Thesis (Ph.D.)--Mississippi State University. Department of Agricultural and Biological Engineering. / Title from title screen. Includes bibliographical references.

Thesis (M.S.)--Mississippi State University. Department of Wildlife and Fisheries. / Title from title screen. Includes bibliographical references.

Austroglanis gilli and A. barnardi are endemic to the Clanwilliam-Olifants System in the Western Cape, South Africa. The populations of each of these species are considered to be threatened by various anthropogenic activities, which include inappropriate agricultural practice and impacts of alien invasive fish species. The purpose of this thesis was to assess the life-history of these two endangered species in order to contribute to understanding their biology. Such information is vital for the development of strategies for their conservation. Marginal zone and marginal increment analyses from sectioned lapilliar otoliths of both A. gilli and A. barnardi showed a unimodal peak, suggesting a single annulus formation. The oldest specimens of A. gilli and A. barnardi were 12+ and 14+ years, respectively. The growth of A. gilli and A. barnardi was relatively slow and was best described by the von Bertalanffy growth curve as: L, = 131.56(1 - exp(- 0.27(t - 1.18 ))) for male and L, = 113.86(1 - exp(- 0.43(1- 0.74))) for female A. gilli from the Rondegat River. In the Noordhoeks River, growth was L, = 99.67(1 - exp(- 0.53(t - 0.35))) for male and L, = 96.60(1 - exp(- 0.64(t - 0.11 ))) for female A. gilli, and L, =71.02(1-exp(-0.26(1-3.07))) and L, = 69.50(1-exp(-0.36(1 - 1.88))) for male and female A. barnardi, respectively. The average natural mortality for the combined sexes was estimated using catch curve analysis at 0.37 ± 0.12 per year for A. gilli from the Rondegat River, and at 0.71 ± 0.05 and 0.39 ± 0.04 per year for A. gilli and A. barnardi from the Noordhoeks River, respectively. For A. gilli in the Rondegat River, the first maturity was estimated at 3.3 years (97.3 mm SL) for males and 3.1 years (94.3 mm SL) for females. In the Noordhoeks River, the first maturity for A. gilli was estimated at 2.0 years (71.9 mm SL) for males and 1.7 (66.4 mm SL) for females, and for A. barnardi at 2.0 (55.0 nun SL) for males and 2.9 years (58.9 mm SL) for females. Maturity corresponded closely to the asymptotic sizes from the von Bertalanffy curves, suggesting a shift in energy use from somatic growth to gonad development. Macroscopic assessment of the state of gonads, the Ganado-somatic index and histological examinations revealed that both A. gilli and A. barnardi have a single spawning season. The presence of oocytes in different stages of development in each of the ovaries of mature females collected between November and January suggested asynchronous, iteroperous serial spawning. The resorption of yolk was observed from ovaries collected between February and March and no vitellogenic oocyte was visible from ovaries collected between April and August. A similar trend was observed for males, with spermatozoa filling the lumen between November and January and some residual spermatozoa being present in the lumens soon after the breeding season. Spermatocytes and spermatids were dominant in the testes until October. An Index of Relative Importance revealed that A. gilli feeds predominantly on the benthic macroinvertebrate larvae of Ephemeroptera (particularly Baetidae), Diptera (particularly Chironomidae and Simuliidae) and Trichoptera. Austroglanis barnardi feeds predominantly on dipteran larvae (particularly Chironornidae and Simuliidae). Chi square contingency tables showed a significant difference in the dominant prey items of A. gilli and A. barnardi in the Noordhoeks River (X₂= 53.79, d.f. = 4, p > 0.001) and A. gilli between Rondegat and Noordhoeks rivers (x₂ = 34.74, d.f. = 4, p > 0.001). The Spearman's rank correlation test showed no shifts in the diet of A. barnardi from Noordhoeks River and A. gilli from Rondegat River with a change in size and season (p>O.OS). However, there was a shift in the diet of A. gilli from the Noordhoeks River which could suggest a distinct patchiness of benthic macroinvertebrates between the riffle feeding areas used by juveniles and other biotopes used by adults. The occurrence, in stomach contents, of other prey items from a wide variety of taxa and the presence of allochthonous material from the terrestrial environment could suggest an opportunistic feeding guild for both Austroglanis species. The life-history traits of A. gilli and A. barnardi, which are charaterized by slow growth, long life span and low relative fecundity, indicate that both species are relatively precocial and K-selected. The population of a precocial species is relatively stable and if population numbers were to be greatly reduced, they would require a long time to rebuild. An urgent conservation intervention is therefore recommended for Austroglanis spp. so as to maintain the diversity of populations within these species. The creation of protected river reserves and raising public conservation awareness may minimise activities that result in altered river hydrology and the destruction of complex benthic habitats.

M.Sc. (Zoology) / The freshwater indicator fish species, Clarias gariepinus, was used to assess and compare the health status of fish from the Hartbeespoort Dam (HBPD) and the Groot Marico Bosveld Dam (GM) which was used as a reference site. HBPD is known to be polluted and renowned for its extreme eutrophic state. GM receives water from the Marico River and is said to be in an unmodified natural ecological state. Adult Clarias gariepinus were sampled using gill nets; during low-flow (n=17) and high-flow (n=20) seasons from the HBPD, and once from the GM (n = 20). A histology-based fish health assessment was done using a necropsy based health assessment index and a qualitative and semi-quantitative histological assessment on selected target organs namely the gills, liver, kidney and gonads. Focus was also placed on reproductive health aspects by staging the gonads according to their reproductive development and assessing the motility of activated sperm using computer assisted sperm analysis (CASA). Water samples were analyzed for selected physical parameters and for selected metals. The results showed distinct macroscopic differences in the livers and testes comparing the two sites. Fish from HBPD had fatty livers and the macroscopic morphology of the testes showed abnormalities regarding the interstitial tissue, possibly due to the proliferation of connective tissue. The macroscopic abnormalities of the livers were reflected in the histological assessment, which concluded steatosis, vacuolation, hepatocyte nuclear alterations and the presence of large numbers of melanomacrophage centers (MMCs). Of these alterations, only MMCs and intracellular deposits were found in fish from the GM. When comparing the HBPD low-flow (LF) and high-flow (HF) sampling trips, the fish from the low-flow had more alterations present in all organs. While the CASA results showed that the motility, velocity and progression of sperm were lower in fish from the HBPD for all parameters, results from GM showed the ideal trend expected from the moment of sperm activation until degeneration. The velocity and progression were significantly (p value <0.05) different between HBPD samples and fish from the GM. The water quality showed increased concentrations of selenium, as well as the endocrine disrupting chemicals (EDCs) nonylphenol and di-n-butyl phthalate. According to the selected parameters assessed, it seems like the water of the HBPD has increasing detriment upon fish health.

Bacillary Necrosis of Pangasius (BNP) caused by Edwardsiella ictaluri is considered to be the most serious disease occurring in farmed striped catfish (Pangasianodon hypophthalmus) in Vietnam. This disease has had an increasing impact over the last ten years and has been reported to cause 50-90% mortality of stocks during a single outbreak. Data obtained from natural outbreaks of E. ictaluri in striped catfish showed the role of environmental factors in the establishment and progression of this disease. At present, factors affecting the virulence and transmission of E. ictaluri in striped catfish are poorly understood. The central hypothesis of this thesis focuses on the complex picture of the environmental factors and infectivity of E. ictaluri in striped catfish. In this study, 80 isolates of E. ictaluri recovered from natural clinical disease outbreaks occurring in striped catfish farms between 2002 and 2011 located in 4 distinct geographical areas within Vietnam were characterised using a variety of methods. The biochemical profiles showed that E. ictaluri isolates from striped catfish in Vietnam have similar phenotypic characteristics to other E. ictaluri isolates from other infected fish species. These data showed high levels of phenotypic homogeneity between the E. ictaluri isolates investigated. The status of isolates recovered from natural infections over time and from geographically distinct farms was evaluated using pulsed-field gel electrophoresis (PFGE), plasmid profile identification and antibiotic sensitivity tests. The PFGE results showed 6 main groups with a similarity of 82% and the corresponding genotypes of the prevalent isolates illustrated annual differences. Three plasmid groups were identified distributed among the isolates investigated, in which high molecular weight plasmids of approximately 35 and 140 kb were found in two of the groups. Plasmid profiles of the present study did not show any trend of geographical region or year of isolation. The 140 kb plasmid has been considered as a multi-antibiotic resistance plasmid which confers resistance to tetracycline, trimethoprim and sulphonamides. All Vietnamese isolates showed a high level of resistance to Oxolinic acid, Sulfadimethoxine/Ormetoprim (Romet), Oxytetracycline and Amoxicillin. A reproducible bacterial immersion challenge model was developed and the LD60 estimated prior to performing subsequent experimental challenge studies. Fish were exposed to 107 cfu ml-1 of E. ictaluri by immersion for up to 30 seconds, resulting in a cumulative percentage mortality of 63%. Edwardsiella ictaluri was recovered and identified from all the dead and moribund fish during these experiments and affected fish showed similar clinical signs and pathology to those reported from natural E. ictaluri infections. The present study resulted in a successful experimental immersion challenge model for E. ictaluri infection in healthy striped catfish. Cohabitation challenges were also developed and produced 15-40% mortality, typical clinical signs and pathology, and successful recovery of the challenge organism demonstrating horizontal transmission of E. ictaluri in striped catfish. Experimental studies were then conducted to investigate the association between pH or salinity of water and susceptibility to E. ictaluri infection in striped catfish. The first experiments were performed in in vitro conditions in which E. ictaluri isolates were cultured in a variety of pH and salt concentrations. In vivo experiments were then designed where striped catfish were exposed to 107 cfu ml-1 of E. ictaluri for 30 seconds and then held at 4 different water pHs (5.5, 6.5, 7.5 and 8.5) or NaCl concentrations (0, 0.5, 1 and 1.5%). The results of in vitro experiments showed that a pH value between 5.5 to 6.5 and salt concentration between 0-0.5% were optimal for the growth of E. ictaluri. The in vivo experiments demonstrated that the cumulative mortality of striped catfish in water at pH 5 and pH 6 was significantly higher than that of fish maintained in more alkaline water (p<0.05). By contrast, the cumulative mortality of the striped catfish maintained in 0.5% salt concentration was significantly lower than those kept in 0%, 1% and 1.5% salt concentration (p<0.05). Clinical signs, lesions and histopathological changes in the affected fish were consistent with those reported in natural infections. This study highlighted the use of pH 8.5 and salinity of 0.5% NaCl as a means of decreasing the susceptibility of striped catfish to E. ictaluri. In conclusion, this study used a variety of methods in order to enhance the understanding of the biochemical, biophysical characteristics, plasmid profile and antibiotic resistance as well as the relatedness of E. ictaluri isolates recovered from farmed striped catfish in Vietnam. This study provided two reliable and reproducible bacterial challenge models (immersion and cohabitation) and emphasised the link between pH and salinity with the infectivity and pathogenicity of E. ictaluri in striped catfish.

Orientador: Reinaldo José da Silva / Resumo: Peixes da família Loricariidae (Siluriformes) apresentam grande plasticidade fenotípicaintraespecífica durante toda sua ontogenia. O conhecimento limitado sobre os aspectosbiológicos, padrões biogeográficos e elevada variabilidade morfológica destes peixesdificultam estudos sobre a biodiversidade acerca deste grupo, incluindo estudos sobre afauna parasitária. Assim, o objetivo deste estudo foi realizar levantamento dabiodiversidade de parasitas de peixes da família Loricariidae em áreas sob a influência daconstrução de Pequenas Centrais Hidrelétricas (PCHs) no rio Sapucaí-Mirim, Estado deSão Paulo, Brasil. Ademais, avaliar a estrutura das comunidades parasitárias doshospedeiros analisados (ao nível de infracomunidade e comunidade componente) epossíveis mudanças na abundância das infracomunidades baseadas em variáveisexplanatórias (espaciais, temporais e fatores intrínsecos ao hospedeiro). Para tanto, duranteos anos de 2012 e 2013 foram realizadas duas amostragens anuais (período seco/chuvoso),em oito áreas amostrais situadas nos reservatórios de três PCHs: Palmeiras, Anhanguera eRetiro. Foram necropsiados 334 loricarídeos pertencentes a 10 espécies: Loricaria prolixa,Hypostomus margaritifer, Hypostomus heraldoi, Hypostomus strigaticeps, Hypostomusregani, Hypostomus ancistroides, Hypostomus cf. margaritifer, Hypostomus topavae,Hypostomus aff. topavae, além de uma espécie não identificada pertencente ao gêneroHypostomus. Foram encontrados 29 ta... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Loricariid fishes (Siluriformes) presents great intraspecific phenotypic plasticity throughouttheir ontogeny. The limited knowledge about the biological aspects, biogeographic patternsof distribution and high morphological variability of these fishes make the studies onbiodiversity of this group difficult, including that about parasites. Therefore, the aim of thisstudy was to survey the biodiversity of parasites of Loricariidae fishes from an area underthe influence of the construction of Small Hydro Power Plants (SHPPs) in the Sapucaí-Mirim River, São Paulo State, Brazil. Moreover, the study evaluated the structure ofparasitic communities of these hosts (at both the component community andinfracommunity levels), assessing the possible variation in infracommunity abundanceamong sites and fish species based on explanatory variables (spatial, temporal, and hosttraits). During 2012 and 2013, two annual samples (dry/rainy seasons) were carried out, ineight sampling sites situated in the reservoirs of three SHPPs: Palmeiras, Anhanguera, andRetiro. Specimens of Loricaria prolixa, Hypostomus regani, Hypostomus ancistroides,Hypostomus strigaticeps, Hypostomus heraldoi, Hypostomus margaritifer, Hypostomus cf.margaritifer; Hypostomus topavae; Hypostomus aff. topavae and Hypostomus sp., wereanalyzed, totaling 334 fishes. Twenty-nine taxa were found, totaling 15,957 parasitespecimens, and Monogena was the dominant group, which showed the greatest richness ... (Complete abstract click electronic access below) / Doutor

Made available in DSpace on 2014-07-29T15:07:29Z (GMT). No. of bitstreams: 1 Dissertacao_Dunya_Moraes.pdf: 432826 bytes, checksum: 63ffc1c5c83c7f760eb90cca2350b35f (MD5) Previous issue date: 2010-03-26 / The objective of this research to investigate the presence of Salmonella sp. in raw materials of animal origin used in the manufacture of feed for broilers, in diets collected directly from bird feeders, and in organs ceca contents and liners carry case for newly hatched chicks, in environmental samples, in samples from swabs of the hands of officials of the farm and slaughterhouse samples and classify and determine the resistance of strains of Salmonella sp. found, before the action of chemotherapeutic nine. For data analysis was descriptive frequency results. 1200 samples were collected from flour and Salmonella sp. was found in 10.5% of samples with a predominance of serovar Enteritidis. The frequency of bacteria in meat meal was 12%, 6.8% in blood, the feathers of 4.3% and 14.6% in the viscera. Were also isolated Salmonella Cerro, Salmonella Montevideo, Salmonella anatum, Salmonella Tennessee, and Salmonella typhimurium among others. Regarding the resistance of strains found in the various categories of flour was observed resistance to sulfonamides, neomycin, tetracycline, sulphamethoxazole-to trimetopim and florfenicol. Of the three strains of bacteria isolated from two diets were of a Salmonella enteritidis and S. Anatum, showing resistance to sulfonamides and neomycin. Of the 32 batches of newly hatched chicks 9.4% were positive for Salmonella and 32 batches of liners carrying case 9.4%. Environmental samples, before bed accommodation, swabs of feeder and drinker and the drinking water of birds tested negative for Salmonella sp .. Drag swabs of poultry manure, and samples Alphitobius diaperinus swabs from the hands of officials of the farms had a frequency of 12.5%, 12.5% and 6.5% respectively. In samples from swabs of drag serovar Enteritidis was the most frequent and catfishes of the samples and swabs of hands was the only serovar isolated. In samples from slaughterhouse 26.7% of the lots from crop and 33.3% of batches of ceca were positive for Salmonella sp .. Regarding the resistance of strains, there was resistance sulfonamides, the amoxicillin and enrofloxacin in samples of newly hatched chicks and amoxicillin in the samples of liners carrying case. In drag swabs and samples of catfishes, the bacteria were resistant to sulfonamides. In samples from crop, were resistant to sulfonamide and enrofloxacin and the caeca to sulfonamides, the trimetopim-sulphamethoxazole, tetracycline, amoxicillin and ampicillin to. / Objetivou-se com esta pesquisa investigar a presença de Salmonella sp. em matérias primas de origem animal utilizadas na fabricação de rações de frangos de corte, em rações coletadas diretamente dos comedouros das aves, em órgãos e conteúdos de cecos e forros de caixa de transporte de pintos de um dia, em amostras ambientais, em amostras de suabes de mãos de funcionários de granjas e em amostras de abatedouro bem como tipificar e determinar o perfil de resistência das cepas de Salmonella sp. encontradas, frente à ação de nove quimioterápicos. Para análise dos dados foi feita freqüência descritiva dos resultados encontrados. Coletou-se 1200 amostras de farinhas e Salmonella sp. foi encontrada em 10,5% das amostras com predominância do sorovar Enteritidis. A freqüência da bactéria em farinhas de carne foi de 12%, nas de sangue 6,8%, nas de penas 4,3% e nas de vísceras 14,6%. Foram isoladas também Salmonella Cerro, Salmonella Montevideo, Salmonella Anatum, Salmonella Tennessee e Salmonella Typhimurium entre outras. Em relação ao perfil de resistência das cepas encontradas nas diversas categorias de farinhas foi observado resistência à sulfonamidas, à neomicina, à tetraciclina, ao trimetopim-sulfametoxasol e ao florfenicol. Das três cepas da bactéria isoladas de rações duas eram de Salmonella Enteritidis e uma de S. Anatum, apresentando resistência à sulfonamidas e à neomicina. Dos 32 lotes de pintos de um dia 9,4% apresentaram positividade para Salmonella e dos 32 lotes de forros de caixa de transporte 9,4%. As amostras ambientais, cama antes do alojamento, suabes de comedouro e de bebedouro e água de bebida das aves apresentaram resultados negativos para Salmonella sp.. Suabes de arrasto de cama de aviários, amostras de Alphitobius diaperinus e suabes de mãos de funcionários das granjas apresentaram freqüência de 12,5%, 12,5% e 6,5% respectivamente. Nas amostras de suabes de arrasto o sorovar Enteritidis foi o mais freqüente e nas amostras de cascudinhos e suabes de mãos foi o único sorovar isolado. Nas amostras de abatedouro 26,7% dos lotes de inglúvio e 33,3% dos lotes de cecos foram positivos para Salmonella sp.. Com relação ao perfil de resistência das cepas isoladas, observou-se resistência à sulfonamidas, à amoxacilina e à enrofloxacina nas amostras de pintos de um dia e à amoxacilina nas amostras de forros de caixa de transporte. Nos suabes de arrasto e amostras de cascudinhos, as bactérias foram resistentes à sulfonamidas. Nas amostras de inglúvios, foi observada resistência à sulfonamidas e à enrofloxacina e nos cecos à sulfonamidas, ao trimetopim-sulfametoxasol, à tetraciclina, à amoxacilina e à ampicilina.

Invasive species are of particular concern as they have the potential to alter community structure and food web relationships within their invaded habitats. African sharptooth catfish Clarias gariepinus, a generalist predator, was introduced through an inter-basin water transfer scheme into the Great Fish and Sundays Rivers, Eastern Cape, South Africa, where it threatens the native riverine biota. This thesis assessed its impact from a trophic perspective. Patterns in catfish distribution and abundance revealed an upstream to downstream gradient that was associated with spatial distribution of most species within the mainstream, and a mainstream to tributary gradient that was associated with the spatial distribution of native minnows. The catfish was predicted to occur widely within the mainstem habitats and to decrease progressively along the mainstrem to tributary gradient with the physico-chemical environment being a good proxy for predicting both its occurrence and abundance. The results suggest the catfish proliferated within mainstem habitats where invasion resistance was possibly reduced due to alteration of flow. Population dynamics and size structuring of two native cyprinid minnows Pseudobarbus afer and Barbus anoplus, threatened by catfish, were examined within uninvaded headwater streams in relation to their proximate physical habitats. Their habitats were characterised by seasonal variation in physico-chemical conditions and a spatial variation in substrata compositions. No evidence of differences was found between seasons for density and capture probability for either species. The population size and density for P. afer was found to increase with increasing proportion of boulders. In comparison, B. anoplus population size and probability of capture increased with increasing proportion of bedrock and bank vegetation, respectively. Size structuring was explained predominantly by seasonality and habitat variables for P. afer and B. anoplus, respectively. Stable isotope ratios of carbon and nitrogen were used to compare the spatial variation in both the community-wide and catfish-specific niches and to estimate catfish prey sources from different habitats within the invaded systems. Aquatic community and catfish niches were statistically different among localities, suggesting that each locality had a distinct community-wide trophic structure. Dispersion metrics indicated no evidence of differences in the clustering among individuals, but provided evidence of differences in path trajectories for the comparisons of catfish populations that suggested dietary plasticity within different localities. Dietary studies revealed both ontogenetic shift and omnivory that suggested that catfish may exhibit less pronounced top-down effects within its invaded habitats. Manipulative experiments were used to test the response of benthic macroinvertebrates within two rivers that were differentially impacted by catfish as a presstype disturbance. Macroinvertebrates were non-responsive to catfish presence within a system where catfish had previously been established. In contrast, excluding catfish in this system indicated a response that suggested the importance of refuge within invaded habitats and the possible recovery pattern of certain macroinvertebrate taxa. By comparison, introduction of catfish within previously uninvaded localities provided evidence of direct catfish impact through elimination of conspicuous taxa. Acoustic telemetry was used to investigate catfish movement patterns within an invaded lentic habitat and provided evidence that habitat utilisation was non-random. The shallow and structured river mouth habitat, which was most utilised, was probably the most ideal for its breeding and feeding. This inferred potential overlap with native species and suggested the risk of predation and competitive interference. Catfish also exhibited both nocturnal and diurnal activity patterns that were probably related to feeding.

This thesis presents an evaluation of the dispersive solid-phase extraction (d-SPE) method referred to as the quick, easy, cheap, effective, rugged and safe (QuEChERS) method for the determination of four organochlorine pesticide residues in fish samples. The pesticides investigated in this study were o, p′-DDT, p, p′-DDE, aldrin and dieldrin. The combined use of Gas Chromatography with an Electron Capture Detector (GC-ECD) and sensitive Time of Flight (TOF) mass detector facilitated the identification of the target analytes. In the absence of certified reference material, the overall analytical procedure was validated by systematic recovery experiments on spiked samples at three levels of 2, 5 and 10 ng/g. The targeted compounds were successfully extracted and their recovery ranged from 76 to 96% with relative standard deviations of less than 13%. The optimum QuEChERS conditions were 2g of fish powder, 10 ml acetonitrile and 1 min shaking time. The optimal conditions were applied to assess the levels of chlorinated pesticides in blunt-tooth catfish (Clarias ngamensis), tigerfish (Hydrocynus vittatus), Oreochromis andersonii and red-breasted tilapia (Tilapia rendalli) from the Okavango Delta, Botswana. Dieldrin, p, p′-DDE and aldrin were detected in all the analysed samples with a concentration range of 0.04 – 0.29, 0.07 – 0.33, 0.04 – 0.28 and 0.03 – 0.24 ng/g per dry weight in O. andersonii, C. ngamensis, T. rendalli and H. vittatus respectively. These concentrations were below the US-EPA 0.1 μg/g allowable limit in edible fish and the Australian Maximum Residue Limit (MRL) of 50 - 1000 ng/g in fresh fish. DDT was not detected in all the fish species investigated. The mean lipid content recorded in the fish samples were 1.24, 2.16, 2.18 and 4.21% for H. vittatus, T. rendalli, O. andersonni and C. ngamensis respectively. No systematic trend was observed between fish age and pesticide levels in fish. Acetylcholinesterase (AChE) activity assays were performed to assess the effects of organochlorine pesticides in Clarias ngamensis. The enzyme activity recorded in Clarias ngamensis from the Okavango Delta and the reference site was 12.31 μmol of acetylcholine iodide hydrolysed/min/g brain tissue. The enzyme activity remained the same indicating no enzyme inhibition. The conclusions drawn from this study are that the QuEChERS method is applicable for the determination of organochlorine pesticide residues in fish matrices. The fish from the Okavango Delta are safe for human consumption.