<p>Like most Archaea, the hypersaline-adapted organism Halobacterium salinarum exhibits characteristics from all three domains of life, including a eukaryotic histone protein, a universal propensity to genetic rearrangements, and homologs of bacterial cell division proteins. Here we investigate the ancestral function of histone protein in the Archaea. Transcriptomics, proteomics, and phenotypic assays of histone mutants determine that histone regulates gene expression and cell shape but not genome compaction in H. salinarum. We further explore the regulation of gene expression on a genome-wide scale through the study of genomic instability. Genomic deletions and duplications are detected through the meta-analysis of 1154 previously published gene expression arrays and 48 chromatin immunoprecipitation arrays. We discover that a 90 kb duplication event in the megaplasmid pNRC100 directly leads to increased gene expression, and find evidence that the chromosome is far more unstable than previously assumed. These events are all linked with the presence of mobile insertion elements. Finally, in response to questions generated by these experiments, we develop a novel time-lapse protocol for H. salinarum and ask basic questions about single cell dynamics during division. Fluorescent labeling of homologs to bacterial cell division proteins confirms their involvement in cell division but localization dynamics contradict the basic bacterial model. The discovery of unusual facets of morphology during cell division is consistent with these novel protein dynamics and opens up new avenues of inquiry into archaeal cell division.</p> / Dissertation

Made available in DSpace on 2014-06-11T19:32:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-08-12Bitstream added on 2014-06-13T18:44:31Z : No. of bitstreams: 1 neves_mc_dr_jabo.pdf: 5007913 bytes, checksum: dbd1f98db55ea3fe7154227df200f61f (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Estratégias para reduzir o aquecimento da Terra e aumentar a produção animal requerem novos sistemas, onde devem ser consideradas as emissões de metano e de outros gases que possam provocar danos ao meio ambiente. O objetivo deste trabalho foi a mensuração da produção de metano por arquéias e aplicação da metagenômica para detecção destas na fração sólida do conteúdo ruminal. Para a análise da produção de metano foi colhido o conteúdo ruminal seguido do preparo da solução a ser fermentada e armazenamento dos gases. A amplificação da região 168 rDNA foi obtida por PCR e a seguir foram feitas clonagem, seqüenciamento e análise das seqüências pelos programas Sequencing Analysis 3.4 e Phred/Phrap/Consed, submetendo-as ao programa BLA8T. Maiores produções de metano e relações acetato:propionato foram observadas nos tratamentos contendo 70% de volumoso. As análises do BLA8T permitiram identificar nos tratamentos com 70% e 30% de feno, 96 seqüências relacionadas à família Methanobacteriaceae, 47 seqüências a arquéias não cultiváveis e 60 seqüências foram de arquéias desconhecidas (T1), 125 seqüências relacionadas à família Methanobacteriaceae, 42 seqüências a arquéias não cultiváveis e 32 seqüências foram de arquéias não conhecidas (T2). Para os tratamentos feitos com 70% e 30% de silagem de milho, foram observadas 30 seqüências referentes à família Methanobacteriacea, 18 seqüências à família Methanomicrobiacea, 43 seqüências a arquéias não cultiváveis e 118 seqüências foram de arquéias desconhecidas (T3) e 173 seqüências referentes à família Methanobacteriacea, 31 seqüências a arquéias não cultiváveis e 25 seqüências foram de arquéias desconhecidas (T4). As análises deste experimento mostraram variação na produção de metano quanto às diferentes proporções V:C e a metagenômic... / Strategies to reduce the Earth worming and raise animal production require new systems, where it must be considered methane and other gases emission that might cause environmental damages. The aim of this work was to evaluate the archaea methane production and the metagenomic evaluation of these bacteria present on the solid phase of the bovine ruminal content. For methane production analysis the ruminar content was collected followed by the proper manipulation for the fermentation process to take place and produced gas storage. The ribosomal 16S rRNA region was obtained by PCR amplification which was followed by cloning and DNA sequencing. The data was later analyzed by the software Sequencing Analysis 3.4, Phred/Phrap/Consed and BLAST. The highest methane production and acetate:propionate ratios were observed for the treatments containing 70% of roughage. The BLAST analysis allowed to identify 96 DNA sequences related to the Methanobacteriaceae family, 47 DNA sequences related to unculturable archaea and 60 DNA sequences were related to unknown archaea (T1), 125 DNA sequences related to Methanobacteriaceae, 42 DNA sequences do unculturable archaea and 32 DNA sequences were considered related to unknown archaea (T2) for the treatments containing 70% and 30% of hay. For those containing 70% and 30% of com silage it was possible to detect 30 DNA sequences related to Methanobacteriaceae, 18 DNA sequences related to Methanomicrobiaceae, 43 sequences related to unculturable archaea, 118 DNA sequences related to unknown archaea (T3) and 173 DNA sequences related to Methanobacteriaceae, 31 sequences related to unculturable archaea, and 25 to unknown archaea (T4). The analysis carried out in this experiment have shown a variation of the methane production as different R:C ratio were used and metagenomic with the rDNA conserved region together with archaea taken from the ruminal content DNA... (Complete abstract click electronic access below)

Bioinformatics is a valuable tool to understand gene regulatory networks. Cis-regulatory elements (CREs) previously found in promoter regions are known to recruit transcription in signaling pathways. In this work it has been hypothesized to consider CREs as a family of related words that interact/bind to a family of related transcription factors, and thus have similar but distinct regulation patterns. A 1460 microarray gene expression collection was obtained via online databases to create a transcriptomic meta-dataset. A novel bioinformatic algorithm was applied to annotate all 65536 (64k) potential 8-letter CREs in the 500 bp upstream promoter region of all A. thaliana genes across the transcriptomic meta-dataset. Of the possible words, only 2,498 were significantly associated with a pattern of regulation in any of the 1,460 microarrays tested whereas the remaining motifs appeared not to be regulatory. Unique CREs were categorized into 4 regulatory types: inducer, suppressor, biregulator and insulator. A predicted protein protein interactome was created for an economically important plant Coffea canephora. Here, it has been hypothesized that evolutionary conservation of many core biological processes enable generation of predicted protein interactome for species with few resources other than sequenced genome. Of over 12,000 genes identified, 939 were predicted to have 4,587 interactions. Gene Ontology analysis revealed enrichment of processes conserved in all eukaryotes but depletion in unique plant processes. A third study was conducted to determine if homology modeling, evolutionary analysis, and structural evolution could determine key factors involved in function, and interaction specificity in Pus10 (EC 5.4.99.25) found in Archaea and Eukaryotes. Redundancy of Pus10 and the bacterial TrmA and TruB orthologs appear to have resulted in significant molecular evolution of Pus10 function. Neofunctionalization was identified in animal kingdom where thiouridine synthase, methylases and PSUSs (THUMP)-domain modification in early animal evolution coincides with appearance of TNF-related apoptosis-inducing ligand (TRAIL) apoptosis components. Subfunctionalization was identified for Thermococcales lineage of Archaea where a shorter forefinger-loop coincides with the loss of Ψ54 specificity as experimentally verified in P. furiosus. Absence of Pus10 was observed in Sulfolobus and higher fungi whereas in plant kingdom Pus10 function remains unknown with possible pseudogene in some lineages

Kyoto University (京都大学) / 0048 / 新制・論文博士 / 博士(工学) / 乙第12200号 / 論工博第3989号 / 新制||工||1438(附属図書館) / 26272 / UT51-2008-C970 / (主査)教授 今中 忠行, 教授 青山 安宏, 教授 森 泰生 / 学位規則第4条第2項該当

Submitted by WELLINGTON PINE OMORI null (wpomori@hotmail.com) on 2018-03-02T14:43:37Z No. of bitstreams: 1 Tese_Wellington_Pine_Omori.pdf: 3601697 bytes, checksum: 300108bd7832f7e80a842293e639462a (MD5) / Approved for entry into archive by Alexandra Maria Donadon Lusser Segali null (alexmar@fcav.unesp.br) on 2018-03-05T18:02:24Z (GMT) No. of bitstreams: 1 omori_wp_dr_jabo.pdf: 3601697 bytes, checksum: 300108bd7832f7e80a842293e639462a (MD5) / Made available in DSpace on 2018-03-05T18:02:24Z (GMT). No. of bitstreams: 1 omori_wp_dr_jabo.pdf: 3601697 bytes, checksum: 300108bd7832f7e80a842293e639462a (MD5) Previous issue date: 2018-02-07 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A torta de filtro apresenta bagaço residual oriundo do processo de extração do caldo de cana-de-açúcar e quando armazenada por longos períodos, se torna um habitat ideal para o desenvolvimento de comunidades microbianas que atuam na desconstrução da lignocelulose. Nossas análises de dados de sequenciamento de DNA metagenômico sugerem que a torta de filtro armazenada por 40 dias possui uma microbiota com características funcionais e ecológicas exclusivas em relação a outros ambientes com elevada disposição de material lignocelulósico. Assim como em ambientes de compostagem, os filos mais abundantes são Actinobacteria, Proteobacteria, Firmicutes e Bacteroidetes. Dentre os principais genes que estes micro-organismos possuem, estão Glicosiltransferases, Carboidrato Esterases e Glicosil Hidrolases, que atuando em conjunto, são passíveis de desconstruírem a lignocelulose e participarem na liberação de açúcares menores, ácidos orgânicos e outros nutrientes. Neste trabalho, identificamos novas enzimas da família AA10 que oxidam a celulose cristalina, demostrando o potencial deste ambiente em possibilitar a adaptação de micro-organismos que expressam enzimas capazes de desestruturar a celulose altamente condensada, possibilitando a liberação de moléculas de glicose. A comunidade microbiana pode acessar nutrientes como Fósforo e Nitrogênio através da despolimerização da biomassa vegetal ou decomposição da microbiota morta. No ciclo biogeoquímico do nitrogênio, a evaporação de amônia é reduzida pela assimilação desta substância pela comunidade microbiana, sendo que a amônia é produzida pela via de amonificação de nitrato e nitrito. Outro ciclo biogeoquímico identificado na torta de filtro foi o do carbono, ocorrendo diminuição da emissão de metano e gás carbônico devido ao uso destas moléculas no metabolismo microbiano. Por apresentar muitas espécies de micro-organismos termofílicos e funções ecológicas similares a compostagens que alcançaram fase termofílica, a torta de filtro armazenada por 40 dias não aparenta conter micro-organismos patogênicos em elevada abundância, o que poderia ser um indício de sua segurança biológica se usado como adubo no solo. No entanto, recomenda-se que novos estudos sejam realizados neste tipo de ambiente agrícola, afim de avaliar como se comportam principalmente os fungos Neosartorya fumigata e Paracoccidioides brasiliensis, os quais são identificados como agentes patogênicos mas que também são encontrados vivendo na natureza como organismos saprofíticos e em interação com alguns mamíferos, sem causar doença. / The filter cake presents residual bagasse from the process of extracting the sugarcane juice and when stored for long periods, it becomes an ideal habitat for the development of microbial communities that act in the deconstruction of lignocellulose. Our analyzes of metagenomic DNA sequencing data suggest that the filter cake stored for 40 days has a microbiota with unique functional and ecological characteristics compared to other environments with high lignocellulosic material. Thus in composting environments, the most abundant phyla are Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. Glycosyltransferases, Carbohydrate Estersases and Glycoside Hydrolases, which act together, are capable of deconstructing lignocellulose and participate in the release of smaller sugars, organic acids and other nutrients. In this work, we identify new enzymes of the AA10 family that oxidize crystalline cellulose, demonstrating the potential of this environment to enable the adaptation of microorganisms that express enzymes capable of destabilizing highly condensed cellulose, allowing the release of glucose molecules. The microbial community can access nutrients such as Phosphorus and Nitrogen through the depolymerization of the plant biomass or decomposition of the dead microbiota. In the biogeochemical cycle of nitrogen, the evaporation of ammonia is reduced by the assimilation of this substance by the microbial community, and ammonia is produced by ammonification of nitrate and nitrite. Another biogeochemical cycle identified in the filter cake was that of carbon, with a decrease in the emission of methane and carbon dioxide due to the use of these molecules in microbial metabolism. Because it contains many species of thermophilic microorganisms and ecological functions similar to composting that reached the thermophilic phase, the filter cake stored for 40 days does not appear to contain pathogenic microorganisms in high abundance, which could be an indication of its biological safety if used as soil fertilizer. However, it is recommended that new studies be carried out in this type of agricultural environment, in order to evaluate the behavior of the fungi Neosartorya fumigata and Paracoccidioides brasiliensis, which are identified as pathogens but are also found living in nature as saprophytic organisms and in interaction with some mammals, without causing disease.

Made available in DSpace on 2014-12-17T14:10:15Z (GMT). No. of bitstreams: 1 CiaxaresMC.pdf: 595430 bytes, checksum: 97825450a670945169f3df28f7765add (MD5) Previous issue date: 2008-03-14 / The human activities responsible for the ambient degradation in the modern world are diverse. The industrial activities are preponderant in the question of the impact consequences for brazilian ecosystems. Amongst the human activities, the petroliferous industry in operation in Potiguar Petroliferous Basin (PPB) displays the constant risk of ambient impacts in the integrant cities, not only for the human populations and the environment, but also it reaches the native microorganisms of Caatinga ground and in the mangrove sediment. Not hindering, the elaboration of strategies of bioremediation for impacted areas pass through the knowledge of microbiota and its relations with the environment. Moreover, in the microorganism groups associated to oil, are emphasized the sulfate-reducing prokaryotes (SRP) that, in its anaerobic metabolism, these organisms participate of the sulfate reduction, discharging H2S, causing ambient risks and causing the corrosion of surfaces, as pipelines and tanks, resulting in damages for the industry. Some ancestries of PRS integrate the Archaea domain, group of microorganisms whose sequenced genomes present predominance of extremophilic adaptations, including surrounding with oil presence. This work has two correlated objectives: i) the detection and monitoring of the gene dsrB, gift in sulfate-reducing prokaryotes, through DGGE analysis in samples of mDNA of a mangrove sediment and semiarid soil, both in the BPP; ii) to relate genomic characteristics to the ecological aspects of Archaea through in silico studies, standing out the importance to the oil and gas industry. The results of the first work suggest that the petrodegraders communities of SRP persist after the contamination with oil in mangrove sediment and in semiarid soil. Comparing the populations of both sites, it reveals that there are variations in the size and composition during one year of experiments. In the second work, functional and structural factors are the probable cause to the pressure in maintenance of the conservation of the sequences in the multiple copies of the 16S rDNA gene. Is verified also the discrepancy established between total content GC and content GC of the same gene. Such results relating ribosomal genes and the ambient factors are important for metagenomic evaluations using PCR-DGGE. The knowledge of microbiota associated to the oil can contribute for a better destination of resources by the petroliferous industry and the development of bioremediation strategies. Likewise, search to lead to the best agreement of the performance of native microbiota in biogeochemical cycles in Potiguar Petroliferous Basin ecosystem / S?o diversas as atividades humanas respons?veis pela degrada??o ambiental observada no mundo moderno. As atividades industriais s?o preponderantes na quest?o das conseq??ncias impactantes para os ecossistemas brasileiros. Entre as atividades antr?picas, a ind?stria petrol?fera atuante na Bacia Petrol?fera Potiguar (BPP), exp?e a risco constante de impactos ambientais nos munic?pios integrantes, n?o s? as popula??es humanas e o meio ambiente, mas tamb?m atinge os microrganismos nativos do solo da Caatinga e no sedimento do manguezal. N?o obstante, a elabora??o de estrat?gias de biorremedia??o de ?reas impactadas perpassa, dentre outros aspectos, pelo conhecimento da microbiota e suas rela??es com o meio. Entre os grupos de microrganismos associados ao petr?leo, destacam-se os procariotos redutores de sulfato (PRS) que, em seu metabolismo anaer?bico, participam da redu??o do sulfato, liberando g?s sulf?drico, causando riscos ambientais e ocasionando a corros?o de superf?cies, como tubula??es e tanques, resultando em preju?zos para a ind?stria. Algumas linhagens de PRS integram o dom?nio Archaea, grupo de microrganismos cujos genomas seq?enciados apresentam predomin?ncia de adapta??es extremof?licas, incluindo ambientes com presen?a de petr?leo. Este trabalho tem dois objetivos correlacionados: i) detectar e monitorar o gene dsrB, presente em procariotos redutores de sulfato, por perfis de DGGE gerados a partir de amostras ambientais de mDNA do manguezal de Diogo Lopes, e do solo do semi-?rido da regi?o da BPP; ii) relacionar caracter?sticas gen?micas aos aspectos ecol?gicos de Archaea, ressaltando sua import?ncia para a ind?stria do petr?leo, atrav?s de estudos in silico. Os resultados do primeiro trabalho sugerem que as comunidades petrodegradadoras de PRS persistem ap?s a contamina??o por petr?leo em sedimento de manguezal e do solo do semi?rido. A compara??o entre as popula??es dos dois locais de amostragem revela que as mesmas apresentam varia??es em seu tamanho e composi??o ao longo de um ano de experimento. No segundo trabalho especula-se que fatores funcionais e estruturais s?o a causa da press?o para a manuten??o da conserva??o das seq??ncias nas m?ltiplas c?pias do gene 16S rDNA. Verifica-se tamb?m a discrep?ncia observada entre o conte?do GC total e conte?do GC do mesmo gene. Tais resultados relacionando genes ribossomais a fatores ambientais s?o importantes para avalia??es metagen?micas empregando PCR-DGGE. O conhecimento da microbiota associada ao petr?leo pode contribuir para uma melhor destina??o de recursos por parte da ind?stria petrol?fera e o desenvolvimento de estrat?gias de biorremedia??o. Outrossim, busca contribuir para o melhor entendimento da atua??o da microbiota nativa nos ciclos biogeoqu?micos em ecossistemas da Bacia Petrol?fera Potiguar

The aim of this thesis was to characterize the group of Archaea within the total microbial community in soils from three areas differently impacted by grazing cattle. The size and the structure of the archaeal community were estimated by the analysis of the cell-membrane etherlipids.

Alguns ecossistemas chamam atenção devido à particular combinação de condições ambientais únicas, que resultam na evolução de espécies capazes de colonizar estes ambientes. Os manguezais compõem um bioma composto por espécies de plantas, animais e microrganismos que interagem neste ambiente, que tem como principal característica a interface entre o continente e o oceano em regiões intertropicais. Nosso objetivo foi acessar via sequenciamento massivo de DNA e RNA (via Illumina HiSeq 2000) o perfil taxonômico e funcional da comunidade microbiana de quatro manguezais com distintos níveis de contaminação. As sequências foram analisadas na plataforma MG-RAST, para a análise taxonômica foi utilizado BlastN contra a base de dados RDP ou M5NR, enquanto que a análise funcional foi baseada na comparação por BlastX das sequências obtidas com as disponíveis no banco de dados M5RNA e M5Nr. Na análise funcional, as sequências classificadas foram ainda integradas na classificação hierárquica SEED (subsystems), KEGG (Kyoto Encyclopedia of Genes and Genomes) e COG (Clusters of Orthologous Group). No total, foram obtidas 682 milhões de sequências válidas ( 88,2, 303,1 e 290,9 milhões a partir das análises de DNA, RNA total e RNA purificado, respetivamente). Estas indicaram como grupos taxonômicos mais abundantes as classes Gammaproteobacteria e Deltaproteobacteria (dentro do domínio Bacteria), e Methanomicrobia e Methanobacteria (dentro do domínio Archaea). Além destas observações, alterações na representação de determinados grupos quando as análises de DNA e RNA são comparadas. Em relação a classificação funcional das sequências, foi possível observar uma similaridade no número de funções encontradas nos diferentes manguezais, mas uma maior quantidade de sequências anotadas foi observada, como esperado, na análise de DNA. De maneira mais detalhada, o estudo das funções relacionadas a transformação de nitrogênio e enxofre indicou que há uma correlação entre a abundância de sequências de um referido gene na análise metagenômica, e sua correspondente quantidade dentro dos grupos de dados de metatranscriptômica. Os grupos microbianos mais representados nestes ciclos foram Deltaproteobacteria e Gammaproteobacteria, atuantes principalmente nos processos de fixação de nitrogênio atmosférico (N2), desnitrificação e redução de sulfato, enquanto que para oxidação do enxofre as classes mais frequentes foram Gammaproteobacteria, Betaproteobacteria e Epsilonproteobacteria. De maneira geral, este estudo fornece indícios sobre a atividade microbiana nos manguezais, e indica que as frequentemente correlações observadas entre os resultados da análise metagenômica e metatranscriptômica, porém essas correlações se tornam menos evidentes quando analisamos em nível de ordem ou em níveis mais específicos. / Some ecosystems call particular attention due to unique combination of environmental conditions that result in evolution of species capable of colonizing these environments. Mangroves constitute a biome composed of species of plants, animals and micro-organisms that interact in this environment, whose main characteristic is the interface between the continent and the ocean in tropical areas. Our goal was to access via massive sequencing of DNA and RNA (via Illumina HiSeq 2000) the taxonomic and functional profile of the microbial community four mangroves with different levels of contamination. The sequences were analyzed on MG-RAST platform for taxonomic analysis was performed using BLASTN against the RDP database or M5NR, while the functional analysis was based on comparison of the sequences obtained by BlastX available on M5RNA with the database and M5Nr . In functional analysis, the sequences were classified yet integrated into the hierarchical classification SEED (subsystems), KEGG (Kyoto Encyclopedia of Genes and Genomes) and COG (Clusters of Orthologous Group). A total of 682 million valid sequences were obtained (88.2, 303.1 and 290.9 million from DNA analyzes, purified total RNA and RNA, respectively). These indicated as the most abundant taxa Gammaproteproteobacteria and Deltaproteobacteria classes (within the domain Bacteria), and Methanomicrobia and Methanobacteria (within the domain Archaea). In addition to these observations, changes in the representation of particular groups when analyzes of DNA and RNA are compared. Regarding the functional classification of the sequences was observed in the number of a similarity functions found in different mangrove, but a greater amount of annotated sequences was observed, as expected, the analysis of DNA. In more detail, the study of the functions related to transformation of nitrogen and sulfur indicated that there is a correlation between the abundance of sequences of said gene in metagenomic analysis, and its corresponding quantity within the metatranscriptômica data groups. The microbial groups were over-represented in these cycles and Deltaproteobacteria Gammaproteobacteria mainly active in nitrogênioatmosférico fixation processes (N2), the denitrification and sulfate reduction, while for sulfur oxidation were the most frequent class Gammaproteobacteria, and Betaproteobacteria Epsilonproteobacteria. Overall, this study provides evidence of microbial activity in the mangroves, and often indicates that the correlations observed between the results of metagenomics and metatranscriptômica analysis, but these correlations become less evident when we look at order level or other specific levels.

Estudos sobre a diversidade de Bacteria em solos de mangue (Brasil) e marisma (Espanha) são escassos. A vegetação de mangue, composta por espécies como Spartina alterniflora, Rhizophora mangle, Avicennia schaueriana e Laguncularia racemosa, pode ser um dos fatores que determinam a estruturação das comunidades de procariotos. Determinações das estruturas das comunidades e de diversidade de Bacteria podem ocorrer em função das diferentes condições físico-químicas dos solos, refletindo na configuração dos processos biogeoquímicos. O objetivo deste trabalho foi avaliar a variação das estruturas das comunidades de Bacteria e Archaea, bem como a diversidade, em solos de mangue e marisma utilizando DGGE e sequenciamento parcial do rDNA 16S. As estruturas das comunidades de procariotos apresentaram variações em função de condições de vegetação. Proteobacteria e Bacteroidetes estão presentes em todos os solos estudados. A comunidade de Bacteria destes ambientes é dominada por Proteobacteria. Vários dos táxons detectados estão relacionados com ciclos biogeoquímicos importantes para os ambientes estudados. As estimativas não-paramétricas de riqueza de espécies (ACE e Chao1) mostram que solos de mangue e marisma podem conter milhares de espécies de bactérias. As comunidades de Bacteria dos solos de mangue e marisma são significativamene diferentes. Na camada mais superficial do sedimento de mangue predomina Euryarchaeota metanogênicas enquanto que na camada mais profunda predomina Crenarchaeota. Bactérias das ordens Desulfobacterales, Desulfovibrionales e Desulfuromonales podem estar relacionadas com a atividade de sulfato-redução e formação de pirita na camada anaeróbia do perfil de solo de marisma. De uma maneira geral, pode-se concluir que a diversidade e estrutura das comunidades de procariotos de ambientes estuarinos pode variar em função da vegetação estabelecida e do tipo de ambiente. Adicionalmente, solos de mangue e marisma possuem grande diversidade de procariotos, grande parte da qual é desconhecida, podendo representar elevado potencial genético para utilização biotecnológica. / The bacterial diversity in mangrove (Brazil) and marisma (Espanha) soils are largely unknown. Bacterial communities participate in biogeochemicals processes that occurs in soils of estuarine ecosystems. Determinations of the bacterial communities structures and diversity can occur in function of different physico-chemical conditions, reflecting in the biogeochemical processes. The aim of this work was to evaluate the variation of bacterial an archaeal communities structures utilizing DGGE and partial sequencing of 16S rDNA. Bacterial community structures showed more similarity between repetitions samples than the areas under different vegetation. Phylogenetic afiliation shows that several sequences were not clamped into known phyla. Proteobacteria prevails in bacterial communities of mangrove and marisma soils. Several taxa detected are associated to important biogeochemical cycles that occur in estuarine ecosystems. Analysis of species richness showed that mangrove and marisma soils can contain 200 to 6000 species of bacteria. Methanogenic Euryarchaeota was found specially in the upper sample of mangrove sediment analysed whereas the Crenarchaeota was found specially in the lower. Based on the data obtained, it can be concluded that the vegetation is one of the factors affecting the structure of bacterial and archaeal communities in mangrove soils. Additionaly, the effects of edafic factors and seasonal variations have to be considered as determining the prokaryotic community sctuctures, and bacterial and archaeal communities can respond independently to the factors that determine their community structures. Bacterial diversity can vary with the studied estuarine ecosystem. Studies are necessary concerning to diversity of Bacteria, it variation and correlation with biogeochemical process in the mangrove and marisma soils. These soils show a great diversity of bacteria, much of than unknown, which represent a great genetic potential to the biotechnology.

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.