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  • 1
    Call number: AWI Bio-20-93988
    Type of Medium: Dissertations
    Pages: x, 181 Seiten , Illustrationen, Diagramme
    Language: English
    Note: Dissertation, Universität Potsdam, 2017 , Contents Abstract Kurzfassung Contents 1. List of figures 2. List of tables Chapter 1. General introduction 1. Motivation 2. Scientific background 3. Objectives of the thesis 4. Thesis outline Chapter 2. Manuscript 1: Treeline dynamics in Siberia under changing climates as inferred from an individual-based model for Larix 1. Abstract 2. Introduction 3. Material and Methods 4. Results 5. Discussion 6. Acknowledgements Chapter 3. Manuscript 2: Field and simulation data reveal dissimilar responses of Larix gmelinii stands to increasing temperature across the Siberian treeline ecotone 1. Abstract 2. Introduction 3. Methods 4. Results 5. Discussion 6. Acknowledgements Chapter 4. Manuscript 3: High gene flow and complex treeline dynamics on the Taymyr Peninsula (north-central Siberia), revealed by nuclear microsatellites of Larix 1. Abstract 2. Introduction 3. Materials and methods 4. Results 5. Discussion 6. Acknowledgements Chapter 5. Manuscript 4: Dispersal distances at treeline in Siberia - genetic guided model improvement 1. Abstract 2. Introduction 3. Methods 4. Results 5. Discussion 6. Acknowledgements Chapter 6. Synopsis 1. Towards a better understanding of Siberian treeline dynamics 2. Methodological challenges to reconstruct and predict the treeline advance 3. Conclusions 4. Outlook Appendix 1. Supplementary information for manuscript 1 (Chapter 2) 2. Supplementary information for manuscript 2 (Chapter 3) 3. Supplementary information for manuscript 3 (Chapter 4) 4. Supplementary information for manuscript 4 (Chapter 5) Bibliography Acknowledgements - Danksagung Declaration
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  • 2
    Call number: AWI G5-20-93989
    Type of Medium: Dissertations
    Pages: viii, 139 Seiten , Illustrationen, Diagramme
    Language: English
    Note: Dissertation, Universität Potsdam, 2018 , Table of Content I. Abstract II. Deutsche Zusammenfassung 0 Preface 1 Scientific Background 1.1 Paleoenvironmental changes since the gLGM in arid Central Asia and north-western High Asia 1.1.1 Paleoclimatic changes 1.1.2 Lake level fluctuations following climatic changes 1.1.3 Inferred terrestrial vegetation responses to environmental changes and possible human impact 1.2 The role of proxy records in tracing environmental changes 1.2.1 Archives and Proxies investigated in environmental studies in Central Asia 1.2.2 Limnological systems as environmental archives 1.2.3 The multiproxy approach as a tool to decipher environmental change 1.3 Study area 1.4 Material and Method Overview 1.4.1 Field based sampling 1.4.2 Outline of material and methods 1.5 Aim and objectives ofthis thesis 1.6 Thesis outline 1.7 Contribution of the authors 1.7.1 Manuscript I - published 1.7.2 Manuscript II - published 1.7.3 Manuscript III - published 1.7.4 Manuscript IV - in preparation 2 Manuscript I Climatic and limnological changes at Lake Karakul (Tajikistan) during the last ~29 cal ka 2.1 Abstract 2.2 Introduction 2.3 Study Area 2.4 Material and methods 2.4.1 Fieldwork 2.4.2 Laboratory analysis 2.5 Results 2.5.1 Age-depth relationship in core KK12-1 2.5.2 TIC, TOC, TOC/TN, δ18Ocarb and δ13CCarb 2.5.3 Grain-size distribution and results ofend-member modelling 2.5.4 XRF data 2.5.5 Ordination results of sediment parameters 2.6 Discussion 2.6.1 Paleoenvironmental indicators from sediment variables 2.6.2 Implications ofthe Lake Karakul sediment record 2.6.3 Linking lake internal development to climate change 2.7 Conclusions 2.8 Acknowledgements 2.9 Data availability 3 Manuscript II Aquatic macrophyte dynamics in Lake Karakul (Eastern Pamir) over the last 29 cal ka revealed by sedimentary ancient DNA and geochemical analyses of macrofossil remains 3.1 Abstract 3.2 Introduction 3.3 Material and Methods 3.3.1 Sample acquisition and treatment 3.3.2 Genetic approach 3.3.3 Elemental isotopic analyses ofaquatic macrophyte remains 3.4 Results 3.4.1 Macrophyte records along lake depth transects in Lake Karakul 3.4.2 Submerged plant content 3.4.3 Ancient DNA analyses 3.4.4 C, N, δ13C and δ15N of Stuckenia cf. pamirica remains 3.5 Discussion 3.5.1 Assessment of aDNA and chemical aquatic macrophyte data as proxies for the macrophyte composition and the paleo-productivity 3.5.2 Changes of past submerged plant composition and productivity and potential drivers 3.6 Conclusions 3.7 Acknowledgements 3.8 Data Availability 4 Manuscript III Radiocarbon and optical stimulated luminescence dating of sediments from Lake Karakul, Tajikistan 4.1 Abstract 4.2 Introduction 4.3 Regional setting 4.4 Methods 4.4.1 Collection and correlation of cores 4.4.2 Radiocarbon dating 4.4.3 Optically stimulated luminescence (OSL) dating 4.4.4 Establishment ofage-depth model 4.4.5 Investigation of exposed lake sediments 4.5 Results 4.6 Discussion 4.6.1 Recovered sediments and correlation ofcores from Lake Karakul 4.6.2 Age-depth model, and assessment of radiocarbon and OSL age data 4.6.3 Significance ofexposed sediments at section KK13-S1 4.6.4 Implications ofthe chronological data 4.7 Conclusion 4.8 Acknowledgements 5 Manuscript IV Vegetation change in the Eastern Pamir Mountains inferred from Lake Karakul pollen spectra of the last 28 ka 5.1 Abstract 5.2 Introduction 5.3 Study site 5.4 Material and Methods 5.4.1 Sediment cores and chronology 5.4.2 Pollen sample preparation and pollen analyses 5.4.3 Pollen data treatment 5.5 Results 5.5.1 Composite core (KK12-1/2; 27.6 cal ka BP to present) 5.5.2 Short core TAJ-Kar-08-lB 5.6 Discussion 5.6.1 Interpretation of pollen data 5.6.2 Terrestrial vegetation change in the Eastern Pamir Mountains in response to past climate change 5.7 Conclusions 5.8 Acknowledgements 5.9 Data Availability 6 Synthesis 6.1 Proxy evaluation 6.1.1 Age-depth relationship 6.1.2 Limnological proxies 6.1.3 Terrestrial proxies 6.2 The potential of Lake Karakul as archive for long term environmental change in the Eastern Pamir 6.3 Climate and moisture availability changes over time - inferred from sedimentary proxies 6.4 Assessment ofthe aquatic macrophyte composition and paleoproductivity within Lake Karakul 6.5 Inferred terrestrial vegetation changes as responds to climatic changes over the last 28 cal ka 6.6 Comparison inferred regional vegetation, lake internal and lake external variations and changes in climate reconstructed in other studies 6.6.1 Pre- gLGM and global Last Glacial Maximum (27.6 to 19 cal ka BP) 6.6.2 Late glacial 6.6.3 Early to middle Holocene 6.6.4 Middle to late Holocene 6.7 Outlook 7 Appendix 7.1 Supplementary information for Manuscript I 7.2 Supplementary information for Manuscript II 7.3 Supplementary information for Manuscript III 8 References Danksagung Eldesstattliche Erklärung
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  • 3
    Call number: AWI Bio-22-95014
    Description / Table of Contents: The deciduous needle tree larch (Larix Mill.) covers more than 80% of the Asian boreal forests. Only a few Larix species constitute the vast forests and these species differ markedly in their ecological traits, most importantly in their ability to grow on and stabilize underlying permafrost. The pronounced dominance of the summergreen larches makes the Asian boreal forests unique, as the rest of the northern hemisphere boreal forests is almost exclusively dominated by evergreen needle-leaf forests. Global warming is impacting the whole world but is especially pronounced in the arctic and boreal regions. Although adapted to extreme climatic conditions, larch forests are sensitive to varying climatic conditions. By their sheer size, changes in Asian larch forests as range shifts or changes in species composition and the resulting vegetation-climate feedbacks are of global relevance. It is however still uncertain if larch forests will persist under the ongoing warming climate or if they will be replaced by evergreen forests. It is therefore of great importance to understand how these ecosystems will react to future climate warmings and if they will maintain their dominance. One step in the better understanding of larch dynamics is to study how the vast dominant forests developed and why they only established in northern Asia. A second step is to study how the species reacted to past changes in the climate. The first objective of this thesis was to review and identify factors promoting Asian larch dominance. I achieved this by synthesizing and comparing reported larch occurrences and influencing components on the northern hemisphere continents in the present and in the past. The second objective was to find a possibility to directly study past Larix populations in Siberia and specifically their genetic variation, enabling the study of geographic movements. For this, I established chloroplast enrichment by hybridization capture from sedimentary ancient DNA (sedaDNA) isolated from lake sediment records. The third objective was to use the established method to track past larch populations, their glacial refugia during the Last Glacial Maximum (LGM) around 21,000 years before present (ka BP), and their post-glacial migration patterns. To study larch promoting factors, I compared the present state of larch species ranges, areas of dominance, their bioclimatic niches, and the distribution on different extents and thaw depths of permafrost. The species comparison showed that the bioclimatic niches greatly overlap between the American and Asian species and that it is only in the extremely continental climates in which only the Asian larch species can persist. I revealed that the area of dominance is strongly connected to permafrost extent but less linked to permafrost seasonal thaw depths. Comparisons of the paleorecord of larch between the continents suggest differences in the recolonization history. Outside of northern Asia and Alaska, glacial refugial populations of larch were confined to the southern regions and thus recolonization could only occur as migration from south to north. Alaskan larch populations could not establish wide-range dominant forest which could be related to their own genetically depletion as separated refugial population. In Asia, it is still unclear whether or not the northern refugial populations contributed and enhanced the postglacial colonization or whether they were replaced by populations invading from the south in the course of climate warming. Asian larch dominance is thus promoted partly by adaptions to extremely continental climates and by adaptations to grow on continuous permafrost but could be also connected to differences in glacial survival and recolonization history of Larix species. Except for extremely rare macrofossil findings of fossilized cones, traditional methods to study past vegetation are not able to distinguish between larch species or populations. Within the scope of this thesis, I therefore established a method to retrieve genetic information of past larch populations to distinguish between species. Using the Larix chloroplast genome as target, I successfully applied the method of DNA target enrichment by hybridization capture on sedaDNA samples from lake records and showed that it is able to distinguish between larch species. I then used the method on samples from lake records from across Siberia dating back up to 50 ka BP. The results allowed me to address the question of glacial survival and post-glacial recolonization mode in Siberian larch species. The analyzed pattern showed that LGM refugia were almost exclusively constituted by L. gmelinii, even in sites of current L. sibirica distribution. For included study sites, L. sibirica migrated into its extant northern distribution area only in the Holocene. Consequently, the post-glacial recolonization of L. sibirica was not enhanced by northern glacial refugia. In case of sites in extant distribution area of L. gmelinii, the absence of a genetic turn-over point to a continuous population rather than an invasion of southern refugia. The results suggest that climate has a strong influence on the distribution of Larix species and that species may also respond differently to future climate warming. Because species differ in their ecological characteristics, species distribution is also relevant with respect to further feedbacks between vegetation and climate. With this thesis, I give an overview of present and past larch occurrences and evaluate which factors promote their dominance. Furthermore, I provide the tools to study past Larix species and give first important insights into the glacial history of Larix populations.
    Type of Medium: Dissertations
    Pages: x, 121 Seiten , Illustrationen
    Language: English
    Note: Dissertation, Universität Potsdam, 2022 , Table of Contents Summary Deutsche Zusammenfassung Table of Contents 1 Introduction 1.1 Larix forests in a changing climate 1.2 The genus Larix 1.3 Larix distribution in the world and their dominance in northern Asia 1.4 Methods to study past species dynamics 1.4.1 Modern genetic marker studies 1.4.2 Lake sediments as archives of the past 1.4.3 Pollen and macrofossils 1.4.4 Metabarcoding of sedimentary ancient DNA 1.4.5 Metagenomic shotgun sequencing 1.4.6 Target enrichment by hybridization capture 1.5 Thesis Objectives 1.6 Thesis outline & author contributions 2 Manuscript I 2.1 Abstract 2.2 Introduction 2.3 Material and methods 2.3.1 Bioclimatic limits 2.3.2 Pollen, macrofossil, and DNA datasets 2.3.3 Ice sheets 2.4 Results 2.4.1 Bioclimatic limits of Larix and its distribution on permafrost 2.4.2 Glacial occurrence patterns of Larix 2.5 Discussion 2.5.1 Are differences in species bioclimatic limits responsible for disparity in Larix distribution across continents? 2.5.2 Do high latitude glacial refugia guarantee larch dominance? 2.5.3 What role does postglacial migration play in larch dominance? 2.5.4 Fire as an additional factor 2.5.5 Outlook 2.6 Conclusion 2.7 Acknowledgements 2.8 Author contributions 2.9 References 3 Manuscript II 3.1 Abstract 3.2 Introduction 3.3 Methods 3.3.1 Sample material 3.3.2 Laboratory work 3.3.3 Data analysis 3.4 Results 3.4.1 Overview of the shotgun and hybridization capture data sets 3.4.2 Ancient DNA authenticity 3.4.3 Retrieval of the Larix chloroplast genome 3.5 Discussion 3.5.1 Taxonomic classification—conservative approach results in low numbers of assignment 3.5.2 Target enrichment success—Larix reads increased by orders of magnitude along with other taxonomic groups 3.5.3 Complete retrieval of ancient Larix chloroplast genomes 3.5.4 Larix sibirica variants present over time 3.5.5 Larch forest decline over the last 7000 years 3.6 Conclusion 3.7 Acknowledgments 3.8 Author contributions 3.9 References 4 Manuscript III 4.1 Abstract 4.2 Introduction 4.3 Results & Discussion 4.3.1 Chloroplast and repetitive DNA enrichment in the sedaDNA samples 4.3.2 A wider pre-glacial distribution of L. sibirica 4.3.3 Larix gmelinii formed northern LGM refugia across Siberia 4.3.4 Postglacial colonization history - differences among larch species 4.3.5 Environment likely plays a more important role than biogeography 4.4 Conclusion 4.5 Material & methods 4.5.1 Sample material 4.5.2 Sequence data analysis 4.6 Data availability 4.7 Acknowledgments 4.8 Author contributions 4.9 References 5 Discussion and synthesis 5.1 Hybridization capture is a well-suited method to study ancient species dynamics 5.1.1 Advantages and limitations of shotgun sequencing 5.1.2 Successful hybridization capture enrichment using chloroplast DNA 5.1.3 Challenges in single-copy target enrichment 5.1.4 Limitations and potentials to improve sedaDNA capture studies 5.2 Factors promoting Asian larch dominance 5.3 Drivers of Larix species distribution 5.3.1 Implications for larch forests under climate warming 5.4 Conclusion 5.5 Outlook 6 References 7 Appendix 7.1 Appendix to manuscript I 7.2 Appendix to manuscript II 7.3 Appendix to manuscript III 7.3.1 Material and Methods 7.3.2 Additional Results & Discussions 7.3.3 References Acknowledgements Eidesstattliche Erklärung
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  • 4
    Call number: AWI Bio-23-95302
    Description / Table of Contents: Climate change of anthropogenic origin is affecting Earth’s biodiversity and therefore ecosystems and their services. High latitude ecosystems are even more impacted than the rest of Northern Hemisphere because of the amplified polar warming. Still, it is challenging to predict the dynamics of high latitude ecosystems because of complex interaction between abiotic and biotic components. As the past is the key to the future, the interpretation of past ecological changes to better understand ongoing processes is possible. In the Quaternary, the Pleistocene experienced several glacial and interglacial stages that affected past ecosystems. During the last Glacial, the Pleistocene steppe-tundra was covering most of unglaciated northern hemisphere and disappeared in parallel to the megafauna’s extinction at the transition to the Holocene (~11,700 years ago). The origin of the steppe-tundra decline is not well understood and knowledge on the mechanisms, which caused shifts in past communities and ecosystems, is of high priority as they are likely comparable to those affecting modern ecosystems. Lake or permafrost core sediments can be retrieved to investigate past biodiversity at transitions between glacial and interglacial stages. Siberia and Beringia were the origin of dispersal of the steppe-tundra, which make investigation this area of high priority. Until recently, macrofossils and pollen were the most common approaches. They are designed to reconstruct past composition changes but have limit and biases. Since the end of the 20th century, sedimentary ancient DNA (sedaDNA) can also be investigated. My main objectives were, by using sedaDNA approaches to provide scientific evidence of compositional and diversity changes in the Northern Hemisphere ecosystems at the transition between Quaternary glacial and interglacial stages. In this thesis, I provide snapshots of entire ancient ecosystems and describe compositional changes between Quaternary glacial and interglacial stages, and confirm the vegetation composition and the spatial and temporal boundaries of the Pleistocene steppe-tundra. I identify a general loss of plant diversity with extinction events happening in parallel of megafauna’ extinction. I demonstrate how loss of biotic resilience led to the collapse of a previously well-established system and discuss my results in regards to the ongoing climate change. With further work to constrain biases and limits, sedaDNA can be used in parallel or even replace the more established macrofossils and pollen approaches as my results support the robustness and potential of sedaDNA to answer new palaeoecological questions such as plant diversity changes, loss and provide snapshots of entire ancient biota.
    Description / Table of Contents: Der vom Menschen verursachte Klimawandel wirkt sich auf die biologische Vielfalt der Erde und damit auf die Ökosysteme und ihre Leistungen aus. Die Ökosysteme in den hohen Breitengraden sind aufgrund der verstärkten Erwärmung an den Polen noch stärker betroffen als der Rest der nördlichen Hemisphäre. Dennoch ist es schwierig, die Dynamik von Ökosystemen in den hohen Breitengraden vorherzusagen, da die Wechselwirkungen zwischen abiotischen und biotischen Komponenten sehr komplex sind. Da die Vergangenheit der Schlüssel zur Zukunft ist, ist die Interpretation vergangener ökologischer Veränderungen möglich, um laufende Prozesse besser zu verstehen. Im Quartär durchlief das Pleistozän mehrere glaziale und interglaziale Phasen, welche die Ökosysteme der Vergangenheit beeinflussten. Während des letzten Glazials bedeckte die pleistozäne Steppentundra den größten Teil der unvergletscherten nördlichen Hemisphäre und verschwand parallel zum Aussterben der Megafauna am Übergang zum Holozän (vor etwa 11 700 Jahren). Der Ursprung des Rückgangs der Steppentundra ist nicht gut erforscht, und die Kenntnis über die Mechanismen, die zu den Veränderungen in den vergangenen Lebensgemeinschaften und Ökosystemen geführt haben, ist von hoher Priorität, da sie wahrscheinlich mit denen vergleichbar sind, die sich auf moderne Ökosysteme auswirken. Durch die Entnahme von See- oder Permafrostkernsedimenten kann die vergangene Artenvielfalt an den Übergängen zwischen Eis- und Zwischeneiszeiten untersucht werden. Sibirien und Beringia waren der Ursprung der Ausbreitung der Steppentundra, weshalb die Untersuchung dieses Gebiets hohe Priorität hat. Bis vor kurzem waren Makrofossilien und Pollen die gängigsten Methoden. Sie dienen der Rekonstruktion vergangener Veränderungen in der Zusammensetzung der Bevölkerung, haben aber ihre Grenzen und Schwächen. Seit Ende des 20. Jahrhunderts kann auch sedimentäre alte DNA (sedaDNA) untersucht werden. Mein Hauptziel war es, durch den Einsatz von sedaDNA-Ansätzen wissenschaftliche Beweise für Veränderungen in der Zusammensetzung und Vielfalt der Ökosysteme der nördlichen Hemisphäre am Übergang zwischen den quartären Eiszeiten und Zwischeneiszeiten zu liefern. In dieser Arbeit liefere ich Momentaufnahmen ganzer alter Ökosysteme und beschreibe die Veränderungen in der Zusammensetzung zwischen Quartärglazialen und Interglazialen und bestätige die Vegetationszusammensetzung sowie die räumlichen und zeitlichen Grenzen der pleistozänen Steppentundra. Ich stelle einen allgemeinen Verlust der Pflanzenvielfalt fest, wobei das Aussterben der Pflanzen parallel zum Aussterben der Megafauna verlief. Ich zeige auf, wie der Verlust der biotischen Widerstandsfähigkeit zum Zusammenbruch eines zuvor gut etablierten Systems führte, und diskutiere meine Ergebnisse im Hinblick auf den laufenden Klimawandel. Mit weiteren Arbeiten zur Eingrenzung von Verzerrungen und Grenzen kann sedaDNA parallel zu den etablierteren Makrofossilien- und Pollenansätzen verwendet werden oder diese sogar ersetzen, da meine Ergebnisse die Robustheit und das Potenzial von sedaDNA zur Beantwortung neuer paläoökologischer Fragen wie Veränderungen der Pflanzenvielfalt und -verluste belegen und Momentaufnahmen ganzer alter Biota liefern.
    Type of Medium: Dissertations
    Pages: vi, 217 Seiten , Illustrationen, Diagramme, Karten
    Language: English
    Note: Dissertation, Universität Potsdam, 2023 , TABLE OF CONTENTS Acknowledgements Summary Zusammenfassung 1 General introduction 1.1 A changing world 1.1.1 Global changes of anthropogenic origin 1.1.2 Amplified crisis in the high latitudes 1.2 The past is the key to the future 1.2.1 The Quaternary glacial and interglacial stages 1.2.2 The Beringia study case 1.3 Investigating past biodiversity 1.3.1 Traditional tools 1.3.2 Newest sedaDNA proxies 1.4 Motivation and aims of the thesis 1.5 Structure of the thesis 1.6 Author’s contributions 2 Manuscript I 2.1 Abstract 2.2 Introduction 2.3 Materials and Methods 2.3.1 Geographical settings 2.3.2 Fieldwork and subsampling 2.3.3 Core splicing and dating 2.3.4 Sediment-geochemical analyses 2.3.5 Pollen analysis 2.3.6 Molecular genetic preparation 2.3.7 Processing of sedaDNA data 2.3.8 Statistical analysis and visualization 2.4 Results 2.4.1 Age model 2.4.2 Sediment-geochemical core composition 2.4.3 Pollen stratigraphy 2.4.4 sedaDNA composition 2.4.5 Comparison between pollen and sedaDNA 2.4.6 Taxa richness investigation 2.5 Discussion 2.5.1 Proxy validation 2.5.2 Vegetation compositional changes in response to climate inferred from pollen and sedaDNA records 2.5.3 The steppe-tundra of the Late Pleistocene 2.5.4 The disrupted Pleistocene-Holocene transition 2.5.5 The boreal forest of the Holocene 2.5.6 Changes in vegetation richness through the Pleistocene/Holocene transition inferred from the sedaDNA record 2.6 Conclusion Data availability statement Funding References 3 Manuscript II 3.1 Abstract 3.2 Introduction 3.3 Material and Method 3.3.1 Site description and timeframe 3.3.2 Sampling, DNA extraction and PCR 3.3.3 Filtering and cleaning dataset 3.3.4 Identification of taxa – species signal 3.3.5 Resampling 3.3.6 Assessment of the species pool stability 3.3.7 Quantification of extinct and extirpated taxa 3.3.8 Characterisation of species and candidate species 3.4 Results 3.4.1 Changes in the composition and species pool at the Pleistocene - Holocene transition 3.4.2 Decrease in the regional plant species richness between the Pleistocene and the Holocene 3.4.3 Identification of loss taxa events 3.4.4 Characterisation of lost taxa 3.5 Discussion 3.5.1 Biotic and abiotic changes in the ecosystem - a cocktail for extinction 3.5.2 Identification and quantification of potential plant taxa loss 3.5.3 Characterisation of potential taxa loss 3.5.4 Limits of the method 3.5.5 Conclusions and perspectives Funding References 4 Manuscript III 4.1 Abstract 4.2 Introduction 4.3 Material & Methods 4.3.1 Fieldwork and subsampling 4.3.2 Chronology 4.3.3 Pollen analysis 4.3.4 Isolation of sedimentary ancient DNA 4.3.5 Metabarcoding approach 4.3.6 Shotgun approach 4.3.7 Bioinformatic processing 4.4 Results 4.4.1 General results of the three approaches: pollen, metabarcoding and shotgun sequencing 4.4.2 Plants (Viridiplantae) 4.4.3 Fungi 4.4.4 Mammals (Mammalia) 4.4.5 Birds (Aves) 4.4.6 Insects (Insecta) 4.4.7 Prokaryotes (Bacteria, Archaea) and Viruses 4.5 Discussion 4.5.1 Interglacial communities 4.5.2 Glacial communities 4.5.3 Potential and limitations of the sedaDNA shotgun approach applied to ancient permafrost sediments 4.6 Conclusions Data availability statement Funding References 5 Synthesis 5.1 Ecological changes between glacial and interglacial stages 5.1.1 Changes in the compositional structure 5.1.2 Loss of plant diversity 5.1.3 Potential drivers of change 5.2 High potential of sedaDNA for past biodiversity reconstruction 5.3 Conclusions and future perspectives Bibliography Appendices Appendix 1: Supplementary material for Manuscript I Appendix 2: Supplementary material for Manuscript II Appendix 3: Supplementary material for Manuscript III Appendix 4: Manuscript IV Eidesstattliche Erklärung
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  • 5
    Call number: AWI Bio-24-95742
    Description / Table of Contents: The arctic is warming 2 – 4 times faster than the global average, resulting in a strong feedback on northern ecosystems such as boreal forests, which cover a vast area of the high northern latitudes. With ongoing global warming, the treeline subsequently migrates northwards into tundra areas. The consequences of turning ecosystems are complex: on the one hand, boreal forests are storing large amounts of global terrestrial carbon and act as a carbon sink, dragging carbon dioxide out of the global carbon cycle, suggesting an enhanced carbon uptake with increased tree cover. On the other hand, with the establishment of trees, the albedo effect of tundra decreases, leading to enhanced soil warming. Meanwhile, permafrost thaws, releasing large amounts of previously stored carbon into the atmosphere. So far, mainly vegetation dynamics have been assessed when studying the impact of warming onto ecosystems. Most land plants are living in close symbiosis with bacterial and fungal communities, sustaining their growth in nutrient poor habitats. However, the impact of climate change on these subsoil communities alongside changing vegetation cover remains poorly understood. Therefore, a better understanding of soil community dynamics on multi millennial timescales is inevitable when addressing the development of entire ecosystems. Unravelling long-term cross-kingdom dependencies between plant, fungi, and bacteria is not only a milestone for the assessment of warming on boreal ecosystems. On top, it also is the basis for agriculture strategies to sustain society with sufficient food in a future warming world. The first objective of this thesis was to assess ancient DNA as a proxy for reconstructing the soil microbiome (Manuscripts I, II, III, IV). Research findings across these projects enable a comprehensive new insight into the relationships of soil microorganisms to the surrounding vegetation. First, this was achieved by establishing (Manuscript I) and applying (Manuscript II) a primer pair for the selective amplification of ancient fungal DNA from lake sediment samples with the metabarcoding approach. To assess fungal and plant co-variation, the selected primer combination (ITS67, 5.8S) amplifying the ITS1 region was applied on samples from five boreal and arctic lakes. The obtained data showed that the establishment of fungal communities is impacted by warming as the functional ecological groups are shifting. Yeast and saprotroph dominance during the Late Glacial declined with warming, while the abundance of mycorrhizae and parasites increased with warming. The overall species richness was also alternating. The results were compared to shotgun sequencing data reconstructing fungi and bacteria (Manuscripts III, IV), yielding overall comparable results to the metabarcoding approach. Nonetheless, the comparison also pointed out a bias in the metabarcoding, potentially due to varying ITS lengths or copy numbers per genome. The second objective was to trace fungus-plant interaction changes over time (Manuscripts II, III). To address this, metabarcoding targeting the ITS1 region for fungi and the chloroplast P6 loop for plants for the selective DNA amplification was applied (Manuscript II). Further, shotgun sequencing data was compared to the metabarcoding results (Manuscript III). Overall, the results between the metabarcoding and the shotgun approaches were comparable, though a bias in the metabarcoding was assumed. We demonstrated that fungal shifts were coinciding with changes in the vegetation. Yeast and lichen were mainly dominant during the Late Glacial with tundra vegetation, while warming in the Holocene lead to the expansion of boreal forests with increasing mycorrhizae and parasite abundance. Aside, we highlighted that Pinaceae establishment is dependent on mycorrhizal fungi such as Suillineae, Inocybaceae, or Hyaloscypha species also on long-term scales. The third objective of the thesis was to assess soil community development on a temporal gradient (Manuscripts III, IV). Shotgun sequencing was applied on sediment samples from the northern Siberian lake Lama and the soil microbial community dynamics compared to ecosystem turnover. Alongside, podzolization processes from basaltic bedrock were recovered (Manuscript III). Additionally, the recovered soil microbiome was compared to shotgun data from granite and sandstone catchments (Manuscript IV, Appendix). We assessed if the establishment of the soil microbiome is dependent on the plant taxon and as such comparable between multiple geographic locations or if the community establishment is driven by abiotic soil properties and as such the bedrock area. We showed that the development of soil communities is to a great extent driven by the vegetation changes and temperature variation, while time only plays a minor role. The analyses showed general ecological similarities especially between the granite and basalt locations, while the microbiome on species-level was rather site-specific. A greater number of correlated soil taxa was detected for deep-rooting boreal taxa in comparison to grasses with shallower roots. Additionally, differences between herbaceous taxa of the late Glacial compared to taxa of the Holocene were revealed. With this thesis, I demonstrate the necessity to investigate subsoil community dynamics on millennial time scales as it enables further understanding of long-term ecosystem as well as soil development processes and such plant establishment. Further, I trace long-term processes leading to podzolization which supports the development of applied carbon capture strategies under future global warming.
    Type of Medium: Dissertations
    Pages: xii, 198 Seiten , Illustrationen, Diagramme
    Language: English
    Note: Dissertation, Universität Potsdam, 2024 , Table of Contents Summary Deutsche Zusammenfassung 1 Introduction 1.1 Arctic ecosystems under global warming 1.2 The plant-associated microbiome 1.3 Drivers of soil development 1.4 Ancient DNA to unravel past ecosystems 1.4.1 Lake sediments as archives of past community changes 1.4.2 Metabarcoding for targeting specific communities 1.4.3 Shotgun sequencing for broader overview 1.5 Thesis objective 1.6 Thesis outline and author contributions 2 Manuscript I 2.1 Abstract 2.2 Introduction 2.3 Materials and Methods 2.3.1 Primer design and evaluation In silico analyses Evaluation of lake sediment core DNA for analyses of fungal paleoecology 2.4 Results Primer design and evaluation Evaluation of lake sediment core DNA for fungal paleoecology 2.4.1 Taxonomic resolution across the cores 2.4.2 Comprehensiveness: Rarefaction and accumulation curves 2.4.3 Amplicon length and GC content to assess bias through degradation 2.4.4 General taxonomic composition of fungi in Siberian lake sediment cores Diversity of fungal paleocommunities from lake CH12 2.5 Discussion 2.5.1 Preservation biases and potential contamination 2.5.2 Characteristics of the optimized sedaDNA ITS1 metabarcoding assay 2.5.3 Potential of lake sediment fungal DNA for paleoecology 2.6 Author contributions 2.7 Acknowledgements 2.8 Conflict of interest 2.9 References 3 Manuscript II 3.1 Abstract 3.2 Introduction 3.3 Geographic setting and study sites 3.4 Materials and Methods 3.4.1 Sampling 3.4.2 DNA extraction and amplification 3.4.3 Bioinformatic analysis 3.4.4 Assessment of negative controls and contamination 3.4.5 Statistical analysis and visualization 3.5 Results 3.5.1 Fungi: sedaDNA sequencing results and overall patterns of alpha diversity and taxonomic composition 3.5.2 Vegetation: sedaDNA sequencing results and overall patterns of alpha diversity and taxonomic composition 3.5.3 Site-specific plant-fungus covariation 3.5.3.1 Fungus and plant covariation in arctic Siberia from MIS3 to the Holocene 3.5.3.2 Quantitative relationships between fungi and plant richness and composition 3.6 Discussion 3.6.1 Fungus and plant diversity along a spatiotemporal gradient in Siberia 3.6.2 Changes in ecosystem functioning over a spatiotemporal gradient 3.6.3 Implications of our results for ecosystem functioning and future research avenues 3.7 Conclusions Funding Availability of data and material Author contribution Declaration of competing interest Acknowledgements 3.8 References 4 Manuscript III 4.1 Abstract 4.2 Introduction 4.3 Results and Discussion 4.3.1 Compositional changes of plants, fungi, and bacteria in ancient metagenomic datasets 4.3.2 Long-term soil development: a trajectory or environmentally driven processes? 4.3.3 Bioweathering supported by lichens and mycorrhiza 4.3.4 Turnover in carbon, nitrogen, and sulphur cycling 4.3.5 Tracing podzolization 4.4 Implications and conclusions 4.5 Material and methods 4.5.1 Geographical setting and study site 4.5.2 X-ray fluorescence scanning of the sediment core 4.5.3 Core sub-sampling 4.5.4 DNA extraction 4.5.5 Single stranded DNA library build 4.5.6 Bioinformatic pipeline for the analysis of the sequencing results 4.5.7 Data analysis 4.5.8 Analysis of the ancient patterns 4.5.9 Statistical analysis of the dataset Acknowledgements 4.6 References Declarations 5 Discussion and synthesis 5.1 Long-term rhizosphere establishment in tundra and taiga areas 5.1.1 SedaDNA as a proxy for soil microbiome 5.1.1.1 Fungal DNA metabarcoding 5.1.1.2 Targeting soil communities with shotgun sequencing 5.1.1.3 Comparison between metabarcoding and shotgun sequencing for the soil microbiome 5.1.2 Fungi-vegetation interaction changes over time 5.1.3 Soil development on a temporal gradient 5.2 Conclusion and future perspectives 6 References 7 Appendix 7.1 Appendix to manuscript I 7.2 Appendix to manuscript II 7.3 Appendix to manuscript III 7.4 Manuscript IV 7.4.1 Abstract 7.4.2 Introduction 7.4.3 Geographical setting and study sites 7.4.4 Material & Methods 7.4.4.1 Sub-sampling of the sediment cores 7.4.4.2 DNA extraction 7.4.4.3 Single stranded DNA library built 7.4.4.4 Bioinformatic pipeline for the analysis of the sequencing data 7.4.4.5 Data analysis 7.4.4.6 Statistical analysis of the datasets 7.4.5 Results 7.4.5.1 Compositional changes of representative plant taxa alongside dynamics in fungal ecologies and bacterial element cycling in ancient metagenomic datasets 7.4.5.2 Impact of abiotic and biotic drivers on soil establishment across geographical locations 7.4.5.3 Relative positive correlations of functional soil taxa with plants across the locations 7.4.5.4 Assessment of the plant taxon-specific microbiome across the locations 7.4.6 Discussion 7.4.6.1 Site-specific soil development 7.4.6.2 Differences in the bedrock 7.4.6.3 Correlation between the lake biota 7.4.6.3.1 General Trends in positively correlated rhizosphere taxa 7.4.6.3.2 Plant taxa specific microbiome 7.4.7 Implications and future directions 7.4.8 References 7.4.9 Supplement to manuscript IV Acknowledgements Eidesstattliche Erklärung Damage pattern analysis – Auflagen Doktorarbeit Summary Main References
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  • 6
    Call number: AWI Bio-24-95736
    Description / Table of Contents: Moss-microbe associations are often characterised by syntrophic interactions between the microorganisms and their hosts, but the structure of the microbial consortia and their role in peatland development remain unknown. In order to study microbial communities of dominant peatland mosses, Sphagnum and brown mosses, and the respective environmental drivers, four study sites representing different successional stages of natural northern peatlands were chosen on a large geographical scale: two brown moss-dominated, circumneutral peatlands from the Arctic and two Sphagnum-dominated, acidic peat bogs from subarctic and temperate zones. The family Acetobacteraceae represented the dominant bacterial taxon of Sphagnum mosses from various geographical origins and displayed an integral part of the moss core community. This core community was shared among all investigated bryophytes and consisted of few but highly abundant prokaryotes, of which many appear as endophytes of Sphagnum mosses. Moreover, brown mosses and Sphagnum mosses represent habitats for archaea which were not studied in association with peatland mosses so far. Euryarchaeota that are capable of methane production (methanogens) displayed the majority of the moss-associated archaeal communities. Moss-associated methanogenesis was detected for the first time, but it was mostly negligible under laboratory conditions. Contrarily, substantial moss-associated methane oxidation was measured on both, brown mosses and Sphagnum mosses, supporting that methanotrophic bacteria as part of the moss microbiome may contribute to the reduction of methane emissions from pristine and rewetted peatlands of the northern hemisphere. Among the investigated abiotic and biotic environmental parameters, the peatland type and the host moss taxon were identified to have a major impact on the structure of moss-associated bacterial communities, contrarily to archaeal communities whose structures were similar among the investigated bryophytes. For the first time it was shown that different bog development stages harbour distinct bacterial communities, while at the same time a small core community is shared among all investigated bryophytes independent of geography and peatland type. The present thesis displays the first large-scale, systematic assessment of bacterial and archaeal communities associated both with brown mosses and Sphagnum mosses. It suggests that some host-specific moss taxa have the potential to play a key role in host moss establishment and peatland development.
    Description / Table of Contents: Während die Beziehungen zwischen Moosen und den mit ihnen assoziierten Mikroorganismen oft durch syntrophische Wechselwirkungen charakterisiert sind, ist die Struktur der Moos-assoziierten mikrobiellen Gemeinschaften sowie deren Rolle bei der Entstehung von Mooren weitgehend unbekannt. Die vorliegende Arbeit befasst sich mit mikrobiellen Gemeinschaften, die mit Moosen nördlicher, naturnaher Moore assoziiert sind, sowie mit den Umweltfaktoren, die sie beeinflussen. Entlang eines groß angelegten geographischen Gradienten, der von der Hocharktis bis zur gemäßigten Klimazone reicht, wurden vier naturbelassene Moore als Probenstandorte ausgesucht, die stellvertretend für verschiedene Stadien der Moorentwicklung stehen: zwei Braunmoos-dominierte Niedermoore mit nahezu neutralem pH-Wert sowie zwei Sphagnum-dominierte Torfmoore mit saurem pH-Wert. Die Ergebnisse der vorliegenden Arbeit machen deutlich, dass die zu den Bakterien zählenden Acetobacteraceae das vorherrschende mikrobielle Taxon der Sphagnum-Moose gleich welchen geographischen Ursprungs darstellen und insbesondere innerhalb des Wirtsmoosgewebes dominieren. Gleichzeitig gehörten die Acetobacteraceae zum wesentlichen Bestandteil der mikrobiellen Kerngemeinschaft aller untersuchten Moose, die sich aus einigen wenigen Arten, dafür zahlreich vorkommenden Prokaryoten zusammensetzt. Die vorliegende Arbeit zeigt zudem erstmals, dass sowohl Braunmoose als auch Torfmoose ein Habitat für Archaeen darstellen. Die Mehrheit der Moos-assoziierten Archaeen gehörte dabei zu den methanbildenden Gruppen, wenngleich die metabolischen Aktivitätsraten unter Laborbedingungen meistens kaum messbar waren. Im Gegensatz hierzu konnte die Bakterien-vermittelte Methanoxidation sowohl an Braunmoosen als auch an Sphagnum-Moosen gemessen werden. Dies zeigt eindrucksvoll, dass Moos-assoziierte Bakterien potenziell zur Minderung von Methanemissionen aus nördlichen, aber auch wiedervernässten Mooren beitragen können. Ein weiteres wichtiges Resultat der vorliegenden Arbeit ist die Bedeutung des Moortyps (Niedermoor oder Torfmoor), aber auch der Wirtsmoosart selbst für die Struktur der Moos-assoziierten Bakteriengemeinschaften, während die archaeellen Gemeinschaftsstrukturen weder vom Moortyp noch von der Wirtsmoosart beeinflusst wurden und sich insgesamt deutlich ähnlicher waren als die der Bakterien. Darüber hinaus konnte erstmalig gezeigt werden, dass sich die bakteriellen Gemeinschaften innerhalb der unterschiedlichen Moorsukzessionsstadien zwar ganz erheblich voneinander unterscheiden, ein kleiner Teil der Bakterien dennoch Kerngemeinschaften bilden, die mit allen untersuchten Moosarten assoziiert waren. Bei der hier präsentierten Arbeit handelt es sich um die erste systematische Studie, die sich auf einer großen geographischen Skala mit den bakteriellen und archaeellen Gemeinschaften von Braunmoosen und Torfmoosen aus naturbelassenen nördlichen Mooren befasst. Die vorliegenden Ergebnisse machen deutlich, dass die untersuchten Moose ein ganz spezifisches mikrobielles Konsortium beherbergen, welches mutmaßlich eine Schlüsselrolle bei der Etablierung der Wirtspflanzen am Anfang der Moorentwicklung spielt und darüber hinaus das Potential hat, die charakteristischen Eigenschaften von Mooren sowie deren weitere Entwicklung zu prägen.
    Type of Medium: Dissertations
    Pages: XX, 139, liv Seiten , Illustrationen, Diagramme
    Language: English
    Note: Dissertation, Universität Potsdam, 2024 , Content Preface Acknowledgements Summary Zusammenfassung Abbreviations 1. Introduction 1.1. Peatlands 1.1.1. Peatland development and peat bog succession 1.1.2. Characteristic peatlands of the northern hemisphere 1.1.3. Anthropogenic threats of northern peatlands 1.1.4. Peat bog restoration 1.2. Peatland bryophytes 1.2.1. Brown mosses 1.2.2. Sphagnum mosses 1.3. Moss microbiota 1.3.1. Moss-associated bacteria 1.3.2. Moss-associated archaea 1.3.3. Endophytic prokaryotic communities 1.4. Biotic and abiotic influences on moss-associated microorganisms 1.5. Objectives 1.6. Study sites 1.6.1. High Arctic peatlands of Svalbard (SV) 1.6.2. Polygonal Tundra of Samoylov (SA) 1.6.3. Palsa Bogs of Neiden (NEI) 1.6.4. Kettle Bog Peatlands of Mueritz National Park (MUE) 2. Material and Methods 2.1. Sampling scheme overview 2.2. Sampling of pore water 2.3. Sampling of moss plantlets 2.4. Analysis of pore water chemistry 2.5. Cell wall analysis 2.5.1. Cation exchange capacity (CEC) 2.5.2. Holocellulose (HC) 2.5.3. Lignin and Lignin-like polymers (LLP) 2.5.4. Bulk moss litter analysis 2.6. Moss surface sterilisation and separation of putative epiphytic and endophytic microbial communities 2.7. DNA extraction and sequencing 2.8. Sequence analyses and bioinformatics 2.9. Statistical analyses 2.10. Potential methane production and oxidation assays 2.10.1. Surface sterilisation prior to activity tests 2.10.2. Methane production 2.10.3. Methane oxidation 3. Results 3.1. Peatland bulk and pore water characteristics 3.2. Diversity and structure of natural peatland microbial communities 3.3. Environmental drivers of moss-associated microbial communities 3.4. Microbial taxa associated with brown mosses and Sphagnum mosses 3.4.1. Moss-associated bacteria 3.4.2. Moss-associated archaea 3.4.3. Bacterial and archaeal core communities 3.4.4. Acetobacteraceae as dominant taxon of the bacterial core community 3.5. Sphagnum bacteriomes of disturbed, rewetted and pristine temperate kettle bog 3.6. Potential moss-associated methane production and methane oxidation rates 3.6.1. Moss-associated methane production 3.6.2. Moss-associated methane oxidation 4. Discussion 4.1. Environmental influences on moss-associated bacterial communities 4.2. Moss-associated archaeal communities and their environmental drivers 4.3. Distinct patterns of endophytic bacteria 4.4. The core microbiota and their possible role for peatland succession 4.5. The potential role of Acetobacteraceae for Sphagnum host mosses and bog ecosystems 4.6. Moss-associated microbial communities of the methane cycle and their potential metabolic activity 4.7. Diversity and structure of Sphagnum bacteriomes from pristine, disturbed and rewetted kettle bogs 5. Conclusion 6. Critical remarks and outlook 6.1. Critical remarks 6.2. Outlook Bibliography Supplementary
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  • 7
    Call number: AWI Bio-20-93993
    Type of Medium: Dissertations
    Pages: III, 127 Seiten , Illustrationen
    Language: English
    Note: Dissertation, Universität Potsdam, 2014 , Table of contents I - Abstract II - Zusammenfassung Chapter 1 - Introduction 1.1. Introduction 1.1.1 Motivation 1.1.2 Organisation of thesis 1.1 Scientific background 1.2.1 Arctic and wetland bryophytes 1.2.2 Bryophyte remains as palaeo-environmental indicators 1.2.3 Regional setting 1.3 Objectives ofthe thesis 1.4 Overview of the manuscripts 1.5 Contribution of the authors Chapter 2 - Manuscript #1 Abstract 2.1 Introduction 2.2 Geographic setting 2.3 Materials and methods 2.3.1 Fieldwork 2.3.2 Radiocarbon dating 2.3.3 Geochemical, stable carbon isotope, and granulometric analyses 2.3.4 Analyses of moss remains and vascular plant macrofossils 2.3.5 Pollen analysis 2.3.6 Diatom analysis 2.3.7 Statistical analysis 2.4 Results 2.4.1 High-resolution spatial characteristics oft the investigated polygon and vegetation pattern 2.4.2 Geochronology and age-depth relationships 2.4.3 General properties of the sedimentary fill 2.4.4 Bioindicators 2.4.5 Characterization oftwo different types of polygon pond sediment 2.5. Discussion 2.5.1 Small-scale spatial structure of polygons 2.5.2 Age-depth relationships 2.5.3 Proxy value of the analysed parameters 2.5.4 The general polygon development 2.5.5 Polygon development as a function of external controls and internal adjustment mechanisms 2.6 Conclusions Chapter 3 - Manuscript #11 Abstract 3.1 Introduction 3.2 Material und methods 3.2.1 Regional setting 3.2.3 Field methods and environmental data collection 3.2.4 Data analysis 3.3 Results 3.3.1 Major characteristics of the investigated polygons 3.3.2 Vegetation cover and its relationships with micro-relief and vegetation type 3.3.3 Vegetation alpha-diversity and its relationship with micro-relief and vegetation type 3.3.4 Vegetation composition and its relationship with micro-relief and vegetation type 3.4 Discussion 3.4.1 Patterns of cover, alpha-diversity and compositional turnover of vascular plants and bryophytes along the rim-pond transect (local-scale) 3.4.2 Patterns of cover, alpha-diversity and compositional turnover of vascular plants and bryophytes along the regional-scale forest-tundra transect 3.4.3 Indicator potential ofvascular plant and bryophyte remains from polygonal peats for the reconstruction of local hydrological and regional vegetation changes 3.4.4. Implications of the performed vegetation transect studies for future Arctic warming 3.5 Acknowledgements 2.4.4 Bioindicators 2.4.5 Characterization of two different types of polygon pond sediment 2.5. Discussion 2.5.1 Small-scale spatial structure of polygons 2.5.2 Age-depth relationships 2.5.3 Proxy value of the analysed parameters 2.5.4 The general polygon development 2.5.5 Polygon development as a function of external controls and internal adjustment mechanisms 2.6 Conclusions Chapter 3 - Manuscript #II Abstract 3.1 Introduction 3.2 Material und methods 3.2.1 Regional setting 3.2.3 Field methods and environmental data collection 3.2.4 Data analysis 3.3 Results 3.3.1 Major characteristics of the investigated polygons 3.3.2 Vegetation cover and its relationships with micro-relief and vegetation type 3.3.3 Vegetation alpha-diversity and its relationship with micro-relief and vegetation type 3.3.4 Vegetation composition and its relationship with micro-relief and vegetation type 3.4 Discussion 3.4.1 Patterns of cover, alpha-diversity and compositional turnover of vascular plants and bryophytes along the rim-pond transect (local-scale) 3.4.2 Patterns of cover, alpha-diversity and compositional turnover of vascular plants and bryophytes along the regional-scale forest-tundra transect 3.4.3 Indicator potential of vascular plant and bryophyte remains from polygonal peats for the reconstruction of local hydrological and regional vegetation changes 3.4.4. Implications of the performed vegetation transect studies for future Arctic warming 3.5 Acknowledgements Chapter 4 - Manuscript #3 Abstract 4.1 Introduction 4.2 Material and methods 4.2.1 Sites 4.2.2 Sampling 4.2.3 Investigated moss species 4.2.4 Measurements 4.2.5 Statistical Tests 4.3 Results 4.4 Discussion Chapter 5 - Discussion 5.1 Bryophytes of polygonal landscapes in Siberia 5.1.1 Modern bryophytes in the Siberian Arctic 5.1.2 Biochemical and isotopic characteristics of mosses 5.1.3 Reliability and potential of fossil bryophyte remains as palaeoproxies 5.2 Dynamics of low-centred polygons during the late Holocene 5.3 Outlook Appendix I - Preliminary Report Motivation Material and methods Results and first interpretation Appendix II Additional tables and figures of manuscript #1 Appendix III Additional figures of manuscript #2 Appendix IV - Quantitative approach of Standard Moss Stem (SMS3) Bibliography Acknowledgements Eidesstattliche Erklärung
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  • 8
    Call number: AWI Bio-20-93992
    Type of Medium: Dissertations
    Pages: XIII, 137 Seiten , Illustrationen, Diagramme , 1 CD-ROM
    Language: English
    Note: Dissertation, Universität Potsdam, 2017 , Content List of Abbreviations List of Figures List of Tables Summary Zusammenfassung Motivation Chapter 1 1. Scientific background 1.1 Late Quaternary climate changes and treeline transition in northern Siberia 1.2 Natural archives and proxies to assess vegetation history 1.3 Study area 1.3 Objectives of the thesis 1.4 Thesis outline 1.4.1 Chapters and manuscripts 1.4.2 Author's contribution 1.4.2.1 Manuscript I - published 1.4.2.2 Manuscript II - submitted 1.4.2.3 Manuscript III - prepared for submission Chapter 2 2. Manuscript I: Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia) 2.1 Abstract 2.2 Introduction 2.3 Geographical settings 2.4 Material and methods 2.4.1 Core material 2.4.2 Subsampling of the permafrost core 2.4.3 Molecular genetic laboratory work 2.4.4 Analysis of sequence data and taxonomic assignments 2.4.5 Pollen sample treatment and analysis 2.4.6 Statistical analyses and visualization 2.5 Results 2.5.1 SedaDNA 2.5.1.1 SedaDNA of terrestrial plants 2.5.1.2 SedaDNA of swamp and aquatic plants 2.5.1.3 SedaDNA of bryophytes and algae 2.5.2 Pollen 2.5.2.1 Pollen of terrestrial plants 2.5.2.2 Pollen and spores of swamp and aquatic plants 2.5.2.3 Spores and algae 2.5.3 Ratios of terrestrial to swamp and aquatic taxa and Poaceae to Cyperaceae 2.6 Discussion 2.6.1 Quality and proxy value of sedaDNA and pollen data 2.6.2 Environmental conditions during the pre-LGM (54-51 kyr BP, 18.9-8.35 m) and composition of deposited organic matter 2.6.3 Environmental conditions during the post-LGM (11.4-9.7 kyr BP (13.4-11.1 cal kyr BP)) and composition of deposited organic matter 2.7 Conclusions 2.8 Acknowledgements Chapter 3 3. Manuscript II: Genetic variation of larches at the Siberian tundra-taiga ecotone inferred from the assembly of chloroplast genomes and mitochondrial sequences 3.1. Abstract 3.2. Introduction 3.3. Material and methods 3.3.1 Plant material 3.3.2 DNA isolation and sequencing 3.3.3 Sequence processing and de novo assembly 3.3.4 Chloroplast genome assembly, annotation and variant detection 3.3.5 Mitochondrial sequences 3.3.6 Analyses of genetic variation 3.4 Results 3.4.1 Chloroplast genome structure and genetic variation 3.4.2 Mitochondrial sequences and genetic variation 3.5 Discussion 3.5.1 De novo assembly and genetic variation of chloroplast genomes and mitochondrial sequences 3.5.2 The distribution of genetic variation at the tundra-taiga ecotone 3.6 Conclusions 3.7 Acknowledgements Chapter 4 4. Manuscript III: The history of tree and shrub taxa and past genetic variation of larches on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the last interglacial uncovered by sedimentary ancient DNA 4.1 Abstract 4.2 Introduction 4.3 Materials and methods 4.3.1 Geographic setting 4.3.2 Core material 4.3.2.1 Core L14-02: Yedoma Ice Complex 4.3.2.2 Core L14-03: Thermo terrace 4.3.2.3 Core L14-04 and hand-pieces L14-04B and L14-04C: Thermo terrace including Eemian deposits 4.3.2.4 Core L14-05: Alas 4.3.3 Core sub-sampling 4.3.4 Molecular genetic laboratory work 4.3.4.1 Sedimentary ancient DNA metabarcoding approach 4.3.4.2 Specific amplification of Larix from sedimentary ancient DNA 4.3.5 Filtering of Illumina sequencing data and taxonomic assignments 4.3.6 Statistical analyses and visualization 4.3.7 Geochronology 4.4. Results 4.4.1 Overall composition of the DNA metabarcoding data 4.4.2 Terrestrial vegetation composition 4.4.2.1 Core L14-02: Late Pleistocene Yedoma Ice Complex 4.4.2.2 L14-03: Deeper late Pleistocene deposits 4.4.2.3 L14-04 Thermo terrace including Eemian deposits 4.4.2.4 Core L14-05: Alas with Holocene lake deposits and taberits of the Yedoma Ice Complex 4.4.2.5 The multivariate structure of the terrestrial vegetation among samples and cores 4.4.3 Genetic variation ofsediment-derived Larix sequences 4.5 Discussion 4.5.1 Tree taxa in the sedaDNA record - where do they come from? 4.5.2 Terrestrial plant community changes of warm phases since the last interglacial 4.5.3 Past genetic diversity of larch populations on Bol'shoy Lyakhovsky Island 4.6 Conclusion 4.7 Acknowledgements Chapter 5 5. Synopsis 5.1 The proxy potential of sedaDNA in paleobotanical reconstructions from sedimentary deposits 5.1.1 Combining sedaDNA and pollen to assess plant diversity and vegetation composition 5.1.2 Current limits and opportunities of sedaDNA approaches 5.2 Using genomic data to trace modern and past treeline dynamics 5.2.1 Modern genomic variation at the Siberian treeline 5.2.2 PCR-based markers for paleoenvironmental genetics 5.3 Terrestrial plant community changes and treeline dynamics in north-eastern Siberia since the last interglacial 5.3.1 Vegetation changes in north-eastern Siberia since the last interglacial 5.3.2 Implications for treeline dynamics 5.4 Conclusion 5.5 Outlook Appendix 1. Supplementary material for Manuscript I (Chapter 2) 2. Supplementary material for Manuscript II (Chapter 3) 3. Supplementary material for Manuscript III (Chapter 4) References Acknowledgements Erklärung
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  • 9
    Call number: AWI G5-22-94780
    Type of Medium: Dissertations
    Pages: xxi, 201 Seiten , Illustrationen, Diagramme
    Language: English
    Note: Dissertation, Universität Potsdam, 2021 , Contents List of Figures List of Tables I Preamble 1 Introduction 1.1.1 The Journey from Weather to Climate 1.1.2 The Climate Background 1.1.3 Pollen as Quantitative Indicators of Past Changes 1.2 Overview and Aims of Manuscripts 1.2.1 List of Manuscripts 1.2.2 Short Summaries of the Manuscripts 1.3 Author Contributions to the Manuscripts II Manuscripts 2 Comparing estimation of techniques for temporal Scaling 2.1 Introduction 2.2 Data and Methods 2.2.1 Scaling estimation methods 2.2.2 Evaluation of the estimators 2.2.3 Data 2.3 Results 2.3.1 Effect of Regular and Irregular Sampling 2.3.2 Effect of Time series length 2.3.3 Application to database 2.4 Discussion 2.5 Conclusions 3 Land temperature variability driven by oceans at millennial timescales 4 Variability of surface climate in simulations of past and future 4.1 Introduction 4.2 Data and Method 4.2.1 Model simulations 4.2.2 The Last Glacial Maximum experiment 4.2.3 The mid Holocene experiment (midHolocene) 4.2.4 The warming experiments 1pctCO2 and abrupt4xCO2 4.2.5 Preprocessing of model simulations 4.2.6 Comparisons across the ensemble 4.2.7 Diagnosing variability changes 4.2.8 Changes in precipitation extremes 4.2.9 Timescale-dependence of the variability changes 4.3 Results 4.3.1 Hydrological sensitivity across the ensemble 4.3.2 Changes in local interannual variability 4.3.3 Changes in modes of variability 4.3.4 Circulation patterns underlying extratropical precipitation extremes 4.3.5 Changes in. the spectrum of variability 4.4 Discussion 4.4.1 Changes in climate variability with global mean temperature 4.4.2 Temperature vs. precipitation scaling 4.4.3 Comparison to climate reconstructions and observations 4.4.4 Limitations 4.5 Conclusions 5 Holocene vegetation variability in the Northern Hemisphere 5.1 Introduction 5.2 Data and Methods 5.2.1 Pollen Database 5.2.2 Principal Component Analysis 5.2.3 Timescale-dependent Estimates of Variability 5.2.4 Biome Classification 5.3 Results 5.3.1 General Vegetation Variability Analysis 5.3.2 Comparison of Forested and Open Land Vegetations 5.3.3 Comparison of Broadleaf and Needleleaf Fore ts 5.3.4 Comparison of Temperate and Boreal Coniferous Forests 5.3.5 Comparison of Evergreen and Deciduous Boreal Forests 5.4 Discussion 5.5 Conclusion III Postamble 6 General discussion and conclusion 6.1 Overview 6.2 Timescale-Dependent Estimates of Variability 6.3 Climate and Vegetation Variabilities in the Holocene 6.4 Implications for the 21th Century 6.5 Outlook IV Appendix A Supplementary figures from "Comparing estimation techniques for temporal scaling in paleo-climate timeseries" A.1 Block Average Results A.2 First-Order Correction for the Effect of Interpolation A.3 Change in Bias and Standard Deviation B Methods and supplementary information from "Land temperature variability driven by oceans at millennial timescales" B.1 Methods B.1.1 Reconstructions B.1.2 Significance Testing B.1.3 Testing for Anthropogenic Impacts B.1.4 Instrumental Data B.1.5 Model Data B.1.6 Spectral Estimates B.1.7 Variance Ratios B.1.8 Sub-Decadal Variability Binning B.1.9 Correlation B.1.10 Moran's I B.2 Supplementary Information B.2.1 Tree Ring Data Analysis B.2.2 Energy-Balance Equations B.3 Extended Data Figures C Supplementary figures from "Variability of surface climate in simulations of past and future" D Supplementary figures from "Characterization of holocene vegetation variability in the Northern Hemisphere" Bibliography
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  • 10
    Call number: AWI Bio-22-94840
    Description / Table of Contents: Vegetation change at high latitudes is one of the central issues nowadays with respect to ongoing climate changes and triggered potential feedback. At high latitude ecosystems, the expected changes include boreal treeline advance, compositional, phenological, physiological (plants), biomass (phytomass) and productivity changes. However, the rate and the extent of the changes under climate change are yet poorly understood and projections are necessary for effective adaptive strategies and forehanded minimisation of the possible negative feedbacks. The vegetation itself and environmental conditions, which are playing a great role in its development and distribution are diverse throughout the Subarctic to the Arctic. Among the least investigated areas is central Chukotka in North-Eastern Siberia, Russia. Chukotka has mountainous terrain and a wide variety of vegetation types on the gradient from treeless tundra to northern taiga forests. The treeline there in contrast to subarctic North America and north-western and central Siberia is represented by a deciduous conifer, Larix cajanderi Mayr. The vegetation varies from prostrate lichen Dryas octopetala L. tundra to open graminoid (hummock and non-hummock) tundra to tall Pinus pumila (Pall.) Regel shrublands to sparse and dense larch forests. Hence, this thesis presents investigations on recent compositional and above-ground biomass (AGB) changes, as well as potential future changes in AGB in central Chukotka. The aim is to assess how tundra-taiga vegetation develops under changing climate conditions particularly in Fareast Russia, central Chukotka. Therefore, three main research questions were considered: 1) What changes in vegetation composition have recently occurred in central Chukotka? 2) How have the above-ground biomass AGB rates and distribution changed in central Chukotka? 3) What are the spatial dynamics and rates of tree AGB change in the upcoming millennia in the northern tundra-taiga of central Chukotka? Remote sensing provides information on the spatial and temporal variability of vegetation. I used Landsat satellite data together with field data (foliage projective cover and AGB) from two expeditions in 2016 and 2018 to Chukotka to upscale vegetation types and AGB for the study area. More specifically, I used Landsat spectral indices (Normalised Difference Vegetation Index (NDVI), Normalised Difference Water Index (NDWI) and Normalised Difference Snow Index (NDSI)) and constrained ordination (Redundancy analysis, RDA) for further k-means-based land-cover classification and general additive model (GAM)-based AGB maps for 2000/2001/2002 and 2016/2017. I also used Tandem-X DEM data for a topographical correction of the Landsat satellite data and to derive slope, aspect, and Topographical Wetness Index (TWI) data for forecasting AGB. Firstly, in 2016, taxa-specific projective cover data were collected during a Russian-German expedition. I processed the field data and coupled them with Landsat spectral Indices in the RDA model that was used for k-means classification. I could establish four meaningful land-cover classes: (1) larch closed-canopy forest, (2) forest tundra and shrub tundra, (3) graminoid tundra and (4) prostrate herb tundra and barren areas, and accordingly, I produced the land cover maps for 2000/2001/2002 and 2016/20017. Changes in land-cover classes between the beginning of the century (2000/2001/2002) and the present time (2016/2017) were estimated and interpreted as recent compositional changes in central Chukotka. The transition from graminoid tundra to forest tundra and shrub tundra was interpreted as shrubification and amounts to a 20% area increase in the tundra-taiga zone and 40% area increase in the northern taiga. Major contributors of shrubification are alder, dwarf birch and some species of the heather family. Land-cover change from the forest tundra and shrub tundra class to the larch closed-canopy forest class is interpreted as tree infilling and is notable in the northern taiga. We find almost no land-cover changes in the present treeless tundra. Secondly, total AGB state and change were investigated for the same areas. In addition to the total vegetation AGB, I provided estimations for the different taxa present at the field sites. As an outcome, AGB in the study region of central Chukotka ranged from 0 kg m-2 at barren areas to 16 kg m-2 in closed-canopy forests with the larch trees contributing the highest. A comparison of changes in AGB within the investigated period from 2000 to 2016 shows that the greatest changes (up to 1.25 kg m 2 yr 1) occurred in the northern taiga and in areas where land cover changed to larch closed-canopy forest. Our estimations indicate a general increase in total AGB throughout the investigated tundra-taiga and northern taiga, whereas the tundra showed no evidence of change in AGB within the 15 years from 2002 to 2017. In the third manuscript, potential future AGB changes were estimated based on the results of simulations of the individual-based spatially explicit vegetation model LAVESI using different climate scenarios, depending on Representative Concentration Pathways (RCPs) RCP 2.6, RCP 4.5 and RCP 8.5 with or without cooling after 2300 CE. LAVESI-based AGB was simulated for the current state until 3000 CE for the northern tundra-taiga study area for larch species because we expect the most notable changes to occur will be associated with forest expansion in the treeline ecotone. The spatial distribution and current state of tree AGB was validated against AGB field data, AGB extracted from Landsat satellite data and a high spatial resolution image with distinctive trees visible. The simulation results are indicating differences in tree AGB dynamics plot wise, depending on the distance to the current treeline. The simulated tree AGB dynamics are in concordance with fundamental ecological (emigrational and successional) processes: tree stand formation in simulated results starts with seed dispersion, tree stand establishment, tree stand densification and episodic thinning. Our results suggest mostly densification of existing tree stands in the study region within the current century in the study region and a lagged forest expansion (up to 39% of total area in the RCP 8.5) under all considered climate scenarios without cooling in different local areas depending on the closeness to the current treeline. In scenarios with cooling air temperature after 2300 CE, forests stopped expanding at 2300 CE (up to 10%, RCP 8.5) and then gradually retreated to their pre-21st century position. The average tree AGB rates of increase are the strongest in the first 300 years of the 21st century. The rates depend on the RCP scenario, where the highest are as expected under RCP 8.5. Overall, this interdisciplinary thesis shows a successful integration of field data, satellite data and modelling for tracking recent and predicting future vegetation changes in mountainous subarctic regions. The obtained results are unique for the focus area in central Chukotka and overall, for mountainous high latitude ecosystems.
    Type of Medium: Dissertations
    Pages: 149 Seiten , Illustrationen, Diagramme
    Language: English
    Note: Dissertation, Potsdam, Universität Potsdam, 2022 , Contents Abstract Zusammenfassung Contents Abbreviations Motivation 1 Introduction 1.1 Scientific background 1.2 Study region 1.3 Aims and objectives 2 Materials and methods 3.1 Section 4 - Strong shrub expansion in tundra-taiga, tree infilling in taiga and stable tundra in central Chukotka (north-eastern Siberia) between 2000 and 2017 3.2 Section 5 - Recent above-ground biomass changes in central Chukotka (NE Siberia) combining field-sampling and remote sensing 3.3 Section 6 - Future spatially explicit tree above-ground biomass trajectories revealed for a mountainous treeline ecotone using the individual-based model LAVESI 4 Strong shrub expansion in tundra-taiga, tree infilling in taiga and stable tundra in central Chukotka (north-eastern Siberia) between 2000 and 2017 Abstract 1 Introduction 2 Materials and methods 2.1 Field data collection and processing 2.2 Landsat data, pre-processing and spectral indices processing 2.3 Redundancy analysis (RDA) and classification approaches 3 Results 3.1 General characteristics of the vegetation field data 3.2 Relating field data to Landsat spectral indices in the RDA model 3.3 Land-cover classification 3.4 Land-cover change between 2000 and 2017 4 Discussion 4.1 Dataset limitations and optimisation 4.2 Vegetation changes from 2000/2001/2002 to 2016/2017 Conclusions Acknowledgements Data availability statement References Appendix A. Detailed description of Landsat acquisitions Appendix B. MODIS NDVI time series from 2000 to 2018 Appendix C. Landsat Indices values for each analysed vegetation site Appendix D. Fuzzy c-means classification for interpretation of uncertainties for land-cover mapping Appendix E. Validation of land-cover maps Appendix F. K-means classification results Appendix G. Heterogeneity of natural landscapes and mixed pixels of satellite data Appendix H. Distribution of land-cover classes and their changes by study area 5 Recent above-ground biomass changes in central Chukotka (NE Siberia) combining field-sampling and remote sensing Abstract 1 Introduction 2 Materials and methods 2.1 Study region and field surveys 2.2 Above-ground biomass upscaling and change derivation 3 Results 3.1 Vegetation composition and above-ground biomass 3.2 Upscaling above-ground biomass using GAM 3.3 Change of above-ground biomass between 2000 and 2017 in the four focus areas 4 Discussion 4.1 Recent state of above-ground biomass at the field sites 4.2 Recent state of above-ground biomass upscaled for central Chukotka 4.3 Change in above-ground biomass within the investigated 15–16 years in central Chukotka 5 Conclusions Data availability statement Author contributions Competing interests Acknowledgements References Appendix A. Sampling and above-ground biomass (AGB) calculation protocol for field data 6 Future spatially explicit tree above-ground biomass trajectories revealed for a mountainous treeline ecotone using the individual-based model LAVESI Abstract 1 Introduction 2 Materials and methods 2.1 Study region 2.2 LAVESI model setup, parameterisation, and validation 2.2.4 LAVESI simulation setup for this study 2.2.5 Validation of the model’s performance 3 Results 3.1 Dynamics and spatial distribution changes of tree above-ground-biomass 3.2 Spatial and temporal validation of the contemporary larch AGB 4 Discussion 4.1 Future dynamics of tree AGB at a plot level 4.2 What are the future dynamics of tree AGB at the landscape level? 5 Conclusions Data availability Acknowledgements References Appendix B. Permutation tests for tree presence versus topographical parameters Appendix C. Landsat-based, field, and simulated estimations of larch above-ground biomass (AGB). 7 Synthesis 7.1 What changes in vegetation composition have happened from 2000 to 2017 in central Chukotka? 7.2 How have the above-ground biomass (AGB) distribution and rates changed from 2000 to 2017 in central Chukotka? 7.3 What are the spatial dynamics and rates of tree AGB change in the upcoming centuries in the northern tundra-taiga from 2020 to 3000 CE on the plot level and landscape level? References Acknowledgements
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