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Bioremediation is a waste management technique that uses organisms such as plants, bacteria, and fungi to remove or neutralize pollutants from a contaminated site. According to the United States EPA, bioremediation is a “treatment that uses naturally occurring organisms to break down hazardous substances into less toxic or non-toxic substances.”

Bioremediation is widely used to treat human sewage and has also been used to remove agricultural chemicals (pesticides and fertilizers) that leach from soil into groundwater. Bioremediation can also remove toxic metals from water, such as selenium and arsenic compounds. Mercury is an example of a toxic metal that can be removed from an environment by bioremediation. Mercury is an active ingredient in some pesticides and is also a byproduct of certain industries, such as battery production. Mercury is usually present in very low concentrations in natural environments, but it is highly toxic because it accumulates in living tissues. Several species of bacteria can carry out the biotransformation of toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas aeruginosa, can convert Hg²⁺ to Hg, which is less toxic to humans.

One of the most useful and interesting examples of the use of prokaryotes for bioremediation is the cleanup of oil spills. The importance of prokaryotes to petroleum bioremediation has been demonstrated in several oil spills in recent years, such as the Exxon Valdez spill in Alaska (1989) (Figure 1), the Prestige oil spill in Spain (2002), the spill into the Mediterranean from a Lebanon power plant (2006,) and more recently, the BP oil spill in the Gulf of Mexico (2010). To clean up these spills, bioremediation is promoted by adding inorganic nutrients that help bacteria already present in the environment to grow. Hydrocarbon-degrading bacteria feed on the hydrocarbons in the oil droplet, breaking them into inorganic compounds. Some species, such as Alcanivorax borkumensis, produce surfactants that solubilize the oil, while other bacteria degrade the oil into carbon dioxide. In the case of oil spills in the ocean, ongoing, natural bioremediation tends to occur since there are oil-consuming bacteria in the ocean before the spill. Under ideal conditions, it has been reported that up to 80 percent of the nonvolatile components in oil can be degraded within one year of the spill. Researchers have genetically engineered other bacteria to consume petroleum products; the first patent application for a bioremediation application in the U.S. was for a genetically modified oil-eating bacterium.

There are a number of cost/efficiency advantages to bioremediation, which can be employed in areas that are inaccessible without excavation. For example, hydrocarbon spills (specifically, oil spills) or certain chlorinated solvents may contaminate groundwater, which can be easier to treat using bioremediation than more conventional approaches.  This is typically much less expensive than excavation, followed by disposal elsewhere, incineration, or other off-site treatment strategies.  It also reduces or eliminates the need for “pump and treat,” a practice common at sites where hydrocarbons have contaminated clean groundwater. Using prokaryotes for the bioremediation of hydrocarbons also has the advantage of breaking down contaminants at the molecular level instead of simply chemically dispersing the contaminant.