Caribbean coral reefs have undergone changes in coral cover, structural complexity and assemblage composition since the 1970s. Although some of the ecological consequences associated with these changes have been well documented, the consequences for ecosystem functions dependent on reef structure are less well understood. In particular, there has been little research into the effects of change, on carbonate production and bioerosion; both are critical controls of structural complexity. Currently, there is only a very limited understanding of how both processes vary within and between different habitat types and what this means for ecosystem functioning. Carbonate framework production and bioerosion were investigated within three habitat types (hardgrounds, Acropora palmata reef and Orbicella reef) under sheltered and exposed wave energy regimes on Grand Cayman. Census based assessments were used, allowing the identification of functionally important species. Additionally, habitat specific calcification rates were measured for calcareous encruster communities to improve estimations of carbonate production; mean rates of calcification ranged from 0.19 to 1.14 G (1G = 1 kg CaCO3 m-2 yr-1) within hardgrounds (4–7 m), Acropora palmata reef (1–8 m) and Orbicella reef habitats (8–15 m) and were significantly higher at wave exposed sites. The rates of bioerosion for two sponge species, Siphonodictyon brevitubulatum and Cliona tenuis, were also measured and new approaches to estimating excavating sponge community bioerosion were developed to improves bioerosion estimates. Mean carbonate framework production was 0.38 G within hardgrounds, 2.65 G within Acropora palmata reef habitat and 3.54 G within Orbicella reef habitat but not significantly different between wave exposure regimes. Calcareous encruster communities, dominated by coralline algae, were identified as key carbonate producers within shallow reef habitats on the exposed south coast. They may be important to the maintenance of reef structure in these degraded reef habitats. Orbicella species were the most important carbonate producers within all reef habitats. Mean total bioerosion was 1.32, 2.27 and 2.28 G within hardgrounds, Acropora palmata reef and Orbicella reef habitats respectively. 4 Total bioerosion was not significantly different between wave exposure regimes for any habitat type, but almost completely dominated by parrotfish (29–86 %). On Grand Cayman, both carbonate framework production and bioerosion were less than that measured in comparative habitats, across the Caribbean, despite the presence of a well-managed marine protected area on the sheltered west coast. The highest rates of net carbonate production occurred in the deepest habitat - Orbicella reef (exposed: +1.45 G, sheltered: +1.07 G). Sheltered and exposed Acropora palmata reef habitat had net production rates of +0.53 and +0.30 G respectively. Hardgrounds were net erosional (-0.94 G). Overall the results suggest a change in the focal point for reef accumulation on Grand Cayman that may alter geomorphology over time. Additionally, Acropora palmata reef habitats are likely to be in a state of accretionary stasis, which may have shutdown reef growth in reef crest environments as carbonate framework produced within these habitats is a major contributor to reef accumulation at the reef crest.

Despite high temperature and salinity conditions that challenge reef growth in other oceans, the Red Sea maintains amongst the most biodiverse and productive coral reefs worldwide. It is therefore an important region for the exploration of coral reef functioning, and expected to contribute valuable insights towards the understanding of coral reefs in challenging environments. This dissertation assessed the baseline variability of in situ abiotic conditions (temperature, dissolved oxygen, pH, and total alkalinity, among others) in the central Red Sea and highlights these environmental regimes in a global context. Further, focus was directed on biotic factors (biofilm community dynamics, calcification and bioerosion), which underlie reef growth processes and are crucial for maintaining coral reef functioning and ecosystem services. Using full-year data from an environmental cross-shelf gradient, the dynamic interplay of abiotic and biotic factors was investigated. In situ observations demonstrate that central Red Sea coral reefs were highly variable on spatial, seasonal, and diel scales, and exhibited comparably high temperature, high salinity, and low dissolved oxygen levels, which on the one hand reflect future ocean predictions. Under these conditions epilithic bacterial and algal assemblages were mainly driven by variables (i.e., temperature, salinity, dissolved oxygen) which are predicted to change strongly in the progression of global climate change, implying an influential bottom up effect on reef-building communities. On the other hand, measured alkalinity and other carbonate chemistry value were close to the estimates of preindustrial global ocean surface water and thus in favor of reef growth processes. Despite this beneficial carbonate chemistry, calcification and carbonate budgets in the reefs were not higher than in other coral reef regions. In this regard, seasonal calcification patterns suggest that summer temperatures may be exceeding the optima of calcifiers. As a possible interpretation of the here observed environmental regimes, it can be concluded that the central Red Sea may be less sensitive to ocean acidification, but is already impacted by ocean warming. Importantly, this dissertation provides valuable present-day baseline data of the natural variability of relevant abiotic drivers together with benthic community and reef growth dynamics. These data will be important for future comparative studies and efforts to quantify the impact of future environmental change in the region.

Caribbean coral reefs are in crisis. Degradation of living coral and fish assemblages has accelerated during the past half century, with a suite of anthropogenic drivers –from local fishing pressure to unprecedented global scale climate change– implicated. Accompanying these losses is the physical disintegration of the three-dimensional calcium carbonate reef structure. Flattening of reefs, synonymous with loss of ecosystem function and provision of services, is caused by an imbalance in the carbonate budget: a trade-off between carbonate production and consolidation by calcifying organisms (principally coral-algal symbioses) and framework breakdown by bioeroding organisms and storms. This thesis focuses on expanding our understanding of two functionally critical issues that strongly influence Caribbean coral reef community composition and dynamics, and which look likely to have a key bearing on the future state of reefs in the region: coral photosynthetic endosymbionts, and carbonate budgets. The former exert an important role in the production of the coral carbonate framework, whilst the latter reflect the dynamics of reef carbonate production and erosion. In the first part of the thesis, existing information on rates of carbonate production and erosion on Caribbean reefs is utilised to construct a detailed theoretical carbonate budget model. The model is used to chart historic changes in Caribbean carbonate budgets, tracking reef flattening across time and identifying key ecological drivers of these changes. This “eco-geomorphic” model is then coupled with state-of-the-art climate and ecological models, to project reef processes to the end of the century, asking the question ‘at what point will Caribbean reefs shift to net erosional regimes?’. The models are also used to explore the efficacy of local management and climate mitigation in altering the negative trajectory of reefs under projected warming and ocean acidification. In the second part of the thesis, 632 corals from across the wider Caribbean are screened, to construct the largest recorded baseline of symbiont biogeography for the region’s key remaining reef framework builder, Montastraea annularis. Spatial patterns of symbiont diversity are explored in terms of environmental, geographic and genetic factors, contributing to the growing body of work currently in the early stages of cataloguing symbiont diversity and its ecological significance. Although carbonate budget models forecast a bleak outlook for the Caribbean, detection of widespread low-level prevalence of thermally-tolerant endosymbionts in M. annularis provides a weak ‘nugget of hope’ for potential coral acclimation. Combined local management and aggressive mitigative action on carbon emissions are pre-requisites for maintenance of functioning reefs into the next century. Coral reef conservation efforts can be improved if we fully appreciate the contributions of all reef components –not just the enigmatic ones– to healthy reef functioning.