Deep ocean microbes fix carbon through unexpected pathways

For nearly a decade, marine scientist Angelicque Santoro kept running into a problem that wouldn't add up. The math simply didn't work.

Researchers knew the ocean was pulling carbon from the atmosphere and storing it in the deep, dark waters miles below the surface. They even had measurements of how much. But when they tried to trace the energy sources that powered this process, the numbers fell apart. There wasn't enough energy available to explain the carbon-fixing rates they were measuring.

"We basically couldn't get the budget to work out for the organisms that are fixing carbon," Santoro, a marine microbiologist at UC Santa Barbara, explained. The microbes needed energy to do their work, but the traditional energy source—ammonia oxidation by deep-sea archaea—didn't seem sufficient to account for what was happening.

Rewriting the deep-ocean rulebook

That discrepancy drove a decade-long investigation. The leading hypothesis was that ammonia-oxidizing archaea were simply more efficient than anyone realized, needing less energy to fix the same amount of carbon. But when Santoro's team tested this idea, it didn't hold up.

So they asked a different question: What if these archaea weren't the main carbon fixers after all?

Lead researcher Barbara Bayer designed an elegant experiment. Using a specialized chemical called phenylacetylene, she selectively shut down the ammonia oxidizers in deep-ocean water samples while leaving everything else intact. If these microbes were the primary carbon fixers, carbon fixation rates should have plummeted.

They didn't. The rate dropped, but far less than expected.

"That told us something else is going on," Santoro said. The culprits appear to be heterotrophic bacteria and archaea—microorganisms that typically feed on decomposing organic matter. These organisms, it turns out, are also taking up inorganic carbon directly from the water and converting it into their cells. They're fixing carbon dioxide while simultaneously doing their normal feeding.

This wasn't theoretically impossible. Scientists had long known it could happen. But for the first time, they now have actual numbers on how much of the deep ocean's carbon fixation comes from these heterotrophs versus the traditional autotrophic pathways.

Why this matters for the ocean food web

The implications ripple outward. If heterotrophs are significant carbon fixers in the deep ocean, it changes how we understand the entire food web down there. The "base" of that food web—the organisms that power everything else—works differently than we thought.

"There are basic aspects of how the food web works in the deep ocean that we don't understand," Santoro noted. This finding is a piece of that puzzle.

The ocean absorbs roughly a third of human carbon dioxide emissions, playing a crucial role in regulating global temperature. Understanding exactly how carbon moves from the atmosphere into the deep sea, and which organisms do the moving, is essential for predicting how this natural buffer will respond as the climate changes.

Santoro's team is now pursuing the next layer of questions. How does fixed carbon actually become available to the rest of the food web. What organic compounds leak from these microbes to feed their neighbors. And how do the nitrogen, carbon, iron, and copper cycles all interact in these deep waters.

The deep ocean, it seems, keeps its secrets carefully. But each answer opens new doors.