A gradual rise in Earth's surface temperature marks a transition from the late Paleocene to the early Eocene ca. 58-51 Ma. Paleocene/Eocene boundary (∼55.5 Ma) sediments deposited in the midst of this slow warming ubiquitously reveal evidence for a massive isotopically light carbon injection and an associated rapid but transient global warming event, or hyperthermal, that has been termed the Paleocene Eocene Thermal Maximum (PETM) and attributed to a carbon injection from multiple potential sources. The PETM has gained importance over the past two decades as a potential geologic analog to the modern anthropogenic carbon injection and climate change. However significant questions surrounding the nature of the carbon injection at the onset of the PETM remain. The Clarence River valley, located in the Marlborough region, South Island, New Zealand, contains a series of outcrops of lithified late Paleocene to early Eocene sediments originally deposited on a paleo-slope margin. Within these sections, the Lower Limestone Member of the Amuri Limestone Formation records the interval of interest. A Lower Limestone prominent recessed unit consisting of multiple marl-rich beds and recording a pronounced negative carbon isotopic excursion (CIE) marks the PETM at sections that have been bisected by tributaries to the Clarence River, including Mead Stream and Dee Stream. Here I detail and discuss Clarence valley Lower Limestone sections and relate these records to global trends with an emphasis on adding constraints to the PETM carbon injection. Specifically, I document the lithologic and carbon isotopic expression of the PETM and two younger paired sets of early Eocene events that, similar to the Mead Stream and Dee Stream PETM sections, reveal negative CIEs and expanded marl-rich units coincident to identical CIEs and condensed carbonate dissolution horizons in deep-sea sections. I further quantify the abundance of bioturbating macrofauna trace fossils through the PETM at both Mead Stream and Dee Stream and argue that New Zealand margin intermediate waters became hypoxic precisely coincident to the PETM carbon injection. In concert, these findings suggest a PETM carbon addition mechanism capable of both diminishing intermediate water dissolved oxygen and of repeated early Eocene injections. / U.S. National Science Foundation (NSF); Joint Oceanographic Institutions (JOI), Inc.

The Paleocene and early Eocene (~66–40 Ma) is characterised by a number of transient warming events, also named hyperthermals. A more recent candidate for a hyperthermal of Paleocene age is the Latest Danian Event (LDE, ~62.2 Ma). So far, the LDE was only poorly explored in few deep-sea records and Tethyan shelf settings. Planktic data characterizing the surface ocean were almost completely missing. In this thesis, it was studied whether the LDE satisfies the requirements for a hyperthermal and the impact on the planktic foraminfera fauna. Samples from three late Danian deep-sea cores (ODP Sites 1210 and 1262, IODP Site U1407) and one Tethyan shelf section (Qreiya 3, Egypt) were investigated in rather high resolution, which, for the first time, allowed to unravel the impact of the LDE, the evolution of the ocean structure and planktic foraminiferal species abundances on an almost global scale. δ18O paleothermometry revealed a temperature rise of 2–4°C affecting the entire water column in all three depth habitats (sea floor, subsurface and surface ocean) and a contemporary negative carbon isotope excusion of 0.6–0.9 ‰ indicates carbon cycle perturbations. Changes in the planktic foraminiferal assemblages indicate a global biotic response to the LDE.

The iconic pillar coral, Dendrogyra cylindrus, is one of five Caribbean species listed in 2014 under the US Federal Endangered Species Act because of its extreme low abundance and continued decline in US waters. Until recently, little was known about the demographics or genetic diversity of Florida’s D. cylindrus population. This study represents the first time two holobiont partners (coral animal and associated photosynthetic algal endosymbionts) have been closely examined, spatially and temporally, in this little-studied species. The aim was to explore the influences of coral animal genotypes, mutualistic photosynthetic algal strains, and hyperthermal stress on bleaching and disease processes, resistance, and recovery through two consecutive hyperthermal events on the Florida Reef Tract (FRT) in 2014 and 2015. Through geographically stratified, triannual assessments and tissue sampling of D. cylindrus colonies across three regions of the FRT from April 2014 to April 2016, I compared genotypic identities of the coral animal to bleaching and disease status and recovery. Additionally, I characterized the algal endosymbionts (Symbiodiniaceae family) in D. cylindrus between regions of the FRT using Illumina amplicon sequencing of the partial chloroplast 23S rDNA Domain V gene and correlated them to differential responses during bleaching and recovery. Finally, I examined the effects of hyperthermal stress on disease prevalence and changes in disease susceptibility in D. cylindrus throughout two consecutive hyperthermal events in 2014 and 2015. Genotypic differences in D. cylindrus were associated with full or partial bleaching and/or disease resistance associated with some genets. Additionally, this study characterized unexpected diversity in the Symbiodiniaceae community within D. cylindrus and a site-specific, species-level switch in endosymbionts associated with acquired bleaching resistance during the 2015 hyperthermal event. Finally, this study demonstrated that two consecutive hyperthermal events were associated with an increase in prevalence of white plague in D. cylindrus and contributed to its susceptibility to black band disease, documented for the first time on the FRT. Through understanding the response of the D. cylindrus holobiont partners to biotic and abiotic stressors, such as hyperthermal bleaching and associated diseases, we gained valuable insights into how this threatened species may respond to a changing climate.

The assistance of thin film deposition with low-energy ion bombardment influences their final properties significantly. Especially, the application of so-called hyperthermal ions (energy <100 eV) is capable to modify the characteristics of the growing film without generating a large number of irradiation induced defects. The nitrogen ion beam assisted molecular beam epitaxy (ion energy <25 eV) is used to deposit GaN thin films on (0001)-oriented 6H-SiC substrates at 700 C. The films are studied in situ by reflection high energy electron diffraction, ex situ by X-ray diffraction, scanning tunnelling microscopy, and high-resolution transmission electron microscopy. It is demonstrated that the film growth mode can be controlled by varying the ion to atom ratio, where 2D films are characterized by a smooth topography, a high crystalline quality, low biaxial stress, and low defect density. Typical structural defects in the GaN thin films were identified as basal plane stacking faults, low-angle grain boundaries forming between w-GaN and z-GaN and twin boundaries. The misfit strain between the GaN thin films and substrates is relieved by the generation of edge dislocations in the first and second monolayers of GaN thin films and of misfit interfacial dislocations. It can be demonstrated that the low-energy nitrogen ion assisted molecular beam epitaxy is a technique to produce thin GaN films of high crystalline quality.

In this thesis, a custom quadrupole mass filter setup was established to independently investigate the impact of the most prominent ion species that are present during ion-assisted deposition. The setup was applied to the low temperature epitaxial growth of GaN thin films on 6H-SiC substrates. Atomic nitrogen ions at higher ion kinetic energies were for the first time independently identified to be the predominant cause of deteriorating crystalline qualities during growth. Precise control of the ion beam parameters yielded the capability to vary the average GaN phase content from almost purely wurtzite to the meta-stable zinc blende GaN phase. Even in case of comparably high crystalline quality, the atomic and molecular nitrogen ions were independently determined to yield distinct thin film topographies throughout the entire observed evolution of the thin film formation.:Bibliographical Description 1 Introduction 1.1 Epitaxial Thin Film Growth 1.2 Ion-Beam Assisted Deposition 1.2.1 Influence of Energetic Particles 1.2.2 Ion-atom Arrival Ratio 1.3 Gallium Nitride 2 Methods 2.1 Setup of the Deposition System 2.1.1 Knudsen Effusion Cell 2.1.2 Reflection High-Energy Electron Diffraction 2.1.3 Auger Electron Spectroscopy 2.1.4 Ion Sources 2.2 Quadrupole Mass Filter System 2.2.1 Components 2.2.2 Working Principle of a Quadrupole Mass Filter 2.2.3 Alternative Mass Filters 2.3 X-ray Diffraction and Reflectivity 2.4 Atomic Force Microscopy 2.5 Transmission Electron Microscopy 3 Results and Discussions 3.1 Characterization of the Quadrupole Mass Filter System 3.1.1 Mass Filter Performance and Resolution 3.1.2 Ion Beam Characteristics 3.1.3 Space Charge Considerations 3.1.4 Conclusions 3.2 Influence of the I/A Ratio and Ion Kinetic Energy 3.2.1 Determination of the GaN Phase Composition 3.2.2 Film Topography and Growth Mode 3.2.3 Crystal Structure and Orientation 3.2.4 Microstructure at the Interface 3.2.5 Conclusions 3.3 Impact of the Ion Species on Growth Instabilities 3.3.1 Growth Rates and Thin Film Topography 3.3.2 Crystal Structure 3.3.3 Growth Mode and RHEED pattern evolution 3.3.4 Conclusions 4 Summary and Conclusions Bibliography Complete Publication List of the Author Acknowledgments Declaration of Authorship / In dieser Arbeit wurde ein maßgefertigter Quadrupol-Massenfilteraufbau etabliert, um die Auswirkungen der prominentesten Ionenspezies, die während der ionengestützten Abscheidung vorhanden sind, unabhängig voneinander zu untersuchen. Der Aufbau wurde für das epitaktische Niedertemperatur-Wachstum von GaN-Dünnschichten auf 6H-SiC-Substraten angewendet. Atomare Stickstoffionen bei höheren kinetischen Ionenenergien wurden zum ersten Mal in der Abwesenheit anderer Spezies als die dominierende Ursache für die Verschlechterung der kristallinen Qualität während des Wachstums identifiziert. Eine präzise Kontrolle der Ionenstrahlparameter ergab die Fähigkeit, den durchschnittlichen GaN-Phasengehalt von der fast reinen Wurtzit- bis zur metastabilen Zinkblende-GaN-Phase zu variieren. Selbst bei vergleichbar hoher kristalliner Qualität weisen die mit atomaren und molekularen Stickstoffionen hergestellten Schichten unabhängig voneinander verschiedene Topographien auf, die sich während der gesamten beobachteten Entwicklung der Dünnschichtbildung deutlich abzeichneten.:Bibliographical Description 1 Introduction 1.1 Epitaxial Thin Film Growth 1.2 Ion-Beam Assisted Deposition 1.2.1 Influence of Energetic Particles 1.2.2 Ion-atom Arrival Ratio 1.3 Gallium Nitride 2 Methods 2.1 Setup of the Deposition System 2.1.1 Knudsen Effusion Cell 2.1.2 Reflection High-Energy Electron Diffraction 2.1.3 Auger Electron Spectroscopy 2.1.4 Ion Sources 2.2 Quadrupole Mass Filter System 2.2.1 Components 2.2.2 Working Principle of a Quadrupole Mass Filter 2.2.3 Alternative Mass Filters 2.3 X-ray Diffraction and Reflectivity 2.4 Atomic Force Microscopy 2.5 Transmission Electron Microscopy 3 Results and Discussions 3.1 Characterization of the Quadrupole Mass Filter System 3.1.1 Mass Filter Performance and Resolution 3.1.2 Ion Beam Characteristics 3.1.3 Space Charge Considerations 3.1.4 Conclusions 3.2 Influence of the I/A Ratio and Ion Kinetic Energy 3.2.1 Determination of the GaN Phase Composition 3.2.2 Film Topography and Growth Mode 3.2.3 Crystal Structure and Orientation 3.2.4 Microstructure at the Interface 3.2.5 Conclusions 3.3 Impact of the Ion Species on Growth Instabilities 3.3.1 Growth Rates and Thin Film Topography 3.3.2 Crystal Structure 3.3.3 Growth Mode and RHEED pattern evolution 3.3.4 Conclusions 4 Summary and Conclusions Bibliography Complete Publication List of the Author Acknowledgments Declaration of Authorship

The Paleocene-Eocene Thermal Maximum (PETM) (55 million years ago) stands as the largest in a series of extreme warming (hyperthermal) climatic events, which are analogous to the modern day increase in greenhouse gas concentrations. Orbitally triggered (Lourens et al., 2005, Galeotti et al., 2010), the PETM is marked by a large (-3‰) carbon isotope excursion (CIE). Hypothesized to be methane driven, Zeebe et al., (2009) noted that a methane based release would only account for 3.5°C of warming. An isotopically heavier carbon, such as that of soil and C3 plants, has the potential to account for the warming and CIE (Zachos et al., 2005). During the early Eocene, high latitude surface temperatures created favorable conditions for the sequestration of terrestrial carbon. A large untapped terrestrial carbon reservoir, such as that within permafrost regions, contains the potential, if degraded, to account for the CIE as well as the global temperature increase observed during the PETM. Using an fully integrated climate model (GENESIS) with fully coupled vegetation model (BIOME4), we show that adequate conditions for permafrost growth and terrestrial carbon sequestration did exist during the lead up to the PETM. By calculating the flux of net primary production (NPP) and soil respiration (Rs), we demonstrate that the biodegradation of permafrost-based carbon reservoirs had the potential to drive the PETM. Furthermore, we show that the natural planetary response to unbalanced carbon reservoirs resulted in the terrestrial sequestration of atmospheric carbon via permafrost regeneration, yielding a vulnerable carbon reservoir for the subsequent hyperthermal.