There’s nothing like an open septic tank to make a person appreciate the value of clean water.


In Michigan’s Saginaw Bay watershed, many residents rely on septic systems to treat wastewater from toilets and drains. Home septic systems typically consist of underground tanks and specially designed drainage areas that capture and partially treat household wastewater. These systems process microbes and contaminants from human activities, including medications, personal care products, antibiotics, and nutrients like nitrogen and phosphorus.

Without proper maintenance, aging septic systems can leak contaminated loads into the ground and from there into local groundwater and surface waters, contributing to issues like beach closures and algal blooms. 

Contamination from septic systems, agriculture, industry, and other sources is a significant challenge for communities in Bay County, located in the curve of Michigan’s thumb. Unfortunately, it is often difficult to decipher which of these sources is contributing to the problem. Contaminant runoff into nearby Saginaw Bay has caused enough damage to this freshwater resource that the U.S. Environmental Protection Agency has designated the Saginaw Bay watershed an Area of Concern. 

Matthew Schrenk, associate professor at the Michigan State University Department of Earth and Environmental Sciences and the Department of Microbiology and Molecular Genetics, is leading a Michigan Sea Grant-funded project aimed at developing better strategies for detecting and identifying septic system leaks by testing nearby soil and water for unique blends of microbes, compounds, and nutrients that might serve as contamination “fingerprints.” Tests like these could go a long way toward helping curb sources of contamination in the Saginaw Bay watershed.

Opening up the septic systemCONTAMINATION DETECTIVE WORK

Schrenk and his research team are working closely with the Bay County Health Department, which has launched a proactive response to handling septic contamination. “It’s not a punitive thing, where they’re going out to ding specific violators,” Schrenk said. Instead, the county is integrating science, policy, and communication to help homeowners keep their septic systems in good working order. 

For example, the county has introduced new requirements about how septic systems are inspected, especially when homes are sold. “They have opportunities for people getting very old systems replaced,” said Schrenk. “The information is presented in an accessible way. It’s been educational for me to learn how science and policy intersect in that environment.”

Thanks to Bay County’s prior work, Schrenk has access to detailed maps of the area’s septic systems and water resources. “This gives us a great opportunity to look at the chemical and biological characteristics of surface water and the condition and age of nearby septic systems,” Schrenk said. “The septic system replacements are also a big opportunity, where we can look at systems themselves.”

In 2020, Schrenk and his team of researchers and students coordinated with the health department to directly sample a small number of home septic tanks and nearby surface waters. They donned full-body hazmat suits and masks in a sampling mission Schrenk deemed “relevant, if disgusting.” 

In 2021, they drove hundreds of miles around Bay County to collect water from rivers, ditches, and streams. Analyzing these samples will create a profile of the minerals and molecules present in each waterbody, as well as the microbial populations thriving there.


Septic tanks create ecosystems where bacteria are exposed to substances and concentrations they wouldn’t typically encounter in the natural world. Microbes living in septic systems must evolve and adapt to survive exposure to — or even break down and use — compounds like ibuprofen, caffeine, hormonal birth control, laundry detergent, and nitrates. 

“Each person’s system is different, and each person’s input is different,” said Schrenk. “We’re trying to understand how physical and chemical parameters of septic systems, in general,  influence their microbes and the genes they contain.” 

The results of Schrenk’s study could potentially help public health agencies adopt more efficient sampling protocols. It can be difficult to identify tracers that specifically pinpoint septic systems as sources of contamination. Detecting pharmaceuticals and personal care products in streams or groundwater can be clear red flags — if public health departments and other monitoring agencies have proper equipment and techniques to test for them. Other common contamination indicators, like high levels of phosphorus or nitrogen, could also stem from agricultural fertilizer or industrial discharges. 

Public health officials already rely on E. coli, a bacterium found in human and animal guts, as an indicator of low water quality. Finding elevated levels of E. coli can trigger beach closures or no-contact warnings for rivers and streams. But E. coli can also come from other sources, like farm manure or flocks of geese. And the current analytic approach usually involves swabbing a water sample into a petri dish and waiting several days for microbes to grow. Even public health labs using quantitative PCR — a quicker and more efficient way to identify microbes using DNA sequencing — still rely on indicators that were established a decade or more ago. 

Schrenk hopes to pave the way for a wider range of diagnostic and monitoring techniques. To that end, he and his team are currently analyzing microbes from their field samples in search of DNA fingerprints unique to the mucky cocktail of a human septic system. They’re particularly looking for genes that indicate how microbes interact with their environment. For example, if bacteria spent time in a septic tank before reaching a stream, the researchers might see more genes associated with antibiotic resistance, the ability to degrade certain medications, or thrive in high-nitrate conditions. 

Modern laboratory equipment has made DNA sequencing relatively quick and inexpensive, so the team already has plenty of data to crunch. “The individual genomes of microbes contain thousands of genes,” said Schrenk. “And the community of genomes in the environment contain orders of magnitude more information than that. Sequencing machines give little snippets of DNA, but genomes are much larger than that, a million base pairs or so. The trick is to assemble the DNA pieces back together in a coherent way. It’s like solving a puzzle with lots of tiny pieces that look very similar.” Thankfully, computer programs will help speed the reassembly.


After they process the DNA sequencing results, the team will be able to use their field samples to begin painting a larger picture. They will integrate data about the abundance of particular genes with information about water quality and map them across the Bay County landscape. 

“The next steps are to statistically test these relationships to show that the abundance of these particular genes correspond with characteristics of their environment,” said Schrenk. Ideally, this will highlight some genetic or molecular red flags that reliably signal the presence of septic system contamination. 

Schrenk’s current project with Michigan Sea Grant will continue for another year. This fall, Schrenk and his team will have a unique sampling opportunity. “Bay County has grants to help pay to get aging systems replaced,” Schrenk said. “This will allow us to get directly into the drainfields, which are the conduits between the system and surface water resources.” The researchers will collect samples from one or two household septic systems and nearby streams, ditches, and rivers — more clues for the contamination detectives to investigate.

Schrenk is no stranger to pursuing microbes in odd locations. “Historically, a lot of my work has focused on life in extreme environments, like in volcanoes or the bottom of the oceans,” he said. 

While septic tanks in Bay County may not be as exciting as deep-sea thermal vents, Schrenk appreciates how projects like this can be an important gateway for students interested in research. “The students are really keen on it,” he said. “Many of them are interested in environmental health, sustainability, and environmental engineering. I can get them out into the field, taking their own samples, in a way that I couldn’t if I had to fly them to, say, South America. The students have a sense of ownership when they collect their own samples and think about the systems on their own terms.”