Experiments were carried out to identify the environmental factors influencing survival during emersion with the aim of suggesting modifications to present transit conditions in order to minimise physiological stress, thus improving scallop condition and survival. Results showed that increasing the emersion temperature from 5 to 20oC caused a reduction in maximum survival time of 62%. Similarly, reduction in relative humidity, from 95 to 70% saturation, resulted in 27% reduction in maximum survival time. Scallops exposed to a fine sea-water mist showed a 13% improvement in survival and the survival of scallops tested in December was 67% better than those tested in July. This seasonal effect appeared to be correlated with tissue glycogen concentrations which decreased by 29% over the same period. Maximum survival of any emersed scallop was 166 hours, although the animals were not in an edible condition after this time. Experimental factors which were found not to influence survival directly were packing orientation, enforced shell-valve closure and hypertoxic conditions (˜100% oxygen). These results implicated aspects of energy metabolism as the primary causes of scallop death during emersion and therefore this area was investigated in more detail. Further work showed that, heart rate had a positive linear relationship with temperature until ˜19oC. Thereafter, heart rate became irregular and uncoordinated, suggesting that poorer survival at high temperature is caused by loss of physiological integration and difficulty in meeting increased metabolic demands. The oxygen consumption rate of Pecten maximus in air is reduced to only 50% of the aquatic rate within 8 hours of emersion. This decline in respiration rate continued and was typically between 25 and 30% of the aquatic oxygen consumption rate after 60 hours in air. In addition, heart rate, haemolymph PO2, haemolymph pH and mantle cavity fluid PO2 and pH all decreased during emersion, implying that respiratory and circulatory systems were deteriorating.

During the course of this programme of work, two related studies were carried out in collaboration with colleagues in the Division of Ecology & Evolutionary Biology. Together with Hussein Jen-Jan, we explored some hidden costs of an aggressive, proactive life style by examining respiratory function in relation to coping strategy in common carp (chapter 6).  Morphometric analysis of the fine structure of the gills was used to estimate respiratory area and histological analysis of sections through the gill filaments was used to measure the extent to which the secondary lamellae were obscured by epithelial cells. There was a significant relationship between risk-taking phenotype and both the size of the respiratory surface and the extent to which this is exposed as opposed to covered with epithelial cells. Risk-taking fish had larger and more exposed respiratory surfaces than did risk-avoiding fish, with fish with intermediate risk-taking phenotype having intermediate scores. These differences are interpreted as an adaptation to the known high resting metabolic rate of risk-taking fish (Chapter 6).  Together with Priyadarshini, we look at social interactions and growth in relation to risk-taking phenotype in goldfish. Within the social groups, though most goldfish showed no aggressive behaviour, some of the fish attacked their companions at least once per minute of observation and some individuals showed as many as 8 attacks per minute. These levels are surprisingly high for what is usually seen as a non-aggressive species. In groups comprising 3 goldfish of each risk-taking category, the risk-avoiding fish showed relatively little aggression. Overall, fish that showed any aggression within social groups gained preferential access to a restricted food supply (Chapter 6).  There were no differences in weight, length or condition between risk-taking and risk-avoiding goldfish at the point of initial screening, but by the end of the experiment the risk-avoiding fish held in groups with other risk-avoiders had gained less weight and had strikingly lower condition factors compared to the other categories of fish (i.e. all risk-avoiders and risk-takers held in mixed groups). It is suggested that some sort of social facilitation of fear keeps levels of stress high in groups composed entirely of risk-avoiding fish (Chapter 6).  The implications of all these results are considered in a final general discussion (Chapter 7).

Social interactions and aggression among salmonid fish are known to induce stress responses, particularly in subordinate fish, and the physiological effects of these stress responses have implications for fish in both aquaculture and natural environments. The physiological responses exhibited by subordinate fish (i.e. those fish that are low ranking in a social hierarchy) vary depending on the nature and extent of the social interaction and can also be influenced by environmental factors. Artificial environments - typically aquaria - generally elicit a larger stress response in the subordinate fish due to the fish being held in close confinement. The present study has clearly demonstrated that the physiological responses to social interaction and the formation of dominance hierarchies in rainbow trout and brown trough are affected by the environment of the fish e.g. whether the environment is artificial or natural, and stable or subject to fluctuations. In an artificial environment, the present study has confirmed that the effects of the social stress encountered by subordinate fish include decreases in growth rate and condition and increases in plasma cortisol but has also demonstrated decreases in the ability to secrete further cortisol and increases in the standard metabolic rate of subordinates. In a semi-natural environment these physiological consequences of subordinance were seen to be reduced; indeed with the presence of environmental perturbations no physiological differences were noted between dominant and subordinate fish. Finally the present study also investigated the role of cortisol in chloride cell proliferation and the determination of social status and concluded that cortisol appears to play a mineralocorticoid role in the proliferation of chloride cells and may also influence the outcome of social interactions.

Human uses and abuses of rivers have grown and diversified over the last few centuries with increasing urban development. With increasing population growth, there has been increasing demand for the use of rivers to satisfy a diverse range of human needs including solid waste disposal and the discharge of industrial, sewage and mining effluents. Rivers have been abstracted for agricultural and potable water supply and river channels have been modified for navigation, flood defences and hydro-electric power generation. These modifications to the river system disrupt the fabric of the aquatic ecosystem and diminish its integrity, affecting equally the capacity of fish and other organisms to survive. Fish depend on undamaged interactive pathways to enhance their survival, growth and recruitment.The Don, Rother and Dearne catchment in South Yorkshire and North East Derbyshire has suffered from a legacy of pollution and land contamination that dates back to the Industrial Revolution. These rivers have been grossly polluted from industrial, sewage, and mining effluents and from the disposal of solid wastes in the catchment. Much of the lengths of these rivers were fishless into the mid 1980s.Fish populations in the catchment remain low and species diversity is poor at most locations in the Don sub-catchment. Brown trout and coarse fish species are present in the Don catchment, with the salmonid populations confined to the upper reaches. Most tributaries of the River Don provide brown trout recruits to the main rivers but poor water quality and degraded habitats have prevented the successful colonisation of the waters by the species. Coarse fish, where present, were found at the middle and lower reaches of the river.Fish populations and species diversity in the River Dearne are generally poor due to serious water quality problems. Limited numbers of brown trout and coarse fish were found at few locations in the catchment, reflecting the widespread nature of poor water and habitat quality. The sub-catchment receives diverse discharges from sewage, industry and abandoned mines. This is exacerbated by various pollution incidents, the causes of some of which remain unidentified.The River Rother has low fish population densities, and many stretches of the river are fishless due mainly to poor water quality and lack of suitable habitats. Some tributaries of the River Rother, particularly the River Hipper, Redleadmill Brook and Brookside Beck hold considerable numbers of brown trout. The Rother sub-catchment also receives sewage, industrial and mine effluents which impact on the water quality.The benthic macroinvertebrate fauna of the sites studied were mainly pollution-tolerant taxa with low species diversity reflecting poor water quality. Heavy metal levels were generally low and declining which, possibly, relate to the decline in steel and coal industry in the catchment.A concerted programme to improve effluent discharges from major sewage treatment works and industries serving the catchment area coupled with a decline in the coal, steel and manufacturing industries has resulted in marked improvements in water quality of the rivers. Reductions in ammonia and BOD levels have been achieved since 1991 due mainly to improvements to sewage treatment works. As a consequence the fisheries of the rivers have shown some evidence of recovery. Unfortunately these improvements are localised and the fish populations suffer periodic setbacks because of isolated pollution incidents.Despite considerable efforts by the Environment Agency and its predecessors (the National Rivers Authority and Yorkshire Water), to improve the fish populations through stocking and some habitat improvement measures, the general status of the fisheries remains poor particularly in the Rivers Dearne and Rother. A strategic Aquatic Resources Management Plan (ARMP) targeting the bottlenecks to recovery and improvement in the water quality and fisheries habitat is proposed for the long-term sustainable improvement of the fisheries. Project Concept Notes and Logical Project Frameworks have been developed to address the water quality, habitat and fisheries rehabilitation problem. These constitute draft proposals for which additional information would be needed before projects can be progressed.

This study provides an assessment of the fish assemblage of the Humber estuary, using a quarterly sampling interval. Sampling 14 subtidal stations throughout the estuary, and two intertidal sites in the outer estuary, the principal aims of the study were to determine the structure and functioning of the assemblage and the environmental and biological factors influencing the fish distribution.

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Historically sea fish were thought to be an inexhaustible resource, in 1882 Thomas Huxley recognised that it was possible to extirpate some fisheries such as the UK oyster and salmon fishery, but he thought "in relation to our present modes of fishing" sea fish were so abundant that they were inexhaustible. Fishing causes impacts other than overfishing, such as bycatch of non-target and vulnerable species discarding and damage to habitats and ecological communities. Fishing intensity has been increasing since the industrial revolution through which technological advances have given fishing vessels the ability to go further and for longer. This has resulted in the need for an ecosystem focused method of management for fisheries, known as ecosystem based fisheries management (EBFM). EBFM requires the development of indicators which represent the ecosystem with which thresholds can be set against fishing pressure. This was investigated for "Sea-pen and burrowing mud megafaunal communities", which have been identified by OSPAR as a threatened or declining habitat in the North Sea and Celtic Seas. Baited cameras were used to monitor mobile megafauna communities across a gradient of fishing intensity to determine which species are sensitive to fishing pressure and could be used in metrics to monitor recovery in areas proposed for protection. Trawling had a negative effect on species richness of mobile megafauna, Munida rugosa, Cancer pagurus and Liocarcinus depurator, but no effect was found on deep burrowing species (Nephrops norvegicus and Goneplax rhomboides). This study identified species that demonstrated different trends with trawl intensity, the trends are related to the ability to burrow and the species mobility. This gives support to the use of biological traits as indicators to detect changes of communities to fishing pressure. In addition to the development of indicators EBFM supports the use of spatial closures as a tool for fisheries management. This method of management is widely used yet remains controversial, often due to the lack of clear objectives and monitoring. Evidence is growing in support of their use but results are often seen after an extended period of long-term monitoring. Clear objectives for each spatial area closure are essential to be able to set relevant targets and reference points, this allows for robust monitoring and improves the ability to effectively manage the area. Although the use of experimental design and statistical analysis to monitor the effects of area closures throughout the world is increasing, there is still a lack of standardisation and the use of theoretically robust survey designs The use of the Before-After, Control-Impact (BACI) design has been identified as the most robust method to monitor areas closed to fishing Few studies have been conducted using this method due to the difficulty in obtaining sufficient temporal and spatial data prior to the implementation of the area closure. There can also be difficulty in identifying suitable reference sites; monitoring begins after closures have already been established or there are limited funds to allow intense temporal and spatial replication. Area closures are particularly beneficial for species which have key life history stages that congregate, such as for spawning. Although the use of area closures are now common place in the UK, this management approach remains controversial due to the frequent lack of clear objectives, monitoring and impact studies. Providing evidence is therefore vitally important to support decision-making for future area closures and to evaluate whether existing closures are achieving their objectives. This was addressed by evaluating an existing seasonal area closure for Atlantic cod (Gadus morhua) in the Firth of Clyde off the Scottish West Coast. The study uses standardised scientific trawl data and a beyond-BACI approach to compare population trends of the Clyde spawning aggregations with two other sub-populations of the same stock. There was no evidence of local recovery in terms of abundance, biomass or reduced mortality in the Clyde more than a decade after the closure was established. Considering the severely depleted state the Clyde sub-population was in when the closure was implemented it appears that the measure was too little and too late. The advantage of EBFM and using an area closure is when there is uncertainty with regard to the effects of fishing on environment and fish stocks, for example if the sensitivity of a habitat to fishing disturbance is unknown or there is not enough data to accurately assess a stocks biomass. This is applicable for deep-sea in the north east Atlantic where since the onset of deep-sea fishing in the 1970s there has been a decline in the abundance of commercial fish species. Management measures were introduced in 2003 which set Total Allowable Catch (TAC) and restricted days at sea, but this still did not allow for the recovery in biomass of commercial species. Also the fishery has high levels of bycatch, including vulnerable deep-sea sharks, which are estimated to have declined by up to 90%. There has been a recent global debate as to whether there is a depth beyond which fisheries cannot be expected to operate in an economically and ecologically sustainable way. The European Union is currently considering new legislation to manage deep-sea fisheries, including the introduction of a depth limit to bottom trawling. However, there is little evidence to suggest an appropriate depth limit. This was addressed using long-term scientific deep-sea trawl data and calculating important ecological and economical indices. The non-linear trend and first derivatives of these indices were calculated with depth. The results suggest that between 600 and 800 m the commercial benefits derived from fishing start to be outweighed by potentially negative ecological consequences. In the marine environment uncertainty is a great impediment for the sustainable management of resources, this thesis demonstrates that with long-term commitments to monitoring, clear objectives and the development of novel techniques to interrogate data, strong evidence can be established to support policy and decision-making.

This thesis describes a study into two post capture conditions, idiopathic muscle necrosis (IMN) and a post capture opportunistic bacterial infection, affecting the Norway lobster, Nephrops norvegicus, and a comprehensive analysis of the stressors involved in the capture and post capture periods of the fishery process. A multivariate approach was used to study progression in the post capture condition of trawl-caught N. norvegicus for the live transport market. Prolonged periods of aerial exposure resulted in large disruptions to the carbohydrate profile, increases in haemolymph L-lactate and crustacean hyperglycaemic hormone concentrations, and corresponding fluctuations in haemolymph pH. These disruptions increased with the increasing temperature of aerial exposure, which impacted the immunocompetence of the lobsters: circulating haemocytes and phenoloxidase levels were significantly reduced and the degree of bacteraemia increased. The health status of N. norvegicus captured during trials in spring and autumn by means of short trawl (1h duration), long trawl (5h duration) and creeling was assessed using a range of physiological (Haemolymph L-lactate, crustacean hyperglycaemic hormone (CHH), abdominal muscle glycogen concentrations), immunological (total haemocyte counts (THC)) and physical (mortality, damage indices) parameters. Increased duration of trawl did not significantly alter physiological parameters, while time of landing did have a significant effect on L-lactate, where animals landed in the morning exhibited higher concentrations. Seasonal variations in abdominal muscle glycogen concentrations were also apparent. Irrespective of season, individuals captured by short trawls in the morning suffered lowest mortalities. Damage assessment data revealed that a greater proportion of individuals were categorised as heavily damaged following longer trawls conducted in spring. The carbohydrate profile and immunocompetence of N. norvegicus was significantly affected following trawl capture and subsequent handling and aerial exposure post capture. The recovery period was investigated through a range of parameters (L-lactate, glycogen, glucose, THC) and the data suggested that animals should be submerged and unstressed for at least 24h following capture and handling to avoid further alterations to the carbohydrate profile and reduce the window of opportunity for invading bacteria to cause meat spoilage. The influence of air temperature on the condition of N. norvegicus caught for the live export market was assessed by correlating meteorological data with the percentage of catch accepted for live transport. Results illustrated a large degree of variability in the conditions of animals on arrival at the processing plant. Air temperature was the only meteorological factor that had an impact on the morbidity and mortality of the catch. In one instance in particular, mean air temperature on the day of capture had a significant negative impact on the health of the catch.