Sewage Treatment: A Partnership of Man & Microbe


Deer Island Wastewater Treatment Plant location. Image credit: Google maps

This post was written by Mariana G. Matus, a doctoral candidate in the Computational and Systems Biology Program at MIT.

Image Credit - Charles Tyler

Image Credit – Charles Tyler

Have you ever wondered where the stuff you flush ends up?

Maybe you’d prefer not to think about it, but students and researchers from the MIT Underworlds Project were determined to find out. To that end, we visited the Deer Island Wastewater Treatment Plant, located on a small peninsula just east of Boston’s Logan airport.

Deer Island Wastewater Treatment Plant location. Image credit: Google maps

Deer Island Wastewater Treatment Plant location. Image credit: Google maps

If you live in the Greater Boston Area, your morning flush, along with the 100 gallons of water you use at home everyday, is sent through an underground network, is treated at Deer Island, and is dumped deep into the Atlantic ocean in less than two days!

Deer Island, the second largest plant in the United States, was designed to treat sewage from 43 communities in the Greater Boston Area. On any given day, Deer Island cleans ~350 million gallons of sewage. That’s enough water to fill over 300 football-field sized pools!

The herculean task of cleaning this much water is possible thanks to a very successful partnership between man and microbe.



Charles Tyler, the Program Manager of Process at Deer Island, led the tour and showed us how the treatment plant behaves like a giant industrial gut where the bacteria from our poo get the chance to finish off the meal they started inside our gut. In exchange, these microbes clean our water before it is returned to the environment. That’s a true man-microbe partnership and a great deal for everyone!

The process by which engineers and microbes clean our waste can be summarized in four steps:

Step 1: Remove large particles from water

Incoming sewage is slowed down to allow for large particles to settle at the bottom of tanks. The water proceeds to step 2 with a mixture of microbes and light organic solids, while the sedimented particles are sent for digestion in oxygen-free reactors (described below in Microbial Exit Ramp).


Step 2: Remove light organic solids from water

Pure oxygen for the aerobic bioreactors is produced in these tall towers.

Pure oxygen for the aerobic bioreactors is produced in these tall towers.

The light organic solids are then cleared from the water through the use of hungry microbes. Engineers make sure the microbes feed happily on our sewage by growing them in huge bioreactors supplied with plenty of oxygen. These microbes require so much oxygen to feed and grow that Deer Island generates their own pure oxygen by distilling it from very cold liquid air in a sophisticated process which takes place in the tall towers to the left.


Step 3: Remove microbes from water

After a few hours in the oxygen-filled bioreactor, >90% of organic materials have been removed from the sewage and the water is clean enough to move to the next step. Now it is time to remove all microbes which have been growing in the water by allowing the cells to settle to the bottom of a second set of large tanks. The water, now clean of organic solids and microbes, can proceed onto step 4.


Most of the sedimented microbes are returned to the oxygen-filled reactors to continue feeding on the next batch of sewage, while some are considered sludgy waste that needs to be disposed of. It would be difficult to dispose of these large amounts of microbial sludge. Luckily, Deer Island has a smart way to use this waste.


Microbial exit ramp: Excess microbes are converted to energy and fertilizers

Cleaning sewage by giving it as a food source to naturally-occurring bacteria is a brilliant idea. The only caveat is that, in the process, not only are you feeding bacteria, you are also growing more of them. The process continuously generates more bacteria than you need to operate the plant, and you need to remove the excess microbial community and do something with them. Engineers have developed processes to convert this bacterial mass to energy and fertilizers.  


If you incubate microbial sludge in the absence of oxygen, most bacteria will die off. However, a few can survive to feed on the corpses of their fellow microbes and convert them into carbon dioxide, methane and water. This process is especially efficient in a warm (near body temperature) environment. In fact, many of these microbial processes also occur in the human intestinal tract.



Egg-shaped anaerobic bioreactors on a beautiful winter morning. Image credit: Claire Duvallet

These microbes grow much slower than the oxygen lovers, which is why engineers give them 25 days to feed. To make sure the plant always has room for the sludge produced, engineers have built huge 14 story-tall, 3 million gallon capacity, egg-shaped bioreactors (see picture to the right).

The methane generated in these bioreactors is used to furnish most heating needs as well as some of the electricity needed to run the plant, while the remaining solids are dried and sold as crop fertilizers.


Step 4: Sent back into the ocean

After the removal of over 90% of the sewage contaminants and microbes, water is disinfected with

Water undergoing disinfection at the end of treatment.

Water undergoing disinfection at the end of treatment.

chlorine, dechlorinated and finally safely dumped nine miles offshore, deep into the ocean.



To guarantee that sewage is properly treated before being dumped in the ocean, Deer Island assesses the water quality of the outflow at their large laboratory facilities. The lab’s manager, Mark Lambert, walked us through their microbiology and chemistry labs and explained to us that the 50 researchers who work there run protocols established by the Environmental Protection Agency (EPA), and give feedback on a daily basis to the plant’s engineers so they can adjust the treatment parameters if necessary.



The main thing I took away from our visit is that every drop of water we use in the toilet, the sink, or the shower, finds its way back to oceans, lakes and rivers in a matter of days. To make our wastewater safe for disposal, treatment plants clear the water of contaminants and produce useful end products such as methane, for electricity, and solids, for fertilizers. All processes which take place at treatment plants are naturally-occurring, and in a very true sense, an extension of our own digestive tracts. Engineers at treatment plants help harness and enhance these natural processes with the right temperature and oxygen conditions to cope with the huge volume of water we use everyday.



If you live in the Boston area, check out Deer Island. In addition to all the cool science and engineering you’ll learn, it is surrounded by a National Park that offers walking, jogging, picnicking, fishing, and a picturesque view of the Boston skyline.


matusMariana G. Matus is a PhD candidate in Computational and Systems Biology at MIT. Her research focuses on how sewage networks can be leveraged to study the health and behavior of human populations. When not performing research, she likes to drink tea and read.