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Cleaning up with genomics: applying molecular biology to bioremediation

Key Points

  • Microorganisms have the ability to destroy a variety of organic contaminants under either aerobic or anaerobic conditions and can immobilize toxic metals. However, the application of this metabolic potential to environmental restoration has been limited, in part, owing to a poor understanding of the microbiology of bioremediation.

  • An important early application of molecular biology to the study of bioremediation was the evaluation of 16S rRNA genes in contaminated environments, which provided an indication of the microorganisms that naturally inhabited these environments or became important when the environment was manipulated to accelerate bioremediation.

  • Analysis of mRNA levels for genes known to be important in bioremediation can provide an insight into the metabolic activity of microorganisms in contaminated environments.

  • Microorganisms closely related to those that are important in bioremediation in subsurface environments can be recovered in pure culture. Sequencing the genomes of these organisms, evaluating their physiology with gene-expression studies and genetic approaches, and in silico modelling of this physiology, can lead to a better understanding of how these microorganisms are likely to function in contaminated environments.

  • Sequencing of genomic DNA extracted directly from environments of interest can yield important data on the genetic potential of microorganisms in the environment. Comparisons of this information with available pure cultures point out similarities and differences between the physiologies of pure cultures and as-yet-uncultured organisms.

  • The application of genome-enabled techniques to the study of bioremediation is in its infancy, but shows promise to change bioremediation from a largely empirical practice to a science.

Abstract

Bioremediation has the potential to restore contaminated environments inexpensively yet effectively, but a lack of information about the factors controlling the growth and metabolism of microorganisms in polluted environments often limits its implementation. However, rapid advances in the understanding of bioremediation are on the horizon. Researchers now have the ability to culture microorganisms that are important in bioremediation and can evaluate their physiology using a combination of genome-enabled experimental and modelling techniques. In addition, new environmental genomic techniques offer the possibility for similar studies on as-yet-uncultured organisms. Combining models that can predict the activity of microorganisms that are involved in bioremediation with existing geochemical and hydrological models should transform bioremediation from a largely empirical practice into a science.

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Figure 1: Typical bioremediation reactions for oxidizable, organic contaminants and chlorinated solvents in contaminated aquifers.
Figure 2
Figure 3: Genome-enabled techniques contribute to the development of models of how microorganisms function in contaminated environments.
Figure 4
Figure 5

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References

  1. Anderson, R. T. & Lovley, D. R. Ecology and biogeochemistry of in situ groundwater bioremediation. Adv. Microbial. Ecol. 15, 289–350 (1997).

    CAS  Google Scholar 

  2. Wackett, L. P. & Hershberger, C. D. Biocatalysis and Biodegradation (ASM Press, Washington DC, USA, 2001). This book and the associated web site provide a comprehensive overview of many of the important reactions that are involved in bioremediation.

    Google Scholar 

  3. Lovley, D. R. Anaerobes to the rescue. Science 293, 1444–1446 (2001).

    CAS  PubMed  Google Scholar 

  4. Bond, D. R., Holmes, D. E., Tender, L. M. & Lovley, D. R. Electrode-reducing microorganisms harvesting energy from marine sediments. Science 295, 483–485 (2002).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Lovley, D. R., Woodward, J. C. & Chapelle, F. H. Stimulated anoxic biodegradation of aromatic hydrocarbons using Fe(III) ligands. Nature 370, 128–131 (1994).

    CAS  PubMed  Google Scholar 

  7. Lovley, D. R., Coates, J. D., Blunt-Harris, E. L., Phillips, E. J. P. & Woodward, J. C. Humic substances as electron acceptors for microbial respiration. Nature 382, 445–448 (1996).

    CAS  Google Scholar 

  8. Lovley, D. R. in Environmental Microbe–Metal Interactions (ed. Lovley, D. R.) 3–30 (ASM Press, Washington DC, USA, 2000).

    Google Scholar 

  9. Coates, J. D., Woodward, J., Allen, J., Philp, P. & Lovley, D. R. Anaerobic degradation of polycyclic aromatic hydrocarbons and alkanes in petroleum-contaminated marine harbor sediment. Appl. Environ. Microbiol. 63, 3589–3593 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Anderson, R. T. & Lovley, D. R. Anaerobic bioremediation of benzene under sulfate-reducing conditions in a petroleum-contaminated aquifer. Environ. Sci. Technol. 34, 2261–2266 (2000).

    CAS  Google Scholar 

  11. Spormann, A. M. & Widdel, F. Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria. Biodegradation 11, 85–105 (2000).

    CAS  PubMed  Google Scholar 

  12. Mohn, W. W. & Tiedje, J. M. Microbial reductive dehalogenation. Microbiol. Rev. 56, 482–507 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Holliger, C., Wohlfarth, G. & Diekert, G. Reductive dehalogenation in the energy metabolism of anaerobic bacteria. FEMS Microbiol. Rev. 22, 383–398 (1998).

    CAS  Google Scholar 

  14. Coates, J. D. & Anderson, R. T. Emerging techniques for anaerobic bioremediation of contaminated environments. Trends Biotechnol. 18, 408–412 (2000).

    CAS  PubMed  Google Scholar 

  15. Lovley, D. R., Phillips, E. J. P., Gorby, Y. A. & Landa, E. R. Microbial reduction of uranium. Nature 350, 413–416 (1991).

    CAS  Google Scholar 

  16. Anderson, R. T. et al. Stimuating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium contaminated aquifer. Appl. Environ. Microbiol. (in the press).

  17. Water Science and Technololgy Board, Commission on Engineering and Technical Systems, National Research Council. In Situ Bioremediation (National Academy Press, Washington DC, USA, 1993).

  18. Rogers, S. L. & McClure, N. in Bioremediation: A criticial review (eds Head, I. M., Singleton, I. & Milner, M. G.) 27–59 (Horizon Scientific Press, Wymondham, UK, 2003).

    Google Scholar 

  19. Pace, N. R., Stahl, D. A., Lane, D. J. & Olsen, G. J. The analysis of natural populations by ribosomal RNA sequence. Adv. Gen. Microbiol. Ecol. 9, 1–55 (1986).

    CAS  Google Scholar 

  20. Amann, R. I., Ludwig, W. & Schleifer, K. -H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Watanabe, K. & Baker, P. W. Environmentally relevant microorganisms. J. Biosci. Bioeng. 89, 1–11 (2000).

    CAS  PubMed  Google Scholar 

  22. Rooney-Varga, J. N., Anderson, R. T., Fraga, J. L., Ringelberg, D. & Lovley, D. R. Microbial communities associated with anaerobic benzene mineralization in a petroleum-contaminated aquifer. Appl. Environ. Microbiol. 65, 3056–3063 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Snoeyenbos-West, O. L., Nevin, K. P. & Lovley, D. R. Stimulation of dissimilatory Fe(III) reduction results in a predominance of Geobacter species in a variety of sandy aquifers. Microb. Ecol. 39, 153–167 (2000).

    CAS  PubMed  Google Scholar 

  24. Röling, W. F. M., van Breukelen, B. M., Braster, M., Lin, B. & van Verseveld, H. W. Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer. Appl. Environ. Microbiol. 67, 4619–4629 (2001).

    PubMed  PubMed Central  Google Scholar 

  25. Lovley, D. R. et al. Oxidation of aromatic contaminants coupled to microbial iron reduction. Nature 339, 297–299 (1989).

    CAS  Google Scholar 

  26. Holmes, D. E., Finneran, K. T. & Lovley, D. R. Enrichment of Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments. Appl. Environ. Microbiol. 68, 2300–2306 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Fennell, D. E., Carrol, A. B., Gossett, J. M. & Zinder, S. H. Assessment of indigenous reductive dechlorinating potential at a TCE-contaminated site using microcosms, polymerase chain reaction analysis and site data. Environ. Sci. Technol. 35, 1830–1839 (2001). One of the first indications that the microorganisms involved in reductive dechlorination in contaminated sediments are closely related to those available in pure culture.

    CAS  PubMed  Google Scholar 

  28. Richardson, R. E., Bhupathiraju, V. K., Song, D. L., Goulet, T. A. & Alvarez–Cohen, L. Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques. Environ. Sci. Technol. 36, 2652–2662 (2002).

    CAS  PubMed  Google Scholar 

  29. Hendrickson, E. R. et al. Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Appl. Environ. Microbiol. 68, 485–495 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Hayes, L. A. & Lovley, D. R. Specific 16S rDNA sequences associated with naphthalene degradation under sulfate-reducing conditions in harbor sediments. Microb. Ecol. 43, 134–145 (2002).

    CAS  PubMed  Google Scholar 

  31. Hristova, K., Gebreyesus, B., Mackay, D. & Scow, K. M. Naturally occurring bacteria similar to the methyl tert-butyl ether (MTBE)-degrading strain PM1 are present in MTBE-contaminated groundwater. Appl. Environ. Microbiol. 69, 2616–2623 (2003). Evidence that some microorganisms that are involved in aerobic degradation of contaminants in groundwater are also closely related to organisms that can be recovered in pure culture.

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734–740 (1997).

    CAS  PubMed  Google Scholar 

  33. Achenbach, L. A. & Coates, J. D. Disparity between bacterial phylogeny and physiology — comparing 16S rRNA sequences to assess relationships can be a powerful tool, but its limitations need to be considered. ASM News 66, 714–715 (2000).

    Google Scholar 

  34. He, J., Ritalahti, K. M., Aiello, M. R. & Loffler, F. E. Enrichment culture and identification of the reductively dechlorinating population as a Dehalococcoides species. Appl. Environ. Microbiol. 69, 996–1003 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Bunge, M. et al. Reductive dehalogenation of chlorinated dioxins by an anaerobic bacterium. Nature 421, 357–360 (2003).

    CAS  PubMed  Google Scholar 

  36. Schneegurt, M. A. & Kulpa, C. F. Jr The application of molecular techniques in environmental biotechnology for monitoring microbial systems. Biotechnol. Appl. Biochem. 27, 73–79 (1998).

    CAS  Google Scholar 

  37. Fleming, J. T., Sanseverino, J. & Sayler, G. S. Quantitative relationship between naphthalene catabolic gene frequency and expression in predicting PAH degradation in soils at town gas manufacturing sites. Environ. Sci. Technol. 27, 1068–1074 (1993). One of the first studies to demonstrate that mRNA could be recovered from contaminated soils and used to estimate rates of contaminant degradation.

    CAS  Google Scholar 

  38. Nazaret, S., Jeffrey, W. H., Saouter, E., von Haven, R. & Barkay, T. merA gene expression in aquatic environments measured by mRNA production and Hg(II) volatilization. Appl. Environ. Microbiol. 60, 4059–4065 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Jeffrey, W. H., Nazaret, S. & Barkay, T. Detection of the merA gene and its expression in the environment. Microbial Ecol. 32, 293–303 (1996).

    CAS  Google Scholar 

  40. Bakermans, C. & Madsen, E. L. Detection in coal tar waste-contaminated groundwater of mRNA transcripts related to naphthalene dioxygenase by fluorescent in situ hybridization with tyramide signal amplification. J. Microbiol. Meth. 50, 75–84 (2002).

    CAS  Google Scholar 

  41. Palenik, B. & Wood, A. M. in Molecular Approaches to the Study of the Ocean (ed. Cooksey, K. E.) 187–205 (Chapman & Hall, London, 1998).

    Google Scholar 

  42. Nierman, W. C. & Nelson, K. E. Genomics for applied microbiology. Adv. Appl. Microbiol. 51, 201–245 (2002).

    CAS  PubMed  Google Scholar 

  43. Childers, S. E., Ciufo, S. & Lovley, D. R. Geobacter metallireducens accesses Fe(III) oxide by chemotaxis. Nature 416, 767–769 (2002). Demonstration of how whole-genome sequencing can lead to the discovery of previously unsuspected physiological characteristics of a microorganism that is important in bioremediation.

    CAS  PubMed  Google Scholar 

  44. Nevin, K. P. & Lovley, D. R. Mechanisms for Fe(III) oxide reduction in sedimentary environments. Geomicrobiol. J. 19, 141–159 (2002).

    CAS  Google Scholar 

  45. Nevin, K. P. & Lovley, D. R. Mechanisms for accessing insoluble Fe(III) oxide during dissimilatory Fe(III) reduction by Geothrix fermentans. Appl. Environ. Microbiol. 68, 2294–2299 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Newman, D. K. & Kolter. A role for excreted quinones in extracellular electron transfer. Nature 405, 94–97 (2000).

    CAS  PubMed  Google Scholar 

  47. Baldi, P. & Hatfield, G. W. in Systems Biology 135–176 (Cambridge Univ. Press, Cambridge, UK, 2002).

    Google Scholar 

  48. Lloyd, J. R. et al. Biochemical and genetic characterization of PpcA, a periplasmic c-type cytochrome in Geobacter sulfurreducens. Biochem. J. 369, 153–161 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Leang, C., Coppi, M. V. & Lovley, D. R. OmcB, a c-type polyheme cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens. J. Bacteriol. 185, 2096–2103 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Palsson, B. The challenges of in silico biology. Nature Biotechnol. 18, 1147–1150 (2000). An excellent overview of the constraints-based, flux-balance approach to modelling microbial metabolism.

    CAS  Google Scholar 

  51. Covert, M. W. et al. Metabolic modelling of microbial strains in silico. Trends Biochem. Sci. 26, 179–186 (2001).

    CAS  PubMed  Google Scholar 

  52. Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S. & Gilles, E. D. Metabolic network structure determines key aspects of functionality and regulation. Nature 420, 190–193 (2002).

    CAS  PubMed  Google Scholar 

  53. Pramanik, J. & Keasling, J. D. Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model. Biotechnol. Bioeng. 60, 230–238 (1998).

    CAS  PubMed  Google Scholar 

  54. Edwards, J. S., Ibarra, R. U. & Palsson, B. O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotechnol. 19, 125–130 (2001).

    CAS  Google Scholar 

  55. Ibarra, R. U., Edwards, J. S. & Palsson, B. O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186–189 (2002).

    CAS  PubMed  Google Scholar 

  56. Covert, M. W. & Palsson, B. O. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277, 28058–28064 (2002).

    CAS  PubMed  Google Scholar 

  57. Edwards, J. S. & Palsson, B. O. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl Acad. Sci. USA 97, 5528–5533 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Schilling, C. H. et al. Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184, 4582–4593 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Pramanik, J., Trelstad, P. L., Schuler, A. J., Jenkins, D. & Keasling, J. D. Development and validation of a flux-based stoichiometric model for enhanced biological phosphorous removal. Wat. Res. 33, 462–476 (1999).

    Google Scholar 

  60. Lovley, D. R. Analysis of the genetic potential and gene expression of microbial communities involved in the in situ bioremediation of uranium and harvesting electrical energy from organic matter. Omics 6, 331–339 (2003).

    Google Scholar 

  61. DeLong, E. F. Microbial population genomics and ecology. Curr. Opin. Microbiol. 5, 520–524 (2002).

    PubMed  Google Scholar 

  62. Handelsman, J., Liles, M., Mann, D., Riesenfeld, C. & Goodman, R. M. Cloning the metagenome: culture-independent access to the diversity and functions of the uncultivated microbial world. Methods Microbiol. 33, 241–255 (2002).

    CAS  Google Scholar 

  63. Beja, O. et al. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289, 1902–1906 (2000). This paper shows that sequencing genomic DNA extracted from the environment can provide significant new insights into the physiological capabilities of as-yet-uncultured microorganisms.

    CAS  PubMed  Google Scholar 

  64. Beja, O., Spudich, E. N., Spudich, J. L., Leclerc, M. & DeLong, E. F. Proteorhodopsin phototrophy in the ocean. Nature 411, 786–789 (2001).

    CAS  PubMed  Google Scholar 

  65. Quaiser, A. et al. First insight into the genome of an uncultivated crenarchaeote from soil. Environ. Microbiol. 4, 603–611 (2002).

    CAS  PubMed  Google Scholar 

  66. Beja, O. et al. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2, 516–529 (2000).

    CAS  PubMed  Google Scholar 

  67. Schleper, C. et al. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 180, 5003–5009 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Dennis, P., Edwards, E. A., Liss, S. N. & Fulthorpe, R. Monitoring gene expression in mixed microbial communities by using DNA microarrays. Appl. Environ. Microbiol. 69, 769–778 (2003). A successful evaluation of gene expression in a mixture of microorganisms, indicating that evaluation of gene expression in natural environments could be tractable.

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Rodrîguez-Valera, F. Approaches to prokaryotic biodiversity: a population genetics perspective. Environ. Microbiol. 4, 628–633 (2002).

    PubMed  Google Scholar 

  70. Rondon, M. R. et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66, 2541–2547 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Entcheva, P., Liebl, W., Johann, A., Hartsch, T. & Streit, W. G. Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl. Environ. Microbiol. 67, 89–99 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Zinder, S. H. The future for culturing environmental organisms: a golden era ahead? Environ. Microbiol. 4, 14–15 (2002). An excellent discussion of the importance of culturing to environmental microbiology.

    PubMed  Google Scholar 

  73. Rappe, M. S., Connon, S. A., Vergin, K. L. & Giovannoni, S. J. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418, 630–633 (2002). A clear demonstration that, with enough imagination and persistence, environmentally important microorganisms can, in fact, be cultured.

    CAS  PubMed  Google Scholar 

  74. Sait, M., Hugenholtz, P. & Janssen, P. H. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ. Microbiol. 4, 654–666 (2002).

    CAS  PubMed  Google Scholar 

  75. Bruns, A., Cypionka, H. & Overmann, J. Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl. Environ. Microbiol. 68, 3978–3987 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Kaeberlein, T., Lewis, K. & Epstein, S. S. Isolating 'uncultivable' microorganisms in pure culture in a simulated natural environment. Science 296, 1127–1129 (2002).

    CAS  PubMed  Google Scholar 

  77. Emerson, D. & Moyer, C. Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH. Appl. Environ. Microbiol. 63, 4784–4792 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Connon, S. A. & Giovannoni, S. J. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68, 3878–3885 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Zengler, K. et al. Cultivating the uncultured. Proc. Natl Acad. Sci. USA 99, 15681–15686 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Hess, W. G. et al. The photosynthetic apparatus of Prochlorococcus: insights through comparative genomics. Photosynthesis Res. 70, 53–71 (2002).

    Google Scholar 

  81. Beja, O. et al. Comparative genomic analysis of archaeal genomic variant in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68, 3335–3345 (2002).

    Google Scholar 

  82. Prommer, H., Barry, D. A. & Zheng, C. MODFLOW/MT3DMS-based reactive multicomponent transport modelling. Ground Water 41, 247–257 (2003).

    CAS  PubMed  Google Scholar 

  83. Parkhurst, D. L. & Appelo, C. A. J. A user's guide to PHREEQC: a computer program for speciation, reaction-path, 1D-transport, and inverse geochemical calculations. US Geological Survey Water-Resources Investigations Report 99–4259. (1999).

    Google Scholar 

  84. Bethke, C. M. Geochemical Reaction Modelling (Oxford Univ. Press, New York, 1996).

    Google Scholar 

  85. Fetter, C. W. Hydrogeology (Prentice Hall, Engelwood Cliffs, New Jersey, 1994).

    Google Scholar 

  86. US Department of Energy, US Final Site Observational Workplan for the UMTRA Project Old Rifle Site Report no. GJO-99-88–TAR (Grand Junction, Colorado, USA, 1999).

  87. MaymoGatell, X., Chien, Y. T., Gossett, J. M. & Zinder, S. H. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276, 1568–1571 (1997).

    CAS  Google Scholar 

  88. Gibson, J. & Harwood, C. S. Metabolic diversity in aromatic compound utilization by anaerobic microbes. Ann. Rev. Microbiol. 56, 345–369 (2002).

    CAS  Google Scholar 

  89. Nelson, K. E. et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol. 4, 799–808 (2002).

    CAS  PubMed  Google Scholar 

  90. Coates, J. D. et al. The ubiquity and diversity of dissimilatory (per)chlorate-reducing bacteria. Appl. Environ. Microbiol. 65, 5234–5241 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Coates, J. D. et al. Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature 411, 1039–1043 (2001).

    CAS  PubMed  Google Scholar 

  92. Lanthier, M., Villemur, R., Lepine, F., Bisailon, J.-G. & Beaudet, R. Geographic distribution of Desulfitobacterium frappieri PCP-1 and Desulfitobacterium spp. in soils from the province of Quebec, Canada. FEMS Microbiol. Ecol. 36, 185–191 (2001).

    CAS  PubMed  Google Scholar 

  93. Lovley, D. R. & Phillips, E. J. P. Reduction of uranium by Desulfovibrio desulfuricans. Appl. Environ. Microbiol. 58, 850–856 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. Lovley, D. R. & Phillips, E. J. P. Reduction of chromate by Desulfovibrio vulgaris (Hildenborough) and its c3 cytochrome. Appl. Environ. Microbiol. 60, 726–728 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Makarova, K. S. et al. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol. Mol. Biol. Rev. 65, 44–79 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

Research on genomic approaches to bioremediation in the author's laboratory are supported by the Genomes to Life and NABIR programs of the Department of Energy, as well as the Office of Naval research.

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DATABASES

NCBI Taxonomy

Dehalococcoides ethanogenes

Geobacter

TIGR

Shewanella

FURTHER INFORMATION

Derek R. Lovley's laboratory

Glossary

SUBSURFACE ENVIRONMENT

An environment that is below the land surface.

XENOBIOTIC

A chemical that is only man-made, and is otherwise not found in the environment.

AQUIFER

A water-saturated subsurface environment.

ANOXIC

A state lacking in oxygen.

PIEZOMETER

A well in an aquifer for determining water levels to estimate the direction of groundwater flow.

CHELATOR

A compound that binds iron and other metals and holds them in solution.

ELECTRON SHUTTLE

A compound that accepts electrons from a microorganism and transfers them to an electron-accepting compound, such as Fe(III) oxide.

BACTERIAL ARTIFICIAL CHROMOSOME

A vector that can stably maintain a large foreign DNA insert and that can be propagated in E. coli.

PHOTOTROPHY

A process that involves the gain of energy from light.

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Lovley, D. Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev Microbiol 1, 35–44 (2003). https://doi.org/10.1038/nrmicro731

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