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"Remediate" means to solve a problem, and "bio-remediate" means to use biological organisms to solve an environmental problem such as contaminated soil or groundwater. Bioremediation can be defined as any process that uses microorganisms and other living organisms like fungi, green plants or their enzymes to return a contaminated evironment back to its original state. Bioremediation may be employed to attack specific soil contaminants, such as degradation of chlorinated hydrocarbons by bacteria. An example of a more general approach is the cleanup of oil spills by the addition of nitrate and/or sulfate fertilisers to facilitate the decomposition of crude oil by indigenous or exogenous bacteria.

In a non-polluted environment, bacteria, fungi, protists, and other microorganisms are constantly at work breaking down organic matters. But in a polluted environment, some of these organisms may die, while a few others will survive by eating up the organic pollutants. Bioremediation works by encouraging the growth of these pollution-eating organisms providing them with fertilizer, oxygen, and other conditions. These organisms would then be able to break down the organic pollutant at a correspondingly faster rate. Naturally-occurring bioremediation and phytoremediation have been used for centuries. For example, desalination of agricultural land by phytoextraction has a long tradition. Bioremediation technology using microorganisms was reportedly invented by George M. Robinson in 1960s.

Bioremediation provides a good cleanup strategy for some types of pollution. Bioremediation provides a technique for cleaning up pollution by enhancing the same biodegradation processes that occur in nature. Depending on the site and its contaminants, bioremediation may be safer and less expensive than alternative solutions such as incineration or landfilling of the contaminated materials. It also has the advantage of treating the contamination in place so that large quantities of soil, sediment or water do not have to be dug up or pumped out of the ground for treatment.

Bioremediation can be carried out in situ by delivering nutrients to contaminated soils, hence it does not incur removal-disposal costs, like the cost associated physically removing and disposing of contaminated soils. Bioremediation also minimizes site disturbance and post-cleanup costs can be substantially reduced compared to traditional cleaning up processes. Even as some sites, natural microbial processes can remove contaminants without human intervention leading to a substantial cost savings. Some examples of bioremediation technologies are bioventing, landfarming, bioreactor, composting, bioaugmentation, rhizofiltration, and biostimulation.

In 1979, a pipeline carrying crude oil burst and contaminated the underlying aquifer. USGS scientists studying the site found that toxic chemicals leaching from the crude oil were rapidly degraded by natural microbial populations. However, naturally occurring microbial processes remediated the ground water contamination significantly. It was witnessed by ceasing of the contaminated plum after a few years as rates of microbial degradation came into balance with rates of contaminant leaching.

Agricultural chemicals affect the chemical quality of ground water in many Midwestern States. Studies in the midcontinent have traced the fate of nitrogen fertilizers and pesticides in ground and surface waters. These studies have shown that many common contaminants, such as the herbicide atrazine, are degraded by biological (microbial degradation) and non-biological (photolytic degradation) processes.

Gasoline is probably the most common contaminant of ground water in the United States. Studies at this site have demonstrated rapid microbial degradation of gasoline contaminants and have shown the importance of processes in the unsaturated zone (the zone above the water table) in degrading contaminants.

Creosote and chlorinated phenols, which are used extensively as wood preservatives in the United States, were found leaking in the underlying aquifer through several unlined ponds and were transported toward nearby Pensacola Bay. Studies at this site have demonstrated that microorganisms can adapt to extremely harsh chemical conditions and that microbial degradation was restricting migration of the contaminant plume.