published_or_final_version / Environmental Management / Master / Master of Science in Environmental Management

The introduction of trout has been implicated in the declines in native fish fauna in New Zealand and worldwide. Since the introduction of brown (Salmo trutta) and rainbow (Oncorhynchus mykiss) trout to New Zealand in 1867, their distribution has spread and they have been implicated in the fragmentation of native fish distributions, particularly native non-migratory galaxiids. However, in the Upper Waimakariri basin the co-occurrence of trout and galaxiid populations is relatively common, even in streams where trout reach sizes known to be piscivorous. To investigate mechanisms that may regulate trout and galaxiid co-occurrence, I investigated differences in antipredator behaviour and growth rate between stream types with varying levels of trout presence. Using quantitative survey data collected between 1997 and 2006, I found that trout abundance was low and varied annually in frequently disturbed sites compared their high abundance in stable streams. This finding was used to classify streams into three population types, barrier (trout absent), disturbed (trout presence intermittent) and sympatric (constant trout presence). Using this classification, I tested the effects of trout chemical cues on galaxiid activity and refuge use in artificial channels. There were no differences in activity or refuge use between trout odour and there were no effects of population type or galaxiid size during both the day and the night. Using otolith weight-fish length relationships in galaxiids collected from each population type, I found that galaxiid growth rate was higher in disturbed streams than in stable streams either with or without trout. An experiment manipulating trout size and presence, over two months in a natural stream, found galaxiids from treatments without trout grew slower than those with trout. Slow growth rates in galaxiids above trout-migration barriers and in sympatry, combined with low growth rates in treatments without trout suggest that the mechanisms that regulate galaxiid growth are more complex than previously thought.

Fisk är ett hälsosamt livsmedel och allt eftersom världsbefolkningen har växt och hälsotrenden blossat upp, har trycket på fiskerinäringen ökat. Bakgrundens fakta tog upp olika konsekvenser som fiskodling kan medföra och hur stor kunskap konsumenten har om detta och deras makt att påverka industrin. Syftet med studien var att belysa brister i fiskodling kopplat till konsumenters kunskap, samt hur de etiska frågorna påverkar konsumentens val. I metod och materialstycket lades det fram att studien var en litteraturstudie som baserades på vetenskapliga artiklar från olika databaser som gick att tillgå vid Örebro universitet. Resultatet av undersökningen gav inblickar i vad konsumenter visste om odlad fisk, vad de tyckte om produkten och hur eller om de utövade sin makt. Resultatet visar även hur hanteringen av fisk går till på fiskodlingar runt om i Europa. I diskussionsavsnittet i studien lades bakgrundsfakta ihop med fakta ur resultatavsnittet. I diskussionen framkom information om att konsumenters uppfattning och kännedom om odlad fisk inte var tillräcklig, trots de märkningar och informationskällor som presenteras i bakgrunden.I diskussionsavsnittet diskuteras även processen som ledde fram till den här studien och vad som fungerat respektive inte fungerat. / B-uppsatser

Hydropower dams block migration routes and disrupt longitudinal connectivity in rivers, thereby posing a threat to migratory fish species. Various fish passage solutions have been implemented to improve connectivity with varying success. A well-functioning passage solution must ensure safe and timely passage routes that are used by a substantial portion of the migrating fish. In this thesis, I report the results from telemetry studies where the behavior and survival of migrating Atlantic salmon spawners, post-spawners and smolts have been evaluated in relation to hydropower dam passage. I evaluate downstream passage performance at dams with no passage solutions in the River Klarälven, and with simple passage solutions in in the Winooski River. In the River Ätran, I study both upstream- and downstream passage performance at a dam with sophisticated passage solutions based on the best available technology. In addition, I have studied the survival and behavior of post-spawners and hatchery-released smolts. A substantial portion of the spawners survived spawning and initiated downstream migration. Most males migrated downstream in autumn following spawning, whereas females tended to stay in the river until spring. For hatchery-reared smolts, early release was associated with faster initiation of migration and higher survival compared to late release. Multiple dam passage resulted in high mortality for both smolts and kelts. For smolts, dam passage, even with simple passage solutions, was associated with substantial delay and mortality. High spill levels were linked to high survival and short delay for downstream migrating salmon. The best available passage solution, which consisted of a nature-like fishway and a low sloping intake rack to guide fish to a bypass, resulted in rapid passage of a large portion of the adult migrants.

Constructed reefs are used successfully in marine systems to enhance spawning habitat; this study examines the effectiveness of constructed reefs in a tidal-freshwater river. Fish abundance, species diversity and richness, residency, water column position, reproductive guilds, and feeding guilds were analyzed on two constructed reefs in the tidal-freshwater James River and compared to silted regions representing the primary substrate in the river. Reefs were sampled using hydroacoustics, electroshocking, gillnetting, trawling, and egg mats. The constructed reefs had a greater proportion of fish that broadcast spawn over hard substrate and a trend of more overall individual, residential, and demersal fish. The results suggest that the reefs may be attracting a different fish community than their respective comparison sites, though additional research on the effectiveness of constructed reefs in tidal-freshwater rivers is recommended.

Knowledge of biodiversity within an ecosystem is essential when trying to understand the function and importance of that ecosystem. A challenge when assessing biodiversity of reef habitats is cryptobenthic fishes, which encompass many groups that have close associations with the substrate. These fishes can be behaviorally cryptic, by seeking refuge within the reef matrix, or visually cryptic, using cryptic coloration to match the surrounding habitat. These factors make visual surveys inadequate for sampling these fishes. One such group of cryptobenthic fishes are the gobies, family Gobiidae, which currently represent over 1600 species, although new species are continually being discovered. Gobies are often small (less than 5 cm), and many species will be associated with a very specific microhabitat type. Due to the understudied nature of the Red Sea, little is known about habitat preferences of gobies within the region. In order to determine the differences in goby community structure within the central Red Sea, fishes were sampled at one reef using 1 m² enclosed rotenone stations from three distinct microhabitats: hard coral, rubble, and sand. Following collection, specimens were photographed and sequenced using COI, to aid in species identification. 232 individuals were collected representing 31 species of goby. Rubble microhabitats were found to host the majority of collected gobies (69%), followed by hard coral (20.6%), then sand (9.9%). Goby assemblages in the three microhabitats were significantly different from each other, and evidence of habitat-specialists was found. These results provide essential baseline information about the ecology of understudied cryptobenthic fishes that can be used in future large-scale studies in the Red Sea region.

Esta pesquisa objetivou enriquecer e purificar, em quimiostatos, consórcios microbianos capazes de oxidar amônia a nitrogênio (\'N IND.2\'), sob condições anaeróbias utilizando como inóculo: (Q1) biomassa de reator nitrificante-desnitrificante de estação de tratamento de água residuária de indústria produtora de aminoácidos (Ajinomoto) e (Q2) lodo granular de reator UASB de abatedouro de aves (Avícola DACAR, TIETÊ). Os inóculos foram enriquecidos em quimiostatos com vazão afluente de 18ml/h de meio basal específico com concentrações médias de 80 mg \'N-NH IND.4\'POT.+\'/L, 75,2 mg \'N-NO IND.2\'POT.-\'/L e 1000 mg/l de bicarbonato como única fonte de carbono. Nos quimiostatos Q1 e Q2 as eficiências médias de remoção foram de 51,6% e 39,3% de amônia e 60,5% e 53,2% de nitrito, respectivamente, após 296 dias de operação. A eficiência média de remoção de nitrogênio total (\'N-NH IND.4\'POT.+\' + \'N-NO IND.2\'POT.-\') foi de 57,1% e 43% após 296 dias de operação, respectivamente para Q1 e Q2. A purificação dos consórcios enriquecidos foi realizada utilizando-se metodologia de gradiente de densidade por centrifugação Percoll. Os consórcios microbianos foram observados por exames microscópicos e a diversidade foi avaliada por DGGE antes e depois da purificação pelo protocolo Percoll. O DGGE revelou mudança na estrutura dos consórcios presentes em Q1 e Q2 no decorrer do período de operação dos quimiostatos. A técnica de hibridação in situ (FISH) com sonda fluorescente (Amx - 368) confirmou a presença de microrganismos anammox nos dois consórcios microbianos. O seqüenciamento do DNA ribossomal 16S de bandas obtidas do gel de DGGE, utilizando-se primers universais para domínio Bacteria, relacionou por árvore de máxima verossimilhança, duas bandas com o grupo das bactérias verdes não-sulfurosas. / This research aimed to enrich and to purify, in chemostats, microbial trusts capable to realize ammonium oxidation to dinitrogen (\'N IND.2\') under anaerobic conditions, using as inoculum: (Q1) biomass from nitrifying-denitrifying reactor of wastewater treatment plant of amino-acids industry (Ajinomoto) and (Q2) granular sludge from upflow anaerobic sludge blanket UASB reactor treating poultry wastes - Avícola DACAR, TIETÊ. The inoculum was enriched in chemostats with affluent flow of 18 ml/h of specific basal media with mean concentrations of 80 mg \'N-NH IND.4\'POT.+\'/L, 75.2 mg \'NO IND.2\'POT.-\'/L and 1000 mg/l of bicarbonate as sole carbon source. In Q1 and Q2 chemostats the mean efficiency of removal were 51.6% and 39.3% of ammonium, and 60.5% and 53.2% of nitrite, respectively, after 296 days of operation. In Q1 and Q2 chemostats, the mean efficiency of total nitrogen removal (\'N-NH IND.4\'POT.+\' + \'NO IND.2\'POT.-\') were 57.1% and 43%, respectively, after 296 days of operation. The purification of enriched microbial trusts was carried following methodology of density gradient by centrifugation (Percoll). The microbial trusts were observed by microscopic analysis and the diversity was evaluated by DGGE, before and after the purification by the Percoll protocol. The DGGE analysis showed changes in microbial trusts structure in Q1 and Q2 in chemostats operation period. The fluorescence in situ hibridization technique (FISH) with Amx-368 probe confirmed the presence of anammox microrganisms in both microbial trusts. The sequencing of recovered bands of DGGE was carried through ribossomal DNA 16S using universal primers for bacteria Domain that related two bands with green nosulphur bacterium using maximum likelyhood tree.

Thesis (Ph.D (Zoology)) --University of Limpopo, 2018 / Freshwater ecosystems are the most threatened systems globally, suffering from channel modification, over extraction of water and, of particular concern, pollution. In South Africa, Olifants River is categorised as the third most polluted river system. Acid mine drainage seeping from derelict and abandoned mines has been described as the primary stressor in the upper Olifants catchment. The increase of metal concentration in the water, sediment and fish tissues has been evident over the past few decades. As a result, there has been an increasing concern regarding the effects of increased metal concentrations on the health of fish and the safety of communities consuming fish from the polluted Olifants River system. This study used enzymatic and histopathologic biomarkers to assess the physiological response of Oreochromis mossambicus and Labeo rosae to environmental contaminants. The study further investigated the metal accumulation trend of across different fish tissues and assessed the edibility of O. mossambicus and L. rosae from Loskop and Flag Boshielo dams. Water, sediment and fish samplings were carried out concurrently during low flow and high flow seasons in 2014. Water and sediment sampling were done at the inflow, middle and dam wall. A minimum of 10 fish specimens for each species were collected from Loskop and Flag Boshielo dams during each sampling. For bioaccumulation analysis, liver, gill and muscle tissues were dissected out, wrapped with aluminium foil and frozen. Frozen samples were sent to SANAS accredited laboratory for metal analysis. For Histopathology, tissues were fixed in 10% neutral buffered formalin prior processing. Tissue processing was done at the Pathology laboratory of the University of Pretoria, Onderstepoort campus. For biomarker analysis, liver and brain tissues were fixed in liquid nitrogen in the field and transferred to the -80°C biofreezer at the University of Limpopo, Biotechnology Unit laboratory. Metal concentrations in the muscle tissue were used to calculate hazard quotient for human health risk assessment which was based on the assumptions that an adult weighting 70 kg consume 150 g portion once per week. Alkaline pH was observed in the water throughout the study. Most water constituents were within the guidelines at both dams. The water at Flag Boshielo Dam was oligotrophic with Loskop Dam showing mesotrophic conditions. Concentrations were below detection level for most metals; however, significant concentrations were recorded in the bottom sediment. Although Loskop Dam is being described as a repository for pollutants from the upper Olifants catchment, no significant differences (p>0.05) were observed for metal concentrations in sediment between the two dams. Coinciding with sediment metal concentrations, liver, gills and muscle have shown notable concentrations for both species at Loskop and Flag Boshielo dams. The common trend of liver accumulating higher metal concentration followed by gill and muscle (liver>gills>muscle) was observed for most metals on O. mossambicus and L. rosae at both dams. In contrast, lead, strontium and manganese showed higher concentrations in the gills. Muscle exhibited lowest concentrations for most metals. Remarkable trends on the activities of biomarkers, lactate dehydrogenase (LDH), glucose-6-phosphate dehydrogenase (G6PDH), glutathione-S-transferase (GST) and acetylcholinesterase (AChE) were detected for both species at Loskop and Flag Boshielo dams. Labeo rosae population have shown a significantly high (p<0.05) LDH activities at Loskop Dam and no significant difference (p>0.05) was observed for Oreochromis mossambicus. Glucose-6-phosphate dehydrogenase activities exhibited no significant difference (p>0.05) for both species between the two dams. Labeo rosae have shown a significantly high (p<0.05) GST activities at Loskop Dam whereas Oreochromis mossambicus exhibited no significant difference (p>0.05) between the two dams. Acetylcholinesterase (AChE) has shown no significant difference (p>0.05) for both species between the Loskop and Flag Boshielo dams. LDH, G6PDH and GST activities have shown relationship with metal concentrations, which makes them good biomarkers of metal exposure.The condition factor indicated that overall conditions of O. mossambicus and L. rosae from Loskop and Flag Boshielo dams were good. Hepatosomatic index results were not conclusive. Most histopathological alterations were recorded on both species at both dams, but with different magnitude of severity. Regressive changes were more prominent in the liver and gills of both species at Loskop and Flag Boshielo dams followed by progressive change. Gills of Oreochromis mossambicus exhibited moderate modifications (score >20) at Loskop Dam and slight modification (score <20) at Flag Boshielo Dam. Labeo rosae populations have shown slight modifications (score <20) in the gills at both dams. Both species have shown significant difference (p<0.05) on the gill index between the two dams. Liver index has also exhibited significant difference (p<0.05) for each species between Loskop and Flag Boshielo dams. Slight modifications (score <20) were observed in the liver for both species at Loskop and Flag Boshielo dams. Both species have shown to accumulate metals within their tissues with liver accumulating higher concentration for most metals, followed by gills and muscle, respectively. Although muscle showed to accumulate lesser metal concentrations, it still raise a serious concern as it is the tissue consumed by human. Lead, chromium, cobalt and antimony concentrations have been the only metals of concern in this river system over the past few years; nevertheless, the present study has shown that other metals viz. arsenic, silver and selenium have exceeded international levels for safe consumption. Given the metal concentration trend reported over the past two decade in fish tissues, there is a need for urgent intervention to address the acid mine drainage problem to ensure sustainable development of the Olifants River and safety of communities depending on it for their livelihood. / NRFand RAD

Le banc de poisson est un exemple typique d’auto organisation de groupe. Ce système implique des interactions complexes d’individus dans un milieu fluide et fait l’objet de nombreuses recherches multidisciplinaire théoriques, numériques ou expérimentales.Plusieurs hypothèses ont déjà été formulées pour expliquer la formation de ces bancs: la fuite face à des prédateurs, l’optimisation dans la recherche de nutriments ou encore l’économie d’énergie. Dans la plupart des recherches, les travaux se concentrent sur ce que les poissons devraient faire pour optimiser une tâche plutôt que sur des observations directes. Cela conduit à des différences dans les conclusions issus du travail des physiciens théoriciens ou ingénieurs avec ce qui est observé dans la nature par les biologistes. Dans ce travail, nous apportons, basées sur des observations directes tetra Hemigrammus bleheri, de nouveaux éléments sur les interactions des poissons lors de la nage collective comme le phénomène de burst-and-coast ou la synchronisation des cinématiques entre plus proches voisins. Enfin, nous démontrons que les bancs de Hemigrammus bleheri privilégient la configuration en ligne plutôt que celle en diamant souvent mise en avant dans la littérature / Fish school is the classical example of self-emergent system of collective behavior in animal locomotion, which involves complex interactions between individuals and has drawn fascination of numerous multidisciplinary analytical, numerical and experimental researches. Various reasons have been cited for the formation of fish school such as evading predators, enhancing foraging success or advantage in terms of energy consumption. However, most of the works primary focus on what fish should do in a school instead of what fish really do, leading to discrepancies between the works of theoretical physicists and engineers and what is observed in the nature by biologists. This thesis is an attempt to bridge this gap. In this work, we investigate the swimming dynamics of the red nose tetra fish Hemigrammus bleheri in a controlled experiment. The tetra fish are observed to swim using a burst-and-coast strategy, which could be for the purpose of active flow sensing. We also address the case of red nose tetra fish Hemigrammus bleheri swimming in groups in a uniform flow, giving special attention to the basic interactions and cooperative swimming of a single pair of fish. We first bring evidence of synchronization of the two fish, where the swimming modes are dominated by "out of phase" and "in phase" configurations. At last, we challenge the question of energy benefit by discussing the channeling effect versus the vortex interaction hypothesis (Weihs, Nature 241:290-291, 1973) about diamond shape. We provide the experimental observation that fish prefer inline formation or phalanx formation over the diamond shape while swimming in a school

The lipid composition of five species of marine finfish from temperate Australian waters was determined. Claims that the lipids of Australian fish contain high levels of omega-6 fatty acids and arachidonic acid (AA) were investigated. Individual fish were analysed from samples collected at three locations and two seasons, and they were found to have fatty acid compositions of similar nutritional value to those from northern hemisphere temperate waters. Levels of AA, eicosapentaenoic acid and docosahexaenoic acid were also found to be comparable. The variability in fatty acid compositions was greater between samples taken from different locations than from different seasons. Lipid contents and compositions were found to exhibit some species-characteristic nature, indicating a need for accurate species identification. A high-performance liquid chromatographic (HPLC) method for fish identification was developed, which was successful. The application of HPLC to processed fish was investigated and it was found to be suitable for gamma-irradiated and infrared dried fish, but not for those that had been smoked or microwave cooked. / Doctor of Philosophy (PhD)