Unexpected Discovery in Deep Ocean Carbon Fixation: Heterotrophs Play Key Role
Introduction: Deep Ocean Carbon Fixation and Climate Change The deep ocean is Earth’s largest long‑term carbon sink, quietly absorbing roughly one‑third of human‑generated carbon dioxide emissions and playing a crucial role in stabilizing the global climate. Yet, scientists have long struggled to explain how carbon is actually fixed and stored in the dark ocean, far below the reach of sunlight. On December 10, 2025, a research team from UC Santa Barbara published a groundbreaking study in Nature Geoscience, revealing that deep‑ocean carbon fixation works in a very different way than the scientific community has assumed for more than a decade. A Decade‑Long Deep Ocean Carbon Mystery For years, the dominant theory held that deep‑sea carbon fixation was mainly driven by ammonia‑oxidizing archaea, chemolithoautotrophic microorganisms that use nitrogen compounds such as ammonia as an energy source to convert inorganic carbon into organic matter in the absence of light. However, when researchers compared the nitrogen energy available in the deep water column with measured rates of dissolved inorganic carbon fixation, they found a major mismatch that could not be explained by ammonia oxidizers alone. Lead scientist Professor Alyson Santoro and first author Barbara Bayer spent nearly ten years trying to resolve this “missing energy” problem in the deep‑ocean carbon cycle. Targeted Experiments Reveal Hidden Deep‑Sea Carbon Fixers To close this gap, the team designed a targeted experiment using phenylacetylene, a specialized chemical inhibitor that selectively blocks the activity of ammonia‑oxidizing archaea without significantly affecting other microbial processes. In deep‑sea incubation experiments, the inhibitor successfully suppressed these abundant archaea, allowing the researchers to test how much they really contribute to dark ocean carbon fixation. Surprisingly, even after ammonia oxidizers were inhibited, the overall rate of inorganic carbon fixation in the studied deep‑ocean waters did not drop nearly as much as expected, proving that other microbial players must be responsible for a large share of carbon fixation at depth. The Unexpected Role of Heterotrophic Microbes in the Dark Ocean The study points to heterotrophs—microorganisms that usually feed on organic carbon from decomposing plankton and other marine life—as key, previously underestimated contributors to deep‑ocean carbon fixation. These heterotrophic bacteria and archaea appear to take up not only organic matter but also substantial amounts of dissolved inorganic carbon, effectively fixing additional carbon dioxide in the dark ocean. While scientists had long considered this dual role theoretically possible, this is one of the first quantitative estimates of how much of the deep‑ocean carbon budget is actually handled by heterotrophs rather than classic autotrophs. Why This Discovery Matters for Ocean Carbon Cycle Science By resolving the long‑standing “missing deep‑ocean carbon fixers” puzzle, this research reshapes how scientists understand the structure and energy flow of the deep‑sea food web. It shows that deep‑ocean carbon sequestration is supported by a more diverse and dynamic microbial community than previously recognized, which has direct implications for how the ocean buffers atmospheric CO2 under ongoing climate change. The work also highlights that basic aspects of the deep‑ocean food web—who fixes carbon, who consumes it, and how energy flows—are still being uncovered, even in one of the planet’s most important climate regulation systems. Implications for NerOcean and Next‑Generation Ocean Monitoring For NerOcean, a Hong Kong–based ocean technology company developing cost‑effective, high‑precision water quality monitoring solutions, these findings underscore why advanced ocean sensing is so critical. If heterotrophic microbes are major contributors to deep‑ocean carbon fixation, then long‑term ocean monitoring must go beyond simple physical and chemical measurements to include microbial community dynamics and biogeochemical fluxes. This means: Ocean monitoring systems will increasingly need integrated tools that combine chemical parameters (such as dissolved oxygen, nutrients, and trace metals) with insights into microbial activity and carbon transformation pathways. Climate models and ocean carbon cycle models should be updated to include the contribution of heterotrophic microorganisms to deep‑ocean carbon fixation, rather than focusing almost exclusively on ammonia‑oxidizing autotrophs. The response of deep‑sea microbial ecosystems to warming, deoxygenation, and pollution may be more complex than expected, creating both challenges and opportunities for innovation in ocean monitoring technology. As NerOcean continues to develop novel sensing platforms such as dissolved oxygen sensors and passive samplers like Artificial Mussels, these advances in deep‑ocean carbon science highlight the importance of building a “nerve of the ocean” that can capture subtle changes in both chemistry and biology over time. Future Directions: Connecting Carbon, Nitrogen, and Trace Metals in the Deep Sea Looking ahead, Professor Santoro and her collaborators plan to investigate how deep‑ocean carbon fixation interacts with other elemental cycles, including nitrogen, iron, and copper, across different water masses and ocean basins. A key open question is how carbon fixed by these diverse microbes is transferred through the deep‑sea food web, from bacterial biomass to larger organisms and eventually to long‑term carbon storage in deep waters and sediments. As climate change accelerates and pressure mounts to better predict ocean carbon sequestration, high‑resolution monitoring, robust sensor networks, and industry–research collaborations will be essential to translate this new scientific knowledge into actionable ocean management strategies. Conclusion This breakthrough research rewrites our understanding of the deep-ocean carbon cycle, highlighting the complexity of marine microbial ecosystems. As climate change continues to impact ocean health, understanding these fundamental processes is crucial for predicting and responding to future environmental challenges. References Bayer, B., Kitzinger, K., Paul, N. L., Albers, J. B., Saito, M. A., Wagner, M., Carlson, C. A., & Santoro, A. E. (2025). Minor contribution of ammonia oxidizers to inorganic carbon fixation in the ocean. Nature Geoscience, 18(11), 1144. Source: University of California – Santa Barbara, ScienceDailyPublished: December 10, 2025
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