Frontiers for Young Minds

Frontiers for Young Minds
Core Concept Earth Sciences Published: October 16, 2023

Microbial “Janitors” Clean Up Our Liquid Waste


Have you wondered what happens to our pee and poop after we flush the toilet bowl? What about food bits and soapy water from sinks and dishwashers? The liquid waste we all produce when using the toilet, having a bath or shower, or washing our clothes and dishes is called sewage. Sewage also includes rainwater running from the streets and liquid waste from factories. This liquid waste flows in hidden pipes called sewers, to sewage treatment facilities. Sewage treatment facilities are designed such that numerous microbes help to clean our waste so that it does not harm people, rivers, and oceans. In this article, we will explore how microbes are the super cleaners behind sewage treatment and why these microbes are beneficial to us.

What Is Sewage and Why Do We Need to Treat It?

Sewage is liquid waste produced by everyone when using the toilet, having a bath or shower, and washing our clothes and dishes. Liquid waste from factories and shopping malls, as well as rainwater from the streets containing leaves, branches, and anything else that is on the street, are also part of city sewage. This liquid waste travels through a giant, hidden web of pipes called the sewage system to sewage treatment facilities that are centers built to treat this liquid waste before releasing it back into the environment.

Even though sewage consists mostly of what we think of as waste, it is rich in nutrients from our poop and leftover food, for example. What we consider waste can be food to other organisms. If released into lakes, rivers, and oceans without treatment, the nutrients in sewage can lead to a rapid growth of algae—a process known as eutrophication. During an eutrophication event, the excessive growth of algae blocks the sunlight entering the water, killing other aquatic plants. Once all the nutrients are consumed, the algae die and are decomposed by aquatic microbes. As these microbes break down dead algae, they use up all the available oxygen and create “dead zones” where fish and other animals die from lack of oxygen (for more information about problems caused an excess of nutrients, see this Frontiers for Young Minds article). Sewage treatment is the process of reducing the nutrients in sewage so that it does not cause harm to aquatic ecosystems [1].

There are many kinds of microbes in sewage, from the environment, rainwater, or our homes. These microbes can break down and consume nutrients. At sewage treatment facilities, these microbes are stimulated to grow and use up the nutrients available in the sewage. Our waste is their food! With the help of microbes, the treated sewage, also called effluent, can then be released into the environment without causing eutrophication and other pollution problems.

What Happens to the Sewage in Treatment Facilities?

When sewage arrives at sewage treatment facilities, it passes through many stages before it is released as effluent (Figure 1A). First, larger objects, such as tree branches or plastic bags, are removed using a screening gate consisting of parallel bars or wire mesh, which prevents large objects from passing through (Figure 1B).

Figure 1 - (A) Sewage contains solid waste, which is full of nutrients, and environmental microbes that can consume those nutrients.
  • Figure 1 - (A) Sewage contains solid waste, which is full of nutrients, and environmental microbes that can consume those nutrients.
  • (B) Large solids in sewage are removed by a screening gate. (C) Chemicals are added to sewage to make small solids stick together so that they sink to the bottom as sludge. (D) The effluent, or liquid part of the sewage, is sent to a bioreactor for further treatment. (E) Sewage treatment can produce renewable resources like organic fertilizer and “green” energy. Fruits in A and C represent solid waste like rest of food and poop. The brown tray represents chemicals added to make the light solid waste to sink.

The sewage then flows into a tank where it stays until small solids fall to the bottom. Think of pulpy orange juice: the heavy pulp sinks quickly on its own, while the lighter pieces float for a long time. In the tank, heavy solids such as human waste or sand sink to the bottom. Chemicals are added to make lighter suspended solids stick together, resulting in bigger, heavier chunks that quickly sink to the bottom, too. The solids that settle at the bottom of the tank are a thick, muddy mixture called sludge—made up of nutrients, microbes, and small solids—which gets processed in a sludge digestor (Figure 1C).

The remaining liquid waste, the effluent, is also rich in nutrients and microbes. The effluent is piped away for further treatment in bioreactors (Figure 1D), which we will describe in more detail below [1]. Treatment of sludge and effluent produces fertilizer and biogas, a form of “green” energy that does not pollute the Earth (Figure 1E). The treated effluent is then disinfected to remove potentially harmful microbes and then either discharged into the environment or recycled into the water supply.

Role of Microbes in Sludge Digesters

Remember the environmental microbes present in sewage? Inside sludge digesters, some of these microbes consume the nutrients present in muddy sludge. This process is called anaerobic digestion. Anaerobic digestion involves breaking down nutrients without using oxygen, in a multistep process—like cutting up an apple into bite-sized pieces (Figures 2A, B).

Figure 2 - (A) Sludge is a thick, muddy mixture formed from the solids that fall to the bottom of the tank.
  • Figure 2 - (A) Sludge is a thick, muddy mixture formed from the solids that fall to the bottom of the tank.
  • (B) Certain microbes can digest sludge in the absence of oxygen, producing a substance called acetic acid (vinegar) in the process. (C) Acetic acid is converted into biogas by other microbes called methanogens, while the remaining undigested sludge can be dried and used as organic fertilizer. Fruits represent solid waste like rest of food and poop that have been sunk to form the sludge.

Some sludge microbes break food into simpler molecules, making the nutrients more accessible to other microbes. The most important product of anaerobic digestion is acetic acid, also known as vinegar. Yes, like the vinegar you probably have in your kitchen! Acetic acid feeds the most important group of sludge microbes, the methanogens. When they consume acetic acid, methanogens produce an environmentally friendly energy source called biogas, which mainly consists of two gases, methane (CH4) and carbon dioxide (CO2) (Figure 2C) [2]. Biogas can be harvested and used to generate electricity and to heat our homes. Any remaining undigested sludge can be dried and used as fertilizer (Figure 2C).

Effluent: Removal of Nutrients by Microbes in Bioreactors

Now we know what happens to the sludge, but what happens to the effluent? As we mentioned earlier, effluent treatment occurs in bioreactors, where two important nutrients are removed: nitrogen and phosphorus. Effluent microbes are grown in specific conditions to maximize their ability to remove these nutrients from the effluent. These microbes are like “Lego” builders, removing and adding blocks to molecules (Figure 3A).

Figure 3 - (A) Removal of nitrogen from effluent via nitrification and denitrification.
  • Figure 3 - (A) Removal of nitrogen from effluent via nitrification and denitrification.
  • Nitrogen removal from effluent is performed by microbes that convert nitrogen in the form of ammonium (NH4+) into nitrogen gas (N2). The letters on the building blocks represent elements: oxygen (blue); hydrogen (green); nitrogen (orange). (B) PAOs are microbes used to remove phosphorous from effluent. PAOs use energy from their polyphosphate “batteries” and “recharge” them by taking phosphate from the effluent. Excess PAOs are harvested for use as fertilizer.

Microbes in the effluent remove nitrogen from molecules through two processes: nitrification and denitrification, which are part of the nitrogen cycle (for more information about the nitrogen cycle, see this Frontiers for Young Minds article). During nitrification, ammonia (NH4+) is converted into nitrite (NO2-) by certain microbes. These microbes remove hydrogen “blocks,” transforming ammonia molecules into nitrite molecules. Then, other microbes change nitrite (NO2-) to nitrate (NO3-) through the addition of oxygen “blocks” (Figure 3A). Other microbes remove the oxygen blocks, converting nitrate (NO3-) into nitrogen gas (N2). Nitrogen gas is released into the air (Figure 3A).

Phosphorus removal is carried out by other microbes, called polyphosphate-accumulating organisms (PAOs) [3]. Like all living things, PAOs need energy to grow, and they contain a compound called polyphosphate that acts like a rechargeable battery. Polyphosp-hate, which is built from several molecules of phosphate (PO4), is used by PAOs as an energy source. This battery is “recharged” when PAOs collect phosphates from the effluent to replace what they used (Figure 3B). The process removes phosphorus from the effluent and stores it away in PAOs. PAOs are eventually collected and used as fertilizer.

Importance of Microbes in Wastewater Treatment

Thanks to the unseen microbes from the environment that help us process sewage, we can make sure that the treated water released back into the environment is safe. Research on sewage treatment processes is investigating new types of bioreactor setups and biological treatment processes using different types of microbes that can increase the efficiency of sewage treatment facilities. Treating sewage is very important for protecting the environment and our water resources. Sewage microbes do all the hard work, helping to keep our environment safe, kind of like school janitors. What is more, these microbes provide us with useful products like fertilizer and biogas. What a great deal!


Eutrophication: A change in an environment’s nutrient status by an increase of nutrients brought by waterways (lakes, rivers, or oceans). One major consequence is the loss of aquatic life due to the rapid growth of plants and algae.

Effluent: Water or gas outflowing from a structure such as a sewage treatment facilities or pipes to another structure (for example tanks) or to natural body of water (lakes, rivers, or ocean).

Bioreactor: A container in which chemical processes are carried out by living organisms, like microbes.

Anaerobic Digestion: A collection of processes by which microbes break down food to obtain energy and grow in the absence of oxygen (air).

Methanogen: Microbes that produce a specific type of biogas called methane.

Nitrification: A process carried out by microbes that transform ammonia (one form of nitrogen) into nitrates (a different form of nitrogen).

Denitrification: A process carried out by microbes that transform nitrates into nitrogen gas, which is released into the atmosphere.

Polyphosphate-accumulating Organisms: A group of microbes that facilitate the removal of nutrient phosphorus from the environment.

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


[1] Kesari, K. K., Soni, R., Jamal, Q. M. S., Tripathi, P., Lal, J. A., Jha, N. K., et al. 2021. Wastewater treatment and reuse: a review of its applications and health implications. Water Air Soil Pollut. 232:208. doi: 10.1007/s11270-021-05154-8

[2] Enzmann, F., Mayer, F., Rother, M., and Holtmann, D. 2018. Methanogens: biochemical background and biotechnological applications. AMB Express 8:1. doi: 10.1186/s13568-017-0531x

[3] Bunce, J. T., Ndam, E., Ofiteru, I. D., Moore, A., and Graham, D. W. 2018. A review of phosphorus removal technologies and their applicability to small-scale domestic wastewater treatment systems [review]. Front. Environ. Sci. 6:8. doi: 10.3389/fenvs.2018.00008