The use of adaptive feeding systems to deliver feed remotely to Atlantic salmon (Salmo salar) cages has the potential to improve the localised environment through a reduction in particulate waste. This can be achieved through improved growth and lower Feed Conversion Ratio (FCR). The aim of this project was to assess whether adaptive feeding systems confer any environmental benefit at salmon farms through by comparing two fish farm sites, one that uses a Computer Aided System (CAS) adaptive feeding system (AKVAsmart UK limited, Inverness, Scotland) (Portavaide fish farm) and one using hand feeding (Rubha Stillaig). This investigation comprised of 3 elements: 1) a comparative assessment of the quantity and nutrient composition of particulate waste material emanating from the cages; 2) collection of benthic samples plus a video survey along transects at each site including a reference station, with an analysis of differences in benthic fauna, sediment grain size and sediment nutrient composition; and 3) comparison of the distribution of waste under each feeding regime using a GIS-based modelling approach. Particulate waste was collected via sediment traps. Uneaten feed was caught in only 3 out of 184 separate collections and thus no estimate of feed loss for each feeding system could be made. Samples were analyzed for total solids (TS), faecal solids (FS), faecal carbon (FC), faecal nitrogen (FN) content and faecal sedimentation rate (FSR). The highest deposition occurred under the cages and decreased with increased distance from the cage centre. Maximal deposition of TS at Portavadie was higher than at Rubha Stillaig when feed was included, although average TS, FS, Fe and FN per tonne of production did not significantly vary between sites. Carbon sedimentation rate was analyzed using regression analysis and a General Linear Model Factorial ANOVA on faecal waste only and showed no significant differences between sites and, therefore, no difference between feeding methods . There were no differences observed in the diversity and abundance of benthic species under the two feeding systems. By the end of the production period all stations out to 25m from the cage edge were dominated by Capitella capitata at both sites, this species proving a useful indicator of the impact of nutrient deposition. The analysis suggested that Heteromastus filiformis and Corophium sp. provided useful indicators of the onset of nutrient enrichment. Measurement of carbon and nitrogen levels and particle size in sediment showed no difference between sites. Variations between sites in species abundance and diversity and sediment carbon and nitrogen levels reflected the different sediment conditions prevalent at the start of the sampling period. Univariate and multivariate analysis showed there was no difference in species diversity and abundance between the sites as a result of using adaptive feeding systems. Horizontal cage movement, measured at up to 10m, reduced the predicted settlement under the cage by 23% and 11 % for feed and faecal distribution respectively. There was no significant difference in the predicted settlement of waste particulates under adaptive and hand feeding. The GIS model prediction of carbon flux (g C m-2 15-days-1) was validated for faecal settlement using sediment trap data where predictions agreed well with observations from Portavadie fish farm, with an accuracy of ± 53.1 % when all stations were included, improving to ± 27.6% when deposition under the cage was excluded. Overall, the approaches used did not identify specific differences between sites that used adaptive feeding and hand feeding methods. The growth period using the adaptive feeding system was approximately nine weeks shorter than under hand feeding, however, which could be used constructively to increase the fallowing period whilst maintaining current levels of production. This would benefit the localised benthos by increasing the time available for recovery before further production takes place and thus the CAS Adaptive Feeding System could be used as part of a broader sustainable farming strategy for fish culture.

Japanese yellowtail Seriola quinqueradiata has been commercially farmed in Japan since the 1940s. In comparison, sea-cage farming of yellowtail kingfish Seriola lalandi in Australia is still developing, with commercial production commencing in 1998. In Australia, S. lalandi is parasitised by Zeuxapta seriolae and Benedenia seriolae. In Japan, S. quinqueradiata is parasitised by Heteraxine heterocerca and B. seriolae. These monogeneans affect industries in both countries and management of these parasites is required to prevent impacts on fish health and commercial losses. I investigated efficacy (% reduction of mean parasite abundance) for orally administered praziquantel, fenbendzole and oxfendazole against Z. seriolae and B. seriolae on S. lalandi and the efficacy of orally administered praziquantel and febantel against H. heterocerca and B. seriolae on S. quinqueradiata. Medications were administered to fish by surface coating feed pellets or via direct intubation of the stomach. Seriola lalandi administered fenbendazole and oxfendazole by surface coating of feed had lower abundance of the gill parasite Z. seriolae. Seriola quinqueradiata intubated with febantel had lower abundance of the gill parasite H. heterocerca. Neither fenbendazole nor oxfendazole administered to S. lalandi in Australia, nor febantel administered to S. quinqueradiata in Japan resulted in a lower abundance of the skin parasite B. seriolae. Praziquantel was first administered to S. lalandi by surface coating of feed. Fish rejected medicated feed, suggesting praziquantel affected its palatability. Fish treated with feed medicated with praziquantel had fewer Z. seriolae and B. seriolae than untreated fish. Praziquantel administered to S. lalandi by intubation allowed a more accurate dose to be tested without differential feeding or reduced palatability obstructing results, and resulted in fewer Z. seriolae (99.5-100 % reduction) and B. seriolae (91 – 97.7 % reduction). Intubated praziquantel also led to fewer recruitment life stages of Z. seriolae and B. seriolae, even at low doses, but did not completely eliminate them from S. lalandi. Praziquantel administered to S. lalandi alone and combined with cimetidine had high efficacy (>99%) against Z. seriolae. In comparison, praziquantel administered alone resulted in fewer B. seriolae (68.3 – 69.7 % reduction) than the same doses of praziquantel combined with cimetidine (36.9 – 40.9 % reduction). A 90.4 -100% reduction in H. heterocerca was achieved when praziquantel was administered by intubation to S. quinqueradiata in Japan but there was only a 22-77.8 % reduction in B. seriolae. The dose of PZQ (150 mg kg⁻¹ body weight day⁻¹ for 3 days) on the label of a commercially available product used to treat B. seriolae in Japanese aquaculture resulted in a 50.9% reduction against B. seriolae, but completely eliminated H. heterocerca. In trials against Z. seriolae and B. seriolae on S. lalandi in South Australia, I also screened 27 other anthelmintics and antiparasitics from the chemical groups: amprolium derivatives, benzimidazoles, benzyl ureas, diphosphate salts, imidazothiazoles, macrocyclic lactones, nitromidazoles, organophosphates, piperazines, salicylanilides, substituted phenols and tetrahydropyrimidines. Of these, only the benzimidazole, albendazole, was effective against Z. seriolae and none appeared to have an effect against B. seriolae. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1459172 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010

Many studies have investigated the impacts of marine cage fish farming on seabed sediments. Most of these studies have focused on organic loading or toxic chemicals used for the treatment of disease, normally for a single or a small number of sites over short time periods. Only very rarely has there been the opportunity to use large data sets consisting of a large number of fish farm sites over a long time scale. In Scotland, localised nutrient impacts have been well documented for marine cage salmon farms, but mixed effects of nutrient and chemicals such as SLICE (the active ingredient of which is emamectin benzoate) have not been investigated in the long term. The aim of this project was to investigate the ecological impacts on sediments from farming activities using very large spatial and temporal data to investigate the long term effects of nutrient and chemical waste. This was achieved using a metadata set collected from 403 sampling stations at 31 fish farms on the west coast of Scotland over a 9 year period. Data consisted of sediment macrofauna, carbon and nitrogen levels, redox potential, particle size for sediment characterisation and sediment concentrations of SLICE. The data was analysed for trends using statistical and multivariate analysis to look for changes in sediment community and related conditions, and the relationships between these parameters were investigated. At sampling stations that were less than 50 metres from the sea cages, 72% of the macrofauna communities were correlated with regard to their species composition and abundance. A significant relationship between the concentration of SLICE and sediment characteristics was represented as: SLICE= 0.000644*(median size particle size) + 0.0311*(C %) – 0.00213*(redox potential) + 1.453. Annelids were the most sensitive to the presence of emamectin benzoate, with the sipunculid Phascolion strombi, the echinoderm Ophiura affinis, and the custaceans Iphinoe, Diastylis and Iphimedia also showing sensitivity. During the data period, there was a clear change in species composition associated with improved seabed conditions. This correlated with biomass changes at the relevant sites, where there was a consequent decrease in nutrient input and SLICE usage. The statistical comparison of the AMBI and ITI indices indicated a 68.9% correlation, but they differed in their ability to indicate levels of organic disturbance. AMBI was shown to correlate more closely with conditions and thus a more reliable index when working with large databases. Univariate and multivariate analysis indicated that a combination of abundance (N), Shannon Wiener (H’) and AMBI, as biological indices for describing the status of the ecological level associated with the carbon percentage and redox potential of sediments gave the most reliable representation of environmental change over a series of sampling stations. In conclusion, the overall results suggest that, in the long-term, sampling stations which contained significant levels of SLICE had a higher impact status than those affected only by nutrient inputs. The accuracy of multiple regression models were increased by adding biotic and abiotic parameters, though fish biomass at the sites were not considered be as important factor for the prediction of impacts. However, this model could be sensitive to natural environmental conditions and variations. In light of these results and conclusions, recommendations can be made both for updating the existed environmental regulation of marine fish farms and in the development of meaningful models to relate sediment conditions to accurate estimations of overall environmental impacts.

Japanese yellowtail Seriola quinqueradiata has been commercially farmed in Japan since the 1940s. In comparison, sea-cage farming of yellowtail kingfish Seriola lalandi in Australia is still developing, with commercial production commencing in 1998. In Australia, S. lalandi is parasitised by Zeuxapta seriolae and Benedenia seriolae. In Japan, S. quinqueradiata is parasitised by Heteraxine heterocerca and B. seriolae. These monogeneans affect industries in both countries and management of these parasites is required to prevent impacts on fish health and commercial losses. I investigated efficacy (% reduction of mean parasite abundance) for orally administered praziquantel, fenbendzole and oxfendazole against Z. seriolae and B. seriolae on S. lalandi and the efficacy of orally administered praziquantel and febantel against H. heterocerca and B. seriolae on S. quinqueradiata. Medications were administered to fish by surface coating feed pellets or via direct intubation of the stomach. Seriola lalandi administered fenbendazole and oxfendazole by surface coating of feed had lower abundance of the gill parasite Z. seriolae. Seriola quinqueradiata intubated with febantel had lower abundance of the gill parasite H. heterocerca. Neither fenbendazole nor oxfendazole administered to S. lalandi in Australia, nor febantel administered to S. quinqueradiata in Japan resulted in a lower abundance of the skin parasite B. seriolae. Praziquantel was first administered to S. lalandi by surface coating of feed. Fish rejected medicated feed, suggesting praziquantel affected its palatability. Fish treated with feed medicated with praziquantel had fewer Z. seriolae and B. seriolae than untreated fish. Praziquantel administered to S. lalandi by intubation allowed a more accurate dose to be tested without differential feeding or reduced palatability obstructing results, and resulted in fewer Z. seriolae (99.5-100 % reduction) and B. seriolae (91 – 97.7 % reduction). Intubated praziquantel also led to fewer recruitment life stages of Z. seriolae and B. seriolae, even at low doses, but did not completely eliminate them from S. lalandi. Praziquantel administered to S. lalandi alone and combined with cimetidine had high efficacy (>99%) against Z. seriolae. In comparison, praziquantel administered alone resulted in fewer B. seriolae (68.3 – 69.7 % reduction) than the same doses of praziquantel combined with cimetidine (36.9 – 40.9 % reduction). A 90.4 -100% reduction in H. heterocerca was achieved when praziquantel was administered by intubation to S. quinqueradiata in Japan but there was only a 22-77.8 % reduction in B. seriolae. The dose of PZQ (150 mg kg⁻¹ body weight day⁻¹ for 3 days) on the label of a commercially available product used to treat B. seriolae in Japanese aquaculture resulted in a 50.9% reduction against B. seriolae, but completely eliminated H. heterocerca. In trials against Z. seriolae and B. seriolae on S. lalandi in South Australia, I also screened 27 other anthelmintics and antiparasitics from the chemical groups: amprolium derivatives, benzimidazoles, benzyl ureas, diphosphate salts, imidazothiazoles, macrocyclic lactones, nitromidazoles, organophosphates, piperazines, salicylanilides, substituted phenols and tetrahydropyrimidines. Of these, only the benzimidazole, albendazole, was effective against Z. seriolae and none appeared to have an effect against B. seriolae. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1459172 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010

Thesis (Ph.D.)--Flinders University, School of Biological Sciences. / Typescript bound. Includes bibliographical references: (leaves 149-166) Also available online.

The potential for aquaculture to be integrated within a large-scale irrigation system taking a poverty-focused approach was investigated in the Mahaweli System H irrigation system of North Western Province, Sri Lanka. Using a livelihoods approach an initial situation appraisal identified the potential for aquaculture to be integrated within existing livelihoods activities. The appraisal revealed that decreasing returns from farming and fishing seasonality were major sources of household vulnerability. Using fish caught from the tank fishery, small-scale cage-based fattening of tilapia was developed with participants in an attempt to mitigate seasonal vulnerability caused by fishing seasonality. Participatory technology development was conducted with members of two communities within Mahaweli System H. Upon identifying resources and formulating a research agenda with participants, pilot trials were conducted by fisher-farmers in USG village and by a group of female cage operators in RAJ village. The study identified several constraints to sustainability of the culture system such as variable and low availability of small tilapia with which to stock cages, poor feed quality and latterly, competition for feed inputs. Despite their initial enthusiasm, women were particularly disadvantaged in this process as they were unable to catch their own fish with which to stock their cages and became dependent on men to assist them. The study showed that the cage-based fattening system was able to help meet emergency household expenses, although it was not efficient enough nor practiced on a large enough scale to contribute greatly to household security. In this manner, holding and fattening smaller tilapia is comparable with livestock holdings. Further development of cage design and feed administration improvements are needed to reduce production costs and improve the economic viability of the system.

Thesis (MScAgric (Conservation Ecology and Entomology)--University of Stellenbosch, 2007. / Small farm dams (< 20 ha) in the Western Cape Province provide adequate water conditions for intensive cage production of rainbow trout (Oncorhynchus mykiss). A major environmental concern of cage aquaculture, however, is the high inputs of nutrients via commercial diets and the subsequent eutrophication of the water source. Eutrophication can result in the degradation of the general water quality (increasing pH levels, oxygen depletion, increased hydrogen sulphide and free ammonia) and shifts in the phytoplankton structure (increased biomass, single species dominance). Deterioration of water quality will affect the success of the fish farming enterprise as well as the performance of irrigation equipment by increasing the risk of clogging and corrosion. Water quality, phytoplankton and zooplankton compositions were monitored at four sites from June 2005 to November 2006 to determine the effects of cage culture on the farm dam environment, its associated biota as well as irrigation water quality. The distribution of nutrients, nitrogen and phosphorus, was mainly influenced by the stratification and mixing regime of the water bodies. Nutrient concentrations increased during the winter mixing period while in the summer months, they seem to settle to the lower part of the water column. Nutrient concentrations of production sites and reference sites were comparable except for the ammonia levels that were significantly higher at the production sites. Phytoplankton corresponded with nutrient availability resulting in high biomass during winter. In terms of biomass, phytoplankton was approximately two times more abundant in production sites compared to reference sites. Assemblage dominance by cyanophytes (Anabaena circinalis, Microcystis spp.) was found more often in production sites, while reference sites were dominated by dinophytes (Ceratium hirundinella, Peridinium spp.). Zooplankton biomass concurred with high phytoplankton biomass in winter. Zooplankton assemblages in production sites sustained much higher biomass. Effects of cage culture on irrigation water quality are evident from increased algal biomass and shifts in species composition. These results indicated that at its present production level, cage culture had impacts on the farm dam environment and irrigation water quality. The most significant evidence was given by increased plankton biomass and single species dominance in production sites. However, these findings can not solely be ascribed to the introduction of aquaculture as various other factors may also contribute to the water quality of these ecosystems.

There is considerable opportunity to develop new modelling techniques within a Geographic Information Systems (GIS) framework for the development of sustainable marine cage culture. However, the spatial data sets are often uncertain and incomplete, therefore new spatial models employing “soft computing” methods such as fuzzy logic may be more suitable. The aim of this study is to develop a model using Neuro-fuzzy techniques in a 3D GIS (Arc View 3.2) to predict coastal environmental vulnerability for Atlantic salmon cage aquaculture. A 3D hydrodynamic model (3DMOHID) coupled to a particle-tracking model is applied to study the circulation patterns, dispersion processes and residence time in Mulroy Bay, Co. Donegal Ireland, an Irish fjard (shallow fjordic system), an area of restricted exchange, geometrically complicated with important aquaculture activities. The hydrodynamic model was calibrated and validated by comparison with sea surface and water flow measurements. The model provided spatial and temporal information on circulation, renewal time, helping to determine the influence of winds on circulation patterns and in particular the assessment of the hydrographic conditions with a strong influence on the management of fish cage culture. The particle-tracking model was used to study the transport and flushing processes. Instantaneous massive releases of particles from key boxes are modelled to analyse the ocean-fjord exchange characteristics and, by emulating discharge from finfish cages, to show the behaviour of waste in terms of water circulation and water exchange. In this study the results from the hydrodynamic model have been incorporated into GIS to provide an easy-to-use graphical user interface for 2D (maps), 3D and temporal visualization (animations), for interrogation of results. v Data on the physical environment and aquaculture suitability were derived from a 3- dimensional hydrodynamic model and GIS for incorporation into the final model framework and included mean and maximum current velocities, current flow quiescence time, water column stratification, sediment granulometry, particulate waste dispersion distance, oxygen depletion, water depth, coastal protection zones, and slope. The Neuro-fuzzy classification model NEFCLASS–J, was used to develop learning algorithms to create the structure (rule base) and the parameters (fuzzy sets) of a fuzzy classifier from a set of classified training data. A total of 42 training sites were sampled using stratified random sampling from the GIS raster data layers, and the vulnerability categories for each were manually classified into four categories based on the opinions of experts with field experience and specific knowledge of the environmental problems investigated. The final products, GIS/based Neuro Fuzzy maps were achieved by combining modeled and real environmental parameters relevant to marine fin fish Aquaculture. Environmental vulnerability models, based on Neuro-fuzzy techniques, showed sensitivity to the membership shapes of the fuzzy sets, the nature of the weightings applied to the model rules, and validation techniques used during the learning and validation process. The accuracy of the final classifier selected was R=85.71%, (estimated error value of ±16.5% from Cross Validation, N=10) with a Kappa coefficient of agreement of 81%. Unclassified cells in the whole spatial domain (of 1623 GIS cells) ranged from 0% to 24.18 %. A statistical comparison between vulnerability scores and a significant product of aquaculture waste (nitrogen concentrations in sediment under the salmon cages) showed that the final model gave a good correlation between predicted environmental vi vulnerability and sediment nitrogen levels, highlighting a number of areas with variable sensitivity to aquaculture. Further evaluation and analysis of the quality of the classification was achieved and the applicability of separability indexes was also studied. The inter-class separability estimations were performed on two different training data sets to assess the difficulty of the class separation problem under investigation. The Neuro-fuzzy classifier for a supervised and hard classification of coastal environmental vulnerability has demonstrated an ability to derive an accurate and reliable classification into areas of different levels of environmental vulnerability using a minimal number of training sets. The output will be an environmental spatial model for application in coastal areas intended to facilitate policy decision and to allow input into wider ranging spatial modelling projects, such as coastal zone management systems and effective environmental management of fish cage aquaculture.