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The treatment of environmental problems through biological means is known as bioremediation and the specific use of plants for example by using phytoremediation. Bioremediation is sometimes used in conjunction with a pump and treat system. In bioremediation, either naturally occurring or specially bred bacteria are used to consume contaminants from extracted groundwater. This is sometimes referred to as a bio-gac system. Many times the groundwater is recycled to allow for continuously flowing water and enhanced bacteria population growth. Occasionally the bacteria can build up to such a point that they can affect filtration and pumping. The vessel should then be partially drained. Care must be taken to ensure that a sharp change in the groundwater chemistry does not kill the bacteria (such as a sudden change in pH).

Dual-phase extraction utilizes a soil vapor extraction system that produces a high vacuum resulting in the extraction of both contaminated vapors as well as a limited amount of contaminated groundwater. This method is somewhat inefficient due to large amount of energy required by pulling water by vacuum compared to pushing water with a submersible pump.

Mycoremediation is a form of bioremediation, the process of using fungi to return an environment (usually soil) contaminated by pollutants to a less contaminated state.

In an experiment conducted in conjunction with Batelle, a major contributor in the bioremediation industry, a plot of soil contaminated with diesel oil was inoculated with mycelia of oyster mushrooms; traditional bioremediation techniques (bacteria) were used on control plots. After four weeks, more than 95% of many of the PAH (polycyclic aromatic hydrocarbons) had been reduced to non-toxic components in the mycelial-inoculated plots. It appears that the natural microbial community participates with the fungi to break down contaminants into carbon dioxide and water. Wood-degrading fungi are particularly effective in breaking down aromatic pollutants (toxic components of petroleum), as well as chlorinated compounds (certain persistent pesticides; Battelle, 2000). Hair mats inoculated with oyster mushrooms were successfully employed in the clean-up of the San Francisco Bay area oil spill in 2007.

The key to mycoremediation is determining the right fungal species to target a specific pollutant. Certain strains have also been reported to successfully degrade the nerve gases VX and sarin.

Mycofiltration is a very similar process, using mycelial mats to filter toxic waste and microorganisms from polluted water.

» See the BioCycle line