The present study sought to falsify three distinct hypotheses about how the interactions of freshet clay turbidity with Flathead Lake may be affecting its trophic state: 1) that freshet-derived turbidity causes precipitation of organic detritus from the water column by flocculation and/or coagulation of dissolved and colloidal organic carbon and seston; 2) that flocculated clay-organic detritus complexes become increasingly infested with microbial biomass as they sink through the water column; and 3) that primary productivity is reduced and subsequently maintained at low levels throughout the summer and fall because of the phosphorus stripping action of sedimenting clay particles. In addition, this study attempted to firmly document mass balances for some ecologically important elements, nutrient loading rates, steady state nutrient concentrations and annual lake primary productivity. It was also necessary to assess the trophic status of the lake in light of any new findings from this research, especially related to the ecological role of freshet turbidity.

Biofiltration is one of many ecosystem services provided by mussels. Besides filtering and clearing waters from miscellaneous harmful particles and debris, mussels also have the ability to lower the turbidity of the water. How the presence of mussels affect macrophyte growth is however a less researched area of science. In this study I try to assess if the presence of Unio tumidus have an effect on the growth of Eleocharis acicularis. I used mesocosms containing individuals from both species and through continuous measurements of water chemistry as well as the measuring the difference in plant biomass between the start of the experiment and the harvest at the end of the experiment. The only significant effect observed was on conductivity which increased by 82% in aquaria with mussels as opposed to only 74% in those without. Interestingly there was no increase in the mean biomass of the plants, instead there was a decrease in mean plant biomass over time. / Biofiltration är en av många ekosystemtjänster som musslor tillhandahåller. Förutom att rena stora mängder vatten från diverse skadliga ämnen så sänker även musslors biofiltration turbiditeten i vattnet. Hur musslornas närvaro påverkar makrofyter är dock ett mindre utforskat område. I den här studien undersöker jag huruvida närvsaro av Unio tumidus påverkar tillväxt hos Eleocharis acicularis. Jag använde mesocosmer innehållande individer av båda arter och genomförde kontinuerliga mätningar av vattenkemin samt mätte förändringar i biomassan hos växterna. Musslorna hade inte en signifikant effekt på vare sig pH, turbiditet, nivåer av chlorophyll-a eller biomassa hos växterna. Den enda variabeln som musslorna visade sig ha en signifikant effekt på var konduktiviteten, som ökade signifikant med 82% i akvarierna med musslor kontra en ökning på endast 74% i akvarierna utan musslor. Intressant nog så minskade växterna i biomassa över tid.

L’estuaire de la Gironde est le plus grand estuaire macrotidal d’Europe formé par la confluence de la Garonne (où se situe l’agglomération de Bordeaux) et de la Dordogne. L’une de ses principales caractéristiques est la présence d’une zone à forte turbidité (bouchon vaseux) où les processus hétérotrophes (dégradation de la matière organique) sont favorisés et où au contraire les processus autotrophes (production primaire) sont limités par le manque de lumière. Ainsi, des déficits en oxygène pouvant être préjudiciables à la vie aquatique se développent systématiquement dans la zone du bouchon vaseux de la Garonne estuarienne. Ces préoccupations environnementales ont donc conduit à étudier en détail dans le cadre de ce travail de doctorat, les facteurs environnementaux qui provoquent ces hypoxies estuariennes. Dans un premier temps, j’ai réalisé un suivi sur le réseau d’eaux urbaines partiellement séparatif et unitaire de la Communauté Urbaine de Bordeaux, de ses stations d’épurations et déversoirs d’orage afin d’appréhender les apports urbains de matières organique et azotées et de les comparer à ceux en provenance du bassin versant amont. Bien que les deux stations d’épuration réalisent des abattements très significatifs sur la matière organique et l’ammonium, il s’avère que les flux vers le milieu naturel restent importants, notamment durant les périodes estivales, pendant lesquelles des orages peuvent engendrer des déversements d’effluents non traités. Ensuite, des expériences d’incubations ont permis de mettre en évidence le caractère fortement labile de cette matière organique urbaine. Le carbone organique dissous et l’ammonium, contenus dans les eaux usées, sont des composés fortement consommateurs en oxygène. Des expériences de respirométrie ont également permis d’estimer les taux de consommation en oxygène nettement plus importants dans les effluents urbains que dans les eaux de la Gironde. Enfin, l’analyse des données du réseau de mesures en continu de la qualité physico-chimique des eaux MAGEST (MArel Gironde ESTuaire) a démontré que l’estuaire subit dans sa section garonnaise des périodes d’hypoxie lors d’étiages prononcés, la masse d’eau la plus affectée par ces désoxygénations étant celle qui oscille aux alentours de l’agglomération de Bordeaux. Si ces résultats démontrent l’impact significatif de l’agglomération Bordelaise, le traitement statistique des données MAGEST pour la période 2005-2011 montre que les phénomènes de désoxygénation sont accrus en période d’étiage prononcé, en présence du bouchon vaseux et lorsque la température de l’eau est élevée. Dans ces conditions, l’oxygène dissous, déjà présent en faible quantité, peut être rapidement consommé lors d’apports supplémentaires d’eaux urbaines non traitées qui ont lieu pendant de fortes précipitations orageuses. Ce travail démontre également que le type de traitement biologique des eaux usées employé par les stations d’épuration et les capacités de stockage temporaire d’eaux d’orages ont un rôle critique sur les bilans de ces composés rejetés dans le milieu naturel. Enfin, ce travail permet de proposer aux gestionnaires des stratégies de rejets des effluents à court et moyen terme, en fonction des conditions hydrologiques et physico-chimiques du milieu, dans le but de limiter leur impact sur l’oxygénation des eaux estuariennes de la Garonne. / The Gironde Estuary is the largest macrotidal estuary in Western Europa, formed by the Garonne River (where the urban area of Bordeaux is located) and the Dordogne River. One of its main characteristics is the presence of a Turbidity Maximum Zone (TMZ) where heterotrophic processes (organic matter decomposition) are favored and where low penetration of light limits autotrophic processes (photosynthetic activity). Low dissolved oxygen (DO) that could impact aquatic biota occurred exclusively in the fluvial, low salinity and high turbidity sections of the estuary. These environmental concerns have led to study in detail in this work factors that cause estuarine hypoxia. First, I have estimated organic matter and ammonium fluxes from urban inputs in separate and combined sewer network of the Urban Community of Bordeaux, its wastewater treatment plants (WWTP) and combined sewer overflow, to compare them to the upstream watershed inputs. Even if the two WWTPs succeed in significant reduction in organic matter and ammonium contents of effluents, discharges into estuarine waters are important especially during summer, periods while storm events can generate untreated effluent inputs. This work demonstrates the high lability of this urban organic matter through incubation experiments. The dissolved organic carbon and ammonium contents in wastewater consume oxygen. Respirometry experiments allowed us to estimate higher oxygen uptake rates in wastewater than in the waters of the Gironde Estuary. Finally, the analysis of 7-yr data series from the continuous monitoring of the physico-chemical water quality (MAGEST network: MArel Gironde ESTuary) highlights periods of hypoxia in the upstream section of the estuary during pronounced low water around the Bordeaux conurbation. Statistical treatments of the 7-yr time series of DO concentration demonstrate the significant impact of the Bordeaux metropolitan area as it appears that the under-oxygenations increase during marked low water, in the presence of the TMZ, when the water temperature is high, and where the dissolved oxygen content is already low and can be quickly consumed after untreated storm water discharges. This study also shows that the nature of biological treatment used by the WWTPs and the temporary storage capacity of storm water have a critical role in the release of such compounds into the environment. This work finally provides strategies for effluent discharges to water managers, to short and medium terms, based on hydrological and physico-chemical conditions of the environment in order to limit their impact on the water oxygenation of the Garonne River.

Umweltveränderungen kommen natürlicherweise vor und viele Spezies waren im Laufe ihrer Evolutionsgeschichte davon betroffen. Durch die Aktivitäten des Menschen jedoch finden diese in höherer Geschwindigkeit und größerem Umfang statt und stellen so für viele Spezies eine neue Herausforderung dar. Einen großen Einfluss auf die Umwelt nimmt der Mensch durch Verschmutzung, welche zu Veränderungen der Physiologie der Organismen und deren Verhalten führen und damit Einfluss auf die Populationsdynamik und letztendlich auf die Biodiversität haben kann. In meiner Dissertation untersuchte ich den Einfluss durch Bergbau ausgelöster Trübung auf das Verhalten und die soziale Struktur des Guppys. Er nutzt soziale Interaktionen für eine höhere Effizienz bei der Nahrungssuche und Räubervermeidung. Die Nutzung sei-nes dafür eingesetzten Sehsinns ist bei Trübung stark eingeschränkt. Ich untersuchte die Reaktion Trübung unerfahrener Fische aus Labor und Feld auf Trübung. Es zeigte sich, dass beide ihre sozialen Interaktionen in trübem Wasser verringerten. Eine zusätzliche Markow-Ketten-Analyse ergab aber auch, dass Laborfische Kontakte zu bestimmten In-dividuen der Gruppe verstärkten und Feldfische ihre initiierten Kontakte behielten. An-schließend studierte ich den Unterschied der sozialen Struktur Trübung erfahrener und - unerfahrener Fische. Trübung erfahrene Fische erhöhten die Gesamtzahl der Interaktio-nen, reduzierten jedoch die Anzahl der initiierten Kontakte im Gegensatz zu unerfahre-nen Fischen. Diese Strukturänderung, vermute ich, erhöht den Zusammenhalt und damit den In-formationsfluss im Schwarm. Die Ergebnisse von Folgeversuchen, nämlich der Erhalt der Paarungsanzahl und die effektivere Vermeidung einer Räuberattrappe bei Trübung er-fahrenen Fischen, unterstützen diese Vermutung. Die Arbeit zeigt, dass Guppys in der Lage sind, sich durch Änderung Ihrer sozialen Struktur an trübe Verhältnisse anzupas-sen. Dies könnte auch Einfluss auf ihre Populationsstruktur haben. / Most species have been subjected to environmental changes during their evolutionary history. However, due to human activity, environmental changes are currently occurring at higher speeds and on a greater scale, presenting new challenges for many species. Pollution, as a major type of human-induced environmental change, may not only affect physiology but also behaviour, thereby affecting population dynamics and consequently biodiversity. The topic of my dissertation is the effect of turbidity from quarrying on the behaviour and social association pattern of the guppy (Poecilia reticulata). Turbidity impairs the fish’s ability to use visual cues during social interactions, which in turn helps increases efficiency of foraging and avoiding predators. I investigated the initial re-sponse of guppies to turbidity and subsequently tested whether turbidity-experienced vs turbidity-inexperienced populations differ in their social association patterns and how they cope with ecological challenges. Both lab-reared and wild-caught guppies that were inexperienced with turbidity reduced social associations in turbid water in con-trast to turbidity-experienced fish. A Markov chain analysis revealed that lab-reared guppies increased associations with particular neighbours. Similarly, wild-caught gup-pies maintained the number of initiated associations under turbid conditions. The in-crease in non-initiated associations suggests a stronger connectivity within the shoal, leading to higher information transmission in a poor visual environment. Additional results showed that this altered social structure enabled turbidity-experienced fish to maintain the frequency of mating attempts in turbidity and to avoid predation risk. This suggests that guppies have the ability to adjust to turbidity, but with major changes in their social structure, which might have an impact on population dynamics.

This thesis presents a series of studies of quenched random disorder (QRD) on liquid crystals. We have used high-resolution AC-Calorimetry, high-resolution X-Ray Diffraction (XRD), X-Ray Intensity Fluctuation Spectroscopy (XIFS), Turbidity, Integrated Low-Angle Light Scattering (ILALS), as well as Polarizing Microscopy to characterize the effects of a nano-colloidal dispersions of aerosils in the phase transitions of several liquid crystals. The aerosil ($SIL$) is made of 70~AA~ diameter SiO$_{2}$ particles coated with hydroxyl (-OH) groups. The coating allows the $SIL$ particles to hydrogen-bond together, to form a very low density gel in an organic solvent. This provides the quenched random disorder. The liquid crystals of interest are: octyloxycyanobiphenyl ($8OCB$), 4-extit{n}-pentylphenylthiol-4'-extit{n}-octyloxybenzoate (ar{8}$S5), 4'-transbutyl-4-cyano-4-heptyl-bicyclohexane ($CCN47$), and octylcyanobiphenyl ($8CB$). Studies have been carried out as a function of aerosil concentration and temperature spanning the following phase transitions, Isotropic to Nematic (emph{I-N}), nematic to smectic-emph{A} (emph{N-SmA}), smectic-emph{A} to smectic-emph{C} (emph{SmA-SmC}), and crystallization.

Source water protection is important to maintain public health by keeping harmful pathogens out of drinking water. Non-point source pollution is often times a major contributor of pollution to surface waters, and this form of pollution can be difficult to quantify. This study examined physical, chemical, and microbiological water quality parameters that may indicate pollution and may help to identify sources of pollution. These included measures of organic matter, particles, and indicator organisms (fecal coliforms and E. coli). The parameters were quantified in the West Boylston Brook, which serves as a tributary to the Wachusett Reservoir and is part of the drinking water supply for the Metropolitan Boston area. Water quality was determined over four seasons at seven locations in the brook that were selected to isolate specific land uses. The water quality parameters were first analyzed for trends by site and by season. Then, a correlation analysis was performed to determine relationships among the water quality parameters. Lastly, ANOVA analyses were used to determine statistically significant variations in water quality along the tributary.

Jusqu’à présent, la dynamique des fractions végétales n’avait jamais été étudiée dans les estuaires macrotidaux en raison de leur faible quantité, par rapports aux fortes charges en matières en suspension fines, et du manque de protocoles d’étude et d’échantillonnage adéquats. Les débris végétaux sont toutefois à l’origine de perturbations d’activités économiques qui impliquent la filtration de larges volumes d’eau. L’objectif de cette thèse était ainsi de comprendre la dynamique d’apport et de transit de ces débris végétaux dans l’estuaire de la Gironde par la mise en oeuvre d’un suivi spatio-temporel de leur distribution et de techniques nouvelles pour un tel estuaire hyper-turbide (incubations in-situ litter-bag, caractérisation biogéochimique, identification des sources). Les résultats principaux sont la mise en évidence du contrôle du régime hydrologique sur leur distribution et la détermination des échelles de temps de leur persistance dans l’estuaire de la Gironde. / Up to now, vegetal fraction dynamics has not been studied in macrotidal estuaries, due to its low quantity in comparison to the strong charge of suspended particulate matter, and due to the lack of appropriate protocols to sample and examine it. Nevertheless, vegetal debris have been identified as a factor able to disrupt a wide range of stakeholder activities that require huge volumes of water to filter. The objective of this PhD was to understand the input and transfer dynamics of vegetal debris in the Gironde Estuary by the implementation of a spatiotemporal btrack of their distribution and by the development of new techniques for this hyper-turbide estuary (in situ litter-bag incubations, biogeochemical characterization, and identification of the sources). Mean results highlight the influence of the hydrological regime in their distribution and reveal time scales of their persistence in the Gironde Estuary.

<div>Agricultural headwater streams in the Midwestern United States are subject to contaminants from fields, increased sedimentation, and degradation of natural habitat. Previous research has shown that physical instream habitat degradation better explained variation in fish community structure than water chemistry. However, these studies did not include total suspended solids (TSS), which are considered a major freshwater contaminant. The objective of this study is to determine whether total suspended solids better explains fish community structure than other variables in agricultural headwater streams. Mixed linear effects modeling was used to determine the set of independent variables that best predicts each of the fish response variables of species richness, Shannon diversity index, fish density, and index of biotic integrity. Standardized coefficients were used to determine which independent variable in each of the models had the largest influence on fish response metrics. The set of independent variables that best explained species richness were mean total suspended solids, imidacloprid, discharge, and substrate richness. Shannon diversity index was explained best by the combination of maximum total suspended solids, mean total suspended solids, atrazine, total nitrogen, and discharge. Fish density was explained best by the percentage of silt and clay, dissolved oxygen, the percentage of canopy cover, cover type richness, and discharge. IBI was explained best by the combination of the percentage of silt and clay, total phosphorus, mean total suspended solids, and dissolved oxygen. Total suspended solids was the most influential independent variable for fish species richness and Shannon diversity, however the percentage of silt and clay in benthic sediments was the most influential independent variable for fish density and IBI. Results also indicate discharge and total phosphorus as being influential to fish community metrics. The results from this study suggest that models containing a combination of different types of independent variables best explain fish community structure. This study supports the use of conservation and restoration practices that reduce total suspended solids and the amount of silt and clay present in bed sediments to increase fish community integrity of agricultural headwater streams of the Midwestern United States.</div>

Estuarine circulation and its associated transport processes drive the environmental integrity of many near-shore habitats (the coastal ocean, rivers, estuaries and emergent wetlands). A thorough understanding and consideration of this circulation is, therefore, vital in the proper management of these habitats. The aim of this study is to bring together theory and new satellite observations in the Columbia River Estuary to increase our understanding of estuarine circulation and transport. Surface reflectance measurements gathered by the Moderate Imaging Spectroradiometer (MODIS) are first compared to in situ observations to develop an empirical model for remotely derived surface turbidity. Results indicate that MODIS data significantly correlate with in situ measurements of turbidity throughout the CRE (R2 = 0.96). Remote estimates of turbidity are then used to explore the physical processes that drive their spatial distribution. Although the response to different hydrodynamic conditions varies throughout the system, global levels of turbidity are most sensitive to fluvial and tidal inputs and increase during spring tides and high river flow. As a result, the turbidity field has temporal cycles that are consistent with the frequency of these processes. The location of the estuarine turbidity maximum (ETM) is highly dynamic and typically migrates downstream as the tidal velocity or river flow increases. The ETM becomes trapped near the Megler Bridge (river kilometer 20), however, and the presence of strong topography in this region suggests there exists an interaction between bottom topography and sediment transport. A 2-D semi-analytical model, developed herein from the simplified Navier-Stokes equations, confirms that topographic features exhibit substantial influence on longitudinal turbidity distributions. The model considers the coupled, tidally-averaged velocity (composed of gravitational circulation, internal tidal asymmetry, and river flow) and salinity fields and assumes a condition of morphodynamic equilibrium to estimate the distribution of sediment for arbitrary channel configurations. Model simulations demonstrate that topographic highs tend to increase local seaward sediment fluxes, and that topographic lows increase local landward sediment fluxes. Sediment flux convergence near topographic highs compresses the local turbidity distribution, whereas flux divergence near topographic lows dilates the distribution and, under appropriate conditions, produces multiple ETMs. In summary a combination of the model and satellite data has given valuable new insights into the sediment dynamics of estuarine environments; in particular, both show that turbidity distribution and ETM location vary considerably with tidal and river flow conditions, fluctuating on a variety of timescales, and are heavily influenced by bottom topography.

I investigated Lake Sturgeon (Acipenser fulvescens) foraging and anti-predator behaviour. My goals were to understand: (1) The role of environmental change on foraging and anti-predator behaviour trade-offs. (2) The relative cost/benefit trade-off between escape behaviour and cover-seeking behaviour. (3) How development of several independent morphological traits affects anti-predator behaviours. I used simulated river mesocosms to study Lake Sturgeon behavioural ecology under controlled conditions. I found: (1) Foraging intensity was significantly higher during the night than the day as well as in turbid environments versus clear environments, indicating that decreased turbidity alone, may in part drive anti-predator behaviour and constrain foraging activity. (2) In high-risk clear-water environments, Lake Sturgeon responded to danger by evoking an escape response and seeking cover in rocky microhabitats. However, in low-risk turbid environments, Lake Sturgeon responded to danger by seeking cover in rocky microhabitats, but not fleeing to a significant degree. Cover-seeking behaviour may therefore be a relatively low-cost/high-benefit anti-predator strategy. (3) Strong evidence for trait co-dependence between escape responses and body size, where larger fish were able to elicit stronger escape responses. I also found that cover-seeking behaviour exhibited a complex multi-tiered relationship, representing a mixture of trait compensation and trait co-specialization that is dependent on specific combinations of morphological traits. These findings are important because they help us understand: (1) The degree to which anti-predator behaviour can be influenced by changing environmental conditions. (2) The relative cost/benefit trade-off between two common anti-predator behaviours. (3) How behaviour and morphology interact in species with a complex anti-predator phenotype.