Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Corals are increasingly threatened by warming sea surface temperatures and other anthropogenic changes. The delicate symbiosis between corals and their algal endosymbionts (zooxanthellae) is easily disrupted by thermal stress, leading to bleaching and eventual mortality. The use of lipid ratios as biomarkers of environmental conditions is well established. Coral biomass contains abundant lipids, and the potential of lipid parameters to diagnose thermal tolerance in zooxanthellae has been previously suggested. In this thesis, I explore the response of specific fatty acids, sterols, and thylakoid membrane lipids to thermal and disease stress in zooxanthellae grown in culture, as well as those isolated from living corals. I present the discovery of a bioactive thylakoid lipid within zooxanthellae cells, and show how this compound is selectively mobilized in thermally stressed cells. I present a plausible mechanism for the breakdown of this compound into products that may cause apoptosis and disrupt the coral-algal symbiosis, eventually causing bleaching. I present two new lipid biomarkers of thermal stress in zooxanthellae, the C18 fatty acid unsaturation ratio, and the fatty acid to sterol ratio. I calibrate the decline of these two parameters to levels of thermal stress comparable to those needed to cause bleaching. I further show that these parameters are sensitive to pathogen stress as well. In several case studies of diseased and thermally stressed corals, I demonstrate that these lipid biomarkers of coral stress may be applied to zooxanthellae isolated from environmental samples. I show that these same compounds are preserved within coral aragonite, which opens up the potential to retrieve lipid-based historical records of coral health from annual layers of coral skeleton. This work demonstrates the value of using lipid biomarkers to assess coral health and better understand the biochemical mechanisms of coral bleaching. / by Jessie Mary Kneeland. / Ph.D.

by Tam Tze Wai. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1998. / Includes bibliographical references (leaves 107-114). / Abstract also in Chinese. / ABSTRACT --- p.i / ACKNOWLEDGEMENTS --- p.v / TABLE OF CONTENTS --- p.vi / LIST OF TABLES --- p.viii / LIST OF FIGURES --- p.ix / Chapter CHAPTER1 --- INTRODUCTION / Chapter 1.1 --- Modelling the Dynamics of a Coral Community --- p.1 / Chapter 1.2 --- New Paradigm in Understanding Complex System --- p.2 / Chapter 1.3 --- Ecological Models under the New Paradigm --- p.3 / Chapter 1.4 --- Hong Kong Marine Environment and Its Degradation --- p.6 / Chapter 1.5 --- Objectives of the Present Study --- p.8 / Chapter CHAPTER2 --- FIELD STUDIES OF A CORAL COMMUNITY IN HONG KONG / Chapter 2.1 --- Introduction --- p.9 / Chapter 2.2 --- Study Area --- p.10 / Chapter 2.3 --- Materials and Methods --- p.12 / Chapter 2.3.1 --- Preliminary Study of the Coral Cover and Diversity / Chapter 2.3.2 --- Extensive Study of the Coral Cover and Diversity / Chapter 2.3.3 --- Relative Abundance and Species Diversity / Chapter 2.4 --- Results and Discussion --- p.14 / Chapter 2.4.1 --- Preliminary Study / Chapter 2.4.2 --- Extensive Study / Chapter CHAPTER3 --- COMPUTER SIMULATION OF A CORAL COMMUNITY / Chapter 3.1 --- Introduction --- p.40 / Chapter 3.2 --- Object-oriented Programming (OOP) --- p.42 / Chapter 3.2.1 --- Objects / Chapter 3.2.2 --- "Classes, Hierarchies and Inheritance" / Chapter 3.2.3 --- Object-oriented Simulation / Chapter 3.3 --- Object-oriented Simulation of a Five-Coral Community --- p.46 / Chapter 3.3.1 --- Class BenthicEnvir / Chapter 3.3.2 --- Class Coral / Chapter 3.3.3 --- The Objects Behaviour / Chapter 3.3.4 --- The Simulation / Chapter 3.3.5 --- Diversity Index and Statistical Analysis / Chapter 3.4 --- Results and Discussion --- p.66 / Chapter 3.4.1 --- Growing Behaviour of the Corals / Chapter 3.4.2 --- Dynamical Behaviour of the Coral Community in Simulation without Disturbance / Chapter 3.4.3 --- Dynamical Behaviour of the Simulated Coral Community with Disturbance / Chapter 3.4.4 --- Utility of the Object-oriented Model / Chapter CHAPTER4 --- GENERAL DISCUSSION / Chapter 4.1 --- Mechanisms Structuring a Coral Community --- p.94 / Chapter 4.2 --- Comparison between Field Studies and the Computer Model / Chapter 4.3 --- Utilities and Limitations of the Present Model / REFERENCES --- p.107 / APPENDIX --- p.115

Tsang, Yu Man. / "November 2009." / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 268-277). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Abstract --- p.iii / Content --- p.vii / List of Tables --- p.ix / List of Figures --- p.xx / Chapter Chapter One --- General Introduction --- p.1 / Introduction --- p.1 / Coral Reefs --- p.1 / Coral-Algal Symbiosis --- p.2 / The Dinoflagellate Symbiodinium --- p.11 / Coral Communities in Hong Kong --- p.18 / Objectives --- p.21 / Study Sites - Tung Ping Chau Marine Park --- p.21 / Coral Species chosen for the Experiment --- p.23 / Platygyra acuta --- p.23 / Porites lutea --- p.23 / Thesis Outline --- p.24 / Chapter Chapter Two --- Temporal variation in photophysiological parameters of Hong Kong corals and their relationship with the environmental factors --- p.28 / Introduction --- p.28 / Methods and Materials --- p.33 / Study Sites --- p.33 / Coral Sampling for zooxanthellae density and chlorophyll concentration analysis --- p.34 / Measurement of changes in the photosynthtic activity of the corals --- p.38 / Environmental Factors --- p.38 / Data analysis --- p.39 / Results --- p.41 / Density of Zooxanthellae --- p.41 / Concentrations of Chlorophyll a and c2 (per zooxanthella) --- p.43 / Concentrations of Chlorophyll a and c2 (per surface area) --- p.46 / Chlorophyll ratio --- p.49 / Effective quantum yield --- p.51 / Photosynthetically active radiation (PAR) --- p.54 / Intra-colony variation for Platygyra acuta --- p.56 / Comparison between Platygyra acuta and Porites lutea --- p.64 / Environmental factors and their correlations with photophysiological parameters in corals --- p.68 / Discussion --- p.73 / Density of zooxanthellae --- p.74 / Concentrations of Chlorophyll a and c2 --- p.80 / Chlorophyll ratio --- p.85 / Effective quantum yield --- p.88 / Intra-colony variation --- p.94 / Between species comparison --- p.98 / Summary --- p.107 / Chapter Chapter Three --- PCR-RFLP Analysis on Symbiodinium in Platygyra acuta --- p.241 / Introduction --- p.241 / Methods and Materials --- p.244 / Sample collection --- p.244 / Molecular phylotyping --- p.245 / Results --- p.247 / Discussion --- p.249 / Summary --- p.257 / Chapter Chapter Four --- Summary and Conclusion --- p.262 / References --- p.268

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references. / The architecture of coral reef ecosystems is composed of coral skeletons built from the mineral aragonite (CaCO3). Coral reefs are currently being threatened by ocean acidification (OA), which may lower calcification rates, reduce skeletal density, and increase aragonite dissolution. Crystallography and chemistry are what govern the materials properties of minerals, such solubility and strength. Thus, understanding the mineralogical nature of coral aragonite and how it forms are important for predicting bulk skeletal responses under climate change. Different models based on geochemical versus biological controls over coral skeleton biomineralization propose conflicting predictions about the fate of corals under OA. Rather than investigating the mechanism directly, I use a mineralogical approach to study the aragonite end-products of coral biomineralization. / I hypothesize that coral mineralogy and crystallography will lend insights into how coral aragonite crystals form and how sensitive coral aragonite material properties may be to OA. Here I compare the crystallography, bonding environments, and compositions of coral aragonite with aragonite produced by other organisms (mollusk), synthetically (abiogenic precipitation in aragonite-supersaturated seawater and freshwater), and in natural geological settings (abiogenic). Coral aragonite crystallography does not resemble mollusk aragonite (aragonite formed with a strong biological influence), but rather is identical to abiogenic synthetic aragonite precipitated from seawater. I predict that the material properties of coral aragonite are similar to that of abiogenic synthetic seawater aragonites and that coral aragonite formation is sensitive to surrounding seawater chemistry. / To test the effect OA on coral aragonites, I studied deep-sea corals from a natural [omega][subscript sw], gradient (1.15-1.44) in the Gulf of Mexico and shallow-water corals across a natural [omega][subscript sw] (2.3-3.7) and pH (7.84-8.05) gradient in Palau. Minor shifts in crystallography are expressed by coral aragonite in these natural systems, likely governed by skeletal calcite contents, density, and [omega] of the coral calcifying fluid. My results are most consistent with a geochemical model for biomineralization, which implies that coral calcification may be sensitive to OA. However, further work is required to determine whether the modest crystallographic shifts I observe are representative on a global scale and whether they could influence bulk skeletal material properties. / by Gabriela A. Farfan. / Ph. D. / Ph.D. Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution)

Thesis (Ph.D.)--University of Wollongong, 2006. / Typescript. Includes bibliographical references: p. 161-192.

published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

Une nécessaire révision des coraux plocoïdes jurassiques en morphologie, morphométrie, systématique et en nomenclature a été réalisée grâce à des spécimens-types, du matériel de collection, ou issu de la littérature. Des structures dont une nouvelle muraille, l'étallonothèque et des types d'auricules ont été identifiés. Un stade initial ontogénique tétraméral a été observé pour la première fois chez Heliocoenia et Pseudocoenia. Ceci est en désaccord avec la définition traditionnelle sur le développement fondamentalement hexaméral chez les Scleractinia. L'étude systématique aboutit à une réorganisation des familles, des genres et de leurs synonymies. Des espèces sont décrites avec des limites encore parfois ambigües nécessitant une approche morphométrique plus approfondie pour être reproductible. Les positions systématiques prises sont traduites dans le sens de la préservation de la stabilité de l'usage des noms, des actes nomenclaturaux sont proposés dans ce sens. Deux méthodes morphométriques ont été appliquées aux contours 2D des sections de polypiérites. L'analyse de Fourrier Elliptique a été utilisée sur des coupes transversales théoriques et réelles. Les résultats montrent les différentes symétries et certains genres distingués par cette méthode. L'analyse des dimensions fractales de modèles théoriques, des coupes étudiées, ou issues de la littérature ont été analysées. Les formes étudiées se placent selon un gradient de complexité croissante du contour correspondant à la maximisation de l'interface squelette-porosité. Le long de ce gradient, les différents taxons se répartissent, leur distinction restant souvent délicate par suite d'un léger recouvrement / A review of Jurassic plocoid corals in morphology, morphometry, systematics and in nomenclature was necessary. This study was realized with collection materials, type specimens and material from the literature. The morphological study enables identifying structures such as a new type of wall, the etallonotheca and some new types of auricles. A tetrameral initial ontogenetic stage was observed for the first time in Heliocoenia and Pseudocoenia. This is in disagreement with the traditional definition of the septal development supposed to be fundamentally hexameral in Scleractinia. The systematic study led to a significant reorganization of families, genera and their synonyms. Species are described but their limits are still ambiguous and so still require more detailed morphometric approaches to be reproducible. The systematic positions chosen here are translated in terms of nomenclature in order to preserve the stability of names. This requires in various cases nomenclatural acts. Two morphometric methods were applied on 2D contours of calices sections. Elliptical Fourier analysis was used on theoretical and real transversal sections. The results show that the different symmetries and some genera can be distinguished by this method. Analysis of fractal dimensions has also been applied. Theoretical models and the sections studied in this work or issued from the literature were analyzed. The studied forms are placed according to an increasing complexity gradient of the contour corresponding to the maximization of the interface skeleton-porosity. The different taxa are distributed along this gradient, due to their small overlaps; their true distinction often remains difficult

Le changement climatique et l’augmentation des températures globales perturbent l’abondance et la distribution de milliers d’organismes, aquatiques et terrestres, et certains écosystèmes sont particulièrement sensibles à ces changements environnementaux. L’augmentation de température est la principale menace au maintien des populations de coraux, véritables ingénieurs écologiques de ces écosystèmes. Bien que la recherche sur les récifs coralliens se soit d’abord attachée à l’étude des coraux adultes, de nombreuses informations manquent sur la reproduction sexuée et asexuée, et leur rôle dans la conservation et restauration récifale. Le premier axe de ma thèse s’est donc construit sur la réponse des jeunes stades de vie à l’augmentation de température, pour d’abord évaluer les modifications de leur performance et ensuite évaluer dans quelles mesures les jeunes stades seraient capables de s’acclimater à des conditions de températures plus élevées. Au travers de différentes expérimentations en laboratoire sur le genre Acropora, j’ai ainsi mis en évidence 1) une résistance thermique importante (+2-3°C au-dessus des températures ambiantes) des gamètes face à l’augmentation de température, 2) une résistance thermique différente entre spermatozoïdes et ovocytes: ovocytes < spermatozoïdes, 3) et la mise en évidence du rôle majeur de l’environnement dans lequel se rencontre les gamètes une fois libérés, sur la qualité et la quantité de la fécondation. Enfin, j’ai identifié les conditions optimales thermiques de pré-exposition des gamètes pour maximiser leur succès de fécondation. Bien qu’un intérêt croissant soit porté sur la reproduction sexuée ces dernières années, l’utilisation de la reproduction asexuée demeure la méthode la plus utilisée pour restaurer les récifs coralliens, plus connue sous le nom de bouturage. Ainsi le second axe de ma thèse a cherché à mettre en évidence la plasticité phénotypique des coraux en cultivant des boutures provenant de 3 espèces dans 3 environnements différents et en analysant leur taux de croissance, leur état de santé et leur survie. Cet axe a pu montrer qu’il existait des différences à plusieurs échelles, entre espèces, mais aussi au sein d’une même espèce. Mes travaux montrent qu’une sélection des individus basée sur l’étude de la plasticité phénotypique de certains traits d’histoires de vie comme la croissance ou l’état de santé dans des environnements variables permettrait d’améliorer l’efficacité de la restauration récifale. Ainsi le choix des individus au sein d’une même espèce afin de réaliser du bouturage (reproduction asexuée) et le conditionnement de la phase de vie gamètes (reproduction sexuée) peut permettre d’augmenter l’efficacité des méthodes de restaurations tout en nous donnant des informations nouvelles sur la biologie et la physiologie des coraux scléractiniaires face aux changements environnementaux. / Climate change and increasing temperature impact abundance and distribution of thousands of organisms, aquatic and terrestrial, and some ecosystems are particularly sensitive to these global changes. Increasing temperature is the principal threat for coral populations, which are ecological engineers of coral reef ecosystems. While research on coral reefs has first sought to study adult corals, data are still lacking on early life stages of corals. As sexual and asexual reproduction may play a key role in the conservation and restoration of coral reefs, my doctoral research aims to better understand changes on sexual and asexual reproduction in the face of rising temperature. The first axis of my Ph. D. was built on the response of early life stages to increasing temperature, in order to assess whether pre-exposure of early life may improve their ulterior performance. Among the different experiments performed on the genus Acropora, I highlighted 1) a high thermal tolerance (+2-3°C above ambient temperature) of gametes, 2) a higher sensibility of oocytes than sperm to rising temperature exposure, and 3) the pivotal role of gamete thermal history on fertilization output. Finally, I identified optimal pre-exposure conditions in order to maximize fertilization success. While an increasing interest in sexual reproduction was observed these last years, asexual reproduction and fragmentation still remain the main tool to restore damaged reefs. Thus, in the second axis of my doctoral project, I investigated the phenotypic plasticity of corals by growing 3 different species of corals across 3 different environments. Their growth rates, health status and survival probability were determined. Results from this axis showed that differences were observed at the interspecific and intraspecific levels. This work revealed that a selection based on phenotypic plasticity among different life-traits (growth rates and health status) and different environments should allow to increase coral reef restoration strategies. Hence the selection of individuals (asexual reproduction) in a species based on coral common garden experiment allow to identify individuals of interest to use as restoration biological materials. Additionally, thermal pre-conditioning of early life stages (sexual reproduction) is another way to increase efficiency of restoration measures in the face of rising temperature. My doctoral research provided new information regarding physiological and biological processes of scleractinian corals facing environmental changes and proposed new solutions for restorations based on sexual and/or asexual reproduction.

Les traceurs à base de bore (δ11B et B/Ca) dans les carbonates ont reçu une attention considérable au cours des dernières décennies dans le domaine des géosciences de par leur potentiel à recalculer le pH. Cette thèse explore les frontières des applications de ces traceurs à la paléocéanographie et à la biogéochimie. A cause de la montée des teneurs en CO2 d’origine anthropique, il est devenu extrêmement important de comprendre comment les systèmes de la Terre répondront dans le futur. Les organismes marins sont aussi impactés par le réchauffement et l’acidification des océans, c’est pourquoi il est essentiel d’identifier les espèces résilientes et de comprendre les mécanismes sous-jacents à leur acclimatation. Les objectifs de cette thèse sont de répondre à certaines questions fondamentales, comment le CO2 atmosphérique a évolué au cours des transitions climatiques majeures du Néogène? Comment le dégazage ou l’absorption de carbone ont-ils évolué dans l’Est équatorial Pacifique au cours des derniers 6.5 Ma? Les changements de source et puits de carbones peuvent-ils moduler le CO2 atmosphérique passé et expliquer les transitions climatiques? Et pour les organismes marins, comment les mécanismes permettant la biominéralisation sont-ils impactés par l’augmentation des températures et l’acidification des océans dans les coraux tropicaux ? / Boron-based proxies (δ11B and B/Ca) in carbonates have gained considerable attention in the geosciences over the last several decades, given their potential to constrain pH. This thesis explores frontier applications of these proxies to paleoceanography and biogeochemistry. Due to rising anthropogenic CO2 levels, it is becoming increasingly important to understand how Earth’s systems will respond in the future.Marine organisms are also impacted by the warming and acidification of the ocean, therefore it is essential to identify resilient species and understand the underlying mechanisms of acclimatization.The objectives of this thesis are to answer several fundamental questions, for instance, how has atmospheric CO2 changed during major climate transitions over the Neogene? How did degassing or absorption of carbon evolve in the East equatorial Pacific during the last 6.5 Ma? Can changes of sources and sinks modulate past atmospheric CO2 and explain past climate transitions? And for marine organisms, how are the mechanisms allowing biomineralization impacted by increased temperature and the acidification of the ocean in tropical corals?

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 131-143). / Coral reefs are biodiverse ecosystems that are at risk of degradation as a result of environmental changes. Reefs are constantly in a state of flux: the resident species assemblages vary considerably in space and time. However, the drivers of this variability are poorly understood. Tracking these changes and studying how coral reefs respond to natural and anthropogenic disturbance can be challenging and costly, particularly for reefs that are located in remote areas. Because many reef animals produce and use sound, recording the ambient soundscape of a reef might be one way to efficiently study these habitats from afar. In this thesis, I develop and apply a suite of acoustics-based tools to characterize the biological and anthropogenic acoustic activity that largely comprises marine soundscapes. First, I investigate links between reef fauna and reef-specific acoustic signatures on coral reefs located in the U.S. Virgin Islands. Second, I compare those findings to a more expansive study that I conducted in Maui, Hawaii, in which the drivers of bioacoustic differences among reefs are explored. Third, I investigate the distances over which sounds of biological origin may travel away from the reef and consider the range within which these acoustic cues might be usable by pelagic larvae in search of a suitable adult habitat. Fourth, I assess the extent to which the presence of vessel noise in shallow-water habitats changes the ambient soundscape. Finally, I present the results of a modeling exercise that questions how ocean noise levels might change over the next two decades as a result of major projected increases in the number and size of and distance traveled by commercial ships. The acoustics-based tools presented here help provide insight into ecosystem function and the extent of human activity in a given habitat. Additionally, these tools can be used to inform an effective regulatory regime to improve coral reef ecosystem management. / by Maxwell Bernard Kaplan. / Ph. D.