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Climate change perturbs CH4 dynamics in these systems, particularly through increasingly frequent wet\u2013dry cycles in small thermokarst lakes. However, how wet\u2013dry 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\u2013dry alternation exhibit a 41\u201370% decrease in diffusive CH4 emissions compared with perennial lakes. Alternating wet\u2013dry cycles lead to a 33\u201337% decrease in the relative abundances of methanogens and a 39\u201359% 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.<\/jats:p>","DOI":"10.1021\/acs.est.5c17973","type":"journal-article","created":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T08:51:58Z","timestamp":1784623918000},"page":"20939-20950","source":"Crossref","is-referenced-by-count":0,"title":["Microbial Reduction\nof Methane Emissions from High-Altitude\nThermokarst Lakes"],"prefix":"10.1021","volume":"60","author":[{"given":"Mei","family":"Mu","sequence":"first","affiliation":[{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]},{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0630-9423","authenticated-orcid":true,"given":"Cuicui","family":"Mu","sequence":"additional","affiliation":[{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]},{"name":"Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences , , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hebin","family":"Liu","sequence":"additional","affiliation":[{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinyue","family":"Song","sequence":"additional","affiliation":[{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinlong","family":"Du","sequence":"additional","affiliation":[{"name":"Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences , , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongqi","family":"Ge","sequence":"additional","affiliation":[{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengsi","family":"Lei","sequence":"additional","affiliation":[{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxiao","family":"Mo","sequence":"additional","affiliation":[{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuguo","family":"Wei","sequence":"additional","affiliation":[{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunling","family":"Zhang","sequence":"additional","affiliation":[{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changming","family":"Zhao","sequence":"additional","affiliation":[{"name":"Lanzhou University , , ,","place":["Lanzhou, China, 730000"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,21]]},"reference":[{"key":"2026080409303744800_cit1","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/s43017-021-00230-3","article-title":"Permafrost carbon emissions in a changing Arctic","volume":"3","author":"Miner","year":"2022","journal-title":"Nat. Rev. Earth Environ."},{"key":"2026080409303744800_cit2","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1016\/B978-0-323-99931-1.00164-1","article-title":"Organic matter storage\nand vulnerability\nin the permafrost domain","author":"Strauss","year":"2025","journal-title":"Encycl. Quat. Sci."},{"key":"2026080409303744800_cit3","doi-asserted-by":"publisher","first-page":"148358","DOI":"10.1016\/j.scitotenv.2021.148358","article-title":"Spatiotemporal variations\nand regional\ndifferences in air temperature in the permafrost regions in the Northern\nHemisphere during 1980\u20132018","volume":"791","author":"Hu","year":"2021","journal-title":"Sci. Total\nEnviron."},{"issue":"1","key":"2026080409303744800_cit4","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1038\/s43247-022-00498-3","article-title":"The Arctic\nhas warmed nearly four times faster than the globe since 1979","volume":"3","author":"Rantanen","year":"2022","journal-title":"Commun. Earth Environ."},{"issue":"17","key":"2026080409303744800_cit5","doi-asserted-by":"publisher","DOI":"10.1029\/2024GL109616","article-title":"Widespread and rapid\nactivities of retrogressive thaw\nslumps on the Qinghai-Tibet Plateau from 2016 to 2022","volume":"51","author":"Xia","year":"2024","journal-title":"Geophys. Res. Lett."},{"key":"2026080409303744800_cit6","doi-asserted-by":"publisher","first-page":"13043","DOI":"10.1038\/ncomms13043","article-title":"Circumpolar\ndistribution\nand carbon storage of thermokarst landscapes","volume":"7","author":"Olefeldt","year":"2016","journal-title":"Nat. Commun."},{"issue":"1","key":"2026080409303744800_cit7","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1038\/s41561-024-01614-y","article-title":"Substantial\nand overlooked greenhouse gas emissions from deep Arctic lake sediment","volume":"18","author":"Freitas","year":"2025","journal-title":"Nat. Geosci."},{"issue":"1","key":"2026080409303744800_cit8","doi-asserted-by":"publisher","first-page":"1552","DOI":"10.1038\/s41467-019-09592-1","article-title":"High carbon emissions\nfrom thermokarst\nlakes of Western Siberia","volume":"10","author":"Serikova","year":"2019","journal-title":"Nat. Commun."},{"issue":"2","key":"2026080409303744800_cit9","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/ngeo2578","article-title":"Climate-sensitive northern lakes\nand ponds are critical\ncomponents of methane release","volume":"9","author":"Wik","year":"2016","journal-title":"Nat. Geosci."},{"issue":"8067","key":"2026080409303744800_cit10","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1038\/s41586-025-09046-3","article-title":"Global dominance\nof seasonality in shaping lake-surface-extent dynamics","volume":"642","author":"Li","year":"2025","journal-title":"Nature"},{"issue":"3","key":"2026080409303744800_cit11","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1002\/hyp.9642","article-title":"Temporal\nand spatial pattern of thermokarst lake area changes at Yukon Flats,\nAlaska","volume":"28","author":"Chen","year":"2014","journal-title":"Hydrol. Processes"},{"key":"2026080409303744800_cit12","doi-asserted-by":"publisher","first-page":"106497","DOI":"10.1016\/j.catena.2022.106497","article-title":"Abrupt increase\nin thermokarst lakes on the central Tibetan Plateau over the last\n50 years","volume":"217","author":"Luo","year":"2022","journal-title":"Catena"},{"issue":"1","key":"2026080409303744800_cit13","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1038\/s43247-024-01635-w","article-title":"Wetland hydrological\ndynamics and\nmethane emissions","volume":"5","author":"Cui","year":"2024","journal-title":"Commun. Earth Environ."},{"issue":"1","key":"2026080409303744800_cit14","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1038\/s43017-021-00238-9","article-title":"Lake and drained lake\nbasin systems in lowland permafrost regions","volume":"3","author":"Jones","year":"2022","journal-title":"Nat. Rev. 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Sci."},{"issue":"6","key":"2026080409303744800_cit24","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1038\/s41561-024-01446-w","article-title":"Widespread societal and ecological\nimpacts from projected Tibetan Plateau lake expansion","volume":"17","author":"Xu","year":"2024","journal-title":"Nat. Geosci."},{"issue":"1","key":"2026080409303744800_cit25","doi-asserted-by":"publisher","first-page":"2404","DOI":"10.1038\/s41467-025-57745-2","article-title":"Methane emissions from\nthermokarst lakes must emphasize the ice-melting\nimpact on the Tibetan Plateau","volume":"16","author":"Mu","year":"2025","journal-title":"Nat. Commun."},{"issue":"3","key":"2026080409303744800_cit26","doi-asserted-by":"publisher","first-page":"333","DOI":"10.3878\/j.issn.1006-9585.2019.19026","article-title":"Multi-Timescale Features\nof Surface Air Temperature in the Source Region of the Yellow River\nduring 1953\u20132017","volume":"25","author":"Feng","year":"2020","journal-title":"Clim. Environ. Res."},{"issue":"6","key":"2026080409303744800_cit27","doi-asserted-by":"publisher","DOI":"10.1029\/2022ef002652","article-title":"Qinghai-Tibet Plateau\nPermafrost at Risk in the Late 21st Century","volume":"10","author":"Zhang","year":"2022","journal-title":"Earth\u2019s Future"},{"issue":"1","key":"2026080409303744800_cit28","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1002\/ldr.3434","article-title":"Spatiotemporal changes of permafrost\nin the Headwater Area of the Yellow River under a changing climate","volume":"31","author":"Sheng","year":"2020","journal-title":"Land Degrad. Dev."},{"key":"2026080409303744800_cit29","doi-asserted-by":"publisher","first-page":"100175","DOI":"10.1016\/j.srs.2024.100175","article-title":"Identifying\nthermokarst lakes using\ndeep learning and high-resolution satellite images","volume":"10","author":"Zhang","year":"2024","journal-title":"Sci. Remote Sens."},{"key":"2026080409303744800_cit30","doi-asserted-by":"publisher","first-page":"149692","DOI":"10.1016\/j.scitotenv.2021.149692","article-title":"High methane\nemissions from thermokarst lakes on the Tibetan Plateau are largely\nattributed to ebullition fluxes","volume":"801","author":"Wang","year":"2021","journal-title":"Sci. Total\nEnviron."},{"key":"2026080409303744800_cit31","doi-asserted-by":"publisher","first-page":"3121","DOI":"10.1038\/s41467-023-38907-6","article-title":"Characteristics of methane emissions\nfrom alpine thermokarst lakes\non the Tibetan Plateau","volume":"14","author":"Yang","year":"2023","journal-title":"Nat. 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Insights"},{"issue":"7476","key":"2026080409303744800_cit34","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1038\/nature12760","article-title":"Global carbon dioxide emissions from inland waters","volume":"503","author":"Raymond","year":"2013","journal-title":"Nature"},{"key":"2026080409303744800_cit35","doi-asserted-by":"publisher","first-page":"G00A08","DOI":"10.1029\/2007JG000569","article-title":"Methane\nproduction and bubble emissions from arctic lakes: Isotopic implications\nfor source pathways and ages","volume":"113","author":"Walter","year":"2008","journal-title":"J. Geophys. Res.\nBiogeosci."},{"issue":"24","key":"2026080409303744800_cit36","doi-asserted-by":"publisher","first-page":"4645","DOI":"10.3390\/rs16244645","article-title":"Simulation\nand Prediction of Thermokarst\nLake Surface Temperature Changes on the Qinghai\u2013Tibet Plateau","volume":"16","author":"Zhang","year":"2024","journal-title":"Remote Sens."},{"issue":"4","key":"2026080409303744800_cit37","doi-asserted-by":"publisher","first-page":"1426","DOI":"10.1128\/aem.03588-14","article-title":"Diversity of Methane-Cycling Archaea in Hydrothermal\nSediment Investigated by General and Group-Specific PCR Primers","volume":"81","author":"Lever","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"2026080409303744800_cit38","unstructured":"Oksanen, J.; Simpson, G.; Blanchet, F.; Kindt, R.; Legendre, P.; Minchin, P.; O\u2019Hara, R.; Solymos, P.; Stevens, M.; Szoecs, E.; et al.; Community\nEcology Package. 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Evol."},{"key":"2026080409303744800_cit41","doi-asserted-by":"crossref","unstructured":"Wickham, H.\n          \n          ggplot2: Elegant Graphics\nfor Data Analysis; Springer-Verlag: New York2016. https:\/\/ggplot2.tidyverse.org;","DOI":"10.1007\/978-3-319-24277-4_9"},{"issue":"1","key":"2026080409303744800_cit42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.2136\/vzj2018.01.0017","article-title":"Effects of\nWater Regimes on Methane Emissions in Peatland and Gley Marsh","volume":"17","author":"Zhu","year":"2018","journal-title":"Vadose Zone J."},{"issue":"12","key":"2026080409303744800_cit43","doi-asserted-by":"publisher","first-page":"1741","DOI":"10.1016\/S0038-0717(99)00093-0","article-title":"Methane\nproduction and oxidation\npotentials in relation to water table fluctuations in two boreal mires","volume":"31","author":"Kettunen","year":"1999","journal-title":"Soil Biol. 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Total Environ."},{"key":"2026080409303744800_cit45","doi-asserted-by":"publisher","DOI":"10.1111\/gcb.17120","article-title":"Size matters:\nAerobic methane oxidation\nin sediments of shallow thermokarst lakes","volume":"30","author":"Manasypov","year":"2024","journal-title":"Glob\nChang Biol."},{"issue":"7523","key":"2026080409303744800_cit46","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1038\/nature13798","article-title":"Methane dynamics regulated by microbial\ncommunity response to permafrost thaw","volume":"514","author":"McCalley","year":"2014","journal-title":"Nature"},{"issue":"10","key":"2026080409303744800_cit47","doi-asserted-by":"publisher","first-page":"3411","DOI":"10.1111\/gcb.16137","article-title":"Reduced methane emissions in former permafrost soils\ndriven by vegetation and microbial changes following drainage","volume":"28","author":"Keuschnig","year":"2022","journal-title":"Glob Chang Biol."},{"issue":"6","key":"2026080409303744800_cit48","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1007\/s00300-014-1641-4","article-title":"Vertical\nsediment distribution of\nmethanogenic pathways in two shallow Arctic Alaskan lakes","volume":"38","author":"Lofton","year":"2015","journal-title":"Polar Biol."},{"issue":"24","key":"2026080409303744800_cit49","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01832-18","article-title":"Response of the Anaerobic\nMethanotroph \u201cCandidatus Methanoperedens nitroreducens\u201d\nto Oxygen Stress","volume":"84","author":"Guerrero-Cruz","year":"2020","journal-title":"Appl. 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