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Fungal colonies grow on dishes inoculated with rock samples from deep within Earth’s ocean crust. WHOI microbiologist Ginny Edgcomb and guest investigator Gaetan Burgaud are exploring what life forms may be living there. (Photo by Tom Kleindinst, Woods Hole Oceanographic Institution) [ Hide caption ]

Life Dwells Deep Within Earth's Crust

What is living there and how?

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Aboard a drillship in the Indian Ocean, geologists pursued their mission to bore a hole thousands of feet through the seafloor to reach the Moho, the mysterious and never-before-penetrated boundary between Earth’s crust and underlying mantle. For microbiologist Virginia Edgcomb, that hole was a passageway not just through, but into the lower crust. She was on a subseafloor quest of her own: to find whatever intrepid and possibly diverse communities of organisms might be living in rocks deep beneath the seafloor.

Edgcomb, a microbial ecologist at Woods Hole Oceanographic Institution (WHOI), studies how life can survive and even thrive in some of the harshest places on Earth, including environments devoid of oxygen, which most organisms use to breathe. But Edgcomb and others have found fungi, bacteria, and other single-celled organisms called archaea beneath the seafloor that use alternative biochemical reactions and alternative chemicals such as hydrogen, sulfur and methane to produce energy.

“They ‘breathe’ things like metals and other molecules for their respiration instead of oxygen,” Edgcomb explained.

Many of the chemicals the organisms use are produced by chemical reactions that can occur in the particular types of olivine-rich rocks and under the particular conditions found in the crust and mantle.

“It’s pretty exciting to think that life forms could just be living on the rocks themselves, as a result of chemical processes that occur in the rocks,” she said. “And you can imagine that’s a scenario that may have been quite similar to one on early Earth—before our planet’s atmosphere evolved to have oxygen. Also, some of the environments we’re exploring may be analogues for environments people are exploring for extraterrestrial life, such as Enceladus and Europa, the icy moons of Saturn and Jupiter.”

Edgcomb and WHOI geobiologist Joan Bernhard have searched for life in other extreme environments as well, such as ultradense, ultrasalty, oxygen-depleted brine pools on the seafloor. Edgcomb had also analyzed subseafloor rock samples collected from a 2008 International Ocean Drilling Program expedition off the coast of Peru, and she and WHOI biologist Rebecca Gast discovered evidence of fungi living in them. In samples from the same site, Edgcomb and WHOI colleague Bill Orsi discovered the first evidence, based on messenger RNA, of eukaryotic life beneath the seafloor. “The three major domains of life are bacteria, archaea and eukaryotes,” Edgcomb explained. “Humans and other animals, plants, and fungi belong to eukaryotes.”

The Indian Ocean expedition in December 2015 and January 2016 offered a rare opportunity to get samples of deep- ocean crustal rocks. Edgcomb was eager to find out what was living there and how they were managing it. “As we go deep into the crust, we’re likely to find organisms that are even more specialized”—adapted, that is, to the special geological and chemical conditions in the lower crust.

Ultraclean on a dirty ship

Edgcomb’s participation in the Indian Ocean drilling expedition happened almost by accident. WHOI geologist Henry Dick was a co-chief scientist organizing the cruise, but though she and Dick worked in the same building for years, they had next to no involvement with each other’s research.

“We didn’t really know each other well, so it was really a little bit of luck that Henry drifted by my lab and introduced himself to me,” she said. The pair began chatting about adding a microbiology research component to the upcoming expedition, and when the project was funded, Edgcomb was invited aboard.

She had no prior experience with deep-sea drilling and quickly learned to appreciate the dexterity of the drilling crew. “To watch them in motion is like watching a bizarre ballet of danger and sweat and muscle and skill,” she said. “They’re moving and manipulating these enormously heavy sections of drill pipe, and it’s just crazy to watch.”

Aboard the JOIDES Resolution drillship, Edgcomb worked with Jason Sylvan, a microbiologist from Texas A&M University, to examine rock samples cored out of the seafloor as the drilling crew pulled them up.

“About every four hours, a new section of core would come up on deck,” she said. The two scientists undertook elaborate procedures to remove contamination from microorganisms in seawater and drilling debris, and to prevent contamination from air or their own fingers. The cores were taken to an enclosed “clean” lab that had been set up aboard the ship with a HEPA filter to keep out contaminants. “A ship is a really, really dirty place, so it was so cool that they worked with us to set up this space,” Edgcomb said.

Inside the clean lab, “we chiseled away all the exterior material, and we only harvested interior material for our analyses,” she said. They targeted wafer-thin veins, or fractures, in the rocks where seawater had percolated down into the crust.

In their initial analyses, they tested for the presence of adenosine triphosphate (ATP), a key energy-transferring molecule in cells. They found detectable levels of ATP, a good sign that life abided within the rocks.

What’s living down there?

Now back on land, Edgcomb and Sylvan are conducting additional experiments in their respective labs. Sylvan is focusing on bacteria and archaea; Edgcomb is working on fungi with guest investigator Gaetan Burgaud of the University of Brittany. They will also examine biomarkers for lipids and DNA, which will tell them what organisms are present, and for RNA, which provide clues about the enzymes and metabolic pathways these organisms use to live thousands of feet below the seafloor. In addition, WHOI geochemist Frieder Klein will analyze the rocks' mineral properties to learn more about the chemical reactions that occur in subseafloor rocks (see Page 18).

Organisms in extreme environments might not be active all the time, but they may still be very much alive, Edgcomb said. Both eukaryotes and prokaryotes, like bacteria, often form spores, a dormant stage that allows them to survive when conditions aren’t favorable.

“These organisms can basically be hanging out for millions of years in a very quiescent state,” Edgcomb said. “I’m sure even the active microbes are carrying on at a very slow rate relative to those near the surface, but nevertheless, they’re buzzing along.”

Edgcomb and Burgaud have inoculated many petri dishes with rock samples to see what life forms will grow.

“We’re eager to figure out who they are, and if they’re new types of fungi,” Edgcomb said. “Even if they’re the same types of fungi that have been found in other subsurface environments, it’s exciting to know they’re in rocks much farther below the seafloor, because I think this is the first time people have searched for eukaryotic life in the lower ocean crust.” 

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