Microbial pollution of surface waters and coastal zones is one of the foremost challenges facing the water industry and regulatory authorities. Yet despite the concern and increasing pressures on water resources in both developed and developing countries, understanding of microbial pollutants in the aquatic environment is fairly scattered. There is a need for an improved ability to quantify the processes that control the fate and distribution of enteric organisms to support decision - making and risk management activities. The aim of this thesis has been to advance the understanding of the dynamics of microbial pollution in aquatic systems through review, experimentation and numerical modelling. Initially, a new module for simulating the protozoan pathogen, Cryptosporidium, was developed and implemented within a three - dimensional ( 3D ) coupled hydrodynamic - water quality model ( ELCOMCAEDYM ). The coupled 3D model was validated against a comprehensive dataset collected in Myponga Reservoir ( South Australia ), and without calibration, performed to a high degree of accuracy. The investigation then sought to examine the experimental dataset in more detail and found a significant difference between protozoan pathogens and the bacterial and viral indicators. To examine the role of bacterial association with particles in more detail, a second experimental campaign was carried out in Sugarloaf Reservoir ( Victoria ). This campaign was used to gain insights into the association of coliform bacteria with suspended sediment and to quantify their sedimentation dynamics based on in situ measurements. Using an inverse technique, particle profile data was used to create a simple Lagrangian model that was applied to back - calculate the sedimentation rates of the coliform bacteria and the fraction that were attached to the particles. The results indicated that 80 - 100 % were associated with a small - sized clay fraction. This result was in contrast with the Cryptosporidium dynamics in Myponga Reservoir, where it was concluded that oocysts did not settle with the inorganic particles. These findings indicated the current models for simulating the array of organisms of interest to regulatory authorities are inadequate to resolve the level of detail necessary for useful predictions and risk management. Large differences between the protozoa, bacteria and phages were being observed due to different particle association rates and sedimentation dynamics, order of magnitude differences in natural mortality rates, and different sensitivity to sunlight bandwidths. The original model implemented within CAEDYM was therefore rewritten to be more complete and generic for all microbial pollutants and different types of aquatic systems. The model was built using a generic set of parameterizations that describe the dynamics of most protozoan, bacterial and viral organisms of interest. The parameterizations dynamically account for sensitivities to environmental conditions, including temperature, salinity, pH, dissolved oxygen, sunlight, nutrients and turbidity, on the growth and mortality of enteric organisms. The new model significantly advances previous studies in several areas. First, inclusion of the growth term allows for simulation of organisms in warm, nutrient rich environments, where typical die - off models tend to over - predict loss rates. Second, the natural mortality term has been extended to independently account for the effects of salinity and pH, in addition to temperature. The salinity - mediated mortality has also been adapted to account for the nutrient status of the medium to simulate the importance of nutrient starvation on the ability of an organism to survive under osmotic stress. Third, a new model for sunlight - mediated mortality is presented that differentially accounts for mortality induced through exposure to visible, UV - A and UV - B bandwidths. The new expression has capacity to simulate the photo - oxidative and photo - biological mechanisms of inactivation through included sensitivities to dissolved oxygen and pH. Fourth, the model allows for organisms to be split between free and attached pools, and sedimented organisms may become resuspended in response to high shear stress events at the water - sediment interface caused by high velocities or wind - wave action. Fifth, the enteric organism module has been implemented within the bio - geochemical model CAEDYM, thereby giving it access to dynamically calculated concentrations of dissolved oxygen, organic carbon, and suspended solids, in addition to pH, shear stress and light climate information. Without adjustment of the literature derived parameter values, the new model was validated against a range of microbial data from three reservoirs that differed in their climatic zone, trophic status and operation. The simulations in conjunction with the experimental data highlighted the large spatial and temporal variability in processes that control the fate and distribution of enteric organisms. Additionally, large differences between species originate from variable rates of growth, mortality and sedimentation and it is emphasized that the use of surrogates for quantifying risk is problematic. The model can be used to help design targeted monitoring programs, examine differences between species and the appropriateness of surrogate indicators, and to support management and real - time decision - making. Areas where insufficient data and understanding exist are also discussed. / Thesis (Ph.D.)--School of Earth and Environmental Sciences, 2007.

Increased abstraction of water in the catchment results in a reduced or altered pattern of river flow and this holds serious consequences for the downstream estuarine ecosystem. In South Africa this is a serious concern because freshwater is in limited supply and the demand for freshwater can be expected to increase in the future. A large multi-disciplinary consortium of South African scientists are working on projects to determine the freshwater requirements of estuarine ecosystems. As part of this, this thesis reports on research undertaken to develop mathematical models to determine the freshwater requirements of estuarine macrophytes. Three key macrophytes are selected. The macrophytes are Zostera capensis Setchell, Ruppia cirrhosa Grande, and Phragmites australis. They are common macrophytes in South African estuaries. Zostera and Ruppia are submerged macrophytes and Phragmites is an emergent macrophyte. They have different freshwater environments and therefore respond differently to alterations in freshwater flow. A first order differential equation model is used to determine the effect of different combinations of open and closed mouth conditions of the estuary on Zostera and Ruppia. The scenarios are selected to determine whether achieving a switch in states from a Zostera-dominated estuary to a Ruppia-dominated estuary is possible. To predict encroachment rates and colonisation patterns, a cellular automaton of the vegetative spread of existing Zostera beds is developed. After analysing various scenarios accounting for both an increase and a decrease in freshwater supply, the cellular automaton is extended to include interactions between Ruppia and Phragmites. The multi-species model is applied to the Kromme estuary, South Africa and the Great Brak estuary, South Africa. Various freshwater scenarios are examined from the natural runoff condition to the situation of no freshwater inflow. A sensitivity analysis of the spatial model with Zostera, Ruppia and Phragmites is conducted. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 1998.

Increased abstraction of water in the catchment results in a reduced or altered pattern of river flow and this holds serious consequences for the downstream estuarine ecosystem. In South Africa this is a serious concern because freshwater is in limited supply and the demand for freshwater can be expected to increase in the future. A large multi-disciplinary consortium of South African scientists are working on projects to determine the freshwater requirements of estuarine ecosystems. As part of this, this thesis reports on research undertaken to develop mathematical models to determine the freshwater requirements of estuarine macrophytes. Three key macrophytes are selected. The macrophytes are Zostera capensis Setchell, Ruppia cirrhosa Grande, and Phragmites australis. They are common macrophytes in South African estuaries. Zostera and Ruppia are submerged macrophytes and Phragmites is an emergent macrophyte. They have different freshwater environments and therefore respond differently to alterations in freshwater flow. A first order differential equation model is used to determine the effect of different combinations of open and closed mouth conditions of the estuary on Zostera and Ruppia. The scenarios are selected to determine whether achieving a switch in states from a Zostera-dominated estuary to a Ruppia-dominated estuary is possible. To predict encroachment rates and colonisation patterns, a cellular automaton of the vegetative spread of existing Zostera beds is developed. After analysing various scenarios accounting for both an increase and a decrease in freshwater supply, the cellular automaton is extended to include interactions between Ruppia and Phragmites. The multi-species model is applied to the Kromme estuary, South Africa and the Great Brak estuary, South Africa. Various freshwater scenarios are examined from the natural runoff condition to the situation of no freshwater inflow. A sensitivity analysis of the spatial model with Zostera, Ruppia and Phragmites is conducted. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 1998.

Doctor of Philosophy / Department of Geography / Melinda Daniels / Geomorphic properties of streams are linked to ecosystem function through processes related to storage, transport, and other drivers regulating biogeochemical conditions. Disturbances altering the physical template of a stream are associated with cascading impacts on ecosystem function. However, few disturbances are studied at long time scales and so the legacy of such events and the implications for ecosystem structure and function are not well understood. This research investigates the role of historic tie-driving, a channel disturbance legacy, in shaping present-day stream channel conditions in the Rocky Mountain region and the associated implications for organic matter dynamics. Using a combination of geomorphic and riparian surveys, organic matter and vegetation sampling, and modeling, I show that components of mountain stream ecosystems have recovered from tie-driving at varying rates. First, I addressed how tie-driving has altered channel morphology and wood loading. Tie-driven streams are narrower, shallower, less rough, and have less wood than non-driven reference reaches. In a second study, I focused on differences in carbon storage within the stream and riparian area between tie-driven and non-driven streams. Carbon stored on the landscape represents a long-term component of the terrestrial carbon cycle and some, but not all, components have been impacted by tie-driving. Large instream wood, coarse downed wood, and fine downed wood were identified as carbon storage components that were significantly smaller in tie-driven stream-riparian corridors. Finally, I modeled whole stream ecosystem metabolism and tested whether abiotic drivers influenced variations in rates of gross primary productivity (GPP), ecosystem respiration (ER), and net ecosystem productivity (NEP). Results from this work suggest that rates of GPP were significantly different between tie-driven and non-driven streams and were partially explained by variations in light related to canopy structure. However, variations in ER and NEP were not significantly different between tie-driven and non-driven sites. Taken as a whole, this work shows that ecosystems bear the imprint of historic disturbances but individual ecosystem components recover at differing rates. Additionally, integrating stream hydro-geomorphic and ecological dynamics is an effective approach to understanding the impact of channel disturbances in shaping ecosystem function at a variety of spatial and temporal scales.

Inland waters receive substantial amounts of organic carbon from adjacent watersheds. Only about half of the carbon exported from inland waters reaches the oceans, while the remainder is lost en route. This thesis identifies flocculation as an important and significant fate of carbon in the boreal landscape. Flocculation reallocates organic carbon from the dissolved state into particles which are prone to settle. Thus, flocculation relocates organic carbon from the water column to the sediment. The dissolved organic carbon (DOC), mainly originating from terrestrial sources, in a set of Swedish lakes was found to determine the extent of sedimentation of particulate organic carbon. A major fraction of the settling particles were of allochthonous origin. This implies that allochthonous DOC was the precursor of the settling matter in these lakes. The gross sedimentation was of the same magnitude as the evasion of carbon dioxide to the atmosphere. Sunlight, especially in the photosynthetically active region, stimulated flocculation of DOC. The effect of light appeared to involve a direct photochemical reaction. Iron was involved in the flocculation but it could not be unravelled whether the iron catalyzes the flocculation or just co-precipitates with the settling matter. Microbial activity was identified as the main regulator of the flocculation rates. Accordingly, alteration of temperature, oxygen concentration and pH did not affect flocculation only indirectly, via their effects on microbial metabolism. A comparison of fluorescence characteristics of organic matter collected in sediment trap and in the sediment surface layer revealed that autochthonous organic carbon was preferentially lost in the sediments while allochthonous matter increased. The recalcitrant nature of the flocculated matter could favour sequestration of this matter in the lake sediment. Hence, the lakes will act as sinks of organic carbon due to a slower mineralization of the flocculated matter in the sediments.

M.Sc. / This study aims to assess the potential impacts of intense feedlot activity on the aquatic freshwater environment, with reference to three feedlots, ranging in production size and all situated in the upper Vaal catchment area. Field assessments were done over a high flow and low flow period, while controlled exposures were also done to quantify a potential stress reaction to growth hormone exposure (using Clarias gariepinus as test organism). It was ascertained that water quality variables contributing towards differences between upstream and downstream environmental conditions are NH4 concentrations pH and conductivity. Lead concentrations were also periodically higher downstream from feedlot activity, in comparison with upstream. Taking the sediment assimilation potential of growth hormones into consideration, it was determined that Feedlot C showed the highest assimilation potential, while Feedlot A reflected the lowest. Alterations on family level invertebrate community structures indicated a categorical decline in abundances and species richness at sites situated downstream from feedlots. However, some clear seasonal influences were also observed. Further community and diversity analyses reflected alterations in invertebrate community structures that were not reflected in SASS 5 scores. With regards to the biomarkers applied in this study, it was noted that there was a significant (p<0.05) difference in the cellular energy allocation (CEA) between control and hormone exposed groups. The total amount of energy available (Ea) increased significantly for test organisms exposed to Diethylstilbestrol (DES), while there was a significant increase in energy consumption (Ec) of test organisms exposed to Trenbolone acetate (TBA). In addition to CEA, metabolic profiling of blood plasma was also performed, which indicated a definite ordination in metabolic constituents after fifteen days of exposure. This was established by subjecting the data to principle component analysis (PCA), which accounted for 83 % variance observed. The impacts and biotic responses identified in this study were contextualised with known literature on the effects of feedlot activity and growth hormone exposure on the aquatic environment. Finally, conclusions were drawn and recommendations made with regard to improving feedlot operational activities. The results obtained in this study contribute towards an integrated framework for the environmental management of feedlot activities.

M.Sc. (Zoology) / The production of nanoparticles started as early as 1990s (Alkilany & Murphy, 2010). Nanoparticles are utilised in a range of products such as electronics, optics, textiles, medical, devices, cosmetics, food packaging, water treatment technology, fuel cells, catalysts, biosensors and agents for environmental remediation (Handy et al., 2008). Unlike natural particles, which dissolve or aggregate and are often temporary in the environment, engineered nanoparticles (ENPs) maybe persistent due to the stabilization properties of their capping agent (surfactant or organic material). Thus, there is growing concern about the production and fate of ENPs in the environment (Handy et al., 2008).As ENPs pass through the water system they become exposed to different salinities, ionic concentrations and pH changes (Lapresta-Fernández et al., 2012). During this process the ENPs are degraded, transported, altered and accumulated in various ways. Nanoparticles have been found to aggregate in various organelles, for example endocytotic vesicles (Elsaesser & Howard, 2011; Lapresta-Fernández et al., 2012), cytoplasm and the perinuclear region (Mirkin et al., 2010). This can take place via ingestion, endocytosis and or by diffusion (Nowack & Bucheli, 2007). The major question is are NPs toxic and are they more toxic than their metal salts? While bulk gold is distinguished as a chemically inert and a non-toxic substance, (Alkilany & Murphy, 2010) GNPs may be toxic due to their different physicochemical properties such as small particle size, configuration, charge and specific surface area and easy surface alterations (Cho et al., 2009; Goodman et al., 2004; Lapresta-Fernández et al., 2012)...

Individuals within fish populations differ in many traits, such as sex, life-history, habitat residence, diet, and morphology. Such trait differences among individuals (i.e. intra-population variation) may be greater than the differences among populations (i.e. inter-population variation). My dissertation examines intra-population variation, with a focus on trophic relationships and morphology; as well as how variation in these attributes may reflect differences in bioaccumulation of contaminants. The second chapter of my dissertation examines the influence of spatial-temporal variation on the trophic structures of round goby (Neogobius melanstomus) and two age classes of yellow perch (Perca flavescens) within Saginaw Bay, Lake Huron. Using stable isotope ratios (δ13C, δ15N, δ2H, δ18O) and stomach contents as trophic indicators, I examined variation of diets. I found that spatial variation had a greater impact on diet indicators than both annual and seasonal variation. This spatial variation could represent a form of compartmentalization within the community of fish residing in Saginaw Bay, and could provide stability to the community. Chapter three of my dissertation examines intra-population variation in yellow perch morphology through a series of mesocosm experiments. My first mesocosm study determined that yellow perch could be experimentally manipulated to display divergent morphologies using simulated habitats, specifically pelagic and littoral habitats. Following this experiment, I focused on specific environmental drivers (structure, prey resources, and predation risk) as possible influences on yellow perch morphology. Within experimental pools, I exposed yellow perch to one of four treatments (an open pool, a structured pool, pools with chironomid prey resources and pools with a perceived, olfactory, predation risk) in the summer of 2015. Following exposure to these treatments I examined the morphological changes in yellow perch in magnitude and direction. I observed that while each treatment induced some difference in morphology, the open and structured treatments had the greatest magnitude of difference. I repeated the open and structure treatments during the following summer (2016). Again, I found that structure and open morphologies could be induced by my mesocosm treatments, but also observed that shapes differed from the previous year’s structure and open treatments. Finally, my fourth chapter examined how variation in trophic niches and morphology may reflect variation in contaminant concentration of fish in their natural environment. In this chapter, I extended my work with yellow perch to also include black crappie (Pomoxis nigromaculatus) and examined fish from 5 northern Indiana glacial lakes. Using model inference techniques, I found that variation in mercury was closely associated with not only fish total length, but also stable isotopes (δ13C and δ15N) and morphology. Interestingly, morphology-related variables of both species were strong predictors of mercury concentration in fish, following total length. Together, the chapters within my dissertation highlight the importance of considering intra-population variation, in which local factors such as habitat conditions and prey availability can influence individual variation in trophic structuring and morphology. These in turn may reflect other attributes of interest, such as the accumulation of contaminants.

Os estudos em microbacias hidrográficas têm mostrado que as características físicas, químicas e biológicas das águas dos córregos e riachos possuem uma estreita relação com a composição do ambiente terrestre adjacente, refletindo as condições de uso e ocupação dos solos da bacia hidrográfica por eles drenada. A microbacia do Córrego do Cancã, localizada perpendicularmente ao Rio Monjolinho, situa-se em uma maior parte no município de São Carlos (SP), e foi estudada sob uma abordagem ecossistêmica. As coletas e análises de campo foram realizadas em sete transectos do córrego, em dois períodos hidrológicos distintos: seca e chuva. A caracterização física e química da água foi realizada através da análise do pH, da condutividade elétrica, da concentração de oxigênio, da temperatura, da concentração e da carga de nutrientes. Alguns dos parâmetros analisados foram comparados aos limites estabelecidos pela CONAMA segundo a resolução nº 20/1986. O córrego do Cancã, segundo a classificação proposta pela CONAMA, é um rio de classe-2. A água do córrego é levemente ácida tendendo à neutralidade em um gradiente da nascente à foz e caracteriza-se pela baixa condutividade elétrica. A temperatura variou entre os períodos avaliados e espacialmente foi influenciada pelos horários de coleta. As concentrações de nutrientes não foram elevadas, e das formas nitrogenadas as mais abundantes foram o nitrato (na estação mais impactada) e o amônio (após o represamento), com valores mais elevados no período de seca. A maior variabilidade foi observada para o nitrogênio total, sendo as maiores concentrações registradas na estação seca. Com base no índice de estado trófico, as águas do córrego do Cancã foram classificadas como mesotróficas. A forma da microbacia é irregular e ligeiramente alongada e pouco sujeita a enchentes. A área da microbacia foi determinada como sendo de 3,075 Km2. Na análise das comunidades planctônicas foram encontrados poucos representantes, distribuídos principalmente nas estações localizadas nos trechos inicial e médio do córrego, sendo, entretanto mais abundantes na nascente. Ocorreu predominância das clorofíceas e diatomáceas entre os organismos fitoplanctônicos e de rotíferos e cladóceros no zooplâncton. A microbacia está sujeita à práticas agrícolas e atividade pecuária semi-intensiva que alteram o balanço de massa dos principais nutrientes, contribuindo para o aumento da carga de nutrientes que são carreados do sistema terrestre para o aquático particularmente no período chuvoso. / The studies peformed in small hydrographic basins have shown that the physical chemical and biological characteristics of the water in springs and streams have a close relation with the composition of adjacent terrestrial ecosystems, reflecting the uses and activities in the soils in the basin drained by them. The microbasin of Cancã stream belongs to the Monjolinho river basin and is mainly located inside the district of São Carlos (SP). In this study It has been evaluated under the ecosystemic approach. Field sampling and analysis were carried out in seven transects of the stream at two distinct hydrological periods: dry and rainy seasons. Physical and chemical analyses of water were performed by mesuring the pH, electrical conductivity, dissolved oxygen and the nutrient concentrations and loads. The parameters obtained were compared to the CONAMA limits, act nº 20/1986. The Cancã stream according to CONAMA proposed system, is classified as a class 2 water. The pH of Cancã water is slightly acid and there a tendency to the neutral from the source to the mouse. It is also characterized by low electrical conductivity. Water temperature has changed between dry and rainy periods and spatially it was influenced by the sampling timing. Nutrient concentrations are low and the main nitrogen compounds present were nitrate and ammonium, at the most impacted site, with highest values in the dry season. The highest variability was obtained for the total nitrogenvariability with higher concentrations at the dry season. Based on the trophic state index. The water of Cancã stream was classified as mesotrophic. The hydrographic microbasin has a non-regular shape, being slightly elongated and it has low vulnerability to floodings. The area of the catchment was found to be 3,071 Km2. Planktonic communities were composed by few organisms mainly occuring at the upper and middle stream streches, being most abundant at the first stretch. Clorophyceans and diatoms were the dominant groups among phytoplankton and the rotifers and cladocerans among the zooplankton. Cancã microbasin is subjected to a variety of agriculture and semi-intensive cattle enterprises that have changed major nutrient mass balances, contributing to the increase in nutrient loadings mainly via surface terrestrial runoff.

The arrival of a non-native species to has the potential to shape native communities by influencing ecological interactions such as predation, foraging, competition and disease transfer. A designation of invasive is applied to an introduced non-native species that has the potential to threaten the continued wellbeing of a native species, pose a risk to human health or negatively impact the economy. The European bullhead (Cottus perifretum) is a freshwater benthic-dwelling fish that is native to England but considered invasive in Scotland. The species was first reported in Scotland in the 1950's and thriving populations are now established in the waters of the Clyde, Forth and Tweed catchments. Bullhead presence is thought to negatively impact native stone loach (Barbatula barbatula) and brown trout (Salmo trutta) parr, due to shared preferences for habitat and prey resources. They are also thought to prey upon the eggs of native Atlantic salmon (Salmo salar) and brown trout, two species that are of high commercial value in Scotland. In other areas of introduction, bullheads have been found to increase parasite infection rates in native fishes. The species therefore has the capacity to incite competition and alter parasite/host interactions in areas of introduction, to the potential detriment of native fauna and the Scottish economy. The European bullhead has been the subject of considerable taxonomic scrutiny in recent years, resulting in its reclassification as a species complex. What was once considered a single species with a distribution encompassing Europe, Russia, Asia and Scandinavia, has been shown to consist of at least 15 distinct species. Genetic examination of bullheads from England confirmed the presence of Cottus perifretum, not Cottus gobio as traditionally listed in all UK literature and legislation. Native English bullhead is currently protected under Annex II of the European Commission Habitats Directive 92/43/EEC, based on the historic assumption that the species present is C. gobio. Analysis of the taxonomic identity of Scottish bullheads has remained outstanding. In this study the invasive status of bullhead was explored by examining feeding and parasitological interactions between bullheads and native freshwater communities in south-east Scotland. An assessment of the feeding preferences of native brown trout and stone loach in the presence and absence of bullheads tested competition for prey resources. Parasitological interactions were investigated by examining the shared parasite fauna of bullheads and native fish and invertebrate species. Bullheads from the Clyde and Forth catchments were analysed to provide a molecular and morphological description of this introduced species. Phylogenetic analysis of COX1 sequences obtained from Scottish bullheads, and a pair-wise distance calculation based on a Kimura 2-parameter model, showed that samples clustered in a distinct clade with English C. perifretum. Significant intraspecific variation was reported in all morphological features examined, but pooled data also revealed a resemblance to the published description provided for C. perifretum. Scottish bullhead is therefore confirmed to be an introduced pocket of the native English species, which is considered under threat in some areas due to habitat modifications and population decline. Comparisons between the dietary compositions of bullheads, brown trout and stone loach showed that the prey selection of brown trout and stone loach varied in the sample locations that contained co-occuring bullheads, when compared to locations where bullheads were absent. However, no direct evidence of trophic competition between bullheads and either brown trout or stone loach was reported. An examination of parasitological interactions recovered eight parasite species from four distinct taxonomic groups in total, of which four species (Echinorhynchus truttae, Apatemon gracilis, Diplostomum volvens and Raphidascaris acus) were shared between bullheads and one or more native fishes. Echinorhynchus truttae was also shared with gammarid crustaceans. Bullhead presence was found to coincide with D. volvens infections in European minnow (Phoxinus phoxinus) and a reduced prevalence of E. truttae in brown trout. Diplostomum volvens was only reported from minnow found in sites with bullheads, strongly suggesting bullheads were responsible for introducing this parasite to native minnows. Bullheads functioned as an alternative host for E. truttae, diluting brown trout parasite loads and reducing overall infection rates in sites where bullhead and brown trout co-exist. The findings reported for both feeding preference and parasite burdens in the presence and absence of bullheads suggest that bullheads do have some effect on the ecology of native species, but these are considered minimal and unlikely to impact the long-term survival of native species. Eradication of Scottish bullhead may contradict the conservation effort that is currently in place. Given the current lack of evidence to validate bullhead's invasive qualities and the recent confirmation of its genetic lineage, revisiting the designation of the bullhead as invasive is warranted. Active eradication should be treated with caution until a significant negative impact can be proven.