Functional metagenomic approach was performed using total environmental DNA extracted from a temperate forest soil sample and from an Antarctica soil sample. Searching for clones harbouring phenotypes related to the production of new hydrolytic enzyme allows the isolation of several new enzymes. Amongst them, an esterase and a cellulase, named RBest1 and RBcel1 respectively, were characterized. By accurate description of their catalytic proprieties these two new enzymes appear to present interesting features. The RBest1 esterase is an enzyme whose activity is stabilised or improved in presence of non water-miscible organic solvent. By sequence analysis, RBest1 is related to other organic solvent tolerant enzyme. Moreover, in aqueous buffer, RBest1 is highly specific for butyrate compound but surprisingly its specificity appears to be shifted in presence of organic solvent. The RBcel1 cellulase, was thoroughly characterized for its involvement both in cellulose degradation and production. Our data highlight the requirement for such enzyme in the bacterial cellulose synthesis process. According to our results, the mining of metagenomic libraries by functional screening associated to detailed description of the isolated enzymes gives hints for both ecological and microbiological questions.

Bacterial diversity and ecosystem functioning (BEF) relationships have received considerable attention during the last three decades and tend to be positive in most cases. However, most studies were done in closed systems and largely ignored the importance of placing local communities into the metacommunity context, in which dispersal can be a crucial factor modifying community diversity and composition and ecosystem functioning. The aim of this study was to investigate the effects of both diversity and dispersal on the responses of bacterial community to a starvation perturbation. To achieve this, we implemented a batch culture experiment using the dilution-to-extinction approach to create a diversity gradient of local bacterial community richness. Different dispersal rates were manipulated by transferring cells in different quantities from a regional source to the cultures, and they were then exposed to a perturbation by transferring them into water from another lake which differed in organic carbon content and quality. We evaluated the BEF relationship by measuring the bacterial community composition using t-RFLP and multiple ecosystem functions. Generally, our results demonstrated that diversity and dispersal have an interactive and positive effect on ecosystem functioning. In particular, dispersal had a stronger and more pronounced effect on ecosystem functioning when bacterial diversity was low. When evaluating the responses of bacterial community respiration, no significant difference was observed among different treatments, however, there were clear differences in substrate utilization patterns, implying that specific functions, such as decomposing certain substrates, are more sensitive to a perturbation than general functions, such as respiration. Therefore it is important to include multiple functional parameters when studying BEF relationships and, in particular, when applying our knowledge to the conservation of natural environments.

The animal phylogeny and feeding habits would affect the composition of gastrointestinal tract¡]GI tract¡^microbiota. GI tract microbiota plays an important role in host health and nutrient provision. In this study, we used PCR-DGGE and bacterial 16S rDNA sequencing to analyze the GI tract bacterial diversity of four animals with different feeding habits in Shou-Shan zoo, including one carnivore, one omnivore and two herbivores, in which one ruminant and one non-ruminant. The results show a great difference between GI tract bacterial diversity of the four animals. The abundance of GI tract bacterial diversity increased from carnivore, omnivore to herbivore. Comparing the similarity of the GI tract bacterial community structures of these four animals, the carnivore possessed the most different composition, to other animals, the next was the omnivore, while the two herbivores show the highest similarity to each other. Our results also indicated that the GI tract microbiota of these four different animals were very stable during the investigating period. We also found that two individuals of the same species had a very similar bacterial compositions in their GI tracts at different time point. This finding indicated that the bacterial compositions of GI tract in the four animals were affected mostly by the host phylogeny and their feeding habits. Moreover, according to bacterial 16S rDNA sequencing and idencification, results show that the Firmicutes were the dominant bacterial phyum in all four animals GI tracts, the amount of Bacteroides was much less than Firmicutes. This result might caused by the highly starch content in their feed. Large amount of carbohydrate-degrading, protein-degrading, lipid-degrading bacteria were found in all of these different animals. Fiber-degrading bacteria Fibrobacteres were identified in the GI tracts of the herbivores and omnivore, but not the carnivore, showing that GI tract microbiota plays an important role to provide nutrient and assist energy to the host.

Three experiments were conducted to examine restoration of disturbed land in Arizona. The first experiment attempted to revegetate abandoned farmland by direct seeding native seeds and using various soil preparation techniques, amendments, and weeding of Salsola iberica. Only irrigation and weeding had a significant effect on seed germination and canopy cover. Irrigation increased plant cover on plots, but weeds dominated the cover. A seedbank study conducted near the end of the second growing season found the soil was dominated by weeds and contained few viable native seeds. The results illustrate the difficulty of establishing native plants on abandoned desert farmland due to the dominance of weedy species, the presence of salts in the soil, and the lack of adequate soil moisture.The second experiment, a lysimeter study, tested the efficacy of different evapotranspiration (ET) soil cover designs for stabilization of acidic copper mine tailing piles. The study evaluated the effectiveness of capillary barriers (CB) to contain the waste found in tailings and different plants to revegetate the piles. The ET covers reduced infiltration of water into tailings. Copper concentrations increased significantly in plant tissue grown on the ET covers compared to plants grown in the greenhouse. Plants did not exhibit signs of phytotoxicity and concentrations were below levels toxic to all domestic animals except sheep. The CB did not reduce water infiltration into the tailings or upward migration of copper into the soil cover. Vegetation is vital to an effective ET cover. A mix of transplanted shrubs and seeded grasses and forbs establish long-term, sustainable vegetation.The third experiment examined the influence of biosolids on the bacterial communities within mine tailings by bacterial counts and bacterial diversity. The diversity of neutral copper mine tailings two weeks after biosolid application was compared with that of desert soil via cloning and sequencing of PCR amplified community 16S rRNA. Culturable heterotrophic plate counts (HPC) increased following biosolid addition. Total direct counts exceeded HPC by approximately two orders of magnitude. Overall, biosolid-amended tailings contained large numbers of bacteria diverse in nature and with many of the traits of normal desert soil bacterial communities.

Contamination from various sources has a huge impact on soil health and microbial community composition. Metal contamination of soil in mining scenarios is of concern and is not adequately addressed, particularly with respect to the microbial community. The mining industry is one of the largest contributors to heavy metal contamination of soil in South Africa, especially since the country is one of the major mining countries in the world. Platinum mining is of special importance, since the largest percentage of the world’s reserves of platinum group metals are found and mined in South Africa. Metals from mining activities become irreversibly immobilized in soil systems because they cannot be degraded and has a huge impact on soil systems. In this study, bacteria was isolated from soil samples collected from a platinum mine tailings dam outside Rustenburg. During the warm sampling season (March 2006) most isolates were found, especially in sites 3 and 4. During the colder and drier season (May 2006) there were less isolates. Most of the isolated cultures also displayed a wide temperature growth range, mostly between 24°C - 37°C. Paenibacillus lautus and Bacillus subtilus DN-10 had a growth range between 5°C - 40°C. Culturable metal tolerant bacteria were isolated, purified and identified using 16S rDNA sequences. Nine different species were found namely Paenibacillus lautus strain DS19, Paenibacillus lautus, Paenibacillus sp. C15, uncultured Paenibacillaceae, Bacillus subtilis strain DN-10, Bacillus sp. KDNB5, Bacillus cereus, Stenotrophomonas maltophilia and Alcaligenes sp. DJWH 146-2. The ability of these strains to tolerate metal concentrations were explored by determining their minimum inhibitory concentrations for a selection of metals e.g. aluminum, barium, cobalt, chromium, cadmium, copper, iron, lead, manganese, nickel and mercury. Most isolates were able to tolerate >5mM of the Al\Ni alloy and cobalt. Transmission electron microscopy was used to determine the location of metals inside bacterial cells and electron dispersive X-ray analysis was used to determine the levels of metals inside microbial cells. Bacillus subtilis DN-10 (LDK0306) showed a high MIC (>5mM) for most metals used, except Hg. This strain also had a high percentage (10.26%) of Pb detected in its cells by EDX. This was the highest percentage detected. Plasmids were extracted from the identified strains and can help gain a better understanding of metal tolerance mechanisms used by these isolates. / Thesis(MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2013

Contamination from various sources has a huge impact on soil health and microbial community composition. Metal contamination of soil in mining scenarios is of concern and is not adequately addressed, particularly with respect to the microbial community. The mining industry is one of the largest contributors to heavy metal contamination of soil in South Africa, especially since the country is one of the major mining countries in the world. Platinum mining is of special importance, since the largest percentage of the world’s reserves of platinum group metals are found and mined in South Africa. Metals from mining activities become irreversibly immobilized in soil systems because they cannot be degraded and has a huge impact on soil systems. In this study, bacteria was isolated from soil samples collected from a platinum mine tailings dam outside Rustenburg. During the warm sampling season (March 2006) most isolates were found, especially in sites 3 and 4. During the colder and drier season (May 2006) there were less isolates. Most of the isolated cultures also displayed a wide temperature growth range, mostly between 24°C - 37°C. Paenibacillus lautus and Bacillus subtilus DN-10 had a growth range between 5°C - 40°C. Culturable metal tolerant bacteria were isolated, purified and identified using 16S rDNA sequences. Nine different species were found namely Paenibacillus lautus strain DS19, Paenibacillus lautus, Paenibacillus sp. C15, uncultured Paenibacillaceae, Bacillus subtilis strain DN-10, Bacillus sp. KDNB5, Bacillus cereus, Stenotrophomonas maltophilia and Alcaligenes sp. DJWH 146-2. The ability of these strains to tolerate metal concentrations were explored by determining their minimum inhibitory concentrations for a selection of metals e.g. aluminum, barium, cobalt, chromium, cadmium, copper, iron, lead, manganese, nickel and mercury. Most isolates were able to tolerate >5mM of the Al\Ni alloy and cobalt. Transmission electron microscopy was used to determine the location of metals inside bacterial cells and electron dispersive X-ray analysis was used to determine the levels of metals inside microbial cells. Bacillus subtilis DN-10 (LDK0306) showed a high MIC (>5mM) for most metals used, except Hg. This strain also had a high percentage (10.26%) of Pb detected in its cells by EDX. This was the highest percentage detected. Plasmids were extracted from the identified strains and can help gain a better understanding of metal tolerance mechanisms used by these isolates. / Thesis(MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2013

Thesis (M.S.)--Florida State University, 2006. / Advisor: Joel Kostka, Florida State University, College of Arts and Sciences, Dept. of Oceanography. Title and description from dissertation home page (viewed Oct. 24, 2006). Document formatted into pages; contains viii, 101 pages. Includes bibliographical references.

Submitted by Erika Demachki (erikademachki@gmail.com) on 2015-01-16T17:21:43Z No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Paulo Roberto Faria - 2012.pdf: 1827212 bytes, checksum: 3a1276717070b5a5dcde3f3289329041 (MD5) / Approved for entry into archive by Erika Demachki (erikademachki@gmail.com) on 2015-01-16T17:40:49Z (GMT) No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Paulo Roberto Faria - 2012.pdf: 1827212 bytes, checksum: 3a1276717070b5a5dcde3f3289329041 (MD5) / Made available in DSpace on 2015-01-16T17:40:49Z (GMT). No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Dissertação - Paulo Roberto Faria - 2012.pdf: 1827212 bytes, checksum: 3a1276717070b5a5dcde3f3289329041 (MD5) Previous issue date: 2012-08-10 / In micropropagation, plant tissue fragments called explants are isolated aseptically, disinfected and cultured in culture medium. However, oxidation and contamination are the main problems in the initiation of the tissue culture plants. In order to initiate the establishment of in vitro methodologies for selected sugarcane varieties a series of decontaminating treatments were performed in shoot tips with different exposure times and concentrations of sodium hypochlorite, casugamicin, ethanol and mercuric chloride. There were no problems with oxidation in any treatment. The use of reagent concentrations and times tested showed not be phytotoxic. Treatment using longer times of exposure to casugamicin and sodium hypochlorite obtained the lowest levels of contamination by fungi and bacteria. However, bacterial contamination rates were high which indicates the necessity of using new procedures for the decontamination process. It is known that the sugarcane is associated with different endophytic bacteria. In order to better study these endophytic bacteria and their relationship with the host plant, promoted the isolation of bacteria in explants of five different varieties of sugarcane: RB98710, RB34068, RB034130, RB034120 and RB034041 to determinate of morphological and physiological characteristics. The thirteen isolates have diversity for morphological and biochemical staining and are characterized as gram-positive. All of them had a production capacity of plant growth factors, and after antimicrobial susceptibility testing, two antibiotics: Ciprofloxacin and Ceftazidime showed the greatest potential for controlling the growth of the isolates. With microbial contamination controlled, studies were conducted to evaluate the effect of growth regulators on in vitro multiplication of shoot tip culture and its roots in three sugarcane varieties: RB98710, RB034041 and RB034130. We used liquid MS medium containing BAP, KIN, NAA and GA3 in different combinations and concentrations. The results showed that, for the three varieties tested, MS medium with 0.2 mg.L-1 BAP and 0.1 mg L-1 KIN are most suitable for higher production of shoots and that the best rooting results were obtained in semi-solid ½ MS medium with 6% sucrose, 5.0 mg L-1 NAA and 0.2% activated charcoal. The plantlets were acclimatized and survivability under ex vitro conditions was 90%, three weeks after the transfer to the greenhouse. / Na micropropagação, fragmentos de tecidos vegetal chamados explantes são isolados, desinfetados e cultivados assepticamente em meio de cultura. Porém, a oxidação e a contaminação são os principais problemas no início do processo de cultura de tecidos de plantas. Com o objetivo de iniciar metodologias de estabelecimento in vitro de variedades selecionadas de cana-de-açúcar foram realizados tratamentos de descontaminação de ápices caulinares com diferentes tempos de exposição e concentrações de hipoclorito de sódio, casugamicina, etanol e bicloreto de mercúrio. Não houve problemas de oxidação em nenhum dos tratamentos. O uso dos reagentes nas concentrações e tempos testados não mostrou ser fitotóxico, no tratamento utilizando os maiores tempos de exposição à casugamicina e ao hipoclorito de sódio obteve os menores índices de contaminação por fungos e bactérias. Porém, os índices de contaminação bacteriana foram elevados, o que indica a necessidade de uso de novos procedimentos para o processo de descontaminação. Sabe-se que a cana-de-açúcar está associada a diferentes bactérias endofíticas. Com o objetivo de melhor estudar estas bactérias endofíticas e sua relação com a planta hospedeira, promoveu-se o isolamento de bactérias contaminantes de explantes de cinco diferentes variedades de cana-de-açúcar: RB98710, RB034068, RB034130, RB034120 e RB034041 visando à determinação de características morfológicas e fisiológicas. Os treze isolados obtidos possuem diversidade para características morfo-tintoriais e bioquímicas sendo caracterizados como bastonetes gram-positivos. Apresentaram capacidade de produção de fatores de crescimento vegetal e, após teste de sensibilidade a antimicrobianos, dois antibióticos: Ciprofloxacino e Ceftazidima apresentaram maior potencial de controle do crescimento dos isolados. Com as contaminações microbianas controladas, estudos foram realizados para avaliar o efeito de reguladores de crescimento na multiplicação in vitro de culturas de ápices caulinares e seu enraizamento em três variedades de cana: RB98710, RB034041 e RB034130. Utilizou-se meio MS líquido contendo BAP, KIN, ANA e GA3 em diferentes combinações e concentrações. Os resultados mostraram que, para as três variedades testadas, o meio MS com 0,2 mg.L-1 de BAP e 0,1 mg.L-1 de KIN são os mais apropriados para a maior produção de brotos e que os melhores resultados de enraizamento foram obtidos em meio ½ MS semissólido com 6% de sacarose, 5,0 mg.L-1 de ANA e 0,2% de carvão ativado. As plântulas foram aclimatizadas e a capacidade de sobrevivência sob condições ex vitro foi de 90%, três semanas após a transferência para a casa de vegetação.

Made available in DSpace on 2015-04-20T12:31:09Z (GMT). No. of bitstreams: 1 Juliana Vianna Pereira.pdf: 4570056 bytes, checksum: c660fca0452deacfa10d23ee9bc79a2b (MD5) Previous issue date: 2009-08-26 / The complex microbiota of the oral cavity has been intensively studied and saliva is characterized by microorganisms which colonize different regions of mouth, such as tongue, supragengival and subgingival biofilm. Considering this, the purpose of this study was to evaluate the bacterial diversity of the saliva of patients with different levels of oral hygiene according to the Silness, Löe index. In this research, two genomic libraries of saliva source from 15 patients each were constructed. The pooled samples differ in the average index of Silness, Löe being considered as high or low index within the rate 1.0 to 3.0 and 0 to 0.5, respectively. The DNA saliva was extracted by phenol / chloroform method and 16S rRNA gene for the microorganisms of each sample were amplified and cloned. The sequences obtained were compared to those from sequences of the GenBank NCBI and RDP. The library resultant from saliva of patients with high level of dental biofilm showed 23 OTUs grouped as five known genus: Streptococcus, Granulicaella, Gemella, Peptostreptococcus and Veillonella besides 33.3% of uncultured bacteria. The Library made from saliva of patients with low level of dental biofilm, was significantly different from its counterpart (p = 0.000) and was composed by 42 OTUs, distributed among 11 known genus: Streptococcus, Granulicaella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces, and 24.87% of uncultured bacteria. The genus Streptococcus was the more prevalent in the two libraries, constituting 79.08% of the first and 73.64% the second. In conclusion, patients with low dental biofilm index have saliva with higher bacterial diversity than patients with high dental biofilm index, and despite most uncultivated species aggregate with Steptococcus, they still are new and unknown microorganisms / A complexa microbiota da cavidade bucal tem sido intensivamente estudada e a saliva destaca-se por apresentar microrganismos de diferentes regiões, como a língua, biofilme subgengival e supragengival. Diante disto, o objetivo do presente estudo foi avaliar a diversidade bacteriana da saliva de pacientes com diferentes índices de higiene bucal e para isto, foram construídas duas bibliotecas genômicas da saliva, que foram constituídas por amostras de 15 pacientes cada uma, com a média de índice de biofilme de Silness; Löe diferenciado, sendo a primeira com índice de 1,0 a 3,0 (denominada alto índice) e a segunda, entre 0 a 0,5 (denominada baixo índice). O DNA da saliva foi extraído pelo método fenol/clorofórmio e o gene 16S rRNA para cada biblioteca foi amplificado e clonado. As sequências obtidas foram comparadas com aquelas armazenadas no GenBank do NCBI e RDP. A biblioteca composta pela saliva de pacientes com Alto índice de biofilme dental apresentou cinco Gêneros conhecidos: Streptococcus, Granulicaella, Gemella, Veillonella e Peptostreptococcus e 33,3% de bactérias não-cultivadas, agrupados em 23 OTUs. A Biblioteca, composta pela saliva de pacientes com Baixo índice de biofilme dental, foi diferente siguinificativamente da primeira (p=0,000) e foi composta de 42 OTUs, distribuídas em 11 Gêneros conhecidos: Streptococcus, Granulicaella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces, alem de 24,87% de bactérias não-cultivadas. O Gênero Streptococcus foi o mais prevalente nas duas bibliotecas, constituindo 79,08% da primeira e 73,63% da segunda. Conclui-se que existe maior diversidade bacteriana na saliva de pacientes com Baixo índice de biofilme dental em relação à pacientes com Alto índice de biofilme dental e que apesar da maioria das espécies não-cultivadas agruparem-se com os Streptococcus, ainda contituem-se de microrganismos novos e desconhecidos

O Brasil é um dos países com a maior biodiversidade do mundo, embora existam ainda poucos estudos sobre a biodiversidade microbiana dulcícola, assim, o objetivo deste trabalho foi avaliar a diversidade e estrutura das comunidades bacterianas presentes no corpo e afluentes do Rio Tietê e relacioná-las às variáveis ambientais. Foram obtidos 385 fragmentos terminais de restrição representando a temporada de estiagem em 2013 e 217 TRFs representando a temporada de cheias em 2014. As análises de Redundância (RDA) apresentaram separação entre as amostras de acordo com o período de coleta seguida da qualidade da água de origem e a temporada 2013 apresentou maior riqueza e diversidade com relação à 2014. Já a técnica de sequenciamento por MiSeq Illumina, apresentou 2.130.122 sequências com boa qualidade e o parâmetro temperatura representou a principal variável ambiental agindo sobre a riqueza das comunidades avaliadas, além disso, a localização geográfica dos rios e suas conexões representaram fatores importantes para a distribuição dos gêneros observados. / Brazil is considered one of the countries with the highest biodiversity; however, there are few studies on microbial diversity in freshwaters. Thereby, the aim of present work was to evaluate the diversity and structure of bacterial community present in Tietê river and its tributaries, for that, 28 points along Tietê River Basin were evaluated by T-RFLP and 14 points were chosen based on these results for partial sequencing of rRNA 16S gene by MiSeq Illumina. 385 Terminal Restriction Fragments were obtained for season 2013 and 217 for 2014 and Redundancy Analysis presented separation between samples according to seasons followed by water quality group separation. Season 2013 presented higher richness and diversity compared to season 2014 and high throughput sequencing presented 2.130.122 sequences with good quality. Temperature parameter represented the main environmental variable acting on the richness of assessed communities, in addition, the geographic location of the rivers and their connections were important factors for the distribution of observed genera.