Why do we focus on carbon dynamics in thermokarst lakes?
Thermokarst lakes, formed by abrupt permafrost thaw, constitute a typical landform in permafrost regions, covering approximately 7% of the permafrost area. The formation of thermokarst lakes not only triggers substantial methane release, but also mobilizes large quantities of dissolved organic carbon (DOC) from surrounding soils into the aquatic ecosystem. DOC in thermokarst lakes is generally considered highly susceptible to microbial decomposition or photo-degradation, thus rendering these lakes potential hotspots for substantial carbon dioxide (CO2) emissions. The initial motivation of our study was to characterize the biodegradability of DOC in thermokarst lakes on the Tibetan Plateau, thereby assessing their potential to emit CO2.
What did we discover and how did we explain the new findings?
To experimentally address this key scientific question mentioned above, our research team collected surface water samples from 188 thermokarst lakes along a ~1,100-km permafrost transect across the Tibetan Plateau in July and August of 2019 and 2020. Subsequently, we assessed the biodegradability of DOC in thermokarst lakes by determining the variations in DOC concentration during a 28-day laboratory incubation. Surprisingly, contrary to our initial expectations, DOC in approximately one-third of the investigated lakes accumulated rather than decreased. Initially, we suspected that this phenomenon might arise from errors in our experimental operations. However, after double checking the analytical workflow and replicating experiments on a subset of samples, we confirmed that the phenomenon was indeed authentic. After ruling out methodological artifacts, Prof. Yuanhe Yang, the principal investigator of our research team, speculated that chemoautotrophic carbon fixation process might be responsible for the observed DOC accumulation.
To test this deduction, I got involved in an isotope-tracing experiment to verify whether chemoautotrophic carbon fixation occurred in these lakes. With considerable efforts, we established collaborations with the Isotope Laboratory Platform at the Institute of Biophysics, Chinese Academy of Sciences (https://ibp.cas.cn/jg/kypt/dbzkxyj/), and the Analytical and Testing Center of Beijing Normal University (https://atc.bnu.edu.cn/). With their technical support, we designed and performed a tracing experiment using radiolabelled bicarbonate (NaH14CO3). Although methodological precedents were limited and practical challenges emerged during implementation, the experiment was successfully completed within two months under expert guidance. The results confirmed the active microbial carbon fixation in thermokarst lakes, which was directly linked to the observed accumulation of DOC during incubation. Furthermore, by using qPCR and amplicon sequencing, we found that the chemoautotrophic carbon fixation was mainly driven by nitrifying microorganisms via the Calvin-Benson-Bassham cycle. Based on these findings, we prepared a manuscript entitled “Chemoautotrophic carbon fixation in thermokarst lakes on the Tibetan Plateau”.
How did we address the reviewers’ concerns?
Upon submission of this manuscript to Nature Communications, both reviewers evaluated that this research sheds light on overlooked processes affecting carbon cycling in thermokarst lakes, and recognized its ecological implications. They also, however, identified two main limitations. First, the study relied solely on surface water samples, yet chemoautotrophic carbon fixation may occur throughout the whole water column across seasons, making the sampling design oversimplified to support broad generalizations. Second, the reliance on specific primers for key carbon fixation pathway (Calvin-Benson-Bassham cycle and 3-hydroxypropionate/4-hydroxybutyrate cycle) genes, rather than a metagenomic approach, constrained the ability to capture the community’s full genetic potential.
To address the reviewers’ concerns, our research team designed and executed a comprehensive resampling campaign in 2024. As the core member, I led a sampling team to collect water samples in the whole water column of thermokarst lakes across three seasons (spring, summer, and autumn) so as to capture both spatial and temporal variability. The fieldwork was fraught with daunting challenges, including operational disruptions due to altitude-related health issues and persistent severe weather conditions such as heavy rain and snow. Despite these obstacles, our sampling team persevered and successfully completed the six-month campaign from May to October 2024 on the Tibetan Plateau.
Upon completion of field sampling, we carried out a series of laboratory analyses. First, a bioincubation experiment was performed to determine the variations of DOC concentration in water samples collected in 2024, verifying that the phenomenon of DOC accumulation could still be observed in partial thermokarst lakes across different depths and seasons. To confirm the reliability of bioincubation experiment mentioned above, we conducted another biodegradable DOC experiment based on CO2 measurement, and found similar results to those determined based on the variations of DOC concentration. These two lines of evidence proved the existence of dark C fixation process in the whole water column and throughout all the three seasons. Moreover, we performed the radiolabelled bicarbonate incubation to trace microbial CO2 assimilation, and found this carbon fixation process occurred in all thermokarst lakes.
Furthermore, we employed metagenomic sequencing to demonstrate that Calvin-Benson-Bassham cycle was the predominant carbon fixation pathway among chemoautotrophs, outweighing five other known pathways. Nitrification was identified as the key energy source driving this process, as confirmed by quantifying nitrification rates via 15N-isotope incubation experiment and by linking these rates with the abundance of nitrification-associated genes. Overall, this research used multiple lines of evidences to reinforce the robustness and generality of the observed process. More importantly, this study challenges the conventional view by illustrating that chemoautotrophic carbon fixation, rather than DOC mineralization, dominates in partial thermokarst lakes—a mechanism that may attenuate the climate feedback from the permafrost carbon cycle. Our findings underscore the crucial role of microbial carbon fixation in shaping DOC dynamics in these lakes and offer insights for understanding fundamental processes in permafrost carbon cycling.
Laboratory experiments (credit: Futing Liu and Shuqi Qin)
Following resubmission, the reviewers commended the revision for its exceptional thoroughness and noted that this research “now provides strong, well-supported evidence for chemoautotrophic carbon fixation in thermokarst lakes”. We sincerely thank both reviewers for their constructive and insightful comments, which greatly strengthened the paper. Looking back, the entire research journey was full of twists and turns. From confidently drafting and submitting our new findings, to having the paper rejected due to limitations pointed out by the reviewers, my emotions went through a roller coaster—from excitement to frustration. Nevertheless, I remained undaunted. With the tremendous help of members from Prof. Yuanhe Yang’s group, we meticulously analyzed the reviewers’ comments and accordingly redesigned the experimental protocol. As the first author, I once again led the team back to the field for resampling. The high‑altitude, cold, and oxygen‑poor environment of the Tibetan Plateau posed a severe physical challenge. Throughout the sampling period, I relied on medication to sustain myself. After six months of fieldwork, I suffered from a persistent cough lasting two months—a consequence of a prolonged pulmonary chill—and recovered only following treatment from several doctors. This experience was not merely a test of scientific rigor, but a profound trial of resilience and endurance. Furthermore, the subsequent laboratory analyses posed equally formidable challenges. To address the reviewers’ comments, we employed multiple advanced techniques—including 14C-labelled incubations for water samples, DOC and CO2-based bioincubation assays, metagenomic sequencing, and 15N-isotope tracing experiments. Each method required substantial time for optimization and execution. Finally, we devoted nearly eighteen months to conduct field sampling and indoor experiments to resolve the initial limitations of this research. Despite numerous challenges during the revision process, I persisted and successfully completed the project. The night our paper was accepted, I lay awake through the night. What welled up within me was more than the joy of success—it was a profound gratitude for lab members who contributed to the experimental and analytical work. I also extend our deepest gratitude to the field sampling team—Luyao Kang, Ziliang Li, Wei Zhou, Weijie Xu, and Xuning Liu—for their perseverance under extreme weather conditions; their dedication was vital to the completion of this study.
Looking ahead
Although we clarified the critical roles of chemoautotrophs in mediating DOC dynamics of thermokarst lakes in permafrost areas, we wonder whether these findings apply for frozen soils which will thaw under climate warming. It is well known that soils belong to a light-limited system, particularly in subsurface layers where solar radiation cannot penetrate. Furthermore, soils contain higher CO₂ concentrations than the atmosphere and are enriched with reduced compounds—such as nitrogen, sulfur, and iron—that serve as key substrates and energy sources for microorganisms carrying out dark carbon fixation. Accumulating evidences indicate that soils are important hotspots for microbial dark carbon fixation, where plays an important role in extreme environments where plant productivity is constrained (including wetlands, arid grasslands, and desert soils). Nevertheless, whether and to what extent this process operates in permafrost ecosystems remains unclear. Owing to limited systematic understanding of this mechanism, dark carbon fixation is currently omitted from Earth system models, which may underestimate the carbon sink of natural ecosystems. To address this gap, our team plans to conduct a systematic evaluation of chemoautotrophic carbon fixation in permafrost soils on the Tibetan Plateau, aiming to advance the understanding of permafrost carbon cycling under global warming.