Submerged Sinkhole Ecosystems in Northern Lake Huron

Summary: This data set includes 2 pages of data about submerged (underwater) sinkholes in Lake Huron collected in September 2003.

View the Data: sinkhole data.xlsx


Local residents of the Lake Huron coast have known about sinkholes on land and in shallow, nearshore areas for centuries. However, it wasn’t until recently that scientists discovered the unique freshwater ecosystems. Submerged sinkholes, or sinkholes found underwater, were officially discovered by accident during a 2001 expedition looking for shipwrecks in the Thunder Bay National Marine Sanctuary and Underwater Preserve. The discovery prompted subsequent expeditions to gather data in order to learn more about the composition of the Lake Huron sinkhole systems.

The Formation of Sinkholes in Lake Huron

A brief history of how the Great Lakes came to be

The foundation for the present Great Lakes basin was set about 3 billion years ago (Precambrian Era). It was a period of great volcanic activity and tremendous stresses, which helped form the northern portions, called the Canadian Shield, of the Great Lakes basin. During the Pleistocene Epoch, which began about a million years ago, the continental glaciers repeatedly advanced over the Great Lakes region from the north. As they inched forward, the glaciers that were up to 2,000 meters (6,500 feet) thick, scoured the surface of the earth, flattening the terrain and moving boulders thousands of miles. With each retreat, chunks of ice were left in their wake and the melting waters eroded new valleys, rivers and lake basins. Mixtures of sand, silt, clay and rocks — referred to as glacial drift — piled in moraines, drumlins and plains that were also left in the wake of the glaciers’ retreat. The Great Lakes were formed as the last glacier completed its retreat about 4,000 years ago.

See: Timeline graphic (PDF)

The limestone, dolomite and other carbonate rocks laid down in the region during the Paleozoic era still form the underlying bedrock in pockets throughout the Great Lakes basin. These types of rocks are easily dissolved, forming deep and shallow aquifers, caves and sinkholes — referred to as karst topography. Sinkholes are formed when the underlying Paleozoic rock dissolves, and the glacial ceiling collapses to create a vertical hole.

Once the sinkholes were discovered, scientific study began. Observations during expeditions in 2002 and 2003 revealed groundwater actively seeping into three of the sinkholes, including the Middle Island, Misery Bay and Isolated sinkholes. The groundwater vents at the bottom of these sinkholes — the areas where the groundwater seeps into the lake — contain unique biogeochemical conditions different from those found in typical lake water.

Unique, Yet Similar

Until recently, it was thought that such unique habitats (caused by steep environmental gradients) were only found in oceans. Researchers are now considering the Lake Huron sinkholes and groundwater vents to be similar to marine vent ecosystems. Research also found evidence of significant chemosynthesis in the deepwater sinkholes where no sunlight can penetrate. For example, a variety of non-photosynthetic benthic microbial mats were observed in the Lake Huron sinkholes.

The concentration of certain types of ions such as, Cl⁻, Br⁻, F⁻, SiO₂, SO₄⁻2, NO3, P and Fe reveals the presence of dissolved solids in the water. These dissolved solids are picked up when the groundwater moves through the bedrock. Many come from the dissolution of the nearby rock itself; others may be carried miles from surface sources through cracks in the dissolving bedrock.

What is Chemosynthesis?

Chemosynthesis, like photosynthesis, is a process by which certain organisms get their energy. However, unlike photosynthesis that uses sunlight as its energy provider, chemosynthesis energy comes from chemicals. Organisms that use this process are bacteria, which are typically found around the hydrothermal vents (areas where warmer water is seeping into the larger, cooler body of water), like those seen in the Lake Huron sinkholes.

The high temperatures and high concentrations of dissolved minerals in the water seen around sinkhole vents form compounds such as hydrogen sulfide. In a biochemical process, bacteria oxidize hydrogen sulfide and use the liberated energy to produce carbohydrates (i.e., stored chemical energy). Unlike photosynthesis, chemosynthesis requires no light and can occur in deep water. The chemosynthetic food web supports dense populations of uniquely adapted organisms.

See: Photosynthesis (PDF) and Chemosynthesis (PDF)


Prior to finding the Lake Huron submerged sinkholes, little was known about the microbiology of groundwater seeps in large bodies of freshwater. Research has since provided some data and findings to work from. In the first stages of exploration, for example, high concentrations of dissolved organic carbon (DOC) and particulate organic carbon (POC) were found. These are both important in fueling the microbial or bacterial food web. The combination of the large quantity of DOC and POC helps the chemosynthesis process occur in the sinkhole.

Study has also enabled researchers to map the hydrography, develop bathymetric maps of the sinkhole communities, and evaluate microbial growth rates in sinkhole environments in the Great Lakes. The discovery of unique chemical characteristics of these ecosystems and their similarities to the oceanic thermal vent systems led researchers to search for similarities and differences in the biology of these systems that might also parallel their ocean counterparts.

They also found that since the groundwater emerging at these sinkholes contains high sulfate and low dissolved oxygen, the habitats lack the fish and other communities typically found in Lake Huron. Instead, single-celled microorganisms dominate the life found in Lake Huron sinkholes.

A New Frontier

The unique biology of the ocean vents has proven fruitful ground for the discovery of unique microorganisms with important properties that make them valuable to pharmaceutical research. Research on the pharmaceutical value of the organisms in Great Lakes sinkholes is already beginning even as scientists continue to explore the basic ecology of the systems.

Research Methods for Sampling and Analysis

A variety of methods were used to collect data from the sinkhole site. These methods include:

  • Dive teams
  • ROVs (remotely operated vehicles) equipped with CTDs (conductivity, temperature and depth recorders)
  • Side scan sonar
  • Selective sampling gear
  • An acoustic positioning system
  • Instrumented mooring
  • Multiparameter sondes

Detailed research methods and additional figures can be found in the journal article, Exploration of a Submerged Sinkhole Ecosystem in Lake Huron. The full copy can be downloaded here.

How to Use This Data


  • Compare the chemistry and biochemistry of water from the lake and water from the sinkhole.
  • Compare the amount of chemosynthesis in the lake water and sinkhole water with the amount of bacteria in both lake and sinkhole water.
  • Does the sinkhole affect the overlying water or is it really an isolated system? Is there a gradient of influence the farther you get from the sinkhole bottom?
  • Is there a connection between the amount of DOC and the amount of bacterial productivity?
  • Which of the physical factors and chemicals seem most closely associated with bacterial abundance? With bacterial productivity? With chemosynthesis?

Enhanced (combine with other data sets or additional calculations):

  • Are sinkholes related to other physical and chemical differences between the Great Lakes?
  • Based on water chemistry, bathymetry, geology or physics – where else in the Great Lakes should we look if we want to discover more sinkholes?


Data Source:
S. Ruberg, S. Kendall, B. Biddanda, T. Black, W. Lusardi, Russ Green, T. Casserley, E. Smith, S. Nold, University of Wisconsin, G. Lang, S. Constant (accepted), Observations of the Middle Island Sinkhole in Lake Huron – A Unique Hydrogeologic and Glacial Creation of 400 Million Years, Mar. Technol. Soc. J., Winter 2008/2009.

Biddanda, B. A., D. F. Coleman, T. H. Johengen, S. A. Ruberg, G. A. Meadows, H. W. VanSumeren, R. R. Rediske, and S. T. Kendall. Exploration of a submerged sinkhole ecosystem in Lake Michigan. Ecosystems 9:828-842 (2006).

Ruberg, S., D. Coleman, T. Johengen, G. Meadows, H, VanSumeren, G. Lang, and B. Biddanda (2005), Groundwater plume mapping in a submerged sinkhole in Lake Huron, Mar. Technol. Soc. J., 39: 65–69.

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