Coral reef cryptofauna (coelobites) are metazoans that occupy the hidden recesses formed by structural taxa such as corals. While cryptic communities are thought to account for the majority of reef biodiversity and play important roles in reef trophodynamics, little empirical evidence exists supporting these claims. Quantitative sampling of coelobites has been thus far limited due to highly heterogeneous reef topographies as well as difficulties associated with identification of large numbers of species. In the eastern Pacific, monogeneric stands of Pocillopora form reef structures that are homogeneous across a horizontal plane and support a relatively depauperate fauna, thereby permitting detailed multispecies analysis. Sampling of motile cryptofauna associated with live coral and dead coral frameworks typifying four levels of degradation, was conducted at Playa Larga Reef on Contadora Island in the eastern Pacific, Gulf of Panamá. Communities associated with live coral colonies were less diverse than those associated with dead corals and the species richness of cryptofauna living on dead coral substrates was higher in more degraded habitats. Living coral colonies, however, support significantly greater densities of cryptofauna and more biomass per volume substrate than their dead coral counterparts. On dead coral frameworks, numbers of individuals and biomass were significantly greater per volume in areas of intermediate degradation. A field experiment was conducted to test the effects of flow, porosity and coral cover on cryptic communities associated with artificial reef frameworks (ARFs). Coral cover (live vs. dead) was not observed to affect the structure of communities occupying underlying frameworks, however, lower porosity substrates sheltered greater abundances of individuals per volume substrate and low flow environments supported elevated biomass. Additionally, porosity and flow were both found to significantly affect relative species abundances as well as overall community diversity. Data from quantitative sampling of natural reef environments and experimental manipulation of cryptic reef habitats suggest novel and unexplored responses to mass coral mortality and reef habitat degradation. Coral death is considered to be vital to the maintenance of reef ecosystem habitat and biotic diversity. Contrary to the popular paradigm that a healthy reef ecosystem has high coral cover, the most diverse reef ecosystems are those which have experienced intermediate levels of degradation. Furthermore, while living corals support elevated cryptofauna abundances and biomass, the magnitude of communities associated with dead framework materials suggest that abundant cryptofauna populations persist in highly degraded reef environments.

Our chemical investigation on the soft coral Sinularia facile which was collected off the coast of Kengting, Taiwan, has led to the isolation of ten metabolites 1¡Ð10, including four cembranoids and six polyhydroxylated steroids. Cembranoids isolated are two new natural compounds, (3E,7E,11E,15E)-cembra-3,7,11,15-tetraen-1-ol (1) and (1R*,12R*,3E,7E,10E,15E)-cembra-3,7,10,15-tetraen-12-ol (2), and two known compounds diepoxycembrene A (3) and isocembrol A (4). Moreover, five new polyhydroxylated steroids, cholest-5-ene-1£\,3£]-diol- 11£\-monoacetate (5), cholesta-5,24-diene-1£\,3£] -diol-11£\-monoacetate (6), cholesta-5,24-diene-1£\,3£]-11£\-triol (7), 24- methylenecholesta-5-ene-1£\, 3£]-diol-11£\,18-diacetate (8) and 24(S)- methylcholest-5-ene-1£\,3£]-diol- 11£\-monoacetate (9), and one known compound, 24-methylenecholest-5- ene-1£\,3£],11£\-triol (10). The chemical structures of these compounds (1¡Ð10) were elucidated by spectroscopic evidences (IR, MS, 1D NMR, and 2D NMR) and by comparison of the spectral data of these compounds in the literature. Cytotoxicity of these compounds toward various cancer cell lines has also been determined.

During the last three decades of coral reefs studies, the large areal coverage of data derived from satellite images has increasingly been used to complement the more detailed but spatially limited data produced by conventional fieldwork. Continuous improvement in sensor capabilities, along with the development of increasingly refined methods for image processing, has lead to ever more accurate maps of physical and biological variables of importance to reef ecology. During the same period, an abundance of field studies have documented statistical relationships between aspects of the reef habitat and its fish community. Despite numerous stochastic influences, such as spatially concentrated and temporally variable fish recruitment pulses or the selective and patchy mortality caused by fishing, several aspects of habitat have been shown to significantly influence the fish community. Fortunately the most important of these, water depth, the structural complexity of the reef, and the cover of live coral, are possible to estimate from currently available satellite imagery. The research presented in the following pages has combined the statistical relationships between the fish community and its habitat with the capability of satellite imagery to map that habitat, thereby answering the research question: How can remote sensing be used to map coral reef fish communities? In the process, a set of new techniques for predictive modeling of complex relationships have been compared, the influence of a range of habitat variables on the fish community quantified, the spatial scales at which the fish-habitat relationships are strongest have been explored, and new methods for deriving estimates of some aspects of the coral reef habitat from satellite imagery have been developed. The results presented in this thesis thus contribute to the further understanding of fish-habitat relationships, while providing a template for producing spatially explicit predictive models of fish community variables. This is not only of scientific interest, but also of substantial value to the conservation community that tries to protect the world’s remaining healthy coral reef ecosystems, and their fish communities, from an array of man-made influences.

During the last three decades of coral reefs studies, the large areal coverage of data derived from satellite images has increasingly been used to complement the more detailed but spatially limited data produced by conventional fieldwork. Continuous improvement in sensor capabilities, along with the development of increasingly refined methods for image processing, has lead to ever more accurate maps of physical and biological variables of importance to reef ecology. During the same period, an abundance of field studies have documented statistical relationships between aspects of the reef habitat and its fish community. Despite numerous stochastic influences, such as spatially concentrated and temporally variable fish recruitment pulses or the selective and patchy mortality caused by fishing, several aspects of habitat have been shown to significantly influence the fish community. Fortunately the most important of these, water depth, the structural complexity of the reef, and the cover of live coral, are possible to estimate from currently available satellite imagery. The research presented in the following pages has combined the statistical relationships between the fish community and its habitat with the capability of satellite imagery to map that habitat, thereby answering the research question: How can remote sensing be used to map coral reef fish communities? In the process, a set of new techniques for predictive modeling of complex relationships have been compared, the influence of a range of habitat variables on the fish community quantified, the spatial scales at which the fish-habitat relationships are strongest have been explored, and new methods for deriving estimates of some aspects of the coral reef habitat from satellite imagery have been developed. The results presented in this thesis thus contribute to the further understanding of fish-habitat relationships, while providing a template for producing spatially explicit predictive models of fish community variables. This is not only of scientific interest, but also of substantial value to the conservation community that tries to protect the world’s remaining healthy coral reef ecosystems, and their fish communities, from an array of man-made influences.

none

Coral reefs have high biodiversity among the many marine ecosystems. Many hypotheses explain marine biodiversity, e.g., the Intermediate Disturbance Hypothesis, the Lottery hypothesis and the Resource Allocation Hypothesis, but there is no mention of the possible role of seasonal effects. Here, we propose the Seasonal Recruitment Hypothesis to explain the possible role of seasonal recruitment and succession in a disturbed ecosystem. In this investigation, we tested several prediction of the hypothesis: a. Does recruitment have seasonal variation? b. Does variable recruiting communities diverge in succession? c. Are high biodiversities of coral reefs contributed by different communities originating from patches created in different seasons? In this study, we used plastic plates as proxy of empty space generated after disturbance to survey the seasonal patterns of settling benthos. Recruitment plates were placed and retrieved at two-month intervals for two consecutive years. Then, the composition and densities of settled taxa were estimated. The PRIMER software was used to compare the community similarities. We looked for possible seasonal patterns in each benthic populations but found few not real examples of such. Although there is difference between communities started in different seasons, no cyclic pattern in similarity was found by MDS plots in two years of recruitment communities. There are variations of recruitment community between different year and month, and the community structures converged after succession. These results do not support the prediction of the Seasoanl Recruitment Hypothesis.

In order to search for bioactive compounds, we have studied the chemical constituents from the organic extracts of five soft corals including Sinularia lochmodes, Sinularia nanolobata, Sinularia grandilobata, Sinularia depressa and Lobophytum crassum. This study had led to the isolation of eighteen natural compounds 1¡Ð18, including seven new compounds, lochmolins A ¡Ð G (1 ¡Ð 7) from S. lochmodes, a new compound nanolobatolide (8) featuring with a new carbon skeleton from S. nanolobata, two new compounds grandilobatin G (9) and sinugrandisterol E (10) from S. grandilobata, a new compound depressoloide A (11) and a known compound sarcophytol L (12) from S.depressa, and three new compounds crassumolides G¡ÐI (13¡Ð15) along with three known compounds durmolides B and C (16 and 17) and sinularolide C (18) from L. crassum. The structures of compounds 1¡Ð18 were established by detailed spectral data analysis (IR, MS, 1D & 2D NMR) and by comparison with the spectral data of the related known compounds. The relative stereochemistries of compound 8 was further confirmed by X-ray single-crystal diffraction analysis. Among them, compounds 13¡Ð15 and 16¡Ð17 were found to show significant activity against the accumulation of the pro-inflammatory iNOS and COX-2 proteins at 10 £gM.

Terpios hoshinota is coral-killing sponge which grows and covers most stony corals in shallow waters. It was first discovered at Green Island in 2006, and have since killed a lot of coral, yet we know little about the physiology of Terpios hoshinota. This research focuses on the propagation and growth of the sponge. In the sexual reproduction part, we collected tissue samples in 2009 and 2010, the sperm cells were found only in Jun and Aug in 2009. The oocytes were found in Apr, Jul, and Aug. In 2010, embryos occurred. No lunar pattern was found in a high-frequency sampling of tissues comparing the occurrence and sizes of oocytes and embryos. Embryos are more likely to be found in the central part of the sponge; this pattern does not apply to oocytes nor to sperm cells. The sponge may be hermaphroditic male and female gametes are developed at different locations or times. The sponge fragments can reinfect new host corals, although such capability decreased with increasing number of days suspending in the water column. The spicules parallel to each other and to the growth axis in tissue threads, moreover, the sponge quickly extended numerous tissue threads in the absence of adequate coral substrate, which may serve the function of reaching new hosts. The sponge grows faster under light than under dimmed conditions. Fusion of tissues could occur between non-identical genotypes, and allografting pairs of tissues have higher rates of rejection than isografting pairs. After allografting the sponge fragments from different areas, the fusion rates were depended on the distance of two populations in the northern coast of Green Island. The results supported that self-seeding is the mechanism how Terpios hoshinota populations exploded in the north coast Green Island. The ability to cross to the neighboring corals, to propagate by fragments, and to produce embryos may have all contributed to their self-seeding capability.

Terpios hoshinota is a blackish-gray cyanobacteriosponge encrusting on stony corals with fast expansion rates in shallow waters. The sponge population exploded at Green Island and Orchid Island during 2006 to 2008. Here, we surveyed at Green Island and Orchid Island in 2009 and 2010, compared the sponge densities, individual lengths, sponge coverage and scleractinian coral coverage between 2008 and 2010. We also tested the hypothesis that typhoon may play a role inhibiting the sponges by monitoring individual sponges before and after. In these three years, the sponge coverages remained the same; sponge length and densities had no significant difference at 2~3 m depth at Green Island, but densities decreased and length increase at 5 m depth at Green Island and 2~3 m depth at Orchid Island, but the rate increased was significant slower than average growth speed . Although sponge coverages were not significant different between these years, the scleractinian corals coverages decreased at Green Island among these years. The main wind direction was southwest during the Typhoon Marakot at Green Island, and only the sponges at southwest coast of Green Island decreased in size significantly among the three coasts monitored. The population of Sponge T. hoshinota exploded in 2006, the strength of typhoons were smaller than other years during 2005 to 2009. The typhoon may be the main factor that inhibiting the sponge T. hoshinota at these two islands.

Coral bleaching and mortality caused by ocean warming is the largest threaten to modern coral reefs. Understanding the change and acclimatization of coral communities to warming temperature is urgent for management and conservation. Using transect photo-surveys and monitoring of natural substratum quadrats with fluorescence technique, we compare the community structure and recruitment of corals between a reef artificially heated by thermal outfall of a nuclear power plant for more than 25 years (Outlet) and a nearby natural reef (Hobihu) in Nanwan Bay, southern Taiwan. Both reefs are influenced by intermittent upwelling induced by internal wave. Abundance of hard corals in Outlet was significant higher than in Hobihu, while soft corals showed an opposite pattern. Coverages of corals such as Montipora spp., Porites spp., Galaxea spp. and Favia spp. were significant higher, but Seriatopora spp. and Stylophora spp. were significant lower in Outlet than in Hobihu. Coral recruitment rates were higher in Hobihu than in Outlet with Hobihu having more Pocilloporidae recruits while Outlet having more Euphylliidae, majorly Galaxea recruits. Coral recruitment rates and their survivorship were significant higher in spring/summer season than in autumn/winter season. These results suggest that elevated seawater temperature with other contrasting environmental conditions (different exposure and current) may change the structure of coral community by influencing differently on various life stages. Massive and encrusting corals may be more resilient to ocean warming.