Large uncertainties in the budget of atmospheric methane, an important greenhouse gas, limit the accuracy of climate change projections. Thaw lakes in North Siberia are known to emit methane, but the magnitude of these emissions remains uncertain because most methane is released through ebullition (bubbling), which is spatially and temporally variable. Here we report a new method of measuring ebullition and use it to quantify methane emissions from two thaw lakes in North Siberia. We show that ebullition accounts for 95 per cent of methane emissions from these lakes, and that methane flux from thaw lakes in our study region may be five times higher than previously estimated. Extrapolation of these fluxes indicates that thaw lakes in North Siberia emit 3.8 teragrams of methane per year, which increases present estimates of methane emissions from northern wetlands (< 6-40 teragrams per year; refs 1, 2, 4-6) by between 10 and 63 per cent. We find that thawing permafrost along lake margins accounts for most of the methane released from the lakes, and estimate that an expansion of thaw lakes between 1974 and 2000, which was concurrent with regional warming, increased methane emissions in our study region by 58 per cent. Furthermore, the Pleistocene age (35,260-42,900 years) of methane emitted from hotspots along thawing lake margins indicates that this positive feedback to climate warming has led to the release of old carbon stocks previously stored in permafrost.

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.

As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.

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Methane dynamics regulated by microbial community response to permafrost thaw. 4,5,16 . The net effect is that the high methane-emitting fen contributes 7 55 times the greenhouse impact per unit area as the palsa. This thaw progression is also associated 56 with an increase in overall organic matter lability, including a decrease in C:N and an increase in 57 humification rates 9 . We hypothesized, consistent with previous studies of in situ bog and fen 58 systems [17][18][19] , that thaw progression also facilitates a shift from hydrogenotrophic to acetoclastic 59 CH 4 production. 60We used the distinct isotopic signatures of different microbial CH 4 production and 61 consumption pathways to directly relate changes in CH 4 dynamics across the thaw gradient to 62 underlying changes in the microbial community. Methane produced by hydrogenotrophic 63 methanogens generally has lower  13 C and higher D ( 13 C = -110 to -60‰ and D = -250 to -64 170‰) relative to that produced by acetoclastic methanogens ( 13 C = -60 to -50‰ and D = -400 65 to -250‰) 19,20 . If methanotrophic microbes then oxidize CH 4 , lighter molecules are 66 preferentially consumed, leaving the remaining CH 4 13 C-and D-enriched relative to the original 67 CH 4 pool (see expected patterns in Extended Data Fig 1) 19 . Greater fractionation is associated with hydrogenotrophic methanogenesis, and was 85 found in the thawing Sphagnum site (average  C = 1.053 ± 0.002). Significantly less 86 fractionation (p=0.002) associated with more acetoclastic production or with consumption by 87 oxidation was found in the fully thawed Eriophorum porewater (average  C = 1.046 ± 0.001). 88Here, increases in acetoclastic production, not oxidation, best explain isotopic shifts because 89 lower  C and higher  13 C-CH 4 are accompanied by significantly lower D-CH 4 (Extended Data 90 Fig. 1, p< 0.001) 19 . This is consistent with the pattern of isotopes in CH 4 emissions as well as 91 incubations of Stordalen peat 9 and studies showing bog-to-fen shifts from hydrogenotrophic to 92 acetoclastic methanogenesis [17][18][19] . 93The CH 4 flux and isotope results provide compelling but indirect evidence for changes in 94 CH 4 -cycling microbial communities with permafrost thaw. These microbiological changes could 95 be shifts in activity of particular community members or changes in community composition. We 96 examined the role of community composition through 16S rRNA gene amplicon sequencing. All 97 known methanogens belong to a small number of archaeal lineages within the Euryarchaeota 23 . 98As expected, the shift from CH 4 -neutral intact permafrost palsa to CH 4 -emitting wetland 99 corresponded to a substantial increase in the relative abundance of methanogenic archaeal 100 lineages (Fig. 1c, Extended Data Table 2,3). In the aerobic palsa and surface Sphagnum habitats, 101 methanogens were found in low relative abundance (average <0.6%), while the anaerobic 102 environments of the Eriophorum and deeper (below the water table) Sphagnum habitats harbored 10...