This dissertation research explored the capabilities of neuronal networks grown on substrate integrated microelectrode arrays in vitro to be applied to toxicological research and lipid signaling. Chapter 1 details the effects of chlorine on neuronal network spontaneous electrical activity and pharmacological sensitivity. This study demonstrates that neuronal networks can maintain baseline spontaneous activity, and respond normally to pharmacological manipulations in the present of three times the chlorine present in drinking water. The findings suggest that neuronal networks may be used as biological sensors to monitor the quality of water and the presence of novel toxicants that cannot be detected by conventional sensors. Chapter 2 details the neuromodulatory effects of N-acylethanolamides (NAEs) on the spontaneous electrical activity of neuronal networks. NAEs are a group of lipids that can mimic the effects of marijuana and can be derived from a variety of plant sources including soy lecithin. The most prominent NAEs in soy lecithin, palmitoylethanolamide (PEA) and linoleoylethanolamide (LEA), were tested individually and were found to significantly inhibit neuronal spiking and bursting activity. These effects were potentiated by a mixture of NAEs as found in a HPLC enriched fraction from soy lecithin. Cannabinoid receptor-1 (CB1-R) antagonists and other cannabinoid pathway modulators indicated that the CB1-R was not directly involved in the effects of NAEs, but that enzymatic degradation and cellular uptake were more likely targets. The results demonstrate that neuronal networks may also be a viable platform for the elucidation of biochemical pathways and drug mechanisms of action.

Magister Scientiae (Biodiversity and Conservation Biology) / The aim of this study was to use plants to determine the degree of heavy metal contamination in water and sediments in order to effectively monitor and provide possible recommendation to improve the water quality in the aquatic ecosystem of the Bottelary River. / South Africa

Thesis (MScEng)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: The increased water demand to be supplied by municipal water distribution systems, and subsequent increased storage period of reserve water, may have implications with regards to water ageing and subsequently may have an impact on health and safety. Current master planning design standards could have a negative effect on water residence time. The decay of the disinfectant potential is a function of the residence time in the distribution system. The objective of this study is to identify and measure existing systems to optimally increase water quality in a distribution system while supplying an increase in demand, dealing with the deterioration of pipe infrastructure and the introduction of alternative water sources. To do this, one must understand the dynamics of water networks and the parameters that affect water quality. The foundation of a water quality model is based on the construction of an accurate hydraulic model. To identify and measure these systems, one must understand the aspects of water purification and the techniques used to achieve water standards in a distribution system. These techniques and standards play a huge role in the prediction of water quality. In this paper the fundamentals and techniques used to determine and measure such a model are discussed. Consequently, additional design parameters to assess water quality must be incorporated into current master planning practice to optimally design water networks. These models are used to determine the appropriate levels of disinfectant at strategic locations in a system. To illustrate these design parameters and systems currently used in practice, a case study involving Umgeni Water (UW) and EThekwini municipality (EWS) was used to determine the most suitable disinfectant strategy for a municipality’s distribution system. Future scenarios and the impact of disinfectant mixing and increased residence time of the water in the system were also determined. The use of this water quality model in a distribution system will ultimately provide a sustainable platform for a risk monitoring procedure. / AFRIKAANSE OPSOMMING: Die verhoogde aanvraag na water in munisipale voorsieningstelsels, en die daaropvolgende verhoogde stoortydperk van reserwe water, kan implikasies inhou met betrekking tot water veroudering waarna dit ‘n impak op gesondheid en veiligheid kan hê. Huidige meesterbeplanning ontwerpstandaarde kan 'n noemenswaardige uitwerking op water retensietyd hê, veral omdat chloor se vervaltyd op sy beurt 'n funksie van water retensietyd is. Die doel van hierdie studie is om 'n prosedure te identifiseer om watergehalte optimaal te verhoog in 'n waterverspreidingstelsel, terwyl die toename in water aanvraag voortduur. Om dit te kan doen moet die dinamika van water netwerke en die parameters wat die gehalte van water beïnvloed, bestudeer word. Die opstel van 'n waterkwaliteit model is gebaseer op die bou van 'n akkurate hidrouliese model. Om uiteindelik die ontwerp van 'n waterkwaliteit oplossing suksevol uit te voer, moet 'n mens al die aspekte van watersuiwering en die tegnieke wat gebruik word om waterstandaarde te handhaaf in 'n verspreidingstelsel verstaan. In hierdie verslag word die beginsels en tegnieke wat gebruik word om so 'n model op te stel, bespreek. Bykomende waterkwaliteit ontwerpparameters moet by huidige meesterbeplanning gevoeg word om waternetwerke optimaal te ontwerp. Hierdie modelle word gebruik om die geskikte vlakke van ontsmettingsmiddel op strategiese plekke in 'n stelsel te bepaal. 'n Gevallestudie van Umgeni Water (UW) en eThekwini-munisipaliteit (EWS) is gebruik om die mees geskikte ontsmettingsmiddel strategie vir 'n munisipaliteit se verspreiding te illustreer. Toekomstige scenario's en die impak van ontsmettingsmiddelvermenging en verhoogde retensietyd van die water in die stelsel sal ook bepaal kan word. Die gebruik van hierdie gehalte-watermodel in 'n verspreidingstelsel sal uiteindelik 'n volhoubare platform vir 'n risiko moniteringstelsel inhou.

<p align="justify"><i>Typologie des cours d’eau en Wallonie et caractérisation par la faune invertébrée</i><br>Vingt-cinq types de cours d’eau ont été définis en Wallonie d’après les termes de la Directive Cadre pour l’Eau en tenant compte des facteurs obligatoires et optionnels rassemblés sous trois critères : la taille (du « ruisseau » à la « très grande rivière »), la pente (faible, moyenne et forte), et cinq régions naturelles (la région limoneuse, le Condroz, la Famenne, l’Ardenne et la Lorraine belge, résumant les facteurs obligatoires altitude, latitude, longitude et géologie). Une approche par analyses multivariées appliquées à un grand nombre d’échantillons (listes taxonomiques) a permis de définir de façon plus précise certains types de rivières et de distinguer sept groupes typologiques montrant des assemblages faunistiques similaires.</p> <p align="justify"><i>Conditions de référence types et définition de l’état écologique des rivières en Wallonie à l’aide de métriques biocénotiques basées sur les invertébrés</i><br> Les listes faunistiques et les valeurs métriques de l’IBGN (Indice biologique global normalisé) issues du réseau d’évaluation de la qualité biologique en Wallonie ont été utilisées pour discriminer les types de rivières et pour définir les sites de référence, les conditions de référence et les limites des classes des états écologiques. Au sud du sillon Sambre et Meuse, impliquant quatre groupes typologiques de rivières, les valeurs de référence et la définition des états écologiques ont été basées et calculées sur un réseau de référence de sites de très bon état. Les « valeurs de conditions de référence » ont été définies par les médianes des métriques des sites de « très bon état ». Lorsque aucun site de très bon état n’était disponible, c’est-à-dire pour les groupes typologiques au nord du sillon Sambre et Meuse et pour la Meuse et la Sambre, les conditions de référence (ou le « potentiel écologique maximal ») et les limites de classes ont été basées sur des coefficients appliqués aux sites de « bon état » et sur jugement d’expert.</p> <p align="justify"><i>Exercice pilote d’inter-étalonnage</i><br> Cinquante échantillons ont été sélectionnés parmi les rivières du type d’inter-étalonnage européen R-C3 (petite taille, altitude moyenne, substrat siliceux) en Wallonie (correspondant aux « ruisseaux ardennais ») dans toute la gamme de qualités écologiques, du « très bon » au « mauvais » état. Chaque métrique de l’indice « Intercalibration Common Metrics » (ICM) a été comparée (par régression linéaire et polynomiale) aux valeurs de l’IBGN. La plus forte corrélation a été établie avec l’indice synthétique de l’ICM dont le R² très élevé (0,95) permet un inter-étalonnage précis et fiable. A un EQR (Equivalent Quality Ratio) de l’IBGN = 1 correspond un indice ICM très proche (= 1,004). En conséquence, la métrique « cote de l’IBGN » est proposée comme métrique pour l’évaluation de l’état écologique de la faune invertébrée en Wallonie.</p> <p align="justify"><i>Espèces exotiques et invasives</i><br>L’ouverture récente du canal à grand gabarit Main – Danube en 1992 et la navigation qui en résulte a permis à plusieurs espèces de macroinvertébrés ponto-caspiennes d’envahir successivement les bassins du Rhin et de la Meuse. De 1998 à 2000, le réseau de mesure a enregistré quatre nouvelles espèces exotiques dans la Meuse en Belgique : une polychète (<i>Hypania invalida</i>) et trois crustacés (<i>Hemimysis anomala, Dikerogammarus villosus, D. haemobaphes</i>). Peu avant, en 1995, le bivalve asiatique <i>Corbicula fluminea</i> et l’amphipode nord-américain <i>Crangonyx pseudogracilis</i> ont également été enregistrés pour la première fois. La dynamique des invasions a été étudiée et discutée.</p> <p align="justify">L’<i>état biologique actuel</i> (2000-2002) des masses d’eaux de surface en Wallonie et l’évolution des états biologiques sur une décennie (1990-2002) figurent dans l’étude et sont discutés. Une amélioration globale de la qualité de 6 % est enregistrée pour cette période. L’amélioration de la qualité se manifeste principalement pour les états « mauvais » et « médiocre » s’élevant à l’état « moyen ».</p> <b>Abstract</b> <p align="justify"><i>River typology in Wallonia and invertebrate fauna characterization</i><br>Twenty-five river-types in Wallonia were defined according to the Water Framework Directive taking into account obligatory and optional factors gathered in three criteria: the size (from “brook” to “very large river”), the slope (gentle, medium and strong) and five natural regions (Loess, Condroz, Famenne, Arden and Jurassic summarising the obligatory altitude, latitude, longitude and geology factors). A multivariate approach applied to a large amount of samples (i.e. taxa lists) led to give a more accurate definition of some river-types and to discriminate seven river-type groups exhibiting similar faunal assemblages.</p> <p align="justify"><i>Type-specific reference conditions and ecological status definition of rivers in Wallonia using invertebrate biocenotic metrics</i><br> Faunal lists and IBGN (i.e. "Standardized Global Biological Index IBGN") metric values, evolving from the biological quality assessment network in Wallonia, were used to discriminate the river types and to define the reference sites, the reference conditions and the status class limits. South of the axis made by the Sambre & Meuse Rivers, involving four river-type groups, reference values and ecological status definition were based and calculated on a reference network of sites of high status. The "reference condition values” were defined as the median values of the metrics in all “high status” sites. Where no site of high status was available, i.e. in the others river-type groups north of the same axis and in the Rivers Sambre and Meuse themselves, reference conditions (or maximum ecological potential) and class limits were based on coefficients applied to “good status” sites and on expert judgement.</p> <p align="justify"><i>Intercalibration pilot exercise</i><br> Fifty samples were selected from R-C3 rivers (i.e. small, mid-altitude, siliceous) in Wallonia (corresponding to the “Arden’s brooks”) showing the widest range of ecological quality from high to bad status. Each Intercalibration Common Metric (ICM) was compared (linear and polynomial regression) to IBGN scores. The highest correlation was found with the synthetic ICM index, whose high R² (0.95) allows accurate and reliable intercalibration. To IBGN EQR (i.e. Equivalent Quality Ratio) = 1 corresponds a very close ICM index value (= 1.004). Consequently, the metric IBGN score is being proposed to act as the metric for the assessment of the invertebrate fauna ecological status in Wallonia, Belgium.</p> <p align="justify"><i>Exotic and invasive species</i><br> The recent opening of the canal Danube – Main in 1992 and the subsequent navigation allowed several Ponto-Caspian macroinvertebrate species to invade successively the Rhine and the River Meuse basins. From 1998 to 2000, the monitoring network recorded four new alien species in the River Meuse in Belgium: one Polychaeta (<i>Hypania invalida</i>) and three Crustacea (<i>Hemimysis anomala, Dikerogammarus villosus, D. haemobaphes</i>). Earlier, in 1995, the Asian Bivalvia <i>Corbicula fluminea</i> and the North American Amphipod <i>Crangonyx pseudogracilis</i> were also recorded for the first time. The invasions’ dynamics were studied and discussed.</p> <p align="justify"><i>Present biological status</i> (2000-2002) of surface water-bodies in Wallonia and biological status evolution over a one-decade period (1990-2002) is included and discussed in the study. A global quality improvement of 6 % is recorded for the period. Quality improvement concerns mainly the “bad” and “poor” status raising up to “moderate” status.</p>

A brown tide bloom of the pelagophyte Aureoumbra lagunensis caused significant impacts to north Indian River Lagoon (IRL) in 2012-2013, including seagrass die-offs, fish kills, and reduced growth and grazing of ecologically important bivalves. There is potential for another pelagophyte, Aureococcus anophagefferens, to expand into this system. Filtration rates (FR) of the pleated tunicate Styela plicata exposed to Aureoumbra lagunensis and Aureococcus anophagefferens were measured against exposure to a control alga (Tisochrysis lutea) in order to determine its potential use as a bioremediator against these harmful algal blooms (HABs). In addition, whether S. plicata might serve as a vector of HABs was studied by culturing fecal deposits. Short-term exposure to HABs significantly reduced FR, whereas long-term exposure indicates comparable cell removal compared to the control. Vector potential of S. plicata was inconclusive. Results warrant further research to determine whether S. plicata can acclimate or respond to HAB conditions over time. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2015. / FAU Electronic Theses and Dissertations Collection

Lake Tana is a biodiversity and natural reservoir for fresh water supply contributing significantly to the economy of Ethiopia and downstream recipient countries, namely: Sudan and Egypt. The Lake Tana Ecosystem provides a variety of goods and services such as: provisioning, regulating, amenity and supporting services. These services are affected by high human activities which threaten the water quality and biodiversity of the lake. Hence, this study aims to assess the impact of human activities on water quality, biodiversity and livelihood of Lake Tana and its shore sides.To assess the impact of anthropogenic activities of Lake Tana; physicochemical parameters, macroinvertebrates, macrophytes and livelihood of the Lake side communities were collected in the year 2014/2015 during dry and wet seasons for 11 sampling sites as indicated in Figure 1.1 and Table 1.1. The variations of physicochemical, metals and bacterial parameters were investigated. The overall water quality parameters (mean analytical results) of Lake Tana were found to be: Temp (Temperature)23.0OC, pH 7.5, EC (Electrical conductivity)180.1 μS/cm, BOD5 (Biological oxygen demand in 5 days)37.3 mg/l, COD (Chemical oxygen demand)316.5 mg/l, TSS 0.3 mg/l, TDS 93.1 mg/l, SO4 2- 11.0 mg/l, PO4 3- 42.4 mg/l, Cr (0.08 mg/l), (Mn (0.01 mg/l), E. Coli (13.4 Cell/ml), F. Coliform (82.5 Cell/ml), T. Coliform (113.0 Cell/ml), etc. These parameters did not show significant variation among the sites but were significantly different between wet and dry seasons (P<0.05). The highest concentration values were recorded during the wet season. However, most of the parameters under investigation were within the Ethiopian EPA (Environmental protection agency) permissible range except PO4 3-, S2-, E. Coli (Cell/ml), F. Coliform (Cell/ml) and T. Coliform (Cell/ml). Based on the analysis of the water quality index (WQI), Lake Tana water was unfit for drinking purpose and needs treatment. For theMacroinvertebrates analysis, a total number of 629 macroinvertebrate individuals are belonging to 9 orders and 38 families were found. In the study year impacted areas number of identified macroinvertebrates were 478 (76%); of this, 233 (37%) were in the wet season and 245 (39%) in the dry season and the total number of individuals identified in the reference area was 151 (24% of the total) in the wet season 61 (9.7%) and in the dry season 90 (14.3%) individuals. The diversity was more in the dry season. The dominant orders were Odonata (156 individuals), Coleoptera (153 individuals) and Hemiptera (141 individuals). The literature indicated that the presence of more Odonata, Coleptera and Hemipteran larvae is an indication of water quality deterioration due to pollution. From the collected samples, the total number of tolerant individuals was 303 (48.2%) and facultative individuals were 243 (38.7%) while intolerant individuals were 80 (12.7%). Most of the taxa (48.2%) had tolerance scores ranging from 7 to 10. The analysis of different forms of indices showed poor water quality. The water quality of Lake Tana was also determined by developing the LTMI (Lake Tana Metric Index). The index indicated the impairment levels of the study sites. Seven of the sites were in the category of poor (disturbed) and the other three were very poor (highly disturbed). The study on macrophytes recorded 43 species and 18 families during the two seasons (wet and dry), throughout the study year. 2687 individual macrophytes were collected; 1756 in the wet season and 931 in the dry season. Poaceae (15 species) with abundance mean 215.40 ± 421.7 was the most dominant family, followed by Cyperaceae (5 species) 35.40 ± 68.3. Sacciolepis africana was the dominant macrophyte species in Lake Tana. But in the study area Ambobahir, the dominant species was Cyperus papyrus while the Megech study area was invaded by the nuisance exotic weed Eichhornia crassipes. In the present study, the low macrophyte diversity values of Shannon Wiener index (2.90), Simpson Diversity Index (1-D) (0.90), Simpson Dominance Index (D) (0.10), Margalef’s index (M’) richness index (5.32) and Evenness Index (E) (0.77) throughout the study year indicate moderate water quality status while the presence of certain bio-indicator species like Eichhornia, Potamogeton and Cyperus in the lake also confirm pollution. Because of the effect of human activities on water quality and biodiversity, the livelihood of the riparian community is affected indirectly. Hence, to recommend mitigation and remediation actions, this study also focused on the assessment of the change of livelihoods of people living in the study area using qualitative research methods (key informant interview, focus group discussion (FGD), observations, published and unpublished materials and photographes). Lake Tana is a home to different flora and fauna including endemic species. The flora such as macrophytes and forest resources are used mainly for traditional medicine, fuel wood, rope, pole, habitat for birds, animal feed, etc. and the fauna includes fish, hippos, crocodiles, invertebrates, etc. Further, the Lake Tana area is a good habitat for indigenous cattle breeds (Fogera breed) and field crops gene center. The major resources around Lake Tana are land (the major source of livelihood), vegetation resources (macrophytes and forest resources), wildlife resources (fish, the other important source of livelihood) and cultural landscapes (churches and monasteries). Lake Tana is exposed to a set of interrelated environmental problems induced by human influence such as deforestation, erosion, sedimentation, water level reduction, erratic rainfall, flood, and competition for water resources, pollution and introduction of alien species. The causes to these problems were overgrazing, farmland expansion, cultivation of marginal lands (shorelines), encroachment of communal land, pollution and vegetation removal to meet demand for food and fuel wood. It is observed that alteration of Lake Tana and its fringe wetlands has affected the whole dynamics of the Lake’s ecosystem and the livelihood of the surrounding community. Ecosystem components are interlinked; hence correlation analysis was done between physicochemical parameters and macroinvertebrates of Lake Tana. Thus, correlations among many of the physicochemical parameters and macroinvertebrates families have been observed. To mention some of the correlations, the changes in the physical, chemical and biological characteristic of the lake affected the aquatic life forms and significantly affect economic activities that the lake supports. The RDA(Canonical redundency analysis) ordination of the species-environmental variable association indicated that pH, Cd, Pb and SO42- and Velidae, Chironomidae, Physidae, Gerridae, Corixidae, Dytiscidae, Caenidae, Coenogrionidae Simuliidae and Psephenidae were negatively correlated while Mussidae positively correlated with these environmental variables. This study concludes that the main threat to aquatic ecosystems in Lake Tana arises from agricultural activities, urbanization and industrialization that deteriorated water quality and biodiversity. Thus, it is recommended that proper management of Lake Tana should be put in place to prevent further deterioration of water quality and biodiversity of the lake for its sustainable development. / Environmental Sciences / Ph. D. (Environmental Science)

Thesis (MSc.) Zoology)) -- University of Limpopo, 2019 / In South Africa, a high anthropogenic demand of water for domestic, recreational, agricultural, urbanisation and industrial purposes has placed enormous pressure on freshwater resources and has led to a decline in water quality. In addition to measuring water quality variables, the health assessment index (HAI) advocated by AvenantOldewage and Swanepoel (1993), and modified by Crafford and Avenant-Oldewage (2009) by incorporating the inverted parasite index (IPI), and adapted further by Madanire-Moyo et al. (2012) who excluded the white blood cells counts, has been used as a rapid and inexpensive means of assessing and monitoring fish health and, in turn, the state of aquatic ecosystems. However, few studies have evaluated the latter approach in conjunction with other biomonitoring indices to assess the water quality of impoundments. Thus, the aim of this study was twofold. The first was to evaluate the HAI adapted by Madanire-Moyo et al. (2012) as a means to establish the health status of Oreochromis mossambicus (Peters, 1852) sampled from various impoundments based on a once-off survey. The second was to establish if the adapted HAI, in conjunction with selected biomonitoring indices and environmental variables, could describe monthly and seasonal fluctuations of O. mossambicus health. Once-off surveys were conducted between April and May 2016 at five impoundments. The Luphephe-Nwanedi Dam located in the upper catchment of the Limpopo River System and Rhenosterkop Dam situated in the Elands River, a tributary of the Olifants River System, served as control sites due to little or no anthropogenic activities occurring in their catchment areas. In addition, surveys were conducted at Loskop and Flag Boshielo dams and Phalaborwa Barrage situated in the main stem of the Olifants River for comparison purposes. The latter three impoundments were selected because they vary in water quality and pollution levels. Monthly surveys were carried out at Flag Boshielo Dam from February 2016 to February 2017 to establish if the biomonitoring tools and the quantification of water and sediment quality variables, could describe and predict seasonal fluctuations in the health of O. mossambicus. To this end, water quality variables were measured during each survey. Water and sediment samples were collected for analysis of nutrients and metals. Oreochromis mossambicus were collected using gill nets. Fish health was assessed using the adapted HAI that was based on observing parasite burden, haematocrit determination and anomalies in body tissues and organs in conjunction with determining gonad and iv hepato-somatic indices, the condition factor, blood glucose levels, microscopy analyses of fish gills and metal concentrations in fish muscle tissues. Water quality in terms of pH, total dissolved solids and electrical conductivity, nutrients and some aqueous and sediment metals exhibited significant differences (p ˂ 0.05) between impoundments surveyed with water quality from good to poor being in the order of: Luphephe-Nwanedi Dams ˂ Rhenosterkop Dam ˂ Loskop Dam ˂ Phalaborwa Barrage ˂ Flag Boshielo Dam. The HAI scores varied significantly (p ˂ 0.0001) between impoundments and substantiated water quality variables results during once off surveys, indicating that the health of fish from Flag Boshielo Dam were most affected when compared to the health of fish surveyed from the other impoundments. Findings from monthly surveys conducted at Flag Boshielo Dam indicated better conditions in terms of water quality variables during a period of high inflow as opposed to periods of low inflow. The HAI scores obtained for fish exhibited significant (p ˂ 0.0001) differences between the months surveyed and were found to be in agreement with the water quality findings, indicating that flow regimes and water quality of an impoundment have an impact on fish health. The condition and somatic indices findings did not seem to be sensitive enough to discriminate between the impoundments during the once off surveys. While during monthly surveys, these indices were significantly (p ˂ 0.0001) different between the months, showing to be affected by seasonal fluctuations. Knowledge of the HAI in conjunction with blood glucose levels, gill histopathology and the arithmetic mean thickness of gill epithelium (Har) best described the health of fish in both the once off and monthly surveys. In conclusion, the findings of this study emphasised the HAI premise that fish from more polluted sites would be more impacted as opposed to less impacted sites, making the HAI adapted by Madanire-Moyo et al. (2012) an effective and rapid biomonitoring tool that can be used in the field. Furthermore, this study proved that the HAI can be used either solely or in association with the parasite index (PI) or IPI depending on the objectives of the study, as no pronounced differences were evident when using HAI, HAI with PI and HAI with IPI. / National Research Foundation (NRF) and Water Research Commission (WRC)

Interest in the subject of fish welfare is continuing to grow, with increasing public awareness and new legislation in the UK. Water quality has long been recognised as being of prime importance for welfare: water provides the fish with oxygen and removes and dilutes potentially toxic waste metabolites. This thesis investigates the interactions between water quality and the welfare of farmed rainbow trout (Oncorhynchus mykiss Walbaum). A literature review was undertaken to identify current recommended water quality limits for the health and welfare of farmed rainbow trout. Contradictions in the literature regarding suggested ‘safe’ water quality limits were also identified, as were deficiencies in some of the methods used to arrive at conclusions for recommended limits. The literature relating to the effects of poor water quality on welfare were also reviewed. The review ends with a discussion about water quality monitoring in the context of on-farm welfare assessment and how the information might be used in such a scheme. A telephone survey of UK rainbow trout farmers was undertaken to ascertain the level of water quality monitoring currently conducted. Participants in this study accounted for over 80% of 2005 UK rainbow trout production. It was established that 54% of farmers monitored dissolved oxygen to some extent and 69% monitored temperature, the most commonly measured water quality parameters and among the most important for health, welfare and growth. Subsequent visits were made to a sample of the participants in the telephone survey to obtain more detailed information of the farming operations, such as frequency of water quality monitoring, retention of production data and slaughter methods. Monitoring water quality will be an integral part of any on-farm welfare assessment scheme, and while measuring some water quality parameters requires specialist equipment, farmers should be able to monitor the essential parameters, dissolved oxygen and temperature. Any on-farm welfare assessment scheme for rainbow trout should incorparate fish-based measures in addition to resource-based parameters in order to provide as complete an overview of trout welfare as possible. An epidemiological study was undertaken to investigate the current status of welfare on UK rainbow trout farms and to identify risk factors for welfare. Forty-four trout farms from throughout the British Isles were visited between July 2005 and April 2007, sampling a total of 3700 fish from 189 different systems. Farms were visited twice, once in winter and once in summer, to account for any seasonal differences in fish physiology and environmental conditions. Data were collected on a range of fish parameters, together with background information on the batch from which the fish originated. Particular emphasis was placed on water quality due to the potential effects this can have on welfare. The water in each system sampled was monitored for 24 hours, with measurements of dissolved oxygen, temperature, pH, specific conductivity and ammonia taken every 15 minutes. A welfare score was developed for each fish using a multifactorial method, combining data on the condition of the fins, the condition of the gills, the stress hormone cortisol, the splenosomatic index and the mortality levels for the population of fish in the system. Using this welfare score and the individual components of the score as response variables, multi-level models were developed using the water quality, system and husbandry data collected. The primary risk factor that was associated with deteriorating welfare was disease. The purpose for which the fish was being farmed was also important, as fish farmed for the table market had on average worse welfare than those farmed for restocking fisheries. Seasonal effects, linked to higher water temperatures in summer, were associated with poorer welfare scores. Aside from seasonal effects, there is not much evidence that poor water quality is a major problem for the welfare of farmed rainbow trout in the UK. While deteriorating water quality certainly has the potential to affect the welfare of farmed rainbow trout, water quality measurements were within recommended ranges for the majority of farms visited. The results of this epidemiological study suggest that factors other than water quality may have a greater impact on trout welfare, such as exposure to diseases and production differences between farming for the table and restocking markets.

This study assessed the quality of the Umgeni River in Durban South Africa seasonally from March 2011 to January 2012, according to standard protocol. Water samples were collected from Inanda dam-U5, KrantzKloof Nature Reserve-U4, New Germany-U3, Reservoir Hills –U2 and River mouth – U1 areas of the Umgeni River. A two-step tangential flow filtration (TFF) process was setup for the concentration of viruses from water samples. Virus like particles (VLPs) was detected using electron microscopy. Canonical correspondence analysis (CCA) was used to statistically evaluate the data sets. All water samples had turbidity values which exceeded the South African water quality guideline value of 0.1 NTU for turbidity. Large seasonal variations in BOD5, COD and conductivity levels were observed. Chloride concentrations were extremely high at point U1 (19234 mg/ℓ) Cl during summer. Total heterotrophic bacterial (THB) population was highest at 13.67 x 106 cfu/100ml (U1 – summer). Enterococci (EC) concentrations were detected at points U1, U2, U3, and U4 during the autumn and spring period. pH, electrical conductivity, temperature, and turbidity positively correlated with the microbial communities, and were the key parameters responsible for water pollution according to CCA. Most water samples contained high populations of somatic (659 pfu/mℓ, U1 – summer) and F-RNA coliphages (550 pfu/mℓ, U2 – summer). VLPs were detected throughout all seasons, with point U1 (summer) having the highest population of 2086 VLP/mℓ. Several presumptive viruses including Adenoviridae, Picornaviridae, Poxviridae, and Reoviridae were detected based on their morphologies. Six cell culture lines were used to determine cytopathic effect (CPE) of the VLPs. VLP samples produced CPEs on the Vero, Hek 293, Hela and A549 cell lines. Integrated cell culture (ICC) - PCR confirmed the presence of infectious VLPs in the river water samples. Adenoviruses, Enteroviruses, rotaviruses and Hepatitis B viruses were detected and quantified in all water samples by nested PCR/RT-PCR and Real-Time PCR respectively, against positive control viruses. These results indicate the potential of viruses in the water samples especially from the lower catchment areas to infect the human hosts throughout the year. These observations have public health care implications and establish a need to monitor the viral population in addition to traditional water quality indicators. / Thesis (Ph.D.)-University of KwaZulu-Natal, Westville, 2013.

Submitted in partial fulfillment for the Degree of Master of Applied Sciences in Biotechnology, Durban University of Technology, Durban, South Africa, 2017. / The study aims to assess and compare the concentration of microbial contaminants, their sources and distribution in surface water and sediment, and to determine the impact of seasonal variations and corresponding risks of faecal contamination using conventional and molecular methods. Historical data analysis was conducted using E. coli values from the eThekwini Water and Sanitation (EWS) department for 66 months (2009-2014). E. coli and Enterococci were analysed in surface water and sediment samples using the mFC/ spread plate and Colilert-18 (IDEXX) methods. The impact of seasonal variations was assessed using E. coli and Enterococci data collected during rainfall and no rainfall events, using an auto-sampler and sediment trap in parallel. Conventional standard membrane filtration methods using mFC agar, Slanetz & Bartley/ Bile Esculin and Brilliance E. coli selective agar were compared to the enzymatic Colilert-18 and Enterolert (IDEXX) test methods along the Isipingo and Palmiet Rivers. In addition, comparison of the analytical performance of droplet digital PCR (ddPCR) and qPCR for the detection of Salmonella targeting ttr gene in river sediment samples collected from the four sites of the Palmiet River in Durban, South Africa was done. In order to assess the public health risk associated with exposure of men, women and children to microbial pathogens in polluted surface water during recreational activities, the QMRA tool was employed in relation to the risk exposure to pathogenic E. coli, Campylobacter, Salmonella and Shigella. Also, the risk associated with crop irrigation (on farmers) as well as the consumption of crops irrigated with surface water from the Isipingo river was determined. Analysis of the historical data gave a baseline of the two rivers of interest, thus helps understand the current situation of the rivers enabling researchers to pick up potential gaps. In this study after the analysis of the historical data it was evident that at the Palmiet river, microbial analysis must be conducted around the QRI settlements which is a major pollution source. Also, from this study it was found that sampling points situated close to wastewater treatment plants, pump stations or informal settlements were of major concern, thus were considered for the study. It was found that sediment exhibited higher microbial concentrations than surface water, which was observed in both rivers. Also, rainfall had a significant impact on microbial variability. Higher microbial concentrations (indicator organisms) were observed in surface water after a heavy rainfall as appose to when there was no rainfall. This was due to contamination that is washed off into the river and sediment resuspension. Methodology comparison revealed that Colilert-18 and Brilliance E. coli were more selective compared to mFC agar. Brilliance E. coli /Coliform agar was comparable with Colilert-18 IDEXX, which was also observed with Slanetz & Bartley and Enterolert IDEXX. However, when mFC agar was compared with Colilert-18 IDEXX, significant difference was observed. In comparison of two Molecular methods, ddPCR were found to be fully amenable for the quantification of Salmonella and offer robust, accurate, high-throughput, affordable and more sensitive quantitation than qPCR in complex environmental samples like sediments. Quantitative Microbial Risk Assessment (QMRA) relating to recreational and occupational exposure showed that children were at the highest risk of getting infected. Also, it was observed that the probability of infection upon exposure to surface water from the Isipingo and Palmiet rivers was significantly high, hence exceeded the WHO guidelines values. Risk assessment on crops revealed that pathogenic bacteria may pose a risk to the consumer, however, a 9-log reduction may be achieved according to the WHO multi-barrier approach which involves proper washing and proper cooking of the crop before ingestion. Overall the sampling points that had the highest pollution level and constantly exceeded the WHO and DWAF guidelines at the Isipingo river were the points situated and named “Next to the WWTP”, and “Downstream of QRI” at the Palmiet River. / M