Breakthrough discovery identifies bacteria behind toxins in St. Louis river estuary

Duluth, Minn. — Minnesota Sea Grant-supported researchers studying harmful algal blooms in the St. Louis River Estuary that separates Minnesota and Wisconsin have made a breakthrough discovery: for the first time, they’ve linked a known cyanotoxin directly to a specific cyanobacteria species, Microcystis aeruginosa, in the Duluth-Superior harbor. 

Cyanobacteria, also known as blue-green algae, can produce toxins, called cyanotoxins, which pose significant health risks to humans, pets, livestock and wildlife. 

Cody Sheik, a microbial ecologist at the University of Minnesota Duluth, led the research in collaboration with Chris Filstrup, a limnologist at the University of Minnesota Natural Resources Research Institute, and Abby Smason, a UMD graduate student researcher and "bloom catcher." 

Smason presented a poster, "A Metagenomic Approach to Tracking Lake Superior's Cyanobacterial Blooms,” about the project at the 2025 International Association for Great Lakes Research conference June 2-6, 2025, in Milwaukee, Wisconsin. Sheik and Filstrup also attended the conference. 

"We’ve known that cyanobacteria blooms have been increasing in frequency around Barkers Island and other parts of the estuary," said Sheik. "But this is the first time we’ve confirmed, with genetic evidence, that a specific Microcystis strain has the complete set of genes needed to produce microcystin, a potentially harmful cyanotoxin." 

The researchers’ discovery was made using metagenomic sequencing, a technique that allows researchers to analyze the DNA of microbial communities directly from environmental samples. 

“This is the first time we’ve actually been able to go out, grab a sample and then sequence the DNA from that sample,” said Sheik. “In the samples that Abby collected from across the estuary we found Microcystis to be the dominant cyanobacteria during bloom events.” 

The project team now wants to figure out if there are specific locations within the estuary that are more prone to growing cyanobacteria. 

“The bigger implication is if these blooms can become super intense and make their way into Lake Superior,” said Sheik. 

For now, Lake Superior’s vast size and low phosphorus levels, which cyanobacteria feed on, make it difficult for the organisms to survive long enough to trigger blooms along the south shore. 

"This is a significant finding for public health and water resource managers," said Filstrup. "Knowing which organism is responsible helps us track where the toxins may be coming from and better understand how to prevent or respond to outbreaks." 

Although toxin levels detected to date have remained relatively low, the researchers say the findings underscore the need for regular monitoring, especially as warmer water temperatures that favor bloom development happen more frequently and for longer periods of time. 

Areas like Barkers Island draw thousands of visitors each summer for swimming, paddling, boating, festivals and family outings. The high public use around these nearshore areas means that even low-level harmful algal bloom could pose health risks or lead to recreational advisories. Studying these locations can help protect the health of the people and pets who use the water. 

"We don’t have a magic solution to harmful cyanobacterial blooms yet," said Smason. "But tracking and sharing information with the public is the best step we can take right now." 

The team is exploring future partnerships with the National Oceanic and Atmospheric Administration and state agencies to expand monitoring efforts and better predict bloom behavior in Lake Superior and its connected waterways. 

ADDITIONAL INFORMATION 

For more information about this project see the Minnesota Sea Grant-funded project Blooming Threats: Assessing Future Cyanobacterial Threats to Lake Superior.

Minnesota Sea Grant is a systemwide program of the University of Minnesota and one of 34 federal-university Sea Grant partnerships across the country supported by the National Oceanic and Atmospheric Administration in Great Lakes and coastal states that encourage the wise stewardship of our marine resources through research, outreach, communication, education and technology transfer. 

CONTACTS:

Cody Sheik, Associate Professor of Biology, Swenson College of Science and Engineering, Large Lakes Observatory, University of Minnesota Duluth, cssheik@d.umn.edu 

Chris Filstrup, Lake Scientist, Natural Resources Research Institute, University of Minnesota, filstrup@d.umn.edu 

Abby Smason, Ph.D. student, Water Resources Science Graduate Program, University of Minnesota Duluth, smaso003@d.umn.edu

Marie Thoms, Communications Director, Minnesota Sea Grant, University of Minnesota and University of Minnesota Duluth, methoms@d.umn.edu.