Description: The Arctic treeline ecotone is characterized by a steep vegetation gradient from arctic tundra to northerntaiga 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 diatomdiversity and richness, which so far has only been documented by microscopic surveys. We applied nextgenerationsequencing to analyse the diatom composition of lake sediment DNA extracted from 32 lakesacross the treeline in the Khatanga region, Siberia, using a short fragment of the rbcL chloroplast gene as agenetic barcode. We compared diatom richness and diversity obtained from the genetic approach withdiatom counts from traditional microscopic analysis. Both datasets were employed to investigate diversityand relationships with environmental variables, using ordination methods. After effective filtering of theraw 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 sequencesobtained per genetic sample (median 50,278), compared with microscopic counts (median 426). Dissolvedorganic 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-taigatransition. Differences between the two approaches are mostly a consequence of the filtering process ofgenetic data and limitations of genetic references in the database, which restricted the determination ofgenetically identified sequence types to the genus level. The morphological approach, however, allowedidentifications 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 DNAwill, in the future, enable reliable investigations of diatom composition from lake sediments that will havepotential applications in both paleoecology and environmental monitoring.

Description: 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.

Description: The Arctic treeline ecotone is a large environmental gradient covering a vast area in Siberia. It sensitively reacts to changes in the environment, which is observable, for instance, in he responding vegetation. The vegetation across the treeline is known to influence the water chemistry of thermokarst lakes in this region. Sensitive algae, such as diatoms, respond to these changes and thus, diatom compositions correlate with the surrounding vegetation. Most studies on the diatom compositions across the treeline ecotone used the classic morphological approach, whereas little is known about the genetic diversity and composition of diatoms. In this Master study NGS sequencing data were used to analyze the diatom composition of 32 lakes and two lake sediment cores in comparison to morphological data sets. Furthermore, the correlation of diatom assemblages with environmental factors was analyzed and compared to morphological data. All analyses were conducted on two taxonomic levels, i.e. species and genera, in order to check the taxonomic resolution of the analyses. The results showed a significant relationship between the diatom composition and specific environmental parameters, i.e. DOC and maximal depth for both methodologies. Calcium and sulfate also had a significant influence on the genetic obtained data, while hydrogen carbonate and conductivity had a significant influence on the morphological data. It was possible to gain similar results with both approaches regarding the diatom compositions of both the recent and the ancient sediment material. Furthermore, it could be shown that there are only slight differences between the taxonomic assignment on species and genus level in the genetic approach, due to incomplete reference databases. Altogether, it could be concluded that even though the analyzed and compared methods are very different, their results are highly comparable.

Description: Large, old and heterogenous lake systems are valuable sources of biodiversity. The analysis of current spatial variability within such lakes increases our understanding of the origin and establishment of biodiversity. The environmental sensitivity and the high taxonomic richness of diatoms make them ideal organisms to investigate intra-lake variability. We investigated modern intra-lake diatom diversity in the large and old sub-arctic Lake Bolshoe Toko in Siberia. Our study uses diatom-specific metabarcoding, applying a short rbcL marker combined with next-generation sequencing and morphological identification to analyse the diatom diversity in modern sediment samples of 17 intra-lake sites. We analysed abundance-based compositional taxonomic diversity and generic phylogenetic diversity to investigate the relationship of diatom diversity changes with water depth. The two approaches show differences in taxonomic identification and alpha diversity, revealing a generally higher diversity with the genetic approach. With respect to beta diversity and ordination analyses, both approaches result in similar patterns. Water depth or related lake environmental conditions are significant factors influencing intra-lake diatom patterns, showing many significant negative correlations between alpha and beta diversity and water depth. Further, one near-shore and two lagoon lake sites characterized by low (0-10m) and medium (10-30m) water depth are unusual with unique taxonomic compositions. At deeper (〉30m) water sites we identified strongest phylogenetic clustering in Aulacoseira, but generally much less in Staurosira, which supports that water depth is a strong environmental filter on the Aulacoseira communities. Our study demonstrates the utility of combining analyses of genetic and morphological as well as phylogenetic diversity to decipher compositional and generic phylogenetic patterns, which are relevant in understanding intra-lake heterogeneity as a source of biodiversity in the sub-arctic glacial Lake Bolshoe Toko.

Description: 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.