This thesis investigates the variation of the chlorophyll-a concentration near Dongsha Atoll derived from MODIS Aqua and Terra satellite images, and their relationship to physical environments including sea surface temperature, CTD water qualities, tides, currents and surface winds for the period 2005 to 2008. The results revealed that the seasonal variation of chlorophyll-a concentration was higher in the winter than in the summer, and had inverse relationship with sea surface temperature. The increased chlorophyll-a concentration was due to entrainment of lower layer cold water with high nutrient. The upwelling water was induced by mixing of surface wind and internal wave shoaling. When the internal waves propagated westward to the Dongsha Atoll, the bottom topography and coastline oriented the cold deep water surged up slope to the northeastern corner of the Atoll, which produced high chlorophyll-a concentration a few days after. The comparison of MODIS images and CTD data revealed that the chlorophyll-a concentration didn¡¦t increase immediately after the passage of internal waves.

Abstract Internal waves have been identified as one of the most active mechanisms producing vertical mixing in continental slope and shelf waters. The major contribution of mixing are due to internal tides, however, shorter period internal waves are unlikely to be the main source of energy for mixing, especially on the inner part of the continental shelf. In this study, we observe the vertical mixing of huge internal waves in the Dongsha Atoll South China Sea. These solitary waves were originate near the Luzon Strait, propagated westward across the basin, evolving into internal solitary wave trains and dissipated at the western shallow continental shelf. The wave energy and phase speed reduced significantly during the shoaling process. Internal waves and their likely related induced mixing phenomena are analyzed based on multiple cruises of observations consisted of CTD hydrographic measurements, water samples and moored thermister strings. Data analyses show that the mixing processes are related to depths of water and the interfacial of wave. For depression wave in the deep water zone, upper layer water may push downward producing vertical mixing beyond the thermocline. The mixing usually dilutes the nutrients in the upper layer of water column. Statistics suggest that the N:P ratio is 12:1 which is lower than the standard value (16:1) indicating the region is nitrogen deficit, similar to most of the surface water in South China Sea. The depression solitons in deep water may evolved to a packet of elevation waves in the shallow water area at ¡§turning point¡¨ of approximately equal depth of upper and lower layers. The mixing of shallow water internal waves can entrain cold nutrient rich water from the lower layer into the frequently nutrient depleted subsurface layer to enhance the local coral reef ecosystem. For example, CTD profiles (2008.5.7) before and after the passage of internal wave show large differences. The vertical density distribution has dramatic change. The column was stratified in two layers in normal condition. The internal waves perturbed the water column into stepwise multi-layer density distribution. The water at 50 m showed temperature decrease by 6 ¢J, salinity increase by 23 psu, density increase by 1.8 , fluorescence decrease by 0.065 £gg/L etc. The MODIS chlorophyll images confirm the high concentration fertilized by the internal wave pumping near the NE region of the Dongsha Atoll.

Abstract This study investigates the distributions and controls of transparent exopolymer particles (TEP) in marginal seas around Taiwan. In the euphotic zone of Kuroshio Water off southeast Taiwan, the concentration of TEP generally reached a maximum in the subsurface and then decreased with depth. The maximum concentration of TEP in every station in the Kuroshio Water coincides with the subsurface maximum of chlorophyll a (Chl. a). This implied that TEP in the euphotic zone was controlled by biological rather than physical processes. Furthermore, the ratios of TEP /POC and TEP/DOC increased with Chl. a indicating that the increase of primary production may enhance DOC transformation to POC through the formation of TEP. Concentrations of TEP in the Taiwan Strait and Gaoping coastal sea decreased generally with the increase of seaward distance, showing the same pattern of nutrient distribution. Apparently, the terrestrial input of nutrient may increase phytoplankton abundance and enhance the formation of TEP. Positive correlations were significant between TEP and Chl. a, suggesting that the distribution of TEP in the euphotic zone of Taiwan Strait and Gaoping coastal sea are also controlled by biological processes. During the study period, the concentrations of nutrient and Chl. a were elevated in the surface water around the Dongsha Island in the South China Sea (SCS), due to the influence of internal wave. According to the close relation between TEP and Chl. a, concentrations of TEP around Dongsha Island were also likely controlled by phytoplankton activity, but the different strength of internal wave may lead to the different conditions of TEP, Chl. a and POC distributions. The results of factor analysis support the fact that distributions of TEP are mainly controlled by biological processes, but various physical conditions could also influence distributions of TEP in the water column. Overall, concentrations of TEP are generally higher in the Taiwan Strait and Gaoping coastal sea than in the Donshia shelf sea and Kuroshio Water off southeast Taiwan. Nevertheless, distributions of TEP are all comparable with previous findings in other coastal and marginal seas.

Many coral reefs around the world were damaged during the 1998 mass bleaching event. The acroporids in the lagoon of Dongsha Atoll were eliminated during massive bleaching, and they are still not recovered. Three hypotheses were proposed to explain how the lagoon of Dongsha Atoll has not recovered during the past twelve years¡G1. the lack of recruitment, 2. the persistent interfering on newly recruiting acroporids by hot water, 3.the interfering on those acroporids by predators. Four types of habitats, i.e., reef tops, reef slopes, reef bases, and inter-patch-reefs were surveyed on their coral communities, densities of juvenile corals, growth rates, pests and diseases of corals. The tissue samples were collected to assess reproductive status of corals. Moreover, Acropora muricata branches were transplanted from north coast of Dongsha Island to 3 m and 9 m depths in the lagoon of Dongsha Atoll for testing suitability of the environment. The acroporids were mature, and they spawned between March and May in 2010. Live coral coverage was 16% on average; small coral densities were 1.5/m2, much lower than other lagoons. Besides, acroporid represented 8% of coral coverage and 4% of juvenile corals which are lower than those of other lagoon. Water temperatures were higher in 2010 than 2009. However, coral skeletal extension rates do not show any reign of reduction. In addition, most acroporids survived 2010 summer¡]sea water temperature exceeded 30¢J¡G40-64%¡^ in the transplantation experiment. During two years of survey, only 6 individuals Acanthaster planci. So the lack of recruits might be the bottleneck to the recovery of acroporid in Dongsha lagoon.

Dongsha Island has Taiwan¡¦s only well developed and integrated coral atoll ecosystem. The numbers of fish species and coral varieties in its waters have topped 679 and 286 respectively, which illustrates its biodiversity and wealth of fishery resources; therefore, it has drawn plenty of Chinese fishing boats to illegally enter into the area for fishing. Over the years, the fishery resources and terrain ecology of the Dongsha Island have been damaged as a result of illegal fishing. On the other hand, even though Taiwan¡¦s Coast Guard Administration in charge of patrolling the waters of the Dongsha Marine National Park, due to the vast sea area and varying depths of the atoll, the effect of the law enforcement on the vessels is limited, and cannot provide effective deterrence. By using existing information technology to gain knowledge on the distribution of the Chinese fishing boats, this study proposes to make the most of the limited law enforcement capacity to enhance the efficiency of law enforcement. With the coastal radar station established by Taiwan¡¦s Coast Guard Administration in 2003, this study scanned the waters around the clock and digitally journalized the data regarding times and locations of the voyages of the fishing boats, to further explore the time and space distribution of the Chinese fishing boats at the Dongsha atoll. Based on the annual, quarterly, monthly, day to night and tidal periods, five periods in total, this study used the Geographic Information System (GIS) to map out the distribution of the Chinese fishing boats, and probed into the distribution patterns in different times and spaces. The results will provide a scientific reference for law enforcement; it is hoped that the law will be effectively enforced and the ecological environment will be well preserved under limited resources. The study results indicate that the Chinese fishing boats operating at the Dongsha atoll are mainly small boats; a large boat can carry 10 to 30 small boats. Furthermore, the fishery catches are mainly live fish, sea cucumbers and conches, and are mostly carried back to the port by transport vessels for sale. The Chinese fishing boats often gather at two hot spots of the south atoll platform and the north atoll platform. In terms of the distribution of seasonal gathering, the study found that most of the Chinese fishing boats return home for the Chinese New Year holiday, the gathering density is higher during full moon periods and the gathering may slightly move towards the north when affected by the southwest monsoon. These results can serve as an important reference for Dongsha Marine National Park¡¦s resource management and Coast Guard Administration¡¦s sea area law enforcement.

The surface circulation of the northern South China Sea (NSCS) for the period of 1986-2006 is studied using the data of more than 505 satellite-tracked drifters from NOAA/AOML database and the data from ten drifters which were released by our lab in the Penghu channel and in the Luzon Strait in 2006. In this study, the spatial structure and the temporal variability of the surface currents, at mesoscale to seasonal cycle, are described in terms of Eulerian and Lagrangian statistics from the drifter velocities that have been processed. Maps of mean currents, velocity variance ellipses and mean kinetic energies were produced in domain of 0.5¢X¡Ñ0.5¢X. The mean flow map confirms that during the winter monsoon, there is a global cyclonic circulation in the NSCS and the southwestward current which passes Dongsha Island and is called the ¡§Dongsha Current¡¨. Its continuation is the southward coastal jet off Vietnam which is called the ¡§Vietnam Current¡¨. Maximum velocities in the Vietnam Current can exceed 100 cm/s. During the summer monsoon, the Dongsha Current became very weak and the drifters looped near Dongsha Island. The drifter data shows that part of Kuroshio water intrudes into South China Sea through Luzon Strait, Dongsha Current and Vietnam Current were coherent flows. Values of 5.12¡Ñ107 cm2/s, 2.56 days and 64.43 km were obtained for the diffusivity, Lagrangian time scale and spatial scale in the meridional direction in the NSCS, respectively. In the zonal direction, the statistics are half of the above values which show that the characteristic time and space scale are anisotropic. The mean velocity in the Dongsha Current is 0.33 m/s. The domain of Dongsha Current is subdivided into ten boxes of size 2¢X¡Ñ 2¢X in order to analyze the spatial structure of Lagrangian statistics. The result shows that the eddy kinetic energy is considerably higher than the mean kinetic energy in the region 113-121¢XE, indicating that the mesoscale motions are particularly frequent. The eddy kinetic energy gradually decreases toward the west and has a maximum value near the Luzon Strait. The drifters that flow southward along the east coast of Vietnam shows that the width of the Vietnam Current varies between 80 and 100 km and has a mean core speed of 60-150 cm/s. In winter, Maximum southward velocities could reach 130 cm/s at 38 km off the coast. In spring, a weaker maximum speed (around 100 cm/s) exists at about 18 km off the Vietnam coast. There were not enough drifter data in summer and fall.

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 stellatum, collected from Dongsha Atoll. This study had led to the identification of sixteen natural diterpenoids, including six new compounds, stellatumonone (1), stellatumolides A¡VC (2¡V4) and stellatumonins A¡VB (5¡V6), along with ten known compounds. The structures of compounds 1¡V16 were established by detailed spectroscopic data (IR, MS, 1D, 2D NMR) and by comparison of the spectral data with those of the related known compounds. The cytotoxicity of compounds 1¡V16 against the HepG2 (human liver hepatocellular carninoma cells), MDA-MB231 (human breast cancer cells) and A549 (human respiratory epithelial cells) cancer cell lines were determined. Among them, compound 16 showed cytotoxic activity toward the A549 cancer cells.

The exchange of water mass into and out of Dongsha Atoll is analyzed based on field measurements, in the region of 116.7-116.92E 20.58-20.78N during year 2008-2010. Measured parameters include sea level, currents, waves, water temperature and bottom depth. The results show that (1) tidal current is the major driven force of water exchange in the Dongsha Atoll. (2) The major water pathway is the two channels at the northwest and southwest by the side of the Dongsha island. The north channel is more important than the south. (3) The volumn transport of wave contribution is small. (4) The estimated residual time of water in the atoll is about 2 days.

Internal waves include soliton of period 10-20 minutes and tidal frequency waves. Large internal solitons with amplitude over 100 m were observed frequently in the South China Sea (SCS). There were convergence zones of 500-1000 m wide in the wave front of solitons which can be detected by satellite from the space. The hypothesis of this study is the internal wave signal can be extracted from the sea surface anomalies of satellite altimetry. Data analyzed include TOPEX/Poseidon altimeter from August 2002 to October 2005 in the northern SCS and Kuroshio regions. Methods applied include (1) standard deviation analysis, (2) harmonic analysis and (3) wavenumber spectrum analysis. The results show that¡]1¡^there is an annual variation in the sea surface height, which is explained due to water temperature changes in different seasons. (2) The results of harmonic analysis show that the amplitude of M2 aliasing is only a few centimeters on the sea surface. The different is small between internal active region and that of without. (3) The absolute values of slope, of internal wave energy and wavenumber spectrum, are 2-3 in the wave active region. This suggests that there are wave motions of scale 100 km or larger, which matches with the length scale of internal waves in the northern SCS.