Deep life: exploring microbial dark matter


Extremophile life accounts for perhaps 23 billion tonnes of carbon. Lauren Fuge reports.


The colours of the Morning Glory Pool in America's Yellowstone National Park are the result of heat-loving extremophile microbes.

The colours of the Morning Glory Pool in America's Yellowstone National Park are the result of heat-loving extremophile microbes. They are just one small sample of the massive array of deep life remaining to be discovered.

Kenneth_Keife/Getty Images

“Zombie” bacteria and other forms of life constitute an immense amount of carbon deep within Earth’s subsurface – hundreds of times greater than the carbon mass of all humans on the surface, scientists say.

Carbon is the chemical backbone of all known life and is found in everything from oil to diamonds, but the carbon we can access in the land, air and sea is only a small fraction of the total amount on Earth. The other 90% resides deep in the planet’s interior. Despite its importance, remarkably little is known about this carbon or its interaction with life on the surface.

Now, on the eve of the autumn meeting of the American Geophysical Union, an international team of more than 1000 scientists from the Deep Carbon Observatory (DCO), a global research collaboration, has highlighted major discoveries made over the past decade about the Earth’s innermost secrets.

Among the findings are the nature and extent of the microbial biosphere deep underground. It turns out that 70% of the planet’s bacteria and archaea live in these extreme environments, not only under radical pressures and temperatures, but also in pitch darkness with restricted nutrient sources.

The results are fascinating. In these vast and unexplored territories, almost untouched by humans, so much is unknown that all research is pioneering.

“A decade ago, we had no idea that the rocks beneath our feet could be so vastly inhabited,” says Isabelle Daniel, a scientist at the University of Lyon 1 in France who specialises in materials in extreme environments.

“Experimental investigations told us that microbes could potentially survive to great depth, but at that time, we had no evidence.”

In 2009, the DCO was founded to facilitate collaboration on this topic between geologists, chemists, physicists and biologists. Formulated as a 10-year project, its vast scientific network is dedicated to exploring what has been termed the ‘Galapagos of the deep’ – essentially, unravelling the mysteries of the planet’s carbon cycles.

Scientists in the collaboration have since sampled hundreds of sites around the world, including drilling 2.5 kilometres below the sea floor off the coast of Japan to show that microbes thrive deep in the oceanic crust.

Other studies have sampled microbes from up to five-kilometre-deep mines and boreholes, and identified unique microbes thriving more than two kilometres deep in the hot, saline ecosystems created by the hydraulic fracturing of shale.

After gathering detailed data from these and dozens of other sites, DCO scientists have spent the past few years synthesising the information to create models of the processes happening in subsurface ecosystems. Among other things, the models reveal the incredible size of the deep biosphere – over two billion cubic kilometres, equal to almost twice the volume of all oceans.

The research has also produced estimates of the total carbon mass of the life that lurks in there: between 15 and 23 billion tonnes, which is 245 to 385 times more than the combined carbon mass of humans.

“Exploring the deep subsurface is akin to exploring the Amazon rainforest,” says Mitch Sogin, senior scientist at the Marine Biological Laboratory in Woods Hole, US, and co-chair of DCO’s Deep Life community.

“There is life everywhere, and everywhere there’s an awe-inspiring abundance of unexpected and unusual organisms.”

Research shows that the deep biosphere contains members of all three domains of life: bacteria, archaea and eukarya, though it is dominated by the former two. There are millions of distinct types, most of which are not yet characterised or even discovered. Such populations are nicknamed “microbial dark matter”, because scientists are unable to culture them in the lab due to incredibly slow replication times or extreme growing conditions.

However, advances in DNA sequencing technologies mean that the critters now can be studied in their natural environment.

Scientists have found that these subsurface creatures are incredibly genetically diverse and differ widely according to their environments, though some types are common across the entire planet. They are wildly different from their surface relatives – some, for example, have life cycles that are almost on geological timescales and are sustained solely on energy from rocks, seeming barely alive and zombie-like from our human perspective.

“We know that in many places they invest most of their energy to simply maintaining their existence and little into growth, which is a fascinating way to live,” notes Karen Lloyd, a microbiologist at the University of Tennessee in Knoxville, US.

Indeed, the entire underground microbial community seems alien to surface-dwellers. It dramatically expands concepts of the tree of life. Scientists keep finding extremophiles in more and more radical environments, constantly breaking records for life found in hotter, more pressurised and more nutrient-scarce places.

A current frontrunner for the Earth’s hottest organism, for instance, is the single-celled Geogemma barossii, which lives in hydrothermal vents on the seafloor and thrives at temperatures of 121 degrees Celsius.

“Even in dark and energetically challenging conditions, intraterrestrial ecosystems have uniquely evolved and persisted over millions of years,” says Fumio Inagaki, geomicrobiologist at the Japan Agency for Marine-Earth Science and Technology.

“Expanding our knowledge of deep life will inspire new insights into planetary habitability, leading us to understand why life emerged on our planet and whether life persists in the Martian subsurface and other celestial bodies.”

A great many mysteries remain on Earth, too.

“Our studies of deep biosphere microbes have produced much new knowledge, but also a realisation and far greater appreciation of how much we have yet to learn about subsurface life,” says Rick Colwell, a microbiologist at Oregon State University, US.

There are hundreds of questions left to address, largely relating to the origins, movements and energy sources of the subsurface biosphere.

For example, did life start deep in the Earth and migrate up, or on the surface and migrate down? How do zombie-like microbes reproduce and what are their most important energy sources? Does deep life spread around the globe, perhaps with the help of geological events like plate tectonics and earthquakes? And do these populations interact with life on the surface?

As Colwell says, “For now, we can only marvel at the nature of the metabolisms that allow life to survive under the extremely impoverished and forbidding conditions for life in deep Earth.”

The Deep Carbon Observatory will issue its final report in October 2019.


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