The ocean’s twilight zone, often regarded as one of the planet’s most enigmatic biochemical theaters, relies heavily on intricate microbial processes that drive carbon fixation in the absence of sunlight. Among these processes, chemolithoautotrophy—where microorganisms derive energy from the chemical oxidation of inorganic compounds—plays a fundamental role in sustaining life. Until now, ammonia-oxidizing microorganisms have been widely considered the primary engines behind this dark ocean carbon fixation, primarily because of the relatively abundant nitrogen content in marine organic matter compared to other energy sources such as sulfur or iron. However, groundbreaking new research challenges this prevailing assumption, revealing a surprisingly minor contribution from ammonia oxidizers to the fixation of inorganic carbon in marine environments.
Marine nitrogen cycling has long emphasized the importance of ammonia oxidation as a critical step fueling chemolithoautotrophic activities. In this process, ammonia is converted into nitrite, which is then oxidized to nitrate through tight biochemical coupling between ammonia and nitrite oxidizers. The close metabolic interdependence means that any perturbation to ammonia oxidation typically suppresses nitrite oxidation as well, assuming no other nitrite sources are available. Yet, in regions characterized by oxygen-deficient zones (ODZs), an alternative pathway emerges through nitrate reduction which can generate nitrite independently of ammonia oxidation. This discovery invites a reevaluation of the drivers underpinning dark carbon assimilation.
To delve deeper into these dynamics, researchers strategically assessed nitrite oxidation rates at varying ocean depths. By applying the average dark inorganic carbon (DIC) fixation yields derived from cultured strains of marine nitrite oxidizers, the team was able to project possible contributions of nitrite oxidation to overall dark DIC fixation. Their results indicate that ammonia and nitrite oxidizers together could account for roughly 70% of dark DIC fixation in the upper mesopelagic zone. Interestingly, their contribution within the sunlit euphotic zone amounted to only about 36%, hinting at additional processes operating closer to the ocean surface.
Despite these significant estimates, caution must be exercised. Molecular analyses demonstrate that open ocean nitrite oxidizers are phylogenetically distinct and distantly related to those cultured in laboratories. This divergence suggests that their actual carbon fixation efficiencies and metabolic pathways in situ might differ substantially from laboratory-based predictions. Furthermore, empirical measurements show that environmental ammonia oxidation yields less DIC fixation than previously expected from cultured analogues, implying that nitrite oxidizers’ contributions may be overestimated. Hence, the conventional understanding exaggerates the role ammonia-based chemolithoautotrophy plays in dark ocean carbon cycling.
Beyond the nitrogen cycle, the ocean’s chemical tapestry includes sulfur compounds that potential chemolithoautotrophs might exploit. The genomic landscape reveals a widespread genetic potential among microbial communities in the dark ocean to oxidize sulfur compounds and drive carbon fixation through sulfur-based energy metabolism. Indeed, sulfur-oxidizing bacteria were detected at all sampled stations, indicating their ubiquitous presence and possible ecological significance.
However, the availability of reduced sulfur compounds in marine environments is heavily constrained. Organic sulfur content in sinking particulate matter is estimated to be approximately seventeen times lower than its nitrogen content. This stark disparity suggests that sulfur compounds constitute a much scarcer energy source for chemolithoautotrophy. Even accounting for the fact that cultured sulfide oxidizers display higher DIC fixation yields—ranging between 0.15 and 0.35 carbon atoms fixed per atom of reduced sulfur oxidized—compared to ammonia oxidizers’ yields around 0.05, the overall contribution of sulfur-fueled chemolithoautotrophy appears limited. Estimates suggest it may represent only about one-third of the ammonia-fueled chemolithoautotrophic carbon fixation.
The complexity deepens when considering heterotrophic microorganisms, which have historically been overshadowed by chemolithoautotrophs in discussions of dark ocean carbon fixation. Recent evidence suggests that heterotrophs—organisms deriving energy from organic compounds—may also play a more substantial role in DIC assimilation, particularly near the ocean’s surface. Measurements indicate that in some circumstances, heterotrophic microbial communities can fix dark DIC at rates ranging from 40 to 200 nanomolar carbon per day, a substantial contribution when contrasted with other processes.
Intriguingly, collated data from hundreds of heterotrophic production and dark DIC fixation measurements across the Atlantic and Pacific oceans reveal a consistently positive linear relationship between overall heterotrophic carbon production and dark DIC fixation. This correlation is further strengthened in the eastern tropical Pacific Ocean, where heterotrophic microbial activity strongly corresponds with elevated dark inorganic carbon fixation rates. Within these communities, it is postulated that a fraction—estimated between 1 and 10%—of heterotrophic biomass carbon originates from the assimilation of dissolved inorganic carbon, rather than solely from organic carbon sources.
Assuming heterotrophs assimilate roughly 10% of their cellular carbon from DIC, researchers calculated that heterotrophic microbes could independently explain approximately 30% of dark DIC fixation rates in both the euphotic and upper mesopelagic zones. This finding shakes up prior assumptions that chemolithoautotrophs dominate inorganic carbon fixation in these regions. Instead, it suggests a more balanced interplay between heterotrophic and chemolithoautotrophic processes in sustaining microbial carbon fluxes in the ocean’s dimly lit waters.
Altogether, this emerging picture from marine biogeochemistry paints a more nuanced understanding of carbon cycling under the ocean’s surface. The evidence challenges the long-held dogma that ammonia oxidizers principally drive dark carbon fixation, instead positioning their contribution as notably minor. It acknowledges the significance of alternative energy metabolisms, such as sulfur oxidation, albeit constrained by substrate availability, and elevates the role of heterotrophic microbes assimilating inorganic carbon to new prominence.
Understanding the exact contributions of these various microbial groups requires further investigation, especially given the genetic and physiological dissimilarities between cultured microbes and their wild ocean counterparts. Enhanced molecular approaches coupled with improved in situ rate measurements will be pivotal in refining estimates for carbon fixation yields across different metabolic guilds. Such insights are vital as ocean carbon cycles profoundly influence global biogeochemical dynamics and, ultimately, the planet’s climate regulation.
Moreover, the exploration of oxygen-deficient zones provides a window into unique nitrogen transformations where nitrate reduction produces alternative nitrite sources, decoupling it from classic ammonia oxidation pathways. This pathway’s geochemical ramifications and the role it plays in sustaining niche microbial populations underscore the ocean’s metabolic diversity and resilience under varying chemical regimes.
These findings not only urge a scientific recalibration but also emphasize the ocean’s microbial complexity and its adaptive agility, sustaining productivity through alternative biochemical routes. The minor role of ammonia oxidizers uncovered here urges the research community to reconsider models of inorganic carbon assimilation that have shaped marine ecology thinking for decades.
In closing, this seminal work opens a new chapter in oceanographic research by reframing the microbial contributions to dark carbon fixation. Far from a monolithic process overwhelmingly driven by ammonia oxidation, dark DIC fixation emerges as a multifaceted mosaic of interwoven microbial pathways. Such revelations are paramount for predicting how ocean ecosystems will respond to environmental changes and for modeling the marine carbon cycle with greater precision.
By expanding investigative efforts into the genomic and metabolic capacities of elusive marine microbes, the field moves closer to unraveling the ocean’s hidden carbon sinks. This knowledge has critical implications for understanding the global carbon budget and developing strategies to mitigate anthropogenic carbon emissions. As the ocean’s twilight zone reveals its secrets, it reaffirms the ocean’s undying innovation in harnessing chemical energy to sustain life even in the absence of light.
Subject of Research: Marine microbial chemolithoautotrophy and its contribution to inorganic carbon fixation in the dark ocean
Article Title: Minor contribution of ammonia oxidizers to inorganic carbon fixation in the ocean
Article References:
Bayer, B., Kitzinger, K., Paul, N.L. et al. Minor contribution of ammonia oxidizers to inorganic carbon fixation in the ocean. Nat. Geosci. (2025). https://doi.org/10.1038/s41561-025-01798-x
