The figures in the deep ocean just didn’t add up for years. Researchers kept detecting more fixation than the known chemistry could account for when they measured the amount of dissolved inorganic carbon being fixed in the sunless layers below the photic zone, which is where photosynthesis terminates and sunlight cannot reach.
The widely accepted theory was that the majority of the work was being done by ammonia-oxidizing archaea, which are microscopic organisms that can extract energy from nitrogen molecules. The issue was that the ambient water’s nitrogen content was insufficient to support the carbon fixation rates that the instruments were capturing. The work was being done, or at least assisted, by something else. No one knew what.
Instead of trying to resolve the disparity, Alyson Santoro, a microbial oceanographer at the Marine Science Institute at UC Santa Barbara, chose to test the hypothesis directly. Her team’s strategy was elegantly simple: they used a substance called phenylacetylene to chemically inhibit the ammonia-oxidizing archaea, which had been demonstrated to selectively block their activity without interfering with other community processes. They then measured the rates of carbon fixation.
According to the established model, there would be a notable decline if the archaea were inhibited. The findings presented a different picture when they were published in Nature Geoscience in September 2025. Rates of carbon fixing hardly changed. It turns out that the archaea accounted for a far lesser portion than previously thought. The microbial community was picking up the slack, and it had been doing so all along without anyone noticing.
Heterotrophic bacteria, which are typically thought of as consumers rather than producers, seem to be that something else. They feed on organic matter as it descends from the surface in the form of particles and decaying cells. Heterotrophs in the deep ocean were traditionally thought of as organisms that break down organic matter and release its constituent parts back into the water column, much like a cleanup crew.
According to this study, heterotrophs are doing something else at the same time: using metabolic pathways that operate concurrently with their primary feeding activity, they are extracting dissolved inorganic carbon from the water and incorporating it into their own cellular material. Photosynthesis is not being replaced by them. “They’re not just consuming organic material — they’re fixing carbon, too,” Santoro told UCSB’s own news office, describing a parallel process that was not included in the models. She pointed out that the numbers ultimately add up. That statement is more significant than it first appears.
When a long-standing accounting gap in ocean chemistry closes, it typically indicates that the mechanism in question was genuine and functioning at a significant scale all along. Approximately one-third of all carbon dioxide emissions from humans are absorbed by the deep ocean. Every climate prediction model currently in use revolves around how it accomplishes that and how much it can absorb under various future conditions.
If those models consistently underestimate heterotrophic carbon fixation in the deep ocean, they are also underestimating the ocean’s overall capacity to store carbon. The direction in which this underestimation affects warming estimates depends on variables that Santoro’s team is still trying to measure.
This is challenging to instantly incorporate into global biogeochemical models due to a well-known issue in ocean science: microbial communities differ greatly throughout water columns, data are difficult to get, and sampling environments is challenging. The environment in the deep ocean is not consistent.
The rates of heterotrophic carbon fixation in the eastern tropical Pacific, where this study was carried out, may be very different from those in the deep water of the Southern Ocean or the mesopelagic region of the North Atlantic. Accurately incorporating these contributions into climate models necessitates data at a temporal and geographic precision that is currently lacking throughout the whole ocean.
