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Coral reef cryptofauna (coelobites) are metazoans that occupy the hidden recesses formed by structural taxa such as corals. While cryptic communities are thought to account for the majority of reef biodiversity and play important roles in reef trophodynamics, little empirical evidence exists supporting these claims. Quantitative sampling of coelobites has been thus far limited due to highly heterogeneous reef topographies as well as difficulties associated with identification of large numbers of species. In the eastern Pacific, monogeneric stands of Pocillopora form reef structures that are homogeneous across a horizontal plane and support a relatively depauperate fauna, thereby permitting detailed multispecies analysis. Sampling of motile cryptofauna associated with live coral and dead coral frameworks typifying four levels of degradation, was conducted at Playa Larga Reef on Contadora Island in the eastern Pacific, Gulf of Panamá. Communities associated with live coral colonies were less diverse than those associated with dead corals and the species richness of cryptofauna living on dead coral substrates was higher in more degraded habitats. Living coral colonies, however, support significantly greater densities of cryptofauna and more biomass per volume substrate than their dead coral counterparts. On dead coral frameworks, numbers of individuals and biomass were significantly greater per volume in areas of intermediate degradation. A field experiment was conducted to test the effects of flow, porosity and coral cover on cryptic communities associated with artificial reef frameworks (ARFs). Coral cover (live vs. dead) was not observed to affect the structure of communities occupying underlying frameworks, however, lower porosity substrates sheltered greater abundances of individuals per volume substrate and low flow environments supported elevated biomass. Additionally, porosity and flow were both found to significantly affect relative species abundances as well as overall community diversity. Data from quantitative sampling of natural reef environments and experimental manipulation of cryptic reef habitats suggest novel and unexplored responses to mass coral mortality and reef habitat degradation. Coral death is considered to be vital to the maintenance of reef ecosystem habitat and biotic diversity. Contrary to the popular paradigm that a healthy reef ecosystem has high coral cover, the most diverse reef ecosystems are those which have experienced intermediate levels of degradation. Furthermore, while living corals support elevated cryptofauna abundances and biomass, the magnitude of communities associated with dead framework materials suggest that abundant cryptofauna populations persist in highly degraded reef environments.

Coral reefs have declined globally due to anthropogenic stressors increasing the frequency and severity of bleaching and disease events. In 2014, a stony coral tissue loss disease (SCTLD) outbreak occurred off the coast of southeast Florida and subsequently spread throughout the region. Data collected by the Southeast Florida Reef Evaluation and Monitoring Project (SECREMP) were used to examine the regional impacts of the disease event on the Southeast Florida stony coral assemblage. A long-term annual monitoring project, SECREMP samples permanent sites along the Southeast Florida Reef Tract (SEFRT) from Miami-Dade County north to Martin County. Analysis of stony coral demographic data from 21 sites revealed regional SCTLD prevalence increased significantly, and significant region-wide declines in stony coral diversity and density were observed. From 2014 to 2018, species-specific susceptibility to the disease were evident, with Meandrina meandritesand Dichocoenia stokesiboth losing > 90% of all live tissue by 2016. The reef building, complexity-contributing species Montastraea cavernosaand Orbicellaspp. lost significant tissue (55% and 70% respectively) as a result of this disease event. Overall, up to 64% of all live tissue was lost and at least 11 of 28 total species were impacted by SCTLD. Of the colonies that suffered complete mortality, many were among the largest individuals in the dataset. Loss of large, sexually mature colonies lowers reproductive capabilities and thus severely inhibits the potential for recovery. Juvenile surveys showed many of the large, structurally complex species had little to no juveniles within the sample sites, while eurytopic generalist species made up more than 76% of all juveniles. This disease event resulted in acute mortality and altered ecosystem function to the point where recovery is uncertain. To facilitate recovery, local resource managers need to understand the severity of the disease outbreak on the coral assemblage and mitigate local anthropogenic stressors.

<p> A study of two shallow fringing reefs off the coast of Zanzibar Island was conducted. The study site was Grave Island, 1 km off the shore of Zanzibar town. The comparison site was Chumbe Island, 10 km upcurrent of the town, adjacent a less densely inhabitated coast. The major anthropogenic stress on these reefs could be considered nutrient loading from sewage discharge.</p> <p> Studies of the sea urchin Diadema setosum, indicated mean densities at Grave Island of 6.4 urchins/m^2 and 1.2 urchins/m^2 at Chumbe Island. Urchin densities comparable to those at Grave Island have been related to overfishing and reduced coral recruitment. Coral associate densities were also considered with a mean density of 87/m^2 at Grave Island and 31/m^2 at Chumbe Island. High coral associate densities have been linked to structurally and physiologically weakened coral.</p> <p> Transect studies were conducted and suggested there were significantly reduced coral cover and reduced amounts of live coral at Grave Island (cf Chumbe Island). As well, coral species diversity was significantly lower at Grave Island than at Chumbe Island. Lowered species diversity suggests an unstable community structure, and reduced coral cover may indicate a faltering reef.</p> <p> Stable Isotope studies were conducted on tissue samples from both sites. They showed no significant difference.</p> <p> This study reflects the poor health of Grave Island. The high abundance of urchins and filter feeders, combined with reduced coral cover and diversity, suggest high nutrient loading on these reefs. The high abundance of urchins and associates also suggest coral mortality will be high and recruitment low. If these trends continue, it is unlikely the reef at Grave Island will be able to survive.</p> / Thesis / Bachelor of Science (BSc)

Porites lobata is an important reef building coral in the tropical eastern Pacific and the dominant Porites species in the Galápagos archipelago. Following the 1982-83 El Niño-Southern Oscillation the Galápagos Islands experienced 97-99% coral mortality, leaving many areas throughout the archipelago denuded of corals. Because very few long term assessments have been conducted on the growth and resilience of P. lobata to natural disturbances in the Galápagos Islands (Glynn et al., 2001; Glynn et al., 2009), benthic surveys were performed on a uniquely dense aggregation of P. lobata colonies at Devil’s Crown, Floreana Island between 1993 and 2011. Annual changes in live tissue area were calculated for the majority of the population (n=17) using Coral Point Count with Excel extensions (CPCe 3.6) software to determine growth and recovery trends for this aggregation. Total live tissue area (n=10) increased from 1993 to 2011, however due to high interannual variability this increase was not significant. Within this overall pattern, a general trend of decline was observed in live tissue cover from 1993 to 2000, with increases in tissue area observed from 2000 to 2011. Severe bleaching (85-100%) was observed during the 1998 survey, followed by 42% tissue loss (n=10), coinciding with sea water warming associated with the very strong 1997-1998 El Niño-Southern Oscillation event. Subsequent regrowth of coral tissue was observed during the 2001 survey with continued recovery through 2009. Multiple comparison testing revealed a significant difference between the impacted state (1999) and the recovered state (2009), (p = 0.002, Dunn’s method, n=17), suggesting this aggregation required a period of ten years to recover from this disturbance. During this recovery period the moderately strong 2007-2008 La Niña, with accompanying stressful low temperatures, occurred but did not interrupt tissue regrowth. Warmer than average sea surface temperatures occurred during the warm months from 2008 to 2011, during which time a cool period occurred from 2010 to 2011. While the magnitude and duration of temperature anomalies during warming were not as great as those observed during the 1997-98 ENSO, low temperatures observed during the cool period were similar to those experienced throughout the 2007-08 La Niña. During this time total live tissue cover was reduced by 19% (n=10); however it is unknown whether this was due to warming or the following cool period. Based on results from the 1997-98 El Niño and 2007-08 La Niña, this reduction in live tissue was most likely caused by elevated sea surface temperatures. Data on the growth and resilience of P. lobata populations at Devil’s Crown will be used for conservation and management of this important resource.