The deep-sea hypersaline lakes in the Red Sea are among the most challenging, extreme, and unusual environments on the planet Earth. Despite their harshness to life, they are inhabited by diverse and novel members of prokaryotes. Methanogenesis was proposed as one of the main metabolic pathways that drive microbial colonization in similar habitats. However, not much is known about the identities of the methane-producing microbes in the Red Sea, let alone the way in which they could adapt to such poly extreme environments. Combining a range of microbial community assessment, cultivation and omics (genomics, transcriptomics, and single amplified genomics) approaches, this dissertation seeks to fill these gaps in our knowledge by studying archaeal composition, particularly methanogens, their genomic capacities and transcriptomic characteristics in order to elucidate their diversity, function, and adaptation to the deep-sea brines of the Red Sea. Although typical methanogens are not abundant in the samples collected from brine pool habitats of the Red Sea, the pilot cultivation experiment has revealed novel halophilic methanogenic species of the domain Archaea. Their physiological traits as well as their genomic and transcriptomic features unveil an interesting genetic and functional adaptive capacity that allows them to thrive in the unique deep-sea hypersaline environments in the Red Sea.

Bifenilas policloradas (PCBs) são compostos de difícil degradação presentes na composição de ascarel, muito utilizado como fluidos dielétricos e isolantes. Neste contexto, a presente pesquisa teve como objetivo avaliar a diversidade de microrganismos em biofilmes de reatores anaeróbios na presença de PCB empregando Métodos de Microbiologia de Anaeróbios Estritos e de Biologia Molecular. Em reator anaeróbio horizontal de leito fixo (RAHLF), alimentado com etanol, formiato, Triton X-100 (0,1%) e ascarel (1 mL/L), operado com tempo de detenção hidráulica (TDH) de 24 horas, foi retirado a comunidade microbiana do biofilme da espuma de poliuretano. Os grupos microbianos encontrados por meio da clonagem e sequenciamento do gene RNAr 16S para o domínio Bacteria foram relacionados aos filos Thermogae, Proteobacteria (Brachymonas petroleovorans, 100% de similaridade e Methylobacillus, 98% de similaridade), Firmicutes (Clostridium, 97% de similaridade, Syntrophomonas, 100% de similaridade e Sporomusa com 100% de similaridade), Synegistetes (Synergistes, 98% de similaridade), Spirochaetes (Leptonema illini, 98% de similaridade), Aminanaerobia, Deferribacteres, Chlorobi, Chloroflexi e Armatimonadetes. Além disso, como nesse biofilme foram identificadas bactérias redutoras de ferro, procedeu-se a sua quantificação por meio da técnica de tubos múltiplos (NMP, Número Mais Provável) obtendo 5,26 x \'10 POT.12\' NMP/g STV de bactérias redutoras de ferro. Ensaio em batelada foi realizado separadamente sob duas condições: (1) metanogênica e (2) ferro redutora. Em ambas as condições foram adicionadas aroclor 1260 (PCB). Os reatores, sob condição metanogênica, foram alimentados com meio de cultivo Angelidaki e substratos orgânicos (formiato e etanol), além de aroclor 1260 (0,2 \'mü\'g/L). Para simular a condição redutora de ferro foi acrescido ao meio de cultura Angelidaki, EDTA férrico (1,86 g/L). A produção de metano, na presença de aroclor 1260 foi de 3,8 x \'10 POT.-4\' mmol \'CH IND.4\'/g STV. A presença de bactérias ferro redutoras foi confirmada indiretamente pela taxa média de redução férrica (90%) nos reatores em batelada, após 60 dias de operação. Por meio de PCR/DGGE, elaborou-se um dendograma das amostras deste ensaio em batelada (metanogênico e redutor de ferro) comparativamente com as do reator RAHLF (biofilme presente na parede do reator e no material suporte). Os reatores em batelada apresentaram similaridade entre si de 79% e 92% para os domínios Bacteria e Archaea, respectivamente. As amostras do reator RAHLF foram 80% (Bacteria) e 96% (Archaea) similares. A existência de bactérias degradadoras de PCB, bem como, bactérias redutoras de ferro no biofilme anaeróbio contribuiu com informações sobre o consórcio microbiano e sua diversidade. / Polychlorinated biphenyls (PCBs) are compounds of difficult degradation, a component of askarel, which were used widely as coolants and lubricants. Hence, this study evaluated the diversity of microorganisms in the presence of PCBs in anaerobic reactors. For such, methods as Strict Anaerobic Microbiology and Molecular Biology were employed. The microbial community of the biofilm, developed in a fixed horizontal bed anaerobic reactor (RAHLF), was studied using the technique of cloning and sequencing of RNAr 16S gene for the Bacteria domain. The reactor had immobilized cells in polyurethane foam with ethanol and formate as a carbon source, Triton X-100 (0.1%) and polychlorinated biphenyls (1 mL/L), and operated with 24 hours HRT. The microbial groups found in this biofilm were related to phyla Thermogae, Proteobacteria (Brachymonas petroleovorans, 100% similarity and Methylobacillus, 98% similarity), Firmicutes (Clostridium, 97% similarity Syntrophomonas, and 100% similarity with Sporomusa 100% similarity), Synegistetes (Synergistes, 98% similarity), Spirochaetes (Leptonema Illini, 98% similarity), Aminanaerobia, Deferribacteres, Chlorobi, Chloroflexi and Armatimonadetes. Furthermore, as bacteria that reduce iron were found, we proceeded the quantification by the multiple tube method (MPN) for this group, obtaining 5.26 x \'10 POT.12\' MPN/g STV of iron-reducing bacteria. The batch reactors evaluated the growth of microorganisms in two condictions: (1) methanogenic e (2) iron reduction, both had the presence of PCBs (Aroclor 1260). The reactor, under methanogenic condition, was fed with synthetic substrate Angelidaki, ethanol and formate, used as carbon source, and aroclor 1260 (0.2 \'mü\'g /L). To simulate the condition of iron reducing, the same synthetic substrate was supplemented with ferric EDTA (1.86 g/L). The production of methane in the presence of aroclor 1260, was 3.8 x \'10 POT.-4\' mmol \'CH IND.4\'/g STV. The presence of iron reducing bacteria, after 60 days, was confirmed indirectly by the average rate of iron ferric reduction (90%). Filogenetics analysis (PCR/DGGE) compared the samples of this batch reactor - methanogenic and reduction of iron ferric -, with the samples of RAHLF - the biofilm in the reactor wall and the support material. The two condictions in batch reactors showed similarity of 79% and 92% respectively for the Bacteria and Archaea domain. Therefore, both samples of RAHLF showed 80% (Bacteria) and 96% (Archaea) of similarity. In other words, more similarity were presented due configuration of the reactor as well as the type of PCB added. As a result, the existence of PCBs degrading bacteria and iron-reducing bacteria in anaerobic biofilm, provided informations about the microbial consortium and its diversity in the presence of PCB.

Despite general concern that the massive deposits of methane stored under permafrost underground and undersea could be released into the atmosphere due to rising temperatures attributed to global climate change, little is known about the methanogenic microorganisms in permafrost sediments, their role in methane emissions, and their phylogeny. The aim of this thesis was to increase knowledge of uncultivated methanogenic microorganisms in submarine and terrestrial permafrost deposits, their community composition, the role they play with regard to methane emissions, and their phylogeny. It is assumed that methanogenic communities in warmer submarine permafrost may serve as a model to anticipate the response of methanogenic communities in colder terrestrial permafrost to rising temperatures. The compositions of methanogenic communities were examined in terrestrial and submarine permafrost sediment samples. The submarine permafrost studied in this research was 10°C warmer than the terrestrial permafrost. By polymerase chain reaction (PCR), DNA was extracted from each of the samples and analyzed by molecular microbiological methods such as PCR-DGGE, RT-PCR, and cloning. Furthermore, these samples were used for in vitro experiment and FISH. The submarine permafrost analysis of the isotope composition of CH4 suggested a relationship between methane content and in situ active methanogenesis. Furthermore, active methanogenesis was proven using 13C-isotope measurements of methane in submarine permafrost sediment with a high TOC value and a high methane concentration. In the molecular-microbiological studies uncultivated lines of Methanosarcina, Methanomicrobiales, Methanobacteriacea and the Groups 1.3 and Marine Benthic from Crenarchaeota were found in all submarine and terrestrial permafrost samples. Methanosarcina was the dominant group of the Archaea in all submarine and terrestrial permafrost samples. The archaeal community composition, in particular, the methanogenic community composition showed diversity with changes in temperatures. Furthermore, cell count of methanogens in submarine permafrost was 10 times higher than in terrestrial permafrost. In vitro experiments showed that methanogens adapt quickly and well to higher temperatures. If temperatures rise due to climate change, an increase in methanogenic activity can be expected as long as organic material is sufficiently available and qualitatively adequate. / Trotz allgemeiner Bedenken, dass auf Grund des Temperaturanstieges im Zusammenhang mit der globalen Klimaerwärmung große Mengen des in terrestrischen und submarinen Permafrostsedimenten gespeicherten Methans freigesetzt werden könnte, ist bisher wenig über die in diesen Böden lebenden methanogenen Mikroorganismen, ihre Phylogenese und sowie ihre Bedeutung hinsichtlich der Methanemissionen bekannt. Das Ziel dieser Doktorarbeit war die Erweiterung der bisherigen Kenntnisse über unkultivierte methanogene Mikroorganismen in submarinen und terrestrischen Sedimentablagerungen, die Zusammensetzung ihrer Lebensgemeinschaft, ihrer Phylogenese und ihrer Bedeutung bei der Emission von Methan. Es wird vermutet, dass methanogene Gemeinschaften submarines Permafrostes zur Erstellung von Modellen genutzt werden können, um Aussagen bezüglich potenzieller Reaktionen methanogener Gemeinschaften des kälteren terrestrischen Permafrostes auf steigende Temperaturen, zu ermöglichen. Die Zusammensetzung der methanogenen Gemeinschaft wurde in terrestrischen und submarinen Permafrostproben untersucht. Der im Rahmen dieser Forschungsarbeit untersuchte submarine Permafrost wies eine im Vergleich zum terrestrischen Permafrost um circa 10°C höhere Temperatur auf. Mittels Polymerasenkettenreaktion (PCR) wurde von jeder der Proben DNA extrahiert und mittels weiterer molekular-mikrobiologischen Methoden wie DGGE, RT-PCR und Klonierung analysiert. Des Weiteren wurden die Proben für in vitro Experimente und Zellzählungen (DAPI und FISH) verwendet. Die Analyse der Isotopenzusammensetzung von CH4 in submarinen Permafrostsedimenten ließ einen Zusammenhang zwischen Methangehalt und aktiver in situ Methanogenese vermuten. Überdies konnte aktive Methanogenese, mittels 13C-Isotopenmessungen von Methan in submarinem Permafrostsediment mit hohem TOC-Wert und hoher Methankonzentration, bewiesen werden. Im Rahmen der molekular-mikrobiologischen Untersuchungen wurden in allen submarinen und terrestrischen Permafrostproben unkultivierte Linien von Methanosarcina, Methanomicrobiales, Methanobacteriacea und den Gruppen 1.3 und Marine Benthic von Crenarchaeota gefunden. Methanosarcina war in allen submarinen und terrestrischen Permafrostproben die dominierende Gruppe der Archaeen. Die Zusammensetzung der archaealen Gemeinschaft, insbesondere die Zusammensetzung der methanogenen Gemeinschaft, variierte zwischen den submarinen und terrestrischen Proben. Des Weiteren fand sich bei der Zellzählung der Methanogenen im submarinen Permafrost eine 10-fach höhere Zellzahl als im terrestrischen Permafrost. Die in vitro Experimente zeigten, dass Methanogene sich schnell und gut an höhere Temperaturen anpassen können. Im Falle weiter steigender Temperaturen auf Grund der Klimaveränderungen, kann – bei ausreichender Verfügbarkeit und Qualität organischen Materials – mit einer Zunahme der methanogenen Aktivität gerechnet werden.

Le méthane (CH4) est un des principaux gaz à effet de serre. L’élevage est à l’origine d’un tiers du CH4 produit par l’activité humaine en Europe. En plus, la production de CH4 représente une perte de 2% à 12 % de l’énergie consommée par l’animal. La méthanogenèse est le résultat de l’activité d’un groupe de microorganismes particuliers - les Archaea méthanogènes. La production de CH4 permet de d’éliminer du milieu ruminal l’hydrogène produit au cours de la fermentation des aliments par les autres microorganismes (bactéries, protozoaires, champignons). En effet, l’accumulation d’hydrogène affecte le fonctionnement optimal du rumen. La réduction des émissions de CH4 par les ruminants présente donc un intérêt économique et environnemental non négligeable et passe inévitablement par une modification de l’écosystème microbien du rumen. L’objectif de ce travail de thèse était de relier la production de CH4 avec la structure et l’activité de la communauté méthanogène du rumen. Différents modèles de manipulation de l’écosystème microbien ruminal comme la défaunation (élimination des protozoaires) et l’utilisation d’aliments connus pour modifier la méthanogenèse ont été utilisés. Le rumen étant un écosystème complexe, les interactions fonctionnelles entre les Archaea méthanogènes et les autres microorganismes présents (bactéries et protozoaires) ont également été étudiées. Dans cette optique, des outils de biologie moléculaire, permettant de cibler les principales communautés microbiennes, ont été optimisés. Nos travaux permettent de conclure sur l’absence de relation claire entre le nombre (et/ou la concentration) des Archaea méthanogènes et la méthanogenèse dans le rumen. Cependant les réductions des émissions de CH4 ont été attribuées aux changements dans la diversité de la communauté méthanogène et la disponibilité en hydrogène. Ce travail de thèse a mis en évidence que les modifications de la composition et/ou de l’activité métabolique de la communauté des Archaea méthanogènes seraient à l’origine des réductions des émissions de CH4 par les ruminants. Une meilleure connaissance des mécanismes microbiens impliqués dans la production de méthane permettra d’envisager de nouvelles pistes pour diminuer les émissions chez les ruminants. / Methane (CH4) is a major greenhouse gas. Livestock contributes to one third of CH4 produced by human activity in Europe. Methanogenesis is the result of the activity of a specific group of microorganisms, the methanogenic Archaea. This natural process prevents hydrogen accumulation in the rumen, which may affect the optimal feed degradation, but it represents a loss of 2% to 12% of energy consumed by the animal. Reduction of CH4 emissions from ruminants presents therefore economic and environmental benefits and inevitably involves a change in rumen microbial ecosystem. However microbial mechanisms of CH4 production in the rumen are still poorly understood. The objective of this thesis was to relate the production of CH4 with the structure and/or the activity of the methanogenic rumen community. Different models of manipulation of the rumen microbiota such as defaunation (removal of protozoa) and the use of feed known to affect methanogenesis were used. Interactions between methanogenic Archaea and other microorganisms (bacteria and protozoa) were also studied in the complex rumen ecosystem. In this context, tools of molecular biology, to identify key microbial communities, were optimized. Our work allows to conclude that there is no clear relationship between the number of methanogenic Archaea and methanogenesis rate in the rumen. However, reduction in CH4 emissions could be attributed to changes in the diversity of the methanogenic community and the availability of hydrogen. This thesis has shown that changes in the composition and / or metabolic activity of methanogenic Archaea community were associated to the reductions in CH4 emissions observed in our animal trials. A better understanding of microbial mechanisms involved in the production of methane will consider new ways to reduce emissions in ruminants.

Bifenilas policloradas (PCBs) são compostos de difícil degradação presentes na composição de ascarel, muito utilizado como fluidos dielétricos e isolantes. Neste contexto, a presente pesquisa teve como objetivo avaliar a diversidade de microrganismos em biofilmes de reatores anaeróbios na presença de PCB empregando Métodos de Microbiologia de Anaeróbios Estritos e de Biologia Molecular. Em reator anaeróbio horizontal de leito fixo (RAHLF), alimentado com etanol, formiato, Triton X-100 (0,1%) e ascarel (1 mL/L), operado com tempo de detenção hidráulica (TDH) de 24 horas, foi retirado a comunidade microbiana do biofilme da espuma de poliuretano. Os grupos microbianos encontrados por meio da clonagem e sequenciamento do gene RNAr 16S para o domínio Bacteria foram relacionados aos filos Thermogae, Proteobacteria (Brachymonas petroleovorans, 100% de similaridade e Methylobacillus, 98% de similaridade), Firmicutes (Clostridium, 97% de similaridade, Syntrophomonas, 100% de similaridade e Sporomusa com 100% de similaridade), Synegistetes (Synergistes, 98% de similaridade), Spirochaetes (Leptonema illini, 98% de similaridade), Aminanaerobia, Deferribacteres, Chlorobi, Chloroflexi e Armatimonadetes. Além disso, como nesse biofilme foram identificadas bactérias redutoras de ferro, procedeu-se a sua quantificação por meio da técnica de tubos múltiplos (NMP, Número Mais Provável) obtendo 5,26 x \'10 POT.12\' NMP/g STV de bactérias redutoras de ferro. Ensaio em batelada foi realizado separadamente sob duas condições: (1) metanogênica e (2) ferro redutora. Em ambas as condições foram adicionadas aroclor 1260 (PCB). Os reatores, sob condição metanogênica, foram alimentados com meio de cultivo Angelidaki e substratos orgânicos (formiato e etanol), além de aroclor 1260 (0,2 \'mü\'g/L). Para simular a condição redutora de ferro foi acrescido ao meio de cultura Angelidaki, EDTA férrico (1,86 g/L). A produção de metano, na presença de aroclor 1260 foi de 3,8 x \'10 POT.-4\' mmol \'CH IND.4\'/g STV. A presença de bactérias ferro redutoras foi confirmada indiretamente pela taxa média de redução férrica (90%) nos reatores em batelada, após 60 dias de operação. Por meio de PCR/DGGE, elaborou-se um dendograma das amostras deste ensaio em batelada (metanogênico e redutor de ferro) comparativamente com as do reator RAHLF (biofilme presente na parede do reator e no material suporte). Os reatores em batelada apresentaram similaridade entre si de 79% e 92% para os domínios Bacteria e Archaea, respectivamente. As amostras do reator RAHLF foram 80% (Bacteria) e 96% (Archaea) similares. A existência de bactérias degradadoras de PCB, bem como, bactérias redutoras de ferro no biofilme anaeróbio contribuiu com informações sobre o consórcio microbiano e sua diversidade. / Polychlorinated biphenyls (PCBs) are compounds of difficult degradation, a component of askarel, which were used widely as coolants and lubricants. Hence, this study evaluated the diversity of microorganisms in the presence of PCBs in anaerobic reactors. For such, methods as Strict Anaerobic Microbiology and Molecular Biology were employed. The microbial community of the biofilm, developed in a fixed horizontal bed anaerobic reactor (RAHLF), was studied using the technique of cloning and sequencing of RNAr 16S gene for the Bacteria domain. The reactor had immobilized cells in polyurethane foam with ethanol and formate as a carbon source, Triton X-100 (0.1%) and polychlorinated biphenyls (1 mL/L), and operated with 24 hours HRT. The microbial groups found in this biofilm were related to phyla Thermogae, Proteobacteria (Brachymonas petroleovorans, 100% similarity and Methylobacillus, 98% similarity), Firmicutes (Clostridium, 97% similarity Syntrophomonas, and 100% similarity with Sporomusa 100% similarity), Synegistetes (Synergistes, 98% similarity), Spirochaetes (Leptonema Illini, 98% similarity), Aminanaerobia, Deferribacteres, Chlorobi, Chloroflexi and Armatimonadetes. Furthermore, as bacteria that reduce iron were found, we proceeded the quantification by the multiple tube method (MPN) for this group, obtaining 5.26 x \'10 POT.12\' MPN/g STV of iron-reducing bacteria. The batch reactors evaluated the growth of microorganisms in two condictions: (1) methanogenic e (2) iron reduction, both had the presence of PCBs (Aroclor 1260). The reactor, under methanogenic condition, was fed with synthetic substrate Angelidaki, ethanol and formate, used as carbon source, and aroclor 1260 (0.2 \'mü\'g /L). To simulate the condition of iron reducing, the same synthetic substrate was supplemented with ferric EDTA (1.86 g/L). The production of methane in the presence of aroclor 1260, was 3.8 x \'10 POT.-4\' mmol \'CH IND.4\'/g STV. The presence of iron reducing bacteria, after 60 days, was confirmed indirectly by the average rate of iron ferric reduction (90%). Filogenetics analysis (PCR/DGGE) compared the samples of this batch reactor - methanogenic and reduction of iron ferric -, with the samples of RAHLF - the biofilm in the reactor wall and the support material. The two condictions in batch reactors showed similarity of 79% and 92% respectively for the Bacteria and Archaea domain. Therefore, both samples of RAHLF showed 80% (Bacteria) and 96% (Archaea) of similarity. In other words, more similarity were presented due configuration of the reactor as well as the type of PCB added. As a result, the existence of PCBs degrading bacteria and iron-reducing bacteria in anaerobic biofilm, provided informations about the microbial consortium and its diversity in the presence of PCB.

Anaerobic Digestion (AD) is an essential component in wastewater treatment to recover energy from waste and deals with sludge management issues effectively. AD is a treatment process that converts organic matter to methane and carbon dioxide with multi-step biological reactions. Methanogenesis, the subprocess of AD that produces methane, is an important indicator of the stability of AD and is influenced by pH, temperature, ammonia, volatile fatty acids (VFAs), and solids concentrations among other factors. Ammonia is an essential nutrient for methanogenic bacteria but at certain ammonia concentrations and pH levels, ammonia is said to be a toxicant for methanogenic archaea. Substrates that are high in ammonia content can include those high in protein, such as food waste, which can be inhibitory to methanogens in the digestion process. Thickened waste activated sludge (TWAS) also contains a large amount of nitrogen with its higher solids concentration, promoting methane production. VFAs are produced during acidogenesis and they can negatively affect methanogenic archaea. High organic loading rates into AD can lead to an accumulation of VFAs and thus inhibition of methanogenic activity. Even with well-known inhibitory effects of ammonia and VFAs on methanogenesis, there are limited tools available for modelling these inhibitions, especially when evaluating diverse compositions of substrate. The objectives of this research work are to experiment for various pairings of pH, ammonia, and acetate levels using batch reactors and to quantify the inhibition on the overall methane production using an AD-based model focused on biological reactions. / Thesis / Master of Applied Science (MASc)

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.

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.

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.

L’étude du microbiote digestif a connu un regain d’intérêt au début des années 2000, avec l’avènement des techniques moléculaires. La culturomics a démontré sa complémentarité depuis 2010 en réduisant une partie des biais des méthodes moléculaires. Une revue sur les techniques d’étude du microbiote digestif et l’analyse du microbiote des sujets africains. Les études de métagénomique en Afrique ont révélé une augmentation de la biodiversité, en particulier des Spirochaetes et des Prevotella chez les africains par rapport aux occidentaux. Sur les 1162 bactéries isolées par culturomics, 476 n'étaient pas africaines, 445 étaient communes et 241 étaient d’origine africaine dont 68 nouvelles espèces. Pour ma participation au travail de culturomics, 102750 colonies testées par MALDI-TOF,ont permis d'identifier 377 espèces incluant 40 nouvelles espèces,17 nouveaux genres et 2 nouvelles familles.Ces nouvelles espèces ont été décrites par taxonogenomics ou new species announcement.Les archaea méthanogènes ont une prévalence de 97,4% pour M. smithii et associés à des pathologies comme l’abcès du cerveau,les parodontites etc. La culture est fastidieuse et nécessitait une source extérieure d’hydrogène. Sous enceinte anaérobie, nous avons cultivé avec succès M. smithii à partir d’un milieu de culture liquide inoculé d’échantillon de selle. L’isolement en culture pure a été un succès sur milieu gélosé en réalisant une coculture avec Bacteroides thetaiotaomicron. Nous avons aussi testé avec succès la coculture de M. smithii avec d’autres bactéries productrices d’hydrogène connues. Les tests de chromatographie en phase gazeuse montraient que ces souches produisaient de l’hydrogène. / The study of the digestive microbiota was a renewed interest in the early 2000s, with the advent of molecular techniques. The culturomics has demonstrated its complementarity since 2010 by reducing some of the biases of molecular methods. A review on the techniques of studying the digestive microbiota and the analysis of the microbiota of African subjects. Metagenomic studies in Africa have revealed an increase in biodiversity, especially Spirochaetes and Prevotella among Africans compared to Westerners. Of the 1162 bacteria isolated by culturomics, 476 were non-African, 445 were common, and 241 were of African origin, including 68 new species. For my participation in the work of culturomics, 102750 colonies tested by MALDI-TOF, identified 377 species including 40 new species, 17 new genera and 2 new families. These new species have been described by taxonogenomics or new species announcement.Methanogenic archaea have a prevalence of 97.4% for M. smithii and associated with pathologies such as brain abscess, periodontitis and so on. The cultivation is tedious and required an external source of hydrogen. Under anaerobic enclosure, we successfully cultivated M. smithii from a liquid culture medium inoculated with a stool sample. The isolation in pure culture was a success on agar medium by performing a coculture with Bacteroides thetaiotaomicron. We have also successfully tested the co-culture of M. smithii with other known hydrogen-producing bacteria. Gas chromatographic tests showed that these strains produced hydrogen.