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.

Coral reefs are arguably the most threatened marine habitat because of multiple anthropogenic stressors degrading the health and resilience of these systems. In the past 20 years there have been increasing observations of mass coral bleaching and mortality associated with increasing water temperatures in the tropics. Reefs provide ecosystem services worth billions of dollars to people living in tropical coastal areas and are the architects of one of the most beautiful structures found on earth. Conserving these habitats is paramount, and conservation planning must contend with climate change along with local and regional stressors. In this thesis Watamu Marine National Park in Kenya is used as a case study of the current challenges facing the conservation of reefs in a warming world. The Western Indian Ocean suffered dramatic bleaching during 1998, which caused the mortality of 70% of Watamu's corals. Using datasets from the 1980s to present the historical trajectory of Watamu's reef community is presented. The current ecosystem resilience is assessed to suggest how this reef will respond to future climate stress. It appears that Watamu's coral community has remained in an altered state post-1998, which, based on its past thermal stress and current coral community, should be resistant to future bleaching. Watamu's resilience and reef health is compared with other locations in the Indian Ocean, including reefs in Kenya and the Maldives that bleached in 1998 and examples from Mozambique and Sumatra of reefs with little evidence of historical thermal stress. Resilience is a multi-faceted process with different major components and numerous interacting factors, which act synergistically on the reef community. Conservation options and opportunities are discussed for the 6 locations examined, using current resilience models and theory as a framework for identifying priority actions. Local and regional-scale human impacts on shallow marine habitats during the last 50 years has been dramatic, and with global-scale climate change as an additional major threat, the next 50 years will be critical for the future of reefs. The locations visited during this study showed encouraging signs of resilience to past thermal stress, with evidence to suggest that corals are acclimatising and/or adapting to increasing water temperatures. The future of reefs in locations like Watamu is uncertain. Better understanding of reef ecology, appropriate conservation techniques and ultimately greater public concern for reefs is required to ensure that there is a future for these ecosystems in the Indian Ocean.

The world’s coral reefs are being impacted by myriad disturbances, from localized overfishing and nutrient pollution to global climate change-induced temperature increases and ocean acidification. Conservation of coral reefs in the face of increasing variability and uncertainty requires an understanding of the interacting effects of multiple stressors on the diverse components of these vital ecosystems. In this thesis, I use data from reefs around Kiritimati atoll (Republic of Kiribati) in the central equatorial Pacific Ocean to examine the effects of a severe pulse heat stress event and local human disturbance on two important components of the coral reef ecosystem – three-dimensional (3D) structural complexity and reef fish assemblages. Using 3D reef models constructed through structure-from-motion photogrammetry, I examined changes in reef structural complexity in the year following the 2015-2016 El Niño and mass coral bleaching event. I found that exposure to prolonged thermal stress and subsequent coral mortality resulted in declines in reef structural complexity, particularly reef surface rugosity and terrain ruggedness. Baseline levels of structural complexity were also negatively influenced by local human disturbance, while complexity was positively related to the densities of branching and massive coral growth forms. These findings have important implications for the maintenance of healthy reef ecosystems, as high levels of structural complexity are important for supporting diverse reef-associated fish assemblages. Next, using underwater visual censuses of reef fish assemblages, I quantified fish abundance, biomass, species richness, and assemblage structure before, during, and after the 2015-2016 El Niño. Total reef fish abundance, biomass, and species richness declined during the El Niño, suggesting that pulse heat stress events may have short-term, negative consequences for reef fish. Although these metrics did not vary substantially across the local human disturbance gradient, recovery of assemblages following the heat stress event was impeded by higher levels of local human disturbance. Reef fish assemblage structure was influenced by a more diverse array of factors, showing significant shifts in response to heat stress, human disturbance, and net primary productivity. Given the many important roles that fish play on coral reefs, declines such as those observed here may impair the ecological functioning of these ecosystems. Together, my results highlight the negative impacts of heat stress and local human disturbance on coral reefs, demonstrating ways in which these stressors may interact to limit reef resilience in the face of increasing anthropogenic pressures. / Graduate / 2019-12-07

Water flow is an important abiotic factor for corals and other cnidarians. This study shows how water flow influences bleaching in Palythoa caribaeorum. Colonies were exposed to flow (low = 3 cm s-1, high = 15 cm s-1) in two temperature regimes (low: 26.5°C, which is within natural variability on the reef where specimens were collected; high: 33.5°C, which is 3.5°C above usual summer temperature) in a unidirectional flume for 48 hours. Two sizes (small = 2.3 ± 0.2 cm, large = 7.3 ± 0.4 cm in diameter) were tested in six repeats per flow regime. Bleaching was determined by zooxanthellae count using a hemocytometer and by chlorophyll a concentration using fluorometry. Results suggest that onset of bleaching is rapid (within 48 hours) in high temperature. The low temperature did not cause significant bleaching. In the high temperature treatment, P. caribaeorum consistently bleached less in high flow. Upstream sides of large colonies bleached less than the downstream sides in high flow. In high flow, small colonies bleached less than large colonies. This suggests that enhanced diffusion of toxic oxygen species is important to mitigate bleaching and is more easily accomplished in small colonies, which may thus have an advantage during bleaching events, as has been observed in the literature.

Coral bleaching is now the main driver of reef degradation. The common notion is that most corals bleach and suffer mortality at just 1-2°C above their mean summer maximum temperatures, but some species and genotypes resist or recover better than others. Here we conducted a series of 18-hour short-term heat stress assays side-by-side with a long-term heat stress experiment to assess the ability of both approaches to resolve putative differences in coral thermotolerance and provide a measure of in situ reef temperature thresholds. Using a suite of measures (photosynthetic performance, coral whitening, chlorophyll a, host protein, algal symbiont counts, and algal type association), we assessed bleaching sensitivity/resilience of Stylophora pistillata colonies from the exposed and protected sides of a near-shore coral reef in the central Red Sea. As suggested by the differential mortality during a previous bleaching event, coral colonies from the protected site exhibited less impacted physiological performance in comparison to their exposed site counterparts, and these differences were resolved using both experimental setups. Notably, the long-term experiment provided better resolution with regard to the different measures collected, but at the price of portability, cost, and duration of the experiment. Variability in resilience to ocean warming is critical to reef persistence, yet we lack standardized diagnostics to rapidly assess bleaching severity or resilience across different corals and locations. Using a newly developed portable experimental system termed CBASS (the Coral Bleaching Automated Stress System), we demonstrate that mobile, short-term heat stress assays can resolve fine-scale differences in coral thermotolerance across reef sites. Based on our results, photosynthetic efficiency measured by non-invasive PAM fluorometry provides a rapid and representative proxy of coral resilience. Our system holds the potential to be employed for large-scale determination of in situ bleaching temperature thresholds across reef sites and species. Such data can then be used to identify resistant genotypes (and reefs) for downstream experimental examination and to complement existing remote-sensing approaches.

Coral reefs are the proverbial rainforests of the ocean, but these spectacular structures are under threat from globally rising sea surface temperatures and ocean acidification. The Red Sea and the Persian/Arabian Gulf (PAG) display unusually high sea surface temperatures, and therefore, provide a model for studying environmental change. Corals are so-called holobionts consisting of the coral host, photosynthetic algae (Symbiodiniaceae), along with other microorganisms, such as bacteria, archaea, fungi, and viruses. While the importance of bacteria to coral holobiont functioning is acknowledged, little is known about changes in the microbial communities under natural environmental stressors in the Red Sea and the PAG. Accordingly, I investigated microbial community and mucus differences in bleached, healthy, and diseased corals. Analysis of the composition of mucus-associated microbial communities of bleached and healthy Porites lobata colonies from the Red Sea and the PAG were stable, although some regional differences were present. In a distinct study investigating coral disease, a broad range of corals in the Red Sea were shown to be infected with black band disease (BBD). Investigating the microbial community associated with BBD revealed the presence of the three main indicators for BBD (cyanobacteria, sulfate-reducing bacteria (SRB), and sulfide-oxidizing bacteria (SOB). Last, I investigated the chemical composition (carbohydrates) of the surface mucus layer of a range of Red Sea corals. Given that coral mucus represents a first line of defense, I was interested to examine whether mucus carbohydrate composition would point to a role of adaptation to the extreme environment of the Red Sea. This analysis showed that mucus consists of conserved sugars that are globally conserved. In summary, this thesis characterizes the microbial communities associated with a range of coral species in different health states (bleached, healthy, and diseased). The microbial community patterns I characterized support the notion that bacteria contribute to coral holobiont health and possibly adaptation to extreme environmental conditions in the Red Sea and PAG.

Coral bleaching is a worldwide result of climate change that is affecting the marine ecosystems greatly. Methods to help solve the issue have been previously explored and Beneficial Microorganisms for Corals (BMCs) have been proven to help mitigate coral bleaching in laboratory trials. In their efforts to test its effectiveness on the field, scientists have found that it would be beneficial to have a constant, biocompatible, source of BMCs. We have tested Calcium Alginate microspheres, what we call Alginate Beads, in terms of release rate and cell viability to determine if they are fit to be used as vectors for the BMC consortia. By placing the Beads in two different temperatures representing winter and summer temperatures in the Red Sea in agitation we were able to understand their dynamics more clearly. By using Flow Cytometry, Colony Forming Units, and microscopy techniques we were able to see that Alginate Beads incorporate bacteria into their matrix and keep them viable for up to two weeks. We also observed that the Beads release more bacterial cells at higher temperatures compared to lower temperatures. This suggests that when used in the field, Alginate Beads are able to sustain the bacteria for a prolonged time period and it will release bacteria at a higher rate in warmer temperatures potentially either season or region-wise. Hence, we believe that Alginate Beads could be suitable as vectors for field research and should be explored further.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Global climate models project a 21st century strengthening of the Pacific Equatorial Undercurrent (EUC). The consequent increase in topographic upwelling of cool waters onto equatorial coral reef islands would mitigate warming locally and modulate the intensity of coral bleaching. However, EUC water is potentially more acidic and richer in dissolved inorganic nutrients (DIN), both widely considered detrimental to coral reef health. My analysis of the Simple Ocean Data Assimilation product indicates that the EUC has indeed strengthened over the past 130 years. This result provides an historical baseline and dynamical reference for future intensification. Additionally, I reared corals in laboratory experiments, co-manipulating food, light and CO2 (acidity) to test the role of nutrition in coral response to elevate CO2 conditions. Heterotrophy yields larger corals but CO2 sensitivity is independent of feeding. Conversely, factors that enhance zooxanthellate photosynthesis (light and DIN) reduce CO2 sensitivity. Corals under higher light also store more lipid but these reserves are not utilized to maintain calcification under elevated CO2 My results suggest that while mitigation of CO2 effects on calcification is not linked to energetic reserve, EUC fueled increases in DIN and productivity could reduce effects of elevated CO2 on coral calcification. / by Elizabeth Joan Drenkard. / Ph. D.

The iconic pillar coral, Dendrogyra cylindrus, is one of five Caribbean species listed in 2014 under the US Federal Endangered Species Act because of its extreme low abundance and continued decline in US waters. Until recently, little was known about the demographics or genetic diversity of Florida’s D. cylindrus population. This study represents the first time two holobiont partners (coral animal and associated photosynthetic algal endosymbionts) have been closely examined, spatially and temporally, in this little-studied species. The aim was to explore the influences of coral animal genotypes, mutualistic photosynthetic algal strains, and hyperthermal stress on bleaching and disease processes, resistance, and recovery through two consecutive hyperthermal events on the Florida Reef Tract (FRT) in 2014 and 2015. Through geographically stratified, triannual assessments and tissue sampling of D. cylindrus colonies across three regions of the FRT from April 2014 to April 2016, I compared genotypic identities of the coral animal to bleaching and disease status and recovery. Additionally, I characterized the algal endosymbionts (Symbiodiniaceae family) in D. cylindrus between regions of the FRT using Illumina amplicon sequencing of the partial chloroplast 23S rDNA Domain V gene and correlated them to differential responses during bleaching and recovery. Finally, I examined the effects of hyperthermal stress on disease prevalence and changes in disease susceptibility in D. cylindrus throughout two consecutive hyperthermal events in 2014 and 2015. Genotypic differences in D. cylindrus were associated with full or partial bleaching and/or disease resistance associated with some genets. Additionally, this study characterized unexpected diversity in the Symbiodiniaceae community within D. cylindrus and a site-specific, species-level switch in endosymbionts associated with acquired bleaching resistance during the 2015 hyperthermal event. Finally, this study demonstrated that two consecutive hyperthermal events were associated with an increase in prevalence of white plague in D. cylindrus and contributed to its susceptibility to black band disease, documented for the first time on the FRT. Through understanding the response of the D. cylindrus holobiont partners to biotic and abiotic stressors, such as hyperthermal bleaching and associated diseases, we gained valuable insights into how this threatened species may respond to a changing climate.

Understanding coral disease dynamics within the heterogeneous populations in which they act is critical for predicting how the structure of reefs may change as a result of enzootic or epizootic levels of these important sources of mortality. This work focused on combining field studies and the development and testing of a spatially-explicit, individual-based epizootiological computer model with the aim of gaining a greater understanding of the dynamics and impact of white plague, a significant source of mortality on reef-building corals in the Caribbean region. Field studies focused on the incidence and distribution of all sources of coral mortality, including suspect white plague in situ, at two locations; the Florida Keys (United States of America) and Little Cayman Island (Cayman Islands, British West Indies). Results indicated that in both regions disease was the most significant source of mortality during the monitoring time periods, and that suspect white plague type II in Cayman is likely contributing to major structural changes. In Florida, observations made during a mass bleaching event indicated that a significant relationship exists between bleaching severity and disease incidence, and that mortality during the event was largely the result of disease and not bleaching. The simulation model was developed using a long-term data set from Little Cayman, and results of calibration indicated that suspect white plague type II on these reefs is transmissible between colonies within a limited field and require a yearly input from an outside source, and that host susceptibility to infection is low and likely not variable among species. Parameters describing the distribution and composition of the coral population were varied, and results indicated a significant effect of colony density, aggregation, and mean size on the impact of disease. Scenario testing of various disease management strategies indicated that should local prevention measures be developed in the future, it is they, and not treatment, that will likely be the most effective in limiting the impact of disease.