Population replenishment through recruitment is an essential process for the long term viability of corals and their associated communities, particularly under increasing stresses that threaten their vitality. Although many researchers have identified specific factors that influence individual processes in the early life cycle of corals, few studies to date have attempted to determine the cumulative success of a cohort's progression through these stages in natural reef settings. Specifically, there is a paucity of knowledge regarding appropriate and realistic techniques to forecast the success of recruitment in natural settings, while taking into account both the individual and environmental factors that regulate these recruitment dynamics at local scales. Because of this need, the overall goals of this dissertation research were to (1) assess key life stage processes leading to recruitment - specifically, settlement and early post-settlement processes - for which previous knowledge was limited or absent; and (2) using this knowledge, develop a local-scale recruitment model that assessed the cumulative success of a cohort's progression through all the early life stages and identified those processes that had a strong relative influence on regulating recruitment dynamics. Focusing on the common western Atlantic brooding coral, Porites astreoides, this dissertation research was divided into three main sections to address the overall objectives: (1) identification and quantification of recruitment patterns in natural reef settings, in order to guide the development and testing of the recruitment model (Chapter 2); (2) assessment of the focal species' behaviors, survivorship rates, and factors affecting those rates during its progression through the primary early life stage processes (i.e., basic habitat preferences during the settlement stage, Chapter 3; early post-settlement survivorship, Chapters 4 and 5); and (3) development of a local recruitment model that accounted for the full complement of early life stage processes in a spatially-explicit simulation framework (Chapter 6). While unique study-specific insights were gained from each of the individual chapters, a few general insights emerged with respect to the overarching study objectives from this dissertation research. First, larval supply is a key driver for recruitment, where a high degree of larval loss, either through direct larval mortality or export from the reef, occurs prior to settlement on the substrate. Rates of loss were 96-99% in the model analyses, and as such represent the first major population bottleneck for this species and others with similar life histories. Compounding this larval loss is a second population bottleneck during the early post-settlement stage, where mortality was typically greater than 75% within the first week after settlement. Such high rates of loss have important implications for future population dynamics, as relatively minor changes to these rates of loss can have relatively strong influences on future dynamics. Second, habitat influences on recruitment were found to be relatively minimal when compared to high rates of mortality in both the larval supply and early post-settlement stages. Although the relative influence of habitat may be strong under unique situations where substantial space preemption limits settlement (e.g., high macroalgal cover, sedimentation, or adult coral cover), these effects may not be reflective of average systems. However, the influence of habitat may still be crucial for ensuring that the few individuals who survive the larval supply and the early post-settlement bottlenecks recruit into the future adult population, and these influences may interact with other density-dependent processes as adult cover increases. Overall, this research presents valuable and novel insights on a number of the under-studied early life stage processes. By identifying the key processes which regulate recruitment, this work highlights those stages whose responses to environmental change will have strong impacts on recruitment and subsequent population dynamics. In addition to the process-based insights gained on these dynamics, this work provides informative criteria for managers on the stages most responsive to conservation efforts aimed at promoting resilience and recovery.

Ocean acidification (OA) refers to the increase in acidity (decrease in pH) of the ocean’s surface waters resulting from oceanic uptake of atmospheric carbon dioxide (CO2). Mounting experimental evidence suggests that OA threatens numerous marine organisms, including reef-building corals; however, few studies have focused on the effects on early life history stages. Coral recruitment is critical to the persistence and resilience of coral reefs and is regulated by several early life processes, including: larval availability (gamete production, fertilization, etc.), larval settlement, post-settlement growth, and survival. Environmental factors that disrupt these early life processes can result in compromised or failed recruitment and profoundly affect future population dynamics. To evaluate the effects of OA on the sexual recruitment of corals, sexual reproduction (including fertilization and sperm swimming speeds) and several critical early life history stages (including larval metabolism, larval settlement, and post-settlement growth) were tested in common Caribbean coral species. Three pCO2 levels were used: ambient seawater (380 µatm) and two pCO2 scenarios that are projected to occur by the middle (560 µatm) and end (800 µatm) of the century as determined by the Intergovermental Panel on Climate Change. Results show that fertilization success, larval metabolic rates, larval settlement rates, and post-settlement growth rates are all compromised with increasing pCO2. This dissertation demonstrates that OA has the potential to negatively impact sexual reproduction and multiple early life history processes of several common Caribbean coral species and may contribute to substantial declines in sexual recruitment that are felt at the community and/or ecosystem scale.

Thesis (M.S.)--University of Delaware, 2006. / Principal faculty advisor: Mark E. Warner, College of Marine and Earth Studies. Includes bibliographical references.

In order to search for bioactive compounds, we have studied the chemical constituents from the organic extracts of two Formosan soft corals Sarcophyton crassocaule and Paralemnalia thyrsoides. This study had led to the isolation of forty-six natural compounds 1¡V46, including sixteen new cembrane¡Vtype diterpenoids, crassocolides A¡VP (1¡V16) and four known cembrane¡Vtype compounds 17¡V20 from S. crassocaule; nineteen new sesquiterpenoids and norsesquiterpenoids, paralemnone (21), isoparalemnone (22), paralemnol (23) and paralemnolins A¡VP (24¡V39), along with seven known compounds 40¡V46 from P. thyrsoides. The structures of these compounds were established by the detailed spectroscopic analysis (IR, MS, 1D¡B2D NMR) and by comparison with related physical and spectral data from other known compounds. The absolute configurations of 1-46 were determined using a modified Mosher's method for 1, 7, 22 and 27. The structures of 5, 21, 24 and 37 were further proven by X-ray diffraction analysis. The cytotoxicity of compounds 1-46 against a limited panel of cancer cell lines was also determined. Also, the activity of compounds 21-28, 35-37 and 41-42 to inhibit the pro-inflammatory iNOS and COX-2 protein expression of LPS-stimulated RAW264.7 macrophage cells has been estimated.

Marine organisms have attracted much attention as potential source for drugs over recent years. Soft corals have yielded many bioactive metabolites. Some of them have been examined for their pharmacological properties. For the process of drug discovery, we have examined bioactive metabolites from the organic extracts of two soft corals Sinularia gibberosa and Sarcophyton sp. collected off Formosan coast. This study had led to the isolation of forty-two natural products (1¡V42), including one new £]-caryophyllene-type sesquiterpenoid (1), four new xeniaphyllane-type norditerpenoids (2, 14, 16, and 17), fourteen new xeniaphyllane-type diterpenoids (3¡V13 and 18¡V20), one novel nor-humulene (15), seven new xeniaphyllane-type diterpenoids (21¡V26) with cyclic peroxyhemiketal (3,6-dihydro-1,2-dioxin-3-ol) moiety, and one new steroid (27), along with five known compounds (28¡V32) from Sinularia gibberosa. Three new cembrane-type diterpenoids (33¡V35), along with seven known cembranolides (36¡V42) were isolated from Sarcophyton sp. The structures of metabolites 1¡V42 including their stereochemistry have been established by detailed spectroscopic analyses, particularly mass, 2D NMR (1H¡V1H COSY, HMQC, HMBC, and NOESY) spectroscopy and by comparison with the related physical and spectral data from other known compounds. In above metabolites, two compounds (8, 9) exhibited cytotoxicity against the growth of MCF-7, Hep 3B, Ca9-22 cancer cell lines. Furthermore, nine compounds (4, 8, 9, 11, 12, 13, 21, 31, 39) exhibited cytotoxicity against the growth of MDA-MB-231, Hep G2 and A-549 cancer cell lines.

<p>Coral reef fish coexist in a state of high diversity that has not been successfully explained by niche diversification, larval supply, differential mortality, or a suite of other proposed factors. These processes are all occurring on a diverse substrate that would be expected to affect the abundance and distribution of fish by directing habitat preferences as well as affecting competitive and predatory success. I conducted correlational studies on healthy and degraded Caribbean reefs that addressed fish abundances at the levels of community, species, and age class. I also experimentally tested habitat preferences in two ways: choice experiments on adults of common species that determined preferences for live coral and rugosity in an isolated environment, and monitoring of artificial reefs differing in live coral cover that tested habitat selection of adults and juveniles in the field. These observations all show that live coral had no effect on community parameters such as abundance or diversity, but that rugosity was positively related to species richness. However, these measures of the community masked differences at the species and age class level. A handful of species exhibited positive or negative preferences for live coral, but these selections did not follow a taxonomic or trophic-level classification. Species within the genus Stegastes, for example, could either aggregate towards or avoid live coral. One species even reversed its habitat preference as it matured. Field distributions were not determined solely by these habitat preferences, but inclusion of competitive interactions into a multi-factorial model explained distribution of some species. Results suggest that changes in live coral cover, an increasingly common phenomenon, would not affect fish at a community level, but could affect a few species through changes to recruitment or alteration of competitive interactions.</p> / Dissertation

Determining the relative roles of top-down vs. bottom-up forces in controlling the structure of ecological communities is of primary importance because anthropogenic nutrient loading, overharvesting of consumers, and potential interactions of these forces are pervasively changing ecosystems throughout the world. Here I use both field experimentation and meta-analyses to investigate the role of predators in controlling community composition, the relative roles of herbivores vs. nutrient enrichment in controlling the abundance of benthic primary producers, and the influence of herbivore diversity on the community structure of coral reefs. On a coral reef in the Florida Keys, I showed that release from predation by large fishes and invertebrates via exclusion cages allowed population increases in the gorgonian-eating gastropod Cyphoma gibbosum which increased predation rates on gorgonian corals. To directly address the relative roles of top-down and bottom-up forces in controlling primary producers in benthic marine habitats, I used factorial meta-analysis of 54 field experiments that orthogonally manipulated herbivore pressure and nutrient loading to quantify the effects of consumers and nutrient enrichment on community structure. The relative effects of herbivores vs. nutrient enrichment were context dependant, varying with latitude, the type of primary producer, and the nutrient status of the system. To address the influence of herbivore diversity on the community structure of Caribbean coral reefs, I used manipulative field experiments over two years to show that a Caribbean reef changes dramatically as a function of herbivorous fish diversity. The effects of herbivore diversity on community structure were strong in both years of the experiment due to different diet preferences among herbivores. Higher herbivore diversity suppressed macroalgal abundance, increased abundance of crustose coralline algae, reduced coral mortality, and increased coral growth when compared to treatments with lower herbivore diversity. Complementary feeding by different fishes drove these patterns because macroalgae were unable to effectively deter feeding by fishes with different attack strategies. Thus, herbivore diversity appears to play an important role in the healthy function of coral reef ecosystems via complementary feeding of different herbivore species.

The purpose of this study is to investigate the factors that are responsible for the distribution of coral communities in the lagoon of the Dongsha Atoll. Previous surveys proposed that there was significant difference of coral cover between the east and west sides of the lagoon. Two hypotheses, seawater temperature and water depth, were proposed to explain the spatial variation of coral distribution. In addition, the growth rate of poritid corals, coral recruits, sexual reproduction, and the occurrence of coral predators and diseases were also studied. Ten patch reefs 5 on the west and 5 on the east sides in the lagoon were selected and the corals on reef tops (1-3 m) and deep reef bases (10-15 m) were investigated. The growth rates of poritid corals on reef tops were higher on reef bases than those on reef tops, and higher in eastern lagoon than those in western lagoon. On average, the growth rate is 0.9 cm/year. A total of 10 families of small corals were recorded in which Faviidae (61.6%), Fungiidae (16.6%) and Poritidae (9.7%) constituted the majority. Diversity index comparisons indicated that reef bases have higher diversities than reef tops. The densities of small corals, ranging between 0.1-3.0 ind./m2, are higher on reef bases than on reef tops. In fungiids, individuals in the eastern lagoon were larger than those in the western lagoon. Tissues of corals were sampled in June 2009 for examination of gonads. However, no reproductive tissues were found after decalcification and histology. The morphological classes, live-coral coverage, dead-coral coverage and dead-coral ratio among the comparisons of reef bases vs reef tops and western vs eastern lagoons, only dead-coral coverage was found to be higher in eastern than in western lagoon. The live-coral coverage was 0.3-46%, dead-coral coverage was 8%-76% and dead-coral ratio was 10%-100%. Among the 10 patch reefs, patch reefs 6, 7, 9 and 10 are represented by mostly K type competitors and belongs to Conservation Class 2, patch reefs 1, 2 and 3 are presented by mostly S type stress-tolerated corals and belongs to Conservation Class 1. The remaining 3 patch reefs 4, 5 and 8 belong to the highest Conservation Class 4 and are represented by diverse types of corals. The water temperature exceeded 30¢XC in 36% of the time at reef tops, and 13% of the time at reef bases, during the summer period, i.e., between June and September, 2009. And the water temperatures were found in 95% of the time to be ~ 1¢XC higher at reef tops than at reef bases. The water temperatures were also higher in the west than in the east of the lagoon that 29% of the time exceeded 30¢XC in the west and 9% in the east only. No coral diseases or pests were found that may pose a large-scale threat in the near future. The variations of coral fauna found among habitats in the lagoon are consistent with the temperature patterns, i.e., the higher the temperature the poorer the coral condition. To the two hypothesis, in the eastern or western lagoon and the different depth are the factors of coral distribution in the lagoon.

In order to search for bioactive compounds, we have studied the chemical constituents from the organic extracts of the soft coral Sarcophyton crassocaule. This study had led to the isolation of twenty-six natural cembrane-type diterpenoids, compounds 1¡V26, including eighteen new compounds, sarcocrassocolide A¡VR (1¡V18), along with six know compounds, crassocolide A, B, D, E, L, sarcocrassolide, sinularolide E and 13-acetoxysarcocrassolide (19¡V26). The structures of compounds 1¡V26 were established by detailed spectroscopic data analysis (IR, MS, 1D, 2D NMR) and by comparison of the spectral data with those of the related known compounds. The structures of 8, 9 and 11 were further established by orgamic methods, and the absolute configuration of 1 was determined using a modified Mosher¡¦s method. The cytotoxicity of compounds 1¡V17 and 19¡V21 against the Daoy (human medulloblastoma), HEp2 (human laryngeal carcinoma), MCF-7 (human breast adenocarcinoma), WiDr (human colon adenocarcinoma), DLD-1 (human colon adenocarcinoma), CCRF-CEM (human T-cell acute lymphoblastic leukemia), and HL-60 (human promyelocytic leukemia) tumor cell lines were determined, and structure-activity relationship was presented by statistic method. Compounds 3 and 9 showed significant activity toward the above Daoy, HEp2, MCF7 and WiDr, and compounds 18, 19, 20, 22 and 24 were found to show significant activity toward the above DLD-1, CCRF-CEM and HL-60. Compounds 1¡V26 were shown to exert significant anti-inflammatory activity in LPS-stimulated RAW264.7 macrophage cells. Compounds 9, 17, 19, 22 and 24 also significantly inhibited the accumulation of pro-inflammatory COX-2 protein.

The methods of denaturing gradient gel electrophoresis (DGGE) and DNA sequencing were used to analyze the ribotypes of microbial communities associated with corals. Both healthy and diseased coral of different species were collected at three locations off the southern coast of Taiwan. Ribotyping results suggested that the microbial communities were diverse. The microbial community profiles, even among the same species of corals from different geographical locations or different times, differ significantly. The coral-associated bacterial communities contain many bacteria common to the habitants of various invertebrates. One ribotype presented on the Black Disease coral tissue is closely related to the Clostridium sp. previously identified from White Plaque-diseased and BBD corals. This Clostridium sp. may be relatived to coral diseased, as this species was also found in many types of diseased coral. The other one ribotype presented on our healthy and diseases coral is closed to denitrifying bacterium Pseudovibrio sp. which had been previously discovered in Kenting National Park Nanwan Bay as a new marine, facultative anaerobic bacterium. However, some bacteria were unexpected. The presence of some unusual species, such as Staphylococcus, Legionella and soil bacteria, associated with corals that were likely the results of human activities. Human activities, such as active fishing and tourism industries in the region might have all contributed to the change in bacterial communities and the death of coral colonies around the region.