Urbanisation is increasingly recognised as a major ecological pressure at the coast. By 2035, the Department for Environment, Food and Rural Affairs will have to spend £1 billion each year on flood defence and erosion control infrastructure if current levels of protection are to be sustained in England and Wales; this represents a substantial commitment to building new hard structures. Ecological research has shown that structures like seawalls, breakwaters, and harbour and port infrastructure are poor surrogates for undisturbed rocky shores. This, alongside substantial international policy drivers, has led to an interest in the ways in which structures might be enhanced for ecological gain. Virtually all of this research has been undertaken by ecologists, while the contribution of geomorphological understanding has not been fully recognised. This thesis presents an assessment of the two-way interactions between colonising organisms and the materials used to build hard coastal structures under a framework of biogeomorphology. The influence of material type and small-scale surface texture on early colonisation is assessed alongside detailed observations of the ways in which biota are involved in the alteration of substratum properties and behaviours through weathering and erosion in the intertidal zone. The research demonstrates that biotic (organisms) and abiotic (material substrata) components of coastal structures are inherently linked at various spatial and temporal scales through complex biogeomorphic interactions and feedbacks. Importantly, these interactions have consequences for the subsequent operation of ecological and geomorphological processes that are of relevance to urban marine ecology, weathering and rock coast geomorphology, and engineering. This thesis demonstrates the considerable potential to manipulate substratum-biota interactions on artificial structures for ecological gain, both directly and indirectly. More broadly, the explicitly interdisciplinary methodological approach adopted shows the value and necessity of integrated research for achieving useful, applied outcomes.

The main goal of this thesis was to develop a multi-technique approach to characterise high molecular weight (colloidal) dissolved organic matter (DOM) occurring in estuarine and coastal marine environments and to investigate how these bulk properties may relate to their ability to influence the physicochemical speciation of metals such as iron and copper. This characterisation was undertaken systematically on the pre-filtered (0.4 μm) estuarine or marine sample, referred to here as the ‘bulk’, as well as on the ultrafiltered (< 5 kDa) and colloidal (> 5 kDa) fractions. Three successive studies were carried out. The first one took place in the estuarine mixing zone of a high pH, low turbidity black water river (River Thurso) and the other two in the receiving coastal waters (Thurso Bay). The optical and size distribution properties of these waters were examined in detail in the first study while their iron and copper-binding properties were examined in the second and third studies, respectively. Size fractionation results showed that the proportion of colloidal to soluble organic carbon (DOC) tended to decrease from the upper estuary (~ 60%) to coastal waters (~ 20%). With respect to trace metals, similar trends were observed as one progressed from the mouth of the river towards the open sea. In relation to their molecular absorption, fluorescence and size fractionation properties, both River Thurso DOM and Nordic Reservoir NOM Reference Material presented the same characteristics and mixing behaviour, indicating the dominance of humic and fulvic substances in the Thurso river-ocean system. The river-borne, humic colloids underwent two types of transformations upon mixing with the seawater end-member. The first one was the coiling or contraction of individual macromolecules ―monomers― with increasing salinity. The second one was the concurrent aggregation of these small monomer units (d = 2 – 4 nm) to form entities that were still colloidal, i.e. smaller than 0.4 μm. As a result of extensive association of iron and copper with the colloidal and soluble fractions respectively, not only organic carbon but also iron and copper behave conservatively in the River Thurso estuary. Throughout the coastal region of freshwater influence (S = 29 - 35) colloidal iron accounted for 30 - 80% of total dissolved iron and was present as iron-humic complexes supplied by the river and showing a uniform stability constant (log KFe’HS’ = 11.3  0.1, i.e. log KFe3+ HS’ = 21.3  0.1). Soluble iron was found to be largely complexed to ligands of marine origin with log K’Fe’HS’ = 11.9  0.1, thus revealing for the first time a difference between the iron-binding strengths of colloidal and soluble ligands. Terrestrial colloidal iron was found to be entirely, if slowly (~ 10 hours), accessible to the added competing ligand 2-(2-thiazolylazo)-pcresol (TAC) used for the determination of K’Fe’HS’. Furthermore, iron appeared to play a role in holding these terrestrial colloids together. Evidence for this came from variations in humic fluorescence intensity over time in response to dissociation of the ironhumic colloidal associations induced by a chelating resin. These results are consistent with the concept that iron derived from a peat-draining river is strongly but reversibly bound to humic substances and remains so under marine conditions. In the same coastal region, two types of high-affinity ligands binding over 99.99% of total copper were detected. The stronger ligand (L1, log KCu2+L1’ = 15.5 - 16.1), of riverine origin, was present in very low concentrations of 1 - 4 nM that correlated with ―but systematically fell short of― total copper concentrations. Its conditional binding constant tended to increase with salinity, with most of the increase taking place in the near-field portion of the river plume. The weaker, more abundant ligand (L2, log KCu2+L2’ = 11.8 - 12.8) was present in total concentrations of 60 – 170 nM and had a controlling influence on the value of the labile (i.e. inorganic) copper concentration which ranged from 0.001 to 0.0001 nM. Both organic ligands were fairly evenly partitioned between soluble and colloidal phases but their sources appeared to differ significantly. Ligand L1 appeared to be of riverine origin (although one cannot exclude active microbial production, as opposed to passive release from peat) while ligand L2 distributions suggested in situ production within Thurso Bay.

Much of the world's oceans lie below a depth of 200 meters, but very little is known about the creatures that inhabit these deep-sea environments. The deep-sea fish family Melamphaidae (Stephanoberyciformes) is one such example of an understudied group of fishes. Samples from the MAR-ECO (www.mar-eco.no) project represent one of the largest melamphaid collections, providing an ideal opportunity to gain information on this important, but understudied, family of fishes. The key to the family presented here is the first updated, comprehensive key since those produced by Ebeling and Weed (1963) and Keene (1987). Samples from the 2004 MAR-ECO cruise and the U.S. National Museum of Natural History provided an opportunity to review two possible new species, the Scopelogadus mizolepis subspecies, and a Poromitra crassiceps species complex. Results show that Scopeloberyx americanus and Melamphaes indicoides are new species, while the two subspecies of Scopelogadus mizolepis are most likely o nly one species and the Poromitra crassiceps complex is actually several different species of Poromitra. Data collected from the MAR-ECO cruise provided an opportunity to study the distribution, reproductive characteristics and trophic ecology of the family Melamphaidae along the Mid-Atlantic Ridge (MAR). Cluster analysis showed that there are five distinct groups of melamphaid fishes along the MAR. This analysis also supported the initial observation that the melamphaid assemblage changes between the northern and southern edges of an anti-cyclonic anomaly that could be indicative of a warm-core ring. Analysis of the reproductive characteristics of the melamphaid assemblage revealed that many of the female fishes have a high gonadosomatic index (GSI) consistent with values found for other species of deep-sea fishes during their spawning seasons. / This may indicate that melamphaids use this ridge as a spawning ground. Diets of the melamphaid fishes were composed primarily of ostracods, a mphipods, copepods and euphausiids. Scopelogadus was the only genus shown to have a high percent of gelatinous prey in their digestive system, while Melamphaes had the highest concentration of chaetognaths. This work presents data on the ecology and taxonomy of the family Melamphaidae and provides a strong base for any future work on this biomass-dominant family of fishes. / by Kyle Allen Bartow. / Thesis (Ph.D.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

The sea anemone Aiptasia pallida is a biological model for anthozoan research. Like all cnidarians, A. pallida possesses nematocysts for food capture and defense. Studies have shown that anthozoans, such as corals, can rapidly increase nematocyst concentration when faced with competition or predation, suggesting that nematocyst production may be an induced trait. The potential effects of two types of tissue damage, predator induced (Lysmata wurdemanni) and artificial (forceps), on nematocyst concentration was assessed. Nematocysts were identified by type and size to examine the potential plasticity associated with nematocyst production. While no significant differences were found in defensive nematocyst concentration between shrimp predation treatments versus controls, there was a significant difference in small-sized nematocyst in anemones damaged with forceps. The proportions of the different types of nematocysts between treatment types were also found to be different suggesting that nematocyst production in A. pallida is a plastic trait. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

Posthatchling green (Chelonia mydas) and loggerhead (Caretta caretta) turtles overlap ecologically but differ morphologically. This study compared hydrodynamic stability between the two species during swimming to test for functional differences in body shape. Flipper movement paths, four stability measures (yaw, pitch, heave, and sideslip), and the relative positions of the centers of buoyancy and gravity were compared between species. Both centers of buoyancy and gravity lie in the anterior body; their positions relative to one another differed with species, but showed no functional consequences. Neither species demonstrated substantial yaw, sideslip, or pitch. Both experienced upward heave with the flippers' downstroke and downward heave with the upstroke; however phase relationships differed between these limb and body motions. No differences were found between the two species. Despite obvious morphological differences, loggerheads and green turtles were similarly stable during swimming, suggesting that the species use different mechanisms to achieve stability. / by Erin Dougherty. / Thesis (M.S.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web.

Masking or decorator crabs, conceal themselves partially through camouflage, by selecting or indiscriminately attaching materials from their environment to their exoskeleton. Functional aspects of decorating behavior and morphology in this group have not been documented. Using Microphrys bicornutus as a model species, this dissertation demonstrates clearly that decorating is an advantageous phenotype that has evolved to serve several functions. Decorating is a complex behavior that begins when a crab approaches an algal substrate and results in the attachment of algae to hooked setae on the exoskeleton. Once decorated, crabs remain motionless on the substrate until disturbed or until another behavior is initiated. This was confirmed for M. bicornutus, as crabs spent a significant amount of time feeding, remaining motionless, picking, and walking when compared to decorating. Crabs displayed agonistic behaviors during encounters with conspecifics conspecifics. These included both active aggressive behavior and display behavior. Crabs showed a decrease in motility during these encounters, helping maintain dispersed distributions, thereby decreasing intrsapecific encounters in the field. Trials were done to determine the effect of conspecifics, predators and feeding preferences on algal utilization. M. bicornutus showed a significant decrease in the amount of algae used for decoration in the highest density trials (i.e., 4 and 8 crabs). Agonistic displays and aggressive behavior between these crabs likely affected the time available for decorating. Decorated crabs isolated from an algal substrate were more likely to survive in the presence of either of two sympatric fish predators. Thus, being protected by the algal decoration on their exoskeletons. Trials also showed a parallel between algal consumption and algal materials used for decoration. In addition to its protective function, algae used by M. bicornutus for decoration simultaneously serve as short term food supplies for the crabs. Eleven morphologically complex structures were identified and mapped on the exoskeleton. Hooked setae were the primary structures used to attach algae to the crab’s body. Ten additional setal structures were present, including two novel types of setae. On the basis of location and morphological variation exhibited among these latter structures, a primary sensory function may be inferred. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2013.

Thesis (MTech (Oceanography))--Cape Peninsula University of Technology, 2016. / Similarities in marine fauna found off the coasts of southern Madagascar and KwaZulu-Natal (KZN, South Africa) led to the development of the “Suitcase Project”, with the aim of establishing whether eddies that form off southern Madagascar may package and transport biological material, as if in a suitcase, across the Mozambique Channel. In pursuit of this question, sampling was conducted on the southern Madagascan shelf and along a transect across a cyclonic eddy which originated off the southern tip of Madagascar, between the 15th and 23rd of July 2013. Bongo nets (300 and 500 μm-mesh) and a neuston net (900 μm-mesh) were used to collect zooplankton within the upper 200 m and at the surface, respectively. Samples were sorted for meroplankton (larval stages of fish and benthic invertebrates) under a stereo microscope, particularly seeking species known to be common to both the east coasts of Madagascar and South Africa and, thus potential indicators of connectivity between these regions. Larvae of crabs, rock lobster, and fish were used for DNA barcoding. Zooplankton biovolume and abundance were compared between the eddy core, eddy periphery and outer regions of the eddy, as well as stations from the Madagascan shelf. Mean neuston biovolume on the Madagascan (0.08 mL m-3) was not significantly higher than that in the eddy (0.06 mL m-3). Mean bongo biovolume in the upper 200 m was much higher on the Madagascan shelf (0.62 mL m-3) than in the eddy (0.16 mL m-3) although only 2 stations were sampled on the shelf. Highest biovolume in the eddy was recorded in the west eddy zone (0.25 mL m-3) and west outer zone (0.23 mL m-3), which was not statistically significantly higher than the eddy core (0.12 mL m-3) and east eddy zone (0.17 mL m-3). Meroplankton was comprised of coastal origin taxa and was most abundant on the shelf and in the eddy perimeters. Larval goat-fish, Parupeneus fraserorum was identified, a newly described mullid, and has been recorded on both the coasts of Madagascar and KZN, SA. Larvae of coastal invertebrate species identified, include the squat lobster Allogalathea elegans and camel shrimp Rhynchocinetes durbanensis. Other larval fish identified, but not found in high abundance include the families of reef associated fishes, for example: Apogonidae, Labridae, Pomacentridae, Priacanthidae, Serranidae and Sparidae. Higher zooplankton biovolumes, larval abundances and reef-associated larval assemblages found on the Madagascan shelf and in the periphery of the cyclonic eddy compared to the core in this study provide support for the suitcase hypothesis that planktonic organisms are entrained within eddies as they propagate south-westwards of the Madagascan shelf. However, further studies are required to determine whether planktonic larvae are able to cross the Mozambique Channel and reach the KZN coast in time to settle.

Planktonic organisms form the base of the marine food web and may be impacted by environmental change in many ways. The interactive effects of multiple, simultaneous climate-driven changes on these organisms are not well understood. This dissertation examined the impacts of ocean acidification in combination with other environmental stressors on marine plankton and determined spatial patterns of one of these potential interactive drivers. Chapter 2 investigated the synergistic effects of ocean acidification and hypoxia on the harmful dinoflagellate Amphidinium carterae. Findings indicated that empirical studies may be crucial to accurately predict organismal responses to multi-stressors. Results also suggested that photorespiration may serve a previously unrecognized role in dinoflagellate metabolism. Chapter 3 examined the combined effects of ocean acidification and lithogenic trace metals on the growth of another harmful dinoflagellate, Cochlodinium polykrikoides. Results indicated that high suspended sediment loads may deliver toxic concentrations of trace elements to marine phytoplankton in acidified coastal ecosystems. Chapter 4 examined the interactive effects of ocean acidification and bacteria on the severity and extent of dissolution in the shells of larval gastropods and the adult pteropod Limacina helicina. Research findings indicated that microbial communities on the shell surfaces of some planktonic molluscs may mediate certain types of shell dissolution in acidified, upwelled waters. Chapter 5 explored the use of thorium isotope fluxes as a proxy for dust and lithogenic iron in the Indian Ocean. Results suggested that the gradient of dust fluxes in the region could impose thresholds for biological productivity. Together, these interdisciplinary studies demonstrate coupled biological and chemical changes in marine ecosystems as a result of increased anthropogenic environmental change.

This thesis addresses time-series analyses of microbial (i.e. marine heterotrophic bacteria and phytoplankton) and microbially relevant ecosystem variables at two ocean time series stations - Palmer Station in the coastal Western Antarctic Peninsula (WAP) and the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea. Using a diverse spectrum of statistical analyses and models, the aim of this thesis is to gain the better insight into 1) variability of microbial and ecosystem processes across varying time scales, from seasonal to interdecadal, and 2) how each process is influenced by variability of surrounding local physical forcing factors as well as regional and global-scale climate variability along the study region. Chapter 1 provides an introduction to the two study sites as well as a brief history of the ocean time-series programs there. Chapter 2 deals with phytoplankton and nutrient drawdown variability over an interdecadal (1993-2013) period using seasonal time-series variables collected at Palmer Station during full 6-months of Austral growing seasons (October-March). Specifically, the linkage between large-scale climate modes relevant to the WAP area and phytoplankton and nutrient patterns is explored to establish the underlying mechanisms of the observed ecosystem variability, which is ultimately triggered by climate conditions via mediatory physical forcing factors. Chapter 3 addresses a decadal (2002-2014) variability of heterotrophic bacterial variables collected at Palmer Station in Antarctica. This Chapter 3 provides an insight into why bacterial activity was shown to be restricted in this very productive ecosystem from diverse aspects gained using different statistical approaches. Furthermore, the linkage between bacterial properties and surrounding environmental conditions is explored. Finally, Chapter 4 concerns an event-scale phenomenon - the frequency of winter storms - and its impact on bacterial dynamics and ecological processes at the BATS site. Using a previously developed storm tracking algorithm, this study benefits from establishing a mechanistic connection between storm forcing and bacterial processes via storm-induced variability of physical environments - the extent of wind-mixing and entrainment of cold water into the upper mixed-layer. The finding of Chapter 4 is novel in the aspect that prevalent negative North Atlantic Oscillation (NAO) conditions, which lead to frequent arrivals of winter storms over the BATS region, in part, explain a significant decreasing bacterial trend over the past 24-year period. Overall, my thesis, in conjunction with work performed by fellow microbial oceanographers, aims to provide evidence of microbial responses to physical forcings across varying time scales in the strongly coupled climate-biogeochemical systems at two contrasting ocean sites based on a variety of statistical approaches.

Although more than 1300 marine reserves have already been established around the world, they still present a relatively new tool for environmental conservation and fisheries management. In accordance with this new approach towards marine protection, conservationists currently call for rapid establishment of a reserve network, which would encompass 10% to 30% of the oceans. Representative habitats from coastal areas as well as high seas would be included. Such a network should serve as a haven for marine species, ensuring their sustainability and aiding them to recover from fishery pressure. Furthermore, reserves are expected to enhance yields to the fishing industry through spillover and larval export. The paper attempts to determine, whether and under which conditions do marine reserves bring net benefits to economies.