Genetic and morphologic determination of diatom community composition in surface sediments from glacial and thermokarst lakes in the Siberian Arctic

Lakes cover large parts of the climatically sensitive Arctic landscape and respond rapidly to environmental change. Arctic lakes have different origins and include the predominant thermokarst lakes, which are small, young and highly dynamic, as well as large, old and stable glacial lakes. Freshwater diatoms dominate the primary producer community in these lakes and can be used to detect biotic responses to climate and environmental change. We used specific diatom metabarcoding on sedimentary DNA, combined with next-generation sequencing and diatom morphology, to assess diatom diversity in five glacial and 15 thermokarst lakes within the easternmost expanse of the Siberian treeline ecotone in Chukotka, Russia. We obtained 163 verified diatom sequence types and identified 176 diatom species morphologically. Although there were large differences in taxonomic assignment using the two approaches, they showed similar high abundances and diversity of Fragilariceae and Aulacoseiraceae. In particular, the genetic approach detected hidden within-lake variations of fragilarioids in glacial lakes and dominance of centric Aulacoseira species, whereas Lindavia ocellata was predominant using morphology. In thermokarst lakes, sequence types and valve counts also detected high diversity of Fragilariaceae, which followed the vegetation gradient along the treeline. Ordination analyses of the genetic data from glacial and thermokarst lakes suggest that concentrations of sulfate, an indicator of the activity of sulfate-reducing microbes under anoxic conditions, and bicarbonate, which relates to surrounding vegetation, have a significant influence on diatom community composition. For thermokarst lakes, we also identified lake depth as an important variable, but sulfate best explains diatom diversity derived from genetic data, whereas bicarbonate best explains the data from valve counts. Higher diatom diversity was detected in glacial lakes, most likely related to greater lake age and different edaphic settings, which gave rise to diversification and endemism. In contrast, small, dynamic thermokarst lakes are inhabited by stress-tolerant fragilarioids and are related to different vegetation types along the treeline ecotone. Our study demonstrated that genetic investigations of lake sediments can be used to interpret climate and environmental responses of diatoms. It also showed how lake type affects diatom diversity, and that such genetic analyses can be used to track diatom community changes under ongoing warming in the Arctic

Paleo-Ecology of the Yedoma Ice Complex on Sobo-Sise Island (Eastern Lena Delta, Siberian Arctic)

Late Pleistocene permafrost of the Yedoma type constitutes a valuable paleo-environmental archive due to the presence of numerous and well-preserved floral and faunal fossils. The study of the fossil Yedoma inventory allows for qualitative and quantitative reconstructions of past ecosystem and climate conditions and variations over time. Here, we present the results of combined paleo-proxy studies including pollen, chironomid, diatom and mammal fossil analyses from a prominent Yedoma cliff on Sobo-Sise Island in the eastern Lena Delta, NE Siberia to complement previous and ongoing paleo-ecological research in western Beringia. The Yedoma Ice Complex (IC) cliff on Sobo-Sise Island (up to 28 m high, 1.7 km long) was continuously sampled at 0.5 m resolution. The entire sequence covers the last about 52 cal kyr BP, but is not continuous as it shows substantial hiatuses at 36–29 cal kyr BP, at 20–17 cal kyr BP and at 15–7 cal kyr BP. The Marine Isotope Stage (MIS) 3 Yedoma IC (52–28 cal kyr BP) pollen spectra show typical features of tundra–steppe vegetation. Green algae remains indicate freshwater conditions. The chironomid assemblages vary considerably in abundance and diversity. Chironomid-based TJuly reconstructions during MIS 3 reveal warmer-than-today TJuly at about 51 cal kyr BP, 46-44 and 41 cal kyr BP. The MIS 2 Yedoma IC (28–15 cal kyr BP) pollen spectra represent tundra-steppe vegetation as during MIS 3, but higher abundance of Artemisia and lower abundances of algae remains indicate drier summer conditions. The chironomid records are poor. The MIS 1 (7–0 cal kyr BP) pollen spectra indicate shrub-tundra vegetation. The chironomid fauna is sparse and not diverse. The chironomid-based TJuly reconstruction supports similar-as-today temperatures at 6.4–4.4 cal kyr BP. Diatoms were recorded only after about 6.4 cal kyr BP. The Sobo-Sise Yedoma record preserves traces of the West Beringian tundra-steppe that maintained the Mammoth fauna including rare evidence for woolly rhinoceros’ presence. Chironomid-based TJuly reconstructions complement previous plant-macrofossil based TJuly of regional MIS 3 records. Our study from the eastern Lena Delta fits into and extends previous paleo-ecological Yedoma studies to characterize Beringian paleo-environments in the Laptev Sea coastal region

Impact of climate change and industrialization on remote Lake Bolshoe Toko, Siberia 

&amp;lt;p&amp;gt;To test if recent climate change and pollution affected remote lake ecosystems without direct human influence, we used paleolimnological methods on lake sediments from a large, prestine, and deep lake in Yakutia, Russia. We compared diatoms and sediment-geochemistry from before and after the onset of industrialization in the mid-nineteenth century, at water depths between 12.1 and 68.3 m in Lake Bolshoe Toko. We analyzed diatom species changes and geochemical changes including mercury concentrations. Chronologies were established using &amp;lt;sup&amp;gt;210&amp;lt;/sup&amp;gt;Pb and &amp;lt;sup&amp;gt;137&amp;lt;/sup&amp;gt;Cs revealing sedimentation rates between 0.018 and 0.033 cm y&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at shallow- and deep-water sites, respectively. Increase in light planktonic diatoms (&amp;lt;em&amp;gt;Cyclotella&amp;lt;/em&amp;gt;) and decrease in heavily silicified euplanktonic &amp;lt;em&amp;gt;Aulacoseira&amp;lt;/em&amp;gt; through time at deep-water sites can be related to warming air temperatures and shorter periods of lake-ice cover, causing pronounced thermal stratification. Diatom beta diversity changed only significantly in shallow-water communities which can be related to the development of new habitats with macrophyte growth. Mercury concentrations increased by a factor of 1.6 as a result of atmospheric fallout. Increases in the chrysophyte &amp;lt;em&amp;gt;Mallomonas&amp;lt;/em&amp;gt; indicates a trend towards acidification. We conclude that also remote boreal lakes are susceptible to human-induced long-distance pollution and recent climate change.&amp;lt;/p&amp;gt;</jats:p

Effects of climate change and industrialization on Lake Bolshoe Toko, eastern Siberia

AbstractIndustrialization in the Northern Hemisphere has led to warming and pollution of natural ecosystems. We used paleolimnological methods to explore whether recent climate change and/or pollution had affected a very remote lake ecosystem, i.e. one without nearby direct human influence. We compared sediment samples that date from before and after the onset of industrialization in the mid-nineteenth century, from four short cores taken at water depths between 12.1 and 68.3 m in Lake Bolshoe Toko, eastern Siberia. We analyzed diatom assemblage changes, including diversity estimates, in all four cores and geochemical changes (mercury, nitrogen, organic carbon) from one core taken at an intermediate water depth. Chronologies for two cores were established using 210Pb and 137Cs. Sedimentation rates were 0.018 and 0.033 cm year−1 at the shallow- and deep-water sites, respectively. We discovered an increase in light planktonic diatoms (Cyclotella) and a decrease in heavily silicified euplanktonic Aulacoseira through time at deep-water sites, related to more recent warmer air temperatures and shorter periods of lake-ice cover, which led to pronounced thermal stratification. Diatom beta diversity in shallow-water communities changed significantly because of the development of new habitats associated with macrophyte growth. Mercury concentrations increased by a factor of 1.6 since the mid-nineteenth century as a result of atmospheric fallout. Recent increases in the chrysophyte Mallomonas in all cores suggested an acidification trend. We conclude that even remote boreal lakes are susceptible to the effects of climate change and human-induced pollution.</jats:p

Late Glacial and Holocene vegetation and lake changes in SW Yakutia, Siberia, inferred from sedaDNA, pollen, and XRF data

Only a few palaeo-records extend beyond the Holocene in Yakutia, eastern Siberia, since most of the lakes in the region are of Holocene thermokarst origin. Thus, we have a poor understanding of the long-term interactions between terrestrial and aquatic ecosystems and their response to climate change. The Lake Khamra region in southwestern Yakutia is of particular interest because it is in the transition zones from discontinuous to sporadic permafrost and from summergreen to evergreen boreal forests. Our multiproxy study of Lake Khamra sediments reaching back to the Last Glacial Maximum 21 cal ka BP, includes analyses of organic carbon, nitrogen, XRF-derived elements, sedimentary ancient DNA amplicon sequencing of aquatic and terrestrial plants and diatoms, as well as classical counting of pollen and non-pollen palynomorphs (NPP). The palaeogenetic approach revealed 45 diatom, 191 terrestrial plant, and 65 aquatic macrophyte taxa. Pollen analyses identified 34 pollen taxa and 28 NPP taxa. The inferred terrestrial ecosystem of the Last Glacial comprises tundra vegetation dominated by forbs and grasses, likely inhabited by megaherbivores. By 18.4 cal ka BP a lake had developed with a high abundance of macrophytes and dominant fragilarioid diatoms, while shrubs expanded around the lake. In the Bølling-Allerød at 14.7 cal ka BP both the terrestrial and aquatic systems reflect climate amelioration, alongside lake water-level rise and woodland establishment, which was curbed by the Younger Dryas cooling. In the Early Holocene warmer and wetter climate led to taiga development and lake water-level rise, reflected by diatom composition turnover from only epiphytic to planktonic diatoms. In the Mid-Holocene the lake water level decreased at ca. 8.2 cal ka BP and increased again at ca. 6.5 cal ka BP. At the same time mixed evergreen-summergreen forest expanded. In the Late Holocene, at ca. 4 cal ka BP, vegetation cover similar to modern conditions established. This study reveals the long-term shifts in aquatic and terrestrial ecosystems and a comprehensive understanding of lake development and catchment history of the Lake Khamra region.</jats:p

Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA

Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate

Dispersal distances and migration rates at the arctic treeline in Siberia – a genetic and simulation-based study

A strong temperature increase in the Arctic is expected to lead to latitudinal treeline shift. This tundra–taiga turnover would cause a positive vegetation–climate feedback due to albedo decrease. However, reliable estimates of tree migration rates are currently lacking due to the complex processes involved in forest establishment, which depend strongly on seed dispersal. We aim to fill this gap using LAVESI, an individual-based and spatially explicit Larix vegetation simulator. LAVESI was designed to simulate plots within homogeneous forests. Here, we improve the implementation of the seed dispersal function via field-based investigations. We inferred the effective seed dispersal distances of a typical open-forest stand on the southern Taymyr Peninsula (northern central Siberia) from genetic parentage analysis using eight nuclear microsatellite markers. The parentage analysis gives effective seed dispersal distances (median ∼10&thinsp;m) close to the seed parents. A comparison between simulated and observed effective seed dispersal distances reveals an overestimation of recruits close to the releasing tree and a shorter dispersal distance generally. We thus adapted our model and used the newly parameterised version to simulate south-to-north transects; a slow-moving treeline front was revealed. The colonisation of the tundra areas was assisted by occasional long-distance seed dispersal events beyond the treeline area. The treeline (∼1&thinsp;tree&thinsp;ha−1) advanced by ∼1.6&thinsp;m&thinsp;yr−1, whereas the forest line (∼100&thinsp;trees&thinsp;ha−1) advanced by only ∼0.6&thinsp;m&thinsp;yr−1. We conclude that the treeline in northern central Siberia currently lags behind the current strong warming and will continue to lag in the near future.</p

Paleo-Ecology of the Yedoma Ice Complex on Sobo-Sise Island (EasternLena Delta, Siberian Arctic)

Late Pleistocene permafrost of the Yedoma type constitutes a valuable paleo-environmental archive due to the presence of numerous and well-preserved floral and faunal fossils. The study of the fossil Yedoma inventory allows for qualitative and quantitative reconstructions of past ecosystem and climate conditions and variations over time. Here, we present the results of combined paleo-proxy studies including pollen, chironomid, diatom and mammal fossil analyses from a prominent Yedoma cliff on Sobo-Sise Island in the eastern Lena Delta, NE Siberia to complement previous and ongoing paleo-ecological research in western Beringia. The Yedoma Ice Complex (IC) cliff on Sobo-Sise Island (up to 28 m high, 1.7 km long) was continuously sampled at 0.5 m resolution. The entire sequence covers the last about 52 cal kyr BP, but is not continuous as it shows substantial hiatuses at 36–29 cal kyr BP, at 20–17 cal kyr BP and at 15–7 cal kyr BP. The Marine Isotope Stage (MIS) 3 Yedoma IC (52–28 cal kyr BP) pollen spectra show typical features of tundra–steppe vegetation. Green algae remains indicate freshwater conditions. The chironomid assemblages vary considerably in abundance and diversity. Chironomid-based TJuly reconstructions during MIS 3 reveal warmer-than-today TJuly at about 51 cal kyr BP, 46-44 and 41 cal kyr BP. The MIS 2 Yedoma IC (28–15 cal kyr BP) pollen spectra represent tundra-steppe vegetation as during MIS 3, but higher abundance of Artemisia and lower abundances of algae remains indicate drier summer conditions. The chironomid records are poor. The MIS 1 (7–0 cal kyr BP) pollen spectra indicate shrub-tundra vegetation. The chironomid fauna is sparse and not diverse. The chironomid-based TJuly reconstruction supports similar-as-today temperatures at 6.4–4.4 cal kyr BP. Diatoms were recorded only after about 6.4 cal kyr BP. The Sobo-Sise Yedoma record preserves traces of the West Beringian tundra-steppe that maintained the Mammoth fauna including rare evidence for woolly rhinoceros’ presence. Chironomid-based TJuly reconstructions complement previous plant-macrofossil based TJuly of regional MIS 3 records. Our study from the eastern Lena Delta fits into and extends previous paleo-ecological Yedoma studies to characterize Beringian paleo-environments in the Laptev Sea coastal region

Multi-omics for studying and understanding polar life

Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss ‘omics’ approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain

Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.</jats:p