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.

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.

Foram estudados três procedimentos para o tratamento prévio de amostras provenientes de três sistemas de biodigestão anaeróbia operados com resíduos sólidos urbanos padronizados (RSUDp), com o fim de promover o desprendimento de células microbianas de fibras e outros materiais, e com isso obter um inóculo mais homogêneo para contagens celulares. Os tratamentos foram os seguintes: (a) suspensão de amostras em tampão fosfato e processamento em liqüidificador; (b) homogeneização mecânica e manual de amostras em solução mineral anaeróbia; (c) amostras submetidas a banho de ultra-som. O método do Número Mais Provável (NMP) foi utilizado para avaliar o número de bactérias celulolíticas e arqueas metanogênicas, em meio mineral contendo celulose em pó. Não foram constatadas diferenças entre os três tratamentos empregados, considerando-se os valores encontrados para ambos os grupos, da ordem de 102 células/mL. O tratamento com ultra-som foi escolhido para outras determinações em função da simplicidade quanto à manipulação. Assim, foram operados dois biorreatores anaeróbios com RSUDp para avaliação da reprodutibilidade dos valores das amostras após tratamento com ultra-som, para a determinação do número de microrganismos (celulolíticos, acetogênicos e metanogênicos) e avaliação da atividade microbiana anaeróbia na degradação do RSUDp. Os resultados das contagens de bactérias celulolíticas e arqueas metanogênicas pelo método do NMP em meio contendo celulose não foram superiores a 103 células/mL, e as réplicas foram bastante semelhantes. O aumento do número do grupo metanogênico pôde ser correlacionado com o aumento dos teores de metano no biorreator amostrado. As contagens de organismos acetogênicos e metanogênicos em meio mineral com fontes específicas revelou valores até 103 células/mL. Os tipos morfológicos predominantes nos exames microscópicos dos sistemas de biodigestão foram bacilos curvos, retos, sarcinas e cistos de sarcinas e as amostras dos tubos de contagem mostraram para celulolíticas, bacilos, cocos e sarcinas, para acetogênicas bacilos, bacilos espessos, cocos e cistos de sarcinas e para as arqueas metanogênicas bacilos fluorescentes e sarcinas. A evolução do processo de biodigestão anaeróbia nos dois últimos sistemas operados mostrou-se bastante próxima a proposta por BARLAZ et al. (1989b), em que o número de bactérias celulolíticas e de arqueas metanogênicas aumenta na fase considerada metânica acelerada. O conteúdo de sólidos totais diminuiu em 50% ao longo do processo e os teores de ácidos orgânicos voláteis diminuíram de 27,5 para 8, 79 g de ác. acético/L. / Three different treatments were applied to samples from three anaerobic biodigestion systems operated with standardized municipal solid waste to promote the release of microbial cells adhered to fibers and other materials, resulting in a more homogeneous inoculum to cellular counting. The following treatments were applied to the samples: a) suspension in phosphate buffer followed by blending; b) mechanical and hand homogenization in anaerobic mineral solution; c) sonication in ultrasound bath. The Most Probable Number (MPN) technique was employed to evaluate the populations of cellulolytic bacteria and methanogenic Archaea, in mineral medium containing powdered cellulose. The populations of both groups of microorganisms were close to 102 cells/mL independently of the treatment applied to release the cells and no clear distinction among them could be made concerning their efficiencies. In view of this fact the ultrasound treatment was employed in all other determinations due to its simple execution. Two anaerobic bioreactors operated with standardized municipal solid waste were monitored to evaluate the reliability of sonication as a procedure for cell release, to determine microorganism populations (cellulolytic, acetogenic bacteria and methanogenic Archaea) and to evaluate the microbial anaerobic activity concerning the biodegradation of the standardized municipal solid waste. Cellulolytic bacteria and methanogenic Archaea had similar populations (lower than 103 cells/mL) as well as acetogenic and methanogenic microorganisms (up to 103 cells/mL). The increase in the methanogenic population could be directly related to the increase of methane production in the studied reactor. The morphological types which predominate in the microscopic examinations of the biodigestion systems were curved and straight rods and sarcina. The tubes for MPN countings showed the presence of rods, coccus and sarcina for cellulolytic bacteria; rods, tick rods, coccus and sarcina for acetogenic bacteria and fluorescent rods and sarcina for methanogenic Archaea. The evolution of the anaerobic biodigestion process in the latter two monitored systems was very similar to the one proposed by BARLAZ et al. ( 1989b) where the number of cellulolytic bacteria and methanogenic Archaea increase during the accelerated methane phase. The total content of solids decreased 50% during the process and the volatile acidity decreased from 27,5 g acetic acid/L to 8,79 g acetic acid/L.

Foram estudados três procedimentos para o tratamento prévio de amostras provenientes de três sistemas de biodigestão anaeróbia operados com resíduos sólidos urbanos padronizados (RSUDp), com o fim de promover o desprendimento de células microbianas de fibras e outros materiais, e com isso obter um inóculo mais homogêneo para contagens celulares. Os tratamentos foram os seguintes: (a) suspensão de amostras em tampão fosfato e processamento em liqüidificador; (b) homogeneização mecânica e manual de amostras em solução mineral anaeróbia; (c) amostras submetidas a banho de ultra-som. O método do Número Mais Provável (NMP) foi utilizado para avaliar o número de bactérias celulolíticas e arqueas metanogênicas, em meio mineral contendo celulose em pó. Não foram constatadas diferenças entre os três tratamentos empregados, considerando-se os valores encontrados para ambos os grupos, da ordem de 102 células/mL. O tratamento com ultra-som foi escolhido para outras determinações em função da simplicidade quanto à manipulação. Assim, foram operados dois biorreatores anaeróbios com RSUDp para avaliação da reprodutibilidade dos valores das amostras após tratamento com ultra-som, para a determinação do número de microrganismos (celulolíticos, acetogênicos e metanogênicos) e avaliação da atividade microbiana anaeróbia na degradação do RSUDp. Os resultados das contagens de bactérias celulolíticas e arqueas metanogênicas pelo método do NMP em meio contendo celulose não foram superiores a 103 células/mL, e as réplicas foram bastante semelhantes. O aumento do número do grupo metanogênico pôde ser correlacionado com o aumento dos teores de metano no biorreator amostrado. As contagens de organismos acetogênicos e metanogênicos em meio mineral com fontes específicas revelou valores até 103 células/mL. Os tipos morfológicos predominantes nos exames microscópicos dos sistemas de biodigestão foram bacilos curvos, retos, sarcinas e cistos de sarcinas e as amostras dos tubos de contagem mostraram para celulolíticas, bacilos, cocos e sarcinas, para acetogênicas bacilos, bacilos espessos, cocos e cistos de sarcinas e para as arqueas metanogênicas bacilos fluorescentes e sarcinas. A evolução do processo de biodigestão anaeróbia nos dois últimos sistemas operados mostrou-se bastante próxima a proposta por BARLAZ et al. (1989b), em que o número de bactérias celulolíticas e de arqueas metanogênicas aumenta na fase considerada metânica acelerada. O conteúdo de sólidos totais diminuiu em 50% ao longo do processo e os teores de ácidos orgânicos voláteis diminuíram de 27,5 para 8, 79 g de ác. acético/L. / Three different treatments were applied to samples from three anaerobic biodigestion systems operated with standardized municipal solid waste to promote the release of microbial cells adhered to fibers and other materials, resulting in a more homogeneous inoculum to cellular counting. The following treatments were applied to the samples: a) suspension in phosphate buffer followed by blending; b) mechanical and hand homogenization in anaerobic mineral solution; c) sonication in ultrasound bath. The Most Probable Number (MPN) technique was employed to evaluate the populations of cellulolytic bacteria and methanogenic Archaea, in mineral medium containing powdered cellulose. The populations of both groups of microorganisms were close to 102 cells/mL independently of the treatment applied to release the cells and no clear distinction among them could be made concerning their efficiencies. In view of this fact the ultrasound treatment was employed in all other determinations due to its simple execution. Two anaerobic bioreactors operated with standardized municipal solid waste were monitored to evaluate the reliability of sonication as a procedure for cell release, to determine microorganism populations (cellulolytic, acetogenic bacteria and methanogenic Archaea) and to evaluate the microbial anaerobic activity concerning the biodegradation of the standardized municipal solid waste. Cellulolytic bacteria and methanogenic Archaea had similar populations (lower than 103 cells/mL) as well as acetogenic and methanogenic microorganisms (up to 103 cells/mL). The increase in the methanogenic population could be directly related to the increase of methane production in the studied reactor. The morphological types which predominate in the microscopic examinations of the biodigestion systems were curved and straight rods and sarcina. The tubes for MPN countings showed the presence of rods, coccus and sarcina for cellulolytic bacteria; rods, tick rods, coccus and sarcina for acetogenic bacteria and fluorescent rods and sarcina for methanogenic Archaea. The evolution of the anaerobic biodigestion process in the latter two monitored systems was very similar to the one proposed by BARLAZ et al. ( 1989b) where the number of cellulolytic bacteria and methanogenic Archaea increase during the accelerated methane phase. The total content of solids decreased 50% during the process and the volatile acidity decreased from 27,5 g acetic acid/L to 8,79 g acetic acid/L.

Thioredoxin (Trx) and thioredoxin reductase (TrxR) along with an electron donor form a thioredoxin system. Such systems are widely distributed among the organisms belonging to the three domains of life. It is one of the major disulfide reducing systems, which provides electrons to several enzymes, such as ribonucleotide reductase, methionine sulfoxide reductase and glutathione peroxidase to name a few. It also plays an important role in combating oxidative stress and redox regulation of metabolism. Trx is a small redox protein, about 12 kDa in size, with an active site motif of Cys-X-X-Cys. The reduction of the disulfide in Trx is catalyzed by TrxR. Two types of thioredoxin reductases are known, namely NADPH thioredoxin reductase (NTR) with NADPH as the electron donor and ferredoxin thioredxoin reductase (FTR) which depends on reduced ferredoxin as electron donor. Although NTR is widely distributed in the three domains of life, it is absent in some archaea, whereas FTRs are mostly found in plants, photosynthetic eukaryotes, cyanobacteria, and some archaea. The thioredoxin system has been well studied in plants, mammals, and a few bacteria, but not much is known about the archaeal thioredoxin system. Our laboratory has been studying the thioredoxin systems of methanogenic archaea, and a major focus has been on Methanocaldococcus jannaschii, a deeply rooted archaeon that has two Trxs and one TrxR. My thesis research concerns the thioredoxin system of the late evolving members of the group which are exposed to oxygen more frequently than the deeply rooted members of the group, and have several Trxs and TrxRs. Methanosarcina mazei is one such organism, whose thioredoxin system is composed of one NTR, two FTRs, and five Trx homologs. Characterization of the components of a thioredoxin system sets the basis to further explore its function. I have expressed in Escherichia coli and purified the five Trxs and three TrxRs of M. mazei. I have shown the disulfide reductase activities in MM_Trx1 and MM_Trx5 by their ability to reduce insulin with DTT as the electron donor, and that in MM_Trx3 through the reduction of DTNB by this protein with NADPH as the electron donor, and in the presence of NTR as the enzyme. MM_Trx3 was found to be the only M. mazei thioredoxin to accept electrons through the NTR, and to form a complete Trx - NTR system. The Trx - FTR systems are well studied in plants, and such a system is yet to be defined in archaea. I have proposed a mechanism of action for one of the FTRs. FTR2 harbors a rubredoxin domain, and this unit is the only rubredoxin in this organism. Superoxide reductase, an enzyme that reduces superoxide radical to hydrogen peroxide without forming oxygen, utilizes rubredoxin as the direct electron source and this enzyme is found in certain anaerobes, including Methanosarcina species. Thus, it is possible that FTR2 provides electrons via a Trx to the superoxide reductase of M. mazei. This activity will define FTR2 as a tool in combating oxidative stress in M. mazei. In my thesis research I have laid a foundation to understand a complex thioredoxin system of M. mazei, to find the role of each Trx and TrxR, and to explore their involvement in oxidative stress and redox regulation. / Master of Science

Altos fluxos positivos de metano para a atmosfera foram detectados na região amazônica. O gás metano é o segundo mais importante gás de efeito estufa e micro-organismos pertencentes ao Domínio Archaea são responsáveis pela produção de aproximadamente 70% do metano emitido para a atmosfera anualmente. O objetivo deste trabalho foi caracterizar a diversidade de arqueias em sedimentos dos rios Floresta e Madeira através de técnicas moleculares e do cultivo de arqueias metanogênicas. A maior parte das sequências obtidas nas duas bibliotecas pertence ao domínio Crenarchaeota, algumas com similaridade menor que 97% às sequências depositadas nos bancos de dados, revelando a existência de grupos ainda não descritos na literatura. Nos enriquecimentos do sedimento do rio Madeira detectaram-se células pertencentes às famílias Methanosarcinaceae e Methanobacteriaceae pelo emprego de sondas fluorescentes de RNA. Culturas dos gêneros Methanosarcina e Methanobacterium foram estabelecidas em laboratório. A grande diversidade de arqueias não cultivadas encontrada vem reforçar a necessidade de se estudar esse grupo, especialmente sua fisiologia e, consequentemente, seu papel ecológico nos diversos ambientes em que são encontrados. / High positive fluxes of methane to the atmosphere have been detected in the Amazonian region. Methane is the second most important greenhouse gas and microorganisms belonging to the Archaea domain are responsible for approximately 70% of the total methane emitted to the atmosphere annually. The objective of this work was to characterize the Archaea diversity in two sites at Madeira and Floresta rivers sediments using molecular techniques and the culturing of methanogenic archaea. Most sequences obtained in the libraries from both rivers belonged to the Crenarchaeota domain, and around half of them presented less than 97% of similarity to sequences available in databases, revealing the existence of new archaea groups yet to be described in the literature. Cells belonging to the Methanosarcinaceae and Methanobacteriaceae families were detected in the enrichment cultures from Madeira River through the use of RNA fluorescent probes. Strains of Methanosarcina sp. and Methanobacterium sp. are being maintained under laboratory conditions. The great diversity of uncultured Archaea found emphasizes the need to study this group, mainly its physiology and, consequently, its role in the diverse environments they occupy.

L’analyse du microbiote oral et de son évolution séculaire se fait principalement à partir de l’analyse du tartre dentaire ancien des populations passées et du biofilm dentaire des populations modernes. Nous avons dans un premier temps fait le point des connaissances sur la paléomicrobiologie des bactéries et des archaea contenues dans le tartre dentaire et montré que les archaea faisaient partie du microbiote oral chez l'homme. Dans la deuxième partie, nous avons mis en évidence le répertoire des archaea méthanogènes vivant dans la cavité orale par la culture (une nouvelle espèce Methanobrevibacter massiliense, Methanobrevibacter smithii et Methanobrevibacter oralis). La prévalence de ces archaea était significativement plus élevée chez les patients atteints de parodontite que chez les personnes contrôles. Ensuite, nous avons développé une méthode de génotypage Multispacer Sequence Typing pour typer M. oralis et M. smithii et révélé différents génotypes. Enfin, nous avons analysé le répertoire des archaea méthanogènes dans des échantillons de tartre dentaire ancien datant du 14ème au 19ème siècle. La prévalence et la diversité des archaea méthanogènes dans la cavité orale ont diminué significativement au cours des sept derniers siècles. Des archaea méthanogènes ont été retrouvées dans 75% des prélèvements de tartre dentaire (Candidatus M. massiliense à 44,6%, M. oralis à 19,6%, Methanomassiliicoccus luminyensis-like à 12,5%, Candidatus Nitrososphaera evergladensis-like dans un prélèvement et Methanoculleus bourgensis dans un autre prélèvement). Un prélèvement de tartre positif pour Candidatus M. massiliense a été documenté par hybridation in situ en fluorescence. / The analyses of oral microbiome and its secular evolution mainly use dental calculus in past populations and dental plaque in modern populations. In our thesis, we initially reviewed the knowledge actual about bacteria and archaea paleomicrobiology of the dental calculus. The review disclosed that archaea taked part in the secular core-microbiota in past and modern populations. In the second work, we demonstrated the repertoire of methanogenic archaea currently living in the oral cavity using culture-based approach and succeeded in isolating for the first time a new species named Methanobrevibacter massiliense in addition to Methanobrevibacter smithii and Methanobrevibacter oralis from dental plaque in periodontitis patients. This work showed that the prevalence of methanogens was significantly higher in periodontitis patients than in controls. Some methanogenic archaea were involved in periodontitis. Then, we developed Multispacer Sequence Typing to evaluate M. oralis and M. smithii and revealed different genetic variants in these archaea. Finally, we examined the repertory of methanogenic archaea in ancient dental calculus dating from the 14th to the 19th century. The prevalence and diversity of methanogenic archaea in the oral cavity decreased significantly during the last seven centuries. Methanogenic archaea were found in 75% of dental calculis (Candidatus M. massiliense, 44.6%; M. oralis, 19.6%; Methanomassiliicoccus luminyensis-like, 12.5%; Candidatus Nitrososphaera evergladensis-like in one and Methanoculleus bourgensis in one specimen). One Candidatus M. massiliense dental calculus was further documented by fluorescent in situ hybridization.

Altos fluxos positivos de metano para a atmosfera foram detectados na região amazônica. O gás metano é o segundo mais importante gás de efeito estufa e micro-organismos pertencentes ao Domínio Archaea são responsáveis pela produção de aproximadamente 70% do metano emitido para a atmosfera anualmente. O objetivo deste trabalho foi caracterizar a diversidade de arqueias em sedimentos dos rios Floresta e Madeira através de técnicas moleculares e do cultivo de arqueias metanogênicas. A maior parte das sequências obtidas nas duas bibliotecas pertence ao domínio Crenarchaeota, algumas com similaridade menor que 97% às sequências depositadas nos bancos de dados, revelando a existência de grupos ainda não descritos na literatura. Nos enriquecimentos do sedimento do rio Madeira detectaram-se células pertencentes às famílias Methanosarcinaceae e Methanobacteriaceae pelo emprego de sondas fluorescentes de RNA. Culturas dos gêneros Methanosarcina e Methanobacterium foram estabelecidas em laboratório. A grande diversidade de arqueias não cultivadas encontrada vem reforçar a necessidade de se estudar esse grupo, especialmente sua fisiologia e, consequentemente, seu papel ecológico nos diversos ambientes em que são encontrados. / High positive fluxes of methane to the atmosphere have been detected in the Amazonian region. Methane is the second most important greenhouse gas and microorganisms belonging to the Archaea domain are responsible for approximately 70% of the total methane emitted to the atmosphere annually. The objective of this work was to characterize the Archaea diversity in two sites at Madeira and Floresta rivers sediments using molecular techniques and the culturing of methanogenic archaea. Most sequences obtained in the libraries from both rivers belonged to the Crenarchaeota domain, and around half of them presented less than 97% of similarity to sequences available in databases, revealing the existence of new archaea groups yet to be described in the literature. Cells belonging to the Methanosarcinaceae and Methanobacteriaceae families were detected in the enrichment cultures from Madeira River through the use of RNA fluorescent probes. Strains of Methanosarcina sp. and Methanobacterium sp. are being maintained under laboratory conditions. The great diversity of uncultured Archaea found emphasizes the need to study this group, mainly its physiology and, consequently, its role in the diverse environments they occupy.

Les archaea constituent l'un des quatre domaines connus du vivant. Contrairement à ce que leur nom laisse supposer, elles ont colonisé tous les écosystèmes et les microbiotes de certains hôtes dont l'Homme. Chez l'homme, certaines espèces d'archaea méthanogènes ont été associées aux muqueuses orale, intestinale et vaginale. Ces archaea méthanogènes sont des procaryotes anaérobies stricts et leurs conditions de culture restent fastidieuses et très mal connues. Quatre archaea methanogènes seulement ont été isolées à partir de prélèvements humains y compris dans le microbiote digestif Methanobrevibacter smithii détectée dans 95,7% des individus, Methanosphaera stadtmanae retrouvée chez environ un tiers des individus et plus récemment dans notre laboratoire Methanomassilicoccus luminyensis détectée en moyenne chez 4% des individus avec une prévalence liée à l'âge ; et dans le microbiote orale Methanobrevibacter oralis isolée à partir de la plaque dentaire. / Archaea is one of four known domains of life. Unlike what their name suggests, they some species of methanogenic archaea have been associated with oral, vaginal and intestinal mucosa. These methanogenic archaea are obligate anaerobic prokaryotes and their culture conditions are fastidious and very poorly known. Only four methanogenic archaea have been isolated from human samples including the digestive microbiota; Methanobrevibacter smithii detected in 95.7% of individuals Methanosphaera stadtmanae found in approximately one third of individuals and more recently in our laboratory Methanomassilicoccus luminyensis detected on average in 4% of individuals with a prevalence of age-related, and in the oral microbiota Methanobrevibacter oralis isolated from dental plaque.

A pesquisa que ora se apresenta visou estabelecer as condições nutricionais adequadas para o uso do sedimento do estuário de Santos - São Vicente do Estado de São Paulo, como inóculo no reator anaeróbio horizontal de leito fixo (RAHLF) no processo de degradação anaeróbia do pentaclorofenol (PCP) em busca da aplicação da tecnologia em escala real, assim como identificar grupos microbianos envolvidos no processo. Para tanto, sedimento do estuário de Santos-São Vicente, com características metanogênicas foi utilizado. Os microrganismos provenientes do sedimento estuarino foram enriquecidos sob condições metanogênicas e halofílicas, visando a utilização do sedimento como inoculo nos ensaios nutricionais e na operação dos reatores do tipo RAHLF. O meio de cultivo salino Biota, suplementado com glicose e formiato, foi utilizado para o desenvolvimento da comunidade microbiana metanogênica halofílica. Testes de degradação do PCP foram realizados previamente sob diferentes concentrações de nitrogênio e fósforo, com vistas a uma melhor compreensão da relação N:P adequada para o processo anaeróbio. Os resultados provenientes do acompanhamento da diversidade microbiana do domínio Bacteria nas diferentes relações testadas indicaram a seleção de distintas comunidades microbianas, resultando em diferentes velocidades de degradação do PCP. A relação N:P de 10:1 foi a que apresentou melhores resultados, pois além da rápida degradação do PCP quando comparada com as outras relações, apresentou a maior diversidade de microrganismos. Posteriormente, o sistema RAHLF foi operado com vazão média afluente de aproximadamente 44 mL/hora, com meio mineral salino Biota (DQO:N:P de 1000:130:45) para R1 e com a alteração para relação DQO:N:P de 1000:10:1 para R2. Duas diferentes estratégias foram adotadas para partida dos reatores. Para R1, optou-se por acrescentar PCP na concentração inicial de 10,0 mg/L, durante 110 dias causando desestabilização da metanogênese e acúmulo de PCP, requerendo intervenção para recuperação do reator pelo período de 90 dias. Na partida do RAHLF 2, optou-se pelo aumento gradual de concentração do PCP de 0,5 mg/L a 12,0 mg/L durante 52 dias. Após estabelecimento da metanogêsenese, R1 foi alimentado durante 270 dias com 5,0 mg PCP/L, durante 41 dias com 8,0 mg/L e 59 dias com 12 mg/L. O balanço de massa no reator RAHLF 1 demonstrou que 0,52% do PCP adicionado saiu no efluente e que não ocorreu adsorção no sistema. 22,34 mg de 2,4,6 TCP, intermediário da degradação do PCP, ficaram adsorvidos na biopartícula. Os resultados das análises de diversidade microbiana apontaram para mudança da comunidade microbiana do domínio Bacteria ao longo do período operacional e morfologias de bacilos fluorescentes semelhantes a Methanobacterium sp estiveram presentes no reator. No RAHLF 2, a degradação do PCP foi de 100%, até a concentração de 10,0 mg/L. No final da fase com 12,0 mg PCP/L, a concentração no efluente foi de 1,4 mg PCP/L, com eficiência média de remoção de 93,2 \'+ ou -\' 5,5%. 2,4,6 TCP foi o intermediário principal no efluente do reator. 4,06% do PCP adicionado ao sistema foram encontradas no efluente e 15,94% ficaram adsorvidas nas biopartículas do reator. Portanto, considera-se que 80% do PCP adicionado sofreu degradação anaeróbia microbiana. A presença dos microrganismos Methanocalcullus e Methanosaeta na fase final de operação do RAHLF 2 e determinadas no sedimento coletado foi considerada fundamental para manter estabilidade do reator. Essa descoberta contribui com informações sobre a real diversidade microbiana de ecossistemas tropicais, sobretudo em habitats anaeróbios, bem como sobre as condições nutricionais e os procedimentos necessários para confiná-la em reatores e usá-la em processos de biorremediação. / The research presented here aimed to determine the optimal nutritional conditions for the use of sediment from the Santos-São Vicente estuary in the state of São Paulo, Brazil, as an inoculum for a horizontal-flow anaerobic immobilized biomass reactor (HAIB) applied to the anaerobic degradation of pentachlorophenol (PCP), seeking to apply the technology on the real scale and to identify the microbial groups involved in the process. To this end, sediment with methanogenic characteristics from the Santos-São Vicente estuary was used. The microorganisms from the estuarine sediment were enriched under methanogenic and halophilic conditions, aiming to use the sediment as an inoculum in nutritional assays and in the operation of HAIB reactors. Biota saline culture medium supplemented with glucose and formiate was used to develop the halophilic methanogenic microbial community. PCP degradation tests were carried out previously under different concentrations of nitrogen and phosphorus in order to gain a better understanding of the optimal N:P ratio for the anaerobic process. The findings on the microbial diversity of the domain Bacteria at the various ratios tested here indicated the selection of distinct microbial communities, resulting in different PCP degradation velocities. The N:P ratio utilized was 10:1 since it presented the best results not only in terms of faster PCP degradation than the other ratios but also highest diversity of microorganisms. The HAIB reactor was then operated with a mean inflow of approximately 44 mL/hour, using the biota saline mineral medium with a COD:N:P ratio of 1000:130:45 in R1 (reactor 1) and a COD:N:P ratio of 1000:10:1 in R2. Two distinct strategies were adopted to start up the reactors. In R1 PCP was added at an initial concentration of 10.0 mg/L for 100 days, causing destabilization of the methanogenesis and accumulation of PCP, requiring a 90-day intervention for the reactor\'s recovery. To start up R2, the PCP concentration was increased gradually from 0.5 mg/L to 12.0 mg/L for 52 days. After methanogenesis was established, R1 was fed for 270 days with 5.0 mg of PCP/L, followed by 41 days with 8.0 mg/L and 59 days with 12 mg/L. The mass balance in R1 indicated that 0.52% of the added PCP exited through the reactor\'s outflow and that adsorption of the system did not occur. 22.34 mg of 2,4,6 TCP, an intermediary of PCP degradation, was adsorbed in the bioparticles. The results of the analysis of microbial diversity indicated a change in the microbial community of the domain Bacteria along the operational period, with fluorescent bacilli morphologies resembling Methanobacterium sp present in the reactor. PCP degradation in R2 was 100% up to a concentration of 10.0 mg/L. At the end of the phase with 12.0 mg PCP/L, the effluent concentration was 1.4 mg PCP/L, with a mean removal efficiency of 93.2 \'+ or -\' 5,5%. 2,4,6 TCP was the main intermediary in the reactor\'s effluent. 4.06% of the PCP added to the system was found in the effluent and 15.94% was absorbed in the bioparticles of the reactor. Therefore, it was concluded that 80% of the added PCP underwent microbial anaerobic degradation. The presence of Methanocalcullus and Methanosaeta microorganisms in the final operating phase of R2, which was determined in the collected sediment, was considered fundamental for maintaining the reactor\'s stability. This discovery contributes to the body of information about the real microbial diversity of tropical ecosystems, above all in anaerobic habitats, and about the nutritional conditions and procedures involved in confining these microorganisms in reactors and using them in bioremediation processes.