This dissertation characterizes the genetic diversity and thermal tolerance of the coral holobiont Stylophora pistillata and Pocillopora verrucosa (family Pocilloporidae) across the Saudi Arabian Red Sea coast (~1500 km). The population genetic structure and holobiont diversity was assessed using genome-wide single nucleotide polymorphisms (SNPs) identified with reference genome-based RAD-Seq, while the associated microbial communities of the algal symbiont (Symbiodiniaceae) and bacteria were inferred from metabarcoding analyses of the ITS2 and 16S rRNA gene. Thermal tolerance of Stylophora pistillata colonies was assessed using standardized short-term heat stress assays on the novel Coral Bleaching Automated Stress System (CBASS). Chapter 1 details the assembly and annotation of the P. verrucosa genome (~380 Mbp; 27,439 gene models), which was highly complete and compared well to the already available S. pistillata genome. Chapter 2 presents population genetic analyses of both coral species, which revealed pronounced differences in their population genetic structure. While P. verrucosa seemed to be highly connected across the Red Sea basin with the exception of the far south, S. pistillata depicted a complex population genetic structure. Microbial communities of Symbiodiniaceae and bacteria were overall less diverse in P. verrucosa than in S. pistillata, and followed an association pattern that was partly determined by the environment and partly by host genotype. Chapter 3 identifies thermally tolerant S. pistillata genotypes by comparing the heat stress response of colonies collected at two sites within the same reef. Ex-situ heat-stress assays confirmed that colonies from the more temperature stable site (fore reef) were less thermally tolerant than their conspecifics from the back reef, where the diel temperature is more variable. This chapter also highlights the utility of acute heat-stress assays as a tool to identify thermotolerant colonies. Taken together, the work of this dissertation provides a foundation for coral conservation in the Red Sea. It highlights that the genetic structure differs between coral species, suggesting that effective conservation through marine protected areas need to incorporate data from multiple species. Coral population genetic data should further be complemented by thermal tolerance assays across the Red Sea to associate genetic diversity with patterns of heat stress tolerance.

<p> About half the Caribbean hermatypic corals died out at the Oligocene-Miocene boundary, about 25 Ma. Roughly two thirds of those corals which died out in the Caribbean are still extant in the Indo-Pacific. The coral and coral associate faunas of three Upper Oligocene and three Middle Miocene fossil reefs in western Puerto Rico were compared. Corals on these sites suffered 59% generic extinction, and 54% species extinction. Nearly all coral genera which are tolerant of turbidity or turbidity and cold water survived. All corals found exclusively or principally on Oligocene shelf-edge reefs became regionally extinct. There are no shelf-edge reefs documented from the Miocene in the Caribbean.</p> <p> Coral associates, the endolithic organisms which live in coral skeletons, were almost completely unaffected by this extinction. Likewise, reef and off-reef gastropods, bivalves, and echinoids suffered only insignificant reductions in diversity. Only corals and large benthic foraminifera were strongly affected by the extinction. It is significant that zooxanthellate organisms were the primary victims of this extinction. There is no evidence to suggest effects at higher trophic levels.</p> <p> Paleontological evidence from corals, coral associates, and gastropods suggests enhanced upwelling in the Caribbean during the Miocene and Early Pliocene. This enhanced upwelling could account for the extinction by cooling Caribbean coastal surface waters and restricting reef development to on-shelf patch reefs, where corals would be subject to more intense sedimentation. Paleoceanographic models indicating West to East deep circulation through the Central American Seaway during the Miocene provide a mechanism for this enhanced upwelling.</p> <p> Life history characteristics may have influenced survivorship among the corals, but apparently had no effect on coral associates. Corals which brood their larvae survived in greater proportions than corals which broadcast. This pattern is opposite that observed in studies on molluscs and other invertebrates.</p> <p> This regional extinction was important in the division of a previously cosmopolitan reef fauna into the modern provincial faunas. Explaining this minor mass extinction may contribute to an understanding of the volatile record of reefs in the larger mass extinctions of the Phanerozoic.</p> / Thesis / Master of Science (MSc)

Coral reefs are among the most biodiverse ecosystems in the world, being essential for marine life. The engineers of these ecosystems, reef-building corals, live in association with a great diversity of microorganisms, which can affect their host’s health in beneficial or detrimental manners. Corals are currently threatened by climate change and other environmental stressors, that lead to the phenomenon of coral bleaching, in which these animals lose their endosymbiotic algae. Even though the stressors that cause coral bleaching are known, the exact cellular and molecular mechanisms that provoke this process are still undiscovered. The lack of information regarding micro-scale processes that happen in unhealthy corals could be resolved with more efforts in developing micro-scale studying models. The use of individual polyps that bail-out of the coral skeleton induced by acute stress has been suggested as a model to study these processes. However, little is known about how these polyps change after bailing-out of a colony, which could become a problem once reliable models should be consistent and well understood. Thus, investigating these changes and optimizing a methodology to minimize them is crucial to establish these polyps as models to study corals. Herein, we investigated microbiological changes of isolated polyps by performing an experiment to study shifts in their microbiome after the separation from the colony. Before the experiment, different methods to isolate polyps were tested to find the one that granted the highest survival. After finding that salinity-induced separation was the most efficient, this method was used to study the microbiome of coral polyps. We found that while no significant changes in the microbiome could be observed immediately after the separation of polyps from their colony compared to coral fragments, this pattern changed after two weeks. We propose that the maintenance of polyps without fixation to a substrate might be the cause for such changes, and that polyps able to attach to a substrate and regrow as a colony might still recover a microbiome composition closer to coral fragments. Finally, a new microfluidic device for fixation and maintenance of coral polyps was developed and tested for use in future experiments.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Earth and Planetary Sciences, 1979. / Microfiche copy available in Archives and Science. / Bibliography: p. 110-119. / by Jonathan Erez. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2011. / "June 2011." Cataloged from PDF version of thesis. / Includes bibliographical references (p. 253-293). / Sampling the vast volumes of the ocean requires tools capable of observing from a distance while retaining detail necessary for biology and ecology, ideal for optical methods. Algorithms that work with existing SeaBED AUV imagery are developed, including habitat classification with bag-of-words models and multi-stage boosting for rock sh detection. Methods for extracting images of sh from videos of long-line operations are demonstrated. A prototype digital holographic imaging device is designed and tested for quantitative in situ microscale imaging. Theory to support the device is developed, including particle noise and the effects of motion. A Wigner-domain model provides optimal settings and optical limits for spherical and planar holographic references. Algorithms to extract the information from real-world digital holograms are created. Focus metrics are discussed, including a novel focus detector using local Zernike moments. Two methods for estimating lateral positions of objects in holograms without reconstruction are presented by extending a summation kernel to spherical references and using a local frequency signature from a Riesz transform. A new metric for quickly estimating object depths without reconstruction is proposed and tested. An example application, quantifying oil droplet size distributions in an underwater plume, demonstrates the efficacy of the prototype and algorithms. / by Nicholas C. Loomis. / Ph.D.

Choi Mei Mei. / Thesis submitted in: December 2002. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 214-236). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgements --- p.vi / Table of Contents --- p.viii / List of Tables --- p.xi / List of Figures --- p.xii / Chapter Chapter One: --- General Introduction --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.1.1 --- Coral bleaching --- p.2 / Chapter 1.1.2 --- Predation of corals by corallivorous gastropods --- p.20 / Chapter 1.2 --- Introduction of Study Sites- Tung Ping Chau --- p.33 / Chapter 1.3 --- Objectives of the Study --- p.35 / Chapter 1.4 --- Structure of this Thesis --- p.36 / Chapter Chapter Two: --- "Coral Bleaching and Predation by Corallivorous Gastropods in the Coral Communities of A Ye Wan and A Ma Wan, Tung Ping Chau" --- p.40 / Chapter 2.1 --- Introduction --- p.40 / Chapter 2.2 --- Materials and Methods --- p.45 / Chapter 2.2.1 --- Quantitative surveys --- p.45 / Chapter 2.2.2 --- "Quantifying the colour of corals, Porites lobata, in Tung Ping Chau" --- p.47 / Chapter 2.2.3 --- Physical parameters --- p.49 / Chapter 2.2.4 --- Data and statistical analysis --- p.49 / Chapter 2.3 --- Results --- p.50 / Chapter 2.3.1 --- Live coral coverage in A Ye Wan and A Ma Wan --- p.50 / Chapter 2.3.2 --- Proportion of Porites lobata paled --- p.52 / Chapter 2.3.3 --- Changes in colour intensity of Porites lobata between seasons --- p.54 / Chapter 2.3.4 --- Density of corallivorous gastropods --- p.55 / Chapter 2.3.5 --- Percentage coverage of live and dead Acropora tumida --- p.55 / Chapter 2.3.6 --- Physical parameters --- p.57 / Chapter 2.4 --- Discussion --- p.59 / Chapter 2.4.1 --- Live coral cover in A Ye Wan and A Ma Wan --- p.59 / Chapter 2.4.2 --- Bleaching of Porites lobata in summer and winter --- p.61 / Chapter 2.4.3 --- Colour intensity of Porites lobata in different seasons --- p.67 / Chapter 2.4.4 --- Predation on corals by corallivorous gastropods --- p.69 / Chapter Chapter Three: --- "Study on Coral Bleaching, Pontes bbata, in Tung Ping Chau by using Permanent Quadrats" --- p.103 / Chapter 3.1 --- Introduction --- p.103 / Chapter 3.2 --- Materials and Methods --- p.104 / Chapter 3.2.1 --- Study sites --- p.104 / Chapter 3.2.2 --- Permanent quadrat monitoring --- p.105 / Chapter 3.2.3 --- Corals sampling for zooxanthellae density and chlorophyll a concentration analysis --- p.106 / Chapter 3.2.3.1 --- Tissus collection --- p.106 / Chapter 3.2.3.2 --- Zooxanthellae counting --- p.107 / Chapter 3.2.3.3 --- Chlorophyll a determination --- p.107 / Chapter 3.2.3.4 --- Determination of coral surface area --- p.108 / Chapter 3.2.4 --- Data analysis --- p.108 / Chapter 3.3 --- Results --- p.109 / Chapter 3.3.1 --- Monitoring of bleaching of porties lobata in permanent quadrat --- p.109 / Chapter 3.3.2 --- Density of Zooxanthellae in Porites lobata --- p.111 / Chapter 3.3.3 --- Concentration of Chlorophyll a in Porites lobata --- p.112 / Chapter 3.3.4 --- Chlorophyll a per zooxanthellae --- p.113 / Chapter 3.4 --- Discussion --- p.114 / Chapter Chapter Four --- Study of Predation on coral Acropora tumida by Corallivorous Gastropods in Tung Ping Chau --- p.138 / Chapter 4.1 --- General Introduction --- p.138 / Chapter 4.2 --- Materials and Methods --- p.140 / Chapter 4.2.1 --- Study sites --- p.140 / Chapter 4.2.2 --- Preliminary evaluation of corallivorous gastropods as the coal predator --- p.141 / Chapter 4.2.3 --- Monthly monitoring of permanent quadrat --- p.142 / Chapter 4.2.4 --- Data and statistical analysis --- p.144 / Chapter 4.3 --- Results --- p.145 / Chapter 4.3.1 --- Species of corallivorous gastropods in Tung Ping Chau --- p.145 / Chapter 4.3.2 --- Feeding behavior of corallivorous gastropods in Tung Ping Chau --- p.146 / Chapter 4.3.3 --- Density of corallivorous gastropods --- p.147 / Chapter 4.3.3.1 --- Monthly change in density of corallivorous gastropods --- p.147 / Chapter 4.3.3.2 --- Correlation between gastropod density and temperature --- p.149 / Chapter 4.3.4 --- Cumulative percentage of area of feeding scar over time --- p.149 / Chapter 4.3.5 --- Monthly percentage change in the areas of feeding scar --- p.152 / Chapter 4.3.5.1 --- Monthly percentage change in the areas of feedling scar due to predation by Cronia margariticola and Drupella rugosa --- p.152 / Chapter 4.3.5.2 --- Correlation between gastropod density and monthly percentage change in area of scar --- p.153 / Chapter 4.3.5.3 --- Correlation between temperature and monthly percentage in area of the feeding scar --- p.154 / Chapter 4.3.6 --- Rate of predation --- p.154 / Chapter 4.3.6.1 --- Rate of predation by the corallivorous gastropods --- p.154 / Chapter 4.3.6.2 --- "Correlation between rate of predation, gastropod density and seawater temperature" --- p.155 / Chapter 4.3.7 --- Population size structure of the corallivorous gastropods --- p.156 / Chapter 4.3.7.1 --- Population size structure of Cronia margariticola --- p.156 / Chapter 4.3.7.2 --- Population size structure of Drupella rugosa --- p.158 / Chapter 4.4 --- Discussion --- p.159 / Chapter 4.4.1 --- Feeding behaviours of corallivorous gastropods --- p.159 / Chapter 4.4.2 --- Density of corallivorous gastropods --- p.162 / Chapter 4.4.3 --- Cumulative percentage of area of feeding scar --- p.170 / Chapter 4.4.4 --- Monthly percentage change of area of feeding scar --- p.173 / Chapter 4.4.5 --- Rate of predation --- p.175 / Chapter 4.4.6 --- Size structure of population size --- p.178 / Chapter 4.4.7 --- Predatory pressure from corallivorous gastropods in Tung Ping Chau --- p.185 / Chapter Chapter Five --- Summary and Perspectives --- p.207 / References --- p.214

[Truncated abstract] The extent to which marine populations are connected by larval dispersal is crucial to their distribution, maintenance and diversity. Thus, for the effective conservation of threatened systems such as coral reefs, understanding patterns of connectivity is essential. However, the biophysical mechanisms that retain or disperse larvae within and among populations are poorly understood. Though the open ocean environment provides the opportunity for long-distance dispersal, if this potential is only rarely realised, recruits produced from afar are unlikely to contribute to the local-scale demography of populations over ecological time frames, but will limit broad-scale genetic diversification over evolutionary time. This thesis explores the extent of genetic and demographic connectivity of two species of reef-building corals over a range of spatial scales among the discontinuous reef systems of northwest Australia. ... Putative source and sink dynamics were not random, but were associated with levels of disturbance and recovery from a recent and catastrophic coral bleaching. When S. hystrix samples from another two offshore systems were included in the analysis, large differences among systems showed that gene flow over hundreds of kilometres is rare over microevolutionary time scales that account for connections over multiple generations. Levels of subdivision over the same spatial scales were markedly lower in the acroporid coral, Acropora tenuis, than in S. hystrix. These results are congruent with expectations based on reproductive mode; in contrast to S. hystrix, which releases brooded larvae that are competent to settle immediately, A. tenuis broadcasts its gametes, and after external fertilisation, the larvae need to develop for several days before they are competent to settle. Despite the differences in levels of broad-scale subdivision, in both species significant differentiation was detected between reefs within systems (>10 km), and between sites within some reefs (< 10 km). These results indicate not only that dispersal between reefs and even some reef patches is restricted, but also that hydrodynamics influence retention of brooded and spawned larvae in similar ways. Further analysis of A. tenuis populations from two coastal systems detected significant differences in genetic diversity among the four major systems of northwest Australia. Additionally, genetic divergence between the coastal and offshore zones was greater than expected by the geographic separation of systems, indicating that connectivity between these zones via transport of A. tenuis larvae on oceanic currents occurs rarely even over microevolutionary time scales. This study has two primary implications for conservation. First, since coastal and offshore reefs of northwest Australia appear to be discrete genetic entities, they have independent evolutionary potential to adapt to local conditions and environmental change. Second, systems, reefs and some reef patches of northwest Australia are demographically independent units. Therefore, designs of coral reserve networks should consider routine dispersal distances of kilometres to a few tens of kilometres.

published_or_final_version / Biological Sciences / Master / Master of Philosophy

[Truncated abstract] Most ecological research investigates the demography of organisms, which can be summarised by their population dynamics and structure. Population dynamics are the rates of birth, growth, reproduction and survival of individuals, which determine the number of individuals in different stage classes, or, the population structure. Understanding the demography of organisms is particularly difficult, and requires the application of different methods of investigation. A number of methods of investigation are required because each can only investigate particular aspects of population demography, and is subject to problems of inaccuracy and bias. Thus, population demography is best understood by simultaneously collecting complimentary data using different methods of analysis to quantify how and why the dynamics and structure of populations change with their environment. The need for complimentary methods of investigation to understand population demography is even greater for organisms that have complex life histories, such as corals. The life histories of corals are particularly complex because they display a variety of modes of sexual and asexual reproduction, and their rates of growth, reproduction and survival are strongly influenced by the size of the individual, which can change rapidly. Additionally, the rates of sexual recruitment to populations of corals are notoriously variable in space and time. Thus, corals are an ideal model to investigate the usefulness of combining methods of analysis to better understand the demography of organisms. In this thesis I demonstrate that combining data from a number of methods of analysis provides a much better understanding of the demography of populations of the mushroom coral Fungia fungites that were exposed to contrasting regimes of disturbance. I used methods of analysis that produce unique and complimentary results, in the form of genetic, size-structure, life history and experimental data. Genetic data confirmed that I was correctly identifying life history stages of polyps, indicated the extent to which a stock-recruitment relationship existed between the sexual recruits and the adult polyps at each population, and provided an estimate of the relative contribution of asexual recruitment to population maintenance. Changes in the size-structures of populations were quantified to determine the effects of different regimes of disturbance, and these changes in population structure were explained by quantifying the life history traits of polyps and their rates of transition through their life cycle. An experimental manipulation was conducted to specifically quantify the effects of sedimentation on the rates of survival and asexual recruitment of polyps, because sedimentation was an important disturbance whose effects were confounded by additional variables. Together, the set of complimentary data provided a good understanding of population demography in the context of varying levels of exposure to certain disturbances, and enabled the best possible predictions about the future of each population under a variety of conditions

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.