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Thesis Reference Thesis Microbial and geochemical characterization of a contaminated freshwater ecosystem (the case of Vidy Bay, Lake Geneva, Switzerland) GLASS-HALLER, Laurence Abstract Le Léman représente la plus grande réserve d'eau douce d'Europe Occidentale et fournit de l'eau à environ 700 000 personnes. Il s'agit d'un lac tempéré, monomictique, qui était considéré comme eutrophe dans les années 1970 à 1980, mais qui depuis est redevenu mésotrophe grâce à des réductions drastiques des apports en phosphore. Dû à un accroissement de la population, au développement de l'industrie et une agriculture plus intensive durant ces dernières décennies, certaines parties du lac souffrent de pollution d'origine anthropique. La ville de Lausanne, située sur la rive nord, déverse dans le lac les plus gros volumes d'eaux usées et traitées, au niveau de la Baie de Vidy. Les trois principales sources de contamination de cette baie sont les effluents de la station d'épuration de Vidy (STEP) et les embouchures des rivières Chamberonne et Flon. L'objectif principal de cette étude de thèse était d'évaluer et de caractériser la contamination chimique et microbiologique de la baie de Vidy, et d'étudier en particulier les effets de la pollution sur la composition et la diversité des [...] Reference GLASS-HALLER, Laurence. Microbial and geochemical characterization of a contaminated freshwater ecosystem (the case of Vidy Bay, Lake Geneva, Switzerland). Thèse de doctorat : Univ. Genève, 2010, no. Sc. 4235 URN : urn:nbn:ch:unige-161678 DOI : 10.13097/archive-ouverte/unige:16167 Available at: http://archive-ouverte.unige.ch/unige:16167 Disclaimer: layout of this document may differ from the published version. 1 / 1 UNIVERSITE DE GENEVE FACULTE DES SCIENCES Section des sciences de la terre et de l’environnement Institut F.-A. Forel Professeur W. Wildi Département de botanique et biologie végétale Professeur R. Peduzzi Microbial and geochemical characterization of a contaminated freshwater ecosystem (the case of Vidy Bay, Lake Geneva, Switzerland) THÈSE présentée à la Faculté des sciences de l’Université de Genève pour obtenir le grade de Docteur ès sciences, mention interdisciplinaire par Laurence Glass-Haller de Baden (AG) Thèse N°4235 GENÈVE 2010 Table of contents Abstract ..................................................................................................................................... v Résumé ................................................................................................................................. viii Abbreviation list .................................................................................................................. xii 1. Introduction ......................................................................................................................... 1 1.1 Chemical contaminants in water ......................................................................... 3 1.1.1 Macropollutants in water ............................................................................... 3 1.1.2 Micropollutants in water ................................................................................ 4 1.2 Pathogenic organisms in water ............................................................................ 5 1.3 The role of bacteria in freshwater ecosystems .................................................. 7 1.3.1 Cellular structure ............................................................................................. 8 1.3.2 Metabolic diversity of freshwater bacteria .................................................. 8 1.3.3 Breakdown of organic matter in aerobic and anaerobic environments .. 9 1.3.4 Bacteria in biogeochemical cycles: the case of the carbon, nitrogen, sulphur, phosphorus and iron cycles. ........................................................................ 11 1.4 The role of bacteria in the fate of water contaminants ................................. 18 1.4.1 The effect of microorganisms on pollutants .............................................. 18 1.4.2 The impact of water contaminants on microbial communities .............. 19 1.5 Thesis rationale and objectives ......................................................................... 20 1.5.1 Rationale ......................................................................................................... 20 1.5.2 Study site ........................................................................................................ 22 1.5.3 Objectives ........................................................................................................ 27 1.5.4 Structure .......................................................................................................... 28 1.5.5 Institutional framework ................................................................................ 28 References .............................................................................................................................. 29 i 2. Effects of a Sewage Treatment Plant Outlet Pipe Extension on the Distribution of Contaminants in the Sediments of the Bay of Vidy, Lake Geneva, Switzerland 35 Abstract 36 2.1 Introduction ........................................................................................................... 37 2.2 Materials and methods ........................................................................................ 38 2.2.1 Study site and sediments sampling ............................................................ 38 2.2.2 Grain size, organic matter, phosphorous and nitrogen analysis ............ 40 2.2.3 Metal and hydrophobic compound analysis ............................................. 41 2.2.4 Data analysis .................................................................................................. 42 2.3 Results .................................................................................................................... 42 2.3.1 Grain size, organic matter, phosphorous and nitrogen ........................... 42 2.3.2 Metal concentrations ..................................................................................... 43 2.3.3 Hydrophobic organic compound concentrations ..................................... 47 2.3.4 Lake currents and spatial distribution of organic matter and heavy metals in the surface sediments ................................................................................... 49 2.4 Discussion .............................................................................................................. 51 2.4.1 Time evolution of contaminants in the surface sediments ...................... 51 2.4.2 Heavy metal and hydrophobic organic compound concentration levels: comparison with standard values and potential biological effects. ....................... 56 2.5 Conclusion ............................................................................................................. 58 References .............................................................................................................................. 60 3. Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (Lake Geneva, Switzerland) ............................. 65 Abstract .................................................................................................................................. 66 3.1 Introduction ........................................................................................................... 67 3.2 Materials and methods ........................................................................................ 68 3.2.1 Study site description and sampling procedure ....................................... 68 3.2.2 Chemical analysis .......................................................................................... 69 3.2.3 DNA extraction .............................................................................................. 71 3.2.4 PCR amplification ......................................................................................... 71 3.2.5 Clone library construction and DNA sequencing .................................... 72 3.2.6 Phylogenetic analysis .................................................................................... 73 3.3 Results .................................................................................................................... 74 3.3.1 Chemical analysis .......................................................................................... 74 3.3.2 Bacterial 16S rRNA gene clone libraries ..................................................... 79 3.3.3 Archaeal 16S rRNA gene clone libraries .................................................... 82 3.4. Discussion .............................................................................................................. 83 3.5 Conclusion ............................................................................................................. 95 References 96 ii 4. Origin and spatial-temporal distribution of faecal bacteria contamination in a Bay of Lake Geneva, Switzerland ................................................................................... 103 Abstract ................................................................................................................................ 104 4.1 Introduction ......................................................................................................... 105 4.2 Materials and methods .....................................................................................
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