Microbial Reduction of Methane Emissions from High-Altitude Thermokarst Lakes

Thermokarst lakes, a typical landscape resulting from abrupt permafrost thaw, are expected to be a substantial CH4 source. Climate change perturbs CH4 dynamics in these systems, particularly through increasingly frequent wet-dry cycles in small thermokarst lakes. However, how wet-dry alternation alters microbial communities remains poorly understood, and quantifying the effects of microbial shifts on CH4 emissions from these lakes represents a key challenge. Here, by integrating field observations, laboratory incubation experiments, and amplicon sequencing, we show that seasonal thermokarst lakes with wet-dry alternation exhibit a 41-70% decrease in diffusive CH4 emissions compared with perennial lakes. Alternating wet-dry cycles lead to a 33-37% decrease in the relative abundances of methanogens and a 39-59% decline in syntrophic partners in lake sediments, while the anaerobic methanotrophic archaea Candidatus Methanoperedens increased from 0.2% to 20.8%. Functional gene analyses indicate acetoclastic methanogenesis, dominated by Methanosaeta, is the primary pathway of CH4 production. The reduction in CH4 emissions is associated with changes in sediment properties, as well as decreased abundances of methylotrophic Methanomassiliicoccaceae and syntrophs. Moreover, denitrifying anaerobic CH4 oxidation processes mediated by Candidatus Methanoperedens lead to a further decline in CH4 emissions. This study provides novel insights into the microbial changes and pathways regulating diffusive CH4 emissions from seasonal thermokarst lakes, which is crucial for assessing permafrost carbon-climate feedback and prioritizing CH4 mitigation strategies.