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 trout, Plectropomus Ieopardus, is a high-volume, high-priced species in the international live reef food fish trade. Each year more than 8,000 tonnes of fish, worth over a billion Hong Kong dollars, are exported from the Philippines, Indonesia, Malaysia and Australia for consumption in Hong Kong and Mainland China. Its wild populations are believed to be declining in all major source countries with the exception of Australia which manages its fisheries. Concerns over the sustainability of coral trout fisheries, which are major livelihood for some coastal communities, have been raised. To assess whether the fisheries are biologically sustainable, this study developed two different stock assessments synthesizing the best available scientific knowledge and fisheries data of coral trout or grouper stocks for two major sources of production. For the coral trout fishery in the Municipality of Taytay in the Province of Palawan, Philippines, only stock life-history was available in literature, while for Indonesia only catch and effort data were provided for 11 major fishing grounds for groupers including coral trout, by a major live fish trader. Given the nature of the data available, two types of fisheries models were developed for the assessments. For Taytay, a per-recruit model was constructed to simulate catch and stock response to a range of fishing levels based on life-history processes. With the current fishing level estimated from sampled catch, the model indicated that the fishery was unsustainable in Taytay because the spawning stock was overexploited. Right-based catch control, export quota, minimum size, spawning season and aggregation closures were proposed for the recovery of spawning and the spawning stock. Studying stock abundance, sex change and uses of the fish other than export, for example domestic use and mortality levels, will improve the assessment rigour. For Indonesia, a mult-grouper species per-area-based Fox model was fitted to recent catch and effort data. The assessment determined catch and trade quotas for management and highlighted the need for rights-based adaptive management. The assessment found on fishing ground where the groupers including coral trout were fished much beyond sustainable levels and suggested immediate reduction of catch and number of fishers. Monitoring catch, effort and stock abundance and understanding larval dispersal and recruitment can help verify model assumptions and improve their accuracy. For the great many data-poor, unassessed grouper fisheries, similar assessments can be carried out gather data and evaluate fisheries sustainability, while management measures derived from the two assessments here could be used to inform management until more data and assessments become available. Data gaps for improvement of models were identified in the study. Both assessments in this study viewed community-based management as essential to resolve the weak enforcement capacity of Southeast Asian states in fisheries management. For management in and by communities lacking expertise and resource, a greater synergy between various parties is critical, which includes institutional legitimacy of community’s property rights, outreach and capacity building by NGOs, compliance of traders with regulations, sustainable trade practices as well as financial support from consumer’s choices and philanthropy. / published_or_final_version / Biological Sciences / Master / Master of Philosophy

Global warming from anthropogenic greenhouse gas emissions causes temperature increases in aquatic ecosystems. The rise in environmental temperatures places sensitive organisms under thermal stress. Reef-building corals are a critically important group of animals that provide many ecosystem services for coral reef ecology and the economy and are at a high risk of loss from thermal stress. Thermal stress causes corals to lose their colour, i.e. become bleached, resulting from the loss of symbiont zooxanthellae. This diminishes the energetic benefits that zooxanthellae provide to corals leading to a decline in coral health and high mortality rates. However, corals are also predators and can thus draw nutrients from zooplankton prey to supplement their nutritional requirements. This study investigated whether heterotrophic feeding can ameliorate the effects of thermal stress on coral physiology by providing an alternative energy source to zooxanthellar photosynthesis. Fragmented Pocillopora damicornis coral colonies were exposed to daily maximum temperatures of up to 31°C while being either starved or fed. During the experimental period coral nubbins were monitored for changes in polyp extension, oxygen consumption rate, feeding rate, colour, chlorophyll a content, zooxanthellae density, antioxidant potentials and DNA integrity during stress and after a short recovery period. It was found that, as expected, coral polyp extension, oxygen consumption rate, colour health, chlorophyll a content, zooxanthellae density and DNA integrity were all adversely affected by thermal stress. This indicted that all these measurements were viable biomarkers for assessing the negative effects of thermal stress on coral health. Coral colour, oxygen consumption rate, chlorophyll a content, lipid content, antioxidant potential and DNA integrity were all significantly improved by feeding. These results indicate that feeding does play a role in improving overall coral health and supports the physiological processes in coral tissue during and after thermal stress. The conclusions from this study also have great significance for coral reef ecology and management as predictions of reef resilience can be made from zooplankton ecology and boosting zooplankton availability to corals may be considered to mitigate the harmful effects of thermal stress and bleaching. / M.Sc. University of KwaZulu-Natal, Durban 2013.

Thesis (M.S.)--University of Hawaii at Manoa, 2006. / Includes bibliographical references (leaves 32-38). / v, 38 leaves, bound 29 cm

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.

There is little published information on the distribution, abundance, seasonality and ecological roles of benthic algae on the Great Barrier Reef, although they are of fundamental importance in the ecology of coral reef communities. This study sought to provide information on algal community dynamics in two contrasting reef-flat zones: the live coral and algal turf-dominated outer flat, and the fleshy macroalgaldominated inner flat, at Heron Reef, Great Barrier Reef, Queensland, Australia.Algal community structure on dead coral limestone was studied on the inner and outer reef flat over a three-year period (from May 1986 to February 1989), and algal transplant and grazer exclusion experiments were carried out to determine the role of grazers in producing and maintaining community structure.Changes during ecological succession provide useful information about structuring processes in natural communities. Algal succession was studied using artificial substratum (concrete), because it provided a flat surface which offered logistical advantages over naturally contoured coral substratum, and because previous studies had found that artificial substrata adequately mimicked natural surfaces in marine successional studies. Succession on natural substratum was also studied for comparison, using coral clumps which had died after a bleaching episode in February 1987. The effects of season on algal succession, were investigated using four series of concrete settlement blocks, started in February, May, August and November 1986. The effect of habitat complexity on succession was examined by comparing succession on an exposed concrete surface with succession on a protected concrete surface provided with crevices. Each successional study lasted two years. Cover data for all algal species present on each sample were obtained using a sampling grid of sixty points, and these data were analysed using the non-parametric multivariate analysis program, PRIMER.A total of 105 algal taxa were identified in this study, with 101 of these recorded in the natural reef flat algal community over the three-year period. Fleshy macroalgae were the dominant group on the inner flat (56% cover), and filamentous turf algae iv were dominant on the outer flat (47% cover). The importance of water temperature and grazing intensity in producing the differences in distribution of these two groups of algae on the reef-flat were considered. Temperature was rejected as a factor, because there was virtually no temperature difference between the two sites over a two-year period. Grazing was found to be an important factor, based on a much higher rate of damage to algal transplants on the outer flat than on the inner flat; and on the development of higher algal biomass on caged than on uncaged concrete settlement blocks.Between 58 and 69 algal taxa were recorded in each of the four successional studies on exposed concrete, 78 taxa were recorded on protected concrete, and 85 taxa were recorded on bleached coral. Algal successional trajectories were similar on concrete and on bleached coral, but the rate varied substantially. Succession was fastest on bleached coral, slowest on exposed concrete, and intermediate on protected concrete. On all substrata, at both sites, early dominance by green and brown filamentous algae decreased over time, while the abundance of other forms increased. Dominance in terms of cover by early successional algae (in particular Ectocarpus) was prolonged on concrete in comparison to bleached coral, and this effect was stronger on exposed concrete than on protected concrete.It is hypothesised that inhibition of algal community development on concrete because of a relatively dense growth of early successional algae was due to one or both of two factors: 1. Reduced algal recruitment due to a lower level of substratum heterogeneity; and 2. Reduced grazing by the dominant herbivores in the system, parrotfish (Family Scaridae), because of the hardness of concrete.Succession was faster on the outer flat than on the inner flat. On bleached coral, succession to a community similar to the natural background algal community took between three and nine months on the outer flat, and between one and two years on the inner flat.There was no regular seasonal pattern of change in the reef flat algal community over a three-year period, but during early succession, algal community structure was v strongly influenced by season of initial exposure of the concrete settlement blocks. However, this variability did not persist, and by two years all seasonal series of blocks had similar communities. Six species of algae were fertile within 10 days of establishment, including the common early successional algae Ectocarpus, Enteromorpha and Polysiphonia, illustrating the potential of these species for rapid exploitation of available space.The results of this study provide much needed baseline data on algal community dynamics on the southern Great Barrier Reef, and on succession and community development following a bleaching episode. Given the rapid and dense colonisation of bare substratum by algae, and the very low rate of recruitment by corals, it seems that corals will be at a disadvantage in maintaining their abundance in this reef flat environment if coral bleaching becomes a regular event.

Thesis (Ph.D.) -- McMaster University, 1997. / Includes bibliographical references. Also available via World Wide Web.

Thesis (M.A.)--West Virginia University, 2008. / Title from document title page. Document formatted into pages; contains vi, 36 p. : ill. (some col.), col. map. Includes abstract. Includes bibliographical references (p. 31-36).

Thesis (M. Sc.)--University of Canterbury, 2007. / Typescript (photocopy). "August 2007." Includes bibliographical references (p. 119-127). Also available via the World Wide Web.

Thesis (M.S.)--Oregon State University, 2005. / Printout. Includes bibliographical references (leaves 63-68). Also available online.