Le méthane, un des principaux gaz à effet de serre, est majoritairement produit et consommé par l'activité métabolique de microorganismes affiliés aux domaines des Archaea et des Bacteria. Afin d’appréhender le cycle biogéochimique du méthane, il est essentiel d’identifier l’ensemble des acteurs impliqués dans ce dernier ainsi que les facteurs environnementaux modulant leurs activités. Les lacs d’eau douce constituent une source importante de méthane, car, dans ces écosystèmes, les conditions environnementales favorisent la méthanogenèse au détriment d’autres processus terminaux de la dégradation anaérobie de la matière organique. Au cours de cette thèse, les études sur les communautés impliquées dans le cycle biogéochimique du méthane ont été conduites dans la colonne d’eau et les sédiments anoxiques du Lac Pavin (Auvergne), unique lac méromictique de France. Cet écosystème a été choisi comme site d'étude en raison des fortes concentrations en méthane présentes dans sa couche d'eau profonde qui contrastent avec les faibles émissions de ce gaz vers l'atmosphère. Ces observations géochimiques suggèrent une intense activité de production et de consommation du méthane, offrant un cadre pertinent pour l’étude des communautés ciblées. Les approches moléculaires visant à caractériser la structure spatiale, la composition, les zones d'activité et les facteurs (ascendants et descendants) potentiellement impliqués dans la régulation des communautés de méthanogènes et de méthanotrophes ont été, au cours de ce travail, systématiquement associées à des approches culturales et microcalorimétriques afin d’acquérir des données sur la physiologie des microorganismes impliqués dans le cycle du méthane. Les résultats obtenus mettent en évidence que les communautés de méthanogènes sont distribuées sur l’ensemble de la colonne d’eau anoxique et dans la strate superficielle des sédiments profonds. Ce groupe métabolique, essentiellement représenté par des espèces affiliées aux Methanosaetaceae et aux Methanoregulaceae, est particulièrement actif dans la zone benthique qui constituerait la source principale de méthane dans cet écosystème. Une nouvelle espèce méthanogène, Methanobacterium lacus, a été isolée de ces sédiments et décrite, et vient enrichir le faible nombre d'espèces méthanogènes isolées à ce jour à partir des lacs d'eau douce. L'étude écophysiologique de cette souche suggère que la température pourrait en partie expliquer la faible représentativité des Methanobacteriales dans cet écosystème. Une partie du méthane semble être directement consommée dans la zone anoxique (pélagique et benthique). L’existence de ce processus d’oxydation anaérobie, soutenu par les approches microcalorimétriques, pourrait être, dans les sédiments profonds, sous la dépendance de lignées candidates archéennes dont la physiologie reste encore énigmatique. Le remplacement progressif des méthanogènes par 2 lignées candidates d'archaea (MBG-D et MCG) le long du profil sédimentaire suggère qu'elle se développe dans des niche contrastées. La régulation putative des communautés archéennes par les virus a été analysée. Cette étude est la première à rapporter la présence de particules virales de type "archaeovirus" dans un environnement non-extrême (en termes de température, pH et salinité) ainsi que des particules virales pouvant représentées de nouvelles familles de virus. Une activité virale intense est suggérée dans ces sédiments par le nombre important de cellules infectées, comparativement à d'autres sédiments, et par le changement concomitant de la structure de la communauté virale et procaryotique avec la profondeur. Bien qu’une partie du méthane soit probablement oxydée en anaérobiose, la consommation de ce métabolite est principalement dépendante de l’activité de méthanotrophes aérobies dominées par des espèces affiliées au genre Methylobacter, un des principaux genres de méthanotrophes rencontré en milieu d’eau douce. (...) / Methane, a major greenhouse gas, is produced and consumed mainly by the metabolic activity of microorganisms affiliated to the domains Archaea and Bacteria. In order to understand the biogeochemical cycling of methane, it is essential to identify all the biological actors involved, as well as environmental factors modulating their activity. Freshwater lakes are a major source of methane because environmental conditions occurring in these ecosystems favor methanogenesis over other terminal processes of anaerobic degradation of organic matter. In this thesis, studies of communities involved in the biogeochemical cycling of methane were carried out in the water column and anoxic sediment of Lake Pavin (Auvergne), the unique French meromictic lake. This ecosystem has been selected as study site due to the high concentrations of methane in its deep water layer which contrast with the very low emission of this gas in the atmosphere. These geochemical observations suggest an intense activity of production and consumption of methane, providing an appropriate framework for studying the communities involved. Molecular approaches to characterize the spatial structure, composition, activity areas and factors (bottom-up and top-down) potentially involved in the regulation of methanogens and methanotrophs were, in this work, systematically associated to cultural and microcalorimetric approaches to acquire data on the physiology of microorganisms involved in the methane cycle. The results show that methanogens are distributed throughout the permanent anoxic water column (monimolimnion) and mainly in the superficial layer of the sediment situated under the monimolimnion. This metabolic group, mainly represented by species affiliated to Methanosaetaceae and Methanoregulaceae, is particularly active in the benthic zone which would be the main source of methane in this ecosystem. A new species of methanogen, Methanobacterium lacus, was isolated from these sediments and described. It enhances to the small number of methanogenic species isolated to date from freshwater lakes. The ecophysiological study of this strain suggests that the temperature could partly explain the low representation of Methanobacteriales in this ecosystem. A part of the methane appears to be directly consumed in the anoxic zone (pelagic and benthic). The existence of this process of anaerobic oxidation, supported by microcalorimetric approaches, could be in deep sediments, dependent on archaeal candidate lineages whose physiology remains enigmatic. The gradual replacement of methanogens by two archaeal candidate lineages (MBG-D and MCG) along the sedimentary profile suggests that they live in contrasted niche. The putative regulation of the archaeal communities by virus was analyzed. This study has reported the first observations of archaeovirus-like particles in a non-extreme environment (in term of temperature, pH and salinity) and virus-like particles which might represent new viral families. An intense viral activity in these sediments is suggested by i) the important number of visibly infected cells and ii) the concomitant change of the viral and prokaryotic communities with depth. While a fraction of methane is probably oxidized anaerobically, the consumption of this metabolite is mainly dependent on the activity of aerobic methanotrophs dominated by species affiliated to the genus Methylobacter, one of the main types of methanotrophs found in freshwater environments.These methanotrophs have a large area of activity, extending around both sides of the red/ox interface in the water column. This wide distribution may partly explain the low quantity of methane released by the Lake Pavin. (...)

Lake Tanganyika is a complex, tropical ecosystem in East Africa, harboring an estimated 2,100 species. Extensive watershed deforestation threatens the biodiversity and ecological integrity of the lake. In this dissertation, ecological and paleoecological methods were employed to study the distribution of invertebrate biodiversity through space and time, with particular emphasis on linkages between biodiversity and land –use patterns. Ecological surveys of fish, mollusc, and ostracod crustacean diversity at sites in northern Lake Tanganyika representing different levels of watershed disturbance revealed a negative correlation between biodiversity and intensity of watershed disturbance. To elucidate the long -term relationship between disturbance and biodiversity, paleoecological records of invertebrates offshore from watersheds experiencing different degrees of anthropogenic disturbance were examined. Life, death, and fossil assemblages of ostracod valves were compared to assess the reliability and natural variability inherent to the paleoecological record. These comparisons indicated that paleoecological (i.e. death and fossil) assemblages reliably preserve information on species richness, abundance, and occurrence frequency at comparable -to- annual resolution. Unlike life assemblages, species composition of paleoecological assemblages reflects input of species from multiple habitat types. Ostracod paleoecological assemblages are characterized by spatiotemporal averaging that renders them representative of larger areas and longer time spans than life assemblages. Thus, paleoecological assemblages provide an efficient means of characterizing longer -term, site -average conditions. Natural variability in ostracod fossil assemblages from a sediment core representing the Late Glacial to the present indicates that abundance of individual ostracod species is highly variable. Ostracod assemblages were preserved in only the most recent 2,500 years of sediment. Species composition of ostracod assemblages reflects lake water depth. Core geochemical data indicate that the coring site may have been below the oxycline for ~2,000 years, inhibiting ostracod survival and preservation. Paleoecological, sedimentological, and stable isotope data revealed differences in biodiversity and watershed disturbance through time offshore from a pair of sites. The protected site is offshore from Gombe Stream National Park (Tanzania), the other offshore from a deforested watershed outside the park. Offshore from the deforested watershed, sedimentation rates increased, and turnover in ostracod species composition occurred during the past 50 years. Comparable changes were not observed offshore from the park.

[Truncated abstract] Acidic mine lakes are formed as a result of the oxidation and dissolution of metal sulfide minerals and are primarily characterized by low pH values of 2 – 4. Many strategies for the bioremediation of acidic mine lakes depend on the alkalinity generation capabilities of microbial ferric and/or sulfate reducing bacteria. However nearly all mine lakes are oligotrophic, with very low concentrations of available organic carbon and nutrients; all required for healthy microbial growth. There is also an unusual class of mine lakes characterized by low concentrations of organic carbon and also very low concentrations of dissolved iron and sulfate. Our ability to promote microbial activity in these systems is especially challenging. This study focuses on one of these systems, Lake Kepwari, a coal mine lake in Western Australia. Numerical modeling of remediation strategies is an efficient way of testing scenarios prior to expensive in-field trials. However such modeling relies on good descriptions of microbial processes, including kinetic parameterizations of ferric and sulfate reduction. There has been little research to date on the study of kinetic parameterizations of the chemical and biological alkalinity generation in acidic mine lakes. The objectives of this thesis were to investigate the viability of microbial ferric and sulfate reduction in an ultraoligotrophic, acidic mine lake, to assess the impact of these microbial processes on water quality and to parameterize the Dual Monod kinetics of neutralization under dual limitation conditions. Molecular analyses including most probable number, DNA extraction, polymerase chain reaction, polymerase chain reaction – denaturing gradient gel electrophoresis were used to examine the microbial communities in the lake sediments. ... The Monod maximum specific microbial growth rates with respect to dissolved organic carbon and ferric, and as determined in batch experiments, were 0.07 ± 0.01 and 0.048 ± 0.02 day-1, respectively, and their corresponding Monod half saturation constants and were 14.37 and 5.6 mmol L-1. The Monod maximum consumption rates under ferric and OC limitation were also estimated. The Monod maximum specific microbial growth rates with respect to dissolved organic carbon and sulfate, , and were 0.05 ± 0.01, 0.08 ± 0.01 and 0.07 ± 0.02 day-1, respectively, and their corresponding Monod half saturation constants, and were 75.5, 131.8 and 10.2 mmol L-1. The Monod maximum consumption rates under sulfate and OC limitation were also estimated. The results of this study suggest that strategies for the remediation of ultraoligotrophic, acidic mine lakes may rely on microbial ferric and sulfate reduction, however additions of both organic carbon and sulfate/ferric are essential. These results can be immediately applied to mesocosm studies in outdoor enclosures and to the management of acidic mine lakes. Furthermore, this thesis has provided a new, valuable understanding on the Dual Monod kinetic parameterizations of neutralization for an ultraoligotrophic, acidic mine lake environment. These parameterizations are essential for the lake ecological models that will be used to investigate remediation scenarios for acidic mine lakes.