The researchers have been studying the samples since they reached the lake and have found that an abundance of life lurks beneath Antarctica’s blanket of ice. In this week’s issue of Nature, Priscu and his team report finding 130,000 cells in each millilitre of lake water — a density of microbial life similar to that in much of the world’s deep oceans. And with nearly 4,000 species of bacteria and archaea, the community in the lake is much more complex than might be expected from a world sealed off from the rest of the planet. “I was surprised by how rich the ecosystem was,” says Priscu. “It’s pretty amazing.”

Samples from the lake show that life has survived there without energy from the Sun for the past 120,000 years, and possibly for as long as 1 million years. And they offer the first look at what may be the largest unexplored ecosystem on Earth — making up 9% of the world’s land area.

“There’s a thriving ecosystem down there,” says David Pearce, a microbiologist at Northumbria University, UK, who was part of a team that tried, unsuccessfully, to drill into a different subglacial body, Lake Ellsworth, in 2013. “It’s the first time that we’ve got a real insight into what organisms might live beneath the Antarctic continent,” he says.

Overall, life in Lake Whillans works much like ecosystems at the surface, but its deep denizens do not have access to sunlight and so cannot rely on photosynthesis for the energy needed to fix carbon dioxide dissolved in the lake water.

The genetic analyses by the team show that some of the lake’s microbes are related to marine species that derive energy by oxidizing iron and sulphur compounds from minerals in sediment. But according to the DNA data, the lake’s most abundant microbes oxidize ammonium, which is likely to have a biological origin.

“The ammonium is probably a relic of old marine sediments,” says Priscu, referring to dead organic matter that accumulated millions of years ago when the region was covered by shallow seas rather than glaciers.

Only single-celled bacteria and archaea have turned up in samples from Lake Whillans — but the particular DNA tests used so far were not designed to detect other types of organism. This preserves the possibility that Lake Whillans might yet be found to harbour more complex life, such as protozoa — or even submillimetre animals such as rotifers, worms or eight-legged tardigrades, all known to live in other parts of Antarctica. Air bubbles in the overlying ice supply oxygen to the lake, so that is not a limiting factor. But the low rate of carbon fixation by microbes might provide too little food for multicellular life.

Lake Whillans receives about one-tenth the amount of new carbon per square metre per year as the world’s most nutrient-starved ocean floors, which support sparse animal populations. Although the chances are slim that Priscu and his colleagues will find animals in Lake Whillans, they plan to look for them using better-tailored DNA assays. For now, the researchers are puzzling over the origins of the microbial residents of the lake. The big question is whether Antarctica’s subglacial communities are made of ‘survivors’ or ‘arrivers’.

Survivors would be the descendants of microbes that lived in the sediments when the area was covered by open ocean, as it has been periodically over the past 20 million years. Alternatively, Lake Whillans might be populated by wind-blown microbes — the ‘arrivers’ — that were deposited on the ice and worked their way down over 50,000 years as ice melted off the bottom of the glacier.

It is also possible that some organisms entered the lake more recently, carried in by sea water seeping under the ice sheet. Lake Whillans sits just 100 kilometres from the grounding line, where the ice sheet transitions from resting on ground to floating on the ocean. That line shifts as the ice thins and thickens, so it is possible that the lake exchanged water — and microbes — with the ocean during the past few thousand years, says Christina Hulbe, a glaciologist at the University of Otago in Dunedin, New Zealand, who has long studied that area of Antarctica.

Other findings from the lake samples have led to some tantalizing ideas. Traces of fluoride in its water offer possible evidence of hydrothermal vents in the area — rich sources of chemical energy that have the potential to support islands of exotic life, such as worms or heat-loving microbes. “It’s probable that there are hydrothermal systems in there,” says Donald Blankenship, a glaciologist at the University of Texas at Austin. The lake occupies a broad rift valley where Earth’s crust has thinned, and radar surveys by Blankenship show putative volcanoes under the ice.