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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.


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.
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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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NCBI Taxonomy

Dehalococcoides ethanogenes





Derek R. Lovley's laboratory



An environment that is below the land surface.


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


A water-saturated subsurface environment.


A state lacking in oxygen.


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


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


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


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


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).

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