Microbes are responsible for much of carbon sequestration in the ocean. Photo Credit: pngtree.com
New research from UC Santa Barbara is prompting scientists to revise their understanding of how carbon is captured and stored in the darkest parts of the ocean. A study published in Nature Geoscience by microbial oceanographer Alyson Santoro—a professor in Ecology, Evolution, and Marine Biology and a principal investigator of UCSB’s Marine Science Institute—and her collaborators resolves a long-standing imbalance between nitrogen availability and dissolved inorganic carbon (DIC) fixation in deep waters.
The deep ocean plays a major role in regulating Earth’s climate, acting as the planet’s most important long-term carbon sink. Yet the identity of the microbes responsible for fixing carbon in these lightless zones has remained an open question. For years, scientists assumed ammonia-oxidizing archaea dominated this process, even though measured rates of carbon fixation often exceeded what their nitrogen-based energy supply could plausibly support.
To address the contradiction, lead author Barbara Bayer developed an experiment that selectively inhibited ammonia oxidizers using a chemical that didn’t interfere with other microbes. If these archaea were the primary carbon fixers, their shutdown should have caused a dramatic drop in carbon-fixation rates.
It didn’t. The decrease was far smaller than expected, indicating that other deep-sea microbes must be contributing substantially.
“What this suggests is that deep-sea heterotrophs are taking up more inorganic carbon than anyone realized,” Santoro explained. “They’re not just consuming organic material—they’re fixing carbon, too.”
This discovery reframes the deep ocean’s microbial economy. Heterotrophs—microorganisms typically known for feeding on organic matter—appear to be playing a dual role, supplementing their diet by incorporating inorganic carbon. The result is a clearer, more accurate picture of how the base of the deep-sea food web functions and how carbon is cycled and stored over long timescales.
Looking ahead, Santoro and her colleagues aim to investigate how the carbon fixed by these newly recognized players becomes available to other organisms, and how carbon, nitrogen, and trace-metal cycles intertwine in the deep ocean.
Research in this paper was also conducted by Nicola L. Paul, Justine B. Albers and Craig A. Carlson at UCSB; Katharina Kitzinger and Michael Wagner at the University of Vienna as well as Mak A. Saito at Woods Hole Oceanographic Institution.
Adapted from original reporting by Sonia Fernandez, “The Mystery of the Missing Deep Ocean Carbon Fixers,” The Current, UC Santa Barbara, 2025.