The new research on dark carbon fixation overturns a long held assumption about what fuels life in the deep ocean and why it matters for global climate predictions. Scientists expected ammonia oxidizers to drive most carbon uptake in the dark midwater zone. Instead, the study shows they play a much smaller role, forcing a rethink of how the ocean stores carbon and supports deep living microbes.
Fast Facts
Study: Researchers found ammonia oxidizers play only a minor role in deep ocean carbon fixation. Why it matters: The discovery helps explain long-standing gaps in the ocean carbon budget. Key takeaway: Other microbial pathways, including heterotrophy, support most of the dark carbon uptake that stabilizes Earth’s climate.
The research team studied waters in the eastern tropical and subtropical Pacific and found something surprising. Even though ammonia oxidizing archaea are extremely abundant, they contribute only a small share of the carbon fixed in the dark ocean. Earlier models assumed these microbes powered much of the deep ocean’s carbon processing. The new findings show other microbial metabolisms must be doing the heavy lifting.
To prove this, researchers used a selective chemical inhibitor called phenylacetylene. It blocks the key enzyme that ammonia oxidizers use, so scientists could measure how much carbon fixation stopped when these microbes were shut down. Seawater samples taken from depths between 60 and 600 meters showed that once ammonia oxidizers were inhibited, most carbon fixation still continued. This simple but precise method allowed the team to isolate each metabolism’s role without disrupting the entire ecosystem.
The findings matter because they correct a major gap in our understanding of the dark ocean carbon budget. Scientists have long seen a mismatch between how much organic carbon sinks from above and how much deep ocean microbes consume. This study suggests that hidden microbial pathways, including heterotrophic activity, supply the missing energy. The result helps improve climate models that rely on accurate estimates of how carbon moves and settles in the sea.
Lead researchers note that ammonia oxidizers still contribute in certain zones. In the upper mesopelagic region, about 120 to 175 meters deep, they can account for up to half of the carbon fixation at some locations. But when looking across the whole water column, their average contribution remains low. This contrast creates healthy scientific tension because it challenges earlier interpretations while offering new explanations for long standing puzzles.
The work connects to larger climate and ecosystem issues. Understanding dark carbon fixation is essential for predicting how the ocean will respond to warming, changing oxygen levels, and shifting nutrient flows. The deep ocean acts as a giant carbon sink. Small changes in how microbes process carbon can influence global climate patterns, fisheries, and nutrient cycles.
Next, the team plans to identify the other microbial metabolisms responsible for the majority of dark carbon fixation. Open questions include which organisms dominate in low oxygen zones and how their activity shifts with climate driven changes in circulation. The study also highlights the need for improved tools to measure microbial energy use in the deep sea.
This discovery shows that the deep ocean still holds major surprises. By revealing that ammonia oxidizers supply only a small part of dark carbon fixation, the study reshapes our understanding of Earth’s largest living space and improves the way scientists model the planet’s future.
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Materials provided by Nature Geoscience authors and institutions listed in the study. Content may be edited for style and length.
Journal Reference:
Barbara Bayer, Katharina Kitzinger, Nicola L. Paul, Justine B. Albers, Mak A. Saito, Michael Wagner, Craig A. Carlson, Alyson E. Santoro. Minor contribution of ammonia oxidizers to inorganic carbon fixation in the ocean. Nature Geoscience, 2025. DOI: 10.1038/s41561-025-01798-x