The Middle Island sinkhole is open to Lake Huron, creating a gradient of biological activity. A nine-metre boat is also visible in this aerial photo for sense of scale. (Scott Kendall/Bopi Biddanda/Grand Valley State University)Twenty metres below the surface of Lake Huron, scientists have discovered peculiar sinkholes where a bizarre ecosystem at odds with the rest of the lake flourishes.

The huge lake's freshwater fish shun the dense, salty, oxygen-deprived waters of these sinkholes off northeastern Michigan.

Instead, brilliant purple mats of cyanobacteria — cousins of microbes found at the bottom of permanently ice-covered lakes in Antarctica — and pallid, floating, ponytail-like microbes thrive.

Groundwater from beneath the lake is dissolving minerals from the ancient seabed and carrying them into the lake to form these exotic, extreme environments, says aquatic ecologist Bopaiah Biddanda of Michigan's Grand Valley State University, a leader of the team studying the sinkhole ecosystems.

"These are almost primordial Earth conditions, with high sulphur and low oxygen like in the ancient oceans that covered the Earth three billion years ago," Biddanda told CBC News.

"It gives us a window into the past and who knows what value it will hold."

The researchers describe this little-known underwater habitat in this week's issue of Eos, published by the American Geophysical Union.

Although above-ground sinkholes in the area were discovered decades ago, the submerged sinkholes were only recently uncovered.

Discovered 8 years ago

In 2001, researchers with the Connecticut-based Institute for Exploration stumbled across them during an underwater archeological survey for shipwrecks in Michigan's Thunder Bay National Marine Sanctuary.

Scientists began to explore these sinkholes a couple of years later, finding some just 20 metres below the surface and others extending 100 metres down, where the sun never shines.

But their findings have trickled in over the last few years because of the logistical problems in exploring lakebed sinkholes.

"Finding these little spots in a huge lake — you can't even compare it to looking for a needle in a haystack," said Biddanda.

The most recent findings show an ecosystem that has more in common with Antarctic lakes and deep-sea, hydrothermal vents than it does with a freshwater lake.

"We were amazed to find these brilliant cyanobacteria mats," said Biddanda. DNA sequencing of the purple mats show they are closely related to mats found in the ice-covered, oxygen-poor Antarctic lakes.

Biddanda suspects similar ecosystems once existed all around the Earth but largely disappeared as the planet's atmosphere became increasingly oxygen-rich.

The team, including researchers from the U.S. National Oceanic and Atmospheric Administration, suspects similar sinkholes exist under the other Great Lakes because, with the exception of Lake Superior, the lakebeds are all composed of limestone, with ancient aquifers running beneath.

The researchers will continue to study the sinkholes this summer, keeping a sharp eye out for the possible discovery of never-before-seen organisms and biochemical processes.