The conservation of biodiversity and endemism in South Africa’s freshwater aquatic ecosystems is a high priority, particularly in the Cape Floristic Region. However, the perception that South Africa lacks suitable fish species for recreational angling, aquaculture and biological control, led to the widespread introduction and use of alien fish species. As a result, formal stocking programs have seen the introduction of five of the world’s top 100 invasive species into South Africa (Dudgeon et al. 2006). According to Dudgeon et al. (2006) freshwater ecosystems are the most endangered ecosystem in the world. The threats to freshwater biodiversity, according to Dudgeon et al. (2006), can be grouped into five categories that interact with one another: overexploitation, water pollution, flow modifications, destruction of habitat and invasion by exotic species. This PhD study took place in the Amatola region of the Eastern Cape Province, South Africa. The Amatola region is a rural area with no large-scale mining or industrial developments, only localised settlements. These developments are mainly situated around impoundments, because of the resources such as water and food that they provide. Thus the dams within the Amatola region should theoretically have no major industrial stressors on them. The three impoundments studied were Binfield Park, Sandile and Wriggleswade Dams. Binfield Park Dam is a 260ha impoundment. It impounds the Tyume River and is used by both subsistence anglers from the local communities and occasionally by recreational bass anglers. Sandile Dam is a 146ha impoundment and is the smallest of the three dams in this study. It impounds the Wolf and Keiskamma Rivers. Wriggleswade Dam is a 1000ha impoundment used extensively by recreational bass and carp anglers, and impounds the Kubusi River. There is a paucity of information regarding the health of the indigenous and alien fish species from the study region, as well as on the parasite diversity of these various fish species. In order to fill the gaps in the information the following hypothesis was proposed. That the necropsy based and histology based fish health assessment can be successfully implemented as tools to assess the effects of heavy metal pollution and alien fish parasites in freshwater fish from selected impoundments in the Amatola region, Eastern Cape Province, South Africa. In order to achieve this hypothesis the main aim of this study will be to use the necropsy- and histology- based fish health assessment to determine the health status of the fish species in these impoundments as well as to understand the potential threat of water pollution and fish parasites. Fish were sampled with the aid of gill nets, fyke nets and by angling from each of the three impoundments over three surveys in July 2011, and March and August 2012. Following capture fish were transported to a field laboratory in aerated containers. At the field laboratory the fish were examined and dissected using the methods recommended by Adams et al. (1993) for a necropsy-based fish health assessment. Gills, livers, kidneys and gonads samples were also collected for histological analysis. Macroscopic and histology-based fish health assessment index was used, as well the analysis of muscle tissue of Micropterus salmoides and surface water and sediment from Binfield Park, Sandile and Wriggleswade Dams. It was shown that, according to the macroscopic fish health assessment index, M. salmoides in Wriggleswade Dam had a higher FHAI score compared to those in Binfield Park and Sandile Dam, there were no significant differences between the FHAI scores. However, the cause of the higher FHAI in the Wriggleswade Dam was because of the external skin damage caused by the presence of the alien parasite Lernaea cyprinacea. The histology-based fish health assessment index, however, showed that M. salmoides from Binfield Park had significantly higher histology Fish Index (IFISH) scores compared to those in Sandile and Wriggleswade Dams. The main contributors to the high IFISH score of Binfield Park were the significantly high Liver Index (IL) and Kidney Index (IK). The increased severity of the alterations observed in the liver and kidney tissue of the Binfield Park M. salmoides samples may have been as a result of the high concentration of mercury found in the muscle tissue of M. salmoides. The water quality and metals detected in the water of Binfield Park, Sandile and Wriggleswade Dams were all below the target water quality guideline values, as well as below those of previous research into the nutrients and presence of metals in these impoundments. The sediment metal analysis showed that the levels of Co, Mn and Ni were above the target guideline levels for Binfield Park, Sandile and Wriggleswade Dams, Cu was above target guidelines levels for Sandile Dam, and uranium was above the target guideline concentrations for Wriggleswade Dam. Binfield Park Dam had significantly high levels of mercury in the muscle tissue of M. salmoides, while Sandile Dam had significantly high levels of zinc in the muscle tissue of M. salmoides. It was shown that M. salmoides from each of the three impoundments are in a healthy state according to the parameters assessed. However, the presence of heavy metals, particularly mercury, uranium and zinc, do indicate the presence of human activities. The indigenous parasites of Anguilla mossambica have been well documented including the gastrointestinal nematode Paraquimperia africana, and the stomach nematode Heliconema africanum. Indigenous parasites such as the swimbladder nematode Anguillicola papernai had no effect on the condition factor of infected and uninfected eels. However, the damage caused by the alien parasites were evident, including the first documented effects of the alien gill monogenean Pseudodactylogyrus anguillae on indigenous wild populations of the longin fin eel A. mossambica from the Eastern Cape, South Africa. Histological observations indicated that an alien gill monogenean caused hyperplasia, increase in mucous cells, rupture of pillar cells as well as telangiectasia. This alien parasite has invaded the Keiskamma and Kei River systems in the Eastern Cape, South Africa. According to the macroscopic fish health assessment index, A. mossambica from Binfield Park, Sandile and Wriggleswade Dams are in a healthy state. However, the histology-based health assessment highlighted that the effects on P. anguillae have a severe negative impact on the health of A. mossambica. Using the macroscopic and histology-based fish health assessment, a comprehensive investigation into the fish health status of Mugil cephalus and Myxus capensis from Binfield Park Dam revealed that human effects and parasites are not the only threats to freshwater fish. Nephrocalcinosis is a non-infectious kidney disease which is characterised by abnormal calcium deposition in the kidneys of humans and some fish species. According to the macroscopic and histology-based fish health assessment, the M. cephalus and M. capensis are not in a healthy condition. The macroscopic and histology-based fish assessment indices are not stressor-specific, and therefore the cause of the poor health state of these two fish species could not be determined. A possible suggestion for the poor health of these two species is the age of the species. Because the two mullet species were stocked into Binfield Park Dam, Ellender et al. (2012) could successfully age them accurately to ten years of age, which is the upper limit of the life span for these species. Macroscopic and histology-based fish heath assessments were conducted on Labeo umbratus from Sandile Dam in order to determine the health of this species. Macroscopic and histology-based fish health assessment indicated that its L. umbratus are in a healthy state. The March 2012 survey specimens had a significantly higher macroscopic FHAI score than those from the July 2011 survey. The increased FHAI score was because of parasite infections, as well as discoloured livers and increased total blood plasma protein levels, which are indicators of nutritional state. However, the presence of the anchor worm parasite Lernaea barnimiana in low numbers had no significant impact on the health of L. umbratus. The effect of the alien anchor worm parasite Lernaea cyprinacea was shown on the transloacted small mouth yellowfish Labeobarbus aeneus. It was also shown that L. aeneus are, according the macroscopic FHAI and the histology-based fish health assessment index, in a healthy state. However, the high scores observed in the macroscopic fish health assessment index were primarily as a result of the presence of the alien parasite L. cyprinacea and its associated affects on the fish host. Because of the significant impact of this alien parasite species on the translocated host species, it can be assumed that this alien parasite species will have a negative effect on the health of indigenous fish species in the Great Kei River. It is clear from the results presented in this study that the necropsy based and histology based fish health assessment can be successfully implemented as tools to assess the effects of heavy metal pollution and alien fish parasites in freshwater fish from selected impoundments in the Amatola region, Eastern Cape Province, South Africa, thus the original hypothesis of this thesis is accepted. Based on work done in this research the gaps in research have been identified. Due to the high levels of mercury indentified in the muscle tissue of M. salmoides from Binfield Park Dam. A human health assessment and edibility should be conducted in order to determine if the fish from Binfield Park Dam is safe for human consumption. In order to conserve South Africa’s Freshwater fish biodiversity, country wide surveys of indigenous fish species must be undertaken so that the health and the parasite diversity can be evaluated. / PhD (Zoology), North-West University, Potchefstroom Campus, 2015

The conservation of biodiversity and endemism in South Africa’s freshwater aquatic ecosystems is a high priority, particularly in the Cape Floristic Region. However, the perception that South Africa lacks suitable fish species for recreational angling, aquaculture and biological control, led to the widespread introduction and use of alien fish species. As a result, formal stocking programs have seen the introduction of five of the world’s top 100 invasive species into South Africa (Dudgeon et al. 2006). According to Dudgeon et al. (2006) freshwater ecosystems are the most endangered ecosystem in the world. The threats to freshwater biodiversity, according to Dudgeon et al. (2006), can be grouped into five categories that interact with one another: overexploitation, water pollution, flow modifications, destruction of habitat and invasion by exotic species. This PhD study took place in the Amatola region of the Eastern Cape Province, South Africa. The Amatola region is a rural area with no large-scale mining or industrial developments, only localised settlements. These developments are mainly situated around impoundments, because of the resources such as water and food that they provide. Thus the dams within the Amatola region should theoretically have no major industrial stressors on them. The three impoundments studied were Binfield Park, Sandile and Wriggleswade Dams. Binfield Park Dam is a 260ha impoundment. It impounds the Tyume River and is used by both subsistence anglers from the local communities and occasionally by recreational bass anglers. Sandile Dam is a 146ha impoundment and is the smallest of the three dams in this study. It impounds the Wolf and Keiskamma Rivers. Wriggleswade Dam is a 1000ha impoundment used extensively by recreational bass and carp anglers, and impounds the Kubusi River. There is a paucity of information regarding the health of the indigenous and alien fish species from the study region, as well as on the parasite diversity of these various fish species. In order to fill the gaps in the information the following hypothesis was proposed. That the necropsy based and histology based fish health assessment can be successfully implemented as tools to assess the effects of heavy metal pollution and alien fish parasites in freshwater fish from selected impoundments in the Amatola region, Eastern Cape Province, South Africa. In order to achieve this hypothesis the main aim of this study will be to use the necropsy- and histology- based fish health assessment to determine the health status of the fish species in these impoundments as well as to understand the potential threat of water pollution and fish parasites. Fish were sampled with the aid of gill nets, fyke nets and by angling from each of the three impoundments over three surveys in July 2011, and March and August 2012. Following capture fish were transported to a field laboratory in aerated containers. At the field laboratory the fish were examined and dissected using the methods recommended by Adams et al. (1993) for a necropsy-based fish health assessment. Gills, livers, kidneys and gonads samples were also collected for histological analysis. Macroscopic and histology-based fish health assessment index was used, as well the analysis of muscle tissue of Micropterus salmoides and surface water and sediment from Binfield Park, Sandile and Wriggleswade Dams. It was shown that, according to the macroscopic fish health assessment index, M. salmoides in Wriggleswade Dam had a higher FHAI score compared to those in Binfield Park and Sandile Dam, there were no significant differences between the FHAI scores. However, the cause of the higher FHAI in the Wriggleswade Dam was because of the external skin damage caused by the presence of the alien parasite Lernaea cyprinacea. The histology-based fish health assessment index, however, showed that M. salmoides from Binfield Park had significantly higher histology Fish Index (IFISH) scores compared to those in Sandile and Wriggleswade Dams. The main contributors to the high IFISH score of Binfield Park were the significantly high Liver Index (IL) and Kidney Index (IK). The increased severity of the alterations observed in the liver and kidney tissue of the Binfield Park M. salmoides samples may have been as a result of the high concentration of mercury found in the muscle tissue of M. salmoides. The water quality and metals detected in the water of Binfield Park, Sandile and Wriggleswade Dams were all below the target water quality guideline values, as well as below those of previous research into the nutrients and presence of metals in these impoundments. The sediment metal analysis showed that the levels of Co, Mn and Ni were above the target guideline levels for Binfield Park, Sandile and Wriggleswade Dams, Cu was above target guidelines levels for Sandile Dam, and uranium was above the target guideline concentrations for Wriggleswade Dam. Binfield Park Dam had significantly high levels of mercury in the muscle tissue of M. salmoides, while Sandile Dam had significantly high levels of zinc in the muscle tissue of M. salmoides. It was shown that M. salmoides from each of the three impoundments are in a healthy state according to the parameters assessed. However, the presence of heavy metals, particularly mercury, uranium and zinc, do indicate the presence of human activities. The indigenous parasites of Anguilla mossambica have been well documented including the gastrointestinal nematode Paraquimperia africana, and the stomach nematode Heliconema africanum. Indigenous parasites such as the swimbladder nematode Anguillicola papernai had no effect on the condition factor of infected and uninfected eels. However, the damage caused by the alien parasites were evident, including the first documented effects of the alien gill monogenean Pseudodactylogyrus anguillae on indigenous wild populations of the longin fin eel A. mossambica from the Eastern Cape, South Africa. Histological observations indicated that an alien gill monogenean caused hyperplasia, increase in mucous cells, rupture of pillar cells as well as telangiectasia. This alien parasite has invaded the Keiskamma and Kei River systems in the Eastern Cape, South Africa. According to the macroscopic fish health assessment index, A. mossambica from Binfield Park, Sandile and Wriggleswade Dams are in a healthy state. However, the histology-based health assessment highlighted that the effects on P. anguillae have a severe negative impact on the health of A. mossambica. Using the macroscopic and histology-based fish health assessment, a comprehensive investigation into the fish health status of Mugil cephalus and Myxus capensis from Binfield Park Dam revealed that human effects and parasites are not the only threats to freshwater fish. Nephrocalcinosis is a non-infectious kidney disease which is characterised by abnormal calcium deposition in the kidneys of humans and some fish species. According to the macroscopic and histology-based fish health assessment, the M. cephalus and M. capensis are not in a healthy condition. The macroscopic and histology-based fish assessment indices are not stressor-specific, and therefore the cause of the poor health state of these two fish species could not be determined. A possible suggestion for the poor health of these two species is the age of the species. Because the two mullet species were stocked into Binfield Park Dam, Ellender et al. (2012) could successfully age them accurately to ten years of age, which is the upper limit of the life span for these species. Macroscopic and histology-based fish heath assessments were conducted on Labeo umbratus from Sandile Dam in order to determine the health of this species. Macroscopic and histology-based fish health assessment indicated that its L. umbratus are in a healthy state. The March 2012 survey specimens had a significantly higher macroscopic FHAI score than those from the July 2011 survey. The increased FHAI score was because of parasite infections, as well as discoloured livers and increased total blood plasma protein levels, which are indicators of nutritional state. However, the presence of the anchor worm parasite Lernaea barnimiana in low numbers had no significant impact on the health of L. umbratus. The effect of the alien anchor worm parasite Lernaea cyprinacea was shown on the transloacted small mouth yellowfish Labeobarbus aeneus. It was also shown that L. aeneus are, according the macroscopic FHAI and the histology-based fish health assessment index, in a healthy state. However, the high scores observed in the macroscopic fish health assessment index were primarily as a result of the presence of the alien parasite L. cyprinacea and its associated affects on the fish host. Because of the significant impact of this alien parasite species on the translocated host species, it can be assumed that this alien parasite species will have a negative effect on the health of indigenous fish species in the Great Kei River. It is clear from the results presented in this study that the necropsy based and histology based fish health assessment can be successfully implemented as tools to assess the effects of heavy metal pollution and alien fish parasites in freshwater fish from selected impoundments in the Amatola region, Eastern Cape Province, South Africa, thus the original hypothesis of this thesis is accepted. Based on work done in this research the gaps in research have been identified. Due to the high levels of mercury indentified in the muscle tissue of M. salmoides from Binfield Park Dam. A human health assessment and edibility should be conducted in order to determine if the fish from Binfield Park Dam is safe for human consumption. In order to conserve South Africa’s Freshwater fish biodiversity, country wide surveys of indigenous fish species must be undertaken so that the health and the parasite diversity can be evaluated. / PhD (Zoology), North-West University, Potchefstroom Campus, 2015

The goal of the research conducted in this dissertation was to define and test methods to incorporate oil spill effects into an ecosystem-based assessment model. It was instigated by the Deepwater Horizon oil spill, an unprecedented oil spill in the United States for both depth and volume, with unknown implications for the health of the region. Using an ecosystem-based assessment model like Atlantis, with integrated oil spill dynamics, was the ideal candidate to predict long-term impacts such as decreased abundance or population recovery time. However no previous methodology existed for doing so in any ecosystem-based assessment model. Therefore, first I conducted a literature review to gather data across fish species on lesion frequency and fish body growth impacts from oil exposure. The two data sets were then fitted to four different dose-response models, and an effect threshold log-linear “hockey-stick” model was selected as the best fit and most parsimonious for both lesions and growth. Next, I conducted a similar analysis comparing macrofaunal and meiofaunal abundances to oil exposure concentrations in the Gulf of Mexico collected after Deepwater Horizon. I confirmed that these data had the domed relationship between invertebrate abundances and oil concentration observed in previous invertebrate oil studies. This domed relationship indicates that abundance increases at low to moderate oil levels, and declines at high oil levels. To drive this relationship in an Atlantis ecosystem model, three scenarios were tested in combination with oil toxicity: 1) Mississippi nutrient loading, 2) increased detritus from marine oil snow sedimentation and flocculent accumulation, and 3) predators altering their behavior to avoid oil exposure. At the Atlantis polygon resolution, only scenario 2, increased detritus from marine oil snow sedimentation and flocculent accumulation, generated the domed relationship for invertebrate abundances. Lastly, the “hockey-stick” model for fish mortality and growth was applied to both fishes and invertebrates in combination with scenario 2 for an integrated long-term assessment of the Gulf of Mexico. Newly available fish exposure data were used to generate an uptake-depuration model for this assessment. The combined effect forcings on vertebrates and invertebrates proved to have more severe long-term implications on population size and recovery than simulations with only fish forcings. Large demersal fishes, including elasmobranchs, were the most severely impacted by large biomass declines in the model spill region. Sensitivity analyses indicated that there was the potential for no recovery during 50 years of simulation in the spill region for many functional groups. Analysis of the synergy between fishing mortality F and toxicity from an oil spill identified that some guilds are more sensitive in an oil spill simulation to varied F than others. Snappers are the most sensitive to increased fishing mortality, while groupers respond the most to a reduction in fishing mortality. The invertebrate guild and small pelagic fishes responded the least to different values of F. Changing F also had implications for guild recovery – some guilds only fully recovered to control scenario biomass when F was reduced. A few functional groups were unable to survive with the combined effects of oil toxicity and increased F, and went extinct before the end of the 50-year simulation. Overall, this work provided the first framework for initial integrated modeling of oil spill impacts in an ecosystem-based assessment model, a potentially important component to future ecosystem-based fisheries management. The “hockey-stick” dose response model is applicable beyond Atlantis modeling, and can be tuned to fit specific events based on available data. I have also identified the importance of including marine oil snow sedimentation and flocculent accumulation to accurately drive the response of benthic invertebrates. Findings from the combined vertebrate and invertebrate simulations should help inform research efforts in the Gulf of Mexico and future oil spill response efforts.

To assess anthropogenic impacts of point-source and diffuse discharges on fish populations of the Waikato River, compare responses to different discharges and identify potential sentinel fish species, we sampled wild populations of brown bullhead catfish (Ameiurus nebulosus, (LeSueur, 1819)), shortfin eel (Anguilla australis Richardson, 1848), and common bully (Gobiomorphus cotidianus McDowall, 1975) in the Waikato River. Sites upstream and downstream of: geothermal; bleached kraft mill effluent (BKME); sewage and thermal point-source discharges were sampled. At each site, the population parameters, relative abundance, age structure and individual indices such as: condition factor; and organ (gonad, liver, and spleen) somatic weight ratios; and number and size of follicles per female were assessed. Indicators of fish residence and in some cases exposure to contaminants in discharges were analyzed. Bile chemistry of brown bullhead and shortfin eel was assayed, liver and muscle metal levels were analyzed for brown bullhead and shortfin eel respectively, and stable isotopes of C and N in common bully were measured. Bile, metal and isotopic signatures gave strong evidence that fish had been resident at sites for some time before sampling. Signatures of bile and metal contaminants showed contamination was localised to discharge areas. Gradients in stable isotopes in common bully showed evidence of changes in water sources and anthropogenic effects along the river. Biochemical variables, hepatic ethoxyresorufin-O-deethylase (EROD) and plasma steroids indicated exposure and response of brown bullhead and shortfin eel to pulp and paper contaminants at the BKME site. Physiological (blood) variables showed fish largely responded in a predictable way to elevated water temperatures at discharge sites at time of sampling, however total haemoglobin of brown bullhead and common bully blood failed to increase at the BKME site despite elevated temperatures and low dissolved oxygen. Growth rates, condition factor, age structure, and gonadosomatic index (GSI) suggest that discharges with significant heat or nutrients benefit brown bullhead despite physiological impairment at the BKME site. Shortfin eel individuals also benefited from heated water discharges. No consistent impacts on common bully health were obvious at individual discharge sites, or cumulatively along the river due to the gradual deterioration in water quality downstream. Common bully individuals also benefited from heat in discharges but lack of juveniles at sites where numerous juvenile brown bullhead were found, suggest that unlike brown bullhead populations, common bully populations were not responding with significant recruitment. Although I found little evidence of toxic effects of discharges on shortfin eel, caution is required in assessing the potential of contaminants to impact eel populations due to the life history of shortfin eel, and exploited nature of populations. For example, reproductive damage suffered by adult eels may not immediately manifest itself in the effected population due to temporal delays in gonadal maturation, and recruitment, and single panmictic populations supplementing recruitment of impacted populations. Distinct changes in population parameters at each of the paired sites and changes in individual variables showed that fish responded to discharges. The range of responses in species suggests different sensitivity to contaminants and amount of benefit which each species receives from heat in discharges. In these terms shortfin eel would be the most resistant, then brown bullhead and lastly common bully. Interpretation of population-level impacts at the geothermal and BKME discharge sites is made difficult due to benefits of additional heat. There is also the possibility that detection of sub-lethal or chronic effects on sensitive juvenile life-stages may be being hidden by compensatory density population responses. Responses and life history of common bully made them the preferred indicator species of the three species sampled, and supported overseas examples using small-bodied fish species as sentinels.

In aquaculture worldwide, diseases are a significant constraint to economic expansion. The Scottish salmonid industry has experienced many cycles of development, with episodes of little or negative profitability caused by excess of production, and times of crisis due to different disease problems. In Scotland, the early implementation of regulation largely contributed to the control of infectious disease outbreaks. The recent Chilean outbreak of infectious salmon anaemia (ISA) illustrated the threats and the impacts of disease in the aquaculture industry and the importance of implementing good regulation and husbandry practices to reduce the impact of the spread of infectious disease. Databases of site production data have an important role to play in the investigation and understanding of diseases. They store valuable data collected during the time of production, which are essential for the identification of potential health and production problems during the production cycle of farmed fish. Mortality records are one of the most important sources of information on a farm, especially if it includes the cause of death as deformities, predators and diseases. Any deviation from the expected levels of mortality may indicate production problems, infectious diseases, or inadequate welfare. The investigation of increased rates of mortality must include examining farm records, determining the influence of death rate on production and the potential risk factors of diseases in a farm. This project demonstrated the importance of mortality records for setting industry standards of “expected” mortality losses and for investigating the value of recorded mortalities as a tool for aiding in surveillance and control of infectious diseases. It also aimed to determine the utility of reported mortality in supporting and assisting management-strategy decisions at the farm and industry level. In this project, we developed a baseline benchmark curve for expected mortality losses for Atlantic salmon in seawater. This novel approach constitutes a first attempt to establish a baseline curve for normal mortality, which allows detection of potential production problems based on deviations of mortality from the baseline curve of normal mortality. The results of this study also indicated that mortality levels may vary across production cycles, which can again be identified by using the baseline. We found that site was the factor with the highest contribution to variance in mortality. This site-to-site variation in mortality may have resulted from epidemics and environmental incidents, or other local event/effects. Temperature, and/or geographical area were also characteristics that contribute to variation in mortality. The regulator, Marine Scotland Science, with the backing and support of the salmonid industry has suggested potential mortality thresholds as an indicator of presence of infectious diseases, which could be used as alerts for inspection by the official authority. In this study, high mortality rates on fish farms were investigated as an indicator of the presence of infectious disease. The analysis was performed using several analytical approaches: receiver operating characteristic (ROC) curve analysis, measures of sensitivity and specificity, and bootstrap methods. The study was performed by splitting the production cycle into small fish with mean weight below 750 g and large fish with mean weight over 750 g. In the small fish, the results did not suggest reported mortality as a strong indicator of the presence of infectious disease, which may be caused by the lack of records of infectious disease at this stage of the production cycle. In the larger fish, high mortality rates were found to be a strong potential indicator of the presence of infectious diseases, including the suggested mortality threshold. In a survey, the role of traditional diagnosis in the prevention and control of disease outbreaks was assessed. For that, key informant interviews were performed with open questions to the health or farm manager of several trout and Atlantic salmon farms and we also used the diagnostic reports of the Veterinary Diagnostic Services (VDS) from Stirling University to triangulate the data. We showed that disease diagnoses are of great importance for disease identification and control of actual diseases. Farmer’s experience was also indicated as essential in the identification of the first signs of disease, which was principally through the daily monitoring of fish. This study suggested that disease diagnosis starts at the farm level with the daily monitoring of fish and the records of different parameters by the farmer, including mortality. Those records were showed to be vital to identify problems within the production. This thesis illustrated a novel approach to investigate and interpret recorded mortality at the farm level. The results presented in this thesis indicated reported mortality as a vital on-farm tool for identification of diseases and production problems. This thesis suggested priority areas where further investigation is required.

Orientador: Reinaldo José da Silva / Coorientador: Sérgio Henrique Canello Schalch / Banca: Eduardo Makoto Onaka / Banca: Maurício Laterça Martins / Resumo: O desenvolvimento das atividades relacionadas à aquicultura tem aumentado consideravelmente a relevância dos estudos sobre parasitas e outros patógenos de organismos aquáticos, principalmente, daqueles hospedeiros com potencial para o cultivo e comercialização. O objetivo deste estudo foi avaliar a ocorrência de infecções parasitárias e microbianas na produção de pacu Piaractus mesopotamicus e do híbrido "patinga" (P. mesopotamicus x Piaractus brachypomus) procedentes da região Noroeste do Estado de São Paulo, Brasil. Três pisciculturas foram amostradas bimestralmente, de fevereiro de 2010 a fevereiro de 2011: A - Reprodução e Larvicultura (pacu/patinga), B - Engorda (patinga) e C - Pesque-pague (pacu/patinga), das quais 35 peixes foram submetidos à análise parasitológica e 21 à análise microbiológica. Foram encontrados os parasitas: dactilogirídeos (Monogenea); Trichodina spp., Ichthyophthirius multifiliis, Chilodonella sp. (Protozoa); Myxobolus spp. e Henneguya spp. (Myxozoa); Rondonia rondoni e Contracaecum sp. (Nematoda); e Dolops carvalhoi (Crustacea). Dentre os peixes analisados, 62,9% de "A" e 100% de "B" e "C" estavam infectados/infestados por pelo menos uma espécie de parasita. Pacus (n=44) apresentaram maior suscetibilidade a infestações por Anacanthorus penilabiatus, e as patingas (n=61), por Mymarothecium viatorum (p<0,05). Na análise microbiológica, 23,8% dos peixes de "A" e "B" e 33,3% da propriedade "C" estavam infectados com pelo menos um gênero de bactéria. A sazonalidade influenciou as infestações por Trichodina spp., A. penilabiatus e infecções pela bactéria Enterobacter sp. em patingas (p<0,05). No antibiograma, cepas de Pseudomonas sp., Stenotrophomonas maltophilia e Aeromonas sp. apresentaram resistência a todos antibióticos... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The development of activities related to aquaculture has considerably increased the relevance of studies on parasites and other pathogens of aquatic organisms, especially those with potential for production and marketing. The aim of this study was to evaluate the occurrence of parasitic and microbial infections in the "pacu" Piaractus mesopotamicus and hybrid "patinga" (P. mesopotamicus x Piaractus brachypomus) from the Northwest of São Paulo State, Brazil. Fishes from three fish farms were evaluated every two months: A - Reproduction and larviculture (pacu / patinga), B - Growout (patinga) and C - Fee-fishing property (pacu / patinga). Fishes from each fish farm were collected from February 2010 to February 2011 for parasitological (n = 35 per property) and microbiological (n = 21 per property) analysis. The parasites found were: Dactylogyridae (Monogenea), Trichodina spp., Ichthyophthirius multifiliis, Chilodonella sp. (Protozoa), Myxobolus spp., Henneguya spp. (Myxozoa), Rondonia rondonia, third stage larvae of Contracaecum sp. (Nematoda), and Dolops carvalhoi (Crustacea). Among the fishes examined, 62.9% from "A" and 100% from "B" and "C" were infected / infested with at least one parasite species. Pacu (n = 44) showed higher susceptibility to infestations caused by Anacanthorus penilabiatus and patinga (n = 61) by Mymarothecium viatorum (p < 0.05). In the microbiological analysis, 23.8% of fishes from "A" and "B" properties and 33.3% of fish from the property "C" were infected with at least one bacteria species. Seasonality influenced Trichodina spp. and A. penilabiatus infestations and infection caused by Enterobacter sp. in patingas (p < 0.05). In antibiogram test, strains of Pseudomonas sp., Stenotrophomonas maltophilia and Aeromonas sp. were resistant to all beta-lactam antibiotics... (Complete abstract click electronic access below) / Mestre

Made available in DSpace on 2014-06-11T19:30:13Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-02-27Bitstream added on 2014-06-13T19:39:32Z : No. of bitstreams: 1 franceschini_l_me_botib.pdf: 588829 bytes, checksum: 796cb08752fb62d3915ad06ac0d6aa82 (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O desenvolvimento das atividades relacionadas à aquicultura tem aumentado consideravelmente a relevância dos estudos sobre parasitas e outros patógenos de organismos aquáticos, principalmente, daqueles hospedeiros com potencial para o cultivo e comercialização. O objetivo deste estudo foi avaliar a ocorrência de infecções parasitárias e microbianas na produção de pacu Piaractus mesopotamicus e do híbrido patinga (P. mesopotamicus x Piaractus brachypomus) procedentes da região Noroeste do Estado de São Paulo, Brasil. Três pisciculturas foram amostradas bimestralmente, de fevereiro de 2010 a fevereiro de 2011: A - Reprodução e Larvicultura (pacu/patinga), B - Engorda (patinga) e C - Pesque-pague (pacu/patinga), das quais 35 peixes foram submetidos à análise parasitológica e 21 à análise microbiológica. Foram encontrados os parasitas: dactilogirídeos (Monogenea); Trichodina spp., Ichthyophthirius multifiliis, Chilodonella sp. (Protozoa); Myxobolus spp. e Henneguya spp. (Myxozoa); Rondonia rondoni e Contracaecum sp. (Nematoda); e Dolops carvalhoi (Crustacea). Dentre os peixes analisados, 62,9% de “A” e 100% de “B” e “C” estavam infectados/infestados por pelo menos uma espécie de parasita. Pacus (n=44) apresentaram maior suscetibilidade a infestações por Anacanthorus penilabiatus, e as patingas (n=61), por Mymarothecium viatorum (p<0,05). Na análise microbiológica, 23,8% dos peixes de “A” e “B” e 33,3% da propriedade “C” estavam infectados com pelo menos um gênero de bactéria. A sazonalidade influenciou as infestações por Trichodina spp., A. penilabiatus e infecções pela bactéria Enterobacter sp. em patingas (p<0,05). No antibiograma, cepas de Pseudomonas sp., Stenotrophomonas maltophilia e Aeromonas sp. apresentaram resistência a todos antibióticos... / The development of activities related to aquaculture has considerably increased the relevance of studies on parasites and other pathogens of aquatic organisms, especially those with potential for production and marketing. The aim of this study was to evaluate the occurrence of parasitic and microbial infections in the “pacu” Piaractus mesopotamicus and hybrid patinga (P. mesopotamicus x Piaractus brachypomus) from the Northwest of São Paulo State, Brazil. Fishes from three fish farms were evaluated every two months: A - Reproduction and larviculture (pacu / patinga), B - Growout (patinga) and C - Fee-fishing property (pacu / patinga). Fishes from each fish farm were collected from February 2010 to February 2011 for parasitological (n = 35 per property) and microbiological (n = 21 per property) analysis. The parasites found were: Dactylogyridae (Monogenea), Trichodina spp., Ichthyophthirius multifiliis, Chilodonella sp. (Protozoa), Myxobolus spp., Henneguya spp. (Myxozoa), Rondonia rondonia, third stage larvae of Contracaecum sp. (Nematoda), and Dolops carvalhoi (Crustacea). Among the fishes examined, 62.9% from A and 100% from B and C were infected / infested with at least one parasite species. Pacu (n = 44) showed higher susceptibility to infestations caused by Anacanthorus penilabiatus and patinga (n = 61) by Mymarothecium viatorum (p < 0.05). In the microbiological analysis, 23.8% of fishes from A and B properties and 33.3% of fish from the property C were infected with at least one bacteria species. Seasonality influenced Trichodina spp. and A. penilabiatus infestations and infection caused by Enterobacter sp. in patingas (p < 0.05). In antibiogram test, strains of Pseudomonas sp., Stenotrophomonas maltophilia and Aeromonas sp. were resistant to all beta-lactam antibiotics... (Complete abstract click electronic access below)

No description available.

The U.S. aquaculture industry has become well established in the last three decades, and channel catfish aquaculture is the most significant component of this industry. Virulent Aeromonas hydrophila has been a serious disease problem since 2009 in the U.S. catfish aquaculture, and Aeromonas veronii and Edwardsiella piscicida are emerging pathogens of catfish. Therefore, this study aims to address fundamental questions on virulence mechanisms of these three fish pathogens, which I expect to support the development of control measures for preventing these diseases. In this study, E. piscicida and virulent Aeromonas hydrophila (vAh) genomes were sequenced, and comparative analyses were conducted using the genome sequences. Average nucleotide identity (ANI) calculations showed that E. piscicida strains share high sequence identity, yet they are from diverse host species and geographic regions. vAh isolates share very high sequence identity, while the other A. hydrophila genomes are more distantly related to this clonal group. We applied several comparative genomics approaches to evaluate E. piscicida genomes and E. ictaluri genomes, providing valuable information about unique and shared features of these two important pathogens in the Edwardsiella genus. Comprehensive secretion system analysis of 55 A. hydrophila genomes and deletion of tssD and tssI core elements of T6SS from vAh isolate ML09-119 has provided new knowledge. We sequenced the genome of virulent Aeromonas veronii strain ML09-123 from catfish indicated that it was highly similar to an A. veronii strain from China. Evaluation of all 41 A. veronii genomes available in the National Center for Biotechnology Information (NCBI) provides a base platform to investigate in detail the molecular mechanism of A. veronii biology and virulence. Lastly, we constructed deletion mutants vAhΔsia, vAhΔent, vAhΔcol, vAhΔhfq1, vAhΔhfq2, and vAhΔhfq1Δhfq2 to determine roles of A. hydrophila secreted proteins and regulatory proteins on virulence in catfish. Results showed that sialidase (vAhΔsia) and enterotoxin (vAhΔent) mutants were significantly attenuated.

Following the construction of the Pongolapoort Dam in 1974, the potential impacts on the lower Phongolo River and floodplain due to alterations in the natural flow regime have caused concerns. Fish communities and population structures are directly influenced by these alterations. The only protected section of the Phongolo River is a 15 km reach and its associated pans that flow through the Ndumo Game Reserve. Historic data shows that the community and population structure of the fish in the Phongolo Floodplain has changed as a result of irregular flood releases. The Ndumo Game Reserve plays an important role in the conservation of many ecologically and economically important species as the pans inside the reserve serve as a refuge area in which these species can breed to replenish the fish numbers in the Phongolo River. The fish diversity inside the Ndumo Game Reserve is also higher when compared to outside. During the high flow period fish move into the floodplain pans as a result of the higher water level. Oreochromis mossambicus, the most common species found in this area, utilize Nyamiti Pan for breeding but the health of this species is under pressure due to severe infestations of Lernaea cyprinacaea and nematode parasites. Lernaea cyprinacaea is a parasitic copepod associated with the introduced exotic fish species Cyprinus carpio which is found in large numbers in various pans inside Ndumo Game Reserve. The presence of this alien species in the refuge area raises concerns as it competes for the same resources as the economically important native fish species. Nyamiti Pan is largely populated by adult cichlid species between the ages of six and ten years old. The importance of flood releases which simulate natural flow regime is emphasised by the negative impacts irregular floods have on fish health, community and population structure. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015