Microbial Reduction in Methane Emissions from High-altitude Thermokarst Lakes

Thermokarst lakes, the typical landscape of abrupt permafrost thaw, are expected to be a substantial CH₄ source. The CH₄ dynamics are disrupted by climate change, particularly frequent dry-wet alternation of small thermokarst lakes. However, microbial community changes caused by wet-dry alternation remains uncertain, and it remains a challenge to quantify the impacts of microbial shifts on CH₄ emissions from thermokarst lakes, especially at the high-altitudes. Here, by field observations, laboratory incubation experiments and amplicon sequencing, we show that thermokarst lakes with seasonal wet-dry alternation exhibit a 41–70% decrease in CH₄ emissions compared with perennial lakes. The alternating wet-dry cycles lead to a 33–37% decrease in relative abundances of methanogens and a 39–59% decline in syntrophic partners in lake sediments, whereas a 43-fold increase in anaerobic methanotrophic archaea Candidatus Methanoperedens. Functional gene analyses indicate acetoclastic methanogenesis dominated by Methanosaeta is the primary pathway of CH₄ production. The reduction in CH₄ emissions is due to the decrease in methylotrophic Methanomassiliicoccaceae and syntrophs. Moreover, the denitrifying anaerobic CH₄ oxidation processes mediated by Candidatus Methanoperedens leads to further decline in CH₄ emissions. This study provides novel insights into microbial changes and pathways regulating CH₄ emissions from seasonal thermokarst lakes, which is crucial for assessing permafrost carbon-climate feedback and prioritizing CH₄ mitigation strategy.