Microbial bioremediation is the use of prokaryotes (or microbial metabolism) to remove pollutants. Bioremediation has been used to remove agricultural chemicals (e.g., pesticides, fertilizers) that leach from soil into groundwater and the subsurface. Certain toxic metals and oxides, such as selenium and arsenic compounds, can also be removed from water by bioremediation. The reduction of SeO₄^-2 to SeO₃^-2 and to Se⁰ (metallic selenium) is a method used to remove selenium ions from water. Mercury (Hg) is an example of a toxic metal that can be removed from an environment by bioremediation. As an active ingredient of some pesticides, mercury is used in industry and is also a by-product of certain processes, such as battery production. Methyl 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 Hg⁺² into Hg⁰, which is nontoxic to humans.

One of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills. The significance 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). In the case of oil spills in the ocean, ongoing natural bioremediation tends to occur, since there are oil-consuming bacteria in the ocean prior to the spill. In addition to these naturally occurring oil-degrading bacteria, humans select and engineer bacteria that possess the same capability with increased efficacy and spectrum of hydrocarbon compounds that can be processed. Bioremediation is enhanced by the addition of inorganic nutrients that help bacteria to grow.

Figure 1. (a) Cleaning up oil after the Valdez spill in Alaska, workers hosed oil from beaches and then used a floating boom to corral the oil, which was finally skimmed from the water surface. Some species of bacteria are able to solubilize and degrade the oil. (b) One of the most catastrophic consequences of oil spills is the damage to fauna. (credit a: modification of work by NOAA; credit b: modification of work by GOLUBENKOV, NGO: Saving Taman)

Some hydrocarbon-degrading bacteria feed on hydrocarbons in the oil droplet, breaking down the hydrocarbons into smaller subunits. Some species, such as Alcanivorax borkumensis, produce surfactants that solubilize the oil (making it soluble in water), whereas other bacteria degrade the oil into carbon dioxide. 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. Other oil fractions containing aromatic and highly branched hydrocarbon chains are more difficult to remove and remain in the environment for longer periods of time.