ALBERT

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

Note: Dissertation, Universität Potsdam, 2024 , Contents 1 Introduction 1.1 The Arctic sea-ice cover 1.1.1 Sea ice in the coupled Arctic climate system 1.1.2 Recent changes of the Arctic sea ice 1.2 The atmosphere as driver of sea-ice variability 1.2.1 Large-scale circulation patterns 1.2.2 Role of cyclones 1.3 Thesis structure and research questions 2 Theory and methods 2.1 Synoptic cyclones 2.1.1 Related fundamentals of atmospheric dynamics 2.1.2 Cyclone activity in the Arctic 2.2 Cyclone tracking and cyclone occurrence mask 2.3 Dynamic and thermodynamic sea-ice variability related to cyclones 3 New insights into cyclone impacts on sea ice in the Atlantic sector of the Arctic Ocean in winter 3.1 Abstract 3.2 Introduction 3.3 Data and methods 3.3.1 Database and cyclone identification 3.3.2 Quantification of cyclone impacts on SIC 3.4 Cyclone impacts on SIC 3.4.1 Effects of different time scales and regions 3.4.2 Effects of SIC conditions and cyclone depth 3.4.3 Spatial variability of SIC response to cyclones 3.4.4 Relation to near-surface wind and surface energy budget 3.5 Signature of ’New Arctic’ conditions 3.6 Conclusions 3.7 Supplementary material 4 Impact of three intense winter cyclones on the sea ice cover in the Barents Sea: A case study with a coupled regional climate model 4.1 Abstract 4.2 Introduction 4.3 Data and methods 4.3.1 HIRHAM–NAOSIM simulation 4.3.2 Supplementary evaluation data 4.3.3 Dynamic and thermodynamic contributions to sea-ice changes 4.4 Results 4.4.1 Cyclone cases 4.4.2 Cyclone impacts on SEB 4.4.3 Cyclone impacts on sea-ice concentration (SIC) 4.4.4 Cyclone impacts on sea-ice thickness (SIT) 4.4.5 Context to other cyclone cases during the MOSAiC winter 4.5 Discussion and conclusions 4.6 Supplementary material 5 Cyclone impacts on sea ice concentration in the Atlantic Arctic Ocean: Annual cycle and recent changes 5.1 Abstract 5.2 Introduction 5.3 Data and methods 5.4 Changes in cyclones and traversed sea ice 5.5 Cyclone impacts on SIC 5.5.1 Annual cycle in the old Arctic 5.5.2 Changes in the new Arctic 5.5.3 Regional changes in autumn 5.6 Conclusions 5.7 Supplementary material 6 Conclusions and Outlook 6.1 What is the statistical impact of cyclone passages on sea-ice concentration (SIC) in the Atlantic Arctic Ocean? 6.2 What are the individual contributions of dynamic and thermodynamic processes to sea-ice changes related to cyclones? 6.3 Do the SIC impacts of cyclones change in a warming Arctic and what are the related mechanisms? 6.4 Ways forward Appendix: Cyclones modulate the control of the North Atlantic Oscillation on transports into the Barents Sea Bibliography

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

Note: Contents Foreword Prologue Earth’s Freezer: Introduction to Permafrost Frozen grounds: Permafrost in the Arctic Permafrost in profile: Landscape features Frozen in time: The history of permafrost An icy balance: Arctic permafrost physiography What lies within: Organic carbon in permafrost When ice grows up: Pingo Canadian Landmark Drilling down: Learning the secrets of permafrost Portrait: Annett Bartsch Un/settled: Life on frozen ground Frozen States I: Russian Federation Portrait: Vyacheslav Shadrin Frozen States II: North America Portrait: Jessi Pascal Frozen States III: Nordic region Portrait: Palle Jeremiassen Awakening Giant: Permafrost and Climate Change Warming up, warming down: Increasing ground temperatures The chill is gone: Thickening of the active layer Disappearing act: Declining permafrost extent Microorganisms, macro effects: Permafrost carbon cycle Faster, deeper, stronger I: Speed of thaw in North America Faster, deeper, stronger II: Speed of thaw in Scandinavia and the Russian Federation Crossing the threshold: Future scenarios of carbon release Portrait: Dmitry Streletskiy Moving Grounds: Permafrost Changes Frost and flora: The role of vegetation in permafrost landscapes Fire on ice: Peat, permafrost, and fire State of matter: Water, snow, and permafrost The rivers run through it: Arctic rivers, deltas and hydrology Along the edge of the world: Arctic coastal classification Wear and tear: Erosion of Arctic permafrost coasts Eating into the landscape: Retrogressive thaw slumps Portrait: Angus Alunik Losing ground: Projected rates of Arctic coastal erosion Beneath the waves: Changes in subsea permafrost Arctic Ripples: Impacts of Permafrost Thaw Feeling the heat: Permafrost thaw impacts on infrastructure Risky business I: North American Arctic and Kalaallit Nunaat (Greenland) Risky business II: The Russian Federation and Scandinavian Arctic Terra infirma I: Coastal infrastructure in Yamalo-Nenets Portrait: Susanna Gartler Terra infirma II: Reinforcing runways in Paulatuk Terra infirma III: Keeping cold food cold in Alaska Terra infirma IV: Urban planning in Ilulissat Nothing in isolation: Health and wellness and permafrost Portrait: Gwen Healey Akearok Toxic grounds: Contaminants and environmental health Coming back to life: Reemerging pathogens Frozen assets I: The formal economy Frozen assets II: Traditional and subsistence activities Cultural homeland: Alaas landscapes in Yakutia Holding Tight: Adaptation to Permafrost Thaw Bumpy road ahead: Transportation infrastructure and permafrost Undermined: Mining infrastructure and permafrost Keeping the light on: Energy infrastructure and permafrost No time to waste: Waste management and permafrost Modern history: Preserving Svalbard’s cultural heritage Portrait: Ingrid Rekkavik Going South: Permafrost in Other Areas A planetary perspective: Permafrost outside the Arctic Frozen giants: Permafrost in the mountains The view from the top: The Qinghai-Tibetan Plateau, Hindu Kush Himalaya, and Andes Europe’s frozen heart: Permafrost in the Alps The ends of the Earth I: Permafrost in Antarctica The ends of the Earth II: Antarctic Peninsula The ends of the Earth III: Queen Maud Land, Victoria Land, and the McMurdo Dry Valleys Over the Horizon Authors and contributors Acknowledgments Artist spotlight: Olga Borjon-Privé (Oluko) Artist spotlight: Katie Orlinsky Glossary Acronyms References

Note: J. B. Dawson, D. A. Carswell, J. Hall, and K.H. Wedepohl: Introduction / Geological Society, London, Special Publications, 24:vii-viii, doi:10.1144/GSL.SP.1986.024.01.01 --- R. Meissner: Twenty years of deep seismic reflection profiling in Germany—a contribution to our knowledge of the nature of the lower Variscan crust / Geological Society, London, Special Publications, 24:1-10, doi:10.1144/GSL.SP.1986.024.01.02 --- D. H. Matthews: Seismic reflections from the lower crust around Britain / Geological Society, London, Special Publications, 24:11-21, doi:10.1144/GSL.SP.1986.024.01.03 --- S. B. Smithson: A physical model of the lower crust from North America based on seismic reflection data / Geological Society, London, Special Publications, 24:23-34, doi:10.1144/GSL.SP.1986.024.01.04 --- V. Haak and R. Hutton: Electrical resistivity in continental lower crust / Geological Society, London, Special Publications, 24:35-49, doi:10.1144/GSL.SP.1986.024.01.05 --- J. Hall: The physical properties of layered rocks in deep continental crust / Geological Society, London, Special Publications, 24:51-62, doi:10.1144/GSL.SP.1986.024.01.06 --- D. S. Chapman: Thermal gradients in the continental crust / Geological Society, London, Special Publications, 24:63-70, doi:10.1144/GSL.SP.1986.024.01.07 --- J. F. Dewey: Diversity in the lower continental crust / Geological Society, London, Special Publications, 24:71-78, doi:10.1144/GSL.SP.1986.024.01.08 --- N. J. Kusznir and R. G. Park: Continental lithosphere strength: the critical role of lower crustal deformation / Geological Society, London, Special Publications, 24:79-93, doi:10.1144/GSL.SP.1986.024.01.09 --- K. Weber: Metamorphism and crustal rheology—implications for the structural development of the continental crust during prograde metamorphism / Geological Society, London, Special Publications, 24:95-106, doi:10.1144/GSL.SP.1986.024.01.10 --- S. A. F. Murrell: The role of deformation, heat, and thermal processes in the formation of the lower continental crust / Geological Society, London, Special Publications, 24:107-117, doi:10.1144/GSL.SP.1986.024.01.11 --- K. Fuchs: Intraplate seismicity induced by stress concentration at crustal heterogeneities—the Hohenzollern Graben, a case history / Geological Society, London, Special Publications, 24:119-132, doi:10.1144/GSL.SP.1986.024.01.12 --- K. Lambeck: Crustal structure and evolution of the central Australian basins / Geological Society, London, Special Publications, 24:133-145, doi:10.1144/GSL.SP.1986.024.01.13 --- R. W. Kay and S. M. Kay: Petrology and geochemistry of the lower continental crust: an overview / Geological Society, London, Special Publications, 24:147-159, doi:10.1144/GSL.SP.1986.024.01.14 --- J. Touret: Fluid inclusions in rocks from the lower continental crust / Geological Society, London, Special Publications, 24:161-172, doi:10.1144/GSL.SP.1986.024.01.15 --- S. R. Taylor and S.M. McLennan: The chemical composition of the Archaean crust / Geological Society, London, Special Publications, 24:173-178, doi:10.1144/GSL.SP.1986.024.01.16 --- R. L. Rudnick and S. R. Taylor: Geochemical constraints on the origin of Archaean tonalitic-trondhjemitic rocks and implications for lower crustal composition / Geological Society, London, Special Publications, 24:179-191, doi:10.1144/GSL.SP.1986.024.01.17 --- D. A. Carswell and S.J. Cuthbert: Eclogite facies metamorphism in the lower continental crust / Geological Society, London, Special Publications, 24:193-209, doi:10.1144/GSL.SP.1986.024.01.18 --- S. Moorbath and P.N. Taylor: Geochronology and related isotope geochemistry of high-grade metamorphic rocks from the lower continental crust / Geological Society, London, Special Publications, 24:211-220, doi:10.1144/GSL.SP.1986.024.01.19 --- B. F. Windley and J. Tarney: The structural evolution of the lower crust of orogenic belts, present and past / Geological Society, London, Special Publications, 24:221-230, doi:10.1144/GSL.SP.1986.024.01.20 --- C. Pin and J. D. Sills: Petrogenesis of layered gabbros and ultramafic rocks from Val Sesia, the Ivrea Zone, NW Italy: trace element and isotope geochemistry / Geological Society, London, Special Publications, 24:231-249, doi:10.1144/GSL.SP.1986.024.01.21 --- S. Robertson: Evolution of the late Archaean lower continental crust in southern West Greenland / Geological Society, London, Special Publications, 24:251-260, doi:10.1144/GSL.SP.1986.024.01.22 --- L. Schiøtte, D. Bridgwater, K.D. Collerson, A.P. Nutman, and A.B. Ryan: Chemical and isotopic effects of late Archaean high-grade metamorphism and granite injection on early Archaean gneisses, Saglek-Hebron, northern Labrador / Geological Society, London, Special Publications, 24:261-273, doi:10.1144/GSL.SP.1986.024.01.23 --- D. M. Shaw, J. J. Cramer, M. D. Higgins, and M. G. Truscott: Composition of the Canadian Precambrian shield and the continental crust of the earth / Geological Society, London, Special Publications, 24:275-282, doi:10.1144/GSL.SP.1986.024.01.24 --- M. Raith and P. Raase: High grade metamorphism in the granulite belt of Finnish Lapland / Geological Society, London, Special Publications, 24:283-295, doi:10.1144/GSL.SP.1986.024.01.25 --- R. C. Newton and E.C. Hansen: The South India-Sri Lanka high-grade terrain as a possible deep-crust section / Geological Society, London, Special Publications, 24:297-307, doi:10.1144/GSL.SP.1986.024.01.26 --- H.-G. Stosch, G. W. Lugmair, and H.A. Seck: Geochemistry of granulite-facies lower crustal xenoliths: implications for the geological history of the lower continental crust below the Eifel, West Germany / Geological Society, London, Special Publications, 24:309-317, doi:10.1144/GSL.SP.1986.024.01.27 --- H. Downes and A. Leyreloup: Granulitic xenoliths from the French Massif Central—petrology, Sr and Nd isotope systematics and model age estimates / Geological Society, London, Special Publications, 24:319-330, doi:10.1144/GSL.SP.1986.024.01.28 --- J. R. Broadhurst: Mineral reactions in xenoliths from the Colorado Plateau; implications for lower crustal conditions and fluid composition / Geological Society, London, Special Publications, 24:331-349, doi:10.1144/GSL.SP.1986.024.01.29 --- P. W. C. van Calsteren, N. B. W. Harris, C. J. Hawkesworth, M. A. Menzies, and N. W. Rogers: Xenoliths from southern Africa: a perspective on the lower crust / Geological Society, London, Special Publications, 24:351-362, doi:10.1144/GSL.SP.1986.024.01.30 --- W. L. Griffin and S. Y. O’Reilly: The lower crust in eastern Australia: xenolith evidence / Geological Society, London, Special Publications, 24:363-374, doi:10.1144/GSL.SP.1986.024.01.31

Note: Dissertation, Universität Potsdam, 2023 , Contents 1. Introduction 2. Boundary Layers Types of the Atmosphere 2.1. The Convective Boundary Layer (CBL) 2.2. The Neutral Boundary Layer (NBL) 2.3. The Stable Boundary Layer (SBL) 3. The Closure problem 4. Model description 4.1. Applied model versions 4.2. Governing equations 4.3. Horizontal grid 4.4. Vertical grid 4.5. Lateral boundaries 4.6. Parametrizations 4.6.1. Radiation scheme 4.6.2. Microphysics 4.6.3. Mellor-Yamada scheme 4.6.4. Smagorinsky scheme 4.6.5. Sea ice scheme 4.7. Difference to classical LES Models 5. Experimental Setup 6. MOSAiC Measurements 6.1. ARM Meteorological tower 6.2. Radiosondes 7. Model evaluation for the central Arctic 7.1. Impact of the horizontal resolution 7.1.1. Under cold, light wind conditions 7.1.2. Under stormy conditions 7.2. Impact of the sea-ice scheme 7.3. Impact of the lower boundary conditions 7.4. Impact of the parametrization schemes under cold, light wind conditions 7.4.1. Near-surface variables 7.4.2. Vertical profiles 7.4.3. Surface fluxes 7.4.4. Boundary Layer Height 7.5. Impact of the parametrization schemes under stormy conditions 7.5.1. Near-surface variables 7.5.2. Vertical profiles 7.5.3. Surface fluxes 7.5.4. Boundary Layer height 8. Discussion and Summary Acknowledgements Appendix