By Kelly A. Reynolds, MSPH, Ph.D.

Since the emergence of environmental microbiology in the early 1970s, scientists have been both humbled by the devastating impact of environmentally transmitted microorganisms on human health, and awed by the wide-ranging adaptability and usefulness of microorganisms found in the environment. Today, microorganisms are being manipulated to provide a natural method for cleaning up some of the environment’s worst chemical hazards.

Hazardous waste
Every day, industrial, commercial and personal practices produce waste — many that are hazardous to public health or the ecosystem. Improper management of wastes may lead to contaminated air, soil and water. According to the U.S. Environmental Protection Agency (USEPA), one in four persons lives within four miles of a Superfund site — an uncontrolled or abandoned deposit of hazardous waste — with over 90 percent of these sites posing a threat to the surrounding population or sensitive environments. Exposure to hazardous wastes may result in reproductive disorders, birth defects, chronic illness (such as cancer or respiratory illnesses), neurological effects and weakened immunity.

The Toxic Substances Control Act’s inventory of commercial chemicals alone includes approximately 72,000 substances. While a handful of these agents are actively regulated and controlled, the exposure levels, treatment options, and public health effects of many aren’t well understood. More than 5,000 chemical accidents and 15,000 oil spills are reported each year to the National Response Center and USEPA regional offices.1

Underground storage tanks of petroleum waste products and other chemical hazards are a great concern, due to leakage, overflow or improper storage. Although the USEPA has stated a goal to reduce annual releases of underground storage tanks by 80 percent (57,000 releases in 1994 to 6,800 in 2005), many sites are already contaminated. Underground disposal of hazardous compounds may pose a particular concern for groundwater — the drinking water source for approximately half of Americans.

Manipulating the microbial world via various methods
The impact of hazardous wastes is highly varied depending on the contaminant, site, route of exposure, and sensitivity of the exposed population. Methods to reduce, control or eliminate problematic chemicals are equally varied. One consistency, however, is the adaptable nature of the microbial world. Microbes have been isolated from extreme environments, once thought incapable of sustaining any type of metabolic life. For example, bacteria have been isolated from hot springs where temperatures can be in excess of 100oC. Others inhabit the Great Salt Lake in Utah, where the salt content is higher than marine environments, or survive in acid mine drainage and the defensive mechanisms of the human stomach. In addition, well known to the water treatment industry, but nonetheless perplexing, are the populations of bacteria able to survive and multiply in virtually nutrient-free or ultrapure water.

Scientists haven’t only discovered microbes capable of surviving in hostile or toxic environments, but have found that microbes are also capable of immobilizing, degrading, removing or detoxifying environmental contaminants. In addition, methods of manipulating these populations to enhance their clean-up capabilities have been discovered, leading to the field of study known as bioremediation.

What is bioremediation?
Bioremediation is the breakdown (biodegradation) of contaminating compounds using microorganisms. These microbes often use contaminants as a food source, thereby completely eliminating toxic compounds by changing them into basic elements such as carbon dioxide and water, a process known as mineralization. Incomplete degradation may also occur, or the partial breakdown of the original contaminant to a less complex form. Another result may be the transformation of a compound to a different chemical structure that may affect the toxicity and mobility of the original agent. Sometimes immobilization of a compound occurs where the agent is overcome by the microbe but not eliminated or altered, which is often a potential benefit but rarely a final solution.

Typically, bioremediation provides an efficient and economical way to reduce environmental toxins, using indigenous or introduced microbes that naturally degrade contaminants. In the process of bioremediation, natural microbial populations are exploited to enhance the biodegradation process. This process may occur at the site of contamination (in situ) or in a designated area where the contaminant is removed from the original site (ex situ). Of particular concern is the carrying capacity of the microbial population, meaning the maximum toxic load that the population is able to withstand. Isolated microbes are capable of transforming or degrading a variety of organic and inorganic contaminants such as arsenic, nitrate, MTBE, perchlorate, radionuclides, lead, mercury, petroleum products, etc., at levels beyond suspected health standards.

Many known contaminants aren’t removed by conventional water treatment processes. Perchlorate, for example, is a known groundwater contaminant resistant to conventional chemical and physical removal processes. It is, however, readily biodegradable under proper conditions to undetectable levels by microbes that are widely available in nature.2 In addition, salt tolerant bacteria have been found that are capable of significant reduction of perchlorate concentrations in brines from ion exchange systems.3 Perchlorate is associated with the manufacture of explosives including solid propellant rocket fuel. Excessive amounts of it in drinking water can interfere with thyroid function and result in adverse developmental effects in children or tumors in all age groups.

Nitrates are one of the greatest concerns with regard to inorganic compound contamination of groundwater sources. Nitrates can enter the water supply through a variety of sources but application of fertilizers to agricultural fields is the greatest cause of U.S. nitrate contamination. Excessive nitrates in drinking water can initiate a variety of health problems including blue-baby syndrome, where it interferes with the body’s uptake of oxygen from the bloodstream. Nitrates can be removed from drinking water by ion exchange, reverse osmosis or distillation, but these treatments may result in high saline brines with high levels of nitrates. Denitrification is the microbial process by which nitrate or nitrite is reduced to the gaseous nitrogen species NO, N2O or N2. Denitrifying bacteria utilize a variety of inorganic and organic compounds as sources of carbon and energy, and are commonly found in the environment.

Optimum treatment conditions
Assessing conditions of the contaminated environment and/or the site of bioremediation is vital. Not all environments are well suited for the proliferation of the microbes most adapted for treatment of the particular contaminant. Thus, bioremediation may be augmented by soil additives, used to increase the growth and metabolism of specific microbes. These additives may include moisture, oxygen, chemicals, organic matter, etc. Biodegradation typically occurs more rapidly in the presence of oxygen, i.e., under aerobic conditions. Oxygen, however, isn’t always available in subsurface environments. In the absence of oxygen, biodegradation occurs under anaerobic conditions.

Often intrinsic microorganisms are available from natural environments. If tolerant microbes cannot be isolated from the test environment, they can be isolated from sites of known contamination where they’ve adapted to the presence of the target toxin. An intrinsic population is the most desirable since these microbes will be well adapted to conditions of the surrounding environment and are most likely to survive. Alternately, microbes can be genetically engineered, where their genomes are artificially enhanced to increase their ability to survive under conditions of varied exposures. Similarly, microbes may be artificially adapted to a foreign condition by a process called successive adaptation. This is accomplished in the laboratory by slowly increasing the concentration of the contaminant of interest in the microbial growth media, selecting for pure cultures of resistant populations. These developed microbes are often used in contained, controlled, and aboveground vessels (bioreactors) where conditions of temperature, pH, etc., may be optimized.

The major advantage of bioremediation is that it’s a natural process and can be used at a much lower cost than many other treatment technologies. The first documented successful use of bioremediation on a large scale was the 1989 Exxon Valdez oil spill in Alaska. Other examples of microbial waste management can be found in the treatment of municipal water or waste that commonly involve natural populations of microbes to decompose suspended solids and reduce pathogenic organisms and other pollutants such as MTBE, perchlorate or petrochemicls. Composting also involves use of microbial activity to reduce waste products to primary soil components and has been practiced since ancient times.

Bioremediation has proven to be an effective tool in the reduction of environmental contaminants but can rarely restore the affected environment back to its original condition. Residual contamination may be difficult to completely eliminate. In addition, bioremediation can be an extremely slow process, requiring manipulation of the treated environment to enhance the microbial activity. The diversity of ecosystems and the nature of living systems lead to uncertain outcomes.

Methods of water treatment, including filtration and absorptive media, can be very effective at removing contaminants from waste streams but often produce a highly concentrated waste product in the filtration media. When combined with other treatment systems such as ion exchange, bioremediation can aid in producing a cleaner waste stream, especially for persistent compounds, mixed wastes, or hard-to-reach environments such as the deep subsurface.


  1. USEPA, Environmental Goals for America, December 1996.
  2. Wu, J., et al., “Persistence of perchlorate and the relative numbers of perchlorate- and chlorate-respiring microorganisms in natural waters, soils, and wastewater,” Bioremediation Journal, 5: 119-130, 2001.
  3. Kim, K., and B.E. Logan, “Microbial reduction of perchlorate in pure and mixed culture packed-bed bioreactors,” Water Research Journal, 2001.
  4. Okeke, C.C., T. Giblin and W.T. Frankenberger, “Reduction of perchlorate and nitrate by salt tolerant bacteria,” Environmental Pollution Journal, 118: 357-363, 2002.
  5. Smith, R., “A household-scale treatment system that uses hydrogen-consuming bacteria to remove nitrate from contaminated drinking water,” 102nd General Meeting of the American Society for Microbiology, May 19-23, Salt Lake City, Utah, Session 69, paper O-47, 2002.

About the author
Dr. Kelly A. Reynolds is a research scientist at the University of Arizona with a focus on development of rapid methods for detecting human pathogenic viruses in drinking water. She holds a master of science degree in public health (MSPH) from the University of South Florida and doctorate in microbiology from the University of Arizona. Reynolds also has been a member of the WC&P Technical Review Committee since 1997.



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