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A new study involving University of Delaware Assistant Professor Sunita Shah Walter shows that microbes living in the subseafloor may have a surprising way to access the carbon they need to survive. The study was led by Arizona State University and the Woods Hole Oceanographic Institution and looked to discover how the microbes were consuming organic carbon and using carbon dioxide.

Feeding deep ocean microbes

Illustration by Tammy Beeson

Under the ocean, microbes are active and poised to eat whatever comes their way

The subseafloor constitutes one of the largest and most understudied ecosystems on Earth. While it is known that life survives deep in the fluids, rocks, and sediments that make up the seafloor, scientists know very little about the conditions and energy needed to sustain that life.

An interdisciplinary research team, led by Arizona State University and the Woods Hole Oceanographic Institution (WHOI) and including the University of Delaware, sought to learn more about this ecosystem and the microbes that exist in the subseafloor, finding that the microbes may have a surprising way to access the carbon they need to survive.

The results of their findings were published in Science Advances, with ASU School of Earth and Space Exploration assistant professor and geobiologist Elizabeth Trembath-Reichert as lead author.

From UD, Sunita Shah Walter, assistant professor in the School of Marine Science and Policy, served as a co-author on the paper and measured the natural carbon for the project. 

To study this type of remote ecosystem, and the microbes that inhabit it, the team chose a location called North Pond on the western flank of the Mid-Atlantic Ridge, a plate boundary located along the floor of the Atlantic Ocean. 

North Pond, at a depth of more than 14,500 feet (4,500 meters) has served as an important site for deep-sea scientists for decades. Most recently the International Ocean Discovery Program drilled hundreds of feet through the sediment and crust at the site in 2010 to create access points for studying life and chemistry beneath the seafloor. 

“After drilling, these holes in the crust are cased with a pipe,” said Shah Walter. “There are these platforms at the top of them and fluid lines that extend from the platform all the way down through these holes. They’re called CORK Observatories. You can go to these CORKs and hook up a pump to the fluid lines and draw up fluid from hundreds of meters down.” 

With support from the National Science Foundation, the Gordon and Betty Moore Foundation, and the Center for Dark Energy Biosphere Investigations, the team sampled the crustal fluid samples from the borehole seafloor observatories with the deep sea remotely operated vehicle Jason II on the research vessel Atlantis.

Kristin Yoshimura, who earned her doctorate at UD in 2019 and is now a postdoctoral student at the University of Tennessee, went on this research cruise to help the team retrieve the samples and said it was great to have a multidisciplinary group of scientists out on the ship. 

"The team on the ship was an incredible group of scientists from a number of different specialties including microbiologists, organic and inorganic chemists, and ecologists,” said Yoshimura. “We all had a common goal — to study what life is doing in the Earth’s crust — but were able to come together from our unique angles to be able to ultimately tell a more comprehensive, robust story. This type of interdisciplinary science is crucial to fully understanding what is really going on down there."

These unique samples from the pristine, cool basaltic seafloor were then brought back to the lab and analyzed using a Nanoscale secondary ion mass spectrometer (NanoSIMS), which was used to measure their elemental and isotopic composition. 

“Our experiments use specialized tracers that can only be observed if a microorganism eats something on the buffet of options we provide,” said Trembath-Reichert. “If we see these tracers in the microbes, then we know they must have been active and eating during our experiments and we get an idea of what food sources they can use to survive.”

Through these analyses, the team discovered that the subseafloor microbial community is active and poised to eat, despite an environment with low biomass and low-carbon conditions. 

Shah Walter said that the microbes live in the ocean crust, below about 3,000 meters of water and then about 100 meters or so of sediment.

“It’s a really difficult environment to live in,” said Shah Walter. “There is very little energy available, and the energy that is available is from organic carbon.” 

All living things need some source of carbon and some source of energy to survive. In a previous paper, Shah Walter said that the only energy she and her collaborators were able to identify in this environment was organic carbon based. 

“From that study, we expected these microbes to get their carbon and their energy from the organic carbon,” said Shah Walter. “But it’s really unappetizing organic carbon. It’s like eating tree bark. It has a radiocarbon age that is thousands of years old, and from what we understand, it’s been floating in the open ocean for thousands of years. No open ocean microbes are interested in eating it and then it gets entrained into the crust and that unappetizing organic carbon is all that’s available.” 

This study looked to discover how the microbes were consuming organic carbon and using carbon dioxide. 

Trembath-Reichert and her team expected the microorganisms to use widely available carbon dioxide the way plants do, by “fixing” it into other forms of organic carbon that they can then use to grow on. But the findings suggest the microbes in this isolated environment with low nutrients and degraded organic carbon were being craftier.

“Our theory is that these microbes are being resourceful and using the carbon dioxide directly as a building block without having to convert it into a food source first,” said Trembath-Reichert. “And this could have major implications for the deep ocean carbon cycle.”

The next steps for Trembath-Reichert and her team are to design experiments to better understand the full diversity of ways carbon dioxide can be used by microbes. As a more readily available carbon source for microorganisms, they will be looking into the ways carbon dioxide can be used for survival and growth in the Earth's largest aquifer beneath the seafloor.

To conduct this research, Trembath-Reichert was supported by fellowships from the NASA Postdoctoral Program and The L’Oréal For Women in Science Program.

Additional authors on this study include senior author Julie Huber of WHOI, Marc Fontánez Ortiz of ASU’s School of Life Sciences, Patrick Carter of the University of Massachusetts and Peter Girguis of Harvard University.

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