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Abstract Northern regions are warming faster than the rest of the globe. It is difficult to predict ecosystem responses to warming because the thermal sensitivity of their biophysical components varies. Here, we present an analysis of the authors’ expert judgment regarding the sensitivity of six ecosystem components – permafrost, peatlands, lakes, snowpack, vegetation, and endothermic vertebrates – across northern landscapes ranging from boreal to polar biomes. We identified 28 discontinuous component states across a 3700 km latitudinal gradient in northeastern North America and quantified sensitivity as the transition time from an initial to a contrasting state following a theoretical step change increase in mean annual air temperature of 5 °C. We infer that multiple interconnected state shifts are likely to occur within a narrow subarctic latitudinal band at timescales of 10 to more than 100 years, and response times decrease with latitude. Response times differ between components and across latitudes, which is likely to impair the integrity of ecosystems.

Arctic and subarctic landscapes have unique hydrological and limnological features and are now experiencing rapid change due to climate warming and permafrost thaw. The highly abundant lakes, ponds, and rivers across these landscapes play an increasingly important role in global biogeochemical cycles and are sentinels of environmental changes. However, studying these remote waters poses challenges for both in situ sampling and remote-sensing analysis. Here we developed a synergistic remote-sensing strategy that combined PlanetScope and Sentinel-2 satellite data to estimate limnicity (water fraction per land surface), limnodensity (density of water bodies), and limnodiversity (optical diversity of water bodies) along a boreal forest-tundra transect, from the non-permafrost to the continuous permafrost zones of western Nunavik (Subarctic Canada). Our analyses show that this region hosts 335,281 water bodies, around 90% in the 0.0001 to 0.01 km2 size range. In bedrock outcrops, large water bodies were mostly associated with glacially carved depressions (higher limnicity). In contrast, small water bodies were predominately found in sedimentary infills along valleys (higher limnodensity). The discontinuous permafrost zone had the highest limnodensity and limnodiversity. This was likely due to permafrost thaw (thermokarst), particularly the collapse, subsidence, and erosion of palsas (organic permafrost mounds), resulting in ponds with black- and brown-colored waters, and lithalsas (mineral permafrost mounds), resulting in ponds with brown, light-brown, and sometimes white-colored waters. Some of these limnodense and limnodiverse landscapes, although covering only 2 to 7% of the total area of the study region, contained over one-third (34%) of the total number of water bodies, 97% of which were

Rapid warming in the High Arctic has induced changes in terrestrial environments that have included major recent shifts in lakes and ponds. Numerous studies exist of spatial trends in water chemistry, bioindicator groups, and paleoenvironmental change from High Arctic lakes; however, little is known about lake thermal stratification regimes at high latitudes beyond assumptions based on generalized classification schemes. Here, we report on the presence in late July 2022 of positive thermal stratification during open-water conditions in two freshwater lakes near Clements Markham Inlet, on northern Ellesmere Island. These lakes are situated in the polar desert at 82.6°N, >1000 km north of the generally accepted northern limit of summer thermal stratification. Given their location approaching the northernmost land on Earth, the thermal profiles of these lakes suggest that the occurrence of summer stratification may no longer be discounted anywhere in the Northern Hemisphere.

ABSTRACTWinter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22–3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season.IMPORTANCEMicrobiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.

We describe limnological data sets from Thores Lake, a large ice-contact proglacial lake in northern Ellesmere Island, Nunavut (82.65°N), including longitudinal and cross transects (vertical resolution 0.03 m, horizontal resolution 100–200 m). The lake is formed due to damming by Thores Glacier at its northwest margin, has multi-year ice cover and a cold (

Abstract Global warming is destabilizing the cryosphere, with consequences for glaciers, permafrost, sea ice and lake ice. Polar lakes have short ice‐free seasons, and small changes in ice cover duration have the potential to provoke alterations to ecosystem structure. However, these lakes are understudied, and the consequences for mixing regimes, thermal structures and biogeochemical processes remain unclear. We measured three annual cycles of dissolved oxygen, temperature and specific conductivity in a lake at ∼83°N to investigate limnological processes and their interannual variability. There were sharp interannual contrasts in lake dynamics, with state shifts in mixing, stratification and oxygen regimes due to air temperature variability and meteorological events. We also observed unusual thermal profiles that were associated with solute gradients. These striking differences underscore the sensitivity of high Arctic lakes to interannual variations in meteorological forcing, and their susceptibility to regime shifts in response to ongoing global change.

In parallel to rapid sea-ice loss and other climate impacts in the Arctic Ocean, large-scale changes are now apparent in northern landscapes and associated ecosystems. Arctic communities are increasingly vulnerable to these changes, including effects on food security, water quality, and land-based transport. The project “Terrestrial Multidisciplinary distributed Observatories for the Study of Arctic Connections” (T-MOSAiC) was conducted under the auspices of the International Arctic Science Committee over the period 2017–2022. The aim was to generate multiauthored syntheses, protocols, and observations toward an improved understanding of Arctic terrestrial change, and to identify priorities for northern research, monitoring, and policy development. This special collection of Arctic Science covers a broad range of these themes, including limnological insights into northern lakes and rivers, a set of protocols for permafrost and vegetation monitoring, an integrated perspective on Arctic roads and railways to bridge the social and natural sciences, snow and ice studies at the coastal margin of the Last Ice Area, and Indigenous perspectives on Arctic and global conservation. The contributions summarized in this introductory article to the T-MOSAiC special collection include recommendations for the future, and they illustrate the immense value of Arctic collaborations that bring together researchers across disciplines, nations, and cultures.

While the sentinel nature of freshwater systems is now well recognized, widespread integration of freshwater processes and patterns into our understanding of broader climate-driven Arctic terrestrial ecosystem change has been slow. We review the current understanding across Arctic freshwater systems of key sentinel responses to climate, which are attributes of these systems with demonstrated and sensitive responses to climate forcing. These include ice regimes, temperature and thermal structure, river baseflow, lake area and water level, permafrost-derived dissolved ions and nutrients, carbon mobilization (dissolved organic carbon, greenhouse gases, and radiocarbon), dissolved oxygen concentrations, lake trophic state, various aquatic organisms and their traits, and invasive species. For each sentinel, our objectives are to clarify linkages to climate, describe key insights already gained, and provide suggestions for future research based on current knowledge gaps. We suggest that tracking key responses in Arctic freshwater systems will expand understanding of the breadth and depth of climate-driven Arctic ecosystem changes, provide early indicators of looming, broader changes across the landscape, and improve protection of freshwater biodiversity and resources.

Relatively little is known about the glaciers of northern Ellesmere Island, Canada. Here we describe the first field and remote sensing observations of Thores Glacier, located 50 km inland from the Arctic Ocean. The glacier is slow-moving, with maximum velocities of 26 m a−1 and a maximum observed thickness of 360 ± 4.3 m. There has been little change in terminus position since at least 1959, with a maximum advance of 170 m at the northwest terminus ending on land and retreat up to 130 m at the southeast terminus ending in Thores Lake. There is little evidence for change since the Little Ice Age as bedrock weathering patterns suggest retreat of no more than 20–30 m around most of the glacier margin. The supraglacial drainage network is generally poorly developed, without moulins and with few crevasses, and therefore no evidence of water reaching the glacier bed. This is supported by one-dimensional modelling, which suggests current basal temperatures of −7.0 °C to −12.0 °C along the centerline. Thores Glacier currently dams Thores Lake, which causes drainage to flow to the southeast. However, if the glacier thins or retreats sufficiently, regional drainage will reverse and flow to the north, and Thores Lake would no longer exist.

Land-based transport corridors and related infrastructure are increasingly extending into and across the Arctic in support of resource development and population growth, causing large-scale cumulative changes to northern socio-ecological systems. These changes include the increased mobility of people, goods and resources, and environmental impacts on landscapes and ecosystems as the human footprint reaches remote, unindustrialized regions. Arctic climate change is also generating new challenges for the construction and maintenance of these transport systems, requiring adaptive engineering solutions as well as community resilience. In this review article, we consider the complex entanglements between humans, the environment, and land transportation infrastructure in the North and illustrate these interrelations by way of seven case studies: the Baikal–Amur Mainline, Bovanenkovo Railway, Alaska–Canada Highway, Inuvik–Tuktoyatuk Highway, Alaska Railroad, Hudson Bay Railway, and proposed railways on Baffin Island, Canada. As new infrastructure is built and anticipated across the circumpolar North, there is an urgent need for an integrated socio-ecological approach to impact assessment. This would include full consideration of Indigenous knowledge and concerns, collaboration with local communities and user groups in assessment, planning and monitoring, and evaluation of alternative engineering designs to contend with the impacts of climate change in the decades ahead.

Abstract Background Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identified genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratified, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems. Results Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identified in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean. Conclusions Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our findings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles. Video Abstract

Abstract Missions to detect extraterrestrial life are being designed to visit Europa and Enceladus in the next decades. The contact between the mission payload and the habitable subsurface of these satellites involves significant risk of forward contamination. The standardization of protocols to decontaminate ice cores from planetary field analogs of icy moons, and monitor the contamination in downstream analysis, has a direct application for developing clean approaches crucial to life detection missions in these satellites. Here we developed a comprehensive protocol that can be used to monitor and minimize the contamination of Arctic ice cores in processing and downstream analysis. We physically removed the exterior layers of ice cores to minimize bioburden from sampling. To monitor contamination, we constructed artificial controls and applied culture-dependent and culture-independent techniques such as 16S rRNA amplicon sequencing. We identified 13 bacterial contaminants, including a radioresistant species. This protocol decreases the contamination risk, provides quantitative and qualitative information about contamination agents, and allows validation of the results obtained. This study highlights the importance of decreasing and evaluating prokaryotic contamination in the processing of polar ice cores, including in their use as analogs of Europa and Enceladus.

In ice-covered polar lakes, a narrow ice-free moat opens up in spring or early summer, and then persists at the edge of the lake until complete ice loss or refreezing. In this study, we analyzed the horizontal gradients in Ward Hunt Lake, located in the Canadian High Arctic, and addressed the hypothesis that the transition from its nearshore open-water moat to offshore ice-covered waters is marked by discontinuous shifts in limnological properties. Consistent with this hypothesis, we observed an abrupt increase in below-ice concentrations of chlorophyll a beyond the ice margin, along with a sharp decrease in temperature and light availability and pronounced changes in benthic algal pigments and fatty acids. There were higher concentrations of rotifers and lower concentrations of viruses at the ice-free sampling sites, and contrasts in zooplankton fatty acid profiles that implied a greater importance of benthic phototrophs in their inshore diet. The observed patterns underscore the structuring role of ice cover in polar lakes. These ecosystems do not conform to the traditional definitions of littoral versus pelagic zones but instead may have distinct moat, ice-margin, and ice-covered zones. This zonation is likely to weaken with ongoing climate change.

Abstract Background The sulfur cycle encompasses a series of complex aerobic and anaerobic transformations of S-containing molecules and plays a fundamental role in cellular and ecosystem-level processes, influencing biological carbon transfers and other biogeochemical cycles. Despite their importance, the microbial communities and metabolic pathways involved in these transformations remain poorly understood, especially for inorganic sulfur compounds of intermediate oxidation states (thiosulfate, tetrathionate, sulfite, polysulfides). Isolated and highly stratified, the extreme geochemical and environmental features of meromictic ice-capped Lake A, in the Canadian High Arctic, provided an ideal model ecosystem to resolve the distribution and metabolism of aquatic sulfur cycling microorganisms along redox and salinity gradients. Results Applying complementary molecular approaches, we identified sharply contrasting microbial communities and metabolic potentials among the markedly distinct water layers of Lake A, with similarities to diverse fresh, brackish and saline water microbiomes. Sulfur cycling genes were abundant at all depths and covaried with bacterial abundance. Genes for oxidative processes occurred in samples from the oxic freshwater layers, reductive reactions in the anoxic and sulfidic bottom waters and genes for both transformations at the chemocline. Up to 154 different genomic bins with potential for sulfur transformation were recovered, revealing a panoply of taxonomically diverse microorganisms with complex metabolic pathways for biogeochemical sulfur reactions. Genes for the utilization of sulfur cycle intermediates were widespread throughout the water column, co-occurring with sulfate reduction or sulfide oxidation pathways. The genomic bin composition suggested that in addition to chemical oxidation, these intermediate sulfur compounds were likely produced by the predominant sulfur chemo- and photo-oxidisers at the chemocline and by diverse microbial degraders of organic sulfur molecules. Conclusions The Lake A microbial ecosystem provided an ideal opportunity to identify new features of the biogeochemical sulfur cycle. Our detailed metagenomic analyses across the broad physico-chemical gradients of this permanently stratified lake extend the known diversity of microorganisms involved in sulfur transformations over a wide range of environmental conditions. The results indicate that sulfur cycle intermediates and organic sulfur molecules are major sources of electron donors and acceptors for aquatic and sedimentary microbial communities in association with the classical sulfur cycle. Video abstract

Abstract Ice cover persists throughout summer over many lakes at extreme polar latitudes but is likely to become increasingly rare with ongoing climate change. Here we addressed the question of how summer ice-cover affects the underlying water column of Ward Hunt Lake, a freshwater lake in the Canadian High Arctic, with attention to its vertical gradients in limnological properties that would be disrupted by ice loss. Profiling in the deepest part of the lake under thick mid-summer ice revealed a high degree of vertical structure, with gradients in temperature, conductivity and dissolved gases. Dissolved oxygen, nitrous oxide, carbon dioxide and methane rose with depth to concentrations well above air-equilibrium, with oxygen values at > 150% saturation in a mid-water column layer of potential convective mixing. Fatty acid signatures of the seston also varied with depth. Benthic microbial mats were the dominant phototrophs, growing under a dim green light regime controlled by the ice cover, water itself and weakly colored dissolved organic matter that was mostly autochthonous in origin. In this and other polar lakes, future loss of mid-summer ice will completely change many water column properties and benthic light conditions, resulting in a markedly different ecosystem regime.

Abstract The candidate phyla radiation (CPR) is a diverse group of uncultured bacterial lineages with poorly understood metabolic functions. CPR bacteria can represent a large proportion of the total planktonic microbial community in subarctic thermokarst lakes, but their functional roles remain unexplored. We applied sequential water filtration and metagenomic shotgun sequencing to a peatland permafrost thaw lake, and found high proportions of CPR bacteria in both summer and winter (> 40% of 16S rRNA reads in the 0.02–0.22 μm pore‐size fraction). The metagenome‐assembled genomes of CPR bacteria representatives showed capacities to degrade and ferment permafrost‐ and peatland‐derived organic matter. Potential products of their metabolic activities included acetate, CO2, and hydrogen, implying a syntrophic relationship with other community members, including methanogens and methanotrophs. The results indicate biogeochemical interdependencies in organic matter utilization within thermokarst microbial communities, with CPR members playing a key intermediate role in carbon and methane cycling.

Arctic lakes are experiencing increasingly shorter periods of ice cover due to accelerated warming at northern high latitudes. Given the control of ice cover thickness and duration over many limnological processes, these changes will have pervasive effects. However, due to their remote and extreme locations even first-order data on lake ecology is lacking for many ecosystems. The aim of this study was to characterize and compare the microbial communities of four closely spaced lakes in Stuckberry Valley (northern Ellesmere Island, Canadian Arctic Archipelago), in the coastal margin zone of the Last Ice Area, that differed in their physicochemical, morphological and catchment characteristics. We performed high-throughput amplicon sequencing of the V4 16S rRNA gene to provide inter- and intra-lake comparisons. Two deep (>25 m) and mostly oxygenated lakes showed highly similar community assemblages that were distinct from those of two shallower lakes (

Thermokarst lakes are important features of subarctic landscapes and are a substantial source of greenhouse gases, although the extent of gas produced varies seasonally. Microbial communities are responsible for the production of methane and CO2 but the “top down” forces that influence microbial dynamics (i.e., grazers and viruses) and how they vary temporally within these lakes are still poorly understood. The aim of this study was to examine viral diversity over time to elucidate the seasonal structure of the viral communities in thermokarst lakes. We produced virus-enriched metagenomes from a subarctic peatland thermokarst lake in the summer and winter over three years. The vast majority of vOTUs assigned to viral families belonged to Caudovirales (Caudoviricetes), notably the morphological groups myovirus, siphovirus and podovirus. We identified two distinct communities: a dynamic, seasonal community in the oxygenated surface layer during the summer and a stable community found in the anoxic water layer at the bottom of the lake in summer and throughout much of the water column in winter. Comparison with other permafrost and northern lake metagenomes highlighted the distinct composition of viral communities in this permafrost thaw lake ecosystem.

Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.

Salinization of freshwater is increasingly observed in regions where chloride de-icing salts are applied to the roads in winter, but little is known about the effects on microbial communities. In this study, we analyzed the planktonic microbiomes of four lakes that differed in degree of urbanization, eutrophication and salinization, from an oligotrophic reference lake with no surrounding roads, to a eutrophic, salinized lake receiving runoff from a highway. We tested the hypothesis that an influence of road salts would be superimposed on the effects of season and trophic status. We evaluated the microbial community structure by 16S rRNA sequencing for Bacteria, and by four methods for eukaryotes: 16S rRNA chloroplast analysis, 18S rRNA sequencing, photosynthetic pigment analysis and microscopy. Consistent with our hypothesis, chloride and total nitrogen concentrations were among the most important statistical factors explaining the differences in taxonomic composition. These factors were positively correlated with the abundance of cryptophytes, haptophytes, and cyanobacteria. Ice-cover was also a major structuring factor, with clear differences between the winter communities and those of the open-water period. Nitrifying and methane oxidizing bacteria were more abundant in winter, suggesting the importance of anaerobic sediment processes and release of reduced compounds into the ice-covered water columns. The four methods for eukaryotic analysis provided complementary information. The 18S rRNA observations were strongly influenced by the presence of ribosome-rich ciliates, but revealed a much higher degree of taxonomic richness and greater separation of lakes, seasonal changes and potential salinity effects than the other methods.

ABSTRACT High-latitude, perennially stratified (meromictic) lakes are likely to be especially vulnerable to climate warming because of the importance of ice in maintaining their water column structure and associated distribution of microbial communities. This study aimed to characterize viral abundance, diversity, and distribution in a meromictic lake of marine origin on the far northern coast of Ellesmere Island, in the Canadian High Arctic. We collected triplicate samples for double-stranded DNA (dsDNA) viromics from five depths that encompassed the major features of the lake, as determined by limnological profiling of the water column. Viral abundance and virus-to-prokaryote ratios were highest at greater depths, while bacterial and cyanobacterial counts were greatest in the surface waters. The viral communities from each zone of the lake defined by salinity, temperature, and dissolved oxygen concentrations were markedly distinct, suggesting that there was little exchange of viral types among lake strata. Ten viral assembled genomes were obtained from our libraries, and these also segregated with depth. This well-defined structure of viral communities was consistent with that of potential hosts. Viruses from the monimolimnion, a deep layer of ancient Arctic Ocean seawater, were more diverse and relatively abundant, with few similarities to available viral sequences. The Lake A viral communities also differed from published records from the Arctic Ocean and meromictic Ace Lake in Antarctica. This first characterization of viral diversity from this sentinel environment underscores the microbial richness and complexity of an ecosystem type that is increasingly exposed to major perturbations in the fast-changing Arctic. IMPORTANCE The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation.

Freshwater salinization is an ongoing concern for north temperate lakes; however, little is known about its impacts on microbial communities, particularly for bacteria. We tested the hypotheses that road de-icing salt induces changes in the microbial community structure of lake plankton, and that changes due to chloride would differ from those due to urban snowmelt because of additional chemicals in the snowmelt. In a laboratory incubator experiment, an overwintering plankton community in lake water was exposed for two weeks to either NaCl or municipal road snow with the same level of chloride. Microbial community structure as determined by 16S (prokaryotes) and 18S (eukaryotes) rRNA transcript analysis showed changes in response to the chloride-only enrichment, with some rare taxa becoming more prominent. Consistent with our hypothesis, the salt and the snow treatments induced different community changes. These results indicate that ecotoxicology assays based on a single salt addition may not reflect the in situ effects of salt-contaminated urban snow, and that the combined chemical effects of urban snowmelt require direct testing.

Thermokarst lakes are known to emit methane (CH4) and carbon dioxide (CO2), but little attention has been given to those formed from the thawing and collapse of lithalsas, ice-rich mineral soil mounds that occur in permafrost landscapes. The present study was undertaken to assess greenhouse gas stocks and fluxes in eight lithalsa lakes across a 200 km gradient of permafrost degradation in subarctic Québec. The northernmost lakes varied in their surface-water CO2 content from below to above saturation, but the southern lakes in this gradient had much higher surface concentrations that were well above air-equilibrium. Surface-water CH4 concentrations were at least an order of magnitude above air-equilibrium values at all sites, and the diffusive fluxes of both gases increased from north to south. Methane oxidation in the surface waters from a northern lake was only 10% of the emission rate, but at the southern end it was around 60% of the efflux to the atmosphere, indicating that methanotrophy can play a substantive role in reducing net emissions. Overall, our observations show that lithalsa lakes can begin emitting CH4 and CO2 soon after they form, with effluxes of both gases that persist and increase as the permafrost continues to warm and erode.

Abstract Climate change and permafrost thaw are unlocking the vast storage of organic carbon held in northern frozen soils. Here, we evaluated the effects of thawing ice‐rich permafrost on dissolved organic matter (DOM) in freshwaters by optical analysis of 253 ponds across the circumpolar North. For a subset of waters in subarctic Quebec, we also quantified the contribution of terrestrial sources to the DOM pool by stable isotopes. The optical measurements showed a higher proportion of terrestrial carbon and a lower algal contribution to DOM in waters affected by thawing permafrost. DOM composition was largely dominated (mean of 93%) by terrestrial substances at sites influenced by thawing permafrost, while the terrestrial influence was much less in waterbodies located on bedrock (36%) or with tundra soils unaffected by thermokarst processes (42%) in the catchment. Our results demonstrate a strong terrestrial imprint on freshwater ecosystems in degrading ice‐rich permafrost catchments, and the likely shift toward increasing dominance of land‐derived organic carbon in waters with ongoing permafrost thaw.

Climate change is causing rapid permafrost degradation across Arctic and subarctic regions, resulting in changes in the size, abundance, and structure of thermokarst (thaw) ponds and lakes. The main objectives of this study were to analyze periphytic diatom communities and their affinity to vegetation substrates in thermokarst ecosystems located in the eastern Hudson Bay region and to establish a first inventory of diatom assemblages and the associated littoral vegetation in these systems. Some generalist diatom species, including Tabellaria flocculosa, occupied all ecological niches in the water bodies. In contrast, genera such as Eunotia and Pinnularia were more specialized and generally concentrated on moss substrates. Shoreline vegetation and thermokarst pond/lake littoral morphology (slope) resulted in limnological conditions that differed between sites and ultimately affected diatom community structure. Our results show that both shoreline vegetation and diatom communities are diverse in thermokarst ecosystems, and their species composition depends mostly on site-specific properties (available microhabitats, local pond/lake morphology) rather than limnological conditions that are closely aligned with regional ecoclimatic conditions.

Thermokarst lakes and ponds were sampled across a range of permafrost landscapes in subarctic Québec (Nunavik, Canada) to compare their rotifer and other zooplankton characteristics with a set of rock-basin lakes and ponds in the region. A total of 24 rotifer species were identified, with an average of seven taxa per waterbody. Rotifer abundance was an order of magnitude higher in the thaw ponds than in rock-basin waters. In some thaw ponds, rotifers accounted for >50% of the total zooplankton biomass, but for

Abstract Shallow lakes are common across the Arctic landscape and their ecosystem productivity is often dominated by benthic, cyanobacterial biofilms. Many of these water bodies freeze to the bottom and are biologically inactive during winter, but full freeze-up is becoming less common with Arctic warming. Here we analyzed the microbiome structure of newly discovered biofilms at the deepest site of a perennially ice-covered High Arctic lake as a model of polar microbial communities that remain unfrozen throughout the year. Biofilms were also sampled from the lake’s shallow moat region that melts out and refreezes to the bottom annually. Using high throughput small subunit ribosomal RNA sequencing, we found more taxonomic richness in Bacteria, Archaea and microbial eukaryotes in the perennially unfrozen biofilms compared to moat communities. The deep communities contained both aerobic and anaerobic taxa including denitrifiers, sulfate reducers, and methanogenic Archaea. The water overlying the deep biofilms was well oxygenated in mid-summer but almost devoid of oxygen in spring, indicating anoxia during winter. Seasonally alternating oxic-anoxic regimes may become increasingly widespread in polar biofilms as fewer lakes and ponds freeze to the bottom, favoring prolonged anaerobic metabolism and greenhouse gas production during winter darkness.

Permafrost science and engineering are of vital importance for northern development and climate adaptation given that buildings, roads, and other infrastructure in many parts of the Arctic depend on permafrost stability. Permafrost also has wide-ranging effects on other features of the Arctic environment including geomorphology, biogeochemical fluxes, tundra plant and animal ecology, and the functioning of lake, river, and coastal marine ecosystems. This review presents an Earth system perspective on permafrost landscapes as an approach towards integration across disciplines. The permafrost system can be described by a three-layer conceptual model, with an upper buffer layer that contains vegetation or infrastructure. Snow and liquid water strongly affect the thermal properties and stability of these layers and their associated interfaces, resulting in critical times and places for accelerated degradation of permafrost and for exchanges of mass and heat with the hydrosphere and atmosphere. Northern permafrost landscapes are now in rapid transition as a result of climate warming and socioeconomic development, which is affecting their ability to provide geosystem and ecosystem services. The Earth system approach provides a framework for identifying linkages, thresholds, and feedbacks among system components, including human systems, and for the development of management strategies to cope with permafrost change.

Permafrost thawing and erosion results in the enrichment of northern lakes by soil organic matter. These allochthonous inputs favour bacterial decomposition and may cause the draw-down of dissolved oxygen to anoxic conditions that promote methanogenesis. Our objective in the present study was to determine the seasonal variations in dissolved oxygen in a set of permafrost peatland lakes in subarctic Quebec, Canada, and to relate these changes to metabolic rates, ice cover, and mixing. The lakes had high dissolved organic carbon concentrations, and their surface waters in summer had greenhouse gas concentrations that were up to one (CO2) to three (CH4) orders of magnitude above air-equilibrium values, indicating their strongly heterotrophic character. Consistent with these observations, the peatland lakes had elevated rates of bacterial production and oxygen consumption. Continuous measurements of oxygen by in situ sensors and of ice cover by automated field cameras showed that the lakes became fully anoxic shortly after freeze-up. The waters were partially re-oxygenated by mixing events in spring and fall, but in one lake, the bottom waters remained anoxic throughout the year. These observations provide a foundation for subsequent biogeochemical and modelling studies of peatland thaw lakes as an abundant class of Arctic freshwater ecosystems

Water tracks play a major role in the headwater basin hydrology of permafrost landscapes in Alaska and Antarctica, but less is known about these features in the High Arctic. We examined the physical and hydrological properties of water tracks on Ward Hunt Island, a polar desert site in the Canadian High Arctic, to evaluate their formation process and to compare with water tracks reported elsewhere. These High Arctic water tracks flowed through soils that possessed higher near-surface organic carbon concentrations, higher water content, and coarser material than the surrounding soils. The water track morphology suggested they were initiated by a combination of sorting, differential frost heaving, and eluviation. The resultant network of soil conduits, comparable to soil pipes, dominated the hydrology of the slope. The flow of cold water through these conduits slowed down the progression of the thawing front during summer, making the active layer consistently shallower relative to adjacent soils. Water tracks on Ward Hunt Island, and in polar desert catchments with these features elsewhere in the High Arctic, strongly influence slope hydrology and active-layer properties while also affecting vegetation distribution and the quality of runoff to the downstream lake.

Permafrost thawing results in the formation of thermokarst lakes, which are biogeochemical hotspots in northern landscapes and strong emitters of greenhouse gasses to the atmosphere. Most studies of thermokarst lakes have been in summer, despite the predominance of winter and ice-cover over much of the year, and the microbial ecology of these waters under ice remains poorly understood. Here we first compared the summer versus winter microbiomes of a subarctic thermokarst lake using DNA- and RNA-based 16S rRNA amplicon sequencing and qPCR. We then applied comparative metagenomics and used genomic bin reconstruction to compare the two seasons for changes in potential metabolic functions in the thermokarst lake microbiome. In summer, the microbial community was dominated by Actinobacteria and Betaproteobacteria, with phototrophic and aerobic pathways consistent with the utilization of labile and photodegraded substrates. The microbial community was strikingly different in winter, with dominance of methanogens, Planctomycetes, Chloroflexi and Deltaproteobacteria, along with various taxa of the Patescibacteria/Candidate Phyla Radiation (Parcubacteria, Microgenomates, Omnitrophica, Aminicenantes). The latter group was underestimated or absent in the amplicon survey, but accounted for about a third of the metagenomic reads. The winter lineages were associated with multiple reductive metabolic processes, fermentations and pathways for the mobilization and degradation of complex organic matter, along with a strong potential for syntrophy or cross-feeding. The results imply that the summer community represents a transient stage of the annual cycle, and that carbon dioxide and methane production continue through the prolonged season of ice cover via a taxonomically distinct winter community and diverse mechanisms of permafrost carbon transformation.

Permafrost thaw lakes including thermokarst lakes and ponds are ubiquitous features of Subarctic and Arctic landscapes and are hotspots of microbial activity. Input of terrestrial organic matter into the planktonic microbial loop of these lakes may greatly amplify global greenhouse gas emissions. This microbial loop, dominated in the summer by aerobic microorganisms including phototrophs, is radically different in the winter, when metabolic processes shift to the anaerobic degradation of organic matter. Little is known about the viruses that infect these microbes, despite evidence that viruses can control microbial populations and influence biogeochemical cycling in other systems. Here, we present the results of a metagenomics-based study of viruses in the larger than 0.22 µm fraction across two seasons (summer and winter) in a permafrost thaw lake in Subarctic Canada. We uncovered 351 viral populations (vOTUs) in the surface waters of this lake, with diversity significantly greater during the summer. We also identified and characterized several phage genomes and prophages, which were mostly present in the summer. Finally, we compared the viral community of this waterbody to other habitats and found unexpected similarities with distant bog lakes in North America.

Thermokarst lakes are one of the most abundant types of microbial ecosystems in the circumpolar North. These shallow basins are formed by the thawing and collapse of ice-rich permafrost, with subsequent filling by snow and ice melt. Until now, permafrost thaw lakes have received little attention for isolation of microorganisms by culture-based analysis. The discovery of novel psychrophiles and their biomolecules makes these extreme environments suitable sources for the isolation of new strains, including for potential biotechnological applications. In this study, samples of bottom sediments were collected from three permafrost thaw lakes in subarctic Québec, Canada. Their diverse microbial communities were characterized by 16S rRNA gene amplicon analysis, and subsamples were cultured for the isolation of bacterial strains. Phenotypic and genetic characterization of the isolates revealed affinities to the genera Pseudomonas, Paenibacillus, Acinetobacter,Staphylococcus and Sphingomonas. The isolates were then evaluated for their production of extracellular enzymes and exopolymers. Enzymes of potential biotechnological interest included α and β-glucosidase, α and β-maltosidase, β-xylosidase and cellobiohydrolase. One isolate, Pseudomonas extremaustralis strain 2ASCA, also showed the capability to produce, in the loosely bound cell fraction, a levan-type polysaccharide with a yield of 613 mg/L of culture, suggesting its suitability as a candidate for eco-sustainable alternatives to commercial polymers.

Microbial mats are ubiquitous in polar freshwater ecosystems and sustain high concentrations of biomass despite the extreme seasonal variations in light and temperature. Here we aimed to resolve genomic adaptations for light-harvesting, bright-light protection, and carbon flow in mats that undergo seasonal freeze-up. To bracket a range of communities in shallow water habitats, we sampled cyanobacterial mats in the thawed littoral zone of two lakes situated at the northern and southern limits of the Canadian Arctic permafrost zone. We applied a multiphasic approach using pigment profiles from high performance liquid chromatography, Illumina MiSeq sequencing of the 16S and 18S rRNA genes, and metagenomic analysis. The mats shared a taxonomic and functional core microbiome, dominated by oxygenic cyanobacteria with light-harvesting and photoprotective pigments, bacteria with bacteriochlorophyll, and bacteria with light-driven Type I rhodopsins. Organisms able to use light for energy related processes represented up to 85% of the total microbial community, with 15–30% attributable to cyanobacteria and 55–70% attributable to other bacteria. The proportion of genes involved in anaplerotic CO2 fixation was greater than for genes associated with oxygenic photosynthesis. Diverse heterotrophic bacteria, eukaryotes (including metazoans and fungi) and viruses co-occurred in both communities. The results indicate a broad range of strategies for capturing sunlight and CO2, and for the subsequent flow of energy and carbon in these complex, light-driven microbial ecosystems.

The global biogeography of microorganisms remains poorly resolved, which limits the current understanding of microbial resilience toward environmental changes. Using high-throughput 16S rRNA gene amplicon sequencing, we characterized the microbial diversity of terrestrial and lacustrine biofilms from the Arctic, Antarctic and temperate regions. Our analyses suggest that bacterial community compositions at the poles are more similar to each other than they are to geographically closer temperate habitats, with 32% of all operational taxonomic units (OTUs) co-occurring in both polar regions. While specific microbial taxa were confined to distinct regions, representing potentially endemic populations, the percentage of cosmopolitan taxa was higher in Arctic (43%) than in Antarctic samples (36%). The overlap in polar microbial OTUs may be explained by natural or anthropogenically-mediated dispersal in combination with environmental filtering. Current and future changing environmental conditions may enhance microbial invasion, establishment of cosmopolitan genotypes and loss of endemic taxa.

The thawing of ice-rich permafrost soils in northern peatlands leads to the formation of thermokarst ponds, surrounded by organic-rich soils. These aquatic ecosystems are sites of intense microbial activity, and CO2 and CH4 emissions. Many of the pond systems in northern landscapes and their surrounding peatlands are hydrologically contiguous, but little is known about the microbial connectivity of concentric habitats around the thermokarst ponds, or the effects of peat accumulation and infilling on the microbial communities. Here we investigated microbial community structure and abundance in a thermokarst pond-peatland system in subarctic Canada. Several lineages were ubiquitous, supporting a prokaryotic continuum from the thermokarst pond to surrounding peatlands. However, the microbial community structure shifted from typical aerobic freshwater microorganisms (Betaproteobacteria and Alphaproteobacteria) in the pond towards acidophilic and anaerobic lineages (Acidobacteria and Choroflexi) in the connected peatland waters, likely selected by the acidification of the water by Sphagnum mosses. Marked changes in abundance and community composition of methane cycling microorganisms were detected along the thermokarst pond-peatland transects, suggesting fine tuning of C-1 carbon cycling within a highly connected system, and warranting the need for higher spatial resolution across the thermokarst landscape to accurately predict net greenhouse gas emissions from northern peatlands.

Thermokarst waterbodies caused by permafrost thawing and degradation are ubiquitous in many subarctic and Arctic regions. They are globally important components of the biogeochemical carbon cycle and have potential feedback effects on climate. These northern waters are mostly small lakes and ponds, and although they may be mapped using very high-resolution satellites or aerial photography, these approaches are generally not suitable for monitoring purposes, due to the cost and limited availability of such images. In this study we evaluated the potential use of widely available high-resolution imagery from Sentinel-2 (S2) for the characterization of the spectral reflectance of thermokarst lakes and ponds. Specifically, we aimed to define the minimum lake area that could be reliably imaged, and to identify challenges and solutions for remote sensing of such waters in the future. The study was conducted in subarctic Canada, in the vicinity of Whapmagoostui-Kuujjuarapik (Nunavik, Québec), an area in the sporadic permafrost zone with numerous thermokarst waterbodies that vary greatly in size. Ground truthing lake reflectance data were collected using an Unmanned Aerial System (UAS) fitted with a multispectral camera that collected images at 13 cm resolution. The results were compared with reflectance from Sentinel-2 images, and the effect of lake area on the reflectance response was assessed. Our results show that Sentinel-2 imagery was suitable for waterbodies larger than 350 m2 once their boundaries were defined, which in the two test sites would allow monitoring from 11% to 30% of the waterbodies and 73% to 85% of the total lake area. Challenges for remote sensing of small lakes include the confounding effects of water reflection (both direct radiation and diffuse), wind and shadow. Given the small threshold area and frequent revisit time, Sentinel-2 provides a valuable approach towards the continuous monitoring of waterbodies, including ponds and small lakes such as those found in thermokarst landscapes. UASs provide a complementary approach for ground truthing and boundary definition.

The global latitudinal gradient in biodiversity weakens in the high polar biome and so an alternative explanation for distribution of Arctic and Antarctic photoautotrophs is required. Here we identify how temporal, microclimate and evolutionary drivers of biogeography are important, rather than the macroclimate features that drive plant diversity patterns elsewhere. High polar ecosystems are biologically unique, with a more central role for bryophytes, lichens and microbial photoautotrophs over that of vascular plants. Constraints on vascular plants arise mainly due to stature and ontogenetic barriers. Conversely non-vascular plant and microbial photoautotroph distribution is correlated with favourable microclimates and the capacity for poikilohydric dormancy. Contemporary distribution also depends on evolutionary history, with adaptive and dispersal traits as well as legacy influencing biogeography. We highlight the relevance of these findings to predicting future impacts on polar plant diversity and to the current status of plants in Arctic and Antarctic conservation policy frameworks.

Permafrost thawing leads to the formation of thermokarst ponds that potentially emit CO2 and CH4 to the atmosphere. In the Nunavik subarctic region (northern Quebec, Canada), these numerous, shallow ponds become well stratified during summer. This creates a physico-chemical gradient of temperature and oxygen, with an upper oxic layer and a bottom low-oxygen or anoxic layer. Our objective was to determine the influence of stratification and related limnological and landscape properties on the community structure of potentially active bacteria in these waters. Samples for RNA analysis were taken from ponds in three contrasting valleys across a gradient of permafrost degradation. A total of 1296 operational taxonomic units were identified by high-throughput amplicon sequencing, targeting bacterial 16S rRNA that was reverse transcribed to cDNA. β-proteobacteria were the dominant group in all ponds, with highest representation by the genera Variovorax and Polynucleobacter. Methanotrophs were also among the most abundant sequences at most sites. They accounted for up to 27 % of the total sequences (median of 4.9 % for all samples), indicating the importance of methane as a bacterial energy source in these waters. Both oxygenic (cyanobacteria) and anoxygenic (Chlorobi) phototrophs were also well represented, the latter in the low oxygen bottom waters. Ordination analyses showed that the communities clustered according to valley and depth, with significant effects attributed to dissolved oxygen, pH, dissolved organic carbon and total suspended solids. These results indicate that the bacterial assemblages of permafrost thaw ponds are filtered by environmental gradients, and are complex consortia of functionally diverse taxa that likely affect the composition as well as magnitude of greenhouse gas emissions from these abundant waters.

Cyanobacterial mats are often a major biological component of extreme aquatic ecosystems, and in polar lakes and streams they may account for the dominant fraction of total ecosystem biomass and productivity. In this study we examined the vertical structure and physiology of Arctic microbial mats relative to the question of how these communities may respond to ongoing environmental change. The mats were sampled from Ward Hunt Lake at the northern coast of Arctic Canada, and were composed of three visibly distinct layers. Microsensor profiling showed that there were strong gradients in oxygen within each layer, with an overall decrease from 100 % saturation at the mat surface to 0 %, at the bottom, accompanied by an increase of 0.6 pH units down the profile. 16S rRNA gene clone libraries revealed the presence of Oscillatorian sequences throughout the mat, while Nostoc related species dominated the two upper layers, and Nostocales and Synechococcales sequences were common in the bottom layer. HPLC analyses showed a parallel gradient in pigments, from high concentrations of scytonemin in the upper layer to increasing zeaxanthin and myxoxanthin in the bottom layer, and an overall shift from photoprotective to photosynthetic carotenoids down the profile. Climate change is likely to be accompanied by increased evaporation and osmotic stress of the littoral mat communities. To assess their capacity to adjust to rising osmolarities, mat sections were exposed to a gradient of increasing salinities, and PAM measurements of in vivo chlorophyll fluorescence were made to assess changes in maximum quantum yield. The results showed that the mats were tolerant of up to a 46-fold increase in salinity. These features imply that cyanobacterial mats are resilient to ongoing climate change, and that in the absence of major biological perturbations, these vertically structured communities will continue to be a prominent feature of polar aquatic ecosystems.