Bioremediation

Introduction

Bioremediation comes from two words—bio, which is short for biological, and remediation, meaning to remedy. The term refers to the use of living organisms including bacteria, fungi and plants, or enzymes from these organisms (enzymes are proteins that speed up chemical reactions without being changed by the reaction) to deal with an environmental problem.

The microbes can be added to the contaminated soil or water, which is typically removed from the original site of contamination and transported to another, more controlled site, although bioremediation can be done directly on-site. If successful, the contaminated environment is considerably cleaner, and can sometimes be returned to the state it was prior to the contamination.

Bioremediation exploits the fact that certain microorganisms that have the requisite enzyme(s) are able to use the toxic contaminating compound(s) as food. They degrade the compound to a form that can be used to provide energy for their growth and reproduction. The portions of the pollutant that remain are usually no longer toxic.

Examples of bioremediation include the degradation of chlorinated hydrocarbons including pesticides such as lindane and DDT, polychlorinated biphenyls (PCBs), and toxic compounds such as dioxins and furans. These compounds persistent in the environment for a long time and can accumulate in the food chain. Oil spills can be cleaned up, typically by adding nutrients such as nitrogen and sulfate containing fertilizer that encourages the growth of the microbes that will ultimately degrade the oil.

Although bioremediation can be done using microorganisms that are naturally present in the environment, the process can also be done, sometimes more efficiently and quickly, by deliberately adapting the organism to the presence of high concentrations of the pollutant. As well, organisms can be deliberately manipulated genetically to enhance their ability to degrade the target pollutant.

Historical Background and Scientific Foundations

Since bioremediation is a natural process, it was recognized centuries ago. For example, the first known use of microorganisms to treat wastewater dates back to Roman sewer systems built in 600 BC.

The modern era of bioremediation dates back to March 24, 1989. Then, the oil tanker Exxon Valdez hit a reef off of Prince William Sound in Alaska; the resulting spill of at least 11 million gallons of crude oil fouled an estimated 75 mi (120 km) of coastline in a region rich in sea life. The application of microorganisms and nutrients to oil-contaminated shoreline was successful in helping to remove much of the pollution. Following this success, the use of bioremediation was embraced by the U.S. Environmental Protection Agency (EPA), which had until then been hesitant about the strategy in natural settings.

At about the same time, scientists were gaining expertise in the genetic tools to deliberately insert and delete informational regions (genes) from the genetic material (genome) of bacteria, viruses, and other microorganisms. As well, genes contained in smaller circles of genetic material called plasmids that were capable of making new copies independent of the genome could be added to bacteria. The use of plasmids is particularly advantageous since multiple plasmids can be present in an individual bacterium, enabling more of the gene product to be made.

The ability to genetically modify microorganisms allowed microbes to be adapted more rapidly to a contaminated environment than could naturally occur. One example is the bacterium Deinococcus radiodurans, which is naturally resistant to radioactivity. Genetic engineering has made the organism capable of using the compounds toluene and mercury as nutrients. Since these are pollutants that are typically present in radioactive nuclear waste, D. radiodurans can be used in the bioremediation of radioactive spills.

For natural or engineered bacteria to be used for bioremediation, conditions that are favorable to the survival and, ideally, growth of the bacteria need to be established. This is because living and growing bacteria require nutrients; when the target toxic contaminant is used as a nutrient, biomediation can be successful.

Bioremediation is typically done using one of two strategies. The first approach, which is designed to increase the numbers of the target microbe or groups of microbes that can degrade the pollutant, is termed bioaugmentation. Bioaugmentation involves the deliberate addition of certain microbes that are adept at degrading the particular toxic chemicals, but which are normally not present or present in low and ineffective numbers.

Bioaugmentation was done in the aftermath of the Exxon Valdez spill using bacteria naturally present in seawater. The water was sprayed onto contaminated shoreline along with a mixture of nutrients. More precise bioaugmentation can be done using genetically engineered bacteria; this approach is more common when the contaminated soil or water is physically contained, either by use of an impermeable barrier or by the removal of the contaminated material to another site.

Instead of bioaugmentation, the contaminated site can be changed to enhance the metabolic activity of naturally occurring microbes that are already present in the contaminated soil or water. This process is known as biostimulation. Typical strategies are fertilization (addition of nutrients to the site), increasing the amount of oxygen present in the soil or water (aeration), or the addition of water (irrigation). Aeration encourages the growth and activity of aerobic bacteria, which require or can at least tolerate the presence of oxygen. Anaerobic bacteria, which do not tolerate the presence of oxygen, tend to have a metabolism that is much slower than aerobic bacteria. Although anaerobic bacteria may be capable of bioremediation, the timescale will be too long to be practical or safe in terms of restoring the site. By encouraging the activity of aerobic bacteria, bioremediation can be accomplished faster. Irrigation also increases bacterial activity, since virtually all bacteria require the presence of some moisture.

Bioremediation using microbes is not a solution for every contamination problem, however. For example, contamination involving some heavy metals cannot be easily handled using bacteria, since the metal cannot be easily taken up by the microbes or used as a nutrient.

WORDS TO KNOW

ANABOLISM: The process by which energy is used to build up complex molecules.

BIOAUGMENTATION: The introduction of specific strains of microorganisms to break down pollutants in contaminated soil or water.

CATABOLISM: The process by which large molecules are broken down into smaller ones with the release of energy.

GROUNDWATER: Fresh water that is present in an underground location.

One solution can be to use other living things that can bind the pollutant. The best example is phytoreme-diation—the use of plants. Plant species that have been bred to tolerate the presence of high concentrations of the particular contaminant can be planted on the contaminated site. As the plants grow, the pollutant compounds can accumulate in the stem or leaves. The plants can then be harvested along with the accumulated pollutant, which can be destroyed at very high temperature (incineration) or reclaimed. Successive rounds of planting and harvesting will, over time, greatly reduce the level of the contaminants in the soil.

Impacts and Issues

Bioremediation has and continues to be very successful in dealing with soil and water contamination. If successful, bioremediation of contaminated sites can be less expensive and less damaging to the environment than traditional clean-up technologies.

Although bioaugmentation has been used in the clean-up of contaminated sites since the late 1980s, the use of deliberately engineered bacteria is still not the first choice when the bioremediation is accomplished at the site of the contamination, due to concerns of the potential spread of the engineered organism in the environment. This risk can be engineered to be very low, since the engineered microbes can be genetically crippled to require the presence of a key nutrient that is not normally present in the environment, and so which must be supplied. Without the available nutrient, the engineered microbe dies.

These concerns have been beneficial, since they heightened scrutiny of bioremediation technology and resulted in strict controls over the process.

The use of genetically engineered bacteria is more common when the polluted soil has been removed and taken to another location for treatment in an enclosed container. The on-site use of genetically engineered

IN CONTEXT: BACTERIA AND SOIL REMEDIATION

Soil-modifying bacteria are employed in bioremediation. This process relies on the use of naturally occurring soil bacteria to convert a hazardous compound into a less hazardous or completely nontoxic compound. Some naturally occurring soil bacteria have the ability to break down a wide variety of compounds, including toxic compounds. However, contamination of soil with human-made chemicals, such as gasoline and polychlorinated biphenyls (PCBs, chemicals that used to be used as coolants), can often be most effectively handled by bacteria that have been specifically genetically engineered.

plants is more common and more easily accepted publicly. An example in a different area is the planting of genetically engineered crop plants. Despite ongoing unease by some, as of 2007 genetically engineered soybean, cotton, and corn plants were grown on over 100 million acres in the United States, making these varieties overwhelmingly more dominant than their natural counterparts.

As of 2008, bioremediation has been used to help clean up tens of thousands of sites involving contaminated soil and water around the globe. Included among these are Superfund sites—heavily contaminated sites in the United States that have long since been abandoned, and for which the EPA provides funds for clean up and restoration. Since its inception in 1980, almost 1,300 sites have been designated for remediation under this program.

Research is underway to identify microorganisms that have the genetic capability to be exploited in bioremediation. Much of this research examines microbes recovered from contaminated soil and water, the rationale being that they must have already adapted to the presence of the pollutant(s). The “high throughput” technology that is used can screen thousands of samples daily for the evidence of microbes with superior toxic degradation power.

See Also Chemical Spills; Oil Spills; Spill Remediation

BIBLIOGRAPHY

Books

Atlas, Ronald M., and Jim Philip. Bioremediation: Applied Microbial Solutions for Real-World Environment Cleanup. Washington: ASM Press, 2005.

Pisano, Gary P. Science Business: The Promise, The Reality, and the Future of Biotech. Boston: Harvard Business School Press, 2006.

Walker, Sharon. Biotechnology Demystified. New York: McGraw-Hill Professional, 2006.

Web Sites

Government of Canada. “Biobasics: Bioremediation.” February 9, 2006. http://biobasics.gc.ca/english/View.asp?x=741 (accessed February 7, 2008).

U.S. Geological Survey. “Bioremediation: Nature’s Way to a Cleaner Environment.” June 28, 2006. http://water.usgs.gov/wid/html/bioremed.html (accessed February 7, 2008).

Brian D. Hoyle