Microbes in Groundwater

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Microbes in Groundwater

More than 95 percent of the world's available fresh water (excluding ice caps and glaciers) is underground. This groundwater is valuable as a source of drinking water for most communities in the world, especially small ones. In the United States, about 15 million private wells serve fewer than 25 people each. In addition, about 92 percent of the 168,000 water systems serving 25 people or more get most or all of their drinking water from groundwater. This article focuses on the common microbes in groundwater (bacteria, protozoa, and viruses), primarily from a public health point of view.

Commonly Occurring Microbes

Groundwater near the land surface usually teems with microbial life. Bacteria, which are microscopic single-celled organisms that lack a true nucleus and normally have a cell wall, are far more numerous than any other organism in the soil and groundwater. Near the surface where plant roots are abundant, there may be 100 million to 1 billion bacteria per gram of dry soil. These values decrease dramatically with soil depth below the root zone, with densities depending on the amount of nutrients (food) and water available. Although concentrations of microbes below the root zone are lower than in the root zone itself, as many as 10 to 100 million bacteria per gram of aquifer material may be present. Bacteria have been found in core samples from a depth of 2.8 kilometers (1.7 miles) below the Earth's surface, and at a depth of 3.2 kilometers in South African gold mines.

Protozoa, single-celled organisms that have a nucleus but lack a cell wall, also are common in groundwater. Protozoa typically are much larger than bacteria, and many types in groundwater feed on bacteria. Molds and other fungi also are common in groundwater near the land surface, where plenty of oxygen is present. These microbes are larger than bacteria and, unlike the protozoa, have a cell wall and often grow in long filaments. Most fungi feed on dead or decaying material. Algae may even be present despite the absence of sunlight. Similar to the bacteria, the numbers of protozoa, fungi, and algae decrease with depth.

A large variety of viruses probably are also common in groundwater. Viruses are much smaller than other microbes and cannot be seen with ordinary microscopes. They do not have a nucleus or cell wall, and can multiply only within the cells of larger organisms. The natural viruses in groundwater are able to reproduce only by infecting and usually killing the bacteria and other larger microbes present.

Microbial Habitats.

Microbes below Earth's surface must compete vigorously with each other for limited food and space. Bacteria that are not adapted to this habitat cannot survive long. Normally, nutrients are scarce in this environment, and thus microbes in groundwater grow slowly. Because the microbes in groundwater and other environmental habitats are well adapted to life in these habitats, few of them have the ability or the need to infect and cause illness in humans and other animals. However, a few environmental bacteria and protozoa may cause disease in humans by chance under certain circumstances, especially in individuals with a weakened immune system or major breaks in the skin that allow microbes to enter.

Many naturally-occurring bacteria below the surface may serve a beneficial role by destroying human-made toxic chemicals that migrate from the surface to groundwater. Some toxic chemicals, such as gasoline, are easy for subsurface bacteria to break down, but others, such as dry-cleaning fluid and some pesticides, are destroyed only slowly, if at all.

Disease-Causing Pathways

The groundwater in a drinking-water well may contain a wide variety of microbes without presenting a public health risk. However, groundwater in some areas becomes contaminated by the fecal material of humans and other animals. This is a cause for concern because fecal material may contain pathogenic (disease-causing) microbes that can infect the intestinal tract of humans. Fecal pathogens may be bacterial, viral, or protozoan.

Water containing fecal material may seep into the groundwater from the land surface or from underground sources of contamination. Major surface sources include:

  • Wastewater and biosolids from sewage treatment facilities that have been applied to land as a soil conditioner;
  • Seepage from shallow artificial ponds (lagoons) used for processing sewage;
  • Seepage from contaminated lakes and other surface-water bodies;
  • Urban runoff;
  • Feces from cattle and other livestock operations; and
  • Improperly constructed sanitary landfills where trash and garbage are disposed.

Fecal contamination also can reach the groundwater from underground sources, such as improperly functioning septic tank systems, underground reservoirs for liquid household sewage (cesspools), or leaking underground sewer lines. About 25 million septic tanks exist in the United States.

Pathogen Movement and Persistence.

Most pathogens from fecal matter remain either near the surface, or near the point of origin in the case of an underground source. However, where conditions are favorable, some pathogens travel along with the water flow though pores (tiny openings) in the surrounding soil and rock, and may enter groundwater. Whether a pathogen reaches the groundwater, especially in the area of a well intake, depends on how strongly it is retained by the soil and how long it survives. The extent to which a pathogen is retained by the soil depends on:

  • Soil characteristics, such as the number and size of pores and their interconnections, and how strongly the pathogen adsorbs (binds) to the soil particles;
  • Environmental factors, especially the amount of rainfall; and
  • The characteristics of an organism, including its size and its tendency to attach to other organisms and organic debris.

Rapid pathogen transport may occur in aquifers that have large pores (such as in a gravel-dominated aquifer), as well as in fractured rock, cave systems, and sinkholes .

Pathogen survival depends on a number of factors, including soil moisture content (longer survival when moist), soil temperature (longer survival at low temperatures), soil acidity (shorter survival in acid soils), amount of nutrients (longer survival of bacterial pathogen if high), and the activity of microbes that normally live in the soil. Normal soil bacteria are fully adapted to their environment and should easily outcompete bacterial pathogens for available nutrients. Some will also release one or more chemicals (toxins) that may kill the pathogens.

In most cases, only a small portion of the original pathogen density will reach a well intake unless a rapid pathway exists (such as fractured rock). Despite this, most reported waterborne disease outbreaks reported in the United States each year are associated with groundwater. Between 1971 and 2000, almost 60 percent of the approximately 700 reported outbreaks, with more than 90,000 cases of illness, were associated with water systems using groundwater.

Protecting Public Health

How can the public be protected from fecally contaminated groundwaters? Drinking-water supplies using groundwater can be protected from fecal contamination of the groundwater in several ways. Most importantly, suppliers can ensure that their well meets the state well-construction code. They can identify any sources of fecal contamination near the well intake and take proper corrective measures. Suppliers can also have an expert conduct a periodic on-site inspection, including an assessment of how vulnerable the source water is to nearby sources of fecal contamination.

Another means by which a water supply can be protected is to periodically test its source-water quality. To test for all possible pathogens, however, is not practical; the wide variety of potential waterborne pathogens and the limitations of analytical methods would make testing for all such pathogens extremely difficult, time-consuming, and expensive. Instead, inexpensive and easily measured indicators of fecal contamination are used rather than testing for specific pathogens. These include microbes that are extremely common in the gut of humans and other warm-blooded animals, but not elsewhere. If such indicators are absent, the pathogens whose normal habitat is the intestinal tract of humans and other warm-blooded animals should also be absent. Among the fecal indicators used for environmental waters, including groundwater, are Escherichia coli (a bacterium), fecal streptococci (a small group of bacteria), enterococci (very similar to fecal streptococci), and coliphage (a group of viruses that infect and kill E. coli ).

Water disinfection provides another barrier to pathogen entry and survival in the pipe network that distributes water (distribution system), especially if the source water is contaminated or vulnerable to fecal contamination. Disinfection kills pathogens and other microbes. Commonly used disinfectants for groundwaters include chlorine and ultraviolet light.

The U.S. Environmental Protection Agency develops regulations that apply to every water supplier that serves at least 25 people for at least 60 days during a year (defined as a public water system).* One regulation that protects groundwater systems from pathogens is the Total Coliform Rule (TCR). The TCR requires every public water system to monitor its tap water for a group of closely related bacteria, called total coliforms, at a frequency that depends on the number of people a system serves. While total coliforms are not a fecal indicator, they are used to detect problems in water treatment and in the distribution system. If any sample is total coliform positive, the system must then test for a fecal indicator (normally E. coli ).

Another regulation, the Surface Water Treatment Rule (SWTR), in addition to surface waters, also covers groundwater systems that are directly under the influence of surface waters. Among other requirements, the SWTR requires all such systems to disinfect. An important element in both the TCR and the SWTR, as amended, is a requirement for systems to have a periodic on-site inspection (sanitary survey) by a state official or a state-approved agent.

As of 2002, the Environmental Protection Agency was developing another regulation, the Groundwater Rule, which will require groundwater systems to determine whether the source water is fecally contaminated or is vulnerable to such contamination. If so, the system will be required to take corrective measures.

see also Drinking-Water Treatment; Ecology, Fresh-Water; Environmental Protection Agency, U.S.; Groundwater; Human Health and Water; Karst Hydrology; Land Use and Water Quality; Landfills: Impact on Groundwater; Life in Extreme Water Environments; Microbes in Lakes and Streams; Pollution of Groundwater; Pollution of Groundwater: Vulnerability; Pollution Sources: Point and Nonpoint; Safe Drinking Water Act; Septic System Impacts; Stream, Hyporheic Zone of a; Supplies, Protecting Public Drinking-Water; Supplies, Public and Domestic Water; Wastewater Treatment and Management; Wells and Well Drilling.

Paul S. Berger


Atlas, Ronald M., and Richard Bartha. Microbial Ecology. Redwood City, CA: The Benjamin/Cummings Publishing Company, 1993.

Bitton, Gabriel, and Charles P. Gerba, eds. Groundwater Pollution Microbiology. New York: John Wiley & Sons, 1984.

Chapelle, Francis H. Ground-Water Microbiology and Geochemistry. New York: John Wiley & Sons, 1993.

Frederickson, James K., and Tullis C. Onstott. "Microbes Deep Inside the Earth." Scientific American 275, no. 4 (1996):6873.


Common sources by which diseasecausing viruses enter groundwater are land disposal of sewage, overflow from septic systems, and livestock waste. Leachate from solid waste landfills also can contain viruses.

Contamination of drinking water with hepatitis A virus and other viruses has been documented throughout the world. Knowing how long these viruses can remain infective is important in estimating the probability that groundwater flow will move the viruses to drinking-water wells while they are still active.

Infective viruses have been demonstrated to travel more than 50 meters in depth from septic tanks into drinking-water wells. Viruses can travel great distances horizontally in aquifers with rapid water velocity, such as karst systems or alluvium with coarse cobbles.

Hydrologists are only beginning to understand the community dynamics of groundwater microbes, particularly viruses. More knowledge of the hydrology of soils and sediments also is necessary to better assess the human health problems related to viral contamination of groundwaters.

* The U.S. Environmental Protection Agency's drinking-water regulations can befound on the Internet at <http://www.epa.gov/safewater> .