, S. and Gadd, G. M. (2003). Linked redox-precipitation of sulfur and selenium under anaerobic conditions by sulfate-reducing bacterial biofilms. Applied and Environmental Microbiology 69, 7063–7072.CrossRefGoogle ScholarPubMed
Hockin, S. and Gadd, G. M. (2006). Removal of selenate from sulphate-containing media by sulphate-reducing bacterial biofilms. Environmental Microbiology 8, 816–826.CrossRefGoogle Scholar
Hockin, S. and Gadd, G. M. (2007). Bioremediation of metals by precipitation and cellular binding. In Sulphate-reducing Bacteria: Environmental and Engineered Systems, ed. Barton, L. L. and Hamilton, W. A., pp. 405–434. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Holmer, M. & Storkholm, P. (2001). Sulphate reduction and sulphur cycling in lake sediments: a review. Freshwater Biology 46, 431–451.CrossRefGoogle Scholar
Gall, J. & Xavier, A. V. (1996). Anaerobes response to oxygen: the sulfate-reducing bacteria. Anaerobe 2, 1–9.CrossRefGoogle ScholarPubMed
Lie, T. J., Leadbetter, J. R. & Leadbetter, E. R. (1998). Metabolism of sulfonic acids and other organosulfur compounds by sulfate-reducing bacteria. Geomicrobiology Journal 15, 135–149.CrossRefGoogle Scholar
Rueter, P., Rabus, R., Wilkes, H., Aeckersberg, F., Rainey, F. A., Jannasch, H. W. & Widdel, F. (1994). Anaerobic oxidation of hydrocarbons in crude oil by new types of sulphate-reducing bacteria. Nature 372, 455–458.CrossRefGoogle ScholarPubMed
Schauder, R. & Kroger, A. (1993). Bacterial sulphur respiration. Archives of Microbiology 159, 491–497.CrossRefGoogle Scholar
Villemur, R., Lanthier, M., Beaudet, R. & Lepine, F. (2006). The Desulfitobacterium genus. FEMS Microbiology Reviews 30, 706–733.CrossRefGoogle ScholarPubMed
White, C. and Gadd, G. M. (1998). Accumulation and effects of cadmium on sulphate-reducing bacterial biofilms. Microbiology–UK 144, 1407–1415.CrossRefGoogle Scholar
White, C., Dennis, J. S. and Gadd, G. M. (2003). A mathematical process model for cadmium precipitation by sulphate-reducing bacterial biofilms. Biodegradation 14, 139–151.CrossRefGoogle Scholar
Blaut, M. (1994). Metabolism of methanogens. Antonie van Leeuwenhoek 66, 187–208.CrossRefGoogle ScholarPubMed
Deppenmeier, U., Lienard, T. & Gottschalk, G. (1999). Novel reactions involved in energy conservation by methanogenic archaea. FEBS Letters 457, 291–297.CrossRefGoogle ScholarPubMed
Dybas, M. & Konisky, J. (1992). Energy transduction in the methanogen Methanococcus voltae is based on a sodium current. Journal of Bacteriology 174, 5575–5583.CrossRefGoogle ScholarPubMed
Ferry, J. G. (1992). Biochemistry of methanogenesis. Critical Reviews in Biochemistry and Molecular Biology 27, 473–503.CrossRefGoogle ScholarPubMed
Ferry, J. G. (1999). Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiology Reviews 23, 13–38.CrossRefGoogle ScholarPubMed
Lin, W. C., Yang, Y.-L. & Whitman, W. B. (2003). The anabolic pyruvate oxidoreductase from Methanococcus maripaludis. Archives of Microbiology 179, 444–456.CrossRefGoogle ScholarPubMed
Macario, A. J. L., Lange, M., Ahring, B. K. & Macario, E. C. (1999). Stress genes and proteins in the archaea. Microbiology and Molecular Biology Reviews 63, 923–967.Google ScholarPubMed
Maden, B. E. H. (2000). Tetrahydrofolate and tetrahydromethanopterin compared: functionally distinct carriers in C-1 metabolism. Biochemical Journal 350, 609–629.CrossRefGoogle Scholar
Reeve, J. N., Nolling, J., Morgan, R. M. & Smith, D. R. (1997). Methanogenesis: genes, genomes, and who's on first?Journal of Bacteriology 179, 5975–5986.CrossRefGoogle ScholarPubMed
Schaefer, G., Engelhard, M. & Mueller, V. (1999). Bioenergetics of the Archaea. Microbiology and Molecular Biology Reviews 63, 570–620.Google Scholar
Schink, B. (1997). Energetics of syntrophic cooperation in methanogenic degradation. Microbiology and Molecular Biology Reviews 61, 262–280.Google ScholarPubMed
Shima, S. & Thauer, R. K. (2005). Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic Archaea. Current Opinion in Microbiology 8, 643–648.CrossRefGoogle ScholarPubMed
Thauer, R. K. (1998). Biochemistry of methanogenesis: a tribute to Marjory Stephenson. Microbiology-UK 144, 2377–2406.CrossRefGoogle ScholarPubMed
Valentine, D. L. & Reeburgh, W. S. (2000). New perspectives on anaerobic methane oxidation. Environmental Microbiology 2, 477–484.CrossRefGoogle ScholarPubMed
Bacher, A., Rieder, C., Eichinger, D., Arigoni, D., Fuchs, G. & Eisenreich, W. (1998). Elucidation of novel biosynthetic pathways and metabolite flux patterns by retrobiosynthetic NMR analysis. FEMS Microbiology Reviews 22, 567–598.CrossRefGoogle Scholar
Detkova, E. & Pusheva, M. (2006). Energy metabolism in halophilic and alkaliphilic acetogenic bacteria. Microbiology-Moscow 75, 1–11.CrossRefGoogle Scholar
Diekert, G. & Wohlfarth, G. (1994). Metabolism of homoacetogens. Antonie van Leeuwenhoek 66, 209–221.CrossRefGoogle Scholar
Drake, H. L. & Daniel, S. L. (2004). Physiology of the thermophilic acetogen Moorella thermoacetica. Research in Microbiology 155, 422–436.CrossRefGoogle ScholarPubMed
Ferry, J. G. (1995). CO dehydrogenase. Annual Review of Microbiology 49, 305–333.CrossRefGoogle ScholarPubMed
Grahame, D. A. (2003). Acetate C-C bond formation and decomposition in the anaerobic world: the structure of a central enzyme and its key active-site metal cluster. Trends in Biochemical Sciences 28, 221–224.CrossRefGoogle Scholar
Hansen, T. A. (1994). Metabolism of sulfate-reducing prokaryotes. Antonie van Leeuwenhoek 66, 165–185.CrossRefGoogle ScholarPubMed
Mueller, V. (2003). Energy conservation in acetogenic bacteria. Applied and Environmental Microbiology 69, 6345–6353.CrossRefGoogle Scholar
Ragsdale, S. (2004). Life with carbon monoxide. Critical Reviews in Biochemistry and Molecular Biology 39, 165–195.CrossRefGoogle ScholarPubMed
Russell, M. J. & Martin, W. (2004). The rocky roots of the acetyl-CoA pathway. Trends in Biochemical Sciences 29, 358–363.CrossRefGoogle ScholarPubMed
Siebers, B. & Schonheit, P. (2005). Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Current Opinion in Microbiology 8, 695–705.CrossRefGoogle ScholarPubMed
Sipma, J., Henstra, A. M., Parshina, S. N., Lens, P. N. L., Lettinga, G. & Stams, A. J. M. (2006). Microbial CO conversions with applications in synthesis gas purification and bio-desulfurization. Critical Reviews in Biotechnology 26, 41–65.CrossRefGoogle ScholarPubMed
Abraham, W., Nogales, B., Golyshin, P., Pieper, D. & Timmis, K. (2002). Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Current Opinion in Microbiology 5, 246–253.CrossRefGoogle ScholarPubMed
Borja, J., Taleon, D. M., Auresenia, J. & Gallardo, S. (2005). Polychlorinated biphenyls and their biodegradation. Process Biochemistry 40, 1999–2013.CrossRefGoogle Scholar
Chen, G. (2004). Reductive dehalogenation of tetrachloroethylene by microorganisms: current knowledge and application strategies. Applied Microbiology and Biotechnology 63, 373–377.CrossRefGoogle ScholarPubMed
Fantroussi, El S., Naveau, H. & Agathos, S. N. (1998). Anaerobic dechlorinating bacteria. Biotechnology Progress 14, 167–188.CrossRefGoogle ScholarPubMed
Fetzner, S. (1998). Bacterial dehalogenation. Applied Microbiology and Biotechnology 50, 633–657.CrossRefGoogle ScholarPubMed
Fetzner, S. & Lingens, F. (1994). Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications. Microbiological Reviews 58, 641–685.Google ScholarPubMed
Furukawa, K. (2000). Biochemical and genetic bases of microbial degradation of polychlorinated biphenyls (PCBs). Journal of General and Applied Microbiology 46, 283–296.CrossRefGoogle ScholarPubMed
Hoehener, P., Werner, D., Balsiger, C. & Pasteris, G. (2003). Worldwide occurrence and fate of chlorofluorocarbons in groundwater. Critical Reviews in Environmental Science and Technology 33, 1–29.CrossRefGoogle Scholar
Holliger, C. & Schumacher, W. (1994). Reductive dehalogenation as a respiratory process. Antonie van Leeuwenhoek 66, 239–246.CrossRefGoogle ScholarPubMed
Holliger, C., Wohlfarth, G. & Diekert, G. (1999). Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiology Reviews 22, 383–398.CrossRefGoogle Scholar
Janssen, D. B. (2004). Evolving haloalkane dehalogenases. Current Opinion in Chemical Biology 8, 150–159.CrossRefGoogle ScholarPubMed
Janssen, D. B., Oppentocht, J. E. & Poelarends, G. J. (2001). Microbial dehalogenation. Current Opinion in Biotechnology 12, 254–258.CrossRefGoogle ScholarPubMed
Janssen, D. B., Dinkla, J. T., Poelarends, G. J. & Terpstra, P. (2005). Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities. Environmental Microbiology 7, 1868–1882.CrossRefGoogle ScholarPubMed
McCarty, P. L. (1997). Microbiology: breathing with chlorinated solvents. Science 276, 1521–1522.CrossRefGoogle Scholar
Smidt, H. & Vos, W. M. (2004). Anaerobic microbial dehalogenation. Annual Review of Microbiology 58, 43–73.CrossRefGoogle ScholarPubMed
Vlieg, J. E. T. V., Poelarends, G. J., Mars, A. E. & Janssen, D. B. (2000). Detoxification of reactive intermediates during microbial metabolism of halogenated compounds. Current Opinion in Microbiology 3, 257–262.CrossRefGoogle Scholar
Wiegel, J. & Wu, Q. Z. (2000). Microbial reductive dehalogenation of polychlorinated biphenyls. FEMS Microbiology Ecology 32, 1–15.CrossRefGoogle ScholarPubMed
Arkhipova, O. & Akimenko, V. (2005). Unsaturated organic acids as terminal electron acceptors for reductase chains of anaerobic bacteria. Microbiology-Moscow 74, 629–639.CrossRefGoogle ScholarPubMed
Coates, J. D. & Achenbach, L. A. (2004). Microbial perchlorate reduction: rocket-fueled metabolism. Nature Reviews Microbiology 2, 569–580.CrossRefGoogle ScholarPubMed
Councell, T. B., Landa, E. R. & Lovley, D. R. (1997). Microbial reduction of iodate. Water, Air and Soil Pollution 100, 99–106.CrossRefGoogle Scholar
Geng, J., Jin, X., Wang, Q., Niu, X., Wang, X., Edwards, M. & Glindemann, D. (2005). Matrix bound phosphine formation and depletion in eutrophic lake sediment fermentation: simulation of different environmental factors. Anaerobe 11, 273–279.CrossRefGoogle ScholarPubMed
Kroger, A., Geisler, V., Lemma, E., Theis, F. & Lenger, R. (1992). Bacterial fumarate respiration. Archives of Microbiology 158, 311–314.CrossRefGoogle Scholar
Richardson, D. J. (2000). Bacterial respiration: a flexible process for a changing environment. Microbiology-UK 146, 551–571.CrossRefGoogle ScholarPubMed
Roels, J. & Verstraete, W. (2001). Biological formation of volatile phosphorus compounds. Bioresource Technology 79, 243–250.CrossRefGoogle ScholarPubMed
Slobodkin, A. I., Zavarzina, D. G., Sokolova, T. G. & Bonch-Osmolovskaya, E. A. (1999). Dissimilatory reduction of inorganic electron accepters by thermophilic anaerobic prokaryotes. Microbiology-Moscow 68, 522–542.Google Scholar
Cao, X., Liu, X. & Dong, X. (2003). Alkaliphilus crotonatoxidans sp. nov., a strictly anaerobic, crotonate-dismutating bacterium isolated from a methanogenic environment. International Journal of Systematic and Evolutionary Microbiology 53, 971–975.CrossRefGoogle ScholarPubMed
Bok, F. A. M., Stams, A. J. M., Dijkema, C. & Boone, D. R. (2001). Pathway of propionate oxidation by a syntrophic culture of Smithella propionica and Methanospirillum hungatei. Applied and Environmental Microbiology 67, 1800–1804.CrossRefGoogle ScholarPubMed
Bok, F. A. M., Luijten, M. L. G. C. & Stams, A. J. M. (2002). Biochemical evidence for formate transfer in syntrophic propionate-oxidizing cocultures of Syntrophobacter fumaroxidans and Methanospirillum hungatei. Applied and Environmental Microbiology 68, 4247–4252.CrossRefGoogle ScholarPubMed
Bok, F. A. M., Plugge, C. M. & Stams, A. J. M. (2004). Interspecies electron transfer in methanogenic propionate degrading consortia. Water Research 38, 1368–1375.CrossRefGoogle ScholarPubMed
Grabowski, A., Blanchet, D. & Jeanthon, C. (2005). Characterization of long-chain fatty-acid-degrading syntrophic associations from a biodegraded oil reservoir. Research in Microbiology 156, 814–821.CrossRefGoogle ScholarPubMed
Hattori, S., Galushko, A. S., Kamagata, Y. & Schink, B. (2005). Operation of the CO dehydrogenase/acetyl coenzyme A pathway in both acetate oxidation and acetate formation by the syntrophically acetate-oxidizing bacterium Thermacetogenium phaeum. Journal of Bacteriology 187, 3471–3476.CrossRefGoogle ScholarPubMed
Imachi, H., Sekiguchi, Y., Kamagata, Y., Hanada, S., Ohashi, A. & Harada, H. (2002). Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. International Journal of Systematic and Evolutionary Microbiology 52, 1729–1735.Google ScholarPubMed
Imachi, H., Sekiguchi, Y., Qiu, Y. L., Hugenholtz, P., Kimura, N., Wagner, M., Ohashi, A. & Harada, H. (2006). Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Applied and Environmental Microbiology 72, 2080–2091.CrossRefGoogle ScholarPubMed
Ishii, S., Kosaka, T., Hori, K., Hotta, Y. & Watanabe, K. (2005). Coaggregation facilitates interspecies hydrogen transfer between Pelotomaculum thermopropionicum and Methanothermobacter thermautotrophicus. Applied and Environmental Microbiology 71, 7838–7845.CrossRefGoogle ScholarPubMed
Johnson, M. R., Conners, S. B., Montero, C. I., Chou, C. J., Shockley, K. R. & Kelly, R. M. (2006). The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture. Applied and Environmental Microbiology 72, 811–818.CrossRefGoogle ScholarPubMed
Kendall, M. M., Liu, Y. & Boone, D. R. (2006). Butyrate- and propionate-degrading syntrophs from permanently cold marine sediments in Skan Bay, Alaska, and description of Algorimarina butyrica gen. nov., sp. nov. FEMS Microbiology Letters 262, 107–114.CrossRefGoogle ScholarPubMed
Kosaka, T., Uchiyama, T., Ishii, S., Enoki, M., Imachi, H., Kamagata, Y., Ohasi, A., Harada, H., Ikenaga, H. & Watanabe, K. (2006). Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. Journal of Bacteriology 188, 202–210.CrossRefGoogle ScholarPubMed
Plugge, C. M., Balk, M., Zoetendal, E. G. & Stams, A. J. M. (2002). Gelria glutamica gen. nov., sp. nov., a thermophilic, obligately syntrophic, glutamate-degrading anaerobe. International Journal of Systematic and Evolutionary Microbiology 52, 401–407.CrossRefGoogle ScholarPubMed
Qiu, Y.-L., Sekiguchi, Y., Imachi, H., Kamagata, Y., Tseng, I.-C., Cheng, S.-S., Ohashi, A. & Harada, H. (2003). Sporotomaculum syntrophicum sp. nov., a novel anaerobic, syntrophic benzoate-degrading bacterium isolated from methanogenic sludge treating wastewater from terephthalate manufacturing. Archives of Microbiology 179, 242–249.CrossRefGoogle ScholarPubMed
Qiu, Y. L., Sekiguchi, Y., Hanada, S., Imachi, H., Tseng, I. C., Cheng, S. S., Ohashi, A., Harada, H. & Kamagata, Y. (2006). Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens. Archives of Microbiology 185, 172–182.CrossRefGoogle ScholarPubMed
Zhang, C., Liu, X. & Dong, X. (2004). Syntrophomonas curvata sp. nov., an anaerobe that degrades fatty acids in co-culture with methanogens. International Journal of Systematic and Evolutionary Microbiology 54, 969–973.CrossRefGoogle ScholarPubMed
Zhilina, T., Zavarzina, D., Kolganova, T., Tourova, T. & Zavarzin, G. (2005). Candidatus ‘Contubernalis alkalaceticum’, an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture withDesulfonatronum cooperativum. Microbiology-Moscow 74, 695–703.Google Scholar
Boll, M. (2005). Key enzymes in the anaerobic aromatic metabolism catalysing Birch-like reductions. Biochimica et Biophysica Acta – Bioenergetics 1707, 34–50.CrossRefGoogle ScholarPubMed
Boll, M., Fuchs, G. & Heider, J. (2002). Anaerobic oxidation of aromatic compounds and hydrocarbons. Current Opinion in Chemical Biology 6, 604–611.CrossRefGoogle ScholarPubMed
Carmona, M. & Diaz, E. (2005). Iron-reducing bacteria unravel novel strategies for the anaerobic catabolism of aromatic compounds. Molecular Microbiology 58, 1210–1215.CrossRefGoogle ScholarPubMed
Chakraborty, R. & Coates, J. D. (2004). Anaerobic degradation of monoaromatic hydrocarbons. Applied Microbiology and Biotechnology 64, 437–446.CrossRefGoogle ScholarPubMed
Coates, J. D., Chakraborty, R. & McInerney, M. J. (2002). Anaerobic benzene biodegradation: a new era. Research in Microbiology 153, 621–628.CrossRefGoogle ScholarPubMed
Corvini, P., Schaeffer, A. & Schlosser, D. (2006). Microbial degradation of nonylphenol and other alkylphenols: our evolving view. Applied Microbiology and Biotechnology 72, 223–243.CrossRefGoogle ScholarPubMed
Esteve-Nunez, A., Caballero, A. & Ramos, J. L. (2001). Biological degradation of 2,4,6-trinitrotoluene. Microbiology and Molecular Biology Reviews 65, 335–352.CrossRefGoogle ScholarPubMed
Eyers, L., George, I., Schuler, L., Stenuit, B., Agathos, S. N. & El Fantroussi, S. (2004). Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Applied Microbiology and Biotechnology 66, 123–130.CrossRefGoogle ScholarPubMed
Gibson, J. & Harwood, S. (2002). Metabolic diversity in anaerobic compound utilization by anaerobic microbes. Annual Review of Microbiology 56, 345–369.CrossRefGoogle ScholarPubMed
Meckenstock, R. U., Safinowski, M. & Griebler, C. (2004). Anaerobic degradation of polycyclic aromatic hydrocarbons. FEMS Microbiology Ecology 49, 27–36.CrossRefGoogle ScholarPubMed
Spormann, A. M. & Widdel, F. (2000). Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria. Biodegradation 11, 85–105.CrossRefGoogle ScholarPubMed
Veeresh, G. S., Kumar, P. & Mehrotra, I. (2005). Treatment of phenol and cresols in upflow anaerobic sludge blanket (UASB) process: a review. Water Research 39, 154–170.CrossRefGoogle ScholarPubMed
Zhang, C. & Bennett, G. N. (2005). Biodegradation of xenobiotics by anaerobic bacteria. Applied Microbiology and Biotechnology 67, 600–618.CrossRefGoogle ScholarPubMed
Croal, L. R., Gralnick, J. A., Malasarn, D. & Newman, D. K. (2004). The genetics of geochemistry. Annual Review of Genetics 38, 175–202.CrossRefGoogle ScholarPubMed
Ehrlich, H. L. (2002). Geomicrobiology. New York: Marcel Dekker.Google Scholar
Gal'chenko, V. F. (2004). On the problem of anaerobic methane oxidation. Microbiology-Moscow 73, 599–608.CrossRefGoogle Scholar
Strous, M. & Jetten, M. S. M. (2004). Anaerobic oxidation of methane and ammonium. Annual Review of Microbiology 58, 99–117.CrossRefGoogle ScholarPubMed
Teske, A. P. (2005). The deep subsurface biosphere is alive and well. Trends in Microbiology 13, 402–404.CrossRefGoogle ScholarPubMed
Warren, L. A. & Kauffman, M. E. (2003). Geoscience: microbial geoengineers. Science 299, 1027–1029.CrossRefGoogle ScholarPubMed
Baker, S. C., Ferguson, S. J., Ludwig, B., Page, M. D., Richter, O. M. H. & Spanning, R. J. M. (1998). Molecular genetics of the genus Paracoccus: metabolically versatile bacteria with bioenergetic flexibility. Microbiology and Molecular Biology Reviews 62, 1046–1078.Google ScholarPubMed
Blasco, F., Guigliarelli, B., Magalon, A., Asso, M., Giordano, G. & Rothery, R. A. (2001). The coordination and function of the redox centres of the membrane-bound nitrate reductases. Cellular and Molecular Life Sciences 58, 179–193.CrossRefGoogle ScholarPubMed
Cabello, P., Roldan, M. D. & Moreno-Vivian, C. (2004). Nitrate reduction and the nitrogen cycle in archaea. Microbiology-UK 150, 3527–3546.CrossRefGoogle ScholarPubMed
Cole, J. A. (1996). Nitrate reduction to ammonia by enteric bacteria: redundancy, or a strategy for survival during oxygen starvation?FEMS Microbiology Letters 136, 1–11.CrossRefGoogle ScholarPubMed
Ferguson, S. J. (1994). Denitrification and its control. Antonie van Leeuwenhoek 66, 89–110.CrossRefGoogle ScholarPubMed
Fritz, G., Einsle, O., Rudolf, M., Schiffer, A. & Kroneck, P. M. H. (2005). Key bacterial multi-centered metal enzymes involved in nitrate and sulfate respiration. Journal of Molecular Microbiology and Biotechnology 10, 223–233.CrossRefGoogle ScholarPubMed
Gregory, K. B., Bond, D. R. & Lovley, D. R. (2004). Graphite electrodes as electron donors for anaerobic respiration. Environmental Microbiology 6, 596–604.CrossRefGoogle ScholarPubMed
Hendriks, J., Oubrie, A., Castresana, J., Urbani, A., Gemeinhardt, S. & Saraste, M. (2000). Nitric oxide reductases in bacteria. Biochimica et Biophysica Acta – Bioenergetics 1459, 266–273.CrossRefGoogle ScholarPubMed
Jetten, M. S. M., Logemann, S., Muyzer, G., Robertson, L. A., Devries, S., Loosdrecht, M. C. M. & Kuenen, J. G. (1997). Novel principles in the microbial conversion of nitrogen compounds. Antonie van Leeuwenhoek 71, 75–93.CrossRefGoogle ScholarPubMed
Jetten, M. S. M., Strous, M., Pas-Schoonen, K. T., Schalk, J., Dongen, U., Graaf, A. A., Logemann, S., Muyzer, G., Loosdrecht, M. C. M., & Kuenen, J. G. (1999). The anaerobic oxidation of ammonium. FEMS Microbiology Reviews 22, 421–437.CrossRefGoogle Scholar
Moura, I., Bursakov, S., Costa, C. & Moura, J. J. G. (1997). Nitrate and nitrite utilization in sulfate-reducing bacteria. Anaerobe 3, 279–290.CrossRefGoogle ScholarPubMed
Park, H. I., Kim, J. S., Kim, D. K., Choi, Y. J. & Pak, D. (2006). Nitrate-reducing bacterial community in a biofilm-electrode reactor. Enzyme and Microbial Technology 39, 453–458.CrossRefGoogle Scholar
Philippot, L. (2002). Denitrifying genes in bacterial and archaeal genomes. Biochimica et Biophysica Acta – Gene Structure and Expression 1577, 355–376.CrossRefGoogle ScholarPubMed
Philippot, L. (2005). Denitrification in pathogenic bacteria: for better or worse?Trends in Microbiology 13, 191–192.CrossRefGoogle ScholarPubMed
Philippot, L. & Hojberg, O. (1999). Dissimilatory nitrate reductases in bacteria. Biochimica et Biophysica Acta – Gene Structure and Expression 1446, 1–23.CrossRefGoogle ScholarPubMed
Potter, L., Angove, H., Richardson, D. & Cole, J. (2001). Nitrate reduction in the periplasm of Gram-negative bacteria. Advances in Microbial Physiology 45, 51–86.CrossRefGoogle ScholarPubMed
Richardson, D. J. & Watmough, N. J. (1999). Inorganic nitrogen metabolism in bacteria. Current Opinion in Chemical Biology 3, 207–219.CrossRefGoogle ScholarPubMed
Simon, J. (2002). Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiology Reviews 26, 285–309.CrossRefGoogle ScholarPubMed
Stouthamer, A. H., Deboer, A. P. N., Vanderoost, J. & Vanspanning, R. J. M. (1997). Emerging principles of inorganic nitrogen metabolism in Paracoccus denitrificans and related bacteria. Antonie van Leeuwenhoek 71, 33–41.CrossRefGoogle ScholarPubMed
Takaya, N. (2002). Dissimilatory nitrate reduction metabolisms and their control in fungi. Journal of Bioscience and Bioengineering 94, 506–510.CrossRefGoogle ScholarPubMed
Niftrik, L. A., Fuerst, J. A., Damste, J. S. S., Kuenen, J. G., Jetten, M. S. M. & Strous, M. (2004). The anammoxosome: an intracytoplasmic compartment in anammox bacteria. FEMS Microbiology Letters 233, 7–13.CrossRefGoogle ScholarPubMed
Ward, B. B. (2003). Significance of anaerobic ammonium oxidation in the ocean. Trends in Microbiology 11, 408–410.CrossRefGoogle ScholarPubMed
Zumft, W. G. (2005). Biogenesis of the bacterial respiratory CuA, Cu-S enzyme nitrous oxide reductase. Journal of Molecular Microbiology and Biotechnology 10, 154–166.CrossRefGoogle ScholarPubMed
Zumft, W. G. & Kroneck, P. M. H. (2006). Respiratory transformation of nitrous oxide (N2O) to dinitrogen by bacteria and archaea. Advances in Microbial Physiology 52, 107–227.CrossRefGoogle Scholar
Barkay, T. & Schaefer, J. (2001). Metal and radionuclide bioremediation: issues, considerations and potentials. Current Opinion in Microbiology 4, 318–323.CrossRefGoogle ScholarPubMed
Carmona, M. & Diaz, E. (2005). Iron-reducing bacteria unravel novel strategies for the anaerobic catabolism of aromatic compounds. Molecular Microbiology 58, 1210–1215.CrossRefGoogle ScholarPubMed
Cervantes, C., Campos-Garcia, J., Devars, S., Gutierrez-Corona, F., Loza-Tavera, H., Torres-Guzman, J. C. & Moreno-Sanchez, R. (2001). Interactions of chromium with microorganisms and plants. FEMS Microbiology Reviews 25, 335–347.CrossRefGoogle ScholarPubMed
Chang, I. S., Moon, H., Bretschger, O., Jang, J. K., Park, H. I., Nealson, K. H. & Kim, B. H. (2006). Electrochemically active bacteria (EAB) and mediator-less microbial fuel cells. Journal of Microbiology and Biotechnology 16, 163–177.Google Scholar
Kim, B. H., Kim, H. J., Hyun, M. S. & Park, D. H. (1999). Direct electrode reaction of an Fe(III)-reducing bacterium, Shewanella putrefaciens. Journal of Microbiology and Biotechnology 9, 127–131.Google Scholar
Kim, B. H., Park, H. S., Kim, H. J., Kim, G. T., Chang, I. S., Lee, J. & Phung, N. T. (2004). Enrichment of microbial community generating electricity using a fuel-cell-type electrochemical cell. Applied Microbiology and Biotechnology 63, 672–681.CrossRefGoogle ScholarPubMed
Landa, E. R. (2005). Microbial biogeochemistry of uranium mill tailings. Advances in Applied Microbiology 57, 113–130.CrossRefGoogle ScholarPubMed
Lee, A. K. & Newman, D. K. (2003). Microbial iron respiration: impacts on corrosion processes. Applied Microbiology and Biotechnology 62, 134–139.CrossRefGoogle ScholarPubMed
Lloyd, J. R. (2003). Microbial reduction of metals and radionuclides. FEMS Microbiology Reviews 27, 411–425.CrossRefGoogle ScholarPubMed
Lovley, D. R., Holmes, D. E. & Nevin, K. P. (2004). Dissimilatory Fe(III) and Mn(IV) reduction. Advances in Microbial Physiology 49, 219–286.CrossRefGoogle ScholarPubMed
Messens, J. & Silver, S. (2006). Arsenate reduction: thiol cascade chemistry with convergent evolution. Journal of Molecular Biology 362, 1–17.CrossRefGoogle ScholarPubMed
Mukhopadhyay, R., Rosen, B. P., Phung, L. T. & Silver, S. (2002). Microbial arsenic: from geocycles to genes and enzymes. FEMS Microbiology Reviews 26, 311–325.CrossRefGoogle ScholarPubMed
Nealson, K. & Cox, B. (2002). Microbial metal-ion reduction and Mars: extraterrestrial expectations?Current Opinion in Microbiology 5, 296–300.CrossRefGoogle ScholarPubMed
Newman, D. K. (2001). Microbiology: how bacteria respire minerals. Science 292, 1312–1313.CrossRefGoogle ScholarPubMed
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
Schroder, I., Johnson, E. & Vries, S. (2003). Microbial ferric iron reductases. FEMS Microbiology Reviews 27, 427–447.CrossRefGoogle ScholarPubMed
Slobodkin, A. (2005). Thermophilic microbial metal reduction. Microbiology-Moscow 74, 501–514.CrossRefGoogle ScholarPubMed
Stolz, J. F., Basu, P., Santini, J. M. & Oremland, R. S. (2006). Arsenic and selenium in microbial metabolism. Annual Review of Microbiology 60, 107–130.CrossRefGoogle ScholarPubMed
Valls, M. & Lorenzo, V. (2002). Exploiting the genetic and biochemical capacities of bacteria for the remediation of heavy metal pollution. FEMS Microbiology Reviews 26, 327–338.CrossRefGoogle ScholarPubMed
Wall, J. D. & Krumholz, L. R. (2006). Uranium reduction. Annual Review of Microbiology 60, 149–166.CrossRefGoogle ScholarPubMed
Weber, K. A., Achenbach, L. A. & Coates, J. D. (2006). Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction. Nature Reviews Microbiology 4, 752–764.CrossRefGoogle Scholar
Wilkins, M., Livens, F., Vaughan, D. & Lloyd, J. (2006). The impact of Fe(III)-reducing bacteria on uranium mobility. Biogeochemistry 78, 125–150.CrossRefGoogle Scholar
Angell, P. (1999). Understanding microbially influenced corrosion as biofilm- mediated changes in surface chemistry. Current Opinion in Biotechnology 10, 269–272.CrossRefGoogle ScholarPubMed
Castro, H. F., Williams, N. H. & Ogram, A. (2000). Phylogeny of sulfate-reducing bacteria. FEMS Microbiology Ecology 31, 1–9.Google ScholarPubMed
Colwell, F. S., Onstott, T. C., Delwiche, M. E., Chandler, D., Fredrickson, J. K., Yao, Q. J., McKinley, J. P., Boone, D., Griffiths, R., Phelps, T. J., Ringelberg, D., White, D. C., LaFreniere, L., Balkwill, D., Lehman, R. M., Konisky, J. & Long, P. E. (1997). Microorganisms from deep, high temperature sandstones: constraints on microbial colonization. FEMS Microbiology Reviews 20, 425–435.CrossRefGoogle Scholar
Cypionka, H. (2000). Oxygen respiration by Desulfovibrio species. Annual Review of Microbiology 54, 827–848.CrossRefGoogle ScholarPubMed
Hansen, T. A. (1994). Metabolism of sulfate-reducing prokaryotes. Antonie van Leeuwenhoek 66, 165–185.CrossRefGoogle ScholarPubMed
Hedderich, R., Klimmek, O., Kroger, A., Dirmeier, R., Keller, M. & Stetter, K. O. (1999). Anaerobic respiration with elemental sulfur and with disulfides. FEMS Microbiology Reviews 22, 353–381.CrossRefGoogle Scholar
Hockin, S. and Gadd, G. M. (2003). Linked redox-precipitation of sulfur and selenium under anaerobic conditions by sulfate-reducing bacterial biofilms. Applied and Environmental Microbiology 69, 7063–7072.CrossRefGoogle ScholarPubMed
Hockin, S. and Gadd, G. M. (2006). Removal of selenate from sulphate-containing media by sulphate-reducing bacterial biofilms. Environmental Microbiology 8, 816–826.CrossRefGoogle Scholar
Hockin, S. and Gadd, G. M. (2007). Bioremediation of metals by precipitation and cellular binding. In Sulphate-reducing Bacteria: Environmental and Engineered Systems, ed. Barton, L. L. and Hamilton, W. A., pp. 405–434. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Holmer, M. & Storkholm, P. (2001). Sulphate reduction and sulphur cycling in lake sediments: a review. Freshwater Biology 46, 431–451.CrossRefGoogle Scholar
Gall, J. & Xavier, A. V. (1996). Anaerobes response to oxygen: the sulfate-reducing bacteria. Anaerobe 2, 1–9.CrossRefGoogle ScholarPubMed
Lie, T. J., Leadbetter, J. R. & Leadbetter, E. R. (1998). Metabolism of sulfonic acids and other organosulfur compounds by sulfate-reducing bacteria. Geomicrobiology Journal 15, 135–149.CrossRefGoogle Scholar
Rueter, P., Rabus, R., Wilkes, H., Aeckersberg, F., Rainey, F. A., Jannasch, H. W. & Widdel, F. (1994). Anaerobic oxidation of hydrocarbons in crude oil by new types of sulphate-reducing bacteria. Nature 372, 455–458.CrossRefGoogle ScholarPubMed
Schauder, R. & Kroger, A. (1993). Bacterial sulphur respiration. Archives of Microbiology 159, 491–497.CrossRefGoogle Scholar
Villemur, R., Lanthier, M., Beaudet, R. & Lepine, F. (2006). The Desulfitobacterium genus. FEMS Microbiology Reviews 30, 706–733.CrossRefGoogle ScholarPubMed
White, C. and Gadd, G. M. (1998). Accumulation and effects of cadmium on sulphate-reducing bacterial biofilms. Microbiology–UK 144, 1407–1415.CrossRefGoogle Scholar
White, C., Dennis, J. S. and Gadd, G. M. (2003). A mathematical process model for cadmium precipitation by sulphate-reducing bacterial biofilms. Biodegradation 14, 139–151.CrossRefGoogle Scholar
Blaut, M. (1994). Metabolism of methanogens. Antonie van Leeuwenhoek 66, 187–208.CrossRefGoogle ScholarPubMed
Deppenmeier, U., Lienard, T. & Gottschalk, G. (1999). Novel reactions involved in energy conservation by methanogenic archaea. FEBS Letters 457, 291–297.CrossRefGoogle ScholarPubMed
Dybas, M. & Konisky, J. (1992). Energy transduction in the methanogen Methanococcus voltae is based on a sodium current. Journal of Bacteriology 174, 5575–5583.CrossRefGoogle ScholarPubMed
Ferry, J. G. (1992). Biochemistry of methanogenesis. Critical Reviews in Biochemistry and Molecular Biology 27, 473–503.CrossRefGoogle ScholarPubMed
Ferry, J. G. (1999). Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiology Reviews 23, 13–38.CrossRefGoogle ScholarPubMed
Lin, W. C., Yang, Y.-L. & Whitman, W. B. (2003). The anabolic pyruvate oxidoreductase from Methanococcus maripaludis. Archives of Microbiology 179, 444–456.CrossRefGoogle ScholarPubMed
Macario, A. J. L., Lange, M., Ahring, B. K. & Macario, E. C. (1999). Stress genes and proteins in the archaea. Microbiology and Molecular Biology Reviews 63, 923–967.Google ScholarPubMed
Maden, B. E. H. (2000). Tetrahydrofolate and tetrahydromethanopterin compared: functionally distinct carriers in C-1 metabolism. Biochemical Journal 350, 609–629.CrossRefGoogle Scholar
Reeve, J. N., Nolling, J., Morgan, R. M. & Smith, D. R. (1997). Methanogenesis: genes, genomes, and who's on first?Journal of Bacteriology 179, 5975–5986.CrossRefGoogle ScholarPubMed
Schaefer, G., Engelhard, M. & Mueller, V. (1999). Bioenergetics of the Archaea. Microbiology and Molecular Biology Reviews 63, 570–620.Google Scholar
Schink, B. (1997). Energetics of syntrophic cooperation in methanogenic degradation. Microbiology and Molecular Biology Reviews 61, 262–280.Google ScholarPubMed
Shima, S. & Thauer, R. K. (2005). Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic Archaea. Current Opinion in Microbiology 8, 643–648.CrossRefGoogle ScholarPubMed
Thauer, R. K. (1998). Biochemistry of methanogenesis: a tribute to Marjory Stephenson. Microbiology-UK 144, 2377–2406.CrossRefGoogle ScholarPubMed
Valentine, D. L. & Reeburgh, W. S. (2000). New perspectives on anaerobic methane oxidation. Environmental Microbiology 2, 477–484.CrossRefGoogle ScholarPubMed
Bacher, A., Rieder, C., Eichinger, D., Arigoni, D., Fuchs, G. & Eisenreich, W. (1998). Elucidation of novel biosynthetic pathways and metabolite flux patterns by retrobiosynthetic NMR analysis. FEMS Microbiology Reviews 22, 567–598.CrossRefGoogle Scholar
Detkova, E. & Pusheva, M. (2006). Energy metabolism in halophilic and alkaliphilic acetogenic bacteria. Microbiology-Moscow 75, 1–11.CrossRefGoogle Scholar
Diekert, G. & Wohlfarth, G. (1994). Metabolism of homoacetogens. Antonie van Leeuwenhoek 66, 209–221.CrossRefGoogle Scholar
Drake, H. L. & Daniel, S. L. (2004). Physiology of the thermophilic acetogen Moorella thermoacetica. Research in Microbiology 155, 422–436.CrossRefGoogle ScholarPubMed
Ferry, J. G. (1995). CO dehydrogenase. Annual Review of Microbiology 49, 305–333.CrossRefGoogle ScholarPubMed
Grahame, D. A. (2003). Acetate C-C bond formation and decomposition in the anaerobic world: the structure of a central enzyme and its key active-site metal cluster. Trends in Biochemical Sciences 28, 221–224.CrossRefGoogle Scholar
Hansen, T. A. (1994). Metabolism of sulfate-reducing prokaryotes. Antonie van Leeuwenhoek 66, 165–185.CrossRefGoogle ScholarPubMed
Mueller, V. (2003). Energy conservation in acetogenic bacteria. Applied and Environmental Microbiology 69, 6345–6353.CrossRefGoogle Scholar
Ragsdale, S. (2004). Life with carbon monoxide. Critical Reviews in Biochemistry and Molecular Biology 39, 165–195.CrossRefGoogle ScholarPubMed
Russell, M. J. & Martin, W. (2004). The rocky roots of the acetyl-CoA pathway. Trends in Biochemical Sciences 29, 358–363.CrossRefGoogle ScholarPubMed
Siebers, B. & Schonheit, P. (2005). Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Current Opinion in Microbiology 8, 695–705.CrossRefGoogle ScholarPubMed
Sipma, J., Henstra, A. M., Parshina, S. N., Lens, P. N. L., Lettinga, G. & Stams, A. J. M. (2006). Microbial CO conversions with applications in synthesis gas purification and bio-desulfurization. Critical Reviews in Biotechnology 26, 41–65.CrossRefGoogle ScholarPubMed
Abraham, W., Nogales, B., Golyshin, P., Pieper, D. & Timmis, K. (2002). Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Current Opinion in Microbiology 5, 246–253.CrossRefGoogle ScholarPubMed
Borja, J., Taleon, D. M., Auresenia, J. & Gallardo, S. (2005). Polychlorinated biphenyls and their biodegradation. Process Biochemistry 40, 1999–2013.CrossRefGoogle Scholar
Chen, G. (2004). Reductive dehalogenation of tetrachloroethylene by microorganisms: current knowledge and application strategies. Applied Microbiology and Biotechnology 63, 373–377.CrossRefGoogle ScholarPubMed
Fantroussi, El S., Naveau, H. & Agathos, S. N. (1998). Anaerobic dechlorinating bacteria. Biotechnology Progress 14, 167–188.CrossRefGoogle ScholarPubMed
Fetzner, S. (1998). Bacterial dehalogenation. Applied Microbiology and Biotechnology 50, 633–657.CrossRefGoogle ScholarPubMed
Fetzner, S. & Lingens, F. (1994). Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications. Microbiological Reviews 58, 641–685.Google ScholarPubMed
Furukawa, K. (2000). Biochemical and genetic bases of microbial degradation of polychlorinated biphenyls (PCBs). Journal of General and Applied Microbiology 46, 283–296.CrossRefGoogle ScholarPubMed
Hoehener, P., Werner, D., Balsiger, C. & Pasteris, G. (2003). Worldwide occurrence and fate of chlorofluorocarbons in groundwater. Critical Reviews in Environmental Science and Technology 33, 1–29.CrossRefGoogle Scholar
Holliger, C. & Schumacher, W. (1994). Reductive dehalogenation as a respiratory process. Antonie van Leeuwenhoek 66, 239–246.CrossRefGoogle ScholarPubMed
Holliger, C., Wohlfarth, G. & Diekert, G. (1999). Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiology Reviews 22, 383–398.CrossRefGoogle Scholar
Janssen, D. B. (2004). Evolving haloalkane dehalogenases. Current Opinion in Chemical Biology 8, 150–159.CrossRefGoogle ScholarPubMed
Janssen, D. B., Oppentocht, J. E. & Poelarends, G. J. (2001). Microbial dehalogenation. Current Opinion in Biotechnology 12, 254–258.CrossRefGoogle ScholarPubMed
Janssen, D. B., Dinkla, J. T., Poelarends, G. J. & Terpstra, P. (2005). Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities. Environmental Microbiology 7, 1868–1882.CrossRefGoogle ScholarPubMed
McCarty, P. L. (1997). Microbiology: breathing with chlorinated solvents. Science 276, 1521–1522.CrossRefGoogle Scholar
Smidt, H. & Vos, W. M. (2004). Anaerobic microbial dehalogenation. Annual Review of Microbiology 58, 43–73.CrossRefGoogle ScholarPubMed
Vlieg, J. E. T. V., Poelarends, G. J., Mars, A. E. & Janssen, D. B. (2000). Detoxification of reactive intermediates during microbial metabolism of halogenated compounds. Current Opinion in Microbiology 3, 257–262.CrossRefGoogle Scholar
Wiegel, J. & Wu, Q. Z. (2000). Microbial reductive dehalogenation of polychlorinated biphenyls. FEMS Microbiology Ecology 32, 1–15.CrossRefGoogle ScholarPubMed
Arkhipova, O. & Akimenko, V. (2005). Unsaturated organic acids as terminal electron acceptors for reductase chains of anaerobic bacteria. Microbiology-Moscow 74, 629–639.CrossRefGoogle ScholarPubMed
Coates, J. D. & Achenbach, L. A. (2004). Microbial perchlorate reduction: rocket-fueled metabolism. Nature Reviews Microbiology 2, 569–580.CrossRefGoogle ScholarPubMed
Councell, T. B., Landa, E. R. & Lovley, D. R. (1997). Microbial reduction of iodate. Water, Air and Soil Pollution 100, 99–106.CrossRefGoogle Scholar
Geng, J., Jin, X., Wang, Q., Niu, X., Wang, X., Edwards, M. & Glindemann, D. (2005). Matrix bound phosphine formation and depletion in eutrophic lake sediment fermentation: simulation of different environmental factors. Anaerobe 11, 273–279.CrossRefGoogle ScholarPubMed
Kroger, A., Geisler, V., Lemma, E., Theis, F. & Lenger, R. (1992). Bacterial fumarate respiration. Archives of Microbiology 158, 311–314.CrossRefGoogle Scholar
Richardson, D. J. (2000). Bacterial respiration: a flexible process for a changing environment. Microbiology-UK 146, 551–571.CrossRefGoogle ScholarPubMed
Roels, J. & Verstraete, W. (2001). Biological formation of volatile phosphorus compounds. Bioresource Technology 79, 243–250.CrossRefGoogle ScholarPubMed
Slobodkin, A. I., Zavarzina, D. G., Sokolova, T. G. & Bonch-Osmolovskaya, E. A. (1999). Dissimilatory reduction of inorganic electron accepters by thermophilic anaerobic prokaryotes. Microbiology-Moscow 68, 522–542.Google Scholar
Cao, X., Liu, X. & Dong, X. (2003). Alkaliphilus crotonatoxidans sp. nov., a strictly anaerobic, crotonate-dismutating bacterium isolated from a methanogenic environment. International Journal of Systematic and Evolutionary Microbiology 53, 971–975.CrossRefGoogle ScholarPubMed
Bok, F. A. M., Stams, A. J. M., Dijkema, C. & Boone, D. R. (2001). Pathway of propionate oxidation by a syntrophic culture of Smithella propionica and Methanospirillum hungatei. Applied and Environmental Microbiology 67, 1800–1804.CrossRefGoogle ScholarPubMed
Bok, F. A. M., Luijten, M. L. G. C. & Stams, A. J. M. (2002). Biochemical evidence for formate transfer in syntrophic propionate-oxidizing cocultures of Syntrophobacter fumaroxidans and Methanospirillum hungatei. Applied and Environmental Microbiology 68, 4247–4252.CrossRefGoogle ScholarPubMed
Bok, F. A. M., Plugge, C. M. & Stams, A. J. M. (2004). Interspecies electron transfer in methanogenic propionate degrading consortia. Water Research 38, 1368–1375.CrossRefGoogle ScholarPubMed
Grabowski, A., Blanchet, D. & Jeanthon, C. (2005). Characterization of long-chain fatty-acid-degrading syntrophic associations from a biodegraded oil reservoir. Research in Microbiology 156, 814–821.CrossRefGoogle ScholarPubMed
Hattori, S., Galushko, A. S., Kamagata, Y. & Schink, B. (2005). Operation of the CO dehydrogenase/acetyl coenzyme A pathway in both acetate oxidation and acetate formation by the syntrophically acetate-oxidizing bacterium Thermacetogenium phaeum. Journal of Bacteriology 187, 3471–3476.CrossRefGoogle ScholarPubMed
Imachi, H., Sekiguchi, Y., Kamagata, Y., Hanada, S., Ohashi, A. & Harada, H. (2002). Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. International Journal of Systematic and Evolutionary Microbiology 52, 1729–1735.Google ScholarPubMed
Imachi, H., Sekiguchi, Y., Qiu, Y. L., Hugenholtz, P., Kimura, N., Wagner, M., Ohashi, A. & Harada, H. (2006). Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Applied and Environmental Microbiology 72, 2080–2091.CrossRefGoogle ScholarPubMed
Ishii, S., Kosaka, T., Hori, K., Hotta, Y. & Watanabe, K. (2005). Coaggregation facilitates interspecies hydrogen transfer between Pelotomaculum thermopropionicum and Methanothermobacter thermautotrophicus. Applied and Environmental Microbiology 71, 7838–7845.CrossRefGoogle ScholarPubMed
Johnson, M. R., Conners, S. B., Montero, C. I., Chou, C. J., Shockley, K. R. & Kelly, R. M. (2006). The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture. Applied and Environmental Microbiology 72, 811–818.CrossRefGoogle ScholarPubMed
Kendall, M. M., Liu, Y. & Boone, D. R. (2006). Butyrate- and propionate-degrading syntrophs from permanently cold marine sediments in Skan Bay, Alaska, and description of Algorimarina butyrica gen. nov., sp. nov. FEMS Microbiology Letters 262, 107–114.CrossRefGoogle ScholarPubMed
Kosaka, T., Uchiyama, T., Ishii, S., Enoki, M., Imachi, H., Kamagata, Y., Ohasi, A., Harada, H., Ikenaga, H. & Watanabe, K. (2006). Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. Journal of Bacteriology 188, 202–210.CrossRefGoogle ScholarPubMed
Plugge, C. M., Balk, M., Zoetendal, E. G. & Stams, A. J. M. (2002). Gelria glutamica gen. nov., sp. nov., a thermophilic, obligately syntrophic, glutamate-degrading anaerobe. International Journal of Systematic and Evolutionary Microbiology 52, 401–407.CrossRefGoogle ScholarPubMed
Qiu, Y.-L., Sekiguchi, Y., Imachi, H., Kamagata, Y., Tseng, I.-C., Cheng, S.-S., Ohashi, A. & Harada, H. (2003). Sporotomaculum syntrophicum sp. nov., a novel anaerobic, syntrophic benzoate-degrading bacterium isolated from methanogenic sludge treating wastewater from terephthalate manufacturing. Archives of Microbiology 179, 242–249.CrossRefGoogle ScholarPubMed
Qiu, Y. L., Sekiguchi, Y., Hanada, S., Imachi, H., Tseng, I. C., Cheng, S. S., Ohashi, A., Harada, H. & Kamagata, Y. (2006). Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens. Archives of Microbiology 185, 172–182.CrossRefGoogle ScholarPubMed
Zhang, C., Liu, X. & Dong, X. (2004). Syntrophomonas curvata sp. nov., an anaerobe that degrades fatty acids in co-culture with methanogens. International Journal of Systematic and Evolutionary Microbiology 54, 969–973.CrossRefGoogle ScholarPubMed
Zhilina, T., Zavarzina, D., Kolganova, T., Tourova, T. & Zavarzin, G. (2005). Candidatus ‘Contubernalis alkalaceticum’, an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture withDesulfonatronum cooperativum. Microbiology-Moscow 74, 695–703.Google Scholar
Boll, M. (2005). Key enzymes in the anaerobic aromatic metabolism catalysing Birch-like reductions. Biochimica et Biophysica Acta – Bioenergetics 1707, 34–50.CrossRefGoogle ScholarPubMed
Boll, M., Fuchs, G. & Heider, J. (2002). Anaerobic oxidation of aromatic compounds and hydrocarbons. Current Opinion in Chemical Biology 6, 604–611.CrossRefGoogle ScholarPubMed
Carmona, M. & Diaz, E. (2005). Iron-reducing bacteria unravel novel strategies for the anaerobic catabolism of aromatic compounds. Molecular Microbiology 58, 1210–1215.CrossRefGoogle ScholarPubMed
Chakraborty, R. & Coates, J. D. (2004). Anaerobic degradation of monoaromatic hydrocarbons. Applied Microbiology and Biotechnology 64, 437–446.CrossRefGoogle ScholarPubMed
Coates, J. D., Chakraborty, R. & McInerney, M. J. (2002). Anaerobic benzene biodegradation: a new era. Research in Microbiology 153, 621–628.CrossRefGoogle ScholarPubMed
Corvini, P., Schaeffer, A. & Schlosser, D. (2006). Microbial degradation of nonylphenol and other alkylphenols: our evolving view. Applied Microbiology and Biotechnology 72, 223–243.CrossRefGoogle ScholarPubMed
Esteve-Nunez, A., Caballero, A. & Ramos, J. L. (2001). Biological degradation of 2,4,6-trinitrotoluene. Microbiology and Molecular Biology Reviews 65, 335–352.CrossRefGoogle ScholarPubMed
Eyers, L., George, I., Schuler, L., Stenuit, B., Agathos, S. N. & El Fantroussi, S. (2004). Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Applied Microbiology and Biotechnology 66, 123–130.CrossRefGoogle ScholarPubMed
Gibson, J. & Harwood, S. (2002). Metabolic diversity in anaerobic compound utilization by anaerobic microbes. Annual Review of Microbiology 56, 345–369.CrossRefGoogle ScholarPubMed
Meckenstock, R. U., Safinowski, M. & Griebler, C. (2004). Anaerobic degradation of polycyclic aromatic hydrocarbons. FEMS Microbiology Ecology 49, 27–36.CrossRefGoogle ScholarPubMed
Spormann, A. M. & Widdel, F. (2000). Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria. Biodegradation 11, 85–105.CrossRefGoogle ScholarPubMed
Veeresh, G. S., Kumar, P. & Mehrotra, I. (2005). Treatment of phenol and cresols in upflow anaerobic sludge blanket (UASB) process: a review. Water Research 39, 154–170.CrossRefGoogle ScholarPubMed
Zhang, C. & Bennett, G. N. (2005). Biodegradation of xenobiotics by anaerobic bacteria. Applied Microbiology and Biotechnology 67, 600–618.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×