Modern and ancient DNA in lacustrine sediments – Vegetation signals unraveled

Current climatic changes, mostly triggered by global warming, influence broad parts of the northern latitudes all over the world, and reliable assessments of present and past vegetation are highly relevant to predict the future development of Arctic ecosystems. The northernmost Siberian arcto-boreal treeline areas in the Taymyr lowlands may be particularly affected by climatic changes, with latitudinal shifts of the treeline ecotone and resulting vegetation changes from tundra to taiga. Obtaining reliable information about present vegetation composition in such remote arctic locations is difficult, as vegetation surveys in the field can typically only be carried out during brief visits, and the flowering season is short. Although these techniques are time consuming, methods like vegetation assessment by ground surveys or palynological analyses are common tools to evaluate floral composition and provide valuable, complimentary information. While vegetation surveys mainly provide information about the status quo, pollen analyses also allow investigation of vegetation back in time. In recent years, sedimentary DNA has emerged as an additional and effective tool to improve knowledge about past vegetation. DNA metabarcoding of lake sediments and sediment cores has become more and more relevant as a tool for such research, but an explicit assessment of lake sediment DNA data in comparison to data obtained from pollen and vegetation surveys is still lacking. Here, we present a study comparing these three vegetation assessment methods for 31 lakes within a 300 km transect in arctic Siberia, reaching from Tundra, through the treeline area, to the light Taiga. Surface sediments of lakes were taken, subsampled for DNA and pollen analyses and processed in the respective laboratories. Together with six representative vegetation surveys, we present results of this comparative study. Our results show that taxa assigned by DNA sequence analyses are comparable to those found in the pollen and vegetation analyses. Overall, the DNA provides a higher taxonomical level of identification, while the pollen grains mainly identify to genus level. Compared to the vegetation survey, pollen and DNA provide more information, as they are able to track vegetation elements, which could not been surveyed at the time of the year the surveys were carried out. The results show that the combination and comparison of pollen, DNA and vegetation seems to serve as a calibration set for future investigations of such remote and highly dynamic ecosystems. Our investigation draws a multidisciplinary, comprehensive image of the current composition of the Siberian lowland vegetation by combining well established and promising, newly emerging methods

Characterisation of East Siberian paleodiversity based on ancient DNA analyses of the Batagay megaslump exposure

With the ongoing Arctic warming, permafrost thaw accelerated during the last decade as much as it is now a global concern for biodiversity loss, food webs and biogeochemical cycling. This rapid permafrost degradation forms features such as massive retrogressive thaw slumps that give access to exceptional records for Quaternary biodiversity change investigations. The Batagay megaslump located in northern Yakutia, East Siberia, is the world’s largest thawslump known to date, and along its ~55m high headwall it gives access to Late and Mid Pleistocene permafrost deposits up to more than 500 kyrs in age. During an expedition to this unique site in 2017, sediment samples were collected with ages from more than 500 kyrs to modern time for the analysis of ancient DNA (aDNA). Our aim is to characterise the biodiversity and changes over geological timescales of this region in East Siberia. Using the aDNA extracted from these ancient environmental samples, we first performed a metabarcoding analysis (chloroplast trnL) to investigate past vegetation composition. We then performed a shotgun metagenomic analysis, which enabled a much higher depth of sequence data and allowed us to access the entire biodiversity, from Eukaryotes to Prokaryotes, Archaea and Viruses. This approach opened up new horizons, making it possible not only to investigate biodiversity composition and changes but also to infer on potential interactions across taxa and kingdoms. Both methods together allowed comparison and ensured robustness of the results obtained. We present here one of the very first studies done on the global, past and modern, biodiversity of permafrost regions which holds an enormous potential to reveal new insights into the evolution of this fragile ecosystem

The microbiome of ancient ice wedges in the Muostakh ‘disappearing island’

Climate change-driven thermal erosion makes Muostakh Island in the southern Laptev Sea (70°35´ N, 130° 0´ E) a very fragile ecosystem of the Arctic. Thus, understanding its biodiversity, the changes and loss in response to climate is a timely and pressing scientific objective. Here, we characterize the microbiome associated with several ice wedges covering the past ~45,000 years of climate/ecosystem history. Ice wedges are a specific feature in the northern permafrost landscapes. They develop seasonally by spring-melting of snow that runs through permafrost contraction cracks, accumulates and creates ice formations in the wintertime through congelifraction. Such environment offers ideal conditions for the preservation of microbial cells and DNA over geological time. Our work tackles four main research aspects, requiring an interdisciplinary approach with synergies between microbial ecology, geo- and paleo-sciences. First, we characterize the ice wedge mineral composition as an environmental micro-niche. Second, we analyze the biodiversity of the microbial communities via shotgun metagenomics of the ancient DNA (aDNA) extracted from the ice wedges. Third, we investigate the biomass content by recovering and enumerating microbial cells present in the ice wedges. In addition, we apply infrared spectroscopy to obtain cellular fingerprints that can serve as biomarkers. Finally, we assess the physiological state of microorganisms using stable isotope probing (SIP) experiments in microcosms that reproduce the environmental conditions (subzero temperature and anoxic conditions). By integrating microbial biodiversity with activity and environmental context, this study will provide valuable new insights into Muostakh’s ice wedge microbiome and the dynamics underlying its changes over time and climatic conditions

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

The Arctic treeline ecotone is characterised by a steep vegetation gradient from arctic tundra to northern taiga forests, which is thought to influence the water chemistry of thermokarst lakes in this region. Environmentally sensitive diatoms respond to such ecological changes in terms of variation in diatom diversity and richness, which so far has only been documented by microscopic surveys. We applied next-generation sequencing to analyse the diatom composition of lake sediment DNA extracted from 32 lakes across the treeline in the Katanga region, Siberia, using a short fragment of the rbcL chloroplast gene as a genetic barcode. We compared diatom richness and diversity obtained from the genetic approach with diatom counts from traditional microscopic analysis. Both datasets were employed to investigate diversity and relationships with environmental variables, using ordination methods. Aftereffective filtering of the raw data, the two methods gave similar results for diatom richness and composition at the genus level (DNA 12 taxa; morphology 19 taxa), even though there was a much higher absolute number of sequences obtained per genetic sample (median 50,278), compared with microscopic counts (median 426). Dissolved organic carbon explained the highest percentage of variance in both datasets (14.2 % DNA; 18.7 % morphology), reflecting the compositional turnover of diatom assemblages along the tundra-taiga transition. Differences between the two approaches are mostly a consequence of the filtering process of genetic data and limitations of genetic references in the database, which restricted the determination of genetically identified sequence types to the genus level. The morphological approach, however, allowed identifications mostly to species level, which permits better ecological interpretation of the diatom data. Nevertheless, because of a rapidly increasing reference database, the genetic approach with sediment DNA will, in the future, enable reliable investigations of diatom composition from lake sediments that will have potential applications in both paleoecology and environmental monitoring

Siberian treeline dynamics in a warming climate - results from larch population genetics and vegetation modelling

A vegetation change from open tundra to dense taiga will fuel the global warming by positive feedback caused by albedo decreases. Yet, it is unclear how fast the arctic treeline, formed of Larix species, will advance north in the next decades. The most determinant factor of tree migration is the ability to disperse seeds (and pollen). Hence, to realistically forecast the migration of tree species in a dynamic vegetation model, it is crucial to incorporate reliable estimates of dispersal. Classical methods, for example counting seeds in seed traps, have been used to describe local dispersal abilities but are not applicable to give precise estimates on rare long-distance dispersal events. In this study we overcome this with the help of modern molecular techniques. By using a set of 16 nuclear microsatellites we inferred the cryptic signal of heritage among larch individuals to study the migration history among well-established tree stands and for different time-cohorts. We analyzed the genetic structure of larch populations for several latitudinal transects spanning north-to-south from tundra to open taiga forests in Siberia and additionally of several age cohorts which established throughout the last century in prevailing cold and warm periods. Finally, we present the results of simulations with our individual-based model LAVESI which was developed by us originally to study population dynamics of larch forest stands. Using downscaled global climate models and 'representative carbon pathway' (RCP) scenarios it is feasible to project the future treeline in Siberia

Changes in the composition of marine and sea-ice diatoms derived from sedimentary ancient DNA of the eastern Fram Strait over the past 30 000 years

The Fram Strait is an area with a relatively low and irregular distribution of diatom microfossils in surface sediments, and thus microfossil records are scarce, rarely exceed the Holocene, and contain sparse information about past richness and taxonomic composition. These attributes make the Fram Strait an ideal study site to test the utility of sedimentary ancient DNA (sedaDNA) metabarcoding. Amplifying a short, partial rbcL marker from samples of sediment core MSM05/5-712-2 resulted in 95.7 % of our sequences being assigned to diatoms across 18 different families, with 38.6 % of them being resolved to species and 25.8 % to genus level. Independent replicates show a high similarity of PCR products, especially in the oldest samples. Diatom sedaDNA richness is highest in the Late Weichselian and lowest in Mid- and Late Holocene samples. Taxonomic composition is dominated by cold-water and sea-ice-associated diatoms and suggests several reorganisations – after the Last Glacial Maximum, after the Younger Dryas, and after the Early and after the Mid-Holocene. Different sequences assigned to, amongst others, Chaetoceros socialis indicate the detectability of intra-specific diversity using sedaDNA. We detect no clear pattern between our diatom sedaDNA record and the previously published IP25 record of this core, although proportions of pennate diatoms increase with higher IP25 concentrations and proportions of Nitzschia cf. frigida exceeding 2 % of the assemblage point towards past sea-ice presence

Long-term thermokarst lake development and internal ecological feedbacks: A new reconstruction from Lake Satagay (Yakutia, Siberia)

The permafrost-shaped landscape of Central Yakutia is particularly rich in thermokarst lakes, which provide important cultural and ecosystem services to the local population. Climate warming and an intensification of agriculture in alaas systems (i.e. mostly drained basins of large thaw lakes formed during the early Holocene under warm climatic conditions) in the Central Yakutian Lowlands may lead to pronounced changes in water resources, water quality, nutrient loading and biodiversity. This could in turn threaten the livelihoods of affected communities, who depend on functional alaas ecosystems. To better foresee potential future impacts of environmental changes on internal lake ecological processes, it is important to gain a better understanding of how thermokarst lakes reacted to such changes in the past. Here, we present a new paleoenvironmental reconstruction of ecological changes within Lake Satagay (N 63.078, E 117.998, Nyurbinsky District), covering the last ca. 10,800 years. We use sedimentological and XRF-derived geochemical parameters, in addition to the metabarcoding of sedimentary ancient DNA (sedDNA) for diatoms and aquatic plants, and microscopic diatom analyses, to evaluate sedimentological and biodiversity shifts throughout the Holocene. Our study revealed 53 diatom DNA sequence types and 53 species morphologically. High distributions of Stephanodiscus and Fragilaria, among multiple other diatom genera in the early Holocene, indicate that initial formation of this typical alaas lake occurred earlier than expected (i.e. before 10,800 BP). In recent millennia diatom abundance decreased and their community is almost exclusively composed of Pseudostaurosira and Fragilaria. Composition of aquatic plants show an overall dominance of Ceratophyllaceae and strong fluctuations in Potamogetonaceae likely related to lake level and water chemical changes. All proxies investigated support that lake conditions and biotic composition has been resilient since 4,000 BP, but youngest samples since 47 BP indicate that land use influence has been crucial for the lake quality. This study represents a step towards a better understanding of climate and human-impacted alaas lake development and its consequences for their ecosystem services in eastern Siberia in the near future

Environmental DNA of aquatic macrophytes: The potential for reconstructing past and present vegetation and environments

1. Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Macrophytes are especially good environmental indicators, thus their environmental DNA palaeorecord might shed light on past postglacial environments. 2. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches. 3. We find that, with state-of-the-art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast trnL (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made. 4. From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physicochemical conditions. 5. Combined with the availability of near-exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial communities of aquatic macrophytes

Diatom responses and geochemical feedbacks to environmental changes at Lake Rauchuagytgyn (Far East Russian Arctic)

This study is based on multiproxy data gained from a 14C-dated 6.5 m long sediment core and a 210Pb-dated 23 cm short core retrieved from Lake Rauchuagytgyn in Chukotka, Arctic Russia. Our main objectives are to reconstruct the environmental history and ecological development of the lake during the last 29 kyr and to investigate the main drivers behind bioproduction shifts. The methods comprise age-modeling, accumulation rate estimation, and light microscope diatom species analysis of 74 samples, as well as organic carbon, nitrogen, and mercury analysis. Diatoms have appeared in the lake since 21.8 ka cal BP and are dominated by planktonic Lindavia ocellata and L. cyclopuncta. Around the Pleistocene–Holocene boundary, other taxa including planktonic Aulacoseira, benthic fragilarioid (Staurosira), and achnanthoid species increase in their abundance. There is strong correlation between variations of diatom valve accumulation rates (DARs; mean 176.1×109 valves m2 a1), organic carbon accumulation rates (OCARs; mean 4.6 g m−2 a−1), and mercury accumulation rates (HgARs; mean 63.4 µg m−2 a−1). We discuss the environmental forcings behind shifts in diatom species and find moderate responses of key taxa to the cold glacial period, postglacial warming, the Younger Dryas, and the Holocene Thermal Maximum. The short-core data likely suggest recent change of the diatom community at the beginning of the 20th century related to human-induced warming but only little evidence of atmospheric deposition of contaminants. Significant correlation between DAR and OCAR in the Holocene interglacial indicates within-lake bioproduction represents bulk organic carbon deposited in the lake sediment. During both glacial and interglacial episodes HgAR is mainly bound to organic matter in the lake associated with biochemical substrate conditions. There were only ambiguous signs of increased HgAR during the industrialization period. We conclude that if increased short-term emissions are neglected, pristine Arctic lake systems can potentially serve as long-term CO2 and Hg sinks during warm climate episodes driven by insolation-enhanced within-lake primary productivity. Maintaining intact natural lake ecosystems should therefore be of interest to future environmental policy

Holocene wildfire and vegetation dynamics in Central Yakutia, Siberia, reconstructed from lake-sediment proxies

Wildfires play an essential role in the ecology of boreal forests. In eastern Siberia, fire activity has been increasing in recent years, challenging the livelihoods of local communities. Intensifying fire regimes also increase disturbance pressure on the boreal forests, which currently protect the permafrost beneath from accelerated degradation. However, long-term relationships between changes in fire regime and forest structure remain largely unknown. We assess past fire-vegetation feedbacks using sedimentary proxy records from Lake Satagay, Central Yakutia, Siberia, covering the past c. 10,800 years. Results from macroscopic and microscopic charcoal analyses indicate high amounts of burnt biomass during the Early Holocene, and that the present-day, low-severity surface fire regime has been in place since c. 4,500 years before present. A pollen-based quantitative reconstruction of vegetation cover and a terrestrial plant record based on sedimentary ancient DNA metabarcoding suggest a pronounced shift in forest structure toward the Late Holocene. Whereas the Early Holocene was characterized by postglacial open larch-birch woodlands, forest structure changed toward the modern, mixed larch-dominated closed-canopy forest during the Mid-Holocene. We propose a potential relationship between open woodlands and high amounts of burnt biomass, as well as a mediating effect of dense larch forest on the climate-driven intensification of fire regimes. Considering the anticipated increase in forest disturbances (droughts, insect invasions, and wildfires), higher tree mortality may force the modern state of the forest to shift toward an open woodland state comparable to the Early Holocene. Such a shift in forest structure may result in a positive feedback on currently intensifying wildfires. These new long-term data improve our understanding of millennial-scale fire regime changes and their relationships to changes of vegetation in Central Yakutia, where the local population is already being confronted with intensifying wildfire seasons