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.