Dark carbon fixation dominates life under the ice in China’s largest saline lake

Beneath the frozen surface of Qinghai Lake, the largest saline lake in China, microbes are quietly pulling carbon out of the water even in near-darkness and near-freezing temperatures. A new study reports that during the ice-covered season, dark-driven carbon fixation—not photosynthesis—accounts for the majority of microbial carbon uptake in the lake, a finding that reshapes how scientists think about carbon cycling in high-altitude lakes that spend a large fraction of the year sealed under ice.

Researchers measured microbial inorganic carbon uptake in Qinghai Lake, which sits at 3,260 meters above sea level on the northeastern Tibetan Plateau, using a carbon-13 bicarbonate labelling approach combined with geochemical and microbial analyses. The lake freezes from mid-December to early April, a period lasting more than a third of the year, making it a natural laboratory for studying microbial activity under ice in a saline, alkaline environment.

On March 1, 2024, the team sampled water at three sites near the western, northern, and southern shores of the lake. Surface ice was cut away with a chainsaw, and water was collected with a Niskin sampler at depths ranging from 0.5 to 10 meters depending on the site. In total, 42 samples were gathered, with three replicates at each depth. Water samples were enriched with carbon-13-labelled sodium bicarbonate and sealed in transparent and opaque bottles, which were then returned to their original depths beneath the ice and incubated in situ for six hours around midday.

The transparent bottles captured light-dependent carbon fixation, while the opaque bottles measured dark-driven fixation. After incubation, the samples were filtered, treated to remove carbonate, and analyzed by isotope ratio mass spectrometry to determine how much of the labelled carbon had been incorporated into particulate organic matter. The method allowed the researchers to quantify uptake rates in micrograms of carbon per liter per hour for each pathway separately.

The results showed that microbial carbon fixation remains active throughout the water column during ice cover, with total rates ranging from 4.92 to 13.09 micrograms of carbon per liter per hour. Dark-driven fixation dominated, contributing 61.06 percent of the total on average, with individual measurements ranging from 2.82 to 9.21 micrograms of carbon per liter per hour. Light-dependent fixation ranged from 1.14 to 4.37 micrograms of carbon per liter per hour. A paired statistical test confirmed that dark fixation rates were significantly greater than light-driven rates across the 42 samples.

Perhaps the most surprising result was the vertical structure of the two pathways. Light-dependent fixation increased significantly with depth, the opposite of what conventional light-attenuation models would predict, while dark-driven fixation decreased with depth. The researchers attribute the deepening boost in photosynthetic uptake to a slight rise in water temperature with depth: water temperatures ranged from 0.69 to 2.51 degrees Celsius, and the marginally warmer bottom waters may relieve the low-temperature inhibition of photosynthetic enzymes, compensating for the reduced light. Cold-tolerant, shade-adapted microbial genera such as Leptolyngbya and Navicula were more abundant in deeper layers, supporting this interpretation.

Dark fixation, by contrast, was strongest in upper layers and correlated positively with nitrate concentrations and particulate organic carbon, while declining with depth. The authors suggest that upper water layers offer stable niches with ample nitrate that support chemolithoautotrophic microbes, including nitrite-oxidizing bacteria that assimilate carbon dioxide using reduced compounds as energy sources. The pattern mirrors observations from marine studies of dark carbon fixation.

Microbial community data added another layer to the picture. Sequencing of 16S and 18S rRNA genes revealed that cyanobacteria in the under-ice water belonged mainly to families including Synechococcaceae and Leptolyngbyaceae, while microeukaryotic communities were dominated by Chlorophyta at 49.1 percent, Chrysophyta at 25.1 percent, and Cryptophyta at 14.9 percent. Correlation analyses linked light-dependent fixation to diatom genera such as Amphora, Navicula, and Surirella, whereas dark fixation was associated with distinct taxa including Nannochloropsis, Bacteroides, Pyramimonas, Tetracystis, and Hemiselmis. The researchers hypothesize that these mixotrophic eukaryotes may facilitate dark fixation through synergistic interactions with chemoautotrophic microbes, participating in the turnover of particulate organic matter and creating nutrient-rich microenvironments.

Compared with summer measurements at the same lake, where phototrophic carbon fixation reached roughly 200 micrograms of carbon per liter per hour in open water, the winter light-driven rates of about 3 micrograms represent a dramatic suppression of photosynthesis. The authors attribute this shift to the extreme light attenuation by ice and snow, which reflects or absorbs approximately 90 percent of incident photosynthetically active radiation, combined with near-freezing water temperatures that slow photosynthetic enzymes. Against this backdrop, dark fixation becomes the dominant mechanism sustaining microbial carbon assimilation, aided by the lake’s high alkalinity and abundant dissolved inorganic carbon, which ranged from 172.31 to 221.45 milligrams per liter in the study samples.

The team frames these observations within an environment–microbe–function framework, in which direct physicochemical constraints such as temperature and nutrients set the kinetic limits of carbon fixation, while microbial community composition modulates the outcome through ecological filtering and metabolic coupling. The authors note limitations: only three sampling sites were accessible, deep waters beyond 15 meters could not be reached because of cracks in the lake ice, sequencing focused only on cyanobacteria and phytoplankton rather than the full bacterioplankton community, and measurements came from a single period within the ice-covered season. Nevertheless, they argue that the dominance of dark fixation reflects a characteristic feature of the winter state of the lake, and that understanding these under-ice processes is essential for quantifying the carbon source–sink function of seasonally frozen lakes as climate change alters ice regimes across the world’s high-altitude and high-latitude waters.

Subject of Research: Microbial light-dependent and dark-driven inorganic carbon fixation rates and their regulators in ice-covered Qinghai Lake, China's largest saline lake

Article Title: Microbial inorganic carbon fixation characteristics in the largest saline lake of China during the ice-covered period

Article References: Han, Y., Shi, F., Liu, X., Wang, Z., Wang, R., & Li, X. (2026). Microbial inorganic carbon fixation characteristics in the largest saline lake of China during the ice-covered period. Carbon Research, 5(1), Article 54. https://doi.org/10.1007/s44246-026-00291-3

Image Credits: AI Generated

DOI: 10.1007/s44246-026-00291-3

Keywords: Qinghai Lake, carbon fixation, ice-covered lakes, saline lakes, Tibetan Plateau, carbon-13 labelling, dark carbon fixation, microbial ecology, chemoautotrophy, winter limnology, carbon cycle, mixotrophy