Hong Kong provides a marginal marine environment for coral growth due to its high latitude in addition to massive freshwater run-off from the Pearl River Delta. Previous studies have reported that Hong Kong waters nurture 84 species of scleractinian corals in 28 families distributed in various locations, especially the protected bays in the eastern waters. However, very little is known about the benthic composition and health of coral communities. This study aimed to 1) determine the benthic composition of local coral communities and understand the environmental determinants of coral coverage and coral community composition; 2) record coral colony size frequency distribution across these 33 sites to understand the patterns of coral recruitment in recent years; 3) quantify coral bioerosion and corallivory by the long-spined sea urchin and explore the feasibility of remediating the coral damage by a coral-associated portunid crab. Surveys were conducted at 33 sites in Hong Kong, which cover sites with the highest coral coverages that are mainly located in the north-eastern, east and south-eastern waters. A belt-transect photo quadrant method was applied. 22 hard coral genera were identified, among which the genera Porites, Platygyra and Pavona were found to be the most abundant. Most of the study sites were dominated by few genera of massive corals which led to a low diversity. Coral coverage was negatively associated with nutrient levels including nitrogen, phosphorus and organic matter deposition rates based on sediment trap data. Apart from sedimentary parameters, coral coverage was also found to be strongly negatively correlated with the density of the long-spined sea urchin Diadema setosum. Study sites were categorized into four different conservation classes with sites of higher diversity assigned a higher conservation value. These data could serve as a baseline for measuring changes in benthic composition in the future, and as a reference for management planning such as designating new marine parks. Determining the size structure can help predict how a population may change in the future and whether conservation efforts are effective in promoting the increase in numbers of individuals. To determine coral size structure in local waters, a video transect method was adopted to capture videos on the benthic substrates of the 33 study sites. In the laboratory, the video clips were analyzed to extract information on the size and growth form of all coral colonies along the transects. Size-frequency distribution plots generally showed a highly positive skewness, which indicated a dominance of small-sized (i.e. 10 - 30 cm) colonies, yet low in recruitment-sized (i.e. 5 cm) colonies. An examination of the size distribution of the most common genera showed that the distribution patterns were more genus-dependent rather than site-dependent. Also, massive corals were the most dominant growth form, while branching corals were the least common which was different from healthy tropical reefs. Apart from establishing a baseline of coral communities, coral bioerosion was further studied. Previous studies found that coral coverage and urchin density were negatively correlated in local waters. Further, severe coral bioerosion had been reported to cause community-level coral damage in several locations. Therefore, impact coral bioerosion by the sea urchin Diadema setosum and whether such impact could be remediated were further investigated in a series of controlled experiments in the field. Although sea urchins were reported to prevent shifting from coral-dominant to algae-dominate phase elsewhere, they were found to cause severe tissue loss and bioerosion at high densities in my study. Thalamita prymna, a common portunid crab in local coral communities, was found to effectively reduce coral damages including bioerosion and surface mortality. Crab predation, an overlooked relationship in coral reefs, can thus be exploited to control urchin corallivory and bioerosion. Prohibiting fish trapping in reef areas could reduce the by-catch of these crabs and protect reefs against urchin attack.

In 2005 and 2010, high sea surface temperatures caused widespread coral bleaching on Jamaica’s north coast reefs. Three shallow (9m) reef sites were surveyed during each event to quantify the prevalence and intensity of coral bleaching. In October 2005, 29-57% of the colonies surveyed were bleached. By April 2006, 10% of the corals remained pale/partially bleached. Similarly, in October 2010, 23-51% of corals surveyed at the same sites were bleached. By April 2011, 12% of the colonies remained pale/partially bleached. Follow-up surveys revealed low coral mortality following both events, with an overall mean of 4% partial colony mortality across all species and sites observed in April 2006, and 2% in April 2011. Mixed effects models were used to quantify the relationship between colony size and (a) bleaching intensity, and (b) bleaching related mortality among coral species. The bleaching intensity model explained 51% of the variance in the bleaching response observed during the two events. Of this 51%, fixed effects accounted for ~26% of the variance, 17% of which was attributed to species-specific susceptibility to bleaching , 5% to colony size, <1% colony morphology and 4% to the difference in bleaching intensity between the two events. The random factor (site) accounted for the remaining ~25% of the variance. The mortality model explained 16% of the variance in post bleaching mortality with fixed effects, including colony size, morphology and species explaining ~11% of the variance, and the random effect (site) explaining 5%. On average, there was a twofold difference in bleaching intensity between the smallest and the largest size classes. Modelling the relationship between colony level characteristics and site-specific environmental factors on coral species’ susceptibility to thermal stress can shed light on community level responses to future disturbances.

Thesis (Ph.D.) - James Cook University, 2004. / Typescript (photocopy) Bibliography: leaves 110-130.

In 2005 and 2010, high sea surface temperatures caused widespread coral bleaching on Jamaica’s north coast reefs. Three shallow (9m) reef sites were surveyed during each event to quantify the prevalence and intensity of coral bleaching. In October 2005, 29-57% of the colonies surveyed were bleached. By April 2006, 10% of the corals remained pale/partially bleached. Similarly, in October 2010, 23-51% of corals surveyed at the same sites were bleached. By April 2011, 12% of the colonies remained pale/partially bleached. Follow-up surveys revealed low coral mortality following both events, with an overall mean of 4% partial colony mortality across all species and sites observed in April 2006, and 2% in April 2011. Mixed effects models were used to quantify the relationship between colony size and (a) bleaching intensity, and (b) bleaching related mortality among coral species. The bleaching intensity model explained 51% of the variance in the bleaching response observed during the two events. Of this 51%, fixed effects accounted for ~26% of the variance, 17% of which was attributed to species-specific susceptibility to bleaching , 5% to colony size, <1% colony morphology and 4% to the difference in bleaching intensity between the two events. The random factor (site) accounted for the remaining ~25% of the variance. The mortality model explained 16% of the variance in post bleaching mortality with fixed effects, including colony size, morphology and species explaining ~11% of the variance, and the random effect (site) explaining 5%. On average, there was a twofold difference in bleaching intensity between the smallest and the largest size classes. Modelling the relationship between colony level characteristics and site-specific environmental factors on coral species’ susceptibility to thermal stress can shed light on community level responses to future disturbances.

For millions of years, the nutrient exchange symbiosis between corals and their endosymbiotic algae has formed the foundation of the ecological success of coral reefs. Yet, in recent decades anthropogenic climate change is increasingly destabilizing this symbiosis, and thus the reefs that rely on it. High-temperature anomalies have caused mass mortality of corals due to repeated coral bleaching, the expulsion or digestion of symbionts by the host during stress. Hence, in-depth knowledge of the cellular processes of bleaching is required to conceive strategies to maintain the ecological functioning of coral reefs. In this thesis, we investigated the role of symbiotic nutrient cycling in the bleaching response of corals. For this, we examined the mechanisms that underlie the functioning of the symbiosis in a stable state and how heat stress affects these metabolic interactions during coral bleaching. Our findings reveal that the functioning of the coral – algae symbiosis depends on the resource competition between host and symbionts. In a stable state, symbiotic competition for ammonium limits nitrogen availability for the algal symbiont, thereby ensuring symbiotic carbon translocation and recycling. During heat stress, however, increased metabolic energy demand shifts host metabolism from amino acid synthesis to degradation. The resulting net release of ammonium by the host, coupled with the stimulated activity of associated nitrogen-fixing microbes, substantially increases nitrogen availability for algal symbionts. Subsequently, stimulated algal growth causes selfish retention of carbon, thereby further reducing energy availability for the host. This positive feedback loop disturbs symbiotic nutrient recycling, eventually causing the collapse of carbon translocation by the symbiont. Hence, heat stress causes shifts in metabolic interactions, which directly and indirectly destabilizes the symbiosis, and ultimately undermines the ecological benefits of hosting algal symbionts for corals. In summary, this thesis shows that integrating symbiotic nutrient cycling into our conceptual understanding of coral bleaching is likely to improve our ability to predict coral bleaching in light of environmental conditions and may ultimately help to conceive new strategies to preserve coral reef functioning.

Coral reef ecosystems are under increasing threat from ocean warming and deoxygenation. Mass coral bleaching events in recent years have been linked to marine heatwaves but reporting of hypoxia-induced bleaching has also been increasing. Oxygen availability in coral reefs is driven by community metabolism and they experience a dynamic range of oxygen concentrations throughout diel cycles, hyperoxia during the day and hypoxia during the night. It has been suggested that the highest oxygen concentrations coincide with the hottest part of the day and this may protect marine taxa from high temperatures. We evaluated experimentally whether excess oxygen availability would increase the thermal threshold of the branching coral Stylophora pistillata, from the Southern Red Sea. We did this by exposing coral fragments of this species to varying dissolved oxygen concentrations (hypoxia, normoxia and hyperoxia) and a short-term temperature ramping regime (1˚C h-1). Hyperoxia did extend the thermal tolerance of S. pistillata fragments, with an LT50 of 39.1˚C as opposed to 39.0˚C for the normoxic treatment and 38.7˚C for the hypoxic treatment. Hyperoxia also increased respiration and gross photosynthesis and had a negative effect on photochemical efficiency at high temperatures. Net photosynthesis, P:R ratio and symbiont density were not significantly affected by oxygen concentration. Corals in this experiment displayed exceedingly high thermal thresholds, which were at least 2˚C higher than previously reported for the same species in the Central Red Sea. The corals used in the experiment had previously survived mass bleaching events in 2015 and hence we may have selected for individuals adapted to thermal stress. This is the first study to investigate the role of oxygen in the thermal tolerance of hermatypic corals and the first assessment of thermal thresholds from corals in the Southern Red Sea, where previously thermal thresholds have been based on a 1-2˚C increase in maximum mean monthly temperatures and visual bleaching observations. This highlights the need for increased experimental assessments of thermal thresholds in the Southern regions of the Red Sea and the important role of oxygen in moderating thermal stress.

The pillar coral, Dendrogyra cylindrus, has been commonly described as widely distributed, but rare throughout its geographical range in the Caribbean. Having recently been listed as Threatened under the US Endangered Species Act, an understanding of population status is needed to promote species conservation and population recovery. Previous to this study the status of the pillar coral population in the state waters of Florida, U.S.A, was relatively unknown primarily due to few colonies being recorded and no comprehensive summary of population abundance, distribution or health being completed. Along with various environmental and anthropogenic factors affecting the pillar coral population on the Florida Reef Tract (FRT), it appears that reproductive limitations may also be contributing to species decline and limiting population recovery as evidenced by the lack of reported juvenile D. cylindrus colonies reported on the Florida Reef Tract (FRT) in the past 17 years. The factors contributing to this phenomenon are currently unknown, however are suspected to be derived from the pillar corals reproductive biology. Being described as a gonochoric, broadcast spawner, sexual reproduction relies on the synchronous release of gametes from colonies of separate sexes, and with low adult colony densities reported for the pillar coral on the FRT, gamete concentrations from both sexes may be too low for fertilization to occur. In 2014 submissions of pillar coral locations from the scientific and lay community were compiled and 610 D. cylindrus colonies along Florida Reef Tract were identified (Lunz et al. 2016). In my study, I describe the population structure of D. cylindrus for the southeast Florida region of the FRT which includes 65 of the total 610 colonies. For each of the 65 colonies, colony depth, demographic, and condition data were recorded including size (length, width, and height), percent of recent mortality, and presence and severity of disease and bleaching. Out of all locations identified in this region, about 50% contained only a single colony of D. cylindrus and the maximum number of colonies per site was 14. Throughout the duration of the study, devastating losses of live tissue were observed following the bleaching and disease events impacting the Florida Reef Tract in 2014, 2015, and 2016 and the status of the southeast Florida population of pillar coral is at serious risk of local extinction. To investigate the ability of colonies of D. cylindrus to sexually reproduce (referred to as sexual reproduction potential) tissue samples were collected from 95 colonies within 15 sites along the FRT and were prepared for histological analysis. The sex of each colony, sizes of gametes in mature developmental stages, the abundance of gametes per cm2 of tissue, and sex ratios for locations on the FRT were reported. All tissue samples from male and female colonies contained gametes that were ≥90% mature; however sex ratios were found to be skewed in all locations, deviating significantly from the 1:1 ratio expected for typical resource allocation in random mating. Hermaphroditic colonies of D. cylindrus are described for the first time throughout its geographical range in this study and comparisons to gonochoristic colonies confirmed that these hermaphrodites are sexually reproductive individuals. Results from this effort provide a more thorough understanding of the reproductive biology of D. cylindrus and essential data for the support of future conservation management and restoration strategies for this FRT population and comparative data for other Caribbean populations.

The variability of water-column absorption due to colored dissolved organic matter (CDOM) and phytoplankton in coral reef regions is the focus of this study. Hydrographic and CDOM absorption measurements made on the Bahamas Banks and in Exuma Sound during the spring of 1999 and 2000 showed that values of salinity and CDOM absorption at 440nm were higher on the banks (37.18 psu, 0.06 m^-1), compared to Exuma Sound (37.04 psu, 0.03 m^-1). Spatial patterns of CDOM absorption in Exuma Sound revealed that plumes of CDOM-rich water flow into Exuma Sound from the surrounding banks. To examine absorption variability in reef regions throughout the world, a thirteen-year time series of satellite-derived estimates of water-column absorption due to CDOM and phytoplankton were created from Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and Moderate Resolution Imaging Spectroradiometer (MODIS) data. Time series data extracted adjacent to coral reef regions showed that variability in absorption depends on oceanographic conditions such as circulation patterns and winds as well as proximity to sources of light-absorbing materials that enter the water column, such as from terrestrial runoff. Waters near reef regions are generally clear, exhibiting a lower "baseline" level of CDOM absorption of approximately 0.01 m^-1 at 443nm. The main differences between regions lie in the periods during the year when increased levels of absorption are observed, which can be triggered by inputs of terrestrially-derived material, as in the Great Barrier Reef lagoon, or wind-driven upwelling as in the Andaman Sea and eastern Pacific Ocean near Panama. The lowest CDOM absorption levels found were approximately 0.003 m^-1 at 443nm near the islands of Palau and Yap, which are removed from sources of colored materials. The highest absorption levels near reefs were associated with wind-driven upwelling during the northeast monsoon on the Andaman coast of Thailand where values of CDOM absorption at 443nm reached 0.7 m^-1. Simulations of the underwater light field based on satellite-derived absorption values revealed that changes in absorption have a strong influence on light levels to which corals are exposed, particularly in the ultraviolet region of the spectrum, where CDOM is the primary absorber of light. Episodes of coral bleaching during 1998 and 2002 were found to be associated with elevated seawater temperatures as well as decreased levels of CDOM absorption, indicating that corals were exposed to light stress along with thermal stress during periods of bleaching.

Coral reefs are greatly impacted by the physical characteristics of the water surrounding them. Incidence and severity of mass coral bleaching and mortality events are increasing worldwide due primarily to increased water temperature, but also in response to other stressors. This decline in reef health demands clearer understanding of the compounding effects of multiple stressors, as well as widespread assessment of coral reef health in near-real time. Satellites offer a means by which some of the physical stressors on coral reefs can be measured. The synoptic spatial coverage and high repeat sampling frequency of such instruments allow for a quantity of data unattainable by in situ measurements. Unfortunately, errors in cloudmasking algorithms contaminate satellite derived sea surface temperature (SST) measurements, especially during anomalously cold events. Similarly, benthic interference of satellite-derived reflectance signals has resulted in large errors in derivations of water quality or clarity in coral reef environments. This work provides solutions to these issues for the coral reef environments of the Florida Keys. Specifically, improved SST cloudmasking algorithms were developed for both Advanced Very High Resolution Radiometer (AVHRR; Appendix A) and Moderate Resolution Imaging Spectroradiometer (MODIS) data (Appendix B). Both of these improved algorithms were used to reveal the extent and severity of a January 2010 cold event that resulted in widespread mortality of Florida Keys corals. Applied to SST data from 2010, the improved MODIS cloudmasking algorithm also showed improved quantity of SST retrievals with minimal sacrifice in data quality. Two separate algorithms to derive water clarity from MODIS measurements of optically shallow waters were developed and validated, one focusing on the diffuse downwelling attenuation coefficient (Kd, m-1) in visible bands (Appendix C), the other on Kd in the ultraviolet (Appendix D). The former utilized a semi-analytical approach to remove bottom influence, modified from an existing algorithm. The latter relied on empirical relationships between an extensive in situ training dataset and variations in MODIS-derived spectral shape, determined using a stepwise principal components regression. Both of these algorithms showed satisfactory validation statistics, and were used to elucidate spatiotemporal patterns of water clarity in the Florida Keys. Finally, an approach was developed to use Landsat data to detect concurrent MODIS-derived reflectance anomalies with over 90% accuracy (Appendix E). Application of this approach to historical Landsat data allowed for long-term, synoptic assessment of the water environment of the Florida Keys ecosystem. Using this approach, shifts in seagrass density, turbidity increases, black water events, and phytoplankton blooms were detected using Landsat data and corroborated with known environmental events. Many of these satellite data products were combined with in situ reports of coral bleaching to determine the specific environmental parameters individually and synergistically contributing to coral bleaching. As such, SST and visible light penetration were found to be parsimoniously explaining variance in bleaching intensity, as were the interactions between SST, wind and UV penetration. These relationships were subsequently used to create a predictive model for coral bleaching via canonical analysis of principal coordinates. Leave-one-out-cross-validation indicated that this model predicted `severe bleaching' and `no bleaching' conditions with 64% and 60% classification success, respectively, nearly 3 times greater than that predicted by chance. This model also showed improvement over similar models created using only temperature data, further indicating that satellite assessment of coral bleaching based only on SST data can be improved with other environmental data. Future work should further supplement the environmental parameters considered in this research with databases of other coral stressors, as well as improved quantification of the temperature at the depth of corals, in order to gain a more complete understanding of coral bleaching in response to environmental stress. Overall, this dissertation presents five new algorithms to the field of satellite oceanography research. Although validated primarily in the Florida Keys region, most of these algorithms should be directly applicable for use in other coastal environments. Identification of the specific environmental factors contributing to coral bleaching enhances understanding of the interplay between multiple causes of reef decline, while the predictive model for coral bleaching may provide researchers and managers with widespread, near real-time assessments of coral reef health.

Coral reefs are among the most diverse and productive ecosystems on earth, and are critical to the survival of tropical marine ecosystems and sustenance of local human populations. However, coral reefs are quite vulnerable to disturbances, both natural and anthropogenic. This thesis looks at how coral reef communities have responded to climactic disturbances, particularly the 1997-98 El Niño Southern Oscillation (ENSO) and subsequent coral bleaching and mortality that affected much of the Indian Ocean, including the coastal waters of Tanzania, where the study was conducted. In particular, it investigates the effects of coral bleaching, habitat degradation and reef spatial arrangement on reef fish assemblages. Habitat structural complexity and spatial arrangement of reefs had an effect on reef fish communities. Fish communities showed patterns in distribution among habitats and between patch and continuous reefs. Fishes preferred live to bleached/dead or eroded coral, but trophic groups reacted differently to patch and continuous reefs. There were slight changes in fish abundance and significant changes in fish diversity on experimental, bleached branching Acropora coral plots over a period of one year. While fish abundance on one site increased shortly after a bleaching event, 6 years later fish abundance had decreased significantly. Conversely, coral reef communities in northern Tanzania had changed little over an 8-year period, with minor changes associated with the 1997-98 ENSO and the presence or absence of fisheries management. The coral reefs in the region were found to show high variability in community structure and responses of associated fish and invertebrate communities. The findings of this thesis indicate the importance of habitat structure and spatial arrangement of reefs, the detrimental effects of coral bleaching, and the possibility that some reefs and some (generalist) reef fish taxa may exhibit resilience to climate change. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.