Late Quaternary dynamics of Arctic biota from ancient environmental genomics.

During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

Changes in above- versus belowground biomass distribution in permafrost regions in response to climate warming.

Permafrost regions contain approximately half of the carbon stored in land ecosystems and have warmed at least twice as much as any other biome. This warming has influenced vegetation activity, leading to changes in plant composition, physiology, and biomass storage in aboveground and belowground components, ultimately impacting ecosystem carbon balance. Yet, little is known about the causes and magnitude of long-term changes in the above- to belowground biomass ratio of plants (η). Here, we analyzed η values using 3,013 plots and 26,337 species-specific measurements across eight sites on the Tibetan Plateau from 1995 to 2021. Our analysis revealed distinct temporal trends in η for three vegetation types: a 17% increase in alpine wetlands, and a decrease of 26% and 48% in alpine meadows and alpine steppes, respectively. These trends were primarily driven by temperature-induced growth preferences rather than shifts in plant species composition. Our findings indicate that in wetter ecosystems, climate warming promotes aboveground plant growth, while in drier ecosystems, such as alpine meadows and alpine steppes, plants allocate more biomass belowground. Furthermore, we observed a threefold strengthening of the warming effect on η over the past 27 y. Soil moisture was found to modulate the sensitivity of η to soil temperature in alpine meadows and alpine steppes, but not in alpine wetlands. Our results contribute to a better understanding of the processes driving the response of biomass distribution to climate warming, which is crucial for predicting the future carbon trajectory of permafrost ecosystems and climate feedback.

A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva.

Some organisms in nature have developed the ability to enter a state of suspended metabolism called cryptobiosis when environmental conditions are unfavorable. This state-transition requires execution of a combination of genetic and biochemical pathways that enable the organism to survive for prolonged periods. Recently, nematode individuals have been reanimated from Siberian permafrost after remaining in cryptobiosis. Preliminary analysis indicates that these nematodes belong to the genera Panagrolaimus and Plectus. Here, we present precise radiocarbon dating indicating that the Panagrolaimus individuals have remained in cryptobiosis since the late Pleistocene (~46,000 years). Phylogenetic inference based on our genome assembly and a detailed morphological analysis demonstrate that they belong to an undescribed species, which we named Panagrolaimus kolymaensis. Comparative genome analysis revealed that the molecular toolkit for cryptobiosis in P. kolymaensis and in C. elegans is partly orthologous. We show that biochemical mechanisms employed by these two species to survive desiccation and freezing under laboratory conditions are similar. Our experimental evidence also reveals that C. elegans dauer larvae can remain viable for longer periods in suspended animation than previously reported. Altogether, our findings demonstrate that nematodes evolved mechanisms potentially allowing them to suspend life over geological time scales.

Root-associated fungi and acquisitive root traits facilitate permafrost nitrogen uptake from long-term experimentally warmed tundra.

Root-associated fungi (RAF) and root traits regulate plant acquisition of nitrogen (N), which is limiting to growth in Arctic ecosystems. With anthropogenic warming, a new N source from thawing permafrost has the potential to change vegetation composition and increase productivity, influencing climate feedbacks. Yet, the impact of warming on tundra plant root traits, RAF, and access to permafrost N is uncertain. We investigated the relationships between RAF, species-specific root traits, and uptake of N from the permafrost boundary by tundra plants experimentally warmed for nearly three decades at Toolik Lake, Alaska. Warming increased acquisitive root traits of nonmycorrhizal and mycorrhizal plants. RAF community composition of ericoid (ERM) but not ectomycorrhizal (ECM) shrubs was impacted by warming and correlated with root traits. RAF taxa in the dark septate endophyte, ERM, and ECM guilds strongly correlated with permafrost N uptake for ECM and ERM shrubs. Overall, a greater proportion of variation in permafrost N uptake was related to root traits than RAF. Our findings suggest that warming Arctic ecosystems will result in interactions between roots, RAF, and newly thawed permafrost that may strongly impact feedbacks to the climate system through mechanisms of carbon and N cycling.

Persistent net release of carbon dioxide and methane from an Alaskan lowland boreal peatland complex.

Permafrost degradation in peatlands is altering vegetation and soil properties and impacting net carbon storage. We studied four adjacent sites in Alaska with varied permafrost regimes, including a black spruce forest on a peat plateau with permafrost, two collapse scar bogs of different ages formed following thermokarst, and a rich fen without permafrost. Measurements included year-round eddy covariance estimates of net carbon dioxide (CO2 ), mid-April to October methane (CH4 ) emissions, and environmental variables. From 2011 to 2022, annual rainfall was above the historical average, snow water equivalent increased, and snow-season duration shortened due to later snow return. Seasonally thawed active layer depths also increased. During this period, all ecosystems acted as slight annual sources of CO2 (13-59 g C m-2 year-1 ) and stronger sources of CH4 (11-14 g CH4 m-2 from ~April to October). The interannual variability of net ecosystem exchange was high, approximately ±100 g C m-2 year-1 , or twice what has been previously reported across other boreal sites. Net CO2 release was positively related to increased summer rainfall and winter snow water equivalent and later snow return. Controls over CH4 emissions were related to increased soil moisture and inundation status. The dominant emitter of carbon was the rich fen, which, in addition to being a source of CO2 , was also the largest CH4 emitter. These results suggest that the future carbon-source strength of boreal lowlands in Interior Alaska may be determined by the area occupied by minerotrophic fens, which are expected to become more abundant as permafrost thaw increases hydrologic connectivity. Since our measurements occur within close proximity of each other (≤1 km2 ), this study also has implications for the spatial scale and data used in benchmarking carbon cycle models and emphasizes the necessity of long-term measurements to identify carbon cycle process changes in a warming climate.

Alder expansion stimulates nitrogen oxide (NOx) emissions from southern Eurasian permafrost peatlands.

Nitrogen oxides (NOx) play an important role for atmospheric chemistry and radiative forcing. However, NOx emissions from the vast northern circumpolar permafrost regions have not been studied in situ due to limitations of measurement techniques. Our goals were to validate the offline analytical technique, and based on this, to widely quantify in situ NOx emissions from peatlands in the southern Eurasian permafrost region. To this end, we conducted a comparison of online and offline flux measurements in 2018 and 2019 using the synthetic air flushing, steady-state opaque chamber method. With differences in annual average and cumulative fluxes less than 0.1 µg N m-2 h-1 and 0.01 kg N ha-1 year-1, the online and offline fluxes were in good agreement, demonstrating the feasibility of conducting offline measurements in remote regions without power supply. The flux measurements over 2 years showed obvious NOx emissions of 0.05-0.14 and 0.13-0.30 kg N ha-1 year-1 in the hollow and hummock microtopography of permafrost peatlands, respectively. The rapid expansion of alder (Alnus sibirica) in the peatlands induced by permafrost degradation significantly increased soil mineral N contents and NOx emissions depending on the age of alder (0.64-1.74 and 1.44-2.20 kg N ha-1 year-1 from the alder forests with tree ages of 1-10 years and 11-20 years, respectively). Alder expansion also intensively altered the thermal state of permafrost including the sharp increases of soil temperatures during the non-growing season from October to April and active layer thickness. This study provides the first in situ evidences of NOx emissions from the northern circumpolar permafrost regions and uncovers the well-documented expansion of alders can substantially stimulate NOx emissions and thus, significantly affect air quality, radiative forcing, and ecosystem productivity in the pristine regions.

Changing climatic controls on the greenhouse gas balance of thermokarst bogs during succession after permafrost thaw.

Permafrost thaw in northern peatlands causes collapse of permafrost peat plateaus and thermokarst bog development, with potential impacts on atmospheric greenhouse gas exchange. Here, we measured methane and carbon dioxide fluxes over 3 years (including winters) using static chambers along two permafrost thaw transects in northwestern Canada, spanning young (~30 years since thaw), intermediate and mature thermokarst bogs (~200 years since thaw). Young bogs were wetter, warmer and had more hydrophilic vegetation than mature bogs. Methane emissions increased with wetness and soil temperature (40 cm depth) and modelled annual estimates were greatest in the young bog during the warmest year and lowest in the mature bog during the coolest year (21 and 7 g C-CH4 m-2 year-1, respectively). The dominant control on net ecosystem exchange (NEE) in the mature bog (between +20 and -54 g C-CO2 m-2 year-1) was soil temperature (5 cm), causing net CO2 loss due to higher ecosystem respiration (ER) in warmer years. In contrast, wetness controlled NEE in the young and intermediate bogs (between +55 and -95 g C-CO2 m-2 year-1), where years with periodic inundation at the beginning of the growing season caused greater reduction in gross primary productivity than in ER leading to CO2 loss. Winter fluxes (November-April) represented 16% of annual ER and 38% of annual CH4 emissions. Our study found NEE of thermokarst bogs to be close to neutral and rules out large CO2 losses under current conditions. However, high CH4 emissions after thaw caused a positive net radiative forcing effect. While wet conditions favouring high CH4 emissions only persist for the initial young bog period, we showed that continued climate warming with increased ER, and thus, CO2 losses from the mature bog can cause net positive radiative forcing which would last for centuries after permafrost thaw.

Carbon Fate, Iron Dissolution, and Molecular Characterization of Dissolved Organic Matter in Thawed Yedoma Permafrost under Varying Redox Conditions.

Permafrost soils store ∼50% of terrestrial C, with Yedoma permafrost containing ∼25% of the total C. Permafrost is undergoing degradation due to thawing, with potentially hazardous effects on landscape stability and water resources. Complicating ongoing efforts to project the ultimate fate of deep permafrost C is the poorly constrained role of the redox environment, Fe-minerals, and its redox-active phases, which may modulate organic C-abundance, composition, and reactivity through complexation and catalytic processes. We characterized C fate, Fe fractions, and dissolved organic matter (DOM) isolates from permafrost-thaw under varying redox conditions. Under anoxic incubation conditions, 33% of the initial C was lost as gaseous species within 21 days, while under oxic conditions, 58% of C was lost. Under anoxic incubation, 42% of the total initial C was preserved in a dissolved fraction. Lignin-like compounds dominated permafrost-thaw, followed by lipid- and protein-like compounds. However, under anoxic incubation conditions, there was accumulation of lipid-like compounds and reduction in the nominal oxidation state of C over time, regardless of the compound classes. DOM dynamics may be affected by microbial activity and abiotic processes mediated by Fe-minerals related to selective DOM fractionation and/or its oxidation. Chemodiversity DOM signatures could serve as valuable proxies to track redox conditions with permafrost-thaw.

Extensive loss of past permafrost carbon but a net accumulation into present-day soils.

Atmospheric concentrations of carbon dioxide increased between the Last Glacial Maximum (LGM, around 21,000 years ago) and the preindustrial era1. It is thought that the evolution of this atmospheric carbon dioxide (and that of atmospheric methane) during the glacial-to-interglacial transition was influenced by organic carbon that was stored in permafrost during the LGM and then underwent decomposition and release following thaw2,3. It has also been suggested that the rather erratic atmospheric δ13C and ∆14C signals seen during deglaciation1,4 could partly be explained by the presence of a large terrestrial inert LGM carbon stock, despite the biosphere being less productive (and therefore storing less carbon)5,6. Here we present an empirically derived estimate of the carbon stored in permafrost during the LGM by reconstructing the extent and carbon content of LGM biomes, peatland regions and deep sedimentary deposits. We find that the total estimated soil carbon stock for the LGM northern permafrost region is smaller than the estimated present-day storage (in both permafrost and non-permafrost soils) for the same region. A substantial decrease in the permafrost area from the LGM to the present day has been accompanied by a roughly 400-petagram increase in the total soil carbon stock. This increase in soil carbon suggests that permafrost carbon has made no net contribution to the atmospheric carbon pool since the LGM. However, our results also indicate potential postglacial reductions in the portion of the carbon stock that is trapped in permafrost, of around 1,000 petagrams, supporting earlier studies7. We further find that carbon has shifted from being primarily stored in permafrost mineral soils and loess deposits during the LGM, to being roughly equally divided between peatlands, mineral soils and permafrost loess deposits today.

Genome-centric view of carbon processing in thawing permafrost.

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.

Dissolved organic matter quality in thermokarst lake water and sediments across a permafrost gradient, Western Siberia.

Thermokarst (thaw) lakes of permafrost peatlands are among the most important sentinels of climate change and sizable contributors of greenhouse gas emissions (GHG) in high latitudes. These lakes are humic, often acidic and exhibit fast growing/drainage depending on the local environmental and permafrost thaw. In contrast to good knowledge of the thermokarst lake water hydrochemistry and GHG fluxes, the sediments pore waters remain virtually unknown, despite the fact that these are hot spots of biogeochemical processes including GHG generation. Towards better understating of dissolved organic matter (DOM) quality at the lake water - sediment interface and in the sediments pore waters, here we studied concentration and optical (UV, visual) properties of DOM of 11 thermokarst lakes located in four permafrost zones of Western Siberia Lowland. We found systematic evaluation of DOM concentration, SUVA and various optical parameters along the vertical profile of lake sediments. The lake size and hence, the stage of lake development, had generally weak control on DOM quality. The permafrost zone exhibited clear impact on DOM porewater concentration, optical characteristics, aromaticity and weight average molecular weight (WAMW). The lowest quality of DOM, reflected in highest SUVA and WAMW, corresponding to the dominance of terrestrial sources, was observed at the southern boundary of the permafrost, in the sporadic/discontinuous zone. This suggests active mobilization of organic matter leachates from the interstitial peat and soil porewaters to the lake, presumably via subsurface or suprapermafrost influx. Applying a substitute space for time scenario for future evolution of OM characteristics in thermokarst lake sediments of Western Siberia, we foresee a decrease of DOM quality, molecular weight and potential bioavailability in lakes of continuous permafrost zone, and an increase in these parameters in the sporadic/discontinuous permafrost zone.

Methane release from carbonate rock formations in the Siberian permafrost area during and after the 2020 heat wave.

Anthropogenic global warming may be accelerated by a positive feedback from the mobilization of methane from thawing Arctic permafrost. There are large uncertainties about the size of carbon stocks and the magnitude of possible methane emissions. Methane cannot only be produced from the microbial decay of organic matter within the thawing permafrost soils (microbial methane) but can also come from natural gas (thermogenic methane) trapped under or within the permafrost layer and released when it thaws. In the Taymyr Peninsula and surroundings in North Siberia, the area of the worldwide largest positive surface temperature anomaly for 2020, atmospheric methane concentrations have increased considerably during and after the 2020 heat wave. Two elongated areas of increased atmospheric methane concentration that appeared during summer coincide with two stripes of Paleozoic carbonates exposed at the southern and northern borders of the Yenisey-Khatanga Basin, a hydrocarbon-bearing sedimentary basin between the Siberian Craton to the south and the Taymyr Fold Belt to the north. Over the carbonates, soils are thin to nonexistent and wetlands are scarce. The maxima are thus unlikely to be caused by microbial methane from soils or wetlands. We suggest that gas hydrates in fractures and pockets of the carbonate rocks in the permafrost zone became unstable due to warming from the surface. This process may add unknown quantities of methane to the atmosphere in the near future.

Reduced microbial stability in the active layer is associated with carbon loss under alpine permafrost degradation.

Permafrost degradation may induce soil carbon (C) loss, critical for global C cycling, and be mediated by microbes. Despite larger C stored within the active layer of permafrost regions, which are more affected by warming, and the critical roles of Qinghai-Tibet Plateau in C cycling, most previous studies focused on the permafrost layer and in high-latitude areas. We demonstrate in situ that permafrost degradation alters the diversity and potentially decreases the stability of active layer microbial communities. These changes are associated with soil C loss and potentially a positive C feedback. This study provides insights into microbial-mediated mechanisms responsible for C loss within the active layer in degraded permafrost, aiding in the modeling of C emission under future scenarios.

Plant uptake of CO2 outpaces losses from permafrost and plant respiration on the Tibetan Plateau.

High-latitude and high-altitude regions contain vast stores of permafrost carbon. Climate warming may result in the release of CO2 from both the thawing of permafrost and accelerated autotrophic respiration, but it may also increase the fixation of CO2 by plants, which could relieve or even offset the CO2 losses. The Tibetan Plateau contains the largest area of alpine permafrost on Earth. However, the current status of the net CO2 balance and feedbacks to warming remain unclear, given that the region has recently experienced an atmospheric warming rate of over 0.3 °C decade-1 We examined 32 eddy covariance sites and found an unexpected net CO2 sink during 2002 to 2020 (26 of the sites yielded a net CO2 sink) that was four times the amount previously estimated. The CO2 sink peaked at an altitude of roughly 4,000 m, with the sink at lower and higher altitudes limited by a low carbon use efficiency and a cold, dry climate, respectively. The fixation of CO2 in summer is more dependent on temperature than the loss of CO2 than it is in the winter months, especially at higher altitudes. Consistently, 16 manipulative experiments and 18 model simulations showed that the fixation of CO2 by plants will outpace the loss of CO2 under a wetting-warming climate until the 2090s (178 to 318 Tg C y-1). We therefore suggest that there is a plant-dominated negative feedback to climate warming on the Tibetan Plateau.

The effect of freeze-thaw action on the dynamic change of supra-permafrost water sources: A stable isotope perspective.

Due to the continuous degradation (gradual thawing) of permafrost, supra-permafrost water has become an important component of runoff that occurs in cold regions. However, current research has only focused on the amount of water provided by permafrost, and little has been reported regarding the source and formation mechanisms of supra-permafrost water. Due to the difficulty of observation and sampling in cold regions and insufficient data accumulation, model simulations face various difficulties in regard to solving problems related to hydrological processes. Considering the advantages of stable isotope tracer methods in hydrology, the source of supra-permafrost water in Qilian Mountain was analyzed based on 1,840 samples, and the source of supra-permafrost water was determined by end-member mixing analysis (EMMA). Negative line-conditioned excess (lc-excess), lower slope, and particularly the negative intercept of the evaporation line (EL) indicates strong evaporation effects on supra-permafrost water. Remarkably, the evolutionary process, influencing factors, and relationship with other water bodies all indicate that supra-permafrost water is replenished by precipitation, ground ice meltwater, and snow meltwater. The results indicated that from May to October, the contributions of precipitation to the supra-permafrost water were 79%, 83%, 90%, 84%, 87%, and 83%, respectively. Snow meltwater contributed 11%, 13%, 10%, 16%, 11%, and 9%, respectively. Permafrost degradation impacts the water cycle and can increase the minimum monthly runoff and increase groundwater storage. To mitigate the effects of this change, monitoring and early warning systems are essential for detecting signs of permafrost degradation in a timely manner so that appropriate measures can be taken. This may involve the use of remote-sensing technologies, sensor networks, and other methods for real-time monitoring. Establishing mechanisms for sharing information with the relevant departments is crucial. The research results provide scientific and technological support and aid in decision-making to mitigate the negative effects of continuous permafrost degradation in a changing environment.

Unraveling the impact of wildfires on permafrost ecosystems: Vulnerability, implications, and management strategies.

Permafrost regions play an important role in global carbon and nitrogen cycling, storing enormous amounts of organic carbon and preserving a delicate balance of nutrient dynamics. However, the increasing frequency and severity of wildfires in these regions pose significant challenges to the stability of these ecosystems. This review examines the effects of fire on chemical, biological, and physical properties of permafrost regions. The physical, chemical, and pedological properties of frozen soil are impacted by fires, leading to changes in soil structure, porosity, and hydrological functioning. The combustion of organic matter during fires releases carbon and nitrogen, contributing to greenhouse gas emissions and nutrient loss. Understanding the interactions between fire severity, ecosystem processes, and the implications for permafrost regions is crucial for predicting the impacts of wildfires and developing effective strategies for ecosystem protection and agricultural productivity in frozen soils. By synthesizing available knowledge and research findings, this review enhances our understanding of fire severity's implications for permafrost ecosystems and offers insights into effective fire management strategies.

Experimental warming altered plant functional traits and their coordination in a permafrost ecosystem.

Knowledge about changes in plant functional traits is valuable for the mechanistic understanding of warming effects on ecosystem functions. However, observations have tended to focus on aboveground plant traits, and there is little information about changes in belowground plant traits or the coordination of above- and belowground traits under climate warming, particularly in permafrost ecosystems. Based on a 7-yr field warming experiment, we measured 26 above- and belowground plant traits of four dominant species, and explored community functional composition and trait networks in response to experimental warming in a permafrost ecosystem on the Tibetan Plateau. Experimental warming shifted community-level functional traits toward more acquisitive values, with earlier green-up, greater plant height, larger leaves, higher photosynthetic resource-use efficiency, thinner roots, and greater specific root length and root nutrient concentrations. However, warming had a negligible effect in terms of functional diversity. In addition, warming shifted hub traits which have the highest centrality in the network from specific root area to leaf area. These results demonstrate that above- and belowground traits exhibit consistent adaptive strategies, with more acquisitive traits in warmer environments. Such changes could provide an adaptive advantage for plants in response to environmental change.

The start of frozen dates over northern permafrost regions with the changing climate.

The soil freeze-thaw cycle in the permafrost regions has a significant impact on regional surface energy and water balance. Although increasing efforts have been made to understand the responses of spring thawing to climate change, the mechanisms controlling the global interannual variability of the start date of permafrost frozen (SOF) remain unclear. Using long-term SOF from the combinations of multiple satellite microwave sensors between 1979 and 2020, and analytical techniques, including partial correlation, ridge regression, path analysis, and machine learning, we explored the responses of SOF to multiple climate change factors, including warming (surface and air temperature), start date of permafrost thawing (SOT), soil properties (soil temperature and volume of water), and the snow depth water equivalent (SDWE). Overall, climate warming exhibited the maximum control on SOF, but SOT in spring was also an important driver of SOF variability; among the 65.9% significant SOT and SOF correlations, 79.3% were positive, indicating an overall earlier thawing would contribute to an earlier frozen in winter. The machine learning analysis also suggested that apart from warming, SOT ranked as the second most important determinant of SOF. Therefore, we identified the mechanism responsible for the SOT-SOF relationship using the SEM analysis, which revealed that soil temperature change exhibited the maximum effect on this relationship, irrespective of the permafrost type. Finally, we analyzed the temporal changes in these responses using the moving window approach and found increased effect of soil warming on SOF. In conclusion, these results provide important insights into understanding and predicting SOF variations with future climate change.

Climate warming has direct and indirect effects on microbes associated with carbon cycling in northern lakes.

Northern lakes disproportionately influence the global carbon cycle, and may do so more in the future depending on how their microbial communities respond to climate warming. Microbial communities can change because of the direct effects of climate warming on their metabolism and the indirect effects of climate warming on groundwater connectivity from thawing of surrounding permafrost, especially at lower landscape positions. Here we used shotgun metagenomics to compare the taxonomic and functional gene composition of sediment microbes in 19 peatland lakes across a 1600-km permafrost transect in boreal western Canada. We found microbes responded differently to the loss of regional permafrost cover than to increases in local groundwater connectivity. These results suggest that both the direct and indirect effects of climate warming, which were respectively associated with loss of permafrost and subsequent changes in groundwater connectivity interact to change microbial composition and function. Archaeal methanogens and genes involved in all major methanogenesis pathways were more abundant in warmer regions with less permafrost, but higher groundwater connectivity partly offset these effects. Bacterial community composition and methanotrophy genes did not vary with regional permafrost cover, and the latter changed similarly to methanogenesis with groundwater connectivity. Finally, we found an increase in sugar utilization genes in regions with less permafrost, which may further fuel methanogenesis. These results provide the microbial mechanism for observed increases in methane emissions associated with loss of permafrost cover in this region and suggest that future emissions will primarily be controlled by archaeal methanogens over methanotrophic bacteria as northern lakes warm. Our study more generally suggests that future predictions of aquatic carbon cycling will be improved by considering how climate warming exerts both direct effects associated with regional-scale permafrost thaw and indirect effects associated with local hydrology.