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.

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.

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.

This study focuses on the relationship between hydrological and nutrient conditions in seawater surrounded by Dongsha Atoll. Dongsha Atoll is located in the northern South China Sea (NSCS), the water properties should be in coherence with the NSCS water masses. However, due to the semi-enclosed topography the water inside Dongsha Atoll is largely affected by local insolation and rainfall. Significant relationships between SiO2 or PO43- and salinity indicate that rainfall could be a major source of these nutrients. Insignificant relationship between N+N and salinity indicates that rainfall and nitrogen fixation both might affect the distribution of N+N. Temporal variations of temperature and chlorophyll a were alike, except for which occurred in July, 2011. It was probably caused by photo inhibition on phytoplankton growth. The inventory of chlorophyll a was positively correlated with both N+N and SiO2 but not with of PO43-, indicating that phytoplankton growth in Dongsha Atoll was mainly affected by N+N and SiO2. Phytoplankton growth maybe limited by N+N but not by SiO2, as the concentration of SiO2 was mostly beyond the limitation concentration for phytoplankton. According to close relationships between chlorophyll a and TSM, POC and PN, the particulate matter maybe mainly derived from biological origins. The inventory of chlorophyll a was positively correlated with both dissolved organic carbon (DOC) and dissolved organic nitrogen (DON), manifesting the importance of biological origins for DOC and DON concentration. The ratios of DOC/DON, DON/DOP and DOC/DOP within the atoll were in ranges of 7.34-303 (mean: 30.4), 3.00-142 (mean: 22.7) and 104-2546 (mean: 421), respectively. The ratios are higher than those values in NSCS and East China Sea, implying the excretion of carbon-enriched DOM by phytoplankton. The concentration of chlorophyll a, DOC and POC were higher in the Small Lagoon than in the Atoll Lagoon, implying a relatively high productivity in the Small Lagoon. The fluxes of carbonate in the atoll was more than 30 times of the flux in the NSCS, due to its unique characteristics in the coral reef habitat. The organic matter of settling particulates was mainly derived from biological sources. The metal of enrichment factor of settling particulates reveals that Fe and Al are mainly derived from crustal sources, while Cu, Zn and Pb are likely influenced by anthropogenic sources.

The subject of this study was to investigate the species composition and spatial distribution pastern of iving (Rose Bengal stained) benthic foraminifera in sediment surface samples (0-1 cm) off the Southwestern Taiwan and Dongsha Atoll. The main objectives of this study was to document the living benthic foraminiferal assemblages off the Southwestern Taiwan and Dongsha Atoll and to examine their distribution in relation to environmental parameters. Four benthic foraminiferal biofacies were recognized within the substrate type in Dongsha Atoll: A1 (Fine-grained) is represented by Pseudomassilina spp. - Quinqueloculina parkeri, A2 (Fine-grained) is represented by Hauerina spp. - Pseudomassilina spp., B1 (Coarse-grained) is characterised by Calcarina spp. - Quinqueloculina spp., B2 (Coarse-grained) is characterised by Amphistegina spp. - Quinqueloculina spp. Sediment surface samples off the Southwestern Taiwan during May 2009 led to the identification of four assemblages. Assemblage A is characterised by Ammonia spp. - Bolivina spp., Assemblage B between is characterized by Asterorotalia spp. - Globobulimina spp., Assemblage C is represented by Cibicides spp. - Nummulites spp., Assemblage D is represented by Ammonia spp. - Cibicides spp. Sediment surface samples off the Southwestern Taiwan during Nov. 2009 led to the identification of three assemblages. Assemblage A is dominated by Ammonia spp. - Cibicides spp., Assemblage B is characterised by Ammonia spp. - Bolivina spp., Assemblage C is characterised by Asterorotalia spp. - Bolivina spp. Stained benthic foraminifera form Dongsha Atoll correlated with current wave, collected site, coarse fraction and TOC contents. Living benthic foraminifera off the Southwestern Taiwan seems not to be related with TOC contents and coarse fraction, the assemblages were found to be more related to tidal energy and lateral transport.

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.