Dissertations / Theses on the topic 'T-RFLP'
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Rocha, Lidianne Leal. "Estudo de comunidades bacterianas de solos do Manguezal da Barra Grande, Icapuà â CE e SeleÃÃo de cepas com potencial para degradar hidrocarbonetos." Universidade Federal do CearÃ, 2008. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=2773.
Full textMendes, Lucas William. "Análise molecular das estruturas e diversidade de comunidades microbianas em solo de manguezal preservado da Ilha do Cardoso-SP." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-27042010-112316/.
Full textThe tropical mangroves are considered one of the most productive ecosystems of the world, being characterized by the high tax of organic matter and recycling of nutrients, that happens between the oceans and the terrestrial habitats. Although the mangroves are considered areas of environmental protection, the destruction of those ecosystems is progressive, due to industrial and port activities in the estuaries. In mangroves, the recycling of nutrients is directly related to the activities and to the diversity of microbial communities present in the soil. This work is part of a wider project inside of the program BIOTA/FAPESP, with respect to the studies of the biodiversity in the State of São Paulo and use of that biodiversity in a maintainable way. The objective of this work was to evaluate the structures and diversity of communities of Bacteria, Archaea and Fungi present in the soil of preserved mangrove of Ilha do Cardoso-SP. The samples were analyzed by T-RFLP and ARISA techniques, cloning and sequencing in order to obtain a characterization of the microbial communities structure of preserved mangrove area in comparison with the adjacent environments of restinga (tropical moist forest) and forest and also to a degraded mangrove. The results allowed concluding that the mangroves present exclusive characteristics, with the presence of distinct organisms, revealing a possible biotechnological potential to be explored. Additionally, the data revealed that the human action affected the structures of those communities in a way to be noticed a sensitive diversity decrease in the degraded mangrove, evidencing, this way, the importance of the ecosystem preservation
Fiore, Rebecca de Ara?jo. "Potencial de esp?cies florestais para remedia??o de substrato contaminado com atrazine e 2,4-D." UFVJM, 2014. http://acervo.ufvjm.edu.br:8080/jspui/handle/1/338.
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Funda??o de Amparo ? Pesquisa do estado de Minas Gerais (FAPEMIG)
Em se tratando da contamina??o de ecossistemas por res?duos de defensivos agr?colas, especial aten??o ? dada para a classe dos herbicidas, em fun??o do volume de aplica??o. Os que possuem mol?culas sol?veis pass?veis de contamina??o de len??is h?dricos subterr?neos se destacam pela abrang?ncia dos efeitos negativos. Nesse sentido, objetivou-se selecionar esp?cies vegetais arb?reas interessantes na remedia??o de ambientes contaminados por res?duos de atrazine e 2,4-D. Foram avaliados 36 tratamentos compostos pela combina??o de 12 esp?cies florestais [Inga marginata (ing?), Schizolobium parahyba (guapuruvu), Handroanthus serratifolius (ip? amarelo), Jacaranda puberula (carobinha), Cedrela fissilis (cedro), Calophyllum brasiliensis (landin), Psidium mirsinoides (goiabinha), Tibouchina glandulosa (quaresmeira), Caesalpinia f?rrea (pau-ferro), Caesalpinia pluviosa (sibipiruna), Terminalia arg?ntea (capit?o) e Schinopsis brasiliensis (bra?na)] e tr?s solu??es simulando o composto lixiviado (atrazine, 2,4-D e ?gua ? controle), com quatro repeti??es. Foram feitas 3 aplica??es dos herbicidas atrazine e 2,4-D com intervalos de 20 dias (aos 60, 80 e 100 dias ap?s o plantio), sendo cada aplica??o correspondente ? metade da dose comercial dos produtos. Para as avalia??es de crescimento foram mensuradas a altura da planta, o di?metro do caule, o n?mero de folhas, a ?rea foliar e o ac?mulo de biomassa seca. Na estimativa do efeito visual dos herbicidas ?s plantas avaliadas, optou-se pela atribui??o de notas em escala de intoxica??o. Para verifica??o de capacidade remediadora das esp?cies arb?reas procedeu-se a semeadura da esp?cie indicadora para indicativo do res?duo do herbicida no solo, (Cucumis sativus (L.)). Posteriormente em amostras de solo provenientes da esp?cie remediadora mais promissora procedeu-se a an?lise de polimorfismo de comprimento de fragmento de restri??o terminal (T-RFLP), com intuito de caracterizar a diversidade microbiana presente. As esp?cies florestais sobreviveram ? aplica??o dos herbicidas, sendo que umas se mostram mais sens?veis do que outras. O ing? apresentou bons resultados de remedia??o com o bioensaio, assim como o ip? amarelo, apesar da sua sensibilidade aos herbicidas. Observou-se aumento no conte?do relativo de macronutrientes para as plantas sob a??o dos herbicidas, na maioria dos tratamentos. Os resultados de T-RFLP confirmaram a diversidade microbiana diferenciada associada ? rizosfera de ing?, principalmente quando submetida ? a??o de atrazine.
Disserta??o (Mestrado) ? Programa de P?s-Gradua??o em Ci?ncia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 2014.
ABSTRACT In the case of contamination of ecosystems by residues of pesticides, special attention is given to the class of herbicides, according to the application volume. Those with likely contamination of underground water soluble molecules sheets are distinguished by breadth of negative effects. In this sense, the aim of this work was to select interesting woody plant species in the remediation of contaminated by residues of atrazine and 2,4-D environments. Were evaluated 36 treatments consisted of combinations of 12 forest species [Inga marginata (ing?), Schizolobium parahyba (guapuruvu), Handroanthus serratifolius (ip? amarelo), Jacaranda puberula (carobinha), Cedrela fissilis (cedro), Calophyllum brasiliensis (landin), Psidium mirsinoides (goiabinha), Tibouchina glandulosa (quaresmeira), Caesalpinia f?rrea (pau-ferro), Caesalpinia pluviosa (sibipiruna), Terminalia arg?ntea (capit?o) and Schinopsis brasiliensis (bra?na)] and three leachate solutions simulate the compound ( atrazine , 2,4 - D and water - control),with four replicates each. Three applications of atrazine and 2,4-D were made at intervals of 20 days (at 60, 80 and 100 days after planting), each application was corresponding to half of the recommended. Evaluations of growth were measured plant height, stem diameter, number of leaves, leaf area and dry biomass. In estimating the visual effect of herbicides on plants assessed, was opted for the grading scale of intoxication. To check remediation ability of tree species proceeded seeding indicator species for indication of herbicide residue in the soil (Cucumis sativus (L.)). Later in soil samples from the species most promising remedial proceeded to analysis of length polymorphism terminal restriction fragment (T-RFLP), in order to characterize the microbial diversity present. Forest species survived the herbicide application, and some are more sensitive than others. The ing? had good results with the remediation bioassay, as well as the ipe amarelo, despite their sensitivity to herbicides. Observed increase in the relative content of macronutrients for plants under the effect of herbicides in most treatments. The results of T-RFLP confirmed the differentiated microbial diversity associated with the rhizosphere of ing?, especially when subjected to the action of atrazine.
Santana, Maiele Cintra. "Análise da comunidade de fungos em áreas de monoculturas e consórcio de Eucalyptus grandis e Acacia mangium." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-03052018-173930/.
Full textThe fungi represent about 75% of the microbial biomass in forest areas, performing important functions, from the mineralization of the organic residues to the availability of nutrients to plants through mycorrhizal associations, which influences the nutrient cycling and, consequently, the growth of trees. The objective of this work was to evaluate the community of fungi of the soil, rhizosphere and root system of Eucalyptus grandis and Acacia mangium planted in monocultures and consortium, and to find explanations for the observed patterns through the correlation with physical and chemical soil attributes and soil depth. The samples were collected at the Experimental Station of Forest Sciences of Itatinga in 2016, when the plants were 2 years old. Samples were collected in four treatments: monocultures of E. grandis and A. mangium and consortia of E. grandis and A. mangium, in which trenches were constructed to collect samples in the 0-10, 10-20, 20 -50 and 50-100 cm deep. The physical and biological attributes of the soil and the chemical attributes of soil, rhizosphere and roots were characterized. For the mycorrhizal evaluation, the number of spores of arbuscular mycorrhizal fungi (AMF) and the rates of root colonization by AMF and ectomycorrhizal fungi were quantified. The morphology of arbuscular mycorrhizal and ectomycorrhizal (ECM) structures was evaluated. The structure of the soil and rhizosphere fungi community by was evaluated by the technique of Terminal restriction fragment length polymorphism (T-RFLP). For this, the DNA was amplified using primers ITS1f-FAM and ITS4 and restriction of the fragments was performed with the enzyme HaeIII. The abundance of ITS gene copies of soil and rhizosphere was quantified by quantitative PCR (qPCR), using primers ITS1f and 5.8s. The physical, chemical and biological attributes had few variations among the evaluated treatments, being the greatest differences found between the depths. The number of spores (<29) and mycorrhizal colonization rates (<48%) were low in all treatments, and reduced with increasing depth. A. mangium plants did not form FMA. In the roots of E. grandis, there was no formation of arbuscules, but we found the presence of hyphal coils, mycorrhizal structures of the Paris type. The anatomy of the ECM confirmed the colonization of these fungi in the roots of the studied plants. The qPCR showed higher abundance of ITS genes in the rhizosphere in relation to the soil, as well as in the superficial layers (0-10 cm) in relation to the deeper ones (10 cm below). The Principal Coordinates Analysis revealed differences in the structure of the fungal communities in the treatments studied, especially for the rhizosphere region, differentiating the fungal profile of the E. grandis monoculture from the other treatments, as well as the influence of A. mangium on the structure of the community. The redundancy analysis showed the influence of some chemical soil attributes on the rates of colonization and community structuring. Thus, it is concluded that in a consortium system, one plant species seems to be more influential than the other in structuring the fungal community, and this influence is more evident in the rhizosphere. In addition, chemical attributes are important factors in the organization of the fungal community.
Miao, Yu. "Development and use of T-RFLP for studies of take-all infection of wheat." Thesis, University of Nottingham, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.490991.
Full textFornazari, Anna Cristina Zari. "Determinação da comunidade microbiana pelo método molecular T-RFLP em carnes refrigeradas embaladas a vácuo." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/11/11141/tde-22112011-085341/.
Full textThe distension of the packaging of vacuum packed chilled meat, also know as blown pack, is assigned to psichrophilic and psychrotrophic bacteria, among which are part some clostridium, enterobacteria and lactic bacteria.The ability of these microorganisms to grow at refrigeration temperatures makes it an appropriate challenge its control by the industry. Brazil is a major producer of beef in the world and despite the importance of the beef industry represents for the country, there are few studies on the possible causes of deterioration of blown pack type. The importance of this work is based on the dearth of research on this problem that affects the meat industry. The aim of this study was to evaluate the presence of the main microorganisms involved in the deterioration blown pack type, with emphasis on clostridia, enterobacteria and lactic bacteria. Thus, the method-Terminal Restriction Fragment Length Polymorphism, available at Molecular biology laboratory of CENA-USP, was used to allow a rapid and accurate diagnosis for the detection of microorganisms. We analyzed 15 samples of beef chilled, vacuum packed wich abundant gas production, refrigerators from the states of São Paulo, Mato Grosso do Sul and Goiás cuts used for the analysis were striploin, shin, rump, hump, cop of rump and cube roll. The samples showing signs of deterioration such blown pack within the shelf life, with storage periods ranging from 30 to 120 days. Were identified Clostridium algidicarnis, Clostridium gasigenes, Clostridium putrefaciens, Clostridium frigidicarnis, Lactobacillus sakei, Hafnia alvei and Serratia liquefaciens by TRFLP technique, which proved an excellent tool for microbial identification in meat samples. The high prevalence of enterobacteria in samples of meat detected by the technique of TRFLP analysis was performed with conventional isolation and identification of enterobacteria, in order to confirm the presence of viable and culturable microorganisms in the samples. The species of enterobacteria were identified and cultivated H. alvei, Ser. liquefaciens, Citrobacter braakii, Pantoea sp. and Yersinia enterocolitica, the latter being potentially pathogenic and interest in public health. It was observed that H. alvei was the predominant species in the samples evaluated by both the T-RFLP technique and by conventional microbiological tests. In order to complement the results were analyzed conventional cultivation and isolation of Clostridium estertheticum and Clostridium gasigenes in meat samples. The PCR technique was employed for the purpose of identification of isolates.
Paes, Fernanda Araujo. "AnÃlise de comunidades microbianas de solo de manguezal por T-RFLP e microarranjos de DNA." Universidade Federal do CearÃ, 2008. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=2712.
Full textThe mangroves are essistemas important and productive, found along the coastline of tropical and subtropical regions. Important processes such as nutrient cycling, are directly connected to the activity of soil microbial communities. Given its strategic position the mangroves are very impacted the world. In Brazil, important areas such as the Bay of All Saints (BA) are severely affected by the presence of oil. Understanding the adaptation of the microbiota and its local dynamics, before the environmental change is essential to be able to maintain or restore these ecosystems. This thesis investigated the structure and function of microbial communities in a mangrove area of the Bay of All Saints polluted by the oil industry. Two sites were sampled - one located in the refinement of the industry and another, distant location and used as the control. Besides the measured abiotic data, two independent methods of cultivation were used: T-RFLP and DNA microarranjos. The results of both sites in the experiments of T-RFLP showed that the two bacterial communities differ in their structure. For the site sampled in the refinery, a greater number of Otus suggests an environmental stimulus, the bacterial community, a fact associÃvel the high organic matter content of the site. For microarranjos DNA, similar categories of genes were detected in both places, but the specificity of their sequences were distinct. The genes that encode for the remediation organic, were more representative, more than 40% in total in the two sites. Even detecting similar categories, only 4% of the gene sequences were common to the sites. These data show that different bodies are responsible for similar functions at each point. The difference between the sites observed in the experiments can be related with the fact that Site 1 is located in a region heavily affected by oil. Using the ecological data rates of T-RFLP indicated the site 1 as the most diverse, while the results with the DNA microarranjos show the opposite. In conclusion, the structure and function of the local microbiota are affected by the presence of the oil industry. Additional studies may help understand the dynamics of microbial communities, facing the future exposure to the oil and / or derivatives.
Os manguezais sÃo essistemas importantes e produtivos, encontrados ao longo da linha da costa de regiÃes tropicias e subtropicais. Processos importantes como a ciclagem de nutrientes, estÃo diretamente conectados à atividade das comunidades microbianas desses solos. Dada sua posiÃÃo estratÃgica os manguezais sÃo bastante impactados no mundo todo. No Brasil, Ãreas importantes como a da BaÃa de todos os Santos (BA) sÃo severamente afetadas pela presenÃa do petrÃleo. Compreender as adaptaÃÃes da microbiota local e sua dinÃmica, frente Ãs alteraÃÃes ambientais, à essencial para que se consiga manter ou restaurar esses ecossistemas. A presente dissertaÃÃo investigou a estrutura e a funÃÃo de comunidades microbianas em uma Ãrea de manguezal da baÃa de Todos os Santos poluÃda pela indÃstria do petrÃleo. Dois locais foram amostrados - um, situado na Ãrea de refinamento dessa indÃstria e o outro, distante desse local e usado como controle. AlÃm dos dados abiÃticos medidos, dois mÃtodos independentes de cultivo foram utilizados: T-RFLP e microarranjos de DNA. Os resultados de ambos os sÃtios nos experimentos de T-RFLP mostraram que as duas comunidades bacterianas diferem quanto à sua estrutura. Para o sÃtio amostrado na refinaria, um nÃmero maior de OTUs sugere um estÃmulo ambiental, na comunidade bacteriana, fato associÃvel ao alto teor de matÃria orgÃnica desse local. Para os microarranjos de DNA, categorias similares de genes foram detectados, em ambos os locais, mas a especificidade de suas sequÃncias foi distinta. Os genes que codificam para a remediaÃÃo orgÃnica, foram os mais representativos, mais de 40% no total nos dois sÃtios. Mesmo detectando categorias semelhantes, apenas 4% das sequÃncias genÃticas foram comuns aos sÃtios. Estes dados mostram que organismos diferentes sÃo responsÃveis por funÃÃes similares em cada ponto. A diferenÃa entre os locais observadas nos experimentos pode ser relacionada, com o fato do sÃtio 1 situar-se numa regiÃo fortemente afetada por hidrocarbonetos. Utilizando-se Ãndices ecolÃgicos os dados de T-RFLP indicaram o sÃtio 1 como o mais diverso, enquantoo os resultados com os microarranjos de DNA mostram o oposto. Concluindo, a estrutura e funÃÃo da microbiota local sÃo afetadas pela presenÃa da indÃstria do petrÃleo. Estudos adicionais poderÃo ajudar a compreender a dinÃmica dessas comunidades microbianas, frente Ãs futuras exposiÃÃes ao Ãleo e/ou derivados.
Paes, Fernanda Araújo. "Análise de comunidades microbianas de solo de manguezal por T-RFLP e microarranjos de DNA." reponame:Repositório Institucional da UFC, 2008. http://www.repositorio.ufc.br/handle/riufc/4926.
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Os manguezais são ecossistemas importantes e produtivos, encontrados ao longo da linha da costa de regiões tropicais e subtropicias. Processos importantes, como a ciclagem de nutrientes, estão diretamente conectados à atividade das comunidades microbianas desses solos. Dada sua posição estratégica, os manguezais são bastante impactados no mundo todo. No Brasil, áreas importantes como a da Baía de todos os Santos (BA) são severamente afetadas pela presença do petróleo. Compreender as adaptações da microbiota local e sua dinâmica, frente às alterações ambientais, é essencial para que se consiga manter ou restaurar esses ecossistemas. A presente dissertação investigou a estrutura e a função de comunidades microbianas em uma área do manguezal da baía de Todos os Santos, poluída pela indústria do petróleo. Dois locais foram amostrados – um, situado na área de refinamento dessa indústria e o outro, distante desse local e usado como controle. Além dos dados abióticos medidos, dois métodos independentes de cultivo foram utilizados: T-RFLP e microarranjos de DNA. Os resultados de ambos os sítios, nos experimentos de T-RFLP, mostraram que as duas comunidades bacterianas diferem quanto à sua estrutura. Para o sítio amostrado na área da refinaria, um número maior de OTUs sugere um estímulo ambiental, na comunidade bacteriana, fato associável ao alto teor de matéria orgânica desse local. Para os microarranjos de DNA, categorias similares de genes foram detectadas, em ambos os locais, mas a especificidade de suas sequências foi distinta. Os genes que codificam para a remediação orgânica foram os mais representativos, mais de 40% do total nos dois sítios. Mesmo detectando categorias semelhantes, apenas 4% das sequências genéticas foram comuns aos sítios. Estes dados mostram que organismos diferentes são responsáveis por funções similares em cada ponto. A diferença entre os locais, observada nos experimentos, pode ser relacionada com o fato do sítio 1 situar-se numa região fortemente afetada por hidrocarbonetos. Utilizando-se índices ecológicos, os dados de T-RFLP indicaram o sítio 1 como mais diverso, enquanto os resultados dos microarranjos de DNA mostraram o oposto. Concluindo, a estrutura e função da microbiota local são afetadas pela presença da indústria do petróleo. Estudos adicionais poderão ajudar a compreender a dinâmica dessas comunidades microbianas, frente às futuras exposições ao óleo e/ou derivados.
Andrade, Pedro Avelino Maia de. "A composição da comunidade bacteriana do solo como fator determinante na micorrização de cana-de-açúcar por Glomus clarum." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/11/11140/tde-26062013-143930/.
Full textSugarcane is an important Brazilian agricultural system crop and presents currently booming. Nevertheless, land use, and implementation of different management technologies have originated changes in environmental balance, where important microbial interactions occur as essential for plant development. Among the wide diversity of soil microorganisms, the mycorrhizal fungi is highilighted as organisms closely associated with plant roots, helping plants, in any way, to obtain water and nutrients. These fungi however, also interact with other soil organisms, such as for example, bacterial community in these environments. Thus, the present work aimed to study the dynamics of interaction between sugarcane and arbuscularmycorrhizal fungi (AMF) Glomusclarum in soils with different compositions of the bacterial community. The methodology used was \"dilution to extinction\", where serial dilutions (10-1, 10-3, 10-6 and 10-9) of a natural soil were used to inoculate a sterile soil. On this basis, were monitored along a period of 60 days, plant colonization by AMF, and structure of bacterial communities. As a result, we observed a higher colonization of roots of cane sugar for treatments inoculated with lower dilutions of the original community (natural soil and dilutions 10-1 and 10-3), and likewise observed a distinction between these bacterial communities treatments to others. Establishing correlations between microbial groups with observed rates of colonization, it was possible to name, based on the massive sequencing of the region V6 ribosomal gene 16S rDNA, the joint amendment of mycorrhiza with changes in groups of Actinobacteria; Bacteriodetes; Firmicutes, Proteobacteria; Verrucomicrobia and Acidobacteria. In conclusion, this work demonstrates the dependence of an important process, as the AMF, has tosoil bacterial community, and indicates that degraded areas, with lower levels of bacterial diversity, such a process can occur with lower efficiency.
Campana, Felippe Buck. "Monitoramento temporal e espacial de contaminações bacterianas na produção de bioetanol: caracterização molecular por T-RFLP e detecção quantitativa por qPCRde comunidades formadoras de biofilmes." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-25102012-164236/.
Full textBacterial contamination by Lactobacillus, Bacillus and Leuconostoc and other lactic acid bacteria is one of the main factors that affects the yield in alcoholic fermentation process. Biofilm formation protects the bacteria community and it is a permanent source of contamination. For characterization of these contaminations in (1) biofilms from centrifuge, tank fermentation, heat exchanger and water pipe and (2) molasses, must, yeast, yeast treated (with H2SO4) and wine, samples were taken at two different periods from fermentation system characterized by high alcohol yields (16%). Restriction enzymes AluI, BstUI, HaeIII, HinfI, MseI and MspI used in T-RFLP analysis were defined by 16S rRNA gene sequences analysis in silico from common contaminants. These enzymes generate high number of unique T-RFs between 30 and 650 bp. DNA from samples were used as template in T-RFLP reactions in order to obtain molecular profiles of microbial communities present at each sample. Shannon diversity index was calculated based on T-RFs numbers. Principal component analysis (PCA) and phylogenetic inference of contaminants were performed based on T-RFs profiles. The main contaminant bacterial taxa were quantified by qPCR using specific primers designed in this study and considering the average of 16S rRNA gene copies previously counted into the genome of each bacterial taxon. Water pipe biofilm showed the highest rate of bacterial diversity in the samples collected in the first sampling period. For the samples collected in the second sampling, the highest rate of bacterial diversity was revealed for molasses and must. PCA suggested that biofilms (but not external sources) are the main contaminants in the studied fermentation process. It is probably due their similarities with the composition of other analyzed communities. Lactobacillus and Bacillus species predominated in first sampling period. Halomonas, Streptococcus, Lactococcus and Pseudomonas were detected in biofilm and liquid samples. They were the main contaminants from biofilm at this time of sampling. In the second sampling period, Bacillus was the most common genera and other lactic acid bacteria such Streptococcus, Staphylococcus and Lactobacillus were also the most frequent contaminants. These results agree with other reported in the literature about conventional fermentation systems. Only the primers designed in this study to amplify the 16S rRNA gene of Burkholderia, Pseudomonas and Weissella showed specificity in tests with bacterial strains. Halomonas sp. was revealed in biofilms from tank fermentation by DNA sequencing using designed primers for genera. Halomonas can produce levan and may consume sucrose available for generation of alcohol. Centrifugal biofilm had the highest amount of bacteria in both sampling periods (1.93E+06 CFU.mg-1 and 2.14E+07 CFU.mg-1, respectively). In liquid samples, yeast had the highest amount of bacteria in both sampling periods (1.03E+08 CFU.ml-1 and 2.96E+06 CFU.ml-1, respectively); it shows significant levels of contaminants. Burkholderia and Pseudomonas were more abundant among biofilm samples of all samplings. Burkholderia was present in high quantities in the majority of liquid samples taken during the first sampling period; Pseudomonas and Weissella equivalently predominated among samples taken during the second sampling period
Arnaldo, Marcela. "Relações entre fluxos de óxido nitroso (N2O) com umidade e genes associados à desnitrificação em floresta e sistemas agrícolas." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-05112014-152017/.
Full textNitrous oxide (N2O) is an important greenhouse gas (GHG) and, in terrestrial ecosystems, it is mainly produced by denitrification. This process occurs under anaerobic conditions and, therefore, is strongly stimulated by the increase of the soil moisture content. However, soils under different uses may exhibit distinct N2O emission rates, even when they have the same moisture content. It is still not clear whether this is due solely to the fact that they differ in relation to physical and chemical properties that affect the activity of denitrifying organisms or whether this is also due to differences in the size of their populations. The aim of this work was to evaluate the relations between N2O fluxes, moisture and abundance of bacterial genes involved in denitrification process (nirK, norB e nosZ) in soil samples from forest, pasture and sugarcane field, through a microcosm experiment. These samples were collected at Fazenda Capuava, located in Piracicaba, SP. Microcosms established from them were maintained with different moisture contents (original and adjusted to achieve 60% and 90% of field capacity) and incubated at 30 °C for 30 days. During the incubation period, the N2O fluxes from soils were analyzed by gas chromatography. Soil samples from microcosms, collected before and after application of the treatments, were compared regarding the structure of their bacterial communities, by using T-RFLP technique, and the abundance of 16S rRNA, nirK, norB and nosZ genes, through qPCR technique. Only samples that had their moisture content adjusted to 90% of field capacity exhibited significant increases in N2O production. In these samples, changes in the structure of bacterial communities and in the copy numbers of norB and nosZ genes were also detected. Only the latter gene, however, showed a positive correlation with soil moisture. The abundance of the quantified genes showed no significant correlations with the gas emission rates. On the other hand, the cumulative N2O emissions were positively correlated with the amounts of denitrifying genes initially present in the samples. These genes were more abundant in pasture and forest soils, which had higher levels of organic matter, carbon, nitrogen, nitrate and clay than those from sugarcane cropping area. These results indicate that soil water content affects the N2O emission rates. However it is not due to changes in the abundance of bacteria involved in the process, such as those that bear the nirK, norB and nosZ genes. Apparently, it is the size of these organisms\' populations that determines the amount of GHG that the soil is able to produce.
Szekely, Brian. "Determining fecal bacterial profiles of a human-habituated wild chimpanzee population in Mahale Mountains National Park, Tanzania." Thesis, Virginia Tech, 2009. http://hdl.handle.net/10919/31828.
Full textMaster of Science
Beckwith, Matthew. "Coupling of autotrophic and heterotrophic plankton food web components in the tidal-freshwater James River, USA." VCU Scholars Compass, 2009. http://scholarscompass.vcu.edu/etd/1706.
Full textLima, Amanda Barbosa. "Influência da cobertura vegetal nas comunidades de bactérias em Terra Preta de Índio na Amazônia Central brasileira." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-19092012-152431/.
Full textAmazonian Dark Earths (ADEs) in the Brazilian Amazon are highly fertile and its chemical content seems not to get depleted even under tropical humid conditions. For this reason, these soils are frequently searched by local population for subsistence farming. The importance of microbial communities has grown the interest in understanding the relationship between land use, plant communities, microorganisms, and ecosystem processes. Therefore, the main objective of this research was to investigate the effect of vegetation cover in land use systems (secondary forest and cassava plantation) and rhizosphere of native leguminous plants on bacterial communities of ADEs. Furthermore, it was also aimed to investigate denitrifying bacteria in these soils. The study area is located at the Experimental Station of Caldeirão, belonging to Embrapa Amazônia Ocidental, Iranduba, AM. The bacterial community function was determined by Community Level Physiological Profile (CLPP), the bacterial community structure was assessed by Terminal Restriction Fragment Length Polymorphism (T-RFLP), the bacterial community composition and distribution by high-throughput sequencing (pyrosequencing), and the quantification of denitrifier bacteria by Quantitative PCR (qPCR). The studies were performed in the Laboratory of Cell and Molecular Biology (CENA/USP) and the Deparment of Biogeochemistry (Max Planck Institute for Terrestrial Microbiology). T-RFLP analysis showed that land use and seasonality affected bacterial communities in ADE, and also showed a clear rhizosphere effect on bacterial communities. CLPP have shown that ADE functional activity was not affected by seasonality. Furthermore, pyrosequencing technology was an important tool to differentiate rare phylotypes. Distinct differences of some rhizosphere bacterial phyla were also observed, indicating that the root zone contributed to shape these communities. The relative abundance of nirK gene was not affected by land use in both studied soils. Alterations in the community structure of nirK and nosZ genes were observed for both soils. ADE denitrifying communities seemed to be more affected by land use than seasonality, and ACH was more influenced by seasonal variations.
Rocha, Karina da. "Decomposição no solo da torta de filtro derivada do processamento da cana-de-açúcar: emissão de gases de efeito estufa e aspectos microbiológicos." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-05022014-084900/.
Full textBrazil is the greatest worldwide producer of sugarcane with production of sugar, ethanol and derived. Usually applied to soil as fertirrigation, filter cake and vinasse on soil conditioning have contributed to the maintenance of fertility. On the contrary, each agricultural operation is associated to GHG emissions that must be accounted for the balance of products. This work aims evaluate GHG emissions (CO2, N2O and CH4) from the filter cake, as well as evaluate the main differences in the microbiological community available within the decomposition process. After evaluation of a survey about to use the filter cake by industries, the study has been developed at Usina Costa Pinto located in Piracicaba (SP). The filter cake applied to the row of sugarcane planting have been monitored by taking regular samples of the emissions. The concentration of the three gases in the samples has been determined by gas chromatography. The microbiological aspects has been evaluated by biomass, enzymatic activity (acid phosphatase, alkaline phosphatase, and beta-glycosidase) and the community structure through terminal restriction fragment length polymorphism (T-RFLP). Significant GHG emission has been observed; mainly from the filter cake applied to the row of sugarcane planting especially N2O, with ratio twelve times greater than CH4 in 56 days of experiment. For microbiological aspects, the maximum of carbon and nitrogen from the microbial biomass for the treatment usually applied (25 Mg ha-1), within two months of experimentation, with respectively 484,89 ?g C g dry soil-1 e 62,95 ?g N g dry soil-1, and correlated by the coefficient of Pearson with the enzymatic activity existent in the material. The T-RFLP analysis has allowed evaluate the community structures of Archaea, Bacteria e Fungi in the microbiological community of the filter cake. Modification in the community structures was not observed over this time examined. The results obtained reinforce the importance of microbiological aspects combined with chemical and physical factors and their influence on GHG emissions.
Rodrigues, Italo Sarto Carvalho 1983. "Análise da diversidade bacteriana associada ao biofilme dentário por polimorfismo de comprimento de fragmentos terminais de restrição (T-RFLP)." [s.n.], 2011. http://repositorio.unicamp.br/jspui/handle/REPOSIP/290618.
Full textDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba
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Resumo: As comunidades bacterianas presentes na cavidade bucal desempenham papel importante no equilíbrio saúde/doença em seres humanos. Nesse sentido, o estudo da composição de microambientes orais pode contribuir para uma melhor precisão no diagnóstico de doenças infecciosas e, consequentemente, para o desenvolvimento de abordagens terapêuticas mais eficazes. A periodontite é uma doença dos tecidos de suporte do dente, caracterizada por resposta imunológica exacerbada do hospedeiro, frente à presença bacteriana no biofilme dentário. A grande diversidade bacteriana observada na cavidade bucal, aliada aos variados quadros clínicos da periodontite, ressaltam a necessidade de investigações mais aprofundadas sobre a composição bacteriana periodontopatogênica. O objetivo deste trabalho é a caracterização da comunidade bacteriana associada ao biofilme periodontopatogênico, pelo uso da técnica de Polimorfismos de Comprimento de Fragmentos Terminais de Restrição (T-RFLP). Amostras de biofilme dentário supragengival e subgengival foram coletadas de 11 pacientes portadores de periodontite. O DNA amostral foi extraído e submetido à Reação em Cadeia da Polimerase (PCR) direcionada ao gene ribossomal 16S, utilizando-se iniciador senso marcado com molécula repórter fluorescente. Os produtos da PCR foram digeridos pelas endonucleases tetraméricas HhaI, MspI e RsaI e os fragmentos terminais de restrição (T-RFs) resultantes foram analisados em um sequenciador automatizado de DNA, gerando diferentes perfis de fragmentos para cada amostra. Ao todo, 19 T-RFs distintos foram detectados com a enzima RsaI (média = 6,4), 61 com MspI (média = 19,3) e 63 com HhaI (média = 16,3). Uma grande variabilidade nos perfis de restrição foi observada, sendo que 51% a 63% dos T-RFs foram detectados em menos de quatro amostras. A predição taxonômica de T-RFs in silico demonstrou a presença de gêneros bacterianos reconhecidamente periodontais, incluindo Actinomyces, Eubacterium, Fusobacterium, Haemophilus, Porphyromonas, Prevotella e Propionibacter. Embora alguns gêneros tenham sido encontrados em todas as amostras avaliadas, as análises de clusterização e estatística multivariada não demonstraram agrupamentos de perfis T-RFLP conforme paciente ou sítio amostral. Os resultados do estudo permitem concluir que a comunidade bacteriana do biofilme periodontopatogênico é bastante variável entre indivíduos, embora possua alguns gêneros predominantes
Abstract: The bacterial communities present in the oral cavity play an important role in maintaining healh/disease equilibrium. In this sense, studying the microbial compostition of the oral environment may contribute to attain a better precision in diagnosis of infectious diseases and, also, to develop efficient therapeutic approaches. Periodontitis is a disease that affects the supporting tissues of the tooth, characterized by a heightened immunologic response to bacteria present in dental biofilm. The broad microbial diversity present in the oral cavity, along with the various clinical features of periodontitis, highlight the necessity of further investigations on the composition of periodontopathic biofilm. The objective of this study is the characterization of the bacterial communities associated with periodontopathic biofilm, by use of the Terminal Restriction Fragment Length Polymorphism (T-RFLP) techique. Supra and subgingival biofilm samples were collected from 11 periodontitis subjects. Total DNA was extracted from the samples and submitted to the Polymerase Chain Reaction (PCR) targeting the 16S rRNA gene, with a fluorescently labeled forward primer. PCR products were digested with the tetrameric endonucleases HhaI, MspI and RsaI, and the resulting terminal restriction fragments (T-RFs) were analyzed in an automated DNA sequencer. In all, 67 T-RFs (mean = 17.3) were detected with RsaI endonuclease, 61 T-RFs with MspI (mean = 19.3) and 19 T-RFs (mean = 6.4) with HhaI. A great variability in the restriction patterns was observed, since 51% to 63% of T-RFs were detected in less than 4 samples, and two T-RFs were exclusively found in supragingival biofilm (p = 0.018). In silico taxonomical prediction of T-RFs demonstrated the presence of well-known periodontal species belonging to the Acinomyces, Eubacterium, Fusobacterium, Haemophilus, Porphyromonas, Prevotella and Propionibacter genera. Although some species were found in all samples, clustering and multivariate statistical analysis did not reveal evident groupings of T-RFLP profiles according to patient or sampling site. The results of this study indicate that the microbiota of periodontopathic biofilm is highly variable among subjects, albeit a core microbial community may be observed
Mestrado
Microbiologia e Imunologia
Mestre em Biologia Buco-Dental
Abu-Halaweh, Marwan, and n/a. "Molecular Methods for Campylobacter and Arcobacter Detection." Griffith University. School of Biomolecular and Biomedical Science, 2005. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20060223.084457.
Full textAbu-Halaweh, Marwan. "Molecular Methods for Campylobacter and Arcobacter Detection." Thesis, Griffith University, 2005. http://hdl.handle.net/10072/367268.
Full textThesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Biomedical Sciences
Full Text
Heuser, Camila. "Identificação molecular de comunidades microbianas presentes em plântulas cultivadas sob diferentes sistemas de cultivo in vitro." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-18102013-113045/.
Full textIn recent years, several protocols and technologies have been proposed for feasibility and optimization of micropropagation of different cultures as well as to reduce production costs. Among these, the use of liquid culture medium and the temporary immersion bioreactor system (TIB) have gained special attention. However, differences are observed among species and methodologies, being necessary more detailed studies for a better knowledge of the factors that affect the micropropagatiion systems. Recent studies, based on molecular techniques, have revealed that in vitro cultures are not axenic, as thought, presenting ubiquitous endophytic community. Knowing the importance of these microorganisms to field plants we would like to know more about their role in in vitro plants. In this scenario, this work proposes to compare the performance of in vitro cultures under different culture conditions: semisolid medium culture, liquid static and liquid medium under agitation, and where differences in in vitro performance were observed comparative molecular analysis of microbial community in the plantlets was performed. Bromeliads and sugarcane cultures were used seeking for model systems for these analyses. These experiments were conducted with Ananas comosus var. comosus (\'Imperial\' and \'Pérola\') and Aechmea nudicaulis cultured under liquid static medium and liquid under agitation, and with Vriesea hieroglyphica, we compared liquid static medium, liquid medium under agitation and TIB. For sugarcane (Saccharum spp. variety SP80-3280), liquid static medium and TIB was compared. Molecular analyses of Dyckia distachya plantlets, which had been grown in semisolid medium liquid static and liquid medium under agitation, were also carried out. Cultures that showed differences in performance among the systems evaluated were D. distachya, (with liquid medium under agitation as the best condition) and sugarcane (best treatment was BIT) and these were considered adequate to study the differences in the bacterial comunity of plants when grown in different in vitro conditions. The characterization of the microbial community of D. distachya was performed by T-RFLP (Terminal Restriction Fragment Length Polymorphism) and showed that the liquid medium under agitation, which had the highest number of shoots compare to the other culture conditions, also differed as to the relative abundance of Operational Taxonomic Units (OTUs). For sugarcane 16S rRNA gene clone libraries, as well as real-time PCR (qPCR) were performed. These analyses showed no significant differences between the libraries of the two treatments, however, BIT showed 3.54 times more copies of the 16S rRNA gene compared to cultures from static liquid medium, allowing us to infer a higher number of bacteria. This study provides strong evidence that the in vitro system used influences the microbial community present in plants
Cabral, C?ssia Michelle. "Fitorremedia??o por esp?cies arb?reas de solo contaminado com herbicida clomazone: efeito na morfologia, anatomia e rizosfera." UFVJM, 2012. http://acervo.ufvjm.edu.br:8080/jspui/handle/1/488.
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O crescimento da popula??o mundial ocasiona alta na demanda por alimentos. O processo produtivo gera importante montante de res?duos que funcionam como fontes poluidoras de ?gua, solo e ar. Anualmente s?o usados no mundo aproximadamente 2,5 milh?es de toneladas de agrot?xicos. Dentre estes se encontra o clomazone, do grupo das isoxazolidinonas, um inibidor da s?ntese de caroten?ides e altamente lixivi?vel. De acordo com a problem?tica apresentada objetivou-se com este trabalho verificar a toler?ncia, por meio de avalia??es de crescimento, intoxica??o, an?lises anat?micas e de diversidade microbiana do solo, assim como a capacidade remediadora de doze esp?cies florestais nativas. Para montagem do experimento foi utilizado o delineamento em blocos ao acaso com quatro repeti??es. Foram feitas 3 aplica??es do herbicida clomazone com intervalos de 20 dias (aos 60, 80 e 100 dias ap?s o plantio), cada aplica??o foi correspondente ? metade da dose comercial de 2 L ha-1. Para as avalia??es de crescimento foram mensuradas a altura da planta, o di?metro do caule, o n?mero de folhas, a ?rea foliar e o ac?mulo de biomassa seca. Para as verifica??es anat?micas foram coletadas 2 folhas de cada planta sempre aos 7 dias ap?s a aplica??o do herbicida, nas duas primeiras aplica??es. Por meio de avalia??es micromorfom?tricas foram medidas na sec??o transversal das folhas das esp?cies florestais, a espessura e a ?rea ocupada pelos tecidos: epiderme adaxial e abaxial, par?nquima pali??dico e par?nquima lacunoso. Para estimativa de intoxica??o pelas plantas testadas, avaliou-se o efeito do produto por meio de notas de toxicidade. Para verifica??o de capacidade fitorremediadora das esp?cies arb?reas procedeu-se a semeadura da esp?cie indicadora sorgo (Sorghum bicolor (L.) Moench.) para indicativo do res?duo do herbicida no solo. Posteriormente em amostras de solo provenientes do experimento procedeu-se a an?lise de T-RFLP com intuito de caracterizar a diversidade microbiana presente. As esp?cies florestais sobreviveram ? aplica??o de clomazone, sendo que I. marginata, C. ferrea e S. brasiliensis apresentaram maior toler?ncia ao herbicida em rela??o ?s an?lise de crescimento, seguidas de S. parahyba, H. serratifolius repetindo-se I. marginata para avalia??es da integridade anat?mica. No entanto, n?o foi verificado, nas condi??es do experimento, remedia??o do solo para a maioria das esp?cies testadas. Contudo plantas de sorgo tiveram crescimento normal quando cultivadas em solo onde antes havia I. marginata. Os resultados de T-RFLP confirmaram a diversidade microbiana diferenciada associada a rizosfera de I. marginata.
Disserta??o (Mestrado) ? Programa de P?s-Gradua??o em Ci?ncia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 2012.
Venturini, Andressa Monteiro. "Efeito do uso do solo e da rizosfera de cana-de-açúcar na estrutura e abundância de comunidades de Bacteria e do filo Verrucomicrobia." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-07082018-102457/.
Full textThe abundance and diversity of soil microbial communities can be influenced by many factors, mainly associated with soil type, its coverage and use. The soil microbiota has great importance due to the processes performed by its organisms, essential for all terrestrial ecosystems. Despite the great complexity associated with these studies, the factors that affect the microbial communities can be better explained through the research of specific groups. In this sense, the bacterial phylum Verrucomicrobia, a ubiquitous soil group, presents high abundance in different environments, which suggests its great ecological importance. But due to the difficulty of isolating its organisms, little is known about the ecology of the phylum. The present work was developed with the objective of analyzing the effect of land use changes and sugarcane rhizosphere on the structure and abundance of Bacteria and Verrucomicrobia communities. For this purpose, soil samples were collected in areas under different land uses in a sugarcane mill in Piracicaba (SP). The samples were used in two separate studies. In the first, the microbial communities present in soil samples obtained in the sampling areas were analyzed and, in the second, taken from a controlled experiment conducted in a greenhouse to analyze the effect of land use and, especially, the rhizosphere on the communities. The communities were evaluated for their abundance, by the qPCR technique, and structure, by T-RFLP. In the first study, the phylum diversity was also accessed with the development of 16S rRNA gene libraries. The results from the studies indicate that bacterial and, especially, the phylum community were affected by land use and the management adopted in each area, which evidences the importance of conservationist systems. The analysis of the clone library demonstrated that the phylum Verrucomicrobia presented greater diversity in native vegetation than in the sugarcane fields. Additionally, the incidence and abundance of the group subdivisions have been changed in accordance with land use. The structure and abundance of the communities were also influenced by the rhizosphere, results of great interest to the reserach of the phylum, since few studies have analyzed the rhizosphere effect on its organisms. Furthermore, the high abundance of the phylum found in the study, which has been commonly underestimated, emphasizes the importance of research with specific focus on groups of interest
Benitez, Maria Soledad. "Applied T-RFLP Analyses for the Identification and Characterization of Microbial Populations Associated With Damping-Off Incidence in a Transitional Organic Cropping System." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1218471106.
Full textBleul, Catrin. "Molekularbiologische Analyse mikrobieller Gemeinschaften in Talsperrensedimenten." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2004. http://nbn-resolving.de/urn:nbn:de:swb:14-1097570982718-83940.
Full textStauffert, Magalie. "Dynamique des communautés microbiennes en réponse à une contamination pétrolière dans des sédiments bioturbés." Thesis, Pau, 2011. http://www.theses.fr/2011PAUU3031/document.
Full textCoastal areas such as mudflats are affected by oil spills. In these environments, microorganisms play a crucial role in the fate of petroleum hydrocarbons. However, many factors influence microbial activities, especially the bioturbating organisms, which altered the oxygen penetration in sediments. The present work attempts to better understand the impact of petroleum contamination on microbial community associated with petroleum contamination in sediments with low and high bioturbation activity. This study is based on microcosm experiments with a device simulating tidal cycles. Marine sediments were maintained for 9 months in microcosms and subjected to four conditions: (i) no treatment (control), (ii) oil, (iii) bioturbation and (iv) oil and bioturbation. Chemical, microbiological and biological analyses were conducted throughout the experiment. The efficiencies of degradation of petroleum hydrocarbons were similar in both sediments. By molecular approaches, we assessed the dynamic of the functional and taxonomic diversity of the total and metabolically active communities during the oil contamination. Microbial communities showed significant structural rearrangements specific for each treatment that resulted in distinct microbial communities in both sediments. Hence, the overall microbial community structure was changed by bioturbating activity without changing the degradation capacity revealing a functional redundancy of the biodegradation capacity of hydrocarbons. This result was further supported by the isolation and characterization of hydro carbonoclastic communities
Marques, Martins Guilherme. "Communautés microbiennes de la baie de raisin : Incidence des facteurs biotiques et abiotiques." Thesis, Bordeaux 2, 2012. http://www.theses.fr/2012BOR21924/document.
Full textThe study of microbial communities associated with wine grapes under field conditions revealed changes in the size and structure during the berry ripening process, with levels rising gradually and reaching their highest value when the berries were over ripe. During this work several bacteria and fungi species, including fermentative yeast, have been isolated and identified. From cultured bacteria, over 44 species were identified from 21 genera. Concerning fungi population, among eight genera identified, the genus Aureobasidium was the most abundant. Our study reveals the impact of different abiotic and biotic factors over microbial community structure, density and metabolic activity. Comparing different vineyards in the same region, we observed that areas presenting more humid and colder climate favor the growth of microorganisms. Our results also show that the farming system has a clear impact on the microbial community, especially in the bacterial fraction. One of the reasons is the inhibiting effect of copper-based fungicides, frequently used in both organic and conventional farming systems. The presence of Botrytis cinerea in grape berries without visual symptoms of infection can change the microbial community of the grapes, increasing bacterial population density and diversity
Papapostolou, Anastasia. "Role of Genetics in Subgingival and Supragingival Bacterial Colonization." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1243453546.
Full textKirker, Grant Terral. "EFFECTS OF CHLOROTHALONIL AND BUTYLATED HYDROXYTOLUENE ON MICROBIAL COMMUNITIES INVOLVED IN THE DETERIORATION OF WOOD USING TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISM (T-RFLP) ANALYSES." MSSTATE, 2008. http://sun.library.msstate.edu/ETD-db/theses/available/etd-04022008-155301/.
Full textFerrari, Beatriz Maria. "Ocorrência e persistência de fragmentos de transgenia (milho Bt evento MON810) em solos agrícolas brasileiros e avaliação de sua comunidade microbiana." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-20052015-164759/.
Full textThe use of GM (genetically modified) crops has been questioned about the fate of transgenes is derived products on the environment. With the release of exudates from roots of GM plants and the decomposition of its residues, the amount of transgenic DNA in the environment increases, which can be adsorbed to the active surface of soil particles and/or be degraded by the action of microbial enzymes. Soil microbial communities can come into direct contact with these products, raising the probability of horizontal transfer of transgenic DNA fragments to soil microorganisms. Moreover, changes in exudates composition of GM plants and changes depending on the management practices may result in structural and functional alterations in the microbial community. Thus, it is necessary to evaluate the persistence of transgenes is derivatives in the soil and effects on microbial community. The objectives of this study were to assess the persistence of fragments 35S-hsp70, hsp70-cry1Ab and cry1Abplant from the genetic construct of Bt corn (event MON810) in different soil types and temperatures, in microcosm and field conditions; and to determine the abundance of 16S rRNA copy number of Bacteria, Firmicutes, Verrucomicrobria and Archaea and 18S rRNA of Fungi under the same conditions, and to evaluate the structure of bacterial communities in agricultural areas of Bt corn cultivation. In the first study, DNA from Bt corn MON810 was added to sandy and clay soils. As negative control, only sterile water was mixed with soil. Soil samples were incubated at 15 and 25°C. At the field, soils were sampled in three agricultural areas in Fátima do Sul, MS, in two consecutive years. After DNA extraction, fragments were quantified by qPCR. In the second study, the abundance of 16S rRNA of Bacteria, Firmicutes, Verrucomicrobria and Archaea and 18S rRNA of Fungi were determined and the structure of bacterial communities was evaluated by T-RFLP. The results showed that in microcosm conditions, hsp70-cry1Ab and cry1Ab-plants fragments persisted until 291 days and the 35S-hsp70 up to 180 days. The temperature and the type of soil did not affect the persistence of fragments. In field, the copy number of these fragments was greater in the second sampling. In the second study, the copy number of 16S rRNA of Bacteria increased with the addition of DNA from Bt corn in microcosm, and a reduction in copy number was observed for Archaea, Verrucomicrobia and Fungi. The results were not consistent for Firmicutes. Temperatures resulted in no effect in gene abundance, while the soil was effective only for Archaea and Verrucomicrobia. Agricultural areas with five years of Bt corn cultivation showed variations in bacterial community structure at the phylum level, and greater abundance of fungi in the second year of sampling, while in the area with a year of cultivation, a reduction in population of Firmicutes and Verrucomicrobia was observed. The largest effects on the microbial community were observed between the sampled years
Eschenhagen, Martin. "Molekulare Untersuchung zweier Belebtschlammanlagen unter besonderer Berücksichtigung der biologischen Phosphorelimination." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2004. http://nbn-resolving.de/urn:nbn:de:swb:14-1091188675328-95596.
Full textKeriuscia, Gokul Jarishma. "Eukaryotic diversity of miers valley hypoliths." Thesis, University of the Western Cape, 2012. http://hdl.handle.net/11394/4031.
Full textThe extreme conditions of Antarctic desert soils render this environment selective towards a diverse range of psychrotrophic microbial communities. Cracks and fissures in translucent quartz rocks permit an adequate amount of penetrating light, sufficient water and nutrients to support cryptic microbial development. Hypolithons colonizing the ventral surface of these quartz rocks have been classified into three types: cyanobacterial dominated (Type I),moss dominated (Type II) and lichenized (Type III) communities. Eukaryotic microbial communities were reported to represent only a minor fraction of Antarctic communities. In this study, culture independent techniques (DGGE, T-RFLP and clone library construction) were employed to determine the profile of the dominant eukaryotes, fungi and microalgae present in the three different hypolithic communities. The 18S rRNA gene (Euk for eukaryotes), internal transcribed spacer (ITS for fungi) and microalgal specific regions of the 18S rRNA gene, were the phylogenetic markers targeted for PCR amplification from hypolith metagenomic DNA. Results suggest that the three hypolith types are characterized by different eukaryotic, fungal and microalgal communities, as implied by nMDS analysis of the DGGE and T-RFLP profiles. Sequence analysis indicates close affiliation to members of Amoebozoa, Alveolata, Rhizaria (general eukaryote), Ascomycota (fungal) and Streptophyta (microalgal). Many of these clones may represent novel species. This study demonstrates that Dry Valley hypolithons harbour higher eukaryote diversity than previously recognised.Each hypolithon is colonized by specialized microbial communities with possible keystone species. The ecological role of the detected microorganisms in the hypolith environment is also theorized, and a trophic hierarchy postulated.
Altrichter, Adam E. "Landscape history and contemporary environmental drivers of microbial community structure and function." Thesis, Virginia Tech, 2010. http://hdl.handle.net/10919/31883.
Full textMaster of Science
Garcia-Blanco, Susana. "Testing the Resource-Ratio Theory As A Framework Supporting A Bioremediation Strategy For Clean-Up Of Crude Oil-Contaminated Environments." University of Cincinnati / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1098275222.
Full textGustafson, Aubree Marie. "T-RFLP analysis of bacterial 16S rRNA gene sequences isolated from river otter (Lontra canadensis) scat and parasite screening for the presence of Toxoplasma gondii." Scholarly Commons, 2009. https://scholarlycommons.pacific.edu/uop_etds/732.
Full textElsayed, Omniea. "Biodegradation of chloroacetanilide herbicides in wetlands." Thesis, Strasbourg, 2015. http://www.theses.fr/2015STRAJ003/document.
Full textChloroacetanilide herbicides are widely used in agriculture, and thereby contribute to environmental pollution. Their fate, including in redox-dynamic receptor ecosystems such as wetlands, remains poorly understood. In this work, microbial degradation of chloroacetanilides (metolachlor, acetochlor and alachlor) was investigated by emerging chemical and molecular biological approaches, at the lab-scale using microcosm columns, and in situ, in outdoor constructed wetlands designed for the treatment of chemical pollutants originating from agriculture.A novel compound-specific isotope analysis (CSIA) method was developed, and the results indicated biodegradation of chloroacetanilides in wetlands, which was also suggested by detection of ethane sulfonic acid and oxanilic acid degradation products. In lab-scale wetland microcosms, chloroacetanilides were mainly degraded in anoxic rhizosphere zones, suggesting a predominant role of anaerobic processes. Chiral chromatographic analysis of metolachlor revealed preferential degradation of the (S) enantiomer of metolachlor, and further confirmed the role of biological processes in chloroacetanilide dissipation. Changes in hydrochemical variables and hydraulic conditions correlated with differences in wetland bacterial composition detected by terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing analyses of the bacterial 16S rRNA gene, confirming the potential of DNA-based bioindicators for follow-up of ecosystem functioning.On the basis of this work, detecting and identifying the microorganisms and biochemical pathways responsible for chloroacetanilide degradation in wetlands, as well as developing bacterial gene-based indicators of wetland functioning, emerge as research objectives for the near future
Bijelovic, Jelena. "Identification of mould and blue stain fungi on wood using Polymerase Chain Reaction and Terminal Restriction Fragment Length Polymorphism." Thesis, Uppsala University, Department of Medical Biochemistry and Microbiology, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7100.
Full textWood inhabiting fungi oposes a great problem for preservation of wooden surfaces everywhere, being the main problem of economic losses of wooden products.
A reference collection consisting of 9 different genus constituting of 21 different strains of wood-inhabiting fungi was used for identification of unknown species of mould and blue stain fungi on wood. The fungus DNA from the samples was isolated from malt extract agar. PCR (Polymerase Chain Reaction) was conducted on rDNA ITS1 and ITS2 regions for amplification of the DNA. The 21 samples were collected to a reference collection for identification of unknown species of fungi on wooden field samples using PCR and T-RFLP (Terminal Restriction Fragment Length Polymorphism).
PCR-based methods, sequencing and T-RFLP were proven to be simple and
accurate methods for detection and identification of fungi in their early stage.
Bonilla, German Andres Estrada. "Efeito da inoculação de bactérias mobilizadoras de fósforo na compostagem e no desenvolvimento da cana-de-açúcar." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/11/11140/tde-29092015-164939/.
Full textSugarcane industry generates large amounts of waste, filter cake and ashes being the main solid wastes. One of the technologies developed for the management of this waste is composting. The application of compost has shown positive effects on the sugarcane culture with regard to phosphorus fertilization. The objectives of this study are: I. To study the diversity of bacterial communities during composting and the effect of inoculation of phosphorus mobilizing bacterial strains on the phosphorus availability in the final compost; II. To evaluate and compare the effects of the application of different sources of phosphorus and P mobilizing bacteria on the development of sugarcane and the effect on soil bacterial communities. Therefore, compost piles were installed at Usina São José da Estiva in Novo Horizonte, Brazil. Treatments consisted of piles with and without rock phosphate and with and without inoculation of Pseudomonas aeruginosa PSBR12 and Bacillus sp. BACBR1 strains. Samples were taken every two weeks for 60 days. In addition, the enzymatic and chemical composition of the compost was determined. The bacterial community was assessed through T-RFLP (restriction fragment length polymorphism) and was sequenced through the new generation platform MiSeqTM System (Illumina). The abundance of bacteria was evaluated by qPCR. In order to evaluate the effect of compost and of inoculating P mobilizing bacteria on sugarcane development, a greenhouse experiment was installed with sugarcane using compost, rock phosphate and triple superphosphate as P sources, besides inoculations, as follows: Inoculant 1: Pseudomonas sp. (PSBR10) Azotobacter sp. (AZTBR19), Rhizobium sp. (RIZBR01); and Inoculant 2: Bacillus simplex (BACBR04), Bacillus sp. (BACBR06), Rhizobium sp. (RIZBR01). The experiment was conducted during 75 days. At the end of the experiment the following parameters were analyzed: dry plant biomass, accumulation of P, N, and K in the shoot, and phosphatases in soil. Bacterial soil communities were sequenced through the new generation Illumina. The application of P mobilizing bacteria during composting decreased the Ca-linked P. Changes of the bacterial communities during composting were temporal. In the beginning, members of the order Lactobacillales were dominant and after 15 days a succession of bacterial communities occurred, when Bacillales and Clostridiales began to dominate. Bacterial communities are mostly influenced by the parameters pH, temperature and humidity. Moreover, in the greenhouse experiment, the use of inoculants (mainly inoculant 2) increased the accumulation of P, N and K in shoots in the treatments that received compost and triple superphosphate as P source. Inoculant application and compost addition modified soil bacterial community structures. Changes in the soil microbiome when inoculant was applied may be related to the increase in nutrients accumulation. The use of P mobilizing bacteria is a potential technology for use in agriculture, when composting waste from the sugarcane industry with rock phosphate or when increasing P fertilization efficiency in sugarcane in the field.
Eschenhagen, Martin. "Molekulare Untersuchung zweier Belebtschlammanlagen unter besonderer Berücksichtigung der biologischen Phosphorelimination." Doctoral thesis, Technische Universität Dresden, 2003. https://tud.qucosa.de/id/qucosa%3A24360.
Full textSpivey, Mary I. H. "The use of PCR and T-RFLP as a means of identifying sources of fecal bacteria pollution in the tidal creeks of New Hanover County, North Carolina." View electronic thesis, 2008. http://dl.uncw.edu/etd/2008-3/spiveym/maryspivey.pdf.
Full textKirker, Grant Terral. "Effects of chlorothalonil (CTN) and butylated hydroxy-toluene (BHT) on microbial communities involved in the deterioration of wood using terminal restriction fragment length polymorphism (T-RFLP) analyses." Diss., Mississippi State : Mississippi State University, 2008. http://library.msstate.edu/etd/show.asp?etd=etd-04022008-155301.
Full textConn, Vanessa Michelle, and vanessa conn@acpfg com au. "Molecular Interactions of Endophytic Actinobacteria in Wheat and Arabidopsis." Flinders University. School of Medicine, 2006. http://catalogue.flinders.edu.au./local/adt/public/adt-SFU20060320.171412.
Full textScheer, Maria. "Charakterisierung der Diversität von Mikroorganismen im Nationalpark “Unteres Odertal”." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2011. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-63999.
Full textPlassart, Pierre. "Pertinence des indicateurs microbiens dans l'évaluation de l'état des sols agricoles." Rouen, 2010. http://www.theses.fr/2010ROUES048.
Full textMost soils worlwide undergo modifications caused by human activities. For numerous agricultural soils, the intensive practices, as well as the chronical spreading of chemical inputs, lead to a decrease in these soils fertilkity. Yet, while these soils are in danger, only a few relevant soil status evaluation tools exist. The biological component has been neglected for a long time, though soil accomodates a high diversity level of organisms involved in biogeochemical cycles. Among these organisms, microorganisms are likely to be potential bioindicators of soil status. Thus, the aim of this work consists in identifying biological variables describing bacterial diversity that would be sensitive to soil status. Bacterial community structure (abundance, genetic and functionnal diversity) was assessed as a whole, but also through the analysis of Pseudomonas populations, a bacterial genus widely found in soils and sensitive to environmental disturbances. The experimental approach, from the field plot level to the microcosm level, consisted in the confrontation of the impacts of (1) soil copper contamination (agronomical dose x100), (2) natural disturbances (spatial and climatic), and (3) human caused disturbances (agricultural practices) on bacterial communities. The first part of this work was performed in situ on typical silty Haute-Normandie soils managed as grasslands and cultures, in order to define the natural spatial and temporal variation limits of different bacterial descriptors. Besides, this first part enabled the understanding each variable's sensitivity, and validated the different methodological approaches. Thus, the measured variables can be organized in two categories: those which rely on microorganisms cultivation would reflect recent soil disturbances, while those based on molecular approaches would reflect the agricultural history of field plots. In the second part, the impact of a copper contamination on the previously described variables was studied in microcosms. Results showed that variations in the bacterial community structure caused by a single copper contamination were minor, when compared with variations caused by season or agricultural practices. In the same time, a comparative analysis was performed between sieved soil and intact soil microcosms. This revealed that soil status can influence bacterial communities response to a copper contamination; indeed, soil physical disturbance (sieving) induced a transient response of bacterial communities to the copper contamination. This work lead to (1) building, for an agricultural silty soil, a microbiological reference system, which includes spatial and temporal fluctuations of the measured variables, (2) determining for each variable its sensitivity to natural and human impacts, and identifying the limits and complementarities of the cellular and molecular approaches, (3) organizing into a herarchy factors determining the genetic and functionnal sructure of bacterial communities, (4) validating the relevance of using the Pseudomonas genus in the evaluation of the impact of copper on soils
Gillespie, Jaimie. "The effects of saltwater intrusion on methanogen community abundance, structure, and activity." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/3175.
Full textDaniels, Camille Arian. "Microbial Landscapes of Corals and Ctenophores." Scholar Commons, 2011. http://scholarcommons.usf.edu/etd/3061.
Full textGumiere, Thiago. "Biogeografia de comunidades fúngicas em áreas cultivadas com cana-de-açúcar." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/11/11140/tde-15032013-091452/.
Full textThe sugarcane is nowadays, the most important crop in the State of São Paulo, serving as the raw material for the production of sugar and ethanol, besides many others by-products. Considering the expansion of agricultural barriers, and shifts in fields management, such cultivation is under a re-arrangement process, aiming to a higher productivity and sustainability. In order to achieve that, among other factors, the role of microbial communities present in soils can be essential to support plant development. However, a few is known about the microbial community under sugarcane crop production soils. Hence, this work intended to evaluate the fungi diversity and abundance in soils cultivated with sugarcane in the State of São Paulo, exploring areas under distinct chemical and physical attributes and also distinct management practices. It was also aimed to determine the occurrence of biogeographically patterns in the structure of such communities. Indeed, it was made the analysis of the fungal community structure by terminal restriction fragment length polymorphism (T-RFLP), together with the quantification of these communities by real time PCR (qPCR) in 476 soils samples, collected in 11 areas cultivated with sugarcane (mills). Within this dataset, it was found that chemical, physical and management attributes explain higher values of variance within each sampled area, but explain little about the total variance of data, suggesting the occurrence of biogeographically patterns in fungal communities in this environment. It was confirmed by the statistical significance of the correlation between distance and dissimilarity of fungal communities, supporting the generation of very first biogeographically maps in such soils. Additionally, the abundance of fungi revealed to be related with sugarcane productivity, indicating this issue as one of the factors modulating the sugarcane productivity in the evaluated areas.
Calbrix, Raphaël. "Impact des intrants organiques et des conduites culturales sur la biomasse microbienne et la diversité des bactéries telluriques." Rouen, 2005. http://www.theses.fr/2005ROUES028.
Full textThe aim of this work is to analyse the effects of four different organic products (turkey manure, compost of turkey manure and ligneous wastes, sewage sludge and compost of sewage sludge) on soil microbial communities in function of agricultural managements, during a 24 months kinetic. The microbial communities were characterised in a quantitative point of view (enumeration of heterotrophic cultivable bacteria, assay of soil total, microbial carbon assay) and in a qualitative one by potential metabolic fingerprinting (Biolog) and genetic structure of soil bacterial communities (T-RFLP 16S rDNA). A transitory impact specific to the different organic products was shown. The impact of organic products on microbial biomass and on bacterial community structure seemed to depend on their rate of lignin (Van Soest) and of mineralisable carbon. The influence of the tillage and the vegetation was revealed by the evolution of bacterial community structure during the 24 months of the experiments
Fourçans, Aude. "Dynamique des communautés bactériennes detapis microbiens soumis aux stressenvironnementaux." Phd thesis, Université de Pau et des Pays de l'Adour, 2004. http://tel.archives-ouvertes.fr/tel-00151969.
Full textcommunautés bactériennes de tapis microbiens afin de comprendre leurs fonctionnements et
leur mécanismes d'adaptation face aux stress environnementaux. De part le développement
dans des habitats très variés et soumis à des variations des conditions environnementales
importantes, les tapis microbiens constituent des modèles de choix pour ce type d'études. La
biodiversité bactérienne a principalement été abordée par T-RFLP (Terminal Restriction
Fragment Length Polymorphism), approche moléculaire d'écologie microbienne.
Premièrement, ce travail a porté sur la description de deux tapis microbiens
photosynthétiques présents sur deux sites différents de salinité distinctes, marin (Iles
Orcades), et hypersalé (Marais salants de Camargue). La combinaison de différentes
approches d'analyses ont permis d'obtenir une image à l'échelle du micromètre de ces tapis.
Ainsi, la diversité bactérienne des principales communautés (eubactéries, bactéries
phototrophes pourpres, bactéries sulfato-réductrices) de ces tapis microbiens a été décrite par
l'approche moléculaire de T-RFLP. Les résultats de cette analyse, associés à ceux d'analyses
biogéochimiques, moléculaire DGGE (Denaturing Gradient Gel Electrophoresis),
microscopiques (CLSM), et de biomarqueurs lipidiques a permis de relier les communautés
bactériennes présentes et d'appréhender leurs rôles écologiques au sein de ces écosystèmes
complexes. Ces deux tapis bien que très différents révèlent une organisation très fine,
constituée de couches distinctes verticales de quelques micromètres, où s'agencent les
populations bactériennes en fonction de leurs caractéristiques physiologiques et des
conditions environnementales. Le tapis de Camargue est dominé en surface par les
cyanobactéries filamenteuses, principalement Microcoleus chthonoplastes. De plus, la
distribution des bactéries phototrophes pourpres et sulfato-réductrices est répartie en fonction
des gradients mesurés de sulfure, oxygène et lumière. Le tapis des îles Orcades est au
contraire dominé par les bactéries pourpres, très diversifiées, principalement du genre
Thiocapsa. Les cyanobactéries y sont faiblement représentées. La diversité bactérienne
phototrophes et sulfato-réductrices est très finement organisée le long de gradients physicochimiques.
Dans un deuxième temps, la distribution spatio-temporelle du tapis microbien de
Camargue en fonction du cycle nycthéméral a été étudiée. Des comportements adaptatifs chez
les bactéries pourpres, les cyanobactéries et les bactéries sulfato-réductrices ont ainsi pu être
révélés. Parmi ces réponses aux variations des microgradients de sulfure et d'oxygène, la
migration a été mise en évidence chez un grand nombre de ces microorganismes.
L'analyse de l'impact d'hydrocarbures sur les tapis microbiens de Guérande et de
Camargue a été le troisième point abordé. L'influence des paramètres environnementaux sur
la dégradation naturelle du pétrole Erika a pu être démontrée. De plus, l'impact réel de la
pollution sur les communautés du tapis a été observé montrant une succession de différentes
communautés bactériennes. Ceci révèle les capacités d'adaptation de ces écosystèmes face à
ce stress d'hydrocarbures. Même si la dégradation par voie microbiologique n'a pu être mise
en évidence dans ces systèmes, l'analyse de la diversité des gènes codant pour les
dioxygénases montre une grande diversité, suggérant que les tapis microbiens possèdent un
potentiel de dégradation important.
Ce travail a permis de mettre en évidence l'organisation dynamique des bactéries au
sein de tapis microbiens, et d'approcher leurs comportements adaptatifs vis à vis des stress
soumis.
Schreiber, Olof. "Microcirculation, Mucus and Microbiota in Inflammatory Bowel Disease." Doctoral thesis, Uppsala universitet, Integrativ Fysiologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-112718.
Full textOrmiston, Anna Kathleen. "ENVIRONMENTAL, SPATIAL AND TEMPORAL EFFECTS ON MICROBIAL COMPOSITION IN LAKE ERIE." Kent State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=kent1461444253.
Full textLenz, Erin Jennifer. "Rhizobial T-RFLP analysis for differentiating soils and habitats." Diss., 2008. http://proquest.umi.com/pqdweb?did=1606926031&sid=2&Fmt=2&clientId=3552&RQT=309&VName=PQD.
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