@phdthesis{Huang2021, author = {Huang, Sichao}, title = {Past and present biodiversity in northeastern Siberia inferred from sedimentary DNA metabarcoding}, school = {Universit{\"a}t Potsdam}, year = {2021}, abstract = {The arctic-boreal treeline is a transition zone from taiga to tundra covering a vast area in Siberia. It often features large environmental gradients and reacts sensitively to changes in the environment. For example, the expansion of shrubs and a northward movement of the treeline are observable in Siberia as a response to the warming climate. The changes in vegetation across the treeline are known to influence the water chemistry in the lakes. This causes further alteration to the composition and diversity of sensitive aquatic organisms such as diatoms and macrophytes. Despite the rising awareness of the complex climate-feedback mechanisms of terrestrial plants, the understanding of their assembly rules and about responses of aquatic biomes in the surrounding treeline lakes is still limited. The goal of this thesis is to examine the previous and present biodiversity of terrestrial and freshwater biomes from the Siberian treeline ecotone, as well as their reactions to environmental changes. In particular, this thesis attempts to examine the performance of applying sedimentary DNA metabarcoding in terrestrial plants, aquatic macrophytes and diatoms, their spatial patterns along the environmental gradients and their temporal patterns throughout the climate transition from the late Pleistocene to Holocene. Sedimentary DNA metabarcoding combined with next-generation sequencing is applied as a primary tool to explore the composition and diversity of terrestrial plants, diatoms and aquatic macrophytes. The main study area is located in Chukotka of northeastern Siberia in the Arctic, a biodiversity hotspot due to its continental location and the diverse habitats of the glacial refugium. The modern diatom diversity was assessed with a specific diatom metabarcoding marker and morphological identification. Both approaches agree to a dominance of Fragilariaceae and Aulacoseiraceae, as well as on the environmental influential indicators of the diatom community. The high diversity of Fragilariaceae identified in the thermokarst lakes is found to follow the vegetation gradient along the treeline, suggesting that diatom metabarcoding can decipher relationships between diatom assemblage shifts and the relevant environmental changes. In particular, the metabarcoding approach detects diversification of fragilarioids in glacial lakes which is not visible using morphology. Sedimentary ancient DNA records indicate a vegetation mosaic of forb-dominated steppe-tundra during 28-19 ka, followed by a shift to dwarf-shrub tundra during 19-14 ka. During the most recent 14 thousand years, the vegetation consists of deciduous shrublands, then a change to boreal forest is observed. Investigations on the alpha diversity of the vegetation show that species richness is unexpectedly highest during pre-LGM, which is likely related to the extensive area that allows for more taxa. The optimum Holocene warming during 9-6 ka is not accompanied by a high richness as widely believed, but with an evenly distributed community by the fulfilment of erect shrubs. Furthermore, changes in taxonomic and phylogenetic diversity show complementary results in understanding community diversity. The composition and richness in the modern macrophytes community from Siberian Arctic and Chinese alpine are best co-influenced by July temperature and electrical conductivity.. Past macrophyte turnover during the late Pleistocene-Holocene is less noticeable in Siberia, whereas a pronounced community change from emergent to submerged plants is detected from Chinese alpine regions at about 14 ka due to increasing temperature and varying water conductivity. Finally, sedimentary DNA metabarcoding is a cost-effective and powerful proxy for ecological application, whereas completeness of the reference library, coverage and resolution of the metabarcoding marker are the major limitations of sedimentary DNA based diversity monitoring. The composition and richness in modern vegetation and macrophytes across broad spatial gradients is constrained by environmental variables, suggesting a potential usage for environmental monitoring. Diatom distributions are driven by different water variables along the treeline. Past records indicate that the shrub coverage has a noticeable influence on the assemblies of both terrestrial plants and aquatic macrophytes, though the shift in macrophyte community is relatively minor in the past 28 thousand years. In the long-term, the shrub expansion may eventually result in a genetically more diverse vegetation community but reduced species richness. When exceeding the optimal temperatures, further warming may lead to a decrease and putative loss of macrophytes and diatoms.}, language = {en} } @article{StoofLeichsenringHuangLiuetal.2022, author = {Stoof-Leichsenring, Kathleen R. and Huang, Sichao and Liu, Sisi and Jia, Weihan and Li, Kai and Liu, Xingqi and Pestryakova, Luidmila A. and Herzschuh, Ulrike}, title = {Sedimentary DNA identifies modern and past macrophyte diversity and its environmental drivers in high-latitude and high-elevation lakes in Siberia and China}, series = {Limnology and oceanography}, volume = {67}, journal = {Limnology and oceanography}, number = {5}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {0024-3590}, doi = {10.1002/lno.12061}, pages = {1126 -- 1141}, year = {2022}, abstract = {Arctic and alpine aquatic ecosystems are changing rapidly under recent global warming, threatening water resources by diminishing trophic status and changing biotic composition. Macrophytes play a key role in the ecology of freshwaters and we need to improve our understanding of long-term macrophytes diversity and environmental change so far limited by the sporadic presence of macrofossils in sediments. In our study, we applied metabarcoding using the trnL P6 loop marker to retrieve macrophyte richness and composition from 179 surface-sediment samples from arctic Siberian and alpine Chinese lakes and three representative lake cores. The surface-sediment dataset suggests that macrophyte richness and composition are mostly affected by temperature and conductivity, with highest richness when mean July temperatures are higher than 12 degrees C and conductivity ranges between 40 and 400 mu S cm(-1). Compositional turnover during the Late Pleistocene/Holocene is minor in Siberian cores and characterized by a less rich, but stable emergent macrophyte community. Richness decreases during the Last Glacial Maximum and rises during wetter and warmer climate in the Late-glacial and Mid-Holocene. In contrast, we detect a pronounced change from emergent to submerged taxa at 14 ka in the Tibetan alpine core, which can be explained by increasing temperature and conductivity due to glacial runoff and evaporation. Our study provides evidence for the suitability of the trnL marker to recover modern and past macrophyte diversity and its applicability for the response of macrophyte diversity to lake-hydrochemical and climate variability predicting contrasting macrophyte changes in arctic and alpine lakes under intensified warming and human impact.}, language = {en} } @article{HuangStoofLeichsenringLiuetal.2021, author = {Huang, Sichao and Stoof-Leichsenring, Kathleen R. and Liu, Sisi and Courtin, Jeremy and Andreev, Andrej A. and Pestryakova, Luidmila. A. and Herzschuh, Ulrike}, title = {Plant sedimentary ancient DNA from Far East Russia covering the last 28,000 years reveals different assembly rules in cold and warm climates}, series = {Frontiers in Ecology and Evolution}, volume = {9}, journal = {Frontiers in Ecology and Evolution}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-701X}, doi = {10.3389/fevo.2021.763747}, pages = {15}, year = {2021}, abstract = {Woody plants are expanding into the Arctic in response to the warming climate. The impact on arctic plant communities is not well understood due to the limited knowledge about plant assembly rules. Records of past plant diversity over long time series are rare. Here, we applied sedimentary ancient DNA metabarcoding targeting the P6 loop of the chloroplast trnL gene to a sediment record from Lake Ilirney (central Chukotka, Far Eastern Russia) covering the last 28 thousand years. Our results show that forb-rich steppe-tundra and dwarf-shrub tundra dominated during the cold climate before 14 ka, while deciduous erect-shrub tundra was abundant during the warm period since 14 ka. Larix invasion during the late Holocene substantially lagged behind the likely warmest period between 10 and 6 ka, where the vegetation biomass could be highest. We reveal highest richness during 28-23 ka and a second richness peak during 13-9 ka, with both periods being accompanied by low relative abundance of shrubs. During the cold period before 14 ka, rich plant assemblages were phylogenetically clustered, suggesting low genetic divergence in the assemblages despite the great number of species. This probably originates from environmental filtering along with niche differentiation due to limited resources under harsh environmental conditions. In contrast, during the warmer period after 14 ka, rich plant assemblages were phylogenetically overdispersed. This results from a high number of species which were found to harbor high genetic divergence, likely originating from an erratic recruitment process in the course of warming. Some of our evidence may be of relevance for inferring future arctic plant assembly rules and diversity changes. By analogy to the past, we expect a lagged response of tree invasion. Plant richness might overshoot in the short term; in the long-term, however, the ongoing expansion of deciduous shrubs will eventually result in a phylogenetically more diverse community.}, language = {en} } @article{HuangHerzschuhPestryakovaetal.2020, author = {Huang, Sichao and Herzschuh, Ulrike and Pestryakova, Luidmila Agafyevna and Zimmermann, Heike Hildegard and Davydova, Paraskovya and Biskaborn, Boris and Shevtsova, Iuliia and Stoof-Leichsenring, Kathleen Rosemarie}, title = {Genetic and morphologic determination of diatom community composition in surface sediments from glacial and thermokarst lakes in the Siberian Arctic}, series = {Journal of paleolimnolog}, volume = {64}, journal = {Journal of paleolimnolog}, number = {3}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2728}, doi = {10.1007/s10933-020-00133-1}, pages = {225 -- 242}, year = {2020}, abstract = {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 (SO42-), an indicator of the activity of sulfate-reducing microbes under anoxic conditions, and bicarbonate (HCO3-), 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 SO42- best explains diatom diversity derived from genetic data, whereas HCO3- 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.}, language = {en} }