Bioremediation is the process of using living micro-organisms to clean up a contaminated site. Micro-organisms do this by removing toxins from materials. They decompose these compounds by using enzymes, specific proteins that control reactions in living cells. Organisms that produce enzymes capable of degrading petroleum are useful in cleaning up oil spills. Some common ones that break down oil are genetically engineered species of Pseudomonas and Azotobacter. Bioremediation accounts for 5 to 10 percent of all pollution treatment and has been used successfully in cleaning up leaking underground gasoline storage tanks.

Bioremediation has many applications, from the ordinary garden compost to the removal of selenium and other toxic metals from waste. The best agents for bioremediation are the ones that can break down contaminants without becoming contaminated or harmful themselves.