Coastal environments are increasingly under threat due to the climate impacts associated with global warming and increasing terrestrial impacts through coastal development and inappropriate land management. As a result, a third of the world's coral reefs are facing the threat of extinction. In order to conserve and manage coral reef ecosystems, it is important to accurately assess the interactions of natural and anthropogenic (including climatic) stresses that are operating.

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Artificial reefs have been deployed purposely worldwide to influence physical and biological processes around coastlines and in inshore waters; often to augment recreational diving and fishing, support environmental mitigation and habitat restoration and, more recently, for scientific research. The aims of this project were to develop standardised methods and protocols for use in artificial reef studies and to establish whether there were differences in the productivity and biotic interactions between artificial and nearby natural rocky reefs in Loch Linnhe, west coast of Scotland. A comparative study was carried out to evaluate methods used in the assessment of subtidal epibiotic assemblage structure followed by a detailed study to compare epibiotic recruitment to artificial and natural reefs using PVC plastic recruitment panels. Predator exclusion cages were used to assess the effects of predation on epifaunal recruitment at different locations. Epifaunal biomass on concrete reef blocks and infaunal biomass in soft sediments surrounding the artificial reef complex was determined and an estimate made of relative productivity between the Loch Linnhe artificial reef modules and their receiving environment. Finally, the trophic dynamics of artificial and natural reefs were investigated through the use of stable isotope ratios. These studies showed that post-settlement processes appear to be controlling differences in epifaunal recruitment to artificial and natural reefs in Loch Linnhe. Vertically orientated PVC recruitment panels, combined with galvanised wire mesh predator exclusion cages, are recommended for use in comparative recruitment studies of subtidal artificial and natural reefs. It was also concluded that the Loch Linnhe artificial reef complex has increased the productivity to the local area and that the construction design of these artificial reefs would be a suitable option, with respect to the development of biological communities, for future artificial structures such as breakwaters.

In the last decade, ocean acidification (OA) has become a major focus of scientific research. A significant fraction of anthropogenic carbon dioxide (C02) emissions is absorbed by the world's oceans, causing a decrease in pH and shifts in the carbonate chemistry of seawater towards increased CO2(aq) Many reef-building coral species obtain their algal symbionts from environmental populations of free-living Symbiodinium via a mechanism known as horizontal transmission. This thesis examined the effect ofOA upon the productivity and growth of four different phylotypes of Symbiodinium (AI, A2, A13 and BI) and also characterised the carbon concentrating mechanisms (CCMs) ofphylotypes A2 and A13, in culture (i.e. 'free-living'). The response to a doubling of pC02 to ~800 ppmv varied between phylotypes; A I and B I were relatively insensitive to OA whilst the productivity of A2 and the growth rate of A13 increased by 40% and 60%, respectively. This phylotype-specific response to OA is likely to affect population dynamics in free-living Symbiodinium, with further implications for those corals that obtain their symbionts via horizontal transmission. Furthermore, the actual mode of iC- acquisition was shown to differ between phylotypes, with A2 capable of indirect bicarbonate (HC03-) uptake, via the catalytic action of external carbonic anhydrase (eCA), whilst A13 was solely dependent upon the CO2(aq) fraction of the inorganic carbon pool in seawater. These differences in iC-acquisition provide the basis for the phylotype-specific effects of OA on these two phylotypes. Future studies will be able to build on these findings to examine the effect of OA upon a wider representation of the Symbiodinium genus and contrast their ability to regulate the CCM in response to changes in seawater pC02 and, ultimately, contribute towards a better understanding of the effects OA will have upon the form and function of coral reef ecosystems.

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