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Bioremediation means to use a biological remedy to abate or clean up contamination. This makes it different from remedies where contaminated soil or water is removed for chemical treatment or decontamination, incineration, or burial in a landfill. Microbes are often used to remedy environmental problems found in soil, water, and sediments. Plants have also been used to assist bioremediation processes. This is called phytoremediation. Biological processes have been used for some inorganic materials, like metals, to lower radioactivity and to remediate organic contaminants. With metal contamination the usual challenge is to accumulate the metal into harvestable plant parts, which must then be disposed of in a hazardous waste landfill before or after incineration to reduce the plant to ash. Two exceptions are mercury and selenium, which can be released as volatile elements directly from plants to atmosphere. The concept and practice of using plants and microorganisms to remediate contaminated soil have developed over the past thirty years.

The idea of bioremediation has become popular with the onset of the twenty-first century. In principle, genetically engineered plants and microorganisms

factor desired conditions
microbial population suitable kinds of organisms that can biodegrade all of the contaminants
oxygen enough to support aerobic biodegradation (about 2% oxygen in the gas phase or 0.4 mg/liter in the soil water)
water soil moisture should be from 5070% of the water holding capacity of the soil
nutrients nitrogen, phosphorus, sulfur, and other nutrients to support good microbial growth
temperature appropriate temperatures for microbial growth (040˚c)
ph best range is from 6.5 to 7.5

can greatly enhance the potential range of bioremediation. For example, bacterial enzymes engineered into plants can speed up the breakdown of TNT and other explosives. With transgenic poplar trees carrying a bacterial gene, methyl mercury may be converted to elemental mercury, which is released to the atmosphere at extreme dilution. However, concern about release of such organisms into the environment has limited actual field applications.

Natural Bioremediation

Natural bioremediation has been occurring for millions of years. Biodegradation of dead vegetation and dead animals is a kind of bioremediation. It is a natural part of the carbon, nitrogen, and sulfur cycles. Chemical energy present in waste materials is used by microorganisms to grow while they convert organic carbon and hydrogen to carbon dioxide and water.

Managed Bioremediation

When bioremediation is applied by people, microbial biodegradation processes are said to be managed. However, bioremediation takes place naturally and often it occurs prior to efforts to manage the process. One of the first examples of managed bioremediation was land farming (refers to the managed biodegradation of organic compounds that are distributed onto the soil surface, fertilized, and then tilled). Many petroleum companies have used it. High-molecular-weight organic compounds (i.e., oil sludges and wastes) are spread onto soil and then tilled into the ground with fertilizer, as part of the managed bioremediation process. Good conditions for microbial biodegradation are maintained by controlling soil moisture and soil nutrients. In 1974 R.L. Raymond was awarded a patent for the bioremediation of gasoline. This was one of the first patents granted for a bioremediation process.

Since about 1980, prepared bed systems have been used for bioremediation. In this approach, contaminated soil is excavated and deposited with appropriate fertilizers into a shallow layer over an impermeable base. Conditions are managed to obtain biodegradation of the contaminants of concern.


Composting has been used as a bioremediation process for many different organic compounds. It is widely employed to recycle nutrients in garden and yard waste. A finished compost can be used as a soil conditioner. Extending composting technology to new bioremediation applications requires experiments. The biodegradation process must be effective within the context of existing environmental conditions, and odors and gases that are generated by the process have to be strictly controlled.

In Situ Bioremediation

In situ processes (degrading the contaminants in place) are often recommended because less material has to be moved. These processes can be designed with or without plants. Plants have been used because they take up large quantities of water. This helps to control contaminated water, such as a groundwater contaminant plume , in the soil. Aerobic (oxygen-using) processes may occur in the unsaturated layer of soil, the vadose zone, which is found above the water table. The vadose zone is defined as the layer of soil having continuously connected passages filled with air, while the saturated zone is the deeper part where the pores are filled with water. Oxygen moves in the unsaturated zone by diffusion through pores in the soil. Some plants also provide pathways to move oxygen into the soil. This can be very important to increase the aerobic degradation of organic compounds.

Fate of Various Organic Contaminants

Petroleum-contaminated soil has been remediated in situ with plants added to enhance the degradation processes. The biodegradation of phenol, oil, gasoline, jet fuel, and other petroleum hydrocarbons occurs in soil. When plants are present, soil erosion is reduced and more microbes are present in the plant root zone. Methyl tertiary butyl ether (MTBE), used in gasoline to enhance the octane rating of the fuel, is difficult to remediate because it is very soluble in water and is hard to break down using microbes normally present in soil. In vegetation-based bioremediation, MTBE is moved from the soil to the atmosphere along with the water that plants take up from soil and release to the air. The MTBE breaks down rapidly in the atmosphere. Benzotriazoles, used as corrosion inhibitors in antifreeze and aircraft deicer fluids, are treated by plant-based bioremediation. The benzotriazole adsorbs or sticks to the plant roots and ends up as part of the plant biomass. Trichloroethylene (TCE) is a common chlorinated solvent that is biotransformed in the soil. It can be taken up by plants along with water. Then the TCE diffuses into the atmosphere where it is destroyed by atmospheric processes.


Bioremediation requires good nutrient and environmental conditions for biodegradation. When oxygen is needed for oxidation of the organic contaminants, bioventing (pumping air into the soil) is often used. Sometimes, fertilizers are added to the soil. In certain places irrigation is necessary so that plants or microbes can grow.

see also Abatement; Biodegradation; Brownfield; Cleanup.


Alexander, Martin. (1994). Biodegradation and Bioremediation. New York: Academic Press.

Davis, Lawrence C.; Castro-Diaz, Sigifredo; Zhange, Qizhi; and Erickson, Larry E. (2002). "Benefits of Vegetation for Soils with Organic Contaminants." Critical Reviews in Plant Sciences. 21 (5):457491.

Eweis, Juana B.; Ergas, Sarina J.; Chang, Daniel P.Y.; and Schroeder, Edward D. (1998). Bioremediation Principles. New York: McGraw-Hill.

Hannink, Nerissa K.; Rosser, Susan J.; and Bruce, Neil C. (2002). "Phytoremediation of Explosives." Critical Reviews in Plant Sciences. 21(5):511538.

McCutcheon, Steven C.; Schnoor, Jerald L., eds. (2003). Phytoremediation: Managing Contamination by Organic Compounds. New York: Wiley-Interscience.

Pilon-Smits, Elizabeth, and Pilon, Marinus. (2002). "Phytoremediation of Metals Using Transgenic Plants." Critical Reviews in Plant Sciences. 21(5):439456.

Rittmann, Bruce E. (1993). In Situ Bioremediation: When Does It Work? Washington, DC: National Academy Press.

Thomas, J.M.; Ward, C.H.; Raymond, R.L.; Wilson, J.T.; and Loehr, R.C. (1992). "Bioremediation." In Encyclopedia of Microbiology, Vol. 1, edited by Joshua Lederberg, pp. 369385. New York: Academic Press.

Internet Resources

Bioremediation Discussion Group. Available from

Natural and Accelerated Bioremediation Research Web site. Available from

Larry Eugene Erickson and Lawrence C. Davis

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Bioremediation is the use of organisms to break down and thereby detoxify dangerous chemicals in the environment. Plants and microorganisms are used as bioremediators. The technology can take advantage of a natural metabolic pathway or genetically modify an organism to have a particular toxic "appetite."

Natural Microbial Bioremediators

On March 24, 1989, an oil tanker called the Exxon Valdez crashed into a reef in the Prince William Sound in Alaska, spilling 11 million gallons of oil that devastated the highly populated ecosystem . Attempts to clean rescued animals and scrub oily rocks were of little help and actually killed some organisms. Bioremediation was more successful. Ten weeks after the spill, researchers from the U.S. Environmental Protection Agency applied phosphorus and nitrogen fertilizers to 750 oil-soaked sites. The fertilizer stimulated the growth of natural populations of bacteria that metabolize polycyclic aromatic hydrocarbons, which are organic toxins that were present in the spilled oil. Over the next few years, ecologists monitored and compared the areas that the bacteria had colonized to areas where they did not grow, and found that the level of polycyclic aromatic hydrocarbons fell five times faster in the bioremediated areas.

Another environmental disaster being treated with natural bioremediation is the pollution of the Hudson River in New York with polychlorinated biphenyls (PCBs). General Electric Corporation deposited these compounds along a 40-mile stretch of the river between 1947 and 1977. PCBs were used to manufacture hydraulic fluids, capacitors, pigments, transformers, and electrical equipment. PCBs come in 209 different and interconverting forms, and the toxicity of a particular PCB depends upon the number of chlorine atoms it includes. Debate rages over whether it is better to remove and bury the most contaminated sediments, or to allow natural bacteria in the river to detoxify the PCBs.

The bioremediation of the Hudson River is occurring in three stages. First, buried anaerobic bacteria strip off chlorines. In the water column, aerobic bacteria cleave the two organic rings of the PCBs. Finally, other microorganisms degrade the dechlorinated, broken rings into carbon dioxide, water, and chloride. While the process effectively detoxifies the PCBs, it is a long-term process that can take up to two centuries.

Natural Plant Bioremediators

For many millions of years, plants have adapted to the presence of various metals in varying amounts in soils. Some metals, such as zinc, nickel, cobalt, and copper, function as nutrients when eaten by humans in small amounts, but are toxic when consumed in excess. Heavy metals that are toxic even in trace amounts include mercury, lead, cadmium, silver, gold and chromium. Human activities such as mining, municipal waste disposal, and manufacturing have increased heavy metal pollution to dangerous levels in some areas. These chemicals cause oxidative damage, which destroys lipids, DNA, and proteins.

Certain plants, called hyperaccumulators, cope with excess heavy metals in the environment by taking them in and sequestering them in vacuoles , which are bubble-like structures in their cells. Sometimes the plant combines a pollutant with another molecule, a process called chelation. Organic acids often serve this role. Citric acid, for example, surrounds and thereby detoxifies cadmium, and malic acid does the same for zinc. A class of polypeptides called phytochelatins can also bind metals and escort them to vacuoles. Yet a third strategy that plants use to control metal accumulation is to employ a class of small, metal-binding proteins called metal-lothioneins. The intentional use of plants that use any of these ways to take heavy metals from soil is termed phytoremediation. It is a form of bioremediation.

Natural phytoremediators can be amazing. Consider Sebertia acuminata, a tree that lives in the tropical rain forest of New Caledonia, near Australia. Up to 20 percent of the tree's dry weight is nickel. If slashed, the bark oozes a bright green. This plant can perhaps be used to clean up nickel-contaminated soil. Soybeans also preferentially take up nickel from soil. Another phytore-mediator is Astragalus, also know as locoweed. It accumulates selenium from soil to counteract toxic effects of phosphorus, which tends to be abundant in selenium-rich soils. Cattle that munch on locoweed stagger about from selenium intoxication. Some plants act as sponges for metals in their environment. For example, plants that grow near gold mines assimilate gold into their tissues, apparently without harm. Prospectors use the gold content of such plants to locate deposits of the precious metal. Plants that grow near highways take up lead from gasoline exhaust. Near nuclear test sites, plants absorb radioactive strontium.

Genetically Modified Bioremediators

Biotechnology can transfer the ability to manufacture detoxifying proteins from one type of organism to another. One organism that was so modified has earned the distinction of being the first micro-organism to be patented. Called the "oil eater," the microorganism was actually a naturally occurring bacterium that had been given four plasmids that were also naturally occurring (plasmids are rings of DNA that can be transferred from one cell to another). It was the combination of the four transferred plasmids in a single bacterial cell that was novel and therefore patent-worthy. The four plasmids in the oil eater gave the bacterium the ability to degrade four components of crude oil. It was invented by Ananda Chakrabarty at General Electric in 1980.

Today, transgenic technology creates designer bioremediators. A transgenic organism contains a gene from another type of organism in all of its cells. The altered organism then manufactures the protein that the transgene encodes. The technology works because all organisms use the same genetic code. In other words, the same DNA and RNA triplets encode the same amino acids in all species.

Transgenic bioremediation can engineer microbial metabolic reactions into plants whose root cells then produce the needed proteins and distribute them in the soil. For example, transgenic yellow poplar trees can thrive in soil that has been heavily contaminated with mercury if they have been given a bacterial gene that encodes the enzyme called mercuric reductase. This enzyme catalyzes the chemical reaction that converts a highly toxic form of mercury in soil to a less toxic gas. The leaves of the tree then emit the gas to the atmosphere, where it dissipates.

Cleaning up munitions dumps is yet another target of transgenic plants, with some interesting biological participants. In one approach, a bacterial gene that breaks down trinitrotoluene (TNT, the major component of dynamite and land mines) is linked to a jellyfish gene that makes the protein glow green. The bacteria can be spread directly on soil that is thought to contain weapons residues, or the genes can be transferred to various types of plants, whose roots then glow when they are near buried explosives. In the future, plants that have been genetically modified in several ways will be able to detect a variety of pollutants or toxins.

see also Eubacteria; Transgenic Organisms: Ethical Issues.

Ricki Lewis


Bolin, Frederick. "Leveling Land Mines with Biotechnology." Nature Biotechnology 17 (1999): 732.

Eccles, Harry. Bioremediation. New York: Taylor and Francis, 2001.

Hooker, Brian S., and Rodney S. Skeen. "Transgenic Phytoremediation Blasts onto the Scene." Nature Biotechnology 17 (1999): 428.

Lewis, Ricki. "PCB Dilemma." The Scientist 15 (2001): 1.

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Bioremediation is the use of living organisms or ecological processes to deal with a given environmental problem. The most common use of bioremediation is the metabolic breakdown or removal of toxic chemicals before or after they have been discharged into the environment. This process takes advantage of the fact that certain microorganisms can utilize toxic chemicals as metabolic substrates and render them into less toxic compounds. Bioremediation is a relatively new and actively developing technology. Increasingly, microorganisms and plants are being genetically engineered to aide in their ability to remove deleterious substances.

In general, bioremediation methodologies focus on one of two approaches. The first approach, bioaugmentation, aims to increase the abundance of certain species or groups of microorganisms that can metabolize toxic chemicals. Bioaugmentation involves the deliberate addition of strains or species of microorganisms that are effective at treating particular toxic chemicals, but are not indigenous to or abundant in the treatment area. Alternatively, environmental conditions may be altered in order to enhance the actions of such organisms that are already present in the environment. This process is known as biostimulation and usually involves fertilization, aeration, or irrigation. Biostimulation focuses on rapidly increasing the abundance of naturally occurring microorganisms capable of dealing with certain types of environmental problems.

Accidental spills of petroleum or other hydrocarbons on land and water are regrettable but frequent occurrences. Once spilled, petroleum and its various refined products can be persistent environmental contaminants. However, these organic chemicals can also be metabolized by certain microorganisms, whose processes transform the toxins into more simple compounds, such as carbon dioxide, water, and other inorganic chemicals. In the past, concentrates of bacteria that are highly efficient at metabolizing hydrocarbons have been "seeded" into spill areas in an attempt to increase the rate of degradation of the spill residues. Although this technique has occasionally been effective, it commonly fails because the large concentrations of hydrocarbons stimulates rapid growth of indigenous microorganisms also capable of utilizing hydrocarbons as metabolic substrates. Consequently, seeding of microorganisms that are metabolically specific to hydrocarbons often does not affect the overall rate of degradation.

Environmental conditions under which spill residues occur are often sub-optimal for toxin degradation by microorganisms. Most commonly the rate is limited by the availability of oxygen or of certain nutrients such as nitrate and phosphate. Therefore the microbial breakdown of spilled hydrocarbons on land can be greatly enhanced by aeration and fertilization of the soil.

Metals are common pollutants of water and land because they are emitted by many industrial, agricultural, and domestic sources. In some situations organisms can be utilized to concentrate metals that are dispersed in the environment. For example, metal-polluted waste waters can be treated by encouraging the vigorous growth of certain types of vascular plants. This bioremediation system, also known as phytoremediation, works because the growing plants accumulate high levels of metals in their shoots, thereby reducing the concentration in the water to a more tolerable range. The plants can then be harvested to remove the metals from the system.

Many advanced sewage-treatment technologies utilize microbial processes to oxidize organic matter associated with fecal wastes and to decrease concentrations of soluble compounds or ions of metals, pesticides, and other toxic chemicals. Decreasing the aqueous concentrations of toxic chemicals is accomplished by a combination of chemical adsorption as well as microbial biodegradation of complex chemicals into their inorganic constituents.

If successful, bioremediation of contaminated sites can offer a cheaper, less environmentally damaging alternative to traditional clean-up technologies.

See also Economic uses and benefits of microorganisms; Microbial genetics; Waste water treatment; Water purification; Water quality

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The word "bioremediation" was coined by scientists in the early 1980s as a term to describe the use of microorganisms to clean polluted soils and waters. The prefix bio defined the process as biological, that is, carried out by living organisms. The noun remediation defined the process as one that resulted in the cleaning, or remediation, of the environment, via complete degradation, sequestration, or removal of the toxic pollutants as the result of microbial activity. Degradation means that the microorganisms decompose the pollutants to harmless natural products such as carbon dioxide (CO2), water (H2 O), or other nontoxic naturally occurring compounds . Sequestration means that the pollutant is trapped or changed in a way that makes it nontoxic or unavailable to biological systems. Removal means that while the pollutant is not necessarily degraded, the microbes physically remove it from the soil or water so that it can be collected and disposed of safely.

The principal goal of bioremediation is to return polluted environments to their natural state. Examples of the many contaminants that are amenable to bioremediation via degradation include organic chemicals such as pesticides, insecticides, herbicides, and pollutants derived from petroleum as the result of oil or fuel spills, or oil refining activities. Research in the 1990s has shown that even synthetic chemicals previously thought to be totally resistant to degradation, such as the insecticide DDT or the explosive TNT, are, in fact, degradable by microorganisms when they are supplied the right growth conditions. Examples of pollutants that can be sequestered or removed by microorganisms include toxic heavy metals such as lead (Pb), cadmium (Cd), and arsenic (As), and radioactive metals such as uranium (U). Toxic levels of metals are found in soils or waters previously contaminated as the result of military, industrial, or mining activities. Metals are found in various chemical forms, but unlike organic compounds, metals cannot be degraded. They can be changed only to some other chemical form. Therefore, the goal of metal bioremediation is to use microbes to change the metals into a form that is either sequestered in the soil in an insoluble form, or changed into a soluble form that can be removed from the soil with water, and then recovered later.

Various processes are used to carry out bioremediation. They include ex situ techniques, where contaminated soil is excavated, bioremediated in a vessel or pile, and then returned to the environment. Alternatively, with in situ techniques, the contamination is treated where it occurred. This approach is particularly suited to treating contaminated groundwater in deep aquifers. Bioremediation can involve the inoculation of a contaminated environment with the specific microorganisms needed to carry out the bioremediation, or supplementation of the environment with nutrients that will promote the activity of microbes already naturally present. When supplementation is done in situ, it is sometimes called naturally accelerated bioremediation. The microorganisms naturally present in some contaminated environments may sometimes slowly bioremediate that environment without any human intervention. This type of bioremediation is called natural attenuation, a process that usually occurs very slowly over many years. Because it is effective and affordable, bioremediation is often the method of choice for cleaning polluted soils, groundwaters, aquatic areas, wetlands, and other environments.

see also Human Impacts; Soil, Chemistry of.

Don L. Crawford


Chaudhry, G. Rasul, ed. Biological Degradation and Bioremediation of Toxic Chemicals. Portland, OR: Dioscorides Press, 1994.

Crawford, Ronald L., and Don L. Crawford, eds. Bioremediation: Principles and Applications. New York: Cambridge University Press, 1996.

Quensen, J. F., S. A. Mueller, M. K. Jain, and J. M. Tiedje. "Reductive Dechlorination of DDE to DDMU in Marine Sediment Microcosms." Science 280 (1998): 722-24.


Phytoremediation uses plants to remove both soilborne and waterborne pollutants. It is proving especially useful for treating heavy metal contamination, an exceptionally difficult type of cleanup job. Plants need soil nutrients and are efficient absorbers of all kinds of minerals. Some species, called hyper-accumulators, can concentrate metals thousand of times above normal levels. Indian mustard (Brassica juncea ) will hyperaccumulate lead, chromium, cadmium, nickel, selenium, zinc, copper, cesium, and strontium. Detoxifying the soil is as simple as harvesting the plants.

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