Solid surfaces that spend long periods of time in aquatic environments are susceptible to the accumulation of marine fouling organisms and this phenomenon is known as marine biofouling. This is a natural process which has significant impacts on marine industries. Research to develop new antifouling solutions focuses on the development of non-toxic solutions that can deter biofouling. A non-toxic antifouling approach that has gained interest in recent years is to modify the surface’s structure to disrupt organism settlement (Kirschner and Brennan 2012; Magin et al. 2010; Myan et al. 2013). Many studies determined that uniform arrays of single layered, micro-topographies are effective at deterring the initial settlement of fouling organisms. In contrast, most studies that tested uniform arrays of single layered, macro-topographies concluded that these topographies are not suitable for antifouling applications. Both single layered, micro-topographies and single layered, macro-topographies were determined to have limitations at mitigating biofouling. This resulted in the interest to develop hierarchical topographies. Hierarchical topographies are surfaces that consist of features that are varied in size and shape. It was suggested that the diverse nature of hierarchical topographies might be able to deter biofouling from a wider array of organisms. This research fabricated and tested a wide range of topographies (uniform, non-uniform, micro, macro, hierarchical, etc.) in a field study. A field study was preferred over lab experiments because results will reflect the antifouling efficacy of the surfaces in a marine environment. These results will indicate the topographies’ viability and future potential for industrial applications. Antifouling efficiency was evaluated by measuring fouling resistance (during the field test) and fouling removal (after the field test) of all topographies. Physical attributes (pattern geometry, pattern size, and surface roughness) of topographies were characterised with Scanning Electron Microscopy (SEM) and Laser Scanning Confocal Microscopy (LSCM). Statistical analysis was carried out to evaluate the significance of the topographies’ physical attributes on the antifouling efficiency of the topographies. The research hypotheses predicted that topography size, geometry and surface roughness will affect the topographies’ ability to resist biofouling. All patterned surfaces were predicted to have a higher resistance to biofouling in comparison to un-patterned control surfaces (i.e. smooth surfaces). The possibility that hierarchical topographies would have better fouling resistance properties than micro-topographies was considered as well. Hierarchical topographies and micro-topographies were also hypothesised to demonstrate better resistance to biofouling than macro-topographies. Topographies with straight ridges and hierarchical shapes were predicted to be more fouling resistant than sandpaper surfaces. Topographies with average roughness (RSa) that were less than 100µm were assumed to exhibit better antifouling efficacy in comparison to topographies with average roughness greater than 100µm. Results showed that pattern size and pattern geometry affects the antifouling efficiency of topographies. Unexpectedly, surface roughness did not show strong correlations with the fouling resistance of the topographies. With the exception of Sandpaper 50 and Sandpaper 1mm samples, all topographies were more fouling resistant than the control samples (i.e. smooth surfaces). Among the 16 topographies, sandpaper 1mm samples demonstrated the worst defence against biofouling. The mean total fouling coverage on these samples after 10 weeks of tests was 98.7%. Straight, single layer ridges demonstrated the best resistance to total fouling during the field test. Barnacle and polychaete settlement trends were affected by the size and geometry of single layer, single sized topographies. After 10 weeks, the mean total fouling coverage on these ridges was only 37.5%. The field test also showed that the topography with the best prolonged resistance to fouling was the 1mm straight ridges. The combination of structured surfaces and a low modulus material is likely to have contributed to the fouling removal properties of all topographies. Lastly, results from the field study also showed that hierarchical topographies do not necessarily have better antifouling properties than single layer, single sized topographies. The field study demonstrated that the physical attributes of topographies contributed to their antifouling efficiency. It has been suggested that the physical characteristics of topographies induces hydrodynamic variations that affects the surfaces’ antifouling properties. However, it is difficult to observe these changes in lab experiments or through field studies because these variations take place at a very small scale. Recent research has applied Computational Fluid Dynamics (CFD) to numerically simulate and analyse flow characteristics in the surrounding areas of antifouling topographies. As a continuation from the field study, the next study in this research applied CFD to analyse flow characteristics over several topographies that were tested in the field study. This was to determine if the settlement trends exhibited by organisms in the field study could have been affected by hydrodynamic variations that were induced by the presence of the topographies. The CFD analysis showed that rotational vortices formed between topography patterns. These vortices could have aided in the accumulation of biofouling material on all topographies during the field test. The analysis also showed that the topographies’ resistance to fouling could be attributed to high shear stress and strain rate zones at the peaks of the topographies. Comparisons between CFD and field test results indicate that higher stresses and strain rate zones around the topographies are likely to lead to a surface’s better resistance to marine biofouling. This is likely because high shear stress and strain rate zones could have disrupted organism motility and made the surface less conducive for settlement.

- / -

Swimming is important to the ecology of many species of scallop but the effects of temperature upon swimming are not clear. The ecology and natural history of scallops is introduced followed by a description of the state of current knowledge of scallop swimming, muscle physiology and energetics. The effects of temperature and the mechanisms used by ectotherms to compensate for such changes over acute, seasonal and evolutionary timescales are discussed. Scallops are active molluscs, able to escape from predators using jet propelled swimming. Queen scallops (Aequipecten opercularis) were acclimated to 5,10 and 15°C in the laboratory and collected in Autumn (13±3°C) and Winter (8±2°C) in order to investigate seasonal acclimatisation. The first jetting cycle of escape responses in these animals was recorded using high-speed video (200-250fps). Whole-animal velocity and acceleration were determined while measurements of valve movement and jet area allowed the calculation of muscle shortening velocity, force and power output. Peak swimming speed was significantly higher at 15°C (0.37m.s⁻¹) than at 5°C (0.28m.s⁻¹). Peak acceleration was 77% higher at 15°C (7.88m.s⁻²) than at 5°C (4.44m.s⁻²). Mean cyclic power output was also higher at 15°C (31.3W.kg⁻¹) than at 5°C (23.3W.kg⁻¹). Seasonal comparison of swimming in freshly caught animals revealed significantly greater acceleration (x2 at 11°C) and velocity during jetting in Winter than in Autumn animals (ANCOVA). These were associated with significant increases in peak power output (x8 at 11 °C), force production and muscle shortening velocity. Actomyosin ATPase activity was significantly higher (31 % at 15°C) in winter animals with peptide mapping of the Myosin heavy chain showing no differences between groups. Increases in muscle power output were associated with reductions in the length of the jetting phase as a proportion of the overall cycle. As a result large changes in muscle performance resulted in large short-term whole body performance enhancement but little difference to velocity over the cycle. Measurements of the swimming performance of the Antarctic scallop were made from videos of escape responses. Animals were acclimated to +2 and -1 °C in the laboratory and compared to animals maintained at natural water temperature (0±0.5°C) at the time of experimentation. Adamussium was very sensitive to temperature change with the proportion of swimming responses being less common at higher temperatures and where an individual was exposed to temperatures above it's maintenance temperature. Analysis of the first jetting cycle of swimming was carried out as described in Chapter 2. These analyses revealed that over the small temperature range that the animals can tolerate swimming performance is strongly temperature dependent. Q₁₀s above 2 included those for thrust (3.74), mean cyclic swimming speed (2.46), mean cyclic power output (5.71) and mean muscle fibre shortening velocity (2.16). Adamussium did not demonstrate strong phenotypic plasticity with no significant differences in swimming of muscle performance between animals acclimated to different temperatures. Comparison of the relationship between swimming velocity and temperature in Adamussium and other species showed little evidence for evolutionary compensation for temperature with all data fitting to a single relationship with a Q₁₀ of 1.96 (0-20°C). Similar results were obtained for power output and the performance of in vitro muscle preparations. These results are discussed in the light of field studies revealing the low predator pressure and escape performance of wild Adamussium. In vivo ³¹P-Nuclear Magnetic Resonance Spectrometry (MRS) was used to measure the levels of ATP, Phospho-l-arginine (PLA) and inorganic phosphorous (PI) in the adductor muscle of the Antarctic scallop, Adamussium colbecki, and two temperate species, Aequipecten opercularis and Pecten maximus. Graded exercise regimes from light (1-2 contractions) to exhausting (failing to respond to further stimulation) were imposed upon animals of each species. MRS allowed non-invasive measurement of metabolite levels and intracellular pH at high time resolution (30-120s intervals) during exercise and throughout the prolonged recovery period. Significant differences were shown between the magnitude and form of the metabolic response with increasing levels of exercise. Short-term (first 15 minutes) muscle alkalosis was followed by acidosis of up to 0.2 pH units during the recovery process. Aequipecten had significantly higher resting muscle PLA levels than either Pecten or Adamussium, used a five-fold greater proportion of this store per contraction and was able to perform only half as many claps (maximum of 24) as the other species before exhaustion. All species regenerated their PLA store at a similar rate despite widely different environmental temperatures. The major results and their impact on our knowledge of biomechanics and it's temperature dependence are discussed. Suggestions for future research based upon the experimental findings and techniques developed are presented.

Regulatory and academic studies use large numbers of fish annually. The use of fish primary cells offers an in vitro alternative for the assessment of chemical toxicity and the evaluation of environmental samples in ecotoxicology. Their uses however are not without limitations which includes short culture periods (i.e. longevity and loss of organ-specific functionality over time). Three-dimensional (3-D spheroid) technology is now established for in vitro mammalian toxicity studies and offers significant advantages for environmental applications in a model fish species. This thesis reports development of a reproducible six-well plate, gyratory-mediated method for rainbow trout (Oncorhynchus mykiss) hepatocyte spheroid culture and compares morphological, functional and biochemical status with two-dimensional (2-D) monolayer hepatocytes. The work further assesses the bio-transformation potential of developed 3-D spheroids to a range of environmentally relevant pharmaceuticals. The study suggests that mature spheroids retain some organotypic responses over-time in culture including morphological (viz., smooth outer surface, tight cell–cell contacts); functional (viz., histo-architecture; cell adhesion molecule expression) and biochemical properties (viz., protein, glucose, albumin- and enzyme levels) that is superior to conventional 2-D monolayer cells. These 3-D spheroids also demonstrate a capacity for the metabolism of environmentally-relevant pharmaceuticals that could be utilised to better understand their bio-accumulation potential in fish. This is an important step forward for developing alternative in vitro tools in future fish ecotoxicological studies as well as for fundamental understanding of the interaction of chemicals with biomolecules which could potentially lead to detrimental responses at different levels of biological organisation.

Previous psychological research has demonstrated the benefits of visiting natural environments, especially coastal areas. However, research within Marine Biology has shown that such visits can harm natural habitats. Consequently, this thesis uses an integrative approach to examine both the risks to the environment and benefits to the human visitors in the context of rocky shores (intertidal areas where solid rock predominates). This was investigated using seven studies that involved a range of methods. Perception-based surveys (Studies 1 & 2) explored the perceived impacts on the visitor, and the potential impacts these visits can have on the rocky shore. Study 3 then examined the impacts on visitors’ well-being & marine awareness directly using a before-after survey on current visitors to two rocky shores. The most prominent habitat threat (leaving rubbish) was then examined in greater detail. Studies 4 and 5 examined the effects of marine litter on individuals’ well-being using two laboratory experimental designs; comparing individuals’ quantitative (Study 4) and qualitative (Study 5) responses to natural and littered shores. The final two studies then focused on an activity that reduces marine litter: Study 6 adopted a pre-post design to examine the benefits of engaging in beach cleans for current volunteers, whilst Study 7 used an experimental design comparing beach cleans with two other coastal activities on a more naïve sample. Overall, these studies provide evidence that experiencing rocky shores are beneficial for well-being and marine awareness. Counteracting such benefits, litter left behind after recreational visits were found to be detrimental to individuals’ well-being. As one potential solution to this issue, beach cleans were found to have the same, and additional beneficial effects on the individual as other coastal activities. Thus, activities which have a relatively positive impact on the environment can also have similar if not additional benefits to the visitor. This programme of research shows the importance of taking a holistic, integrative approach that takes into account both the risks to the environment and benefits to the individual resulting from recreational visits to natural environments.

Metals and radionuclides are environmentally relevant contaminants, yet their potential impacts on marine organisms have not been adequately evaluated. This is especially true for exposures of longer duration and/or lower contaminant concentration (i.e. chronic) which are often more representative of real world scenarios. In this context, a suite of biomarkers at different levels of biological organisation were investigated in an ecologically relevant bivalve species, Mytilus galloprovin- cialis after exposure to nickel (a metal), zinc pyrithione (an organometal) and tritiated water (a radionuclide). These contaminants were chosen based on their differing properties, and hence, mechanisms of action. All three contaminants produced genotoxicity (DNA strand breaks, as measured by the comet assay, and induction of micronuclei [MN]). For nickel (> 1800 µg L −1 ) and tritiated water (15 MBq L−1 ), biomarkers at lower levels of biological organisation (i.e. DNA strand breaks, MN, changes in the expression of key stress response genes) were more sensitive than those at higher levels (i.e. clearance rate, attachment, tolerance of anoxia). In particular, exposure to tritiated water for 14 days resulted in DNA damage and molecular alterations without affecting higher level responses. As environmental contaminants could interact with other physical or chemical stressors in a complex environment, further exploration of biological responses revealed modulation by hyperthermia with concomitant changes in the transcriptional ex- pression of key defence genes (hsp70, hsp90, mt20, p53 and rad51). In contrast to nickel and tritiated water, exposure to both 0.2 and 2.0 µM zinc pyrithione caused significant deviation from concurrent controls for every biomarker examined, suggesting that further investigation of the environmental impacts of this contaminant is particularly necessary. Variation in biological responses induced by different contaminants suggests that potential links between levels of organisa- tion should be evaluated on a contaminant-specific basis. The integrated, multiple biomarker approach used in the current study provides a robust methodology for such studies, which could be translated to other ecologically relevant species for proper evaluation of risks to both environmental and human health.

Future changes to the pH and temperature of the oceans are predicted to impact the biodiversity of marine ecosystems, particularly those animals that rely on the process of calcification. The marine intertidal gastropod Littorina littorea can be used as a model of intertidal organism for investigating the effects of ocean acidification and high temperature, alone and in combination because its ability to be quickly adapt against environmental stressor. In the first study a single species population of L. littorea was used to test for physiological and biochemical effects underpinning organismal responses to climate change and ocean acidification. Compared with control conditions, snails decreased metabolic rates by 31% in response to elevated pCO2 while by 15% in response to combined pCO2 and temperature. Decreased metabolic rates were associated with metabolic depression, a strategy to match oxygen demand and availability, and an increase in end-product metabolites in the tissue under acidified treatments, indicating an increased reliance on anaerobic metabolism. This study also showed that anthropogenic alteration of CO2 and temperature may also lead to plastic responses, a fundamental mechanism of many marine gastropods to cope environmental variability. At low pH and elevated temperature in isolation or combined showing lower shell growth than individuals kept under control conditions. Percentage change in shell length and thicknesses was also lower under acidified and temperature in isolation or combined than control condition, making shells were more globular and desiccation rates were higher. Further studies to broader latitudinal ranges for six populations of L. littorea showed that shell growth decreased in all six populations under elevated pCO2 compared to control snails particularly those at range edges. Elevated pCO2 also affected to the reduction of shell length and width that causing shell aspect ratio to increase across latitudinal gradients except individuals from Millport, UK. Percentage changes of aperture width and aperture area were also decrease under elevated pCO2 with greater reduction of aperture area were found at populations in the mid-ranges which is assumed this response might be linked to local adaptation of the individual to microclimatic conditions. This study also showed that metabolic rates were negatively affected by high pCO2 and show non-linear trend across latitudinal gradients in compared to individual kept under normal pCO2 conditions. Metabolomic analysis showed that two northern populations of Trondheim and TromsØ were distinct from other populations when exposed to low temperature (15 °C) with elevated pCO2 due to, in part, high concentrations of thymine, uracil, valine and lysine. A similar separation also occurred under medium (25 °C) and high (35 °C) temperature exposure in which one of northern population (Trondheim) was distinct from other populations and had lower concentrations of alanine, betaine and taurine while higher of valine. These results suggest that populations at northern latitudes may apply different ionic transport mechanisms under elevated pCO2 and elevated temperatures and those populations are likely to vary in terms of their physiological responses to this environmental challenge.

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.

In the past, oceans have strongly influenced atmospheric CO2 levels through organic and inorganic carbon cycling. The inorganic carbon pump relies on the formation of calcium carbonate which releases CO2 into the surface ocean and traps alkalinity in solid form which sinks to deeper ocean layers and sediments. After sinking, calcium carbonate can either then become trapped in the sediments or dissolve increasing the alkalinity of deeper ocean layers. The net effect is of acidifying surface oceans and encouraging release of CO2 to the atmosphere. The present thesis focuses on marine teleost (bony) fish in temperate areas as previously poorly understood but potentially major producers of calcium carbonate in the ocean. Fish in temperate areas may be contributing to carbonate sediment production and as such the inorganic carbon pump. Prior to this thesis only tropical fish have been investigated as major piscine sediment producers. The present thesis describes the composition and morphology of carbonates produced by many different species of temperate fish providing a basis for the understanding the fate of these carbonates in the environments and their potential contribution to sediment production and the inorganic carbon cycle. Characteristics of carbonates produced by fish in the wild were fairly consistent within a species upon examination of carbonates produced by poor cod (Trisopterus minutus) over the course of a year. However, despite the likely consistent and distinct characteristics of fish carbonates, little evidence of them was found in temperate shallow sediments beneath pens of farmed Atlantic salmon (Salmo salar) where there theoretically should be very high production rates. Reduced salinity, often a feature of temperate areas compared to tropical areas, was found to reduce production rates of carbonate from fish compared to higher salinities. However, salinity reductions below the ocean average of 35 psu (practical salinity units) had less impact on production rates than increases above 35 psu. As such it is argued that production rates in temperate environments should still be relatively high considering high fish biomasses in some temperate regions and could still mean fish in temperate areas are an important source of carbonate production and potential sediment production.

Lorsqu’un morceau de bois atteint le fond de l’océan, il provoque la mise en place d’un écosystème capable de se développer en absence de lumière. Cet écosystème est qualifié de chimiosynthétique du fait de la présence d’une faune pouvant fixer le carbone inorganique présent dans l’eau de mer. De plus, ce système attire une faune ultra-specialisée qui utilise des symbiontes bactériens pour digèrer le bois. Avant ces travaux, la plupart des études s’interressaient principalement à la macrofaune et le rôle des microorganismes libres demeurait inconnu. Nous avons pu démontrer dans cette thèse le rôle essentiel que jouent les microorganismes libres dans la mise en place de cet écosystème. Nous avons prouvé que des communautés de microorganismes se succédaient au cours de la première année de colonisation et que cette succession était influencée par le type de bois et l’environment dans lequel il se trouve. La première phase de cette succession aboutit au développement après un mois, d’une population de bactéries sulfato-réductrices produisant de l’hydrogène sulfuré et ce, même en l’absence d’organismes foreurs. Cette production d’hydrogène sulfuré est à la base (1) du développement rapide d’un biofilm chimiolithoautotrophe et (2) du recrutement d’espèces possédants des symbiontes chimiosynthétiques. Nos résultats ont permis d’aboutir à la proposition d’une succession d’étapes clés liées permettant la transformation d’un substrat térrigène en un écosysteme qui, il y a plusieurs millions d’années, aurait permis à la faune chimiosynthétique de coloniser les grands fonds. / When wood sinks to the deep-sea floor it creates a new ecosystem that does not depend directly on energy from sunlight. This ecosystem is called chemosynthetic because of the presence of a fauna associated with symbiotic bacteria that can assimilate inorganic carbon from seawater. Furthermore this system is colonized by specialized fauna that use symbiotic bacteria to digest the wood matrix. Previous studies mostly focused on these symbiotic macroorganisms and the role played by non-symbiotic microorganisms in the sunken wood ecosystem remains unknown. We demonstrate in this thesis the important role played by non symbiotic microorganisms during the sunken wood ecosystem establishment. We reveal the ecological succession of microorganisms driven by time and wood structure. The first step of this succession is characterized by a microbial population able to produce hydrogen sulfide after one month of immersion. This hydrogen sulfide production is the basis for (1) a chemolithoautotroph biofilm development on the wood surface and (2) a recruitment of species associated with chemoautotrophic bacteria. Our results suggest a succession of different phases that transform a terrigeneous substrate into an environment that may have helped, million years ago, the colonization of the deep sea by chemosynthetic species.