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

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

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

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

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 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 tree/ha) advanced by ∼1.6 m/yr, whereas the forest line (∼100trees/ha) advanced by only ∼0.6m/yr. 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

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

Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: Overview and prospects

Alpine ecosystems on the Tibetan Plateau are being threatened by ongoing climate warming and intensified human activities. Ecological time-series obtained from sedimentary ancient DNA (sedaDNA) are essential for understanding past ecosystem and biodiversity dynamics on the Tibetan Plateau and their responses to climate change at a high taxonomic resolution. Hitherto only few but promising studies have been published on this topic. The potential and limitations of using sedaDNA on the Tibetan Plateau are not fully understood. Here, we (i) provide updated knowledge of and a brief introduction to the suitable archives, region-specific taphonomy, state-of-the-art methodologies, and research questions of sedaDNA on the Tibetan Plateau; (ii) review published and ongoing sedaDNA studies from the Tibetan Plateau; and (iii) give some recommendations for future sedaDNA study designs. Based on the current knowledge of taphonomy, we infer that deep glacial lakes with freshwater and high clay sediment input, such as those from the southern and southeastern Tibetan Plateau, may have a high potential for sedaDNA studies. Metabarcoding (for microorganisms and plants), metagenomics (for ecosystems), and hybridization capture (for prehistoric humans) are three primary sedaDNA approaches which have been successfully applied on the Tibetan Plateau, but their power is still limited by several technical issues, such as PCR bias and incompleteness of taxonomic reference databases. Setting up high-quality and open-access regional taxonomic reference databases for the Tibetan Plateau should be given priority in the future. To conclude, the archival, taphonomic, and methodological conditions of the Tibetan Plateau are favorable for performing sedaDNA studies. More research should be encouraged to address questions about long-term ecological dynamics at ecosystem scale and to bring the paleoecology of the Tibetan Plateau into a new era

Strengthening global-change science by integrating aeDNA with paleoecoinformatics

Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes