How Microbes Help Us Reclaim Our Wastewater

May 29, 2024

This article was originally published in April 2020 and has since been updated for inclusion in the Spring 2024 issue of Microcosm.

A key challenge to setting up a civilization is the plumbing. This is one reason why major cities, particularly those with a long history, are conspicuously placed along rivers; pressurized water and the kind of plumbing we have today would not be unfamiliar thousands of years ago to civilizations like the Mayans. Despite its long and pivotal role in our success, once wastewater is done swirling down our toilet bowls, most of us are blissfully unaware of what happens next. It may not come as a surprise that microbes are the heroes of this untold story.

Separating the Waste From the Water

Before we examine these little heroes of sanitation, let’s establish the big picture of wastewater management. The ultimate goal is to take water rendered unusable by waste and purify it sufficiently to restore it to the environment. Waste removed during the process is digested by microbes, and what remains is dried and disposed of in landfills, incinerators or applied to soil as a conditioner, depending on the source and process. Large-scale operations manage the bulk of our wastewater and follow a process called activated sludge. Invented a little over 100 years ago, this process incorporates the following basic steps: filtration, activation (aeration), clarification (settling) and disinfection.

Illustration showing the main steps of the activated sludge process used by large-scale wastewater management facilities.
Illustration of the main steps in the activated sludge process used by large-scale wastewater management facilities.
Source: Wikimedia Commons.

Sludge is the euphemistic term used to describe the brown, viscous liquid that results after raw sewage has been filtered to remove grit. The sludge itself is inhabited by a diverse community of microbes, including bacteria, protozoans and even some eukaryotes like tardigrades, that have hitched a ride (perhaps through us) along the sewers connecting our homes to the waste management facility. Sludge comprises an incredibly rich medium, full of organic matter that we find unappetizing, but bacteria find delicious. Once this sludge has been processed by bacteria, it is called activated sludge, which can refer to both the material itself and the waste management process.

The cast of characters varies in each waste management facility, but a recent global survey of the microbiome of wastewater activated sludge found that there are 28 core bacterial members of healthy activated sludge. The most abundant of these are Dokdonella kunshanensis, Zoogloea species and Nitrospira species. These are all aerobic, gram-negative bacteria. We know little about D. kunshanensis, other than it can be readily isolated from activated sludge. We know more about the other 2 species. The name Zooglea means “living glue” because of the species' proclivity to form sticky biofilms. Nitrospira species help oxidize nitrite to nitrate and are important for cycling aquaria because nitrate is much less toxic to fish than the ammonia they excrete. As we shall see, these traits facilitate the activated sludge process. However, these most abundant bacteria still represent only a small percentage (~3% of total abundance) of the diverse bacteria present in activated sludge microbiomes.


After passing through filtration, key bacteria are alive, but are not thriving like we need them to, so we "activate" them through aeration. Stirring or bubbling the sludge introduces oxygen throughout, which encourages air-loving microbes to begin to actively grow and reproduce, while discouraging the growth of other kinds of microbes. This simple selection, inherent to the process, is similar to how home microbiologists cultivate a specific, useful subset of microbes for composting or for a sourdough starter. In fact, facilities sometimes prime incoming sludge with activated sludge to ensure bacterial communities from healthy batches are present from the beginning.

The aerobic bacteria in the sludge digest the organic material around them to reproduce and grow, and change the chemical makeup of the sludge by oxidizing ammonia into nitrate and nitrite in a process called nitrification. The process follows a progression that will be familiar to anyone who has studied microbiology: there is a lag period where these bacteria initially begin to grow, followed by an exponential growth phase, a stationary phase and finally a senescent phase where starving bacteria begin to die off. In their bubbly, sludgy new home, these bacteria are doing most of the work for us, turning sludge into more bacterial cells.

Most of the role that humans play in this process is trying our best to keep the microbes on track. This involves taking samples of the sludge to track its progress. Metrics, like the amount of dissolved oxygen and organic matter, the amount and types of bacteria, such as culturable indicator species (e.g., coliform bacteria), and other indicators, are used to identify various stages of the process. Waste management facilities also use biological oxygen demand (a measure of the amount of oxygen being consumed by microbes) to calculate the food-to-mass (or microbe) ratio. These values allow scientists to chart their course to the stationary phase when the sludge no longer needs to be aerated.

A floc of bacteria at 400X magnification removing phosphorus from medium in the lab.
A floc of bacteria at 400X magnification removing phosphorus from medium in the lab. All bacteria were stained green, and Candidatus Accumulibacter Phosphatis, which accumulates phosphorus, were stained in blue. Courtesy of Connor Skennerton.
Source: Wikimedia Commons.
When things are going well, it’s easy to see. Clumps of bacteria, called flocs, form in the sludge as these microbes help us reclaim the water within. Similar to its homophone, flocculation is a process where these aerobic bacteria produce biofilms composed of extracellular polymeric substances that allow them to stick together. These biofilms help microbiologists monitor when a healthy consortium of bacteria are actively working to digest waste, while signs like excessive foam point to microbes that aren’t team players.

If the wrong microbes show up or the process goes off track, then humans intervene chemically or remove excess sludge. Filamentous bacteria can become the “wrong microbes” if they don’t cooperate with the biofilm consortia of bacteria and produce excessive filaments. This “filament bulking” prevents sludge from settling. In particular, Nocardia species and Microthrix parvicella convert oil and grease into a brown foam by increasing hydrophobicity in the system, which stabilizes the foam.

By the end of the process, a mature food chain of diverse microorganisms capable of biochemically transforming the sludge emerges. Bacteria feed on sludge; amoebae and ciliates (such as peritrichs) feed on the bacteria; and tardigrades (and the occasional nematode) comprise the apex predators. These higher-order members of the food web become more prominent during the exponential phase of bacterial growth, but if they become too common, it’s a sign something has gone wrong (such as aerating the sludge for too long).

Clarification and Disinfection

When it’s time to stop bubbling, the activated sludge enters its next phase: clarification. As it says on the back of juice bottles, “settling is natural,” and so we wait while the flocs and remaining sludge settle out of a now-watery solution. Once the water has clarified to the satisfaction of the facility, the activated sludge, which has concentrated at the bottom, is sent off for further processing.

Remaining sludge goes through a second bacterial digestion without oxygen. Anaerobic bacteria further break down the sludge and reduce nitrate and nitrite into nitrogen gas through a process called denitrification. Biogas (primarily methane and carbon dioxide) produced during this anaerobic digestion is burned off or further purified for sale to energy companies. Such anaerobic digestion can occur at various stages of the process.

The very last of the activated sludge that survives primary and secondary microbial digestion is then dried. This “waste-activated sludge” is ready to leave the facility as fertilizer or smoke, depending on its composition. Here, many weeks and microbial assists later, is the final destination of our modern sewage.

The supernatant (Latin for “great swimmers”) on the top after clarification is disinfected with chemicals, like chlorine, or with ultraviolet (UV) radiation. This final step effectively kills any remaining organisms, pathogenic or otherwise, that have made it this far. If pathogens are a concern, checks are made throughout the process to ensure they are eliminated as the water is reclaimed. Finally, the water that may have once passed through your kidneys is ready to rejoin the ecosystem, often by way of local lakes and rivers.

For most of us, our contribution to this process is pressing the toilet handle. As is often the case, we can thank microbes for doing the hard work and making it look easy.

Interested in learning more about wastewater? Gain a deeper understanding of how wastewater spreads AMR, and learn how such knowledge can help microbiologists mitigate this global health threat. 

Author: Brian Lovett, Ph.D.

Brian Lovett, Ph.D.
Brian Lovett is a postdoctoral researcher working on fungal biology and biotechnology at West Virginia University.