Hundreds of unknown microbial genomes tell story of life deep underground

And old goldmine in South Dakota is teeming with life deep underground – not goldminers, but microbes.

Researchers from Northwestern University have found nearly 600 microbial genomes, some new to science, within fracture fluids up to 1.5 kilometres below the surface.

“The deep subsurface biosphere is enormous; it’s just a vast amount of space,” said Northwestern geoscientist Dr Magdalena Osburn.  

“We used the mine as a conduit to access that biosphere, which is difficult to reach no matter how you approach it. The power of our study is that we ended up with a lot of genomes, and many from understudied groups.

“From that DNA, we can understand which organisms live underground and learn what they could be doing. These are organisms that we often can’t grow in the lab or study in more traditional contexts. They are often called ‘microbial dark matter’ because we know so little about them.”

Similar to the Stawell Underground Physics Laboratory in regional Victoria, the Homestake Mine in South Dakota, is home to the  Sanford Underground Research Facility, with physics and microbial experiments both underway.  

“Researchers mostly perform high-energy particle physics experiments,” said Osburn.

“But they also let us study the deep biospheres that live within the rocks. We can set up experiments in a controlled, dedicated site and check on them months later, which we would not be able to do in an active mine.”

The researchers bore holes into rocks in the old mine, and captured fracture fluids that are up to 10,000 years old. These fluids are made up of water and dissolved gas, plus an amazing variety of microbial life.

From the 600 microbes found, the team discovered that their genes fell into two distinct camps – minimalist or maximalist.

“Many of the microbes we found were either minimalists: ultra-streamlined with one job that it does very well alongside a close consortium of collaborators.

“These maximalists are ready for every resource that comes along. If there is an opportunity to make some energy or transform a biomolecule, it is prepared. By looking at its genome, we can tell it has many options. If nutrients are scarce, it can just make its own.

“The minimalists are extreme specialists, and all together, they make it work. It’s a lot of sharing and no duplication of effort.”

As well as being fascinating, the researchers believe that understanding what our planet’s extreme microbes look like also allows us to look beyond Earth.

“I get really excited when I see evidence of microbial life, doing its thing without us, without plants, without oxygen, without surface atmosphere,” she said.

“These kinds of life very well could exist deep within Mars or in the oceans of icy moons right now. The forms of life tell us about what might live elsewhere in the Solar System.”

The research has been published in Environmental Microbiology.