Wastewater treatment procedures vary depending on the intended use of that water (recreation, water supply, etc.) but usually involves a physical, chemical, or biological process to rid it of harmful microbial species or accumulated chemicals.
The US EPA regulates public drinking water systems, and a complete list of their regulations and methods is available.
Household water treatment methods are widely promoted in developing countries, and their efficacies against various microorganisms have been summarized.
The wastewater treatment process typically involves three stages; Primary, Scondary, and Tertiary Treatment. These are then followed by a Disinfection step typically utilizing chlorine. More recent advances have also allowed for the use of UV light and ozone during this stage.
Primary Treatment is often a purely physical process with the intention of removing larger pollutants from sewage. A screen is typically employed before wastewater ever enters a treatment plant(this is called Preliminary Treatment) to remove very large items such as golf balls, toys, wood, or other debris. Following Preliminary Treatment, the wastewater enters a treatment plant where it is collected in systems designed to remove pollutants that can be settled out of the water by gravity(Primary Sedimentation). Chemical coagulation or filatration are other popular methods used during this step.
Secondary Treatment aims to remove organic material that was not removed during Primary Treatment. This is accomplished using either Attached Growth Processes or Suspended Growth Processes. In both systems, microorganisms are supplied with oxygenated water and build slime layers, or biofilms in a controlled environment. These bacteria can use the organic material within the wastewater as a source of food, while the oxygen is used to keep the system aerobic. Eventually, the biofilm may slough off its attached surface and need to be collected in a Secondary Collection Tank.
In some cases wastewater treatment stops here. If the water is being released into an area that may be used for drinking water, further treatment is necessary.
Support Data to follow
Tertiary Treatment is often used if the water is going to be used for drinking water. Its purpose is to further decrease BOD as well as levels of certain chemicals that algae and bacteria require for growth, such as Phophorous. This is usually carried out with the addition of alum or lime to the water. However, these methods are often expensive as they involove additional volumes of chemicals that must be purchased prior to treatment. New methods aimed at manipulating bacterial life cycles to capture and remove phosphorus are proving to be a money-saving alternative many municipal and industrial companies are watching closely.
The few organisms that remain after Primary, Secondary, and Tertiary Treatment are killed or deactivated in a Disinfection stage. The three most effective disinfection procedures use Chlorine, Ultra-Violet Light, or Ozone.
The most widely used disinfectant is Chlorine. Chlorine oxidizes cellular material, killing bacteria. Depending on the system, chlorine gas, hypochlorite solution, or another liqued or solid form of chlorine may be used for disinfection. The dose typically ranges from 5-20mg/L.
After chlorination, some chlorine residuals may remain in the water. These can be harmful to aquatic life and are usually removed through dechlorination with sulfur dioxide, sodium bisulfate, or sodium metabisulfate.
An Ultraviolet (UV) disinfection system transfers electromagnetic energy from a mercury arc lamp to an organism's genetic material (DNA and RNA). When UV radiation penetrates the cell wall of an organism, it destroys the cell's ability to reproduce. UV radiation, generated by an electrical discharge through mercury vapor, penetrates the genetic material of microorganisms and retards their ability to reproduce.
- EPA Public Water Systems
- Sobsey MD, Stauber C, Casanova L, Brown J and Elliott M (2008) Point of use household drinking water filtration: A practical, effective solution for providing sustained access to safe drinking water in the developing world. Environmental Science & Technology. 42 (12), 4261–4267.
- EPA Wastewater Treatment
- EPA Chlorine Fact Sheet
Both vinegar and baking soda can be used as natural antimicrobial disinfectants. Vinegar has shown a < 3 log10 reduction of both Staphylococcus aureus and Escherichia coli, while baking soda successfully elimintated < 3 log10 of S. aureus, E. coli, Pseudomonas aeruginosa, and Salmonella enterica Choleraesuis. 
Common household commercial disinfectants include: Vesphene IIse, TBQ, Clorox, and Lysol disinfectant spray, Antibacterial Kitchen Cleaner, Mr. Clean Ultra and ethanol. These products have typically been shown to be more effective at eliminating bacteria from fomites than natural products, with reductions in bacterial concentrations ranging from 4-6 log10.
A more complete list of disinfectants as well as their relative effectiveness is found here.
- Household Cleaners Study
- [http://www.unc.edu/depts/spice/dis/ICHE-2000-Jan-p33.pdf W. A. Rutala, S. L. Barbee, N. C. Aguiar, M. D. Sobsey, D. J. Weber Infect Control Hosp Epidemiol. 2000 January; 21(1): 33–38. doi: 10.1086/501694]
Fumigation is typically the most effective air treatment against harmful microbial agents, although it must be done in an enclosed area such as an office building or home. Common fumigating chemicals include phosphine, 1,3-dichloropropene, chloropicrin, methyl isocyanate, hydrogen cyanide, sulfuryl fluoride, formaldehyde, and Iodoform.
In the 2001 bioterrorism attacks in which Bacillus anthracis spores were sent mailed to several individuals in Washington, paraformaldehyde was used to fumigate the buildings where the letters were opened. The full fumigation and disinfection procedure is online.
US EPA has an extensive index on indoor air quality..
Biological contaminants include bacteria, molds, mildew, viruses, animal dander and cat saliva, house dust, mites, cockroaches, and pollen (see more about Asthma triggers at www.epa.gov/asthma). There are many sources of these pollutants. Pollens originate from plants; viruses are transmitted by people and animals; bacteria are carried by people, animals, and soil and plant debris; and household pets are sources of saliva and animal dander. The protein in urine from rats and mice is a potent allergen. When it dries, it can become airborne. Contaminated central air handling systems can become breeding grounds for mold, mildew, and other sources of biological contaminants and can then distribute these contaminants through the home.
By controlling the relative humidity level in a home, the growth of some sources of biologicals can be minimized. A relative humidity of 30-50 percent is generally recommended for homes. Standing water, water-damaged materials, or wet surfaces also serve as a breeding ground for molds, mildews, bacteria, and insects. House dust mites, the source of one of the most powerful biological allergens, grow in damp, warm environments.
- [http://online.liebertpub.com/doi/pdf/10.1089/bsp.2005.3.119 Remediation of Bacillus anthracis Contamination in the U.S. Department of Justice Mail Facility ]
- EPA IAQ
- USEPA Indoor Air Quality Biologial
HACCP (Hazard Analysis & Critical Control Points) is a management system in which food safety is addressed through the analysis and control of biological, chemical, and physical hazards from raw material production, procurement and handling, to manufacturing, distribution and consumption of the finished product.
The U. S. Food and Drug Administration (FDA) publishes the Food Code, a model that assists food control jurisdictions at all levels of government by providing them with a scientifically sound technical and legal basis for regulating the retail and food service segment of the industry (restaurants and grocery stores and institutions such as nursing homes). Local, state, tribal, and federal regulators use the FDA Food Code as a model to develop or update their own food safety rules and to be consistent with national food regulatory policy.  The Food Code was last updated in 2009 
The addition of antimicrobial agents in food products is regulated by the U.S. Food and Drug Administration, and has been successful at eliminating harmful bacterial species as well as improving the shelf life of food products.
The USFDA's jurisdiction over antimicrobials used in or on food can be found here
There are a great variety of antimicrobials currently employed in modern food production, many of which can be found here
Proper food preparation, cooking, and storage are essential for food safety. United States Department of Agriculture fact sheets on safe food handling are online. State and municipal governments also have their own food safety regulations.
By primary and secondary sedimentation
Primary sedimentation tanks, with retention times of 2-6 hours, allow a proportion of the viruses in these wage to adsorb onto solids and settle. Removals reported in the literature suggest between 0 and 83 percent removal from influent to effluent.
Rao and others (1977) recorded a 24-33% removal of enteroviruses by primary settling tanks in Bombay. At other times of the year removal was between 41-83% with a 2-hour retention time. Rao, Lakhe and Waghmare (1978)reported a 50% reduction of viruses in a pilotplant settling tank at Nagpur (India). One report suggests that factors other than settlement maybe operative in removing viruses from sedimentation tank effluent (Clarke and others 1961).
Similar performance may be expected from secondary sedimentation tanks, except that these are often designed with higher overflow rates. The sludge removed from sedimentation tanks will normally contain a 10-100 times higher concentration of enteroviruses than the raw sewage.
Storage is an effective method of virus inactivation, especially at temperatures above 20'C. In any storage vessel, some sedimentation will also be taking place that will remove a proportion of viruses to the sludge layer. Expected removal rates in stored sewage may be derived from the data given above on the survival of enteroviruses in sewage (see also the appendixes of Feachem and others 1980), although little is known about survival under tropical climatic conditions.
By septic tanks
A septic tank is simply a settling chamber (or chambers) with a mean retention time of 3 days or less. In poorly designed tanks, or those requiring desludging, there is very considerable carryover of solids into the effluent. Viruses will be removed both by inactivation in the anaerobic liquor and by adsorption to solids that settle to the sludge layer. A series of laboratory experiments showed that a 99% reduction of poliovirus 1 in septic tank effluent took 14 days at 20°C and 43 days at 7°C (Small Scale Waste Management Project 1978). In practice, enterovirus reductions of 50% and under are to be expected. The inactivation of enteroviruses, both in sludge within the septic tank and in the drainfield, will be considerably enhanced by warm temperatures.
Night Soil & Sludge Treatment
Raw night soil contains all the viruses being excreted by the contributing population. Sewage works sludges are rich in viruses because a high proportion of viruses in sewage are, or become, solids-associated and are therefore concentrated into both primary and secon- dary sludges (Lund 1973; Lund 1976; Lund and Ronne 1973; Wellings, Lewis and Mountain 1976). By pit latrines Francis, Brown and Ainslie (1953) isolated polioviruses (16 out of 220 samples positive) from pit latrines in poor areas of four towns in southern Texas (USA). Pit latrines with polioviruses were not associated with known cases of poliomyelitis, an epidemic of which was taking place at the time (March-July of 1948), but were associated with the isolation of polioviruses from flies in the vicinity. By anaerobic digestion Ward and Ashley (1976) investigated the inactivation rate of poliovirus in digested sludge and found that it was greater than 1 log unit per day at 28°C and about 1 log unit per 5 days at 4°C. They concluded that anaerobically digested sludge contains a specific virucidal agent; in a subsequent study (Ward and Ashley 1977a) they identified this agent as ammonia (see also Fenters and others 1979). Ward and Ashley concluded that ammonia acts as a potent enterovirucide in raw and digested sludges with high pH values. At pH 9.5 and 21°C, greater than 3 log unit and 5 log reductions in poliovirus concentrations were obtained in 72 hours in raw and digested sludges, respectively. Sanders investigated the inactivation by anaerobic digestion of solids-associated poliovirus and found that survival was enhanced by solids incorporation. The inactivation rates at 34 and 37°C were 84-99% per day, respectively, for the first 24 hours. After that time inactivation slowed considerably to between 30-60% per day. At 50°C the inactivation rate was high at more than 7 log units per day. Berg and Metcalf (1978) reported the destruction of between 76-96% of viruses by mesophilic digestion (35°C for 20 days) and between 98.9 and >99.9% by thermophilic digestion (50°C for 20 days). Enterovirus concentrations in raw sludge were 4 x 103 to >1x10^5 per liter, 300 to 4,100 per liter in mesophilically digested sludge, and 0 to 170 per liter in thermophilically digested sludge. Wellings, Lewis and Mountain (1976) isolated enteroviruses and retroviruses, at concentrations of up to 34 per liter, from sludge from an anaerobic digester in Florida (retention time >60 days at 34°C) to which no raw sludge had been added for the previous 7 days. Sattar and Westwood (1979) found excreted viruses in 53 percent of samples of digested sludge (20 days at 35°C) and in 39 percent of dried sludge samples (>6 months' drying time) at a large sewage treatment plant in Ottawa (Canada). Hurst and others (1978) isolated viruses, at concentrations of up to 231 per liter, from sludge that had been thickened, aerobically digested, and centrifuged at a Houston (Texas, USA) treatment plant. Some laboratory studies have reported an inactivation rate of around 1 log unit per day at 30-35°C (for instance, Eisenhardt, Lund and Nissen 1977; Fenters and others 1979; Ward and Ashley 1976). At this rate of inactivation, typical anaerobic digestion at 35°C for 35 days should produce a virus free sludge with a wide margin of safety. Sanders and others (1979) have shown that inactivation rates of solids-associated viruses after the first day of digestion may be very much slower (around 1 log unit every 2-7 days). It is probable that only batch digestion at 35°C, for 35 days, or digestion at temperatures of around 50°C, will produce a virus-free sludge. More field data are required, on the actual virus removal performance of operating plants of these types, to confirm this assumption.