NOAA Great Lakes Environmental Research Laboratory

The latest news and information about NOAA research in and around the Great Lakes


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Millions of Microbes: The Unexpected Inhabitants of Lake Huron’s Underwater Sinkholes

When most people think of sinkholes, a massive cavity in the ground opening up and swallowing a car is what usually comes to mind. But when scientists at the NOAA Great Lakes Environmental Research Laboratory (GLERL) hear “sinkholes,” their minds jump to an unusual place — the bottom of a Great Lake.

Aerial view of research boat on green water
Researchers on GLERL’s R/V Storm study sinkholes in northern Lake Huron off the coast of Alpena, Michigan. (Credit: David J Ruck/Great Lakes Outreach Media)

Thousands of years ago, off the coast of Alpena, Michigan, patches of ground beneath Lake Huron collapsed to form a series of underwater sinkholes — some measuring hundreds of feet across and up to 60 feet deep. You may have read this NOAA.gov article about how these sinkholes are contributing water to Lake Huron, but did you know they also support a huge kingdom of microorganisms?

Microbes might be tiny, but they’re one of the biggest research topics in the Great Lakes. They thrive near the sinkholes because the groundwater seeping in has the perfect chemistry for their survival: low oxygen levels and lots of chloride and sulfate, which come from the dissolved limestone underlying the lake. These factors make the sinkholes inhospitable for fish and other wildlife normally found in the Great Lakes, which means these microbes have a much easier time surviving there than other creatures. With perfect living conditions and little competition, they’re so abundant that they form purple, green, and white microbial mats that cover the lake floor like a colorful carpet.

Floor of Lake Huron covered by purple and white microbial mats with bubbles in them.
Purple microbial mats in the Middle Island Sinkhole in Lake Huron, June 2019. Small hills and “fingers” like this one in the mats are caused by gases like methane and hydrogen sulfide bubbling up beneath them. (Credit: Phil Hartmeyer, NOAA Thunder Bay National Marine Sanctuary)

Scientists at GLERL are collaborating with partners from the University of Michigan and Grand Valley State University to see just what these microscopic lake dwellers can teach us. This video by Great Lakes Outreach Media highlights how they can even give us a deeper insight into the history of Earth itself.

Associate Professor Greg Dick from the University of Michigan discusses cyanobacteria’s important role in Earth science. This clip is from Great Lakes Outreach Media’s upcoming documentary, “The Erie Situation.”

Some sinkholes are so deep that sunlight can’t reach them, but that doesn’t stop some microbes from calling them home. They’re able to live their entire lives in complete darkness, because they get their energy from the added minerals in the water rather than from sunlight — a process called chemosynthesis. But whether they need sunlight or not, several of the microbial species present have proven to be full of surprises.

“In the near-shore systems, the cyanobacteria we found have DNA signatures that come closest to comparing to the cyanobacteria found at the bottom of a lake in Antarctica. So that’s a strange coincidence,” said Steve Ruberg, the scientist in charge of sinkhole research at GLERL. “Some of the other bacteria we’ve found in the deeper systems have only been found off the coast of Africa.”

Fish sitting on a rock, which is covered by purple and white microbes
A burbot resting on rocks covered in purple and white microbial mats inside the Middle Island sinkhole in Lake Huron. (Credit: Phil Hartmeyer, NOAA Thunder Bay National Marine Sanctuary)

The particular sinkholes we’re studying are located within NOAA’s Thunder Bay National Marine Sanctuary, an area of Lake Huron that’s federally protected for the purpose of preserving nearly 200 shipwrecks. In fact, the only reason we know about these sinkholes is because they were discovered by accident only 18 years ago, on a research cruise documenting the shipwrecks.

Close up of rocks covered in  purple, white and green microbes on the bottom of Lake Huron, with a diver in the background.
A diver observes the purple, white and green microbes covering rocks in Lake Huron’s Middle Island Sinkhole (Credit: Phil Hartmeyer, NOAA Thunder Bay National Marine Sanctuary)

So why did this microbial paradise come into existence in the first place? The story goes back much further than the sinkholes’ discovery in 2001. About 400 million years ago, before the Great Lakes even existed, a layer of limestone bedrock formed beneath what is now Lake Huron. Then around 10,000 years ago, underground caves were created when a chemical reaction between the limestone and acidic groundwater dissolved away holes in the bedrock. All that was left were weakly supported “ceilings” that eventually collapsed into the sinkholes we — and the microbes — know and love today.

Close up of rocks covered in purple, white and green microbes on the floor of Lake Huron
Purple cyanobacteria and white chemosynthetic mats on the floor of Lake Huron with Lowell Instruments current meter. (Credit: Phil Hartmeyer, NOAA Thunder Bay National Marine Sanctuary)

Since Lakes Michigan and Erie have the same limestone bedrock as Lake Huron, GLERL scientists think these lakes could be home to more of these fascinating underwater features. So while the excitement of this fieldwork has died down for the year, our research on Great Lakes sinkholes and their tiny inhabitants is far from over.


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NOAA GLERL collaborating with partners to monitor the Lake Huron ecosystem

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The NOAA Great Lakes Environmental Research Laboratory (GLERL) is participating in an international, multi-agency effort to study invasive species, water quality, fisheries, and climate change in Lake Huron this field season—pursuing key knowledge gaps in the ecosystem. The Coordinated Science and Monitoring Initiative (CSMI) coordinates across U.S. and Canadian agencies to conduct intensive sampling in one Great Lake per year, on a five-year cycle. The Great Lakes Restoration Initiative, which is administered by the U.S Environmental Protection Agency (EPA), is funding this research.

“While GLERL has had a long-term research program focused on Lake Michigan, we are using this initiative to advance long-term research on Lake Huron,” said GLERL Director Deborah Lee. “Invasive species, warming temperatures, and changes in nutrient loading are putting as much stress on Lake Huron as on Lake Michigan. We want to better understand the Lake Huron ecosystem and develop modeling tools to predict how the lake is changing.”

Henry Vanderploeg, Ph.D., chief of GLERL’s Ecosystem Dynamics research branch and lead researcher for GLERL’s efforts in the pelagic (open water) portion of the initiative comments, “GLERL plays a critical role in the CSMI, addressing key science questions. GLERL’s high frequency temporal and spatial sampling will help determine nutrient and energy flows from tributaries, nearshore to offshore. This type of data is critical to effectively manage Lake Huron for water quality and fish production.” Frequent spatial surveys are key to understanding food web connections throughout the seasons.

Researchers from GLERL  will expand upon their recent work in Lake Michigan (CSMI 2015) and past work in Huron (2012) to determine fine-scale food-web structure and function from phytoplankton to fishes along a nutrient-rich transect (from inner Saginaw Bay out to the 65-m deep Bay City Basin) and along a nutrient-poor transect (from inner Thunder Bay out to the Thunder Bay basin) during May, July, and September. GLERL will collect additional samples of fish larvae and zooplankton along both transects in June to help estimate larvae growth, diet, density, and mortality and to identify fish recruitment bottlenecks.

“GLERL was instrumental in establishing the long-term monitoring efforts that provide the foundation for current CSMI food-web studies,” said Ashley Elgin, Ph.D., research ecologist in the Ecosystem Dynamics research branch. Elgin serves as the NOAA representative on the CSMI Task Team, part of the Great Lakes Water Quality Act Annex 10, alongside partners from the U.S. Geological Survey (USGS), EPA, the U.S. Fish & Wildlife Service, Environment and Climate Change Canada, and the Ontario Ministries of Natural Resources and the Environment and Climate Change. This year, Elgin is conducting critical mussel growth field experiments in Lake Huron, expanding upon work she developed in Lake Michigan.  She will be addressing the following questions: (1) How does quagga mussel growth differ between regions with different nutrient inputs?; and (2) How do growth rates compare between Lakes Michigan and Huron? Elgin will also coordinate a whole-lake benthic survey, which will update the status of dreissenid mussels and other benthic-dwelling organisms in Lake Huron.  

GLERL’s key research partner, the Cooperative Institute for Great Lakes Research (CIGLR), will deploy a Slocum glider for a total of sixteen weeks to collect autonomous measurements of temperature, chlorophyll, colored dissolved organic matter (CDOM), and photosynthetically active radiation (PAR) between outer Saginaw Bay and open waters of the main basin.  Deployment times and coverage will be coordinated with other glider deployments by the EPA Office of Research and Development (ORD) and/or USGS Great Lakes Science Center, spatial research cruises, and periods of expected higher nutrient loads (i.e., following runoff events).  

CSMI research cruises began in late April and will continue through September. Researchers are using an impressive fleet of research vessels, including EPA’s 180-foot R/V Lake Guardian, GLERL’s 80-foot R/V Laurentian and 50-foot R/V Storm, and two large USGS research vessels, the R/V Articus and R/V Sterling. Sampling missions will also be conducted aboard Environment Canada’s Limnos across Lake Huron. The Laurentian is fitted out with a variety of advanced sensors and sampling gear, making it especially suitable for examining fine-scale spatial structure.

Scientists from the USGS Great Lakes Science Center, the Michigan Department of Natural Resources, and the University of Michigan are also participating in the Lake Huron CSMI.