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  • 1
    Monograph available for loan
    Monograph available for loan
    Potsdam : Alfred-Wegener-Inst. für Polar- und Meeresforschung
    Call number: AWI G3-08-0009
    Type of Medium: Monograph available for loan
    Pages: VIII, 108 S. : Ill., graph. Darst.
    Classification:
    Meteorology and Climatology
    Language: English
    Note: Bremen, Univ., Diss., 2007
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  • 2
    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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  • 3
    Call number: AWI G3-23-95073
    Description / Table of Contents: The Arctic is changing rapidly and permafrost is thawing. Especially ice-rich permafrost, such as the late Pleistocene Yedoma, is vulnerable to rapid and deep thaw processes such as surface subsidence after the melting of ground ice. Due to permafrost thaw, the permafrost carbon pool is becoming increasingly accessible to microbes, leading to increased greenhouse gas emissions, which enhances the climate warming. The assessment of the molecular structure and biodegradability of permafrost organic matter (OM) is highly needed. My research revolves around the question “how does permafrost thaw affect its OM storage?” More specifically, I assessed (1) how molecular biomarkers can be applied to characterize permafrost OM, (2) greenhouse gas production rates from thawing permafrost, and (3) the quality of OM of frozen and (previously) thawed sediments. I studied deep (max. 55 m) Yedoma and thawed Yedoma permafrost sediments from Yakutia (Sakha Republic). I analyzed sediment cores taken below thermokarst lakes on the Bykovsky Peninsula (southeast of the Lena Delta) and in the Yukechi Alas (Central Yakutia), and headwall samples from the permafrost cliff Sobo-Sise (Lena Delta) and the retrogressive thaw slump Batagay (Yana Uplands). I measured biomarker concentrations of all sediment samples. Furthermore, I carried out incubation experiments to quantify greenhouse gas production in thawing permafrost. I showed that the biomarker proxies are useful to assess the source of the OM and to distinguish between OM derived from terrestrial higher plants, aquatic plants and microbial activity. In addition, I showed that some proxies help to assess the degree of degradation of permafrost OM, especially when combined with sedimentological data in a multi-proxy approach. The OM of Yedoma is generally better preserved than that of thawed Yedoma sediments. The greenhouse gas production was highest in the permafrost sediments that thawed for the first time, meaning that the frozen Yedoma sediments contained most labile OM. Furthermore, I showed that the methanogenic communities had established in the recently thawed sediments, but not yet in the still-frozen sediments. My research provided the first molecular biomarker distributions and organic carbon turnover data as well as insights in the state and processes in deep frozen and thawed Yedoma sediments. These findings show the relevance of studying OM in deep permafrost sediments.
    Type of Medium: Dissertations
    Pages: xxiii, 178 Seiten , Illustrationen, Diagramme, Karten
    Language: English
    Note: Table of Contents Abstract Zusammenfassung Samenvatting Acknowledgements List of Figures List of Tables List of Abbreviations 1 Introduction 1.1 Motivation 1.2 Aims and research questions 1.3 Scientific background 1.3.1 The Arctic in a changing climate 1.3.2 Northern Hemisphere permafrost region 1.3.3 Permafrost degradation 1.3.3.1 Thermokarst development 1.3.3.2 Retrogressive thaw slumps 1.3.4 Organic matter in permafrost deposits 1.4 Material and methods 1.4.1 Study sites 1.4.2 Main laboratory methods 1.5 Thesis structure 1.6 Overview of publications 1.6.1 Publication “n-Alkane Characteristics of Thawed Permafrost Deposits Below a Thermokarst Lake on Bykovsky Peninsula, Northeastern Siberia” 1.6.2 Publication “Greenhouse gas production and lipid biomarker distribution in Yedoma and Alas thermokarst lake sediments in Eastern Siberia” 1.6.3 Publication “Organic matter characteristics of a rapidly eroding permafrost cliff in NE Siberia (Lena Delta, Laptev Sea region)” 1.6.4 Publication “Molecular biomarkers in Batagay megaslump permafrost deposits reveal clear differences in organic matter preservation between glacial and interglacial periods” 1.6.5 Contributions to complementary research 2 Bykovsky Peninsula 2.1 Abstract 2.2 Introduction 2.3 Study area 2.4 Material and methods 2.4.1 Field work 2.4.2 Laboratory analyses 2.4.2.1 Biomarker analysis 2.4.2.2 Biomarker indices 2.5 Results 2.5.1 Bulk sediment 2.5.1.1 Long core PG2412 2.5.1.2 Short core PG2420 2.5.2 Hydrochemistry 2.5.3 n-Alkane distributions 2.6 Discussion 2.6.1 Depositional history at the study site 2.6.1.1 Unit I - Early Weichselian fluvial sedimentation 2.6.1.2 Unit II – Yedoma deposition in wetland landscapes dominated by low-centered polygons 2.6.1.3 Unit III/Unit A – Yedoma deposition under cold-dry conditions during the Late Weichselian 2.6.1.4 Unit IV/Unit B – Holocene thermokarst lake formation and lacustrine sedimentation 2.6.2 Organic matter degradation 2.7 Conclusion 2.8 Acknowledgements 3 Yukechi Alas 3.1 Abstract 3.2 Introduction 3.3 Methods and materials 3.3.1 Study area 3.3.2 Field work 3.3.3 Laboratory analyses 3.3.3.1 Organic carbon content 3.3.3.2 Lipid biomarkers 3.3.4 Incubations 3.3.5 Statistical analysis 3.4 Results 3.4.1 Organic matter characteristics 3.4.1.1 Alas lake sediment core YU-L7 3.4.1.2 Yedoma lake sediment core YU-L15 3.4.2 Greenhouse gas production 3.4.2.1 Alas lake sediment core YU-L7 3.4.2.2 Yedoma lake sediment core YU-L15 3.4.2.3 Carbon mineralization 3.4.3 Statistical correlation and regression 3.5 Discussion 3.5.1 Organic matter degradation potential 3.5.1.1 Organic carbon quantity 3.5.1.2 Organic matter preservation and talik formation 3.5.1.3 Presence of methanogenic communities 3.5.2 Greenhouse gas production 3.5.2.1 Carbon dioxide production 3.5.2.2 Methane production 3.5.3 GHG links with other parameters and outlook 3.6 Conclusion 3.7 Acknowledgements 4 Sobo-Sise cliff 4.1 Abstract 4.2 Introduction 4.3 Study area 4.4 Methods 4.4.1 Fieldwork 4.4.2 Sedimentological organic matter parameters 4.4.3 Lipid biomarkers 4.4.3.1 Extraction and fraction separation 4.4.3.2 GC-MS measurements and compound quantification 4.4.4 Biomarker indices 4.4.4.1 Average Chain Length 4.4.4.2 Carbon Preference Index 4.4.4.3 Higher Plant Fatty Acids 4.4.5 Data analysis 4.5 Results 4.5.1 Sedimentological organic matter parameters 4.5.2 Biomarkers 4.5.2.1 n-Alkanes 4.5.2.2 Fatty acids 4.5.3 Clustering 4.6 Discussion 4.6.1 Terrestrial depositional environment 4.6.1.1 Organic matter source 4.6.1.2 Organic matter quality 4.6.2 Implications and outlook 4.7 Conclusion 4.8 Acknowledgements 5 Batagay thaw slump 5.1 Abstract 5.2 Introduction 5.3 Study site 5.4 Methods 5.4.1 Sample collection 5.4.2 Laboratory analyses 5.5 Results 5.5.1 Detected biomolecules 5.5.2 Lower Ice Complex 5.5.3 Lower Sand Unit 5.5.4 Woody Layer 5.5.5 Upper Ice Complex - Yedoma 5.5.6 Holocene Cover 5.6 Discussion 5.6.1 Biogeochemical legacy of glacial periods 5.6.2 Biogeochemical legacy of interglacial periods 5.6.3 Modern organic matter mobilization in the Batagay megaslump 5.7 Conclusion 5.8 Acknowledgements 6 Synthesis 6.1 Lipid biomarkers to characterize permafrost organic matter 6.1.1 Organic matter source 6.1.2 Organic matter quality 6.2 Mobilization of organic matter in thawing permafrost 6.2.1 Methane production vs. emission 6.2.2 Using the data in models 6.2.3 Transport of OM into aquatic systems 6.3 Recommendations for future research References Appendix A Supporting information for Chapter 2 Appendix B Supporting information for Chapter 3 Appendix C Supporting information for Chapter 4 Appendix D Supporting information for Chapter 5
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  • 4
    Call number: AWI Bio-21-94540
    Description / Table of Contents: This thesis investigates how the permafrost microbiota responds to global warming. In detail, the constraints behind methane production in thawing permafrost were linked to methanogenic activity, abundance and composition. Furthermore, this thesis offers new insights into microbial adaptions to the changing environmental conditions during global warming. This was assesed by investigating the potential ecological relevant functions encoded by plasmid DNA within the permafrost microbiota. Permafrost of both interglacial and glacial origin spanning the Holocene to the late Pleistocene, including Eemian, were studied during long-term thaw incubations. Furthermore, several permafrost cores of different stratigraphy, soil type and vegetation cover were used to target the main constraints behind methane production during short-term thaw simulations. Short- and long-term incubations simulating thaw with and without the addition of substrate were combined with activity measurements, amplicon and metagenomic sequencing of permanently frozen and seasonally thawed active layer. Combined, it allowed to address the following questions. i) What constraints methane production when permafrost thaws and how is this linked to methanogenic activity, abundance and composition? ii) How does the methanogenic community composition change during long-term thawing conditions? iii) Which potential ecological relevant functions are encoded by plasmid DNA in active layer soils? The major outcomes of this thesis are as follows. i) Methane production from permafrost after long-term thaw simulation was found to be constrained mainly by the abundance of methanogens and the archaeal community composition. Deposits formed during periods of warmer temperatures and increased precipitation, (here represented by deposits from the Late Pleistocene of both interstadial and interglacial periods) were found to respond strongest to thawing conditions and to contain an archaeal community dominated by methanogenic archaea (40% and 100% of all detected archaea). Methanogenic population size and carbon density were identified as main predictors for potential methane production in thawing permafrost in short-term incubations when substrate was sufficiently available. ii) Besides determining the methanogenic activity after long-term thaw, the paleoenvironmental conditions were also found to influence the response of the methanogenic community composition. Substantial shifts within methanogenic community structure and a drop in diversity were observed in deposits formed during warmer periods, but not in deposits from stadials, when colder and drier conditions occurred. Overall, a shift towards a dominance of hydrogenotrophic methanogens was observed in all samples, except for the oldest interglacial deposits from the Eemian, which displayed a potential dominance of acetoclastic methanogens. The Eemian, which is discussed to serve as an analogue to current climate conditions, contained highly active methanogenic communities. However, all potential limitation of methane production after permafrost thaw, it means methanogenic community structure, methanogenic population size, and substrate pool might be overcome after permafrost had thawed on the long-term. iii) Enrichments with soil from the seasonally thawed active layer revealed that its plasmid DNA (‘metaplasmidome’) carries stress-response genes. In particular it encoded antibiotic resistance genes, heavy metal resistance genes, cold shock proteins and genes encoding UV-protection. Those are functions that are directly involved in the adaptation of microbial communities to stresses in polar environments. It was further found that metaplasmidomes from the Siberian active layer originate mainly from Gammaproteobacteria. By applying enrichment cultures followed by plasmid DNA extraction it was possible to obtain a higher average contigs length and significantly higher recovery of plasmid sequences than from extracting plasmid sequences from metagenomes. The approach of analyzing ‘metaplasmidomes’ established in this thesis is therefore suitable for studying the ecological role of plasmids in polar environments in general. This thesis emphasizes that including microbial community dynamics have the potential to improve permafrost-carbon projections. Microbially mediated methane release from permafrost environments may significantly impact future climate change. This thesis identified drivers of methanogenic composition, abundance and activity in thawing permafrost landscapes. Finally, this thesis underlines the importance to study how the current warming Arctic affects microbial communities in order to gain more insight into microbial response and adaptation strategies.
    Type of Medium: Dissertations
    Pages: VI, 243 Seiten , Diagramme, Illustrationen
    Language: English
    Note: Dissertation, Universität Potsdam, 2020 , Contents Preface Acknowledgements Contents Summary Zusammenfassung List of abbreviations Chapter 1. Introduction 1.1 Motivation 1.2 Carbon storage in Arctic permafrost environments and the permafrost carbon feedback (PCF) 1.3 Methane cycling microorganisms 1.4 The microbial ecology of permafrost 1.5 Plasmids and their potential role in stress tolerance 1.6 Objectives Chapter 2. Study sites 2.1 Regional settings 2.2 Kurungnakh and Samoylov Island 2.3 Bol'shoy Lyakhovsky Island 2.4 Herschel Island Chapter 3. Manuscripts 3.1 Overview of manuscripts, including contribution of co-authors. 3.2 Manuscript I Methanogenic response to long-term permafrost thaw is determined by paleoenvironment 3.3 Manuscript II Methane production in thawing permafrost is constrained by methanogenic population size and carbon density 3.4 Manuscript III Metaplasmidome-encoded functional potential of permafrost active layer soils Chapter 4. Synthesis 4.1 Introduction 4.2 Constraints behind methane production from thawing permafrost 4.3 The methanogenic community response to long-term permafrost thaw 4.4 The adaptive potential of the permafrost micro biota to cope with stress factors during global warming 4.5 Conclusion Chapter 5. Future research directions and perspectives Chapter 6. References Chapter 7. Appendix 7.1 Supporting information for manuscript I 7.2 Supporting information for manuscript II 7.3 Supporting information for manuscript III 7.4 ESR collaboration, manuscript IV
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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
    Publication Date: 2023-08-25
    Description: Since the beginning of the Anthropocene, lacustrine biodiversity has been influenced by climate change and human activities. These factors advance the spread of harmful cyanobacteria in lakes around the world, which affects water quality and impairs the aquatic food chain. In this study, we assessed changes in cyanobacterial community dynamics via sedimentary DNA (sedaDNA) from well-dated lake sediments of Lake Tiefer See, which is part of the Klocksin Lake Chain spanning the last 350 years. Our diversity and community analysis revealed that cyanobacterial communities form clusters according to the presence or absence of varves. Based on distance-based redundancy and variation partitioning analyses (dbRDA and VPA) we identified that intensified lake circulation inferred from vegetation openness reconstructions, δ13C data (a proxy for varve preservation) and total nitrogen content were abiotic factors that significantly explained the variation in the reconstructed cyanobacterial community from Lake Tiefer See sediments. Operational taxonomic units (OTUs) assigned to Microcystis sp. and Aphanizomenon sp. were identified as potential eutrophication-driven taxa of growing importance since circa common era (ca. CE) 1920 till present. This result is corroborated by a cyanobacteria lipid biomarker analysis. Furthermore, we suggest that stronger lake circulation as indicated by non-varved sediments favoured the deposition of the non-photosynthetic cyanobacteria sister clade Sericytochromatia, whereas lake bottom anoxia as indicated by subrecent- and recent varves favoured the Melainabacteria in sediments. Our findings highlight the potential of high-resolution amplicon sequencing in investigating the dynamics of past cyanobacterial communities in lake sediments and show that lake circulation, anoxic conditions, and human-induced eutrophication are main factors explaining variations in the cyanobacteria community in Lake Tiefer See during the last 350 years.
    Description: Virtual Institute of Integrated Climate and Landscape Evolution Analyses -ICLEA-
    Description: Leibniz-Gemeinschaft http://dx.doi.org/10.13039/501100001664
    Description: Helmholtz-Gemeinschaft (DE)
    Description: Deutsche Bundesstiftung Umwelt http://dx.doi.org/10.13039/100007636
    Description: Helmholtz-Zentrum Potsdam Deutsches GeoForschungsZentrum - GFZ (4217)
    Keywords: ddc:577.6 ; Late Holocene ; Methylheptadecanes ; Varves ; Anthropocene ; Sericytochromatia ; Melainabacteria
    Language: English
    Type: doc-type:article
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  • 8
    Publication Date: 2016-04-20
    Print ISSN: 0302-8933
    Electronic ISSN: 1432-072X
    Topics: Biology
    Published by Springer
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  • 9
    Publication Date: 2017-08-01
    Print ISSN: 0038-0717
    Electronic ISSN: 1879-3428
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Elsevier
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  • 10
    Publication Date: 2020-09-01
    Print ISSN: 0966-842X
    Electronic ISSN: 1878-4380
    Topics: Biology
    Published by Cell Press
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