Rickettsiales-like organisms (RLOs) are thought to be related to bacteria in the order Rickettsiales. They have been reported to occur in the staghorn coral (Acropora cervicornis), and this study investigated trends of infection over time, and in relation to the health of infected corals. This study focuses on tissue samples taken mostly from visibly healthy A. cervicornis thickets in Broward County, Florida, and processed for histological examination. Samples were originally collected and analyzed to document reproduction during years 2001 through 2012, and tissue loss diseases (white-band disease [WBD] types I and II, and rapid tissue loss). The presence of suspect RLOs, the presence of ovoid bacterial aggregates in the basal body wall, and the condition of the coral tissue were examined in hematoxylin and eosin (H&E) and Giemsa-stained sections. Determination was made as to whether suspect RLO infection severity, location, or the presence of bacterial aggregates are correlated with changes in tissue condition associated with WBD. To better understand progression, trends, and periodicity in bacterial presence and coral tissue health, these data were then further analyzed for potential correlation with the month, year, and average monthly nighttime sea surface temperatures (categorized into ranges above, within, or below 24–29°C) when samples were collected. The severity of suspect RLO infections and the presence of bacterial aggregates in A. cervicornis varied over time, with no correlation with the location of suspect RLOs within the polyp. High suspect RLO prevalence was correlated with normal tissue conditions, while low suspect RLO prevalence was correlated with abnormal tissue conditions. However, high prevalence of bacterial aggregates was correlated to abnormal tissue conditions. Epidermal RLO and overall suspect RLO prevalence severity scores were significantly higher among samples collected when monthly average nighttime sea surface temperatures were below 24°C in contrast to samples collected when temperatures were between 24–29°C, suggesting direct or indirect effects of sea surface temperatures on infection severity. The areas of suspect RLO intracellular bodies within infected mucocytes were measured using digital image analysis software and found to be positively correlated with worsening coral tissue condition. Semiquantitative variable scores for histoslides stained with H&E were significantly different from those stained with Giemsa, indicating that these stains cannot be used interchangeably to study the presence of bacteria and the condition of coral tissue. Overall, the results of this study indicate that infection severity of suspect RLOs and the presence of bacterial aggregates are variable and correlated with the incidence of WBD-I in A. cervicornis. However, the exact nature of this relationship remains unclear. Further studies are necessary to interpret trends detected during this analysis to develop a better understanding of what contributes to the severe tissue-loss outbreaks and mortalities of A. cervicornis.

Looking at the metabolite profile of an organism provides insights into the metabolomic state of a cell and hence also into pathways employed. Little is known about the metabolites produced by corals and their algal symbionts. In particular, corals from the central Red Sea are understudied, but interesting study objects, as they live in one of the warmest and most saline environments and can provide clues as to the adjustment of corals to environmental change. In this study, we applied gas chromatography – mass spectrometry (GC–MS) metabolite profiling to analyze the metabolic profile of four coral species and their associated symbionts: Fungia granulosa, Acropora hemprichii, Porites lutea, and Pocillopora verrucosa. We identified and quantified 102 compounds among primary and secondary metabolites across all samples. F. granulosa and its symbiont showed a total of 59 metabolites which were similar to the 51 displayed by P. verrucosa. P. lutea and A. hemprichii both harbored 40 compounds in conjunction with their respective isolated algae. Comparing across species, 28 metabolites were exclusively present in algae, while 38 were exclusive to corals. A principal component and cluster analyses revealed that metabolite profiles clustered between corals and algae, but each species harbored a distinct catalog of metabolites. The major classes of compounds were carbohydrates and amino acids. Taken together, this study provides a first description of metabolites of Red Sea corals and their associated symbionts. As expected, the metabolites of coral hosts differ from their algal symbionts, but each host and algal species harbor a unique set of metabolites. This corroborates that host-symbiont species pairs display a fine-tuned complementary metabolism that provide insights into the specific nature of the symbiosis. Our analysis also revealed aquatic pollutants, which suggests that metabolite profiling might be used for monitoring pollution levels and assessing environmental impact.

Most corals worldwide are broadcast spawners that rely on synchronous gamete release for successful fertilization. Spawning synchrony may also decrease the probability of heterospecific fertilization that may produce maladaptive hybrids. Despite the importance of reproductive timing, researchers have only recently begun to collect spawning data across coral species in the Caribbean, but these data remain to be analyzed. This study investigates interannual, seasonal, and environmental patterns that may influence Caribbean scleractinian spawning times. The number of spawning observations varies widely among location and species. Most spawning observations were collected in Florida, Curaçao, and Flower Garden Banks National Marine Sanctuary. Acropora palmata, A. cervicornis, and Orbicella species were the most documented. The Orbicella spp. were very consistent for spawning day annually, while the acroporids were less reliable. However, the acroporids were more consistent for spawning time in minutes after sunset between years. Season and moon cycles were obvious proximate cues for spawning, but a strong influence from wind and tides was absent. Acropora cervicornis was the only species in this study which spawning was significantly affected by water temperature. For some scleractinians, the day of spawning was significantly affected by mass bleaching events; spawning could occur on earlier days than in previous years for up to two years after the event. This study highlights existing data gaps for Pseudodiploria clivosa, A. prolifera and Siderastrea siderea. Documenting spawning patterns is crucial to better understand the potential impacts of future threats on the already imperiled Caribbean corals at risk from reproductive failure.

Coral reefs are an important element of marine ecosystem that are critical to maintain a healthy environment. Unfortunately, in recent years coral reefs are doing poorly and many in parts of the ocean are simply dying. Therefore, study of coral’s structural response to external loads could answer what will happen with their structures, while they exhibit different types of loading. Therefore, the proposition of using in-situ micro-Raman spectroscopy to study skeletons of Acropora cervicornis was used. Coral skeleton samples I subjected to mechanical loading studied their vibrational properties by exciting the material with 532nm visible light. A uniaxial compressive load I applied using a MTS universal testing machine and then using the Raman Spectroscopy to study the vibrational response of coral skeletons. Indentations used Vickers Hardness tester and performed 2D mapping of the coral structure around the indentation. If it’s expected that as a result of the proposed research the better understanding of structural stability of the Acropora Cervicornis coral skeletons will be achieved.

This research explores the instantaneous mechanical behavior of the skeleton of the critically endangered staghorn coral Acropora cervicornis. Both bleached and sanded skeletons were used in this experiment. The Raman spectroscopy test showed that there was no significant change in the Raman shift between the three branches tested. The shifts were nearly identical to Raman shifts of calcium carbonate. Vickers hardness test found that 1 Bleached had the average hardness of 3.44 GPa with a standard deviation of 0.12 GPa. The sanded sample also had a similar value of 3.54 GPa with a standard deviation of 0.13 GPa. Samples from 2 Bleached had a hardness value that was significantly lower at only 2.68 GPa with a standard deviation of 0.37 GPa. The axial compressive stress test determined that the average strength for the bleached samples was 18.98 MPa and for the sanded, 29.16 MPa. This information can be used to assist in the restoration of this species.

Caribbean reef ecosystems have undergone major ecological changes in the last 30 – 40 years, with the result that ecological systems once dominated by structurally complex Acropora cervicornis and Montastraea annularis corals now consist mainly of flattened carbonate substrates with macroalgal overgrowth. A need for greater understanding of coral reef ecosystems is imperative if we are to attempt to conserve them. The threespot damselfish, Stegastes planifrons, is herbivorous damselfish species ubiquitous to Caribbean reefs, where it has been termed a keystone species. Aggressive in nature, S. planifrons defends territories of around 70 cm in diameter from other roving herbivorous fish and urchins, in apparent effort to maintain the algal resources therein for its own use. The predilection of Stegastes planifrons for basing its territories on the now Critically Endangered staghorn coral, Acropora cervicornis, and the Endangered boulder coral Montastraea annularis is well known, however the likely ecological implications of this fact have not been investigated. Using a combination of experimental and observational methodologies we examine the ecological implications of coral microhabitat choice and use by S. planifrons. We also assess the magnitude of the direct and indirect effects of S. planifrons’ territorial behaviour on macroalgal dynamics both within and outside of territory confines, at the reef-wide level. We find that coral microhabitat is a more important determinant of algal community structure than damselfish presence, and that this can be explained by a previously unrecognised effect of coral microhabitat on the grazing behaviour of roving herbivorous fishes - on which S. planifrons’ territorial behaviour has little effect. In a modification of the space availability hypothesis of Williams et al (2001) we suggest that Acropora cervicornis acts as a grazing fish „exclusion zone‟, and we further hypothesise that the existence of large stands of this coral prior to the Caribbean „phase shift‟ may have acted to concentrate the grazing pressure of excluded roving fish onto the remaining areas of the reef. We further hypothesise that the loss of such „exclusion zones‟ and accompanied effective dilution of grazing pressure may have been on a scale large enough to have been a significant underlying factor in the proliferation of macroalgae seen on modern day Caribbean reefs. In the absence of demonstrable direct or indirect effects on benthic algal communities we question the continued keystone status of S. planifrons, particularly since the status 6 was originally based on interference behaviour involving the important grazing urchin Diadema antillarum, which is now functionally absent from Caribbean reefs. Implications of the context-dependant nature of keystone status are also discussed. We find that the effect of S. planifrons on coral community may be more important than its effects on benthic algal community. In examining the factors involved in habitat coral choice we establish a significant preference for 100% live coral substrate over substrates with a supply of algal food. Territory selection was followed by a high rate of coral biting – a behaviour which has previously been shown to result in coral tissue death and the fast establishment of algal turf communities on which S. planifrons likes to feed (Kaufman 1977). We also demonstrate a novel and significant association between S. planifrons presence and disease incidence its primary habitat coral, the Critically Endangered staghorn coral Acropora cervicornis, and a significant correlation between areas of fish biting and the later onset of disease. Changes to the overall role of damselfish on today's Caribbean reefs are discussed in light of these insights.

[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.

Acropora cervicornis and A. palmata were once dominant, reef-building corals of Caribbean reefs. Over the last several decades, population declines of Caribbean Acropora have been dramatic, and both species are now listed as “Threatened” under the United States Endangered Species Act. Numerous restoration efforts now utilize coral gardening techniques to cultivate these species for transplantation, in which A. cervicornis is primarily cultivated both on fixed structures and in line nurseries. This study evaluates growth and survivorship of multiple A. cervicornis genotypes grown via two line nursery techniques, and compares the efficacy of each against the conventional method of fixed nursery puck-mounted culture. Suspended nursery culture resulted in higher post-fragmentation survivorship of corals than puck culture, especially in warmer conditions. Disease incidence was significantly reduced by suspended culture, which also prevented predation from fireworms (Hermodice carunculata) prevalent in puck corals at the same nursery. Genotypic growth rate differences persisted among techniques, and suspended coral growth was comparable to puck culture. Suspended colonies may need more frequent pruning to avoid branch abrasion and breakage, but the technique is an effective means to reduce disease, predation, and post-fragmentation mortality in A. cervicornis nursery culture.

Reef-building coral populations throughout the world are being threatened by numerous stressors and continue to decline. As potent endocrine-disrupting compounds, exogenous sex steroid contamination has been a largely overlooked stressor to corals. Previous research indicates these compounds are prevalent in marine environments, fluctuate annually along with reproductive cycles, can bioaccumulate, and have had variable effects on growth and reproduction in several cnidarian species. This project had three primary objectives: (1) establish environmental estradiol and progesterone concentrations in Broward County and lower Florida Keys reef environments, (2) conduct 17 β-estradiol and progesterone larval assays on P. astreoides larvae to determine the effects of these compounds on settlement and viability, and (3) conduct 17 β-estradiol and progesterone dosing experiments on adult Acropora cervicornis and Porites astreoides fragments to determine the effects on growth, zooxanthellae, reproduction, and overall tissue health. Estradiol was detected in surface and at-depth water samples from Broward County and lower Keys reef sites at effect level concentrations for marine organisms. Broward County larvae treated with low progesterone (5 ng/L) had decreased survival, while lower Keys larvae in low estradiol treatments (1 ng/L) had increased on-disc settlement. No other treatment effects were observed, however, lower Keys larvae had greater overall survival in comparison to Broward County larvae. There were no significant differences between estradiol and progesterone treatments in the adult-dosing experiment for growth, zooxanthellae density, reproduction, and overall tissue health. This is the first study to detect estradiol at Broward County reefs sites and our results, while inconclusive, indicate these compounds may have the potential to affect coral reef ecosystems.

While populations of nearly all stony coral species along the Florida reef tract have exhibited decline, the most notable decline has occurred in the once-dominant acroporid species (Acropora cervicornis, A. palmata). Both species were listed in 2006 as threatened under the Endangered Species Act. This listing, combined with their continued decline, has resulted in large-scale restoration efforts throughout Florida and the Western Caribbean. Currently, there is little to no information regarding spatial prioritization of sites for these restoration efforts. The primary objective of this dissertation was to utilize species distribution modeling, informed by existing data from the Florida reef tract, to identify sites for restoration of acroporid corals that should have strong likelihood for success. The initial focus was to use a database of reported field observations, in combination with benthic habitat maps, to model the extent of suitable habitat for Acropora spp. The mapped coral reef and hardbottom classifications throughout Florida, Puerto Rico, and the US Virgin Island reef tracts were used to generate potential-habitat polygons using buffers that incorporated 95% and 99% of reported observations of Acropora spp. Resulting maps demonstrated that A. palmata habitat is relatively well defined, while that of A. cervicornis is more variable and difficult to constrain. Thus, as the major focus of this dissertation, available monitoring data from the Florida reef tract were used to construct and compare two types of statistical species distribution models, random forest and boosted classification trees, as an approach to inform siting of restoration efforts for A. cervicornis. Boosted classification trees were more accurate than the random forest model at classifying A. cervicornis population trends. Further analyses of the two most important environmental parameters identified by the model, depth and light availability, revealed that reef areas predicted to not have had A. cervicornis present from 1996-2013 were deeper, on average, and had lower light availability and greater variance than areas predicted to have had continuous or transient A. cervicornis presence over this time frame. This study represents a first step at deriving an ecologically-guided approach to spatial prioritization of restoration efforts. The overarching goal of this project has been to design a strategy for creating models to define and predict where conservation and restoration actions should be most effective, that can be utilized for a variety of coral species. With existing populations mapped, the results can also aid in protecting the limited areas in which these species still occur.