By Harshit
SANTA BARBARA, DECEMBER 11 —
New findings from UC Santa Barbara and international collaborators challenge decades of assumptions about how the deep ocean fixes and stores carbon, helping resolve a long-standing mismatch between nitrogen availability and measured carbon fixation rates in the dark ocean. The work, led by microbial oceanographer Alyson Santoro and published in Nature Geoscience, sheds light on how carbon moves into the deep sea — a process central to the planet’s ability to buffer climate change.
“Something that we’ve been trying to get a better handle on is how much of the carbon in the ocean is getting fixed,” Santoro said. “The numbers work out now, which is great.”
The project was supported in part by the National Science Foundation.
The Deep Ocean as Earth’s Carbon Vault
Earth’s oceans absorb roughly one-third of human CO₂ emissions, acting as the planet’s largest carbon sink. For the ocean to regulate climate over centuries, carbon must travel from the atmosphere into the deep ocean. Much of this transfer occurs via microbial activity.
At the surface, photosynthetic phytoplankton convert dissolved CO₂ into organic matter. In the deep ocean — where sunlight never reaches — scientists long believed that most dissolved inorganic carbon (DIC) fixation was performed by ammonia-oxidizing archaea, microbes that use nitrogen compounds rather than sunlight for energy.
But for years, the nitrogen-based energy available simply did not match the amount of carbon scientists were measuring.
A Decade-Long Carbon Cycle Puzzle
“There was a discrepancy between what people measured when they went out on a ship and what was understood to be the energy sources for microbes,” Santoro said.
In other words: the deep ocean appeared to be fixing more carbon than ammonia-oxidizing archaea could theoretically power.
The mismatch persisted through multiple studies over nearly ten years. Earlier hypotheses — such as the possibility that archaea were far more efficient than assumed — did not hold up.
The new study finally resolves the contradiction.
A Targeted Experiment Reveals the Missing Players
To identify who was actually fixing carbon, lead author Barbara Bayer designed a deep-ocean experiment using phenylacetylene, a chemical inhibitor that selectively blocks ammonia oxidation.
If ammonia-oxidizing archaea were responsible for most deep-ocean carbon fixation, the carbon-fixation signal should have dropped sharply.
It did not.
Despite inhibiting these abundant archaea, DIC fixation rates decreased only slightly — a clear sign that other microbial groups were doing far more of the work than previously believed.
A New Model: Heterotrophs Are Fixing More Carbon Than Expected
The unexpected contributors are likely heterotrophic microbes — organisms that feed on organic carbon from dead or decaying marine life but also appear to take up inorganic carbon.
“We think that heterotrophs are taking up a lot of inorganic carbon in addition to the organic carbon they usually consume,” Santoro said. “Meaning they’re also responsible for fixing some carbon dioxide.”
This discovery provides the first quantitative evidence of how much deep-ocean carbon fixation derives from heterotrophs versus autotrophs.
Redefining the Deep-Sea Food Web
The findings reshape fundamental ideas about how the deep-ocean ecosystem functions.
“There are basic aspects of how the food web works in the deep ocean that we don’t understand,” Santoro said. “This helps us figure out the very base of that food web.”
Beyond clarifying carbon storage, the study opens questions about how fixed carbon becomes available to other organisms — whether through leakage of organic compounds or microbial turnover.
Next Questions: How Do Deep Microbes Feed the Planet?
Researchers will now probe how carbon, nitrogen, iron, copper, and other elemental cycles interact in the deep sea, and what types of organic molecules carbon-fixing microbes release into the ecosystem.
“The other thing we’re trying to figure out is once these organisms fix the carbon into their cells, how does it become available to the rest of the food web?” Santoro said.
Collaborating institutions include UCSB, the University of Vienna, and Woods Hole Oceanographic Institution.