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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.

Le corps humain est un ensemble de microflores où cohabitent bactéries, archées, virus et eucaryotes. Ces écosystèmes complexes sont appelés microbiotes. Parmi ceux-ci figure le microbiote intestinal qui compte 1011 à 1014 bactéries/g de selle. Les modifications de la flore intestinale peuvent être à l'origine de pathologies comme les diarrhées infectieuses. Il s'agit d'un véritable problème de santé publique puisqu'environ 2.16 millions de décès sont liés à cette pathologie chaque année. Les virus intestinaux jouent un rôle prépondérant mais les infections bactériennes restent également importantes. Le diagnostic de ces infections bactériennes reste compliqué puisque le microbiote intestinal comporte 75% d'espèces non cultivables. De plus, on ne dispose pas réellement d'une liste exhaustive des bactéries pouvant être responsables de diarrhées infectieuses. Nous avons donc choisi d'étudier le microbiote intestinal dans des selles normales et pathologiques, par une approche polyphasique alliant une étape préliminaire de concentration des selles diarrhéiques par la lyophilisation, à des techniques de culture et des méthodes de biologie moléculaire. Pour cela nous avons mis au point une nouvelle technologie pour la détection des entéropathogènes par hybridation sur puce à ADN permettant la détection des bactéries et des virus ADN entéropathogènes, en présence d'un témoin archae. Notre outil permet le diagnostic multiplexe des diarrhées infectieuses puisque nous avons correctement identifié un adénovirus et la bactérie Campylobacter jejuni présents dans une même selle. / The human body is a collection of microflora where cohabit bacteria, archaea, viruses and eukaryotes. These complex ecosystems are called microbiota. Among these is the intestinal microbiota that counts 1011 to 1014 bacteria/g of stool. Changes in the intestinal flora can cause of pathologies such as infectious diarrhea. This is a real public health problem since about 2.16 million deaths are related to this disease each year. Enteric viruses play a preponderant role but bacterial infections are also important. The diagnosis of bacterial infections is complicated because the intestinal microbiota includes 75% non-cultivable species. In addition, there is not really a list of bacteria could be responsible for infectious diarrhea. We therefore decided to study the intestinal microbiota in normal stool and also pathological stools by a polyphasic approach combining a preliminary step of diarrheal stools concentration by lyophilization, with cultivation techniques and molecular biology methods. We developed a new technology for the detection of enteropathogens by hybridization on DNA microarray for the detection of bacteria and enteric viruses (DNA) in the presence of a control archaea. Our tool allows multiplexed diagnostic of infectious diarrhea since we correctly identified an adenovirus and Campylobacter jejuni present in a same sample. This is the first DNA microarray for multiplex detection of bacteria and viruses (DNA) enteropathogens. An improvement of our protocol for nucleic acid extraction is proposed to allow the detection of RNA viruses such as rotavirus and calicivirus which are currently dominant.

Os impactos da poluição por hidrocarboneto de petróleo sobre a diversidade e funcionalidade das comunidades microbianas em manguezais não são totalmente conhecidos, principalmente devido às limitações metodológicas para acessar os microrganismos nãocultiváveis. No entanto, vários métodos moleculares independentes de cultivo têm sido utilizados para investigar a diversidade e a estrutura das comunidades microbianas em ecossistemas naturais. O objetivo deste trabalho foi avaliar as variações da estrutura das comunidades de Bacteria e Archaea e a diversidade de Bacteria em uma transeção de solo de mangue do rio Iriri (Bertioga, SP) com um gradiente de contaminação por hidrocarbonetos de petróleo. As análises por eletroforese em gel com gradiente desnaturante (DGGE) mostraram que as comunidades de Bacteria e Archaea nas diferentes posições geográficas foram mais similares entre si do que entre diferentes profundidades ao longo do perfil em uma mesma posição geográfica. A análise das seqüências de clones de rDNA 16S de Bacteria dos diferentes pontos amostrados em abril de 2000, mostrou que a diversidade genética, avaliada pelo índice de Shannon, das comunidades microbianas diferem estatisticamente somente entre ponto o P1 (ponto menos contaminado) e P3 (ponto mais contaminado). As estimativas não-paramétricas da riqueza de espécies mostraram que P1, P2 e P3 possuem mais de 3539, 2524 e 1421 espécies bacterianas, respectivamente. Já, para as amostras do ponto P2 coletadas nos anos 2000 e 2004, muito embora os valores dos índices de Shannon tenham sido semelhantes, houve uma provável dominância de grupos específicos nas amostras coletadas em 2004, verificada pelos altos valores da recíproca do índice de Simpson. Os dados mostraram também que o número estimado de espécies bacterianas no ponto P2 diminuiu com o tempo, sendo menor em amostras de 2004, se comparado com amostras de 2000. No geral, a afiliação filogenética dos clones de rDNA 16S mostrou a grande diversidade de espécies, a maioria não conhecidas. Os dados sugerem que a contaminação do solo de mangue do rio Iriri está selecionando microrganismos mais adaptados às fontes de carbono introduzidas no solo. / The impacts of petroleum hydrocarbon pollution on the diversity and functionality of the microbial communities in mangrove soils are not totally understood, mainly due to the methodological limitations to access unculturable microorganisms. However, several cultureindependent molecular methods have been used to investigate the diversity and structure of microbial communities in natural ecosystems. The aim of this work was to evaluate shifts in Bacteria and Archaea community structures and the diversity of Bacteria in a soil transection of the Iriri river mangrove (Bertioga, SP) showing a petroleum hydrocarbon contamination gradient. The analyses by denaturing gradient gel electrophoresis (DGGE) showed that the communities of Bacteria and Archaea in different geographical positions were more similar among them than the communities in different depths along the soil profile at the same geographical position. Sequence analyses of bacterial 16S rDNA clones from different points sampled in April 2000 showed that the genetic diversity of the bacterial communities, based on the Shannon index, differ statistically only between P1 (less polluted) and P3 (more polluted) locations. Nonparametric estimates of species richness showed that P1, P2 and P3 may have more than 3539, 2524 and 1421 bacterial species, respectively. For P2 sampled in years 2000 and 2004, even though the Shannon indices were similar, there was a probable dominance of specific bacterial groups in year 2004, based on the high values of the reciprocal of Simpson\'s index. The data also showed that the estimated number of bacterial species in P2 decreased with the time, being lower in samples collected in 2004, as compared to samples collected in 2000. In the general, the phylogenetic affiliation of the 16S rDNA clones showed high bacterial species diversity, and most of the bacteria were of unknown species. The data suggest that the contamination of Iriri river mangrove soil with petroleum hydrocarbon is selecting microorganisms more adapted to the introduced carbon sources into the soil.

O exossomo é um complexo multiproteico conservado evolutivamente de archaea a eucariotos superiores que desempenha funções celulares essenciais tais como: atividade exoribonucleolítica 3\'→5\', regulação dos níveis de mRNA, maturação de RNAs estruturais e controle de qualidade de RNAs durante os vários estágios do mecanismo de expressão gênica. Em Archaea, o exossomo é composto por até quatro subunidades diferentes, duas com domínios de RNase PH, aRrp41 e aRrp42, e duas com domínios de ligação a RNAs, aCsl4 e aRrp4. Três cópias das proteínas aRrp4 e/ou aCsl4 se associam com o núcleo hexamérico catalítico do anel de RNase PH e completam a formação do complexo. A proteína PaNip7 é um cofator de regulação do exossomo da archaea Pyrococcus abyssi e atua na inibição do complexo enzimático ligando-se simultaneamente ao exossomo e a RNAs. Neste projeto, a reconstituição in vitro do exossomo da archaea Pyrococcus abyssi formado pela proteína de topo PaCsl4 foi obtida. Para tanto foram realizadas análises de interação proteica usando as técnicas de cromatografia de afinidade, gel filtração e SDS-PAGE. Em adição à formação da isoforma PaCsl4-exossomo, um fragmento peptídico correspondente à região C-terminal da PaNip7 foi sintetizado pelo método da fase sólida, purificado por RP-HPLC e o purificado foi caracterizado por LC/ESI-MS almejando realizar futuros experimentos de interação com o exossomo. / The exosome is a multiprotein complex evolutionarily conserved from archaea to higher eukaryotes that performs essential cellular functions such as: 3\'→5\' exoribonucleolytic activity, regulation of mRNA levels, maturation of structural RNAs and quality control of RNAs during the various stages of the gene expression mechanism. In Archaea, the exosome is composed of up to four different subunits, two with RNase PH domains, aRrp41 and aRrp42, and two with RNAs binding domains, aCsl4 and aRrp4. Three copies of the aRrp4 and/or aCsl4 proteins associate with the hexameric catalytic core of the RNase PH ring and complete the formation of the complex. The PaNip7 protein is a regulating cofactor of the Pyrococcus abyssi archaeal exosome and acts in the inhibition of the enzyme complex by binding simultaneously to the exosome and RNAs. In this project, the reconstitution in vitro of the Pyrococcus abyssi archaeal exosome formed by the PaCsl4 top protein was achieved. To this end protein interaction analyses were performed using affinity chromatography, gel filtration and SDS-PAGE techniques. In addition to the formation of the PaCsl4-exosome isoform, a peptide fragment corresponding to the C-terminal region of PaNip7 was synthesized by solid-phase method, purified by RP-HPLC and the purified peptide was characterized by LC/ESI-MS aiming to perform future binding experiments with the exosome.

La sécrétion de vésicules membranaires (VMs) constitue un processus physiologique important qui a particulièrement été étudié chez les Bactéries et les Eucaryotes. La récente découverte de la production de VMs chez les Archées souligne cependant que ce phénomène est universel et suggère que le dernier ancêtre commun aux trois domaines, LUCA (Last Universal Common Ancestor), produisait certainement des VMs. Les VMs des Archées n’ayant pour le moment été étudiées que chez certaines Crénarchées (ex : G/ Sulfolobus), nous avons entrepris de caractériser les VMs produites par un groupe d’Euryarchées hyperthermophiles anaérobies, les Thermococcales. Dans la première partie de cette étude, nous avons examiné le mécanisme de production ainsi que la composition en lipides et en protéines des VMs de trois espèces de Thermococcales: Thermococcus kodakaraensis, Thermococcus gammatolerans et Thermocococus sp. 5-4. Nous avons observé que les VMs sont sécrétées par un processus de bourgeonnement à partir de l’enveloppe cellulaire similaire à la formation des ectosomes par les cellules eucaryotes. De plus, les VMs sont fréquemment libérées en groupes, formant de grosses protubérances ou des filaments ressemblant aux nanopodes récemment décrits chez les Bactéries. Des différences de structure et de composition protéique sont observées entre les VMs des trois souches étudiées. Cependant, les VMs et les membranes cellulaires d’une même souche ont des compositions protéique et lipidique très proches, confirmant que les VMs sont produites à partir des membranes des cellules. Les VMs et les membranes cellulaires des trois souches comportent notamment un récepteur de peptides de la famille OppA (Oligopeptide-binding protein A) et des homologues de cette protéine ont été identifiés dans les VMs de certaines souches de Sulfolobus.Les VMs sécrétées par les Thermococcales sont associées à de l’ADN et cette association les protègent contre la thermodégradation. Nous montrons dans notre étude que les cellules de T. kodakaraensis transformées avec le plasmide navette plC70 relâchent des VMs comportant ce plasmide. De façon intéressante, ces VMs peuvent être utilisées pour transférer pLC70 à des cellules dénuées de plasmides, suggérant que les VMs pourraient être impliquées dans le transfert d’ADN entre cellules à haute température.Dans la seconde partie de cette étude, nous nous sommes particulièrement intéressés à la souche Thermococcus nautilus, une Thermococcale produisant des VMs associées de manière sélective à deux plasmides contenus dans la cellule. L’un d’eux correspond notamment à un génome viral défectueux de la lignée d’adenovirus PRD1. Ceci indique que les VMs peuvent être un moyen de transport pour des génomes viraux et suggère que la production de VMs par des cellules ancestrales pourraient avoir joué un rôle dans l’apparition des virus.En plus d’être impliquées dans le transport de plasmides/virus, les VMs produites par T. nautilus exercent un effet toxique sur certaines souches de Thermococcales, probablement dû au convoyage de toxines. Même si ces « thermococcines » nécessitent d’être caractérisées, il s’agit de la première mise en évidence d’une activité toxique liée aux VMs chez les Thermococcales. / Secretion of membrane vesicles (MVs) is an important physiological process that has been extensively studied in Bacteria and Eukarya. The recent discovery that Archaea produce MVs shows that this process is universal and suggests that the Last Universal Common Ancestor, LUCA, certainly produced MVs. As these archaeal MVs have been only studied in some Crenarchaeota (ex: G/ Sulfolobus), we started characterizing MVs produced by Thermococcales, a group of hyperthermophilic anaerobic Euryarchaeota.In the first part of this study we examined the mechanism of production as well as the protein and lipid composition of MVs produced by three strains of Thermococcales: Thermococcus kodakaraensis, Thermococcus gammatolerans and Thermocococus sp. 5-4. We observed that MVs are released by a budding process from the cell envelope that is similar to ectosome formation in eukaryotic cells. Moreover, clusters of MVs often form filamentous structures and protuberances on cell surfaces, resembling recently described bacterial nanopods. Differences in structure are observable between MVs of the three species, as well as in their protein composition. However, MVs and cell membranes from the same species have a quite similar protein and lipid composition, confirming that MVs are produced from cell membranes. A major protein present in cell membranes and MVs from the three strains is the oligopeptide-binding proteins (OppA), which has homologues in MVs from Sulfolobus species. Thermococcales MVs harbor DNA and protect this DNA against thermodegradation. Here, we show that T. kodakaraensis cells transformed with the shuttle plasmid pLC70 release MVs harboring this plasmid. Interestingly, these MVs can be used to transfer pLC70 into plasmid-free cells, suggesting that MVs could be involved in DNA transfer between cells at high temperature. In the second part of this study, we were specially interested in the strain Thermococcus nautilus, a Thermococcale that produces MVs selectively enriched in two plasmids from the cell. Notably, one of them corresponds to the genome of a defective virus from PRD1-adenovirus lineage. This indicates that MVs can be used as vehicles for the transport of viral genomes and suggests that production of MVs by ancestral cells could have played a role in the origin of viruses.In addition to be involved in transport of plasmids/viruses, MVs from T. nautilus display a toxic effect on some strains of Thermococcales, maybe due to the delivery of toxins. Even if these “thermococcins” remain to be characterized, this is the first time that a toxic activity associated with MVs has been shown in Thermococcales.

Le présent travail s’intéresse à l’étude de la diversité des communautés procaryotiques, basée sur le gène codant pour l’ARNr 16S et sur les gènes codants pour la sous-unité β du sulfite réductase dissimilatrice (dsrB) et la sous-unité alpha de la méthyl-coenzyme M réductase (mcrA), pour étudier la diversité de la communauté des bactéries sulfato-réductrices et des méthanogènes, respectivement à partir des échantillons collectés en saison sèche ou pluvieuse du Chott El Jerid. Les analyses des séquences du gène codant pour l’ARNr 16S ont montré que les bactéries regroupées aux Proteobacteria et Firmicutes sont détectés dans les deux saisons alors que les séquences appartenant au groupe taxonomique Bacteroidetes, Actinobacteria et Betaproteobacteria sont apparues uniquement dans la saison pluvieuse. Le groupe Deinococcus-Thermus sont observés que dans la saison sèche. Dans le domaine des archées, la plupart des séquences appartiennent au phylum Euryachaeota, détecté dans les deux saisons, alors que, le phylum Crenarchaeota apparait uniquement dans la saison pluvieuse. En plus, les bactéries sulfato-réductrices, appartenant à la classe Deltaproteobacteria, sont fréquents notamment à la saison pluvieuse prouvée déjà par les deux techniques DGGE et qPCR. A partir des cultures d’enrichissement, de nombreuses bactéries anaérobies fermentaires appartiennent aux familles Halanaerobiaceae et Halobacteroidaceae. Les analyses phylogénétiques ainsi que les caractéristiques phénotypiques et physiologiques montrent une nouvelle souche Sporohalobacter salinus proche de l’espèce Sporohalobacter lortetii, seule espèce décrite à ce jour du genre Sporohalobacter. / The present work concerns microbial biodiversity of prokaryotic communities, sulfate-reducing bacteria, and methanogens targeting the 16S rRNA gene and functional gene markers encoding the dissimilatory sulfite reductase β-subunit gene (dsrB) and alpha subunit of the methyl-coenzyme M reductase (mcrA), respectively from samples collected in the dry and wet seasons from Chott El Jerid. Phylogenetic analysis targeting the 16S rRNA gene showed that bacteria were grouped to Proteobacteria and Firmicutes detected at both seasons, whereas, Bacteroidetes, Actinobacteria and Betaproteobacteria were present only in the wet season. Deinococcus-Thermus group were observed in the dry season. Archaeal sequences were belonged to the phyla of Euryarchaeota in both seasons and Crenarchaeota was appeared in wet season. Sulfate-reducing bacteria, related to Deltaproteobacteria class were dominant mainly in wet season proved by two techniques DGGE and QPCR. From enrichment cultures, anaerobic fermentative bacteria were isolated in pure cultures, related to Halanaerobiaceae and Halobacteroidaceae families. Phylogenetic analysis, phenotypic and physiological characteristics showed a novel strain Sporohalobacter salinus related to Sporohalobacter lortetii, an unique species of genus Sporohalobacter described until now.

O presente trabalho foi desenvolvido com o objetivo de verificar a eficiência de um reator anaeróbio híbrido (RAH) alimentado com uma mistura de ácidos orgânicos acético, propiônico, butírico, e láctico, bem como do álcool metanol, perfazendo uma DQO de 6,88 g/L, e avaliar nessas condições, a degradação do pentaclorofenol (PCP) na faixa de 2,0 a 21,0 mg/L. O RAH apresentou adequada performance na ausência de PCP, tendo sido inoculado com um lodo com AME cerca de 0,57 g DQO-CH4/g SV.d. Durante os 21 meses de operação do RAH na ausência de PCP verificou-se uma remoção média de DQO de 93% produção média de metano de 84%. Através de testes de toxicidade realizadas em batelada com o lodo granulado do RAH, antes da adição de PCP no reator, calculou-se o IC50, cujos valores foram 10, 12 e 13,69 mg/L. Na presença de PCP na faixa de 2,0 a 2,1 mg/L, o RAH apresentou remoção média de DQO de 96,7%, produção média de metano de 85,5% e remoção dos ácidos voláteis próxima a 74% do acético, 93% do butírico e 64% do propiônico. Individualmente, na presença da maior concentração de PCP adicionada, ocorreu decréscimo na remoção dos ácidos voláteis, principalmente do ácido propiônico e na taxa de conversão DQO/biogás. O PCP foi removido do sistema na ordem de 99% pela ação do lodo granulado com predominância do grupo das Archaea metanogênicas, verificada por exames microscópicos e hibridação \"in situ\". Valores da ordem de grandeza microbiana para os microrganismos metanogênicos nos períodos anteriores e posteriores a adição de PCP permaneceram na faixa de 105 e 106 céls./mL, quando cultivados em metanol e lactato mais sulfato, respectivamente. Os resultados sugerem que as Archaea metanogênicas podem estar envolvidas na degradação do PCP. A velocidade de remoção do organoclorado foi igual a 1,07 mg PCP/g SV.d quando a maior concentração de PCP foi estudada (21,0 mg/L). / The present research aimed to verify the efficiency of an Anaerobic Hybrid Reactor (AHR) supplied with a mixture of fatty acids, acetic, propionic, butyric and lactic and methanol as well. The total amount of COD was 6.88 g/L. The performance of the reactor was remarkably stable and efficient during PCP additions at range from 2.0 to 21.0 mg/L. The AHR showed a great performance in the PCP absence, inoculated with sludge with an specific methanogenic (SMA) activity of 0,057 g.COD-CH4/g. VS.d. During the 21 months of operation without PCP, the reduction of COD was around 93% and methane was up to 84% in the biogas. Before PCP addiction, two toxicity batch tests conducted with the granular sludge presented IC50 values around 10.12 mg/L and 13.69 mg/L. In the presence of PCP, at the range of 2.0 to 21.0 mg/L, the efficiency of volatile fatty acids breakdown was 93%, 64% and 74% respectively for butyric, propionic and acetic acids. Individually, at the presence of the higher PCP concentration studied, a decrease in the conversion of COD to biogas and organic acids removal occurred, mainly with propionic acid. PCP total removal of more than 99% was reached by granular sludge activities formed by the total time of reactor operation with a prevalence of methanogenic Archaea, verified under direct microscopy exams and in situ hybridization. Methanogenic cells predominance was noticed with 105 to 106 cells/mL during enumeration on methanol and lactate plus sulfate culture media, respectively. The results suggest that methanogenic Archaea can be involved in PCP degradation. The organochlorine removal rate was 1.07 mg PCP.g-1 VS.d-1 during the highest PCP (21.0 mg/L) concentration addition.

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.