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1.3: Microorganisms

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    The most important job of a Water Treatment Operator is providing reliable and quality water to the public. This is accomplished through chemical deactivation or physical removal of disease-causing microorganisms in the water. Microorganisms are deactivated by the addition of a chemical such as Chlorine or Ozone while physical removal is accomplished with the use of a filtration system.

    Surface Water Treatment Rule

    The Surface Water Treatment Rule (SWTR) was created in 1990 to further protect the public from waterborne illness. The specific diseases the SWTR seeks to prevent are those caused by viruses, legionella, and Giardia lamblia. Disease-causing microorganisms are also known as pathogens. The microbes that cause most waterborne illnesses are found in most surface water in the United States. Every public agency that uses surface water as source water must adhere to the SWTR. Surface Water is defined as any open body of water that is susceptible to surface runoff. Rainfall and snowmelt that enter open bodies of water such as lakes, rivers, and man-made reservoirs are susceptible to contamination from sewage treatment plants and animal feces.

    At this time there are no simple inexpensive tests for viruses, legionella, and Giardia lamblia; therefore, other protective measures are used to test the source water and treated water. Water regulations provide detailed inactivation and removal regulations for Protozoa, also known as Giardia, and viruses. Bacteria fall somewhere in the middle of both microorganisms so there is no need to “regulate” them. Bacteria will be removed and/or deactivated within the parameters or regulations that are in place. Giardia and Cryptosporidium form hard cysts that are very difficult to deactivate chemically with Chlorine. They are larger than viruses so they or more easily removed through filtration. Newer technological advances such as ozone addition are excellent ways to deactivate Giardia.

    Treatment plants must use a combination of disinfectant (chemical deactivation) and filtration and must achieve 99.9% removal or inactivation of Giardia cysts and 99.99% of viruses. You might also see the percentages expressed as 3 Log and 4 Log. 99.9% will be expressed as 3 Log and 99.99% will be expressed as 4 Log. Treatment plants, which use filtration, achieve their removal factor by monitoring the combined filter effluent turbidity. Turbidity is the measurement of the cloudiness in water. The reason it is important to measure turbidity is because microorganisms can hide behind the very small particles and render treatment techniques ineffective. Turbidity readings are expressed as nephelometric turbidity units (NTU). Most surface source water will not meet standards that would enable a treatment plant to refrain from using approved filtration techniques. The approved treatment techniques currently used by water operators are conventional treatment, direct filtration, slow sand, diatomaceous earth, reverse osmosis, and alternate treatment technologies approved on a case by case basis by the primacy regulating board. Newer technologies such as membrane filtration and UV treatment are being employed by some water agencies.

    Table 3.1: Waterborne Pathogens




    • Campylobacter
    • Escherichia coli (E-coli)
    • Salmonella
    • Yersinia
    • Vibrio
    • Legionella
    • Aermmonas
    • Mycobacterium
    • Shigella
    • Pseudomonas
    • Hepatitis A
    • Reovirus
    • Calicivirus
    • Enterovirus
    • Coxsackievirus
    • Adenovirus
    • Echovirus
    • Poliovirus
    • Giardia Lamblia
    • Cryptosporidium
    • Entameoba
    • Microsporidium

    A continuous disinfectant residual must always be in the distribution system to prevent waterborne illness. A disinfectant residual of .2 mg/L must be present at all times in the distribution system, however, most water operators will maintain somewhere between 2.5 mg/L-3.0 mg/L. The CT calculation is used to make sure proper disinfectant levels are being used during the treatment and distribution process. The effectiveness of the treatment process is calculated with the CT formula and uses data such as disinfectant used, residual of disinfectant, length of time disinfectant is in contact with water, water temperature, and pH of the water. It is important to note that during the treatment process the goal is to disinfect the water (kill all pathogens) and not to sterilize (kill all organisms).

    The “C” is the concentration of disinfectant while the “T” is the amount of time the disinfectant is in contact with water. On days with higher effluent plant rates, an operator may need to raise chlorine doses as the disinfectant will be in contact with the water for less time. Conversely, if plant flow rates are lower, a lower chlorine dose can be used because the disinfectant is in contact with the water for a greater time.

    Case Study: Milwaukee April 1993

    In April of 1993, the largest outbreak of Cryptosporidium on record occurred in Milwaukee, Wisconsin. Over 400,000 people reported illness and 100 people died. All of the people who died after drinking the tainted water had the AIDS virus. It can’t be for certain that the Cryptosporidium was the cause of each of their deaths, but as will be discussed later in this chapter, people with weakened immune systems are much more susceptible to death if they drink tainted water.

    The Milwaukee incident was the catalyst for enhancements to the SWTR. Since Cryptosporidium creates cysts and is not killed by chlorine, the “double barrier” treatment approach was created. Treatment plants were then required to monitor turbidity effluent levels and use alternative treatment techniques, such as ozone or ultraviolet light, that would deactivate the Cryptosporidium. An effective filtration plant using coagulation, flocculation, sedimentation, and filtration, should have been able to handle the outbreak, thus turbidity levels were not within standards.

    The source of the Cryptosporidium was believed to be a sewage spill that was very close to the intake of the Southern Milwaukee treatment plant where the outbreak occurred. Others believe that the operators of the treatment plant were using higher quantities of waste stream water in the treatment process. Recycling washed filter water is a common practice, but after this event, it was established that only 10% of the sourced raw water can come from the wastewater.

    The lesson everybody learned here is water quality is ever-changing and evolving. Mother Nature throws curveballs at us that change the quality of the source water. If something is wrong, it is your duty as an operator to say something. Regulations are all well and good but if they are not being followed, people can become very ill or possibly even die.

    Total Coliform Rule

    The total coliform rule was published in 1989 and was revised in 2014. It set up minimum requirements for the frequency and amount of coliform tests that would be taken by water agencies. As discussed earlier, the coliform bacteria exist in larger quantities than other bacteria. If there is a positive coliform test, there is a greater chance the treatment process is not functioning properly and there is an increased chance of pathogens in the water. Bacterial outbreaks in water cause gastroenteritis with the associated symptoms of nausea, diarrhea, vomiting, and cramps. Very young people, elderly, and people with weakened immune systems are at an even greater danger should there be waterborne illnesses in water. Each water agency is required to have an approved sampling site map approved by the primacy agency.

    The Total Coliform Rule goal is zero positive coliform samples. Water systems that take less than 40 samples per month are only allowed one positive sample while systems that take greater than 40 samples must not find positive results in more than 5% of the coliform samples taken. If a positive coliform sample is found, it is not necessarily an indicator of a problem. Human sampling error could be the culprit. Once a positive is found the coliform sample is retaken within 24 hours at the positive sampling site and two additional samples are taken, one upstream and one downstream of the initial positive site. If there is a second positive coliform result, the water is then tested for E-Coli. If E-Coli is present in the sample, it is an immediate public health risk and is deemed an acute MCL violation. This would be considered a Tier I violation and public notification would have to occur within 24 hours.

    Long-Term 1 Enhanced Surface Water Treatment Rule

    The Long-Term 1 Enhanced Surface Water Treatment Rule (LT1ESWTR) applies to water systems that serve less than 10,000 people. Below is a list of requirements for water agencies that fall under this category:

    • Must achieve 99% or 2 log removal of Cryptosporidium
    • Most systems are required to meet turbidity standards of 0.5 NTU from 95% of combined filter effluent turbidity readings. Smaller systems will get 2 log removal credit of Giardia with a stricter .03 NTU combined filter effluent.
    • Monitoring of individual filter is required. Higher turbidity reading from individual filters will require corrective action.
    • Some states might require a disinfectant byproduct profile
    • Any change in primary disinfectant must be profiled and approved
    • All treated water clearwells must be covered and not open to atmosphere

    Long-Term 2 Enhanced Surface Water Treatment Rule

    The Long Term 2 Enhanced Surface Water Treatment Rule (LT2ESWTR) covers all water systems which serve more than 10,000 customers.

    • This rule added enhancements to the SWTR. Water providers are required to test the source raw water for Cryptosporidium and E-coli for a 2 year period. This step was put in to ensure all treatment plant equipment was capable of properly deactivating and removing pathogens from water.
    • After testing, systems were given a bin number which determined how susceptible the system was to contamination.
    • If systems were susceptible, a time frame was given to correct deficiencies
    • Continuous monitoring of the distribution system influent and maintaining at least .02 mg/L chlorine residual is required

    Filter Back Wash Recycling Rule

    As noted in the Milwaukee case study, water systems are able to use recycled wastewater as a raw water source. Many treatment plants utilize waste ponds, waste lagoons, and waste basins to capture recycled wash water and water from drains throughout treatment plant. In order for plants to use the recycled water, plants must put the wastewater through the same treatment process as raw untreated water. The amount of water that can be returned is based on the plants size and maximum plant flows.

    Lead and Copper Rule

    The lead and copper rule differs from most other water guidelines because these two constituents are usually found in water after it has gone through the treatment cycle. Most raw water has very low levels of lead and copper. Lead and copper are found in drinking water after a chemical reaction takes place in distribution pipes. Water that is more acidic can erode lead and copper pipes causing them to leach into water. The use of lead pipes in drinking water systems was banned in 1986 and they can no longer be used. Lead is known to cause several health problems in fetuses and young children. It can cause developmental problems. Lead can also have effects on the kidney, brain, red blood cells, and is known to cause anemia.

    With optimal corrosion control, the ability of water to chemically react with lead and copper pipes is lowered. Many treatment plants add chemicals such as caustic soda to raise the pH of the water. Treated water with a pH around 8 will keep a thin layer of calcium on the inside of a distribution pipe which protects the pipe from corrosion. Corrosion control is tested by monitoring the conductivity, testing pH of water, water temperature, testing for calcium, testing for alkalinity, and testing for phosphate or silica corrosion inhibiter if used to control corrosion.

    The Lead and Copper rule also differs from other rules because it bases its parameters on action levels. If 10 percent of the customers’ water tests in the 90th percentile of the action level for lead and copper, then further preventative actions must be met. Most customers do not have to worry about this due to advances in corrosion control in the past few decades.

    Lead pipes
    Figure \(\PageIndex{1}\): Image of lead pipes by Borsi112 is licensed under CC BY-SA 3.0

    Stage 1 and 2 Disinfectant Bi-Product Rule

    When natural organic matter mixes with chemical disinfectants, it is possible for disinfectant byproduct formation (DBP). Chemical disinfectants used in water treatment that form DBP’s are chlorine, chlorine dioxide, chloramines, and ozone. The Stage 1 disinfectant byproduct rule established MCL’s for trihalomethane (TTHM), haloacitic acid (HAA5), chlorite, and bromate. Compliance is set up on a running annual average for TTHM, HAA5, and Bromate and on a monthly average for chlorite. The rule also set up maximum disinfection levels for chlorine, chloramines, and chlorine dioxide.

    The Stage 2 disinfectant byproduct rule applies to all community and nontransient noncommunity water systems that add a chemical disinfectant or purchase treated water that has a chemical disinfectant. The purpose of the Stage 2 rule is to monitor local sampling of individual connections. Some parts of the water system have less movement, therefore they are more susceptible to DBP formation. The Stage 2 rule covers TTHM and HAA5 and has the same MCL as the Stage 1 rule. See the chart below:

    Disinfectant Residual

    MRDL* as mg/L

    Compliance Based On


    4.0 mg/L

    Running annual average RAA


    4.0 mg/L

    Running annual average RAA

    Chlorine Dioxide

    0.8 mg/L

    Daily samples

    *Maximum residual disinfectant level

    Disinfection Byproduct

    Maximum Contaminant Level

    Compliance Based On


    .080 mg/L (80 ppb)

    Running annual average

    Haloacetic acid

    .060 mg/L (60 ppb)

    Running annual average


    .010 mg/L (10 ppb)

    Running annual average


    1.0 mg/L (1 ppm)

    Monthly average

    *ppb- parts per billion ppm- parts per million

    Consumer Confidence Reports

    The public has a right to know what is in their drinking water. As you continue to read through the text you will notice that a lot of the terminology is quite a mouthful. In 1998 consumer confidence reports were made available to the public for transparency. Eight groups of information were added to the report:

    • System information including contact info
    • Different sources of water (i.e. lakes, wells, rivers)
    • Definitions non-water personnel can understand including MCL’s, MCLG’s and treatment techniques
    • Any detected contaminants in the system along with a listing of the possible health effects if limits and goals are not met
    • Non-regulated contaminants found
    • List of violations if they occurred
    • Variances and exemptions
    • Educational tools for contaminants and affected populations

    The internet has made it possible for water treatment facilities to post information monthly on company websites; however, a consumer confidence report will be mailed/electronically delivered to its customers on a yearly basis.

    Flow Rate Calculation

    The flow rate calculation will be one of the most frequently used in water math. This calculation tells us a lot about what is going on in our water system. Common flow rates you will see are Gallons per Minute (GPM), Cubic Feet Per Second (CFS), Million Gallons a Day (MGD), and Acre Feet per Year (AFY). Water operators use flow rates for different purposes. If you were running a small treatment plant, you might use GPM or CFS in your day to day operations but when looking at water produced throughout the entire month or year, calculating in Acre Feet may be more appropriate. Like any algebraic formula, there will be an unknown factor you are solving for. In the case of a flow question, there will be 3 values, two known and one unknown.


    Flow Rate Equation

    Flow Rate = Volume ÷ Time

    The algebraic “Wheel” is a very effective way to solve many water math problems. Those students with more “mechanical” minds may find this way of solving math problems easier. Below is an example of how to solve a flow rate equation with both methods.

    Example 1

    In 4 hours, a water tank's volume increases by 30,000 gallons. What was the flow rate of the water entering the tank? Express in gallons per minute.

    Flow Rate = Volume/Time

    Flow Rate = 30,000 gallons/4 hours

    7,500 gallons/1 hour

    7,500 gallons/1 hour = 1 hour/60 min

    = 125 gallons/minute



    We can also use the Flow Rate calculation to solve for volume or time.

    Example 2 - Solve for Time

    How long will it take to drain a 100,000-gallon storage tank where the water is exiting at 2,500 Gallons per minute?

    Time = 100,000 gal/2,500 GPM = 40 minutes

    Always put the unknown in the left part of the formula so your factors cancel out properly.

    Example 3 - Solve for Volume

    Your water tank pump is set to run for 90 minutes. Your pump output is 3,000 GPM. How many gallons of water will enter the tank?

    Volume = 3,000 GPM x 90 min

    Volume = 270,000 gallons

    Example 4

    A water tank’s full capacity is 500,000 gallons. The operator will bring the tank down to half full in an 8-hour period. What is the flow rate of the water exiting the tank?

    (Note: The state gets very creative with their test questions. Remember to read the question multiple times before solving it. Don’t be the test taker that uses 500,000 gallons in the equation instead of 250,000 gallons!)

    Flow Rate = 250,000 gallons/8 hours

    Flow Rate = 31,250 gallons/1 hour

    31,250 gal/1 hour = 1 hour/60 min = 520.83 GPM

    Chapter Review

    1. A disease-causing microorganism:
      1. Pathogen
      2. Colilert
      3. Pathological
      4. Turbidity
    2. According to the Surface Water Treatment Rule, what is the combined inactivation and removal for Giardia?
      1. 1.0 Logs
      2. 2.0 Logs
      3. 3.0 Logs
      4. 4.0 Logs
    3. What is the equivalency expressed as a percentage for the SWTR inactivation and removal of viruses?
      1. 99.9%
      2. 99.99%
      3. 99.0%
      4. 99.999%
    4. A water agency that takes more than 40 coliform samples must fall under what percentile?
      1. 10%
      2. 7%
      3. 5%
      4. No positive samples allowable
    5. The multiple barrier treatment approach includes ___________.
      1. Sterilization and filtration
      2. Disinfection and filtration
      3. Disinfection and sterilization
      4. Infection and filtration
    6. The maximum disinfectant residual allowed for chlorine in a water system is ___________.
      1. .02 mg/L
      2. 2.0 mg/L
      3. 3.0 mg/L
      4. 4.0 mg/L
    7. How do water agencies monitor the effectiveness of their filtration process?
      1. Alkalinity
      2. Conductivity
      3. Turbidity
      4. pH
    8. What is the disinfectant byproduct caused by ozonation?
      1. Trihalomethanes
      2. Bromate
      3. Chlorite
      4. No DBP formation
    9. Haloacitic Acids are also known as ___________.
      1. TTHM
      2. HOCL
      3. Chlorite
      4. HAA5
    10. What is the MCL for trihalomethanes?
      1. .10 mg/L
      2. .06 mg/L
      3. .08 mg/L
      4. .12 mg/L
    11. What is the MCL for Haloacitic Acids?
      1. 100 ppb
      2. 60 ppb
      3. 80 ppb
      4. 120 ppb
    12. What is the MCL for bromate?
      1. .010 mg/L
      2. .020 mg/L
      3. .030 mg/L
      4. .040 mg/L
    13. A treatment plant operator must fill a clearwell with 10,000 ft3 of water in 90 minutes. What is the rate of flow expressed in GPM?
      1. 111 GPM
      2. 831 GPM
      3. 181 GPM
      4. 900 GPM
    14. A water tank has a capacity of 6MG. It is currently half full. It will take 6 hours to fill. What is the flow rate of the pump?
      1. 3,333 GPM
      2. 6,333 GPM
      3. 8,333 GPM
      4. 16,666 GPM
    15. A clearwell with a capacity of 2.5 MG is being filled after a maintenance period. The flow rate is 2,500 GPM. The operator begins filling at 7 AM. At what time will the clearwell be full?
      1. 10:00 PM
      2. 10:40 PM
      3. 11:00 PM
      4. 11:40 PM

    1.3: Microorganisms is shared under a CC BY license and was authored, remixed, and/or curated by LibreTexts.