NC State Extension

Microbial Pathogens and on-Site Soil Treatment Systems

J.S. Meschke and M.D. Sobsey

Department of Environmental Science and Engineering, School of Public Health,

University of North Carolina

Chapel Hill, NC 27599


Onsite waste disposal systems (OSDS) are used to treat domestic waste for roughly 20% of the United States population (Scandura, 1997). These systems typically are comprised of an influent pipe from the house entering a septic tank, which serves as a settling chamber and anaerobic digester. The septic tank then connects to a distribution box which leads to the soil absorption field (SAF). Even under optimal conditions, very little treatment of microbial pathogens occurs in the septic tank. biological stabilization and pathogen removal primarily take place in the SAF. Properly functioning absorption fields are effective in reducing microbes and pose little health risk. However, failure of an absorption field to eliminate pathogens can lead to contaminated groundwater. Approximately half of the drinking water used in the United States is derived from groundwater and nearly half of waterborn outbreaks are attributed to contaminated groundwater (Craun, 1985). Contamination of groundwater from OSDS failure has been implicated in up to 40% of groundwater attributed outbreaks (Cogger, 1988). this review summarizes the factors and conditions that affect pathogen occurrence and persistence in, and removal from septic tank effluent (STE).


The four types of pathogens potentially present in human excreta are viruses, bacteria, protozoan, and helminth eggs. Viruses are very small (20-100nm) obligate intracellular parasites, comprised of nucleic acid enclosed in a protein capsid. Viruses are very host specific. Inside a host, viruses commander the hosts cellular machinery to replicate. Outside of a host, viruses behave as abiotic colloidal particles. The types of viruses in STE, referred to as enteric viruses, can cause a wide variety of diseases ranging form gastroenteritis to infectious hepatitis. Bacteria are prokaryotic cellular organisms (>>1-6 mm in size). the majority of bacteria in STE are not frank pathogens. Most are the normal flora which reside in the gut. enteric bacterial pathogens can cause disease ranging from gastroenteritis to ulcer to typhoid fever. protozoans are unicellular eukaryotic organisms (1-15 mm in size). they are generally shed from the gut in an environmentally stable cyst form. Diseases caused by enteric protozoans include gastroenteritis and dysentery. Helminths are intestinal worms. They are multicellular eukaryotic parasites. Helminth ova (30-100mm) may be shed in feces. Important representatives of the four enteric pathogen types are included in Table 1.

Initial pathogen treatment occurs in the septic tank and consists of removal by settling. A greater percentage of the protozoan cysts and helminth ova may be removed than bacteria or viruses during this process due to the much larger size. Removal of bacteria and viruses at this stage may be due to aggregation or adsorption to larger particles. Removal efficiencies for all four pathogen groups range from 0-2 log10 (0-99%) in the septic tank (Feachem, 1983). Numbers of pathogens in STE may reach 105-106/100ml (Hagedorn, 1981; feachem, 1983). Efficiency of removal for an optimally functioning OSDS, as a whole, may reach 9 log10 (99.9999999%)(Scandura, 1997).

Table 1. Important Human Enteric Microbial Pathogens


Enteroviruses: Polios, Echos

  • Hepatitis A virus
  • Hepatitis E virus
  • Reoviruses
  • Rotaviruses
  • Adenoviruses

Caliciviruses: Norwalk, Snow


  • Salmonella spp.
  • Campvlobacter spp.
  • Escherichia coli
  • Helicobacter pvlori
  • Aeromonas hydrophila
  • Yersinia enterocolitica
  • Vibrio cholerae, other Vibrio spp.
  • Brucella
  • Leptospira
  • Mycobacteria spp. (non-tubercular)
  • Shigel. spp.


  • Cryptosporidium parvum
  • Cyclospora caventensis
  • Giardia lamblia
  • Entamoeba histolvtica
  • Balatidium coli
  • Microsporidia
  • Toxoplasma gondii


  • Ancylostoma duodenale
  • Ascaris lumbridoides
  • Enterbius vermicularis
  • Necator americanus
  • Strongvloides stercoralis
  • Trichuris trichiura


The greatest removal of pathogens from STE occurs in the biological mat or clogging zone at the interface of the trench was and the soil. Only a few centimeters thick in a properly functioning OSDS, the zone serves as a filter by which the majority of the larger pathogens are entrained. However, viral and bacterial pathogens are small enough to pass through the effective pore size of the clogging zone. Removal of these pathogens is controlled primarily by attachment to the soil matrix rather than entrainment.

Attachment of Viruses and Bacteria

Microbial attachment of soil may be through adsorption or adhesion due to sticky coatings or cellular appendages (Gerba, 1984). Chemical binding is another possible attachment mechanism (usually associated with inactivation). Chemical binding of viruses may cause conformational changes in the virus capsid which render the virus inactive or perhaps open the capsid releasing the more easily degradable nucleic acid (Yeager, 1979). Adsorption of microbes is generally a weak attachment and microbes may be easily eluted or desorbed by low ionic strength rainwater (Reneau, 1989).


As a general rule, pathogens survive longer under moist conditions (Hurst, 1980; Gerba, 1984). Inactivation of microbes occurs only when soil moisture levels become very low (perhaps 1- 10%). As soil moisture levels decrease, pathogenic microbes may be inactivated by desiccation or enhanced predation due to a thinner moisture layer around individual soil particles.


Cool temperatures enhance pathogen survival. However, freezing temperatures may cause cellular damage and thus decrease survival (Hurst, 1980; Gerba 1984).

Organic Matter Content

Organic matter has been shown to increase survival of certain enteric bacteria and viruses in soil. However, organic matter may compete with viruses for adsorption sites (Gerba, 1984). Studies have shown that the survival of some viruses may be increased with increased adsorption (Hurst, 1980). Consequently, organic matter may increase virus transport and thereby adversely affect virus survival by preventing or reversing adsorption.

Microbial Antagonism

Ideally the clogging zone is unsaturated and aerobic (Cogger, 1988). This creates an ecological niche in which the facultative anaerobic bacteria of the gut are at a competitive disadvantage. Pathogens entrained in or attached to the matrix may be consumed or out competed for nutrients by the established microflora (Gerba, 1984). Established microflora may include ciliated grazers, amoebae, rotifers, fungi, and aerobic bacteria. Certain pathogens, including certain viruses (Hepatitis A virus), spore forming bacteria, protozoan cyst, and helminth ova, are very persistent in the environment and are not easily degraded in the clogging zone.

pH & Salt Content

Enteric bacteria have been shown to persist better in alkaline soils, rather than acid soils. Furthermore, pH and salt content may directly affect adsorption of viruses and bacteria. Viruses and bacteria have pH dependent surface charges. Near neutral pH the net surface charge of these microbes is negative. Increased cation concentrations, especially for multi-valent cations, increase adsorption (Gerba, 1984).

Soil Type and Topography

the siting of OSDSs is extremely important for proper functioning and efficient microbial reduction. High sand content soils may be too permeable, thus increasing the potential of groundwater contamination. Clayey soils, on the other hand, may not allow enough drainage, thus creating saturated and possible anaerobic conditions. Slope and location of bodies of water must be considered. A steep slope may increase the flow rate through SAF and nearby bodies of water may lead to seasonal saturated conditions.

Hydraulic Regime

Increased flow rate decreases adsorption of bacteria and viruses. Saturated conditions favor pathogen transport (Gerba, 1984). Influences of nearby wells (cones of depression) may affect pathogen movement through the SAF (Weissman, 1976).


Outbreaks attributed to groundwater contaminated by OSDSs are well documented for bacterial, viral and protozoan etiologic agents. Below are three examples of such outbreaks: a Cryptosporidium outbreak in England, a Norwalk Virus outbreak in Washington, and a Shigellosis outbreak in Florida.

In the cryptosporidiosis outbreak 47 cases of illness were reported. A strong correlation between location of cases and two groundwater sources was statistically established. Two well shafts in a single aquifer were implicated. One well was improperly sited such that during heavy rainfall it received surface runoff from a nearby grazing pasture. The second well was found to have a cross connection with a nearby SAF. The lining of this well showed signs of corrosion by aggressive water. The geology of the aquifer is sandstone, which apparently is somewhat karstic. Also, the area was a site of active coal mining (Bridgman, 1995).

In the shigellosis outbreak, roughly 1200 cases were reported from a local population of 6500. In this case a faulty OSDS at a local nursery school combined with a breakdown in chlorination of drinking water was implicated in the outbreak. A fluorescein dye test revealed that a church OSDS was continuously contaminating the source wells. The porosity of the soil was such that the cone of depression from the source well had a radius of up to 400 meters, while OSDSs were within 50 meters (Weissman, 1976).

The Norwalk-related outbreak affected roughly 72% of students and teachers at a grade school. The school received its water from an on-site well and used an OSDS to dispose of waste. A back siphonage of sewage into the well through a cross connection with the OSDS was identified as the probably cause of water contamination (Taylor, 1981).


Several field studies have been performed to determine the potential of groundwater contamination by on-site disposal systems. Below, two sample studies are summarized.

In the early 1980s, Vaugh et al. conducted a study on the entrainment of viruses in SAFs. The study observed movement of naturally occurring human enteroviruses from a OSDS through a shallow aquifer using a series of observation wells. Virus was detected greater than 60 m away from the OSDS and at depths of 18m (Vaughn, 1983).

In another study, Scandura and Sobsey compared the efficacy of four systems for the removal of bacterial and viral contamination. The soil in all systems was sand or sand-loam. Septic tanks were spiked with a model enteric virus several times over the course of a year, and samples were tested from the septic tank, distribution box and observation wells. Even in the most optimally operating system (the one with highest clay content), virus positive samples were found. Further study demonstrated the potential for rapid and extensive movement of viruses in the subsurface with the observation of virus positives in a well 35 m from the distribution lines after only 2 days (Scandura, 1997).


contamination of groundwater and nearby surface waters by microbial pathogens from on-site sewage treatment systems is always a potential risk to human health. Therefore, on-site wastewater treatment systems must be properly sited, designed, installed, operated, and maintained to ensure adequate long term performance in treating microbial pathogens, and other contaminants in sewage.


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