The growth of aquaculture industry, and in particular of salmonids, has dramatically increased in the last decades to supply the growing worldwide demand for fish products. The expansion of aquaculture needs a good management to ensure the sustainability of this activity. In particular, improving feeds for aquaculture to enhance health and performance of reared fish is imperative for this industry. Molecular biological approacches can help interpret responses to new diets and immune responses. Ubiquitin ligases (UbE3s) play a pivotal role in the ubiquitin proteasome pathway of protein degradation and are markers that could be linked to health and performance of fish. Six UbE3s were characterized, 4 are related to muscle catabolism and two involved in NF-kB activation. Atrogin-1 and MuRF genes were increased following food deprivation and a proinflammatory stimulation. MULAN and Mul1b, are mitochondrial activators of NF-kB and the expression of both genes was increased following a proinflammatory immune challenge both in vivo and in vitro. These genes have been used as markers in dietary traits to understand responses. A transcriptome study using Atlantic salmon fed a commercially available functional feed designed for optimal health status compared to a standard feed was performed. Both the liver and muscle were chosen for the transcriptomic analysis. In liver, a number of process were found down regulated, including protein turnover and innate immunity. No significant alterations were found in muscle. To determine the effect of a high plant protein diet (PP), compared to a marine profile diet (MP) in Atlantic a transcriptomic analysis was performed. Fish grew equally well on both diets and no significant histological differences were seen in intestine. The PP diet induced tissue specific changes in gene expression, with the mid intestine showing activation of the adaptive immune response and protein turnover. In liver cell proliferation and apoptosis indicate cellular reorganization and also a general suppression of processes such as immune response was observed. In contrast muscle tissue showed reduced protein metabolism and decrease in immune gene expression suggesting less energy expenditure in this tissue. To assess fish response to Piscirickttsia salmonis, the etiological agent of the salmonid rickettsial seeticemia (SRS), a transcriptomic analysis was carried out. P. salmonis infection has profound effects on transcription in the head kidney, liver and muscle of salmon. Head kidney, liver and muscle tissue showed a decrease in expression of mRNAs related to acquired immune function indicating the pathogen is down regulating this response controlled in part by the inhibition of the G-protein signalling pathway, whereas the innate immune response was increased in head kidney. Liver and muscle also responded, including specific responses in each tissue type. These results improve understanding of the mechanisms by which this bacterium survives and replicates within host cells and may assist selection of molecular biomarkers useful for the development of a diagnostic tools, vaccines and therapeutants for the aquaculture industry. Using markers selected from the previous experiments, the effect of four different diets, a marine profile diet (MP/FO), a plant protein diet (PP/FO), a vegetable oil diet (MP/VO) and PP/VO diet, in Atlantic salmon were examined. Markers for protein and lipid metabolism and immune response were studied in mid intestine, liver and muscle of fish fed for 77 days the four diets. Small but significant changes were observed, but despite of this, fish fed all the four diets showed similar growth rates. Moreover, to study the possible effect of the diets on fish health, the expression of specific SRS markers was studied in head kidney and liver of fish fed the four diets and infected with P. salmonis. The SRS challenge demonstrated that all groups of fish were able to respond efficiently to the pathogen. In conclusion, these new diets may represent good alternatives to fish meal (FM) and fish oil (FO) diets indicating that a replacement of marine diets with vegetable sources is possible in Atlantic salmon without affecting neither fish growth and performance nor the health of fish. The findings presented in this thesis suggest that E3 ligases are good molecular markers, allowing to study performance and health of fish following feeding trial and pathogen challenge. In addition, transcriptomic analysis performed to select further key molecular markers involved in a variety of processes and improved our knowledge of fish physiology and immunology, providing useful information for the development of new alternative diets for aquaculture.

Aquaculture, as an aquatic based economic activity, has risen from relative obscurity to a position of global recognition in just over two decades, and is forecast to become increasingly important in the next century. This growth, however, has been accompanied by increasing concerns over the environmental and social costs associated with the exploitation of the natural resource base on which it depends. This occurs in the broader context of increasing awareness of the finite capacity of the global system, and the need for development of more sustainable resource management regimes. The objective of the study is to examine if and how 'sustainability' can be brought into assessment for aquaculture development. The main concepts of sustainability are discussed, and key issues for assessment identified. The range of impacts associated with aquaculture development is reviewed, and broad categories of sectoral sustainability indicators proposed. Specific issues and assessment approaches are examined in three case studies, focusing on environment interactions, resource use assessment, and the rural development context, respectively. There follows a structured analysis of applicability of selected generic appraisal methods, concluding that while all may contribute, none is sufficiently broad to account for all sustainability perspectives. A more comprehensive framework for the assessment is therefore proposed, by which sustainability features of any system can be described, potential indicators and methods of assessment identified, and results communicated to the decision making process. This does not offer a definitive judgement on sustainability, but presents an holistic view, allowing explicit recognition of trade-offs involved between conflicting sustainability objectives. It is concluded that sufficient information is available for this approach to be developed and applied on a wider basis. Constraints to more sustainable development relate more to the social, political and economic environment than to problems of uncertainty in forecasting biological and physical systems.

Thesis (Ph. D.)--University of Hawaii at Manoa, 2003. / Includes bibliographical references (leaves 109-118).

Understanding that disease is a limiting factor to the aquaculture industry together with the knowledge that drugs and chemotherapeutics can cause newly resistant bacterial strains, has driven attention to finding new prophylactic measures to control diseases that include vaccination and the use of “functional feeds” to modulate the fish immune system. The supplementation of immunostimulants into fish diets is already widely used in aquaculture. However, searching for new and effective substances is one of the targets of many fish feed suppliers, including EWOS Ltd. who have co-funded the work presented in this study. There are a number of immunostimulant molecules used at present. Some bacterial components such as LPS are used to enrich fish diets and have been described to improve the natural immune defences. In contrast, peptidoglycan (PG), another ubiquitous component of the bacterial cell wall, has so far received less attention and is therefore investigated in this present study. Its ability to stimulate innate immunity is assessed using antimicrobial peptides (AMPs) as molecular markers, which are known to be involved in the early response against a broad range of pathogens. To date, AMPs in fish are not well characterised and in most cases the mechanisms of pathogen killing as well as the pathways inducing their expression still remain to be elucidated. Initially the cloning and characterisation of three novel trout β-defensin genes (omDB-2, omDB-3, omBD-4) was performed, and the molecules compared to the previously reported omDB-1. Each β-defensin gene was fully cloned and preliminary expression work in vivo and in vitro revealed the ability of these genes to be induced by bacteria and viruses. Analysis of the gene organization found that all three new genes contained three exons divided by two introns. Constitutive expression of these genes was detected by real time PCR ofmucosal and systemic tissues from healthy fish, with omDB-3 and omDB-4 showing the highest expression levels. Following bacterial challenge in vivo, the defensin genes were induced at the three mucosal sites examined (skin, gill, gut), with levels of omDB-2 and omDB-3 increased some 16-fold in gut and gill respectively. Using polyinosinic polycytosinic RNA (polyI:C) as a viral mimic, all of the four trout -defensin genes were induced in head kidney primary leucocyte cultures at 4h post-stimulation, with omDB-1 and omDB-3 showing particularly high expression. To determine the -defensin spectrum of activity against 10 strains of Gram negative and Gram positive bacteria, transfected RTG-2 cell lines over expressing GFP and the target genes omDB-1, omDB-3 and omDB-4 -defensins were produced and their supernatants used. Results showed highest bioactivity against Gram negative bacteria, in particular the supernatant from omDB-1 transfected cells showed the widest range of activity towards the majority of selected bacteria. In addition immune relevant genes (Toll-like receptors, genes involved in the anti-inflammatory response and in the apoptosis process) were screened in normal cell lines stimulated with the supernatant of omDB-1, as well as in the RTG-2 cells transfected with the three different defensins. Results showed for all the cell lines, a clear link with the viral recognition receptors TLR 3 and TLR 9, which supported the poly I:C data reported in Chapter 2 and by the induction in omDB-1 and omDB-3 transfected cell lines of the IFN- gene known to be involved in the antiviral response. Trout β-defensins also up-regulated MHC II and the CCR6 receptor. To determine the effects of fish diets enriched with different concentrations of PG, three in vivo feeding trial experiments in rainbow trout were carried out. Effectiveness of the diets was assessed using gene expression of selected AMPs, including β-defensins, cathelicidins and liver expressed antimicrobial peptide molecules. Fish fed with diets containing either 10 mg/Kg or 50 mg/Kg of PG respectively, showed the highest up-regulation of AMPs at 14 days of feeding. Data showed omDB-2 in the gut as the most inducible gene in agreement with the results obtained in the first experiment and omDB-3 was the fastest to respond in skin and gill. In addition, after ceasation of feeding the enriched diet, modulation of AMP expression was still detectable 28 days later, although a lower degree of induction was found in such fish relative to those maintained on the enriched diet. A final PG feeding trial was combined with a Yersinia ruckeri bacterial challenge which used two PG supplemented diets containing 10 mg/Kg and 50 mg/Kg of immunostimulant, and a commercial β-glucan supplemented diet (as a positive control), and fed to trout for 7 and 14 days before intraperitoneal injection challenge of the fish. Only a delay in the mortality rate was found in fish fed for 14 days with the 10 mg/Kg diet, with no clear protection from any of the functional feeds assessed. Finally, at least 500 bp of the regulatory 5’ end flanking region of two defensin (omDB-1 and omDB-2) and two liver expressed (hepcidin and LEAP-2A) genes were cloned and sequenced. In addition, the promoter sequence already known for the cathelicidin-1 gene was used in this study. Bioinformatic tools were used to search for putative transcription factor binding sites, and revealed the presence in all promoters of regulatory elements which could enhance or inhibit the expression of these genes, in response to different stimuli.

Most aquaculture tenures in British Columbia (BC) are located in coastal First Nation traditional territories, making the aquaculture industry very important to First Nation communities. Marine aquaculture, in particular salmon farming, has been labeled one of the most controversial industries in BC and various groups with differing opinions have created a wide-spread media debate known as the “aquaculture controversy”. Industry, government, and (E)NGO’s are often the most visible players; First Nations, especially those without aquaculture operations directly in their territories, are often excluded or underrepresented in the conversation. In particular, remote communities from the central and north coast are significantly underrepresented. Aquaculture is predicted to expand in BC, making it crucial to know the opinions of these communities. By drawing on twelve key informant interviews conducted in situ in three central and north coast First Nation communities, as well as other literatures and discourses, this thesis explores the aquaculture controversy and perspectives towards finfish, shellfish, seaweed and Integrated Multi-Trophic Aquaculture (IMTA) systems. The thesis suggests that there is little interest in salmon aquaculture in the communities of Oweekeno, Skidegate and Massett; however there is significant interest in shellfish farming and to a lesser extent seaweed and IMTA. It also sheds light on the major issues and concerns of the current industry and potential interest areas in-line with First Nation values. In doing so, the current research contributes to the knowledge mobilization of First Nation perspectives towards coastal aquaculture in BC. / Graduate / 0366 / ktebbutt@uvic.ca

Most aquaculture tenures in British Columbia (BC) are located in coastal First Nation traditional territories, making the aquaculture industry very important to First Nation communities. Marine aquaculture, in particular salmon farming, has been labeled one of the most controversial industries in BC and various groups with differing opinions have created a wide-spread media debate known as the “aquaculture controversy”. Industry, government, and (E)NGO’s are often the most visible players; First Nations, especially those without aquaculture operations directly in their territories, are often excluded or underrepresented in the conversation. In particular, remote communities from the central and north coast are significantly underrepresented. Aquaculture is predicted to expand in BC, making it crucial to know the opinions of these communities. By drawing on twelve key informant interviews conducted in situ in three central and north coast First Nation communities, as well as other literatures and discourses, this thesis explores the aquaculture controversy and perspectives towards finfish, shellfish, seaweed and Integrated Multi-Trophic Aquaculture (IMTA) systems. The thesis suggests that there is little interest in salmon aquaculture in the communities of Oweekeno, Skidegate and Massett; however there is significant interest in shellfish farming and to a lesser extent seaweed and IMTA. It also sheds light on the major issues and concerns of the current industry and potential interest areas in-line with First Nation values. In doing so, the current research contributes to the knowledge mobilization of First Nation perspectives towards coastal aquaculture in BC. / Graduate / 0366 / ktebbutt@uvic.ca

nÃo hà / O extrativismo pesqueiro jà alcanÃou ou atà jà ultrapassou os limites de captura mÃxima sustentÃvel na maioria das pescarias no mundo. Ao mesmo tempo, o consumo de pescado per capta em nÃvel mundial vem aumentando cada vez mais. O problema à como aumentar a produÃÃo de pescado sem aumentar os esforÃos de pesca. A soluÃÃo pode ser a aqÃicultura, porÃm esta atividade deve ser realizada com inserÃÃo social, responsabilidade ambiental, viabilidade econÃmica e com uma boa governanÃa. No Brasil, a aqÃicultura vem se desenvolvendo bastante, especialmente nos reservatÃrios de Ãguas de domÃnio da UniÃo. Este trabalho se propÃs a analisar a sustentabilidade da aqÃicultura em Ãguas de domÃnio da UniÃo utilizando os parques aquÃcolas do reservatÃrio do CastanhÃo, no estado do Cearà como estudo de caso. Para isto, utilizou-se a elaboraÃÃo de um perfil socioeconÃmico de dois grupos de cessionÃrios (beneficiÃrio e controle), o que demonstrou a influÃncia positiva da piscicultura neste perfil. E elaborou-se subÃndices que englobaram as dimensÃes sociais, ambientais, institucionais (governanÃa) e econÃmicas de sustentabilidade; que por sua vez permitiram a construÃÃo do Ãndice de desenvolvimento sustentÃvel da aquicultura. Verificou-se que o sistema aquÃcola em questÃo obteve um resultado enquadrado como de mÃdia sustentabilidade. / The fisheries activity already reached or exceeded the limits of sustainable maximum capture in the majority of fisheries in the world. At the same time, the consumption of fish products in world-wide level comes more increasing each time. The problem is how to increase the fish production without increasing the fisheries efforts. The solution can be aquaculture, however this activity must be carried through with social insertion, environmental responsibility, economic viability and with a good governance. In Brazil, aquaculture have been a very good developing, specially in the water reservoirs of Union domain. This work had analyzed the sustentability of aquaculture in these waters using the aquÃcolas parks of the reservoir of CastanhÃo, in the state of Cearà as a case study. For this, it was used an elaboration of a socialeconomical profile of two groups of assignees (beneficiary and controll), what it demonstrated the positive influence of the fishculture in this profile. And it was elaborated subÃndexes that involves social, environmental, institucional (governance) and economic dimensions of sustentability; that had allowed the construction of the index of sustainable development of the aquaculture. It was verified that this aquaculture system in question got a result fit as of media sustentability.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Os potenciais impactos ambientais provenientes da aquicultura intensiva tÃm aumentado a preocupaÃÃo da sociedade quanto à sustentabilidade da prÃpria atividade. Com o presente trabalho teve como objetivo avaliar, os parÃmetros zootÃcincos das tilÃpias do Nilo, qualidade de Ãgua, produÃÃo de biomassa algal e taxa de remoÃÃo dos compostos nitrogenados pela microalga Spirulina platensis em um cultivo integrado da tilÃpia do Nilo (Oreocrhomis niloticus) com a microalga S. platensis em um sistema fechado de circulaÃÃo de Ãgua. O experimento foi realizado no Centro de Biotecnologia Aplicada a Aquicultura (CEBIAQUA) do Departamento de Engenharia de Pesca da Universidade Federal do CearÃ. O cultivo das tilÃpias foi inteiramente casualizado e realizado em trÃs tratamentos com quatro repetiÃÃes nas densidades de 0,1; 0,15 e 0,20 juvenis L-1. As tilÃpias foram alimentadas ad libitum com raÃÃo comercial (0.8 mm), contendo 55% de proteÃna bruta (PB), fornecida Ãs 9, 13 e 17 h, sete dias por semana. Para o cultivo de Spirulina platensis, inicialmente, o inÃculo foi cultivado em meio quÃmico alternativo e posteriormente adaptado ao efluente de tilÃpia do Nilo e inoculado em 12 bacias de polietileno. Durante todo o experimento, a Ãgua das caixas dos peixes e das respectivas bacias das microalgas foi reutilizada no sistema de recirculaÃÃo fechado entre as duas culturas, havendo apenas reposiÃÃo de Ãgua por conta da evaporaÃÃo. ApÃs o completo desenvolvimento da S. platensis nas bacias, a coleta da microoalga foi realizada atravÃs de filtragem da Ãgua em telas de 60 Âm. Foram ainda monitorados o pH, temperatura, oxigÃnio dissolvido, bem como determinados os nÃveis de N-amÃnia, N-nitrato e N-nitrito durante o perÃodo experimental. Os resultados mostraram que a densidade de estocagem mais eficiente para o cultivo das tilÃpias foi 0,10 juvenis L-1, pois apesar de ter resultado na mesma biomassa final dos demais tratamentos, foi a que apresentou a menor taxa de conversÃo alimentar. A microalga S. platensis se adaptou facilmente e se desenvolveu muito bem no efluente das tilÃpias do Nilo, independente da densidade de estocagem dos peixes. Com relaÃÃo à qualidade de Ãgua, foi evidenciado que a integraÃÃo das culturas manteve os nÃveis de N-amÃnia (0,26  0,03 mg L-1), N-nitrato (2,55  0,71) e N-nitrito (0,19  0,01) dentro dos valores aceitÃveis para o cultivo da tilÃpia do Nilo. / The environmental potential impacts from intensive aquaculture have increased public concern about the sustainability of the activity itself. The present work aimed to evaluate the zootÃcincos parameters of Nile tilapia , water quality, algal biomass production and rate of nitrogen removal compounds by Spirulina platensis realize an integrated cultivation of Nile tilapia (Oreocrhomis niloticus) with Spirulina platensis in a closed system of water circulation. The experiment took place at the Biotechnology Aquaculture Applied Center (CEBIAQUA) of The Fishing Engineering Department of the Federal University of CearÃ. Tilapias culture was conducted in three treatments with four replicates at densities of 010, 0,15 and 0,20 juveniles L-1. The tilapias were fed ad libitum with a commercial ration (0,8 mm) containing 55% crude protein (CP), administered daily at 9, 13 and 17 h. For Spirulina platensis culture, initially, the inoculum was cultivated in an alternative chemical medium and later adapted to the Nile tilapia effluent and inoculated into 12 polyethylene basins. Throughout the experiment, the water of fishes boxes and of the respective microalgae basins was reused in the closed recirculation system between the two cultures, with only replacement of water due to evaporation. After the full development of S. platensis in the basins, the microalgae was collected using a 60 Âm screen. The pH, temperature, dissolved oxygen, and levels of N-ammonia, N-nitrate and N-nitrite were also monitored during all the experimental period. The results showed that the most efficient stocking density was 0,10 L-1, because despite having the same final biomass of the other treatments it presented the lowest feed conversion ratio. The microalgae S. platensis was easily adapted and developed very well in the Nile tilapiaâs effluent, regardless of fishes stocking density. With respect to water quality, it was evident that the cultures integration maintained the levels of N-ammonia (0,26  0,03 mg L-1), N-nitrates (2,55  0,71 mg L-1) and N- nitrites (0,19  0,01 mg L-1) within acceptable values for the Nile tilapia culture.

There has been a long history of attempts to promote subsistence rural aquaculture within South Africa. Many of these attempts have failed due to inadequate support from government and support agencies. There has been a recent revived interest in promoting rural aquaculture development. Presented in this project are six scenarios demonstrating the potential application of thermal modelling techniques to improving subsistence rural aquaculture. These scenarios were based on a model validated against a real life system, and run with environmental data for the year 2005. Bovine manure, grass thatch, cereal straw and Typha spp. water reeds were tested for thermal performance. These results were then applied to the scenarios. The open and kraal enclosed pond scenarios yielded the widest deviation in temperatures throughout the year, with an average temperature of 3.8oC and 6.0oC above ambient and a temperature range of 10.6oC and 12.4oC for the year respectively. Eliminating solar radiation and reducing wind speed resulted in an average difference of 1.5oC below ambient and a temperature range of 7.5oC for the year. When completely enclosed in a well-sealed traditional Xhosa style hut, the pond had an average difference of 5.6oC below outside ambient temperature, with a range of 7.8oC for the year. A passive solar heating scenario added to the sealed hut scenario, which when run continuously maintained an average difference of 34.7oC above outside ambient temperatures, with a range of 56oC for the year. When a hypothetical 25oC temperature control was included in the model, the system maintained an average of 7.1oC above ambient outside temperatures, with a temperature range of 0.8oC throughout the year. The wider range of temperatures made available through the use of thermal modelling approaches provides a more diverse range of species available for subsistence rural aquaculture at any site, significantly improving its potential.

Over the last three decades there has been a significant increase in aquaculture production and the demand for farmed fish is predicted to rise further. More fish are being caught to become fishmeal in aquaculture, than for direct human consumption use, while a large number of fish stocks are being depleted. Many popular farmed species are carnivores and thus brought up on a diet consisting of fishmeal and fish oil. However, several studies have shown that several fish species can be brought up on a diet consisting of mussel meal instead of fishmeal. If so, this finding can possibly lead to a more sustainable fishing in the future by reducing the number of wild-caught fish. The purpose of this study has been to examine if mussel meal extract can induce foraging in the omnivorous species crucian carp (Carassius carassius), a commercial fish that is mainly farmed in China. Induced foraging can indicate that crucian carp could become accustomed to mussels, even though mussels are not part of its natural food source. The results revealed that foraging was induced in the crucian carp by conventional feed for carp, the control diet, but not by extract of mussels. / Vattenbruket har ökat markant under de senaste tre decennierna och idag går mer fisk till foderproduktion för fiskodlingar än vad som konsumeras direkt av människan. Detta är problematiskt då många fiskbestånd är utarmade, samtidigt ökar efterfrågan på fisk. Många populära matfiskar är rovfiskar som huvudsakligen matas med fiskbaserat foder. Ett flertal studier har emellertid visat att flera fiskarter potentiellt kan födas upp på blåmusslor (Mytilus edulis) istället för fiskbaserat foder. Foder som huvudsakligen baseras på musslor kan därför i framtiden möjligen bidra till att minska överexploatering av fisk. Denna studie undersökte om musselextrakt kan inducera ett födosök hos omnivoren ruda (Carassius carassius), som idag odlas och används som matfisk framförallt i Kina. I så fall kan det indikera att ruda möjligen kan vänjas vid musslor, trots att det inte ingår i fiskens naturliga föda. Resultaten i studien visade att ett födosök inducerades hos ruda gentemot extrakt av vanligt karpfoder, kontrollsubstansen, men inte gentemot musselextrakt.