A degradação da metilamina foi investigada por meio da avaliação da velocidade específica máxima de produção de metano (VEM CH4) e da comunidade microbiana relacionada aos Domínios Bacteria e Archaea. Para isso, foram realizados dois ensaios com reatores anaeróbios em batelada inoculados com lodo granulado oriundo de reator UASB usado no tratamento de água residuária de abatedouro de aves. Em todos os ensaios, os reatores controle, que não receberam adição de metilamina, apresentaram VEM CH4 de 0,04 mmol/L g STV dia. O primeiro ensaio avaliou a degradação da metilamina em diferentes concentrações de inóculo (2,5, 5,0 e 10,0 g STV/L) e substrato (1.550 e 3.100 mg metilamina/L). A concentração de \'CH IND.4\' esperada estequiometricamente foi atingida em todos os reatores (37,50 e 75,00 mmol \'CH IND.4\'/L, para concentrações de 1.550 e 3.100 mg metilamina/L, respectivamente), exceto para aquele com 2,5 g STV/L e 3.100 mg metilamina/L, que produziu somente 2,04 mmol \'CH IND.4\'/L. A maior velocidade específica máxima de produção de \'CH IND.4\' foi 4,42 mmol/L g STV dia, obtida nos reatores com 2,5 g STV/L e 1.550 mg metilamina/L. Os reatores inoculados com 5,0 g STV/L tiveram VEM CH4 de 2,31 e 2,34 para 1.550 e 3.100 mg metilamina/L, respectivamente. Os reatores com 1.550 mg metilamina/L e 10,0 g STV/L apresentaram VEM CH4 de 1,28 mmol/L g STV dia. A concentração de \'N\'-\'NH IND.4\'POT.+\' excedeu em 12,9%, 0,7% e 18,3% o valor esperado (698 mg/L) para os reatores com 1.550 mg metilamina/L e 2,5, 5,0 e 10,0 g STV/L, respectivamente. Nos reatores com 3.100 mg metilamina/L, as concentrações finais de \'N\'-\'NH IND.4\'POT.+\' foram 122 e 1.726 mg/L para concentrações de inóculo de 2,5 e 5,0 g STV/L, respectivamente. O segundo ensaio comparou diferentes relações metilamina/sulfato (0,71, 1,26 e 2,18) em reatores inoculados com 5,0 g STV/L contendo 1.550 mg metilamina/L. As concentrações de \'CH IND.4\' esperadas estequiometricamente foram atingidas em todos os reatores. As velocidades específicas máximas de formação de \'CH IND.4\' foram de 2,54, 2,31 e 3,14 mmol/L g STV dia para as relações metilamina/sulfato 0,71, 1,26 e 2,18, respectivamente. Em todos os reatores, a concentração de \'N\'-\'NH IND.4\'POT.+\' atingiu média final de 1200 mg/L. Os reatores controle consumiram 71,9% do sulfato adicionado. Os reatores com relação metilamina/sulfato 0,71, 1,26 e 2,18 consumiram 49,6%, 61,6% e 83,2% de todo o sulfato adicionado, respectivamente. Nos dois ensaios, os exames microscópicos revelaram a presença de cocos, bacilos, filamentos, cocos e sarcinas fluorescentes. Nos reatores alimentados apenas com metilamina, o seqüenciamento de fragmentos da região 16S do RNAr detectou cinco Filos do Domínio Bacteria (Acidobacteria 4%, Firmicutes 11%, Proteobacteria 14%, Spirochaetes 13% e Synergistes 47%). Nos reatores com metilamina e sulfato, sete Filos foram detectados (Firmicutes 45%, Proteobacteria 7%, Spirochaetes 2%, Synergistes 16%, Chloroflexi 4%, Thermotogae 8% e Planctomycetes 1%). Nos dois ensaios, o Domínio Archaea foi predominantemente representado pelas Famílias Methanomicrobiaceae, Methanosaetaceae e Methanosarcinaceae, com presença de Methanomethylovorans hollandica, uma espécie de arquéia metanogênica com metabolismo especializado na degradação de metilamina. / The degradation of methylamine was investigated assessing the maximum specific methane production rate (MSR CH4) and the microbial community related to Bacteria e Archaea Domains. For this, two tests were performed in anaerobic batch reactors inoculated with granular sludge from an UASB reactor used in the treatment of poultry wastes. In all experiments, the control reactors, without methylamine addition, showed MSR CH4 of 0.04 mmol/L g TVS day. The first experiment evaluated the degradation of methylamine at different inoculum concentrations (2.5, 5.0 and 10.0 g TVS/L) and substrate concentrations (1,550 and 3,100 mg methylamine/L). The stoichiometrically expected \'CH IND.4\' concentration was reached in all reactors (37.50 and 75.00 mmol \'CH IND.4\'/L, for methylamine concentrations of 1,550 and 3,100 mg methylamine/L, respectively), except for the reactor with 2.5 g TVS/L and 3,100 mg methylamine/L, that produced only 2.04 mmol \'CH IND.4\'/L. The highest maximum specific methane production rate was 4.42 mmol/L g TVS day, reached in the reactors with 2.5 g TVS/L and 1,550 mg methylamine/L. The reactors inoculated with 5.0 g TVS/L had MSR CH4 of 2.31 and 2.34 for 1,550 and 3,100 mg methylamine/L, respectively. The reactors with 1,550 mg methylamine/L and 10.0 g TVS/L had MSR CH4 of 1.28 mmol/L g TVS day. The \'N\'-\'NH IND.4\'POT.-\' concentrations exceeded 12.9%, 0.7% and 18.3% the expected value (698 mg/L) for the reactors with 1,550 mg methylamine/L and 2.5, 5.0 and 10.0 g TVS/L, respectively. In the reactors with 3,100 mg methylamine/L, the final concentrations of \'NH IND.4\'POT.+\'-\'N\' were 122 and 1,726 mg/L for inoculum concentrations of 2.5 and 5.0 g TVS/L, respectively. The second experiment compared different methylamine/sulfate ratios (0.71, 1.26 and 2.18) on reactors inoculated with 5.0 g TVS/L containing 1,550 mg methylamine/L. The stoichiometrically expected \'CH IND.4\' concentration was reached in all reactors. The maximum specific methane production rates were 2.54, 2.31 and 3.14 mmol/L g TVS day for methylamine/sulfate ratios of 0.71, 1.26 and 2.18, respectively. In all reactors, the average \'NH IND.4\'POT.+\'-\'N\' final concentration was 1,200 mg/L. The control reactors consumed 71.9% of the added substrate. The reactors with methylamine/sulfate ratios of 0.71, 1.26 and 2.18 consumed 49.6%, 61.6% and 83.2% of all the added sulfate, respectively. In both experiments, the microscopic analysis revealed cocci, rods, filaments, fluorescent cocci and sarcinas. In the reactors fed with methylamine only, the sequencing of 16S rRNA fragments detected five Phyla of the Bacteria Domain (Acidobacteria 4%, Firmicutes 11%, Proteobacteria 14%, Spirochaetes 13% and Synergistes 47%). In the reactors with methylamine and sulfate, seven Phyla were detected (Firmicutes 45%, Proteobacteria 7%, Spirochaetes 2%, Synergistes 16%, Chloroflexi 4%, Thermotogae 8% e Planctomycetes 1%). In both experiments, Archaea Domain was mainly represented by Methanomicrobiaceae, Methanosaetaceae and Methanosarcinaceae Families, with the presence of Methanomethylovorans hollandica, a methanogenic archaea specie with specific metabolism for methylamine degradation.

Les bases fondamentales de la biologie suggèrent que tous les organismes actuels partagent un dernier ancêtre commun, le cenancêtre. Dès que la comparaison moléculaire des organismes des trois domaines du vivant (archées, bactéries et eucaryotes) est devenue possible, d’importants débats ont émergé sur l’habitat du cenancêtre, son rapprochement des origines de la vie, sa nature unique ou communautaire et ses relations avec les trois domaines du vivant. Cependant, jusqu’à il y a peu les informations disponibles sur les organismes modernes n’étaient pas suffisantes pour décrire précisément sa biologie. Notamment, la découverte chez les archées de membranes dont les composants principaux, les phospholipides, sont synthétisés par des mécanismes très différents de ceux des bactéries et les eucaryotes a conduit à proposer que chaque mécanisme de synthèse des phospholipides soit apparu indépendamment dans les lignées modernes. Dans ces hypothèses le cenancêtre aurait été dépourvu de phospholipides et, donc, de membranes. Cela met en cause la nature cellulaire du cenancêtre, qui semblait pourtant soutenue par d’autres indices indirects. Ces contradictions posent la question de l’existence de traces dans les organismes modernes d’une synthèse des phospholipides chez le cenancêtre. Dans cette thèse j’ai profité de l’explosion récente des données génomiques pour répondre à cette question. Il avait déjà montré que des membres de deux superfamilles protéiques universelles pouvaient avoir synthétisé de façon non spécifique chez le cenancêtre les énantiomères de glycérol phosphate servant d’ossature aux phospholipides. Les phospholipides archéens sont composés d’isoprénoïdes et les bactériens et eucaryotes d’acides gras. J’ai donc étudié l’évolution des voies de synthèse de ces molécules ainsi que celle de l’assemblage de tous les composants dans des phospholipides. Mes résultats montrent que la voie de synthèse des isoprénoïdes des eucaryotes et une voie hypothétique de synthèse des acides gras chez les archées avaient probablement des ancêtres moins spécifiques chez le cenancêtre. Une partie au moins de la machinerie d’assemblage des phospholipides semble aussi avoir été présente chez le cenancêtre.Ceci suggère que le cenancêtre avait probablement des mécanismes peu spécifiques de synthèse des phospholipides et que les différences entre les membranes actuelles sont dues à la spécialisation de la machinerie ancestrale dans chaque lignée. Mes observations soulignent aussi l’importance d’étudier le cenancêtre à partir des informations issues des organismes actuels pour éviter toute confusion avec les origines de la vie. / The main bases of Biology suggest that all extant organisms share a last common ancestor, namely the cenancestor. As soon as the comparison of molecular characters of organisms representative of the whole diversity of life became possible, hot debates emerged about the environmental conditions in which the cenancestor lived, its closeness to the origins of life, its single or community nature and its relationships with the three domains of life (Archaea, Bacteria and Eucarya). However, available information about current organisms was for a long time inadequate to precisely describe the biology of this organism. For instance, the observation that the main archaeal membrane components, called phospholipids, are synthesized by different means than their bacterial/eukaryotic counterparts was proposed to reveal that modern phospholipid biosynthesis pathways emerged late in independent lineages and were, therefore, absent in the cenancestor. This hypothesis argued that the cenancestor had no lipid membranes, so it could not be a cellular organism although other indirect clues indicated the opposite. These contradictions raise the question of the presence in modern organisms of traces that the cenancestor had a phospholipid biosynthesis machinery.In this dissertation, I took advantage from the recent accumulation of genomic data to address this issue. Previous work had shown that the members of two universal protein superfamilies could be present in the cenancestor to carry out the non-specific synthesis of the glycerol phosphate enantiomers that are the backbones of modern phospholipids. Bacterial and eukaryotic phospholipids use fatty acids whereas archaeal phospholipids are made up of isoprenoids. Thus, I studied the evolution of the metabolic pathways that synthesize these molecules and build up the phospholipids from their components. My results show that the eukaryotic isoprenoid biosynthesis pathway and a hypothetical archaeal fatty acid biosynthesis pathway are likely to have had less specific ancestors in the cenancestor. In addition, the phospholipid assembly machinery was also probably present in the cenancestor.These results suggest that the cenancestor was likely able to enzymatically synthesize its phospholipids by means less specific than modern ones. Dissimilarities in modern membrane phospholipids would result from the specialization of each biosynthesis system in each lineage. My work also stresses the fact that the cenancestor should be described on the basis of the comparison of modern organisms to avoid frequent confusions between the cenancestor and the origins of life.

A degradação da metilamina foi investigada por meio da avaliação da velocidade específica máxima de produção de metano (VEM CH4) e da comunidade microbiana relacionada aos Domínios Bacteria e Archaea. Para isso, foram realizados dois ensaios com reatores anaeróbios em batelada inoculados com lodo granulado oriundo de reator UASB usado no tratamento de água residuária de abatedouro de aves. Em todos os ensaios, os reatores controle, que não receberam adição de metilamina, apresentaram VEM CH4 de 0,04 mmol/L g STV dia. O primeiro ensaio avaliou a degradação da metilamina em diferentes concentrações de inóculo (2,5, 5,0 e 10,0 g STV/L) e substrato (1.550 e 3.100 mg metilamina/L). A concentração de \'CH IND.4\' esperada estequiometricamente foi atingida em todos os reatores (37,50 e 75,00 mmol \'CH IND.4\'/L, para concentrações de 1.550 e 3.100 mg metilamina/L, respectivamente), exceto para aquele com 2,5 g STV/L e 3.100 mg metilamina/L, que produziu somente 2,04 mmol \'CH IND.4\'/L. A maior velocidade específica máxima de produção de \'CH IND.4\' foi 4,42 mmol/L g STV dia, obtida nos reatores com 2,5 g STV/L e 1.550 mg metilamina/L. Os reatores inoculados com 5,0 g STV/L tiveram VEM CH4 de 2,31 e 2,34 para 1.550 e 3.100 mg metilamina/L, respectivamente. Os reatores com 1.550 mg metilamina/L e 10,0 g STV/L apresentaram VEM CH4 de 1,28 mmol/L g STV dia. A concentração de \'N\'-\'NH IND.4\'POT.+\' excedeu em 12,9%, 0,7% e 18,3% o valor esperado (698 mg/L) para os reatores com 1.550 mg metilamina/L e 2,5, 5,0 e 10,0 g STV/L, respectivamente. Nos reatores com 3.100 mg metilamina/L, as concentrações finais de \'N\'-\'NH IND.4\'POT.+\' foram 122 e 1.726 mg/L para concentrações de inóculo de 2,5 e 5,0 g STV/L, respectivamente. O segundo ensaio comparou diferentes relações metilamina/sulfato (0,71, 1,26 e 2,18) em reatores inoculados com 5,0 g STV/L contendo 1.550 mg metilamina/L. As concentrações de \'CH IND.4\' esperadas estequiometricamente foram atingidas em todos os reatores. As velocidades específicas máximas de formação de \'CH IND.4\' foram de 2,54, 2,31 e 3,14 mmol/L g STV dia para as relações metilamina/sulfato 0,71, 1,26 e 2,18, respectivamente. Em todos os reatores, a concentração de \'N\'-\'NH IND.4\'POT.+\' atingiu média final de 1200 mg/L. Os reatores controle consumiram 71,9% do sulfato adicionado. Os reatores com relação metilamina/sulfato 0,71, 1,26 e 2,18 consumiram 49,6%, 61,6% e 83,2% de todo o sulfato adicionado, respectivamente. Nos dois ensaios, os exames microscópicos revelaram a presença de cocos, bacilos, filamentos, cocos e sarcinas fluorescentes. Nos reatores alimentados apenas com metilamina, o seqüenciamento de fragmentos da região 16S do RNAr detectou cinco Filos do Domínio Bacteria (Acidobacteria 4%, Firmicutes 11%, Proteobacteria 14%, Spirochaetes 13% e Synergistes 47%). Nos reatores com metilamina e sulfato, sete Filos foram detectados (Firmicutes 45%, Proteobacteria 7%, Spirochaetes 2%, Synergistes 16%, Chloroflexi 4%, Thermotogae 8% e Planctomycetes 1%). Nos dois ensaios, o Domínio Archaea foi predominantemente representado pelas Famílias Methanomicrobiaceae, Methanosaetaceae e Methanosarcinaceae, com presença de Methanomethylovorans hollandica, uma espécie de arquéia metanogênica com metabolismo especializado na degradação de metilamina. / The degradation of methylamine was investigated assessing the maximum specific methane production rate (MSR CH4) and the microbial community related to Bacteria e Archaea Domains. For this, two tests were performed in anaerobic batch reactors inoculated with granular sludge from an UASB reactor used in the treatment of poultry wastes. In all experiments, the control reactors, without methylamine addition, showed MSR CH4 of 0.04 mmol/L g TVS day. The first experiment evaluated the degradation of methylamine at different inoculum concentrations (2.5, 5.0 and 10.0 g TVS/L) and substrate concentrations (1,550 and 3,100 mg methylamine/L). The stoichiometrically expected \'CH IND.4\' concentration was reached in all reactors (37.50 and 75.00 mmol \'CH IND.4\'/L, for methylamine concentrations of 1,550 and 3,100 mg methylamine/L, respectively), except for the reactor with 2.5 g TVS/L and 3,100 mg methylamine/L, that produced only 2.04 mmol \'CH IND.4\'/L. The highest maximum specific methane production rate was 4.42 mmol/L g TVS day, reached in the reactors with 2.5 g TVS/L and 1,550 mg methylamine/L. The reactors inoculated with 5.0 g TVS/L had MSR CH4 of 2.31 and 2.34 for 1,550 and 3,100 mg methylamine/L, respectively. The reactors with 1,550 mg methylamine/L and 10.0 g TVS/L had MSR CH4 of 1.28 mmol/L g TVS day. The \'N\'-\'NH IND.4\'POT.-\' concentrations exceeded 12.9%, 0.7% and 18.3% the expected value (698 mg/L) for the reactors with 1,550 mg methylamine/L and 2.5, 5.0 and 10.0 g TVS/L, respectively. In the reactors with 3,100 mg methylamine/L, the final concentrations of \'NH IND.4\'POT.+\'-\'N\' were 122 and 1,726 mg/L for inoculum concentrations of 2.5 and 5.0 g TVS/L, respectively. The second experiment compared different methylamine/sulfate ratios (0.71, 1.26 and 2.18) on reactors inoculated with 5.0 g TVS/L containing 1,550 mg methylamine/L. The stoichiometrically expected \'CH IND.4\' concentration was reached in all reactors. The maximum specific methane production rates were 2.54, 2.31 and 3.14 mmol/L g TVS day for methylamine/sulfate ratios of 0.71, 1.26 and 2.18, respectively. In all reactors, the average \'NH IND.4\'POT.+\'-\'N\' final concentration was 1,200 mg/L. The control reactors consumed 71.9% of the added substrate. The reactors with methylamine/sulfate ratios of 0.71, 1.26 and 2.18 consumed 49.6%, 61.6% and 83.2% of all the added sulfate, respectively. In both experiments, the microscopic analysis revealed cocci, rods, filaments, fluorescent cocci and sarcinas. In the reactors fed with methylamine only, the sequencing of 16S rRNA fragments detected five Phyla of the Bacteria Domain (Acidobacteria 4%, Firmicutes 11%, Proteobacteria 14%, Spirochaetes 13% and Synergistes 47%). In the reactors with methylamine and sulfate, seven Phyla were detected (Firmicutes 45%, Proteobacteria 7%, Spirochaetes 2%, Synergistes 16%, Chloroflexi 4%, Thermotogae 8% e Planctomycetes 1%). In both experiments, Archaea Domain was mainly represented by Methanomicrobiaceae, Methanosaetaceae and Methanosarcinaceae Families, with the presence of Methanomethylovorans hollandica, a methanogenic archaea specie with specific metabolism for methylamine degradation.

Terrestrial inputs of organic matter contribute greatly to the functioning of aquatic ecosystems, subsidizing between 30-70% of secondary production. This contribution of terrestrial resources is especially important in boreal lakes that are largely nutrient-poor and thus more responsive to these additions. Yet the mechanisms underlying initial processing of terrestrial resources by microbial communities at the base of lake food webs remain poorly understood. With this in mind, this thesis aims to advance our understanding of lake sediment microbial community assembly and functioning along abiotic gradients, primarily reflecting variation in terrestrial organic matter inputs that are predicted to increase with future environmental change. Chapter 1 reviews current knowledge on the terrestrial support of lake food webs and highlights gaps in understanding the factors influencing the microbial processing of terrestrial resources. It also provides an overview of metagenomics methods for microbial community analysis and their development over the course of the thesis. Chapter 2 tests how much of ecosystem functioning is explained by microbial community structure relative to other ecosystem properties such as the present-day and past environment. Theory predicts that ecosystem functioning, here measured as CO2 production, should increase with diversity, but the individual and interactive effects of other ecosystem properties on ecosystem functioning remain unresolved. Chapter 3 further questions the importance of microbial diversity for ecosystem functioning by asking whether more diverse microbial communities stabilize ubiquitous functions like CO2 production and microbial abundances through time. It also aims to identify the biotic and abiotic mechanisms underlying positive diversity-stability relationships. Chapter 4 then explores how microbial communities assemble and colonize sediments with varying types and amounts of terrestrial organic matter in three different lakes over a two-month period. Understanding how microbial communities change in relation to sediment and lake conditions can help predict downstream ecosystem functions. Finally, Chapter 5 discusses the main findings of the thesis and ends with proposed avenues for future research.

Neste trabalho foi realizada a caracterização microbiana anaeróbia de reatores anaeróbios diferenciais horizontais e em batelada, operados sob condições sulfetogênicas e mesofílicas (30ºC). Os reatores diferenciais foram preenchidos com diferentes materiais suportes (espuma de poliuretano, carvão vegetal, polietileno reciclado de baixa densidade e cerâmica porosa à base de alumina) visando a seleção do suporte adequado para otimização do processo sulfetogênico, para a relação DQO/sulfato de aproximadamente 0,67. Os reatores diferenciais foram alimentados diariamente com esgoto sintético, contendo aproximadamente 1000 mg/L de DQO e 1500 mg/L de sulfato, durante 28 dias de operação. A caracterização microbiana foi realizada através da técnica de hibridação in situ fluorescente (FISH), microscopia óptica e eletrônica de varredura. Foram realizadas quantificações, em termos de porcentagens, de microrganismos pertencentes ao Domínio Bacteria (EUB338), Domínio Archaea (ARC915) e bactérias redutoras do íon sulfato (BRS) da subdivisão delta de Proteobacteria (SRB385). Nos reatores diferenciais, houve predomínio de bactérias em todos os suportes estudados. Os reatores diferenciais operados com espuma e carvão apresentaram maiores porcentagens de BRS, com valores iguais a 57,6% e 69,7%, respectivamente. A cerâmica foi o material que apresentou melhor equilíbrio de bactérias e arqueas metanogênicas, com 59,6% e 40,9%, respectivamente. Os reatores em batelada foram operados com espuma de poliuretano e carvão vegetal com relação DQO/sulfato de aproximadamente 3. As porcentagens de BRS quantificadas pelo FISH foram iguais a 65,3% e 69,1% para espuma e carvão, respectivamente. Em ambos os reatores o carvão vegetal foi o material mais favorável à sulfetogênese. / This research reports an anaerobic microbial characterization of both, a horizontal differential anaerobic and a batch reactors, operated at sulfidogenic and mesofilic conditions at 30ºC. The differential reactors were filled with four support materials (polyurethane foam, vegetable coal, recycled polyethylene of low density and alumin based porous ceramic) aiming the selection of a more appropriated support for optimization of sulfidogenic processes (ratio COD/sulfate of approximately 0.67). Differential reactors were fed daily with synthetic sewage, containing approximately 1000 mg/L of COD and 1500 mg/L of sulfate concentrations, during 28 days of operation. Microbial characterization was accomplished using fluorescent in situ hybridization (FISH), optic and scanning electronic microscopy. It was realized a quantification, in percentages, of microorganisms belong to Bacteria Domain (EUB338), Archaea Domain (ARC915) and sulfate-reducing bacteria (SRB) of delta subdivision Proteobacteria (SRB385). Differential reactors have shown predominance of bacteria in all the support materials studied. Differential reactors operated with foam and coal presented the greatest percentages of SRB, with values equal to 57.6% and 69.7%, respectively. The ceramic was the material that presented the best equilibrium of bacteria and methanogenic archaea, with 59.6% and 40.9%, respectively. Batch reactors were operated with polyurethane foam and vegetable coal with COD/sulfate ratio of approximately 3. Percentages of SRB quantified by FISH were equals to 65.3% and 69.1% for foam and coal, respectively. In both reactors the vegetable coal have shown to be the most favorable material to sulfidogenesis.

Les organismes cellulaires appartiennent à l'un des trois domaines du vivant : Archaea, Bacteria, Eucarya. Les Archaea sont des organismes unicellulaires avec un phénotype bactérien mais qui possèdent de nombreux caractères moléculaires eucaryotes. En particulier, la machinerie de réplication archéenne est une version homologue et simplifiée de celle des eucaryotes. Au cours de cette thèse, j'ai étudié la réplication de l'ADN chez les Archaea en combinant des approches in vitro et in silico.<br />Premièrement, j'ai essayé de purifier la protéine initiatrice de la réplication Cdc6/Orc1, sous une forme native, dans l'espoir de mettre au point le premier système de réplication de l'ADN in vitro chez les Archaea. Malheureusement, cette approche a été infructueuse en raison de l'instabilité et des propriétés d'agrégation de la protéine.<br />Deuxièmement, j'ai réalisé une analyse comparative du contexte génomique des gènes de réplication dans les génomes d'Archaea. Cette analyse nous a permis d'identifier une association très conservée entre des gènes de la réplication et des gènes liés au ribosome. Cette organisation suggère l'existence d'un mécanisme de couplage entre la réplication de l'ADN et la traduction. De manière remarquable, des données expérimentales obtenues chez des modèles bactériens et eucaryotes appuient cette idée. J'ai ensuite mis au point des outils expérimentaux qui permettront d'éprouver la pertinence biologique de certaines des prédictions effectuées.<br />Finalement, j'ai examiné la distribution taxonomique des gènes de la réplication dans les génomes d'Archaea afin de prédire la composition probable de la machinerie de réplication de l'ADN chez le dernier ancêtre commun des Archaea. Dans leur ensemble, les profils phylétiques des gènes de la réplication suggèrent que la machinerie ancestrale était plus complexe que celle des organismes archéens contemporains.

ABSTRACT PURIFICATION AND CHARACTERIZATION OF CYTOPLASMIC AND PROTEASOME ASSOCIATED CHYMOTRYPSIN-LIKE PROTEASES FROM THERMOPLASMA VOLCANIUM &Ouml / zdemir, F.inci Ph.D., Department of Biology Supervisor: Prof. Dr. Semra Kocabiyik September, 147 pages In this study, two novel cytoplasmic serine proteases were isolated and characterized from thermophilic archaea Thermoplasma volcanium. The first protease was purified by ion exchange and affinity chromatographies and identified as a chymotrypsin-like serine protease mainly based on its substrate profile and inhibition pattern. The presence of protease activity was analyzed by gelatin zymography which was detected as a single band (35 kDa). Optimum temperature was found to be 60oC for azocasein hydrolysis and 50oC for N-Suc-Phe-pNA hydrolysis. Optimum activity was observed in the pH range of 6.0-8.0 with a maximum value at pH 7.0. The Km and Vmax values for the purified protease were calculated to be 2.2 mM and 40 &micro / moles of p-nitroanilide released min-1.ml-1, respectively, for N-Suc-Phe-PNA as substrate. Ca2+ and Mg2+ at 4 mM concentrations were the most effective divalent cations in activating the enzyme. In the second stage of this study, 20S proteasome of Tp. volcanium with substantial chymotrypsin-like activity was purified and characterized. This enzyme complex was purified with 19.1 U/mg specific activities from cell free extract by a four-step procedure. SDS-PAGE analysis revealed two strong bands with relative molecular masses of 26 kDa (&amp / #945 / -subunit) and 21.9 kDa (&amp / #946 / -subunit). Tp. volcanium 20S proteasome predominantly catalyzed cleavage of peptide bonds carboxyl to the acidic residue Glu (postglutamyl activity) and the hydrophobic residue Phe (chymotrypsin-like activity) in short chromogenic peptides. Low-level hydrolyzing activity was also detected carboxyl to basic residue Arg (trypsin-like activity). Chymotrypsin-like activity of Tp. volcanium 20S proteasome was significantly inhibited by chymotrypsin specific serine protease inhibitor chymostatin. When N-CBZ-Arg was used which is a substrate for trypsin, 20S proteasome was strongly inhibited by TLCK. The optimum temperature for Ala-Ala-Phe-pNA hydrolysis by the Tp. volcanium 20S proteasome was 55oC and the optimum pH was 7.5. The chymotryptic activity was significantly enhanced by divalent cations such as Ca+2 and Mg2+ at high concentrations, i.e. 125-250 mM. Keywords:Serine protease, 20S proteasome, archaea, thermophilic protease, Thermoplasma volcanium, chymotrypsin-like serine protease.

Les gènes codant pour des protéines peuvent souvent être regroupés et intégrés en modules fonctionnels par rapport à un organelle. Ces modules peuvent avoir des composantes qui suivent une évolution corrélée pouvant être conditionnelle à un phénotype donné. Les gènes liés à la motilité possèdent cette caractéristique, car ils se suivent en cascade en réponse à des stimuli extérieurs. L’hyperthermophilie, d’autre part, est interreliée à la reverse gyrase, cependant aucun autre élément qui pourrait y être associé avec certitude n’est connu. Ceci peut être dû à un déplacement de gènes non orthologues encore non résolu. En utilisant une approche bio-informatique, une modélisation mathématique d’évolution conditionnelle corrélée pour trois gènes a été développée et appliquée sur des profils phylétiques d’archaea. Ceci a permis d’établir des théories quant à la fonction potentielle du gène du flagelle FlaD/E ainsi que l’histoire évolutive des gènes lui étant liés et ayant contribué à sa formation. De plus, une histoire évolutive théorique a été établie pour une ligase liée à l’hyperthermophilie. / Protein coding gene may often be grouped and integrated in functional modules with respect to an organelle. These modules may have constituents that follow a conditional correlated evolution to a given phenotype. Genes linked to motility posses this characteristic as they follow a cascade in response to external stimuli. Similarly, hyperthermophily is related to reverse gyrase, however no other element that could be associated with certainty is known. This may be caused by an unresolved case of non-orthologous gene displacement. Using a bioinformatic approach, a mathematical model for conditional correlated evolution for three genes has been developed and applied to the phyletic profiles of archaea. This has helped to develop theories about the potential functions of the flagellar gene FlaD/E and the evolutionary history of the genes that are linked to it and that may have contributed to its formation. In addition, a theoretical evolutionary history has been established for a ligase associated with hyperthermophily.

Mars is one of the best candidates among planetary bodies for supporting life. The presence of water in the form of ice and atmospheric vapour together with the availability of biogenic elements and energy are indicators of the possibility of hosting life as we know it. The occurrence of permanently frozen ground – permafrost, is a common phenomenon on Mars and it shows multiple morphological analogies with terrestrial permafrost. Despite the extreme inhospitable conditions, highly diverse microbial communities inhabit terrestrial permafrost in large numbers. Among these are methanogenic archaea, which are anaerobic chemotrophic microorganisms that meet many of the metabolic and physiological requirements for survival on the martian subsurface. Moreover, methanogens from Siberian permafrost are extremely resistant against different types of physiological stresses as well as simulated martian thermo-physical and subsurface conditions, making them promising model organisms for potential life on Mars. The main aims of this investigation are to assess the survival of methanogenic archaea under Mars conditions, focusing on methanogens from Siberian permafrost, and to characterize their biosignatures by means of Raman spectroscopy, a powerful technology for microbial identification that will be used in the ExoMars mission. For this purpose, methanogens from Siberian permafrost and non-permafrost habitats were subjected to simulated martian desiccation by exposure to an ultra-low subfreezing temperature (-80ºC) and to Mars regolith (S-MRS and P-MRS) and atmospheric analogues. They were also exposed to different concentrations of perchlorate, a strong oxidant found in martian soils. Moreover, the biosignatures of methanogens were characterized at the single-cell level using confocal Raman microspectroscopy (CRM). The results showed survival and methane production in all methanogenic strains under simulated martian desiccation. After exposure to subfreezing temperatures, Siberian permafrost strains had a faster metabolic recovery, whereas the membranes of non-permafrost methanogens remained intact to a greater extent. The strain Methanosarcina soligelidi SMA-21 from Siberian permafrost showed significantly higher methane production rates than all other strains after the exposure to martian soil and atmospheric analogues, and all strains survived the presence of perchlorate at the concentration on Mars. Furthermore, CRM analyses revealed remarkable differences in the overall chemical composition of permafrost and non-permafrost strains of methanogens, regardless of their phylogenetic relationship. The convergence of the chemical composition in non-sister permafrost strains may be the consequence of adaptations to the environment, and could explain their greater resistance compared to the non-permafrost strains. As part of this study, Raman spectroscopy was evaluated as an analytical technique for remote detection of methanogens embedded in a mineral matrix. This thesis contributes to the understanding of the survival limits of methanogenic archaea under simulated martian conditions to further assess the hypothetical existence of life similar to methanogens on the martian subsurface. In addition, the overall chemical composition of methanogens was characterized for the first time by means of confocal Raman microspectroscopy, with potential implications for astrobiological research. / Der Mars ist unter allen Planeten derjenige, der aufgrund verschiedener Faktoren am wahrscheinlichsten Leben ermöglichen kann. Das Vorhandensein von Wasser in Form von Eis und atmosphärischem Dampf zusammen mit der Verfügbarkeit biogener Elemente sowie Energie sind Indikatoren für die Möglichkeit, Leben, wie wir es kennen, zu beherbergen. Das Auftreten von dauerhaft gefrorenen Böden, oder auch Permafrost, ist ein verbreitetes Phänomen auf dem Mars. Dabei zeigen sich vielfältige morphologische Analogien zum terrestrischen Permafrost. Permafrostgebiete auf der Erde, welche trotz extremer, Bedingungen durch eine große Zahl und Vielfalt mikrobieller Gemeinschaften besiedelt sind, sind hinsichtlich möglicher Habitate auf dem Mars die vielversprechendste Analogie. Die meisten methanogenen Archaeen sind anaerobe, chemolithotrophe Mikroorganismen, die auf der Marsoberfläche viele der metabolischen und physiologischen Erfordernisse zum Überleben vorfinden. Methanogene Archaeen aus dem sibirischen Permafrost sind zudem extrem resistent gegenüber unterschiedlichen Formen von physiologischem Stress sowie simulierten thermo-physikalischen Marsbedingungen. Die Hauptziele dieser Untersuchung bestehen darin, das Überleben der methanogenen Archaeen unter Marsbedingungen zu beurteilen, wobei der Fokus auf methanogenen Archaeen aus dem sibirischen Permafrost liegt, sowie deren Biosignaturen mit Hilfe der Raman-Spektroskopie zu charakterisieren, einer starken Technologie zur mikrobiellen Identifikation, welche bei der ExoMars-Mission zum Einsatz kommen wird. Zu diesem Zweck wurden methanogene Archaeen aus dem sibirischen Permafrost sowie aus Nicht-Permafrost-Habitaten in Simulationen Marsbedingungen ausgesetzt, wie Austrocknung durch Langzeitversuche bei ultraniedrigen Temperaturen unter dem Gefrierpunkt (-80ºC), Mars-analogen Mineralien (S-MRS und P-MRS) sowie einer Marsatmosphäre. Weiterhin wurden die Kulturen verschiedenen Konzentrationen von Magnesiumperchlorat, einem starken Oxidant, der im Marsboden nachgewiesenen wurde, ausgesetzt. Ferner wurden die Biosignaturen einzelner Zellen der methanogenen Archaeen mit Hilfe der konfokalen Raman-Mikrospektroskopie (CRM) charakterisiert. Die Ergebnisse zeigten für alle untersuchten methanogenen Stämme Überleben und Methanbildung, nachdem diese simulierten Austrocknungsbedingungen ausgesetzt worden waren. Nach Versuchen mit Temperaturen unter dem Gefrierpunkt zeigten die Stämme aus dem sibirischen Permafrost eine schnellere Wiederaufnahme der Stoffwechseltätigkeit, wohingegen bei den Referenzorganismen aus Nicht-Permafrost-Habitaten die Zell¬membranen im größeren Ausmaß intakt blieben. Der Stamm Methanosarcina soligelidi SMA-21 aus dem sibirischen Permafrost zeigte nach dem Belastungstest mit Marsboden und Mars-analoger Atmosphäre signifikant höhere Methanbildungsraten. Zudem überlebten alle untersuchten Stämme die Zugabe von Magnesiumperchlorat in der entsprechenden Konzentration, die auf dem Mars vorkommt. Weiterhin konnten durch die Raman-Spektroskopie beachtliche Unterschiede in der chemischen Zusammensetzung zwischen methanogenen Archaeen aus Permafrost- und Nicht-Permafrost-Habitaten, trotz ihrer phylogenetischen Verwandtschaft, ermittelt werden. Die Konvergenz der chemischen Zusammensetzung der Permafrost-Stämme könnte das Resultat ihrer Anpassung an die Umgebung sein, was auch die Unterschiede hinsichtlich ihrer Resistenz verglichen mit Nicht-Permafrost-Stämmen erklären könnte. Als Teil dieser Studie wurde die Raman-Spektroskopie als Analyse-Technik zur Ferndetektion von methanogenen Archaeen, welche in eine Mineral-Matrix eingebettet sind, evaluiert. Diese Dissertation trägt zu einem besseren Verständnis hinsichtlich der Grenzen für ein Überleben von methanogenen Archaeen unter simulierten Marsbedingungen bei und damit zu einer Beurteilung der Hypothese, ob es ähnliches Leben unter der Marsoberfläche geben könnte. Darüber hinaus wurde erstmalig die chemische Zusammensetzung von methanogenen Archaeen mit Hilfe der Raman-Mikrospektroskopie charakterisiert. Dieser Technologie kommt eine wesentliche Bedeutung für weitere Forschungstätigkeit in der Astrobiologie zu.

Aquesta tesi doctoral va estudiar la diversitat (riquesa i abundància), la distribució i la dinàmica de les comunitats planctòniques d'Archaea presents a diferents llacs estratificats temperats d'aigua dolça per aportar evidencies sobre la seva distribució i la seva possible activitat en aquests ecosistemes en relació als cicles biogeoquímics presents en els mateixos. Es varen estudiar dos estanyols d'origen càrstic (l'Estanyol del Vilar durant cinc anys consecutius (2001-2005) i l'Estanyol de Can Coromina) i un llac d'origen volcànic (Llac Kivu) analitzant, per una banda, la seva comunitat planctònica d'Archaea mitjançant una aproximació molecular i, per una altra, la seva possible activitat en aquests ambients (p.e., la nitrificació i la fixació de carboni). Per contextualitzar els resultats, es va realitzar un anàlisi in silico dels patrons de distribució global dels Archaea mesòfils mitjançant un anàlisi a nivell de llinatge combinant seqüències del gen 16S rRNA amb diferents eines estadístiques i d'ecologia general. / The present PhD thesis analysed the diversity (richness and evenness), distribution and dynamics of planktonic Archaea in several temperate stratified freshwater lakes to shed some light on their distribution and potential activity in these ecosystems in relation to prevalent biogeochemical cycles. In this sense, two karstic lagoons (Lake Vilar during five consecutive years (2001-2005) and Coromina lagoon) and a volcanic lake (Lake Kivu) were studied analysing, in the one hand, their archaeal planktonic community throughout a molecular approach and, in the other hand, their potential acitivity in these environments (e.g., nitrification and carbon fixation). In order to contextualize the obtained results, an in silico phylogenetic lineage-based analysis on the global distribution of lacustrine Archaea was conducted using 16S rRNA gene sequences in combination with statistical and general ecology tools.