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Water microbiology FAQ Frequently Asked Questions

The question library on water related issues

What is microbiology?

Microbiology is the scientific field that is occupied with the study of microscopic organisms, commonly known as microrganisms.

What are microrganisms?

All living creatures consist of cells. Cells are very small basic units of life. They are the smallest structures capable of basic life processes, such as taking in nutrients and expelling waste. Cells can only be made visible by microscopes.
Microrganisms are organisms that usually consist of one single cell. Because of this, they are often referred to as "single-celled organisms". They are so small, that humans cannot visualise them. We can only see them through microscopes, by which the cells are greatly enlarged.

At first, microorganisms were not seen as a separate kind. Microrganisms that carried out photosynthesis (see carbon cycle) were classified in the plant kingdom, and microrganisms that ingested food were placed in the animal kingdom. However, in the 19th century, scientists had identified a wide variety of microrganisms with diverse cell structures, very specific internal structures, and specific reproductive patterns that made them realize these organisms did not belong to the plant or animal kingdom.

What kinds of microrganisms are there?

Microrganisms are divided up by their cell characteristics, in the same way as plants and animals. There are two kinds of (micr)organisms. The first kind is the eukaryotic organism (protista). Most organisms are eukaryotic, which basically means that the cells they consist of contain nucleuses and other internal parts, surrounded by membranes. The second kind of microrganisms is the prokaryotic organism (monera). Prokaryotic cells are surrounded by a membrane, but they contain no nucleus or other internal parts (organelles), contrary to eukaryotic cells.

Monera and protists

The monera are bacteria and cyanobacteria. They are single-celled prokaryotic microrganisms, as was mentioned earlier. Bacteria are very important for other organisms, because they break down organic matter. During this process nutrients are formed, which are reused by plants and animals. Some of the bacteria that live on earth can cause disease, but most of them are quite useful as they aid animals in the decomposition of food in their bodies. Bacteria differ from other types of cells in the fact that they do not have a nucleus. With plants and animals this is where the DNA (genetic information) can be found. With bacteria the genetic material floats within the cell. They reproduce by first copying their DNA and than performing cell division. Bacteria also lack membrane-bound organelles, such as mitochondria, the cell structures involved in energy metabolism.
Bacterial cells are so small that scientists measure them in units called micrometers (µm), a millionth of a meter. An average bacterium is about one micrometer long.
Bacteria know several different kinds of subdivisions, such as spherical (coccus) and rod-shaped (bacillus) bacteria.

Spherical bacteria

Rod-shaped bacteria

The protists are single-celled eukaryotic microrganisms, as mentioned earlier. Examples are amoebas, diatoms, algae and protozoa. These can be a danger to human and animal health, as certain protists can cause diseases, such as malaria and sleeping sickness. There are a wide variety of protists, and they inhabit many different environments; fresh water, seawater, soils, and the intestinal tracts of animals, where they perform crucial digestive processes.
Many species of protists can produce their own nutrients by the process of photosynthesis and many protists can also move around on their own accord. Protists vary greatly in size and shape; the green alga Nanochlorum is only 0.01 mm long, but giant kelps can grow to 65 m or more in length.

Which microrganisms in water cause diseases?

Sometimes microrganisms that cause health effects can be found in drinking water. However, as drinking water is thoroughly disinfected today, disease caused by microrganisms is rarely caused by drinking water.
People that swim in swimming pools will find that the water they swim in is disinfected with either chlorine, ozone, UV or chlorine dioxide. But there are people that swim outside in surface water every year. These are the people that are most susceptible to bacterial infections and infections caused by other microrganisms, because microrganisms often enter surface water through industrial discharge and animal excrements. When you are an outside swimmer, you always have to be careful and read the signs placed by the waterside, because the water you are swimming in may be infected, for example with botulism.
There are various bacteria and protozoa that can cause disease when they are present in surface water.

Bacteria are not only known to cause disease when they enter a human body through food, surface water may also be an important source of bacterial infection. In this table you can see various bacteria that can be found in surface water, and the diseases they cause when swallowed in large amounts, along with the symptoms.


Disease/ infection




Very thin, blood- and mucus-containing diarrhoea

Campylobacter jejuni


Flue, diarrhoea, head- and stomachaches, fever, cramps and nausea

Escherichia coli

Urinary tract infections, neonatal meningitis, intestinal disease

Watery diarrhoea, headaches, fever, homiletic uraemia, kidney damage

Plesiomonas shigelloides


Nausea, stomachaches and watery diarrhoea, sometimes fevers, headaches and vomiting


Typhoid fever



Sickness, intestinal cramps, vomiting, diarrhoea and sometimes light fevers


(Gastro) intestinal disease

Stomachaches, diarrhoea and fevers, sometimes vomiting

Vibrio El Tor (freshwater)

(Light form of) Cholera

Heavy diarrhoea

Protozoa can accumulate in certain body parts, after they have penetrated a human body. The accumulations are called cysts.
Because of their parasitic nature, protozoa can cause various diseases. In this table you can see various protozoa that can be found in surface water, and the diseases they cause when swallowed in large amounts, along with the symptoms.





Amoebic dysentery

Severe diarrhoea, headache, abdominal pain, chills, fever; if not treated can cause liver abscess, bowel perforation and death

Cryptosporidium parvum


Feeling of sickness, watery diarrhoea, vomiting, lack of appetite



Diarrhoea, abdominal cramps, flatulence, belching, fatigue

Toxoplasm gondii


Flu, swelling of lymph glands
With pregnant women subtle abortion and brain infections

How do we eliminate harmful microrganisms from water?

To eliminate harmful microrganisms from water we tend to use disinfectants. Examples of disinfectants are chlorine, UV, ozone (O3) and chlorine dioxide (ClO2). There are several different advantages and disadvantages to the various disinfection techniques, as shown on our disinfection page. Chemicals that are harmful to certain types of microrganisms are often used to eliminate them. These chemicals are known as biocides, because they are mortal to microrganisms.

How can microrganisms be made useful during water treatment?

Microrganisms can be used to decompose contaminants in wastewater. This kind of water treatment is called biological water treatment. During biological water treatment microrganisms break down organic matter, nitrates and phosphates. This is a brief explanation of how these biological water treatment processes work.

Removal of organic matter

Biological water purification is performed to lower the organic load of dissolved organic compounds. Microrganisms, mainly bacteria, do the decomposition of these compounds. There are two main categories of biological treatment: aerobic treatment and anaerobic treatment. Aerobic water treatment means decomposition of organic matter by bacteria that need oxygen during the decomposition process. Anaerobic water treatment means decomposition of organic matter by microrganisms that do not use oxygen.
In aerobic systems the water is aerated with compressed air (in some cases merely oxygen), whereas anaerobic systems run under oxygen free conditions.

Removal of ammonium and nitrates

The removal of ammonium and nitrates is quite complex. It is a water treatment process that takes both aerobic and anaerobic conversion to remove the contaminants.
In the aerobic conversion stage there are two bacterial species involved. Firstly, Nitrosomonas bacteria convert ammonia to nitrite. Secondly, Nitrobacter bacteria convert nitrite to nitrate. These two processes together are commonly known as the nitrification process.

After that, the anaerobic bacteria take over. These bacteria convert nitrate to atmospheric nitrogen gas. This process is called denitrification. Denitrification is accomplished with many anaerobic bacteria, such as Achromobacter, Bacillus and Pseudomonas. The first stage of denitrification is the reverse of the nitrification process, it converts nitrate back to nitrite. The second stage of denitrification converts nitrite to nitrogen gas (N2). This gas can be freely released into the atmosphere without causing environmental damage.

Removal of phosphates

Phosphates can be removed from wastewater by an aerobic (oxygen-dependent) bacterium, called Acinetobacter. This bacterium accumulates polyphosphates in the cell tissues.
The Acinetobacter can take up a higher amount of phosphates than it needs for its cell synthesis. The extra amounts of phosphates are stored in the cells as polyphosphates.
The storage of polyphosphates causes the Acinetobacter to be able to temporarily survive anaerobic circumstances. When the Acinetobacter resides in an anaerobic zone in the wastewater, it takes up fatty acids to store them as spare substances. During this process, polyphosphates are decomposed for energy supply, causing phosphates to be released into the aerobic zone. When the Acinetobacter enters the aerobic zone it takes up phosphates and stores them as polyphosphates in the cell tissues. This causes the phosphate content of the wastewater to decrease.

Sources: Encarta Encyclopedia, Water purification FAQ

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