Rozprawy doktorskie: „T-RFLP”

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Rocha, Lidianne Leal. "Estudo de comunidades bacterianas de solos do Manguezal da Barra Grande, IcapuÃ 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.

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Os manguezais sÃo ecossistemas entremarÃs produtivos e biologicamente importantes que ocorrem em regiÃes tropicais e subtropicais do mundo. Ãreas de manguezais nÃo perturbados fornecem habitats para uma variedade de plantas, animais e microrganismos. Estes ecossistemas recebem materiais sedimentares do mar e continente, tornando-se uma Ãrea de transiÃÃo com elevada produtividade. Importantes processos, tais como ciclagem de nutrientes, estÃo diretamente conectados Ã atividade e diversidade das comunidades microbianas dos solos do manguezal. No entanto, devido a sua localizaÃÃo estratÃgica, manguezais tÃm sido amplamente impactados por todo o mundo. A compreensÃo da estrutura e das funÃÃes das comunidades microbianas e suas adaptaÃÃes Ãs alteraÃÃes ambientais resultantes de xenobiÃticos, alteraÃÃes climÃticas e a prÃtica industrial, tais como a exploraÃÃo petrolÃfera, Ã essencial para manter ou restabelecer funÃÃes desejÃveis do ecossistema. Dessa forma, o presente estudo investigou a estrutura de comunidades bacterianas de amostras de solos do manguezal da Barra Grande, IcapuÃ (37Â 20âW, 4Â 40âS), por mÃtodo independente de cultivo usando Polimorfismo do Tamanho de Fragmentos de RestriÃÃo Terminal (T-RFLP) e tambÃm avaliou o mÃtodo dependente de cultivo (enriquecimento) para isolar cepas de bactÃrias com potencial para degradar petrÃleo e n-Hexadecano. Um total de trÃs pontos foi amostrado ao longo do manguezal, com 150 metros de distÃncia entre cada um deles. Temperatura, pH, salinidade, matÃria orgÃnica e granulometria dos solos foram medidas. AnÃlises de T-RFLP foram feitas apÃs a digestÃo de DNA genÃmico com as enzimas HhaI e MspI e o nÃmero e diversidade de Unidades TaxonÃmicas Operacionais (OTU) de cada amostra foi analisado pelo programa T-Align (Applied Biosystems). A cepa selecionada para testes de diferentes concentraÃÃes de n-Hexadecano foi identificada pelo seqÃenciamento do gene do rRNA 16S. Esta cepa foi tambÃm avaliada em relaÃÃo Ã susceptibilidade a radiaÃÃo UV e antibiÃticos. Os resultados mostraram que as comunidades bacterianas de solos do manguezal sÃo semelhantes em nÃmero de OTUs, mas diferem em composiÃÃo. Provavelmente a peculiaridade das variÃveis fÃsico-quÃmicas e granulometria do solo sÃo responsÃveis pelas diferenÃas na composiÃÃo e estrutura das comunidades bacterianas. Dezoito cepas de bactÃrias foram isoladas de culturas de enriquecimento com petrÃleo e quatro cepas mostraram potencial particular para degradar n-Hexadecano. Uma cepa identificada como Acinetobacter sp. IC18 foi caracterizada como uma boa degradadora de hidrocarboneto, pois foi capaz de degradar 1% do n-Hexadecano em 48 horas. Esta cepa tambÃm utilizou cerca de 30% de uma concentraÃÃo total de 20% (v/v) de n-Hexadecano durante o mesmo perÃodo de incubaÃÃo. AlÃm disso, IC18 foi susceptÃvel a vÃrios antibiÃticos e resistente Ã radiaÃÃo UV. Em conclusÃo, a estrutura da comunidade bacteriana de solos do manguezal da Barra Grande parece nÃo ser afetada pela presenÃa da exploraÃÃo petrolÃfera em IcapuÃ. AlÃm disso, os solos deste manguezal sÃo colonizados por vÃrias cepas com potencial para degradar hidrocarbonetos, que Ã particularmente interessante em virtude do risco de derramamentos de petrÃleo.

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Mendes, 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/.

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Os manguezais tropicais são considerados um dos ecossistemas mais produtivos do mundo, sendo caracterizados pela alta taxa de ciclagem de matéria orgânica e nutrientes que ocorre entre os oceanos e os ambientes terrestres. Embora os manguezais sejam considerados áreas de proteção ambiental, a destruição desses ambientes é progressiva, devido a atividades industriais e portuárias nos estuários. Nos manguezais, a ciclagem de nutrientes está diretamente relacionada às atividades e a diversidade das comunidades microbianas presentes no solo. Este trabalho está inserido em um projeto mais amplo dentro do programa BIOTA/FAPESP, no que tange aos estudos da biodiversidade no Estado de São Paulo e utilização dessa biodiversidade de modo sustentável. O objetivo deste trabalho foi avaliar as estruturas e diversidade das comunidades de Bacteria, Archaea e Fungi presentes no solo de manguezal preservado da Ilha do Cardoso-SP. As amostras foram analisadas pelas técnicas de T-RFLP, ARISA, clonagem e seqüenciamento a fim de obter uma caracterização das estruturas das comunidades microbianas de uma área de manguezal preservado em comparação com os ambientes adjacentes de restinga e floresta e também a um manguezal antropizado. Os resultados permitiram concluir que o manguezal possui características exclusivas, com a presença de organismos distintos, revelando um possível potencial biotecnológico a ser explorado. Adicionalmente, os dados revelaram que a ação antrópica afetou as estruturas dessas comunidades de modo a ser notada uma sensível diminuição de diversidade no manguezal antropizado, evidenciando, dessa maneira, a importância da preservação desse ecossistema
The 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

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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.

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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/.

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Os fungos representam cerca de 75% da biomassa microbiana em áreas florestais, desempenhando funções importantes, desde a mineralização dos resíduos orgânicos até a disponibilização de nutrientes para plantas por meio das associações micorrízicas, o que influencia a ciclagem de nutrientes e, consequentemente, o crescimento das árvores. O objetivo desse trabalho foi avaliar a comunidade de fungos do solo, da rizosfera e do sistema radicular de Eucalyptus grandis e Acacia mangium plantados em monocultivos e em consórcio, e encontrar respostas para os padrões observados por meio da correlação com os atributos físicos, químicos, biológicos e a profundidade do solo. A coleta das amostras foi realizada na Estação Experimental de Ciências Florestais de Itatinga, em 2016, quando as plantas estavam com 2 anos de idade. Foram coletadas amostras em quatro tratamentos: monoculturas de E. grandis e de A. mangium e consórcios de E. grandis e de A. mangium, nos quais foram construídas trincheiras para coleta das amostras nas camadas de 0-10, 10-20, 20-50 e 50-100 cm de profundidade. Foram caracterizados os atributos físicos e biológicos do solo e os atributos químicos do solo, da rizosfera e das raízes. Para a avaliação micorrízica, foi quantificado o número de esporos de fungos micorrízicos arbusculares (FMA) e as taxas de colonização radicular por FMA e por fungos ectomicorrízicos. Foi avaliada a morfologia das estruturas das micorrizas arbusculares e ectomicorriza (ECM). A estrutura da comunidade de fungos do solo e da rizosfera foi avaliada por meio da técnica de Terminal restriction fragment length polymorphism (T-RFLP). Para isso, o DNA foi amplificado utilizando os primers ITS1f-FAM e ITS4 e a restrição dos fragmentos foi realizada com a enzima HaeIII. A abundância de cópias do gene ITS do solo e da rizosfera foi quantificada por PCR quantitativo (qPCR), utilizando os primers ITS1f e 5.8s. Os atributos físicos, químicos e biológicos tiveram poucas variações entre os tratamentos avaliados, sendo as maiores diferenças encontradas entre as profundidades. O número de esporos (<29) e as taxas de colonização micorrízica (<48%) foram baixos em todos os tratamentos, e se reduziram com o aumento da profundidade. As plantas de A. mangium não formaram micorrizas arbusculares. Nas raízes de E. grandis, não houve a formação de arbúsculos, mas foi verificada a presença de hifas enroladas (hyphal coils), estrutura de micorriza do tipo Paris. A anatomia das ECM confirmou a colonização destes fungos nas raízes das plantas estudadas. O qPCR mostrou maior abundância de genes ITS na rizosfera em relação ao solo, assim como nas camadas superficiais (0-10 cm) em relação às mais profundas (10 cm abaixo). A Análise de Coordenadas Principais revelou diferenças na estrutura das comunidades de fungos nos tratamentos estudados, principalmente para a região da rizosfera, diferenciando o perfil de fungos do monocultivo de E. grandis dos demais tratamentos, assim como a influência da A. mangium na estruturação da comunidade. A análise de redundância mostrou a influência de alguns atributos químicos nas taxas de colonização e estruturação da comunidade. Dessa forma, conclui-se que em sistema de consórcio, uma espécie de planta parece ser mais influente do que a outra na estruturação da comunidade de fungos e essa influência é mais evidente na rizosfera. Além disso, os atributos químicos são fatores importantes na organização da comunidade fúngica.
The 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.

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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.

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Take-all of wheat is caused by the soil-borne fungus Gaeumannomyces graminis var. tritici (Ggt), and is a widespread and destructive disease in temperate climates around the world where losses may be as high as 50%. Several practices are used to limit the disease on susceptible crops, including tillage, rotation, choice of variety, N fertilizer, and chemical and biological seed treatments. In relation to biological control, it is necessary to better understand the effects of different treatments on microbial dynamics in the rhizosphere and on roots.

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Fornazari, 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/.

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O estufamento de embalagens a vácuo de carnes refrigeradas, também conhecido como blown pack, é atribuído a bactérias psicrófilas e psicrotróficas, dentre as quais fazem parte algumas espécies de clostrídios, enterobactérias e bactérias lácticas. A capacidade desses microrganismos crescer em temperaturas de refrigeração adequadas torna um desafio o seu controle pela indústria. O Brasil é um dos grandes produtores de carne bovina no mundo e apesar da importância que a indústria de carne representa para o país, existem poucos estudos sobre as possíveis causas da deterioração do tipo blown pack. A importância deste trabalho fundamenta-se na escassez de pesquisas sobre esse problema que afeta a indústria de carne. O objetivo dessa pesquisa foi avaliar a presença dos principais microrganismos envolvidos na deterioração tipo blown pack, com ênfase em clostrídios, enterobactérias e bactérias láticas. Assim, o método Terminal- Restriction Fragment Length Polymorphism, disponível no laboratório de Biologia Molecular do CENA-USP, foi empregado por permitir um diagnóstico rápido e preciso para detecção de microrganismos. Foram analisadas 15 amostras de carne bovinas refrigeradas, embaladas a vácuo e estufadas, provenientes de frigoríficos dos estados de São Paulo, Mato Grosso do Sul e Goiás. Os cortes utilizados para as análises foram contrafilé, músculo, alcatra, cupim, picanha e filé de costela. As amostras apresentavam características de deterioração tipo blown pack dentro da data de validade, com períodos armazenamento variando de 30 a 120 dias. Foram identificadas as espécies Clostridium algidicarnis, Clostridium gasigenes, Clostridium putrefaciens, Clostridium frigidicarnis, Lactobacillus sakei, Hafnia alvei e Serratia liquefaciens pela técnica T-RFLP, que se mostrou uma excelente ferramenta de identificação microbiana nas amostras de carne. Devido à alta prevalência de enterobactérias nas amostras de carnes detectadas pela técnica de T-RFLP, foram realizadas análises convencionais com isolamento e identificação de enterobactérias, a fim de confirmar a presença destes microrganismos viáveis e cultiváveis nas amostras. As espécies de enterobactérias cultivadas e identificadas foram H. alvei, Ser. liquefaciens, Citrobacter braakii, Pantoea sp e Yersinia enterocolitica, sendo esta última potencialmente patogênica e de interesse em saúde pública. Observou-se que a H. alvei foi a espécie predominante nas amostras avaliadas, tanto pela técnica de T-RFLP como pelas análises microbiológicas convencionais. Com o objetivo de complementar os resultados, foram realizadas análises convencionais de cultivo visando o isolamento de Clostridium estertheticum e Clostridium gasigenes nas amostras de carne. A técnica de PCR foi empregada com a finalidade de identificação dos isolados obtidos.
The 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.

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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.

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FundaÃÃo de Amparo Ã Pesquisa do Estado do CearÃ
The 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 Ã 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, Ã 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 Ã 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.

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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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PAES, F. A. Análise de comunidades microbianas de solo de manguezal por T-RFLP e microarranjos de DNA. 2008. XVI; 128 f. Dissertação (Mestrado em Ciências Marinhas Tropicais) - Instituto de Ciências do Mar, Universidade Federal do Ceará, Fortaleza, 2008.
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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.

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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/.

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A cana-de-açúcar é uma das principais culturas do sistema agrícola brasileiro, e apresenta-se atualmente em plena expansão. Porém o uso do solo e a implementação de diferentes tecnologias de manejo têm originado alterações no equilíbrio ambiental, onde importantes interações microbianas ocorrem de forma essencial para o desenvolvimento vegetal. Dentre a vasta diversidade de microrganismos do solo, destacam-se os fungos micorrízicos, organismos intimamente associados as raízes das plantas, auxiliando a mesma, dentre outras formas, na obtenção de água e nutrientes. Estes fungos, no entanto, interagem também com outros organismos do solo, como por exemplo, com a comunidade bacteriana presente neste ambiente. Desta forma, o presente trabalho buscou estudar a dinâmica de interação entre cana-de-açúcar e o fungo micorrízico arbuscular (FMA) G.clarum em solos com diferentes composições da comunidade bacteriana. A metodologia utilizada foi a \'diluição para extinção\', onde diluições seriadas (10-1; 10-3; 10-6 e 10-9) de um solo natural foram usadas para inocular o solo estéril. Sobre esta base, foi monitorada pelo período de 60 dias, a colonização da planta pelo FMA e a estruturação das comunidades bacterianas. Como resultado, foi observada uma maior colonização das raízes de cana-de-açúcar para os tratamentos inoculada com menores diluições da comunidade original (solo natural e diluições 10-1 e 10-3), sendo da mesma forma observada uma distinção entre as comunidades bacterianas destes tratamentos para os demais. Estabelecendo correlações entre os grupos microbianos e as taxas de colonização micorrízica, foi possível nomear, com base no sequenciamento massivo da região V6 do gene ribossomal 16S DNAr, a alteração conjunta da micorrização com mudanças nos grupos de Actinobacteria,Bacteriodetes,Firmicutes,Proteobacteria,Verrucomicrobiae Acidobacteria. Concluindo, este trabalho demonstra a dependência que um processo importante, como a micorrização, possui da comunidade bacteriana do solo, e indica que em áreas degradadas, com menores níveis de diversidade bacteriana, tal processo pode ocorrer com menor eficiência.
Sugarcane 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.

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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/.

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A contaminação bacteriana por espécies dos gêneros Lactobacillus, Bacillus e Leuconostoc entre outras bactérias lácticas é um dos principais fatores que afetam o rendimento da fermentação alcoólica. A formação de biofilmes acaba protegendo as bactérias e é uma fonte permanente de contaminação. Objetivando caracterizar tais contaminações em (1) biofilmes de centrífuga, dorna, trocador de calor e tubulação de água e (2) melaço, mosto, levedo, levedo tratado (com H2SO4) e vinho, amostras foram coletadas em diferentes períodos de um sistema fermentativo de alto teor alcoólico (16%). As enzimas de restrição AluI, BstUI, HaeIII, HinfI, MseI e MspI utilizadas nas análises de T-RFLP foram definidas por análises in silico com sequências do gene 16S rRNA de contaminantes freqüentes. Essas enzimas geram uma maior quantidade de T-RFs únicos entre 30 e 650 pb. Os DNAs extraídos das amostras foram submetidos às análises de T-RFLP para obtenção do perfil molecular das comunidades microbianas dos pontos de coleta. Os índices de diversidade de Shannon foram calculados com base no número dos T-RFs. Foram realizadas as análises dos componentes principais (PCA) e a inferência filogenética dos contaminantes com base nos perfis dos T-RFs. A quantificação dos principais táxons contaminantes foi feita por qPCR utilizando primers específicos delineados neste estudo e considerando a média de cópias do gene 16S rRNA presentes no genoma de cada táxon bacteriano. Na primeira coleta o biofilme de água apresentou maior índice de diversidade microbiana e na segunda, melaço e mosto. PCA sugere que os biofilmes (e não as fontes externas) são os principais contaminantes desse processo fermentativo devido as suas semelhanças com a composição das outras comunidades analisadas. Espécies de Lactobacillus e Bacillus predominaram entre as amostras da primeira coleta. Halomonas, Streptococcus, Lactococcus e Pseudomonas foram detectados em amostras de biofilme e em amostras líquidas, sendo os principais contaminantes provindos de biofilme no momento da primeira coleta. Na segunda coleta Bacillus foi o principal contaminante e novamente gêneros produtores de ácido lático como Streptococcus, Lactobacillus e Staphylococcus foram os mais freqüentes. Os resultados concordam com o reportado na literatura sobre sistemas fermentativos convencionais. Apenas os primers desenhados para amplificação do gene 16S rRNA de Burkholderia, Pseudomonas e Weissella apresentaram especificidade em testes com isolados. Halomonas sp. foi encontrada em biofilme de dorna através do sequenciamento utilizando primers para esse gênero. Halomonas pode produzir levânio podendo haver o consumo da sacarose disponível para fermentação. Biofilme da centrífuga teve a maior quantidade de micro-organismos nos dois momentos de coleta (1,93E+06 UFC.mg-1 e 2,14E+07 UFC.mg-1, respectivamente) assim como as amostra de levedo entre as amostras líquidas (1,03E+08 UFC.ml-1 e 2,96E+06 UFC.ml-1, na primeira e segunda coleta, respectivamente), indicando níveis consideráveis de contaminantes. Burkholderia e Pseudomonas foram os mais abundantes entre as amostras de biofilmes da primeira e segunda coleta. Nas amostras líquidas Burkholderia apresentou-se em maior quantidade na maioria das amostras da primeira coleta; enquanto Pseudomonas e Weissella em geral predominaram equivalentemente entre as amostras da segunda coleta
Bacterial 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

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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/.

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O óxido nitroso (N2O) é um importante gás de efeito estufa (GEE) e, nos ecossistemas terrestres, é produzido principalmente pelo processo de desnitrificação. Esse ocorre em condições anaeróbias e, portanto, é fortemente estimulado pelo aumento do teor de umidade do solo. Entretanto, solos sob diferentes usos podem exibir taxas de emissão de N2O distintas, mesmo quando apresentam teores de umidade equivalentes. Ainda não está claro se isso se deve somente ao fato de os mesmos diferirem quanto a atributos físicos e químicos capazes de afetar a atividade dos organismos desnitrificantes ou se também se deve à diferenças com relação ao tamanho de suas populações. O presente trabalho foi desenvolvido com o objetivo de compreender as relações entre os fluxos de N2O, a umidade e a abundância de genes bacterianos envolvidos no processo de desnitrificação (nirK, norB e nosZ) em solos de floresta, pastagem e cultivo de cana-de-açúcar, utilizando um experimento de microcosmos. Amostras de solo foram coletadas na fazenda Capuava, situada no município de Piracicaba, SP. Os microcosmos estabelecidos a partir das mesmas foram mantidos com diferentes teores de umidade (original e ajustados para atingir 60% e 90% da capacidade de campo) e incubados a 30 °C por 30 dias. Ao longo do período de incubação, os fluxos de N2O a partir desses solos foram analisados por cromatografia gasosa. Amostras coletadas do interior dos microcosmos, antes e depois da aplicação dos tratamentos, foram comparadas quanto à estrutura de suas comunidades bacterianas, utilizando a técnica de T-RFLP, e quanto à abundância dos genes 16S rRNA, nirK, norB e nosZ, através da técnica de qPCR. Somente os solos que tiveram sua umidade ajustada para 90% da capacidade de campo exibiram incrementos significativos na produção de N2O. Em tais amostras, também foi verificada a alteração da estrutura das comunidades bacterianas e do número de cópias dos genes norB e nosZ. Apenas este último, no entanto, apresentou uma correlação positiva com a umidade do solo. A abundância dos genes avaliados não apresentou correlações significativas com as taxas de emissão do GEE. Por outro lado, as emissões cumulativas de N2O se correlacionaram positivamente com as quantidades de genes desnitrificantes presentes inicialmente nas amostras de solo. Estes genes se mostraram mais abundantes nas amostras de pastagem e floresta, as quais apresentavam maiores teores de matéria orgânica, carbono, nitrogênio, nitrato e argila do que aquelas provenientes da área cultivada com cana-de-açúcar. Tais resultados demonstram que o conteúdo de água do solo afeta a taxa de emissão de N2O, mas que isso não se deve a alterações na abundância das bactérias envolvidas no processo, como as que carregam os genes nirK, norB e nosZ. Aparentemente, no entanto, quantidade de GEE que o solo é capaz de produzir está relacionada ao tamanho das populações desses organismos desnitrificantes.
Nitrous 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.

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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.

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Intestinal flora of wild chimpanzee has not been studied. Fecal flora analyses currently give insight to this environment. We collected feces from twelve human-habituated wild chimpanzees in each of three age groups: four juveniles, four sub-adults, and four adults. We analyzed fecal samples using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) of amplified 16S rRNA genes to determine bacterial diversity present. Between 1 and 14 terminal-restriction fragments (T-RFs) were observed in each sample. A total of 26 unique T-RFs were produced from the samples and ranged in size from 92 to 837 base pairs (bps). Twenty-four of these T-RFs corresponded to five bacterial phyla: Actinobacteria, Bacteroidetes, Firmicutes, Mollicutes, and Proteobacteria, as well as uncultured and unidentified bacterial species. The remaining T-RFs corresponded solely to uncultured or unidentified bacteria. Firmicutes was the most common phylum, observed in 11 of the samples. Bacteroidetes was the second-most common phylum, detected in 8 of the samples. Principal Components Analysis (PCA) revealed a discrete clustering of 10 samples when looking at components one and two, and a clustering of 11 samples when looking at component three. These three components accounted for 72.5% of the variation within the data. Morisita indices were computed to compare T-RF profiles of two samples at a time, and were between 0 and 0.886. Results indicated that some fecal bacterial profiles were similar in the study group, but ultimately varied between samples when compared two at a time. Specific diet, physiology, and environmental reservoir exposure may play large roles in shaping such profiles.
Master of Science

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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.

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Empirical studies have shown that algal- and detrital-based food web components are coupled in many pelagic systems as algal carbon enhances bacterioplankton production and growth efficiencies. Such phyto-bacterioplankton coupling impacts carbon flow through plankton food webs, yet the extent of coupling is poorly understood in systems receiving large amounts of allochthonous carbon. To investigate this issue, bacterioplankton abundance (BA) and community composition were compared to chlorophyll a concentrations and phytoplankton production in the tidal-freshwater James River (VA). BA averaged 107 cells mL-1 and was significantly related to chlorophyll a, phytoplankton production, and DOC concentrations. Analysis of DOC quality using fluorescence spectroscopy revealed that the fulvic DOC fraction was dominated by allochthonous compounds. However, estimates of DOC C:N and DOC turnover rates indicated that DOC was more labile in the lower part of the study reach where BA was highest. T-RFLP analysis of 16s rDNA showed that bacterioplankton community composition significantly varied between the upper and lower portions of the sampling reach. These findings suggest that coupling of food web components is an important pathway affecting carbon cycling within the tidal-fresh water James River.

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Lima, 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/.

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As Terras Pretas de Índio (TPIs) na Amazônia Brasileira são altamente férteis e o seu conteúdo químico parece não exaurir mesmo em condições de floresta tropical. Por essa razão, são frequentemente procuradas pelas populações locais para o cultivo de subsistência. A importância das comunidades microbianas tem aumentado o interesse em compreender a relação entre o uso da terra, as comunidades de plantas, os micro-organismos e os processos do ecossistema. Portanto, o objetivo principal desta pesquisa foi investigar as comunidades bacterianas sob a influência da cobertura vegetal em sistemas de uso da terra (floresta secundária e plantio de mandioca) e na rizosfera de plantas leguminonas nativas em comunidades de bactéria das TPIs. Além disso, investigou-se também as bactérias desnitrificantes nesses solos. A área de estudo está localizada na Estação Experimental do Caldeirão, pertencente à Embrapa Amazônia Ocidental, no município de Iranduba-AM. A funcionalidade da comunidade bacteriana foi determinada pela Análise de Perfil Fisiológico da Comunidade Microbiana (CLPP), a estrutura da comunidade bacteriana foi acessada por Polimorfismo do Tamanho do Fragmento de Restrição Terminal (T-RFLP), a composição e distribuição das comunidades bacterianas foram determinadas por sequenciamento em larga escala (pirosequenciamento), e para quantificar as bactérias desnitrificantes foi utilizada a técnica de PCR quantitativa (qPCR). Os estudos foram realizados no laboratório de Biologia Celular e Molecular (CENA / USP) e no departamento de Biogeoquímica (Max Planck Institute for Terrestrial Microbiology). A análise de T-RFLP mostrou que o uso da terra e a sazonalidade afetaram as comunidades bacterianas na TPI, e mostrou também um claro efeito da rizosfera nas comunidades bacterianas. CLPP demonstrou que a atividade funcional da TPI não foi afetada pela sazonalidade. Além disso, a tecnologia de pirosequenciamento foi uma ferramenta importante para diferenciar filotipos raros. Diferenças distintas de alguns filos bacterianos da rizosfera foram observadas, indicando que a zona de raiz contribui para moldar essas comunidades. A abundância relativa do gene nirK não foi afetada pelo uso da terra nos dois tipos de solos. Alterações na estrutura das comunidades dos genes nirK e nosZ foram observadas em ambos os tipos de solos. As comunidades desnitrificantes na TPI pareceram ser mais influenciadas pelo uso da terra do que pela sazonalidade, e ACH foi mais influenciada pelas variações de sazonalidade.
Amazonian 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.

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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/.

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O Brasil é considerado o maior produtor mundial de cana-de-açúcar, voltada para a produção de açúcar, etanol e derivados. O aproveitamento de resíduos da usina, como torta de filtro e vinhaça no condicionamento do solo pode contribuir com a manutenção da sua fertilidade. Por outro lado, a cada operação agrícola necessária para o cultivo da cana-de-açúcar está associada uma emissão de GEE que deve ser contabilizada. O objetivo desta pesquisa foi estimar a emissão dos principais GEE (CO2, N2O e CH4) pela torta de filtro, e avaliar as alterações de alguns atributos das comunidades microbianas durante o processo de decomposição. Após avaliação de uma enquete sobre o modo de utilização da torta de filtro por diversas usinas, um estudo foi desenvolvido na Usina Costa Pinto localizada em Piracicaba (SP). A torta aplicada no sulco de plantio da cana foi monitorada quanto à emissão dos gases, sendo que as concentrações dos mesmos nas amostras foram determinadas por cromatografia gasosa. Os atributos microbiológicos examinados foram a biomassa, a atividade enzimática (fosfatase ácida, alcalina e ?-glicosidase) e a estrutura da comunidade através do polimorfismo de fragmento de restrição terminal (T-RFLP). Foi observada emissão significativa dos principais GEE predominantemente da torta quando aplicada nos sulcos de plantio, com destaque para o N2O, com uma proporção doze vezes maior em massa do que o CH4, em 56 dias de experimento. Quanto aos aspectos microbiológicos, o maior valor encontrado de carbono e nitrogênio da biomassa microbiana para a dose usualmente aplicada (25 Mg ha-1), foi com dois meses de experimento, com respectivamente 484,89 ?g C g solo seco-1 e 62,95 ?g N g solo seco-1, e correlacionado pelo coeficiente de Pearson com a atividade enzimática no material. Pela técnica de T-RFLP foi possível avaliar a estrutura dos Domínios de Archaea, Bacteria e Fungi na comunidade microbiana da torta de filtro. Não houve modificação dessa estrutura ao longo do tempo analisado. Os resultados obtidos reforçam a importância dos atributos microbiológicos aliados a fatores químicos e físicos e a influência dos mesmos sobre as emissões de GEE.
Brazil 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.

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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.

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Orientadores: Daniel Saito, José Francisco Hofling
Dissertação (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

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17

Abu-Halaweh, Marwan, i 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.

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Twenty species and six subspecies of the genera Arcobacter and Campylobacter have been described to date. All are Gram-negative, microaerophilic, curved, spiral or S-shaped cells, and are members of the order Campylobacterales, class Epsilonproteobacteria phylum Proteobacteria. Though most members are pathogenic, C. jejuni, C. coli and A. butzleri are the most frequently isolated species from patients suffering from gastrointestinal illness. The current methods for their detection, identification, and differentiation are cumbersome, time consuming and lack specificity. DNA based molecular techniques including real-time Polymerase Chain Reaction (PCR) and Fingerprinting methods Terminal Restriction Fragments Length Polymorphism (T-RFLP) and Ligase Detection Reaction (LDR) have been used in this project to develop rapid detection and identification methods for Campylobacter and Arcobacter species. Five real-time PCR methods were developed which include: (a) rapid detection and identification of Campylobacter species using real-time PCR adjacent hybridisation probes, (b) rapid identification of C. jejuni using SYBR Green I, (c) rapid detection and differentiation of Arcobacter species using adjacent hybridisation probes, (d) rapid detection and differentiation of Arcobacter species and the Campylobacter group (C. coli, C. jejuni, C. lari, C. hyoilei, C. helviticus, C. hyointestinalis, C. insulaenigrae, C lanienae) using melting temperature (Tm) of adjacent hybridisation probes, and (e) a one tube real-time PCR multiplex for the rapid detection and identification of Campylobacter species, C. coli and C. jejuni using a TaqMan Probe, in an iCycler iQTM (BioRad, USA) and Light CyclerTM (Idaho Technology, USA). [Continued ...]

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18

Abu-Halaweh, Marwan. "Molecular Methods for Campylobacter and Arcobacter Detection". Thesis, Griffith University, 2005. http://hdl.handle.net/10072/367268.

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Twenty species and six subspecies of the genera Arcobacter and Campylobacter have been described to date. All are Gram-negative, microaerophilic, curved, spiral or S-shaped cells, and are members of the order Campylobacterales, class Epsilonproteobacteria phylum Proteobacteria. Though most members are pathogenic, C. jejuni, C. coli and A. butzleri are the most frequently isolated species from patients suffering from gastrointestinal illness. The current methods for their detection, identification, and differentiation are cumbersome, time consuming and lack specificity. DNA based molecular techniques including real-time Polymerase Chain Reaction (PCR) and Fingerprinting methods Terminal Restriction Fragments Length Polymorphism (T-RFLP) and Ligase Detection Reaction (LDR) have been used in this project to develop rapid detection and identification methods for Campylobacter and Arcobacter species. Five real-time PCR methods were developed which include: (a) rapid detection and identification of Campylobacter species using real-time PCR adjacent hybridisation probes, (b) rapid identification of C. jejuni using SYBR Green I, (c) rapid detection and differentiation of Arcobacter species using adjacent hybridisation probes, (d) rapid detection and differentiation of Arcobacter species and the Campylobacter group (C. coli, C. jejuni, C. lari, C. hyoilei, C. helviticus, C. hyointestinalis, C. insulaenigrae, C lanienae) using melting temperature (Tm) of adjacent hybridisation probes, and (e) a one tube real-time PCR multiplex for the rapid detection and identification of Campylobacter species, C. coli and C. jejuni using a TaqMan Probe, in an iCycler iQTM (BioRad, USA) and Light CyclerTM (Idaho Technology, USA). [Continued ...]
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Biomedical Sciences
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19

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/.

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Nos últimos anos, diversos protocolos e tecnologias têm sido propostos a fim de viabilizar ou otimizar a micropropagação de diversas culturas, bem como reduzir custos de produção. Dentre eles, tem ganhado destaque, o uso do meio de cultura líquido e do sistema de biorreator de imersão temporária (BIT). No entanto, observam-se diferenças de resposta entre espécies e metodologias, sendo necessários maiores estudos para um melhor conhecimento dos fatores que afetam os sistemas de micropropagação. Estudos recentes, baseados em técnicas moleculares, têm revelado que as culturas in vitro não são axênicas, como se acreditava, apresentando comunidades endofíticas onipresentes. Sabendo-se da importância desses microrganismos em plantas a campo, passou-se a questionar o papel destes no desenvolvimento e multiplicação de plantas in vitro. Diante deste cenário, este trabalho se propôs a comparar o desempenho de culturas in vitro em diferentes condições de cultivo: meio semissólido, meios líquido estático, sob agitação e, avaliando-se o crescimento/ multiplicação das plântulas e, naqueles onde houve diferença no desempenho, foram realizadas análises moleculares para a caracterização da comunidade microbiana presente na parte aérea das plantas. Foram utilizadas culturas de bromeliáceas e cana-de-açúcar, buscando sistemas que permitissem as avaliações pretendidas. Para isto foram instalados experimentos com Ananas comosus var. comosus (\'Imperial\' e \'Pérola\') e Aechmea nudicaulis, sob cultivo em meio líquido estático e sob agitação; e com Vriesea hieroglyphica E. Morren, sob cultivo em meio líquido estático, sob agitação e em BIT. Para a gramínea, cana-de-acúcar (Saccharum spp., variedade SP80-3280), foram avaliados o cultivo em meio líquido estático e em BIT. Foram também realizadas análises moleculares de plântulas de Dyckia distachya, que haviam sido cultivadas em meios de culturas semissólido, líquido sob agitação e estático. As culturas que apresentaram diferenças de desempenho entre os sistemas avaliados foram D. distachya, (sendo o melhor tratamento o meio líquido sob agitação) e cana-de-açúcar (melhor tratamento foi BIT) e estas foram consideradas como sistemas adequados para o estudo de como diferentes sistemas de cultivo in vitro podem influenciar na comunidade bacteriana das plantas. A caracterização da comunidade bacteriana de D. distachya foi realizada por T-RFLP (Terminal Restriction Fragment Length Polymorphism) e mostrou que o tratamento meio líquido sob agitação, o qual teve a maior produção de brotos em relação aos demais, diferiu quanto à abundância relativa das unidades taxonômicas operacionais (UTOs) encontradas. Para cana-de-açúcar foram realizadas a construção de bibliotecas de clones do gene 16S rRNA e PCR quantitativo em tempo real (qPCR). Estas análises mostraram não haver diferença significativa entre as bibliotecas dos tratamentos avaliados, no entanto, BIT apresentou 3,54 vezes mais cópias do gene 16S rRNA em relação ao tratamento meio líquido estático, nos permitindo inferir que também possui uma maior número de bactérias. Este estudo apresenta fortes indícios de que o sistema de cultivo in vitro utilizado influencia a comunidade microbiana presente nas plantas
In 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

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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.

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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/.

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A abundância e diversidade dos microrganismos do solo podem ser influenciadas por grande número de fatores, associados, principalmente, ao tipo de solo, sua cobertura e uso. A microbiota do solo apresenta grande importância pelos processos desempenhados pelos seus organismos, essenciais para todos os ecossistemas terrestres. Apesar da grande complexidade associada a esses estudos, os fatores que influenciam as comunidades microbianas podem ser melhor elucidados pela pesquisa com grupos específicos. Nesse sentido, o filo bacteriano Verrucomicrobia, grupo ubíquo em solos, apresenta elevada abundância em diferentes ambientes, o que sugere sua grande importância ecológica. Mas, pela dificuldade de isolamento de seus organismos, ainda pouco se sabe a respeito da ecologia do filo. O presente trabalho foi desenvolvido com o objetivo de analisar os efeitos do uso do solo e da rizosfera de cana-de-açúcar nas comunidades de Bacteria e do filo Verrucomicrobia. Com essa finalidade, amostras de solo foram coletadas em áreas sob diferentes usos em uma usina sucroalcooleira na cidade de Piracicaba (SP). As amostras foram utilizadas em dois estudos distintos. No primeiro, foram analisadas as comunidades microbianas presentes nas amostras de solo obtidas na coleta das áreas de estudo e, no segundo, retiradas de um experimento controlado conduzido em estufa para analisar o efeito do uso do solo e, principalmente, da rizosfera nas mesmas. As comunidades foram avaliadas quanto a sua abundância, pela técnica de qPCR, e estrutura, pela técnica de T-RFLP. No primeiro estudo, a diversidade do filo também foi acessada pelo desenvolvimento de bibliotecas do seu gene 16S rRNA. Os resultados dos estudos indicam que a comunidade bacteriana e, principalmente, do filo foram afetadas pelo uso do solo e pelo manejo adotado em cada área, o que evidencia a importância de sistemas conservacionistas. A análise das bibliotecas demonstrou que o filo Verrucomicrobia apresentou maior diversidade na mata nativa do que nos canaviais. Adicionalmente, a incidência e a abundância das subdivisões do grupo foram alteradas de acordo com o uso do solo. As comunidades também foram influenciadas pela rizosfera em sua estrutura e abundância, resultados de grande interesse para o estudo do filo, pois poucos trabalhos analisaram o efeito rizosférico em seus organismos. Além disso, a sua elevada abundância encontrada no estudo, que tem sido comumente subestimada, ressalta a importância de trabalhos com foco específico em grupos de interesse
The 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

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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.

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Bleul, 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.

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Mikrobielle Prozesse spielen eine wichtige Rolle im Sediment von Talsperren und Seen. Demgegenüber stehen nur unzureichende Erkenntnisse über die Zusammensetzung mikrobieller Biozönosen in Sedimenten sowie deren Aktivität zur Verfügung. Das Ziel dieser Studie war die Untersuchung und der Vergleich der Zusammensetzung und der Struktur mikrobieller Gemeinschaften in Sedimenten um eine Abschätzung der mikrobiellen Diversität in Talsperrensedimenten unterschiedlicher Trophie zu erreichen. Durch die Kombination der in dieser Arbeit verwendeten Methoden (Vergleichende 16S rDNA Analyse, Fingerprinttechniken, klassische Methoden) konnte eine Charakterisierung der mikrobiellen Zusammensetzung der obersten 5 cm von den Talsperrensedimenten Neunzehnhain, Muldenberg, Quitzdorf und Saidenbach erzielt werden. Die vergleichende 16S rDNA Analyse offenbarte in 2541 analysierten rekombinanten Klonen 528 verschiedene Sequenztypen, welche zu 293 OTUs zusammengefaßt werden konnten. Obwohl die Gemeinschaften der verschiedenen Talsperren nur schwach auf der Ebene der phylogenetischen Gruppen differierten, konnte durch die Verwendung von Ähnlichkeitsindices gezeigt werden, dass jede Talsperre eine spezifische mikrobielle Sedimentgemeinschaft aufweist. Über 60% aller Klone zeigten Ähnlichkeiten von mehr als 97% zu 16S rDNA-Sequenzen kultivierter Organismen oder phylogenetisch eingeordneten Sequenzen (14 bekannte phylogenetische Gruppen). Alle anderen Klone zeigten hohe Sequenzhomologien zu unidentifizierten, phylogenetisch bisher nicht eingeordneten Bakterien. Diese Bakterien waren mit Anteilen zwischen 19,8% (Muldenberg) und 54,6% (Saidenbach) in den 16S rDNA Bibliotheken repräsentiert. Mittels Fingerprinttechniken (DGGE, T-RFLP, ARISA) konnten komplexe Muster der mikrobiellen Diversität erzeugt werden. Dabei konnten die Ergebnisse der 16S rDNA Analyse bestätigt werden. Durch die verwendeten Methoden konnte eine komplexe mikrobielle Diversität in den Sedimenten aufgedeckt werden und die Ergebnisse weisen darauf hin, dass die mikrobielle Diversität in Sedimenten wesentlich höher ist als bisher angenommen.

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Stauffert, Magalie. "Dynamique des communautés microbiennes en réponse à une contamination pétrolière dans des sédiments bioturbés". Thesis, Pau, 2011. http://www.theses.fr/2011PAUU3031/document.

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Dans les environnements côtiers, soumis à l’impact des marées noires, les microorganismes jouent un rôle crucial dans le devenir des hydrocarbures pétroliers. Toutefois, de nombreux facteurs influencent les activités microbiennes, notamment par les organismes bioturbateurs qui modifient la pénétration de l’oxygène dans les sédiments. Le travail de la thèse vise à mieux comprendre l’impact d’une pollution pétrolière sur les communautés microbiennes dans des sédiments bio turbés. Il s’agissait de comparer les remaniements structuraux de la communauté microbienne liée à la contamination pétrolière dans des sédiments présentant une faible et une forte activité de bioturbation. Des sédiments marins ont été maintenus en microcosmes durant 9 mois et soumis à quatre conditions : (i) pas de traitement (contrôle), (ii) pétrole, (iii) bioturbation et (iv) pétrole et bioturbation. Les efficacités de dégradation des hydrocarbures pétroliers se sont révélées similaires dans les deux types de sédiments. Par des approches moléculaires, la diversité taxonomique et fonctionnelle des communautés microbiennes totales et métaboliquement actives a été évaluée au cours du temps. Les communautés microbiennes ont subi d’importants remaniements structuraux spécifiques à chaque traitement. Nous suggérons que le fonctionnement global de la communauté est modifié par l’activité bioturbatrice sans pour autant modifier l’activité de dégradation. Ces travaux ont mis en évidence une redondance fonctionnelle de l’activité de biodégradation des hydrocarbures pétroliers des communautés microbiennes. L’isolement de communautés hydrocarbonoclastes a permis de confirmer cette redondance fonctionnelle
Coastal 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

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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.

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L’étude des communautés microbiennes de la baie de raisin dans des conditions de production à l’échelle de la parcelle montre une dynamique temporelle des populations cultivables, qui se traduit par une augmentation des niveaux de population à partir des stades de début véraison et début maturité. Concernant la communauté bactérienne cultivable, 44 espèces appartenant à 21 genres ont été identifiées. Parmi les huit genres identifiés pour la population fongique, les espèces appartenant au genre Aureobasidium sont les plus abondantes, contrairement aux espèces fermentaires qui restent minoritaires. L’incidence des facteurs biotiques et abiotiques sur différents paramètres de population microbienne tels que la structure, la densité et l’activité métabolique a été analysée. Nous avons observé que les zones climatiques plus fraîches et humides, favorisent le développement des microorganismes. Ces travaux mettent en évidence l’impact écotoxique du cuivre sur la communauté microbienne, en particulier dans sa fraction bactérienne. Le développement de Botrytis cinerea sur la grappe modifie la communauté microbienne des baies de raisin sain : le nombre d’espèces bactériennes augmente ainsi que leur diversité. La communauté bactérienne de la baie de raisin est proche de celle des feuilles d’un point de vue de sa structure, et mais éloignée de celles des écorces et du sol, avec des indices de diversité et de richesse plus faibles
The 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

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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.

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Kirker, 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/.

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The effects of an organic biocide (CTN) with and without co-added antioxidant (BHT) on microbial communities in SYP were assessed using terminal restriction fragment length polymorphism (T-RFLP) analyses in both field and accelerated decay laboratory studies. Ammoniacal copper quaternary (ACQ-C) was used as a positive control in the field study component, but not in the laboratory test. Field stakes were treated with 0.25 and 0.37% ammoniacal copper quat (ACQ-C), CTN (0.1 and 0.25%), CTN (0.1 and 0.25%) with 2% BHT added, 2% BHT alone, and controls were left untreated. In the field studies, preservative treatment slowed the initial colonization of wood by fungi. Higher species richness and diversity were found in non-biocidal treatments (BHT and untreated controls). Fungal communities in treated wood were different based on their species composition, but eventually became more similar to untreated controls. Preservative treatment increased richness and diversity of basidiomycete fungi, but overall presence of basidiomycetes was low compared to other fungi. Preservatives did not change the species composition of basidiomycetes compared to untreated controls. Preservative treatment initially increased bacterial richness and diversity, but over time these trends diminished to levels consistent with untreated controls. Preservatives changed the species composition of colonizing bacteria so that treated and untreated communities remained different over 15 months of soil exposure. Bacterial diversity was negatively correlated with CTN depletion at the lowest rate. In the accelerated decay laboratory test, the effects of CTN and/or BHT on bacterial, fungal, and basidiomycete communities in composted and uncomposted soil were evaluated over a 12 month period. Composted soil had less fluctuation in changing microbial diversity due to more constant moisture. The consensus of the analyses of the bacterial, fungal, and basidiomycete communities indicate that wood preservatives increased microbial species richness and diversity. Preservative treatment increased species turnover that decreased over time. Eventually, microbial communities approached a stable community structure consistent with untreated controls. Preservatives were completely degraded after 30 days exposure; however, definite changes in bacterial and fungal richness, diversity, and species composition were found. Basidiomycetes again represented the smallest portion of the microbial community involved in the overall decay process.

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Ferrari, 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/.

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O uso de culturas GM (geneticamente modificadas) tem sido questionado quanto ao destino dos produtos derivados da transgenia no ambiente. Com a liberação de exsudatos das raízes das plantas e a decomposição dos resíduos culturais, aumenta-se a quantidade de DNA transgênico no ambiente, que pode ser adsorvido à superfície ativa das partículas do solo e/ou degradado pela ação de enzimas microbianas. A comunidade microbiana do solo pode entrar em contato direto com estes produtos, aumentando a probabilidade de transferência horizontal de fragmentos de DNA transgênico para os microrganismos. Também, alterações na composição dos exsudatos das plantas GM e mudanças em função das práticas de manejo, podem resultar em alterações na composição funcional e estrutural da comunidade microbiana. Assim, faz-se necessário avaliar a persistência dos produtos derivados da transgenia no solo e seus possíveis efeitos sobre a comunidade microbiana. Os objetivos deste estudo foram: avaliar a persistência dos fragmentos 35S-hsp70, hsp70-cry1Ab e cry1Ab-planta da construção gênica do milho Bt (evento MON810) em diferentes tipos de solo e temperaturas, em condições de microcosmo e de campo; e determinar a abundância do número de cópias dos gene 16S rRNA de Bacteria, Firmicutes, Verrucomicrobria e Archaea, e 18S rRNA de Fungo nas mesmas condições, e avaliar a estrutura da comunidade bacteriana em áreas agrícolas de cultivo de milho Bt. No primeiro estudo, o DNA do milho Bt MON810 foi adicionado em solos arenoso e argiloso. Como controle negativo, apenas água estéril foi misturada ao solo. Amostras de solo foram incubadas a 15 e 25ºC. Em campo, os solos foram amostrados em três áreas agrícolas em Fátima do Sul, MS, em dois anos consecutivos. Após extração de DNA, os fragmentos foram quantificados por qPCR. No segundo estudo, foram determinadas a abundância dos genes 16S rRNA de Bacteria, Firmicutes, Verrucomicrobria e Archaea e 18S rRNA de Fungo e avaliada a estrutura da comunidade bacteriana por T-RLFP. Os resultados mostraram que em condições de microcosmo, os fragmentos hsp70-cry1Ab e cry1Ab-planta persistiram até 291 dias, e o fragmento 35S-hsp70 até 180 dias. A temperatura e o tipo de solo não afetaram a persistência dos fragmentos. Em campo, o número de cópias desses fragmentos foi maior na segunda coleta. No segundo estudo, o número de cópias do gene 16S rRNA de Bacteria aumentou com adição de DNA do milho Bt nos microcosmos, e uma redução do número de cópias foi verificada para Archaea, Verrucomicrobia e Fungo. Para Firmicutes, os resultados não foram consistentes. As temperaturas não resultaram em efeito na abundância dos genes, enquanto o tipo de solo teve efeito apenas para Archaea e Verrucomicrobia. Áreas agrícolas com cinco anos de cultivo de milho Bt apresentaram variações na estrutura da comunidade bacteriana em nível de filo, e maior abundância de Fungos no segundo ano de amostragem, enquanto em área com um ano de cultivo, observouse uma redução da população de Firmicutes e Verrucomicrobia. Os maiores efeitos na comunidade microbiana foram verificados entre os anos de amostragem
The 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

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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.

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Aufgrund der ökologischen und ökonomischen Problematik der chemischen Phosphatfällung ist eine Optimierung der Effizienz und Stabilität der biologischen Verfahren zur Phosphat-elimination erforderlich. Hierfür ist jedoch ein fundiertes Wissen über die daran beteiligten Organismen eine entscheidende Vorraussetzung. Das Ziel der vorliegenden Arbeit war es, die mikrobielle Populationstruktur von zwei Belebtschlamm-anlagen im Labormaßstab mit Hilfe von drei unterschiedlichen 16S rDNA basierenden molekular-biologischen Methoden zu charakterisieren. Ein besonderer Schwer-punkt ist hierbei die Analyse der Bakterien, die mit der erhöhten biologischen Phosphat-elimination in Verbindung gebracht werden. Dies sind Vertreter der Rhodocyclus-Gruppe, der Gattung Tetrasphaera und der Gattung Acinetobacter. Als Untersuchungsobjekte wurden zwei Hauptstromverfahren zur erhöhten biologischen Phosphatelimination gewählt, die sich im Schlamm-alter, der Schlammbelastung und der sich daraus resultierenden Nitrifikationsleistung unterscheiden. Aufgrund der gewählten Verfahrensweisen wurde der Einfluss der Nitrifikation auf die Zusammensetzung der Belebtschlammbiozönose ebenfalls untersucht. Um praxisnahe Verhältnisse zu erreichen, wurden die Anlagen mit kommunalem Abwasser beschickt. Für einen Vergleich sollten Proben aus kommunalen Kläranlagen mit deutlich anderen Verfahrensweisen in die Untersuchungen mit einbezogen werden.

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Keriuscia, Gokul Jarishma. "Eukaryotic diversity of miers valley hypoliths". Thesis, University of the Western Cape, 2012. http://hdl.handle.net/11394/4031.

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>Magister Scientiae - MSc
The 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.

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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.

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Recent work in microbial ecology has focused on elucidating controls over biogeographic patterns and connecting microbial community composition to ecosystem function. My objective was to investigate the relative influences of landscape legacies and contemporary environmental factors on the distribution of soil microbial communities and their contribution to ecosystem processes across a glacial till sequence in Taylor Valley, Antarctica. Within each till unit, I sampled from dry areas and areas with visible evidence of recent surface water movement generated by seasonal melting of ephemeral snow packs and hillslope ground ice. Using T-RFLP 16S rRNA gene profiles of microbial communities, I analyzed the contribution of till and environmental factors to community similarity, and assessed the functional potential of the microbial community using extracellular enzyme activity assays. Microbial communities were influenced by geochemical differences among both tills and local environments, but especially organized by variables associated with water availability as the first axis of an NMDS ordination was strongly related to shifts in soil moisture content. CCA revealed that tills explained only 3.4% of the variability in community similarity among sites, while geochemical variables explained 18.5%. Extracellular enzyme activity was correlated with relevant geochemical variables reflecting the influence of nutrient limitation on microbial activity. In addition, enzyme activity was related to changes in community similarity, particularly in wet environments with a partial Mantel correlation of 0.32. These results demonstrate how landscape history and environmental conditions can shape the functional potential of a microbial community mediated through shifts in microbial community composition.
Master of Science

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32

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.

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Gustafson, 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.

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In order to analyze the bacterial community of river otter scat (fecal material) at the class level, river otter scat samples were collected from Grizzly Island Wildlife Area (Solano County, CA) and the Cosumnes River Preserve (Sacramento County, CA). DNA was isolated from each sample with the MOBIO PowerSoil™ DNA Isolation Kit and 16S rRNA gene sequences were amplified from each sample. After digestion with Mspl, TRFLPs were analyzed in an ABI Prism™ 310 Genetic Analyzetin triplicate and data peak information from each electropherogram was uploaded into the Phylogenetic Assignment Tool (PAT). Species belonging to the Class Bacilli were the most abundant followed by unclassified species. Two road killed river otters were necropsied to recover brain and blood tissue. DNA was isolated using the Qiagen Tissue DNeasy Kit. Samples from both otters were amplified with a singe tube nested PCR primer set for the detection of the ITS 1 region of Toxoplasma gondii. Scat samples used in the T-RFLP analysis were also tested for the presence ofT. gondii using the same nested primer set. Neither the river otter tissue samples nor any of the scat samples used in this analysis showed evidence of infeGtion with T. gondii.

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Elsayed, Omniea. "Biodegradation of chloroacetanilide herbicides in wetlands". Thesis, Strasbourg, 2015. http://www.theses.fr/2015STRAJ003/document.

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Les chloroacétanilides sont une famille d'herbicides largement utilisée en agriculture, et contribuent de ce fait à la pollution environnementale. Leur devenir, y compris dans les écosystèmes rédox-dynamiques récepteurs comme les zones humides, est encore mal compris. Dans ce travail, la dégradation microbienne de chloroacétanilides (métolachlore, acétochlore et l'alachlore) a été étudiée par des approches innovantes de chimie analytique et de biologie moléculaire, à l'échelle du laboratoire en utilisant des microcosmes en colonnes, et in situ dans des zones humides construites à ciel ouvert et conçues pour traiter les intrants chimiques issus de l'agriculture.Une nouvelle méthode d’analyse isotopique composés-spécifiques a été développée. Les résultats indiquent la biodégradation des chloroacétanilides dans les zones humides, également suggérée par la détection des produits de dégradation correspondants (acides éthane sulfonique et oxanilique). Dans les expériences en microcosme de laboratoire, les chloroacétanilides ont principalement été dégradés dans les zones anoxiques de la rhizosphère, suggèrant un rôle prépondérant des processus anaérobies. L'analyse par chromatographie chirale du métolachlore a en outre révélé la dégradation préférentielle de l'énantiomère S du métolachlore, confirmant l'importance des processus biologiques dans la dissipation des chloroacétanilides. Les corrélations qui ont pu être observées entre les changements de variables hydrochimiques et de conditions hydrauliques et des différences de composition bactérienne détectées par génotypage par polymorphisme de longueur des fragments de restriction (T-RFLP) et par pyroséquençage du gène ARNr 16S confirme le potentiel de bio-indicateurs basés sur l'ADN pour suivre le fonctionnement des écosystèmes.Sur la base de ce travail, la détection et l'identification des micro-organismes et des voies biochimiques responsables de la dégradation de chloroacétanilides dans les zones humides, ainsi que l'élaboration d'indicateurs génétiques bactériens pour le suivi de la dégradation de chloroacétanilides en zones humides, émergent comme autant d’objectifs de recherche à court-terme
Chloroacetanilide 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

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35

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.

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Wood 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.

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36

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/.

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A indústria sucroenérgetica gera grande quantidade de resíduos, sendo a torta de filtro e as cinzas os principais resíduos sólidos. Uma das tecnologias desenvolvidas para o manejo destes resíduos é a compostagem. A aplicação do composto tem mostrado efeitos positivos na cultura da cana-de-açúcar no que diz respeito à fertilização fosfatada. Os objetivos do presente trabalho foram: I. Observar o comportamento das comunidades bacterianas durante a compostagem e o efeito da inoculação de estirpes bacterianas mobilizadoras de fósforo sobre a disponibilidade de fósforo no composto final; II. Avaliar o efeito da aplicação de diferentes fontes de P e de bactérias mobilizadoras de fósforo no desenvolvimento de plantas de cana-de-açúcar e o efeito sobre as comunidades bacterianas do solo. Nesse sentido, pilhas de compostagem foram instaladas na Usina São José da Estiva em Novo Horizonte, SP. Os tratamentos consistiram de pilhas com e sem rocha fosfática; e pilhas com e sem a inoculação das estirpes Pseudomonas aeruginosa PSBR12 e Bacillus sp. BACBR1. Amostragens foram realizadas quinzenalmente durante 60 dias. Adicionalmente determinou-se a atividade enzimática, e parâmetros químicos do composto. A comunidade bacteriana foi acessada por meio da técnica independente de cultivo T-RFLP (restriction fragment length polymorphism) e sequenciado por meio da plataforma de nova geração MiSeqTM System (Illumina). Com o objetivo de avaliar o efeito do composto e da inoculação de bactérias mobilizadoras de P no desenvolvimento da cana-de-açúcar foi instalado um experimento em casa de vegetação com plantas de cana de açúcar, utilizando-se composto, rocha fosfática e super fosfato triplo como fontes de P, além da inoculação dos seguintes: Inoculante 1: Pseudomonas sp. PSBR10, Azotobacter sp. AZTBR19, Rhizobium sp. RIZBR01; e o Inoculante 2: Bacillus simplex BACBR04, Bacillus sp. BACBR06, Rhizobium sp. RIZBR01. O experimento foi conduzido durante 75 dias. Ao fim do experimento foram analisados os seguintes parâmetros: biomassa seca, acúmulo de P, N, e K na parte aérea, e fosfatases no solo. A estrutura das comunidades bacterianas no solo foram avaliadas por meio do sequenciamento na plataforma Illumina. A aplicação de bactérias mobilizadoras de P durante a compostagem diminuiu o P ligado ao Ca. A mudança nas comunidades bacterianas durante a compostagem foi temporal, no início dominaram membros da ordem Lactobacillales, após 15 dias as ordens Bacillales e Clostridiales passaram a dominar o processo. As comunidades bacterianas são influenciadas principalmente pelos parâmetros pH, temperatura e umidade. Quanto ao experimento em casa de vegetação, o uso dos inoculantes (principalmente o inoculante 2) aumentou o acúmulo de P, N e K na parte aérea nos tratamentos que receberam composto e super fosfato triplo como fonte de P. A aplicação dos inoculantes e a adição do composto modificou a estrutura das comunidades bacterianas do solo; essa alteração quando os inoculantes são aplicados pode estar relacionada com o incremento no acúmulo de nutrientes. O uso de bactérias mobilizadoras de P é uma tecnologia potencial para o uso na agricultura, tanto na compostagem de resíduos da indústria sucroenergética com rocha fosfática, como no aumento da eficiência da fertilização fosfatada na cana-de-açúcar.
Sugarcane 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.

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37

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.

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Aufgrund der ökologischen und ökonomischen Problematik der chemischen Phosphatfällung ist eine Optimierung der Effizienz und Stabilität der biologischen Verfahren zur Phosphat-elimination erforderlich. Hierfür ist jedoch ein fundiertes Wissen über die daran beteiligten Organismen eine entscheidende Vorraussetzung. Das Ziel der vorliegenden Arbeit war es, die mikrobielle Populationstruktur von zwei Belebtschlamm-anlagen im Labormaßstab mit Hilfe von drei unterschiedlichen 16S rDNA basierenden molekular-biologischen Methoden zu charakterisieren. Ein besonderer Schwer-punkt ist hierbei die Analyse der Bakterien, die mit der erhöhten biologischen Phosphat-elimination in Verbindung gebracht werden. Dies sind Vertreter der Rhodocyclus-Gruppe, der Gattung Tetrasphaera und der Gattung Acinetobacter. Als Untersuchungsobjekte wurden zwei Hauptstromverfahren zur erhöhten biologischen Phosphatelimination gewählt, die sich im Schlamm-alter, der Schlammbelastung und der sich daraus resultierenden Nitrifikationsleistung unterscheiden. Aufgrund der gewählten Verfahrensweisen wurde der Einfluss der Nitrifikation auf die Zusammensetzung der Belebtschlammbiozönose ebenfalls untersucht. Um praxisnahe Verhältnisse zu erreichen, wurden die Anlagen mit kommunalem Abwasser beschickt. Für einen Vergleich sollten Proben aus kommunalen Kläranlagen mit deutlich anderen Verfahrensweisen in die Untersuchungen mit einbezogen werden.

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38

Spivey, 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.

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39

Kirker, 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.

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40

Conn, Vanessa Michelle, i 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.

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Wheat is the most economically important crop forming one quarter of Australian farm production. The wheat industry is severely affected by diseases, with fungal pathogens causing the most important economic losses in Australia. The application of fungicides and chemicals can control crop diseases to a certain extent, however, it is expensive and public concern for the environment has led to alternative methods of disease control to be sought, including the use of microorganisms as biological control agents. Microorganisms are abundant in the soil adjacent to plant roots (rhizosphere) and within healthy plant tissue (endophytic) and a proportion possess plant growth promotion and disease resistance properties. Actinobacteria are gram-positive, filamentous bacteria capable of secondary metabolite production such as antibiotics and antifungal compounds. A number of the biologically active endophytes belonging to the Actinobacteria phylum were isolated in our laboratory. A number of these isolates were capable of suppressing the wheat fungal pathogens Rhizoctonia solani, Pythium sp. and Gaeumannomyces graminis var. tritici, both in vitro and in planta indicating the potential for the actinobacteria to be used as biocontrol agents. The aim of this research was to investigate the molecular mechanisms underlying this plant-microbe interaction. The indigenous microbial populations present in the rhizosphere and endophytic environment are critical to plant health and disruptions of these populations are detrimental. The culture-independent technique Terminal Restriction Fragment Length Polymorphism (T-RFLP) was used to characterise the endophytic actinobacteria population of wheat roots under different conditions. Soils which support a higher number of indigenous microorganisms result in wheat roots with higher endophytic actinobacterial diversity and level of colonisation. Sequencing of 16S rRNA gene clones, obtained using the same actinobacteria-biased PCR primers that were used in the T-RFLP analysis, confirmed the presence of the actinobacterial diversity, and identified a number of Mycobacterium and Streptomyces species. It was found that the endophytic actinobacterial population of the wheat plants contained a higher diversity of endophytic actinobacteria than reported previously, and that this diversity varied significantly among different field soils. The endophytic actinobacteria have previously been shown to protect wheat from disease and enhance growth when coated onto the seed before sowing. As the endophytes isolated were recognised as potential biocontrol agents, the impact on the indigenous endophytic microbial population was investigated. Utilising the T-RFLP technique it was established that the use of a commercial microbial inoculant, containing a large number of soil bacterial and fungal strains applied to the soil, disrupts the indigenous endophyte population present in the wheat roots. The hypothesis is that non-indigenous microbes proliferate and dominate in the soil preventing a number of endophytic-competent actinobacterial genera from access to the seed and ultimately endophytic colonisation of the wheat roots. This dramatically reduces diversity of endophytes and level of colonisation. In contrast the use of a single endophytic actinobacteria endophyte inoculant results in a 3-fold increase in colonisation by the added inoculant, but does not significantly affect this indigenous population. Colonisation of healthy plant tissues with fungal endophytes has been shown to improve the competitive fitness with enhanced tolerance to abiotic and biotic stress and improved resistance to pathogens and herbivores. In this study the fungal endophyte population of wheat plants grown in four different soils was analysed using partial sequencing of 18S rRNA gene sequences. Sequence anlaysis of clones revealed a diverse range of fungal endophytes. In this diverse range of fungal endophytes a number sequences were highly similar to those of previously known fungal phytopathogens. A number of sequences detected were similar to fungal species previously identified in soil or plant material but not as endophytes. The remaining sequences were similar to fungal species without a known relationship with plants. Plants have developed an inducible mechanism of defence against pathogens. In addition to local responses plants have developed a mechanism to protect uninfected tissue through a signal that spreads systemically inducing changes in gene expression. In the model plant Arabidopsis thaliana activation of the Systemic Acquired Resistance (SAR) pathway and the Jasmonate (JA)/Ethylene (ET) pathway is characterised by the production of pathogenesis-related (PR) and antimicrobial proteins resulting in systemic pathogen resistance. Endophytic actinobacteria, isolated from healthy wheat roots in our laboratory, have been shown to enhance disease resistance to multiple pathogens in wheat when coated onto the seed before sowing. Real Time RT-PCR was used to determine if key genes in the SAR and JA/ET pathways were induced in response to inoculation with endophytic actinobacteria. Inoculation of wild-type Arabidopsis thaliana with selected strains of endophytic actinobacteria was able to ï¿½primeï¿½ the defence pathways by inducing low level expression of SAR and JA/ET genes. Upon pathogen infection the defence-genes are strongly up-regulated and the endophyte coated plants had significantly higher expression of these genes compared to un-inoculated plants. Resistance to the bacterial pathogen Erwinia carotovora subsp. carotovora was mediated by the JA/ET pathway whereas the fungal pathogen Fusarium oxysporum triggered primarily the SAR pathway. Further analysis of the endophytic actinobacteria-mediated resistance was performed using the Streptomyces sp. EN27 and Arabidopsis defence-compromised mutants. It was found that resistance to E. carotovora subsp. carotovora mediated by Streptomyces sp. EN27 occurred via a NPR1-independent pathway and required salicylic acid whereas the jasmonic acid and ethylene signalling molecules were not essential. In contrast resistance to F. oxysporum mediated by Streptomyces sp. EN27 occurred via a NPR1-dependent pathway but also required salicylic acid and was JA- and ET-independent. This research demonstrated that inoculating wheat with endophytic actinobacteria does not disrupt the indigenous endophytic population and may be inducing systemic resistance by activating defence pathways which lead to the expression of antimicrobial genes and resistance to a broad range of pathogens.

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Scheer, 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.

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Gewässersedimente stellen für den Stoffkreislauf ein wichtiges Ökosystem dar. Durch die Stoffwechselleistungen einer komplexen mikrobiellen Lebensgemeinschaft wird sowohl das Sediment selbst, sein Interstitialwasser, das überstehende Freiwasser als auch die Atmosphäre und die darin lebenden Mikro- und Makroorganismen beeinflusst. Die grundlegenden chemischen Prozesse im Sediment sind bereits gut untersucht. Auch sind die mikrobiellen Großgruppen im Sediment bekannt. Im Hinblick auf die Diversität der Mikroorganismen, insbesondere in Süßwassersedimenten, gibt es noch Forschungsbedarf. Das Auengebiet des Nationalparks „Unteres Odertal“ stellt durch seine jährlich kontrollierten Flutungen ein interessantes und wegen seiner Vielfalt verschiedenartiger Gewässertypen einen idealen Ort zur Untersuchung mikrobieller Biozönosen in Gewässersedimenten dar. Ziel dieser Arbeit war es, eine erste Charakterisierung der mikrobiellen Biozönose in den Gewässersedimenten des Auennationalparks „Unteres Odertal“ durchzuführen und mit den Ergebnissen der Talsperre Saidenbach und der Elbaue bei Dornburg zu vergleichen. Hierfür kam ein breites Spektrum an Methoden zum Einsatz, das klassische mikrobiologische Methoden und molekularbiologische Techniken umfasste. Die Analysen sollten dabei über mehrere Jahre hinweg erfolgen, um die Variabilität der mikrobiellen Populationen in Abhängigkeit von sich ändernden Umweltparametern zu erfassen. Die Charakterisierung der Umweltparameter erfolgte durch Messungen chemisch-physikalischer Parameter im Freiwasser, Sediment und seinem Interstitialwasser. Die untersuchten Probenahmestellen unterschieden sich in ihren chemischen Profilen. Damit waren Unterschiede in der mikrobiellen Zusammensetzung dieser Probenahmestellen zu erwarten. Die Identifizierung und Quantifizierung der Prokaryoten mittels CARD FISH wies auf eine hohe Abundanz von Alpha- und Beta-Proteobakterien sowie Bacteroidetes, Planctomycetes, Verrucomicrobia und Chloroflexi in den Proben des Odertals hin. Die Proben Dornburgs wurden von Planctomyceten und die Proben des Haselbachs von Alpha-Proteobakterien oder Verrucomicrobien dominiert. Obwohl die Hybridisierbarkeit der Proben gut war, wurde mit den angewendeten Sonden in der Summe weniger als 50 % der Gesamtzellzahl erfasst. Die Anwendung der ARISA Methode zeigte strukturelle Unterschiede zwischen den untersuchten Proben in Abhängigkeit von der Sedimenttiefe und dem Probenahmemonat. Die größte Ähnlichkeit besaßen die Biozönosen des Anglerteichs und des Bogengrabens. Ein Einfluss der Flutung auf die Zusammensetzung der mikrobiellen Biozönose konnte deutlich gezeigt werden. Die Identifikation der Eubakterien in den Proben des Odertals durch die Erstellung von 16S rDNA Eubakterien Klonbanken ergab eine Dominanz der Beta-Proteobakterien und Bacteroidetes und wies auf die Bedeutung der Delta-Proteobakterien hin. Die eubakterielle Lebensgemeinschaft im Haselbach wurde von Alpha-Proteobakterien und Acidobakterien dominiert. Variabilitäten im Zusammenhang mit dem Probenahmedatum und der Flutung des Odertals konnten gezeigt werden. Die größte eubakterielle Biodiversität wurde im Sediment der Oder-Zollstation (April 2007) geschätzt. Die Anwendung der Pyrosequenzierung ergab eine hohe Biodiversität in allen Proben und bestätigte die Dominanz der Beta-Proteobakterien im Anglerteich. Im Bogengraben dominierten die Delta-Proteobakterien knapp vor den Beta-Proteobakterien. In der Oder waren neben den Beta-Proteobakterien die Bacteroidetes abundanter. Die genannten Taxa dominierten auch die Bibliotheken der Talsperre Saidenbach. Die höchste Biodiversität wurde für die Bibliothek des Bogengrabens angegeben, dessen Lebensgemeinschaft die meisten Gemeinsamkeiten mit der Bibliothek des Anglerteichs aufwies. Sulfatreduzierende Bakterien (SRB) wurden durch die Sequenzierung von Klonbanken und die Anwendung der Fingerprintmethoden T-RFLP und DGGE charakterisiert. Die hohe Biodiversität der SRB konnte je nach erstellter Klonbank unterschiedlich gut beschrieben werden. Neben zahlreichen nicht identifizierbaren Vertretern waren Desulfobacterales und Clostridiales abundant. Die größte Diversität wurde wiederum in der Bibliothek des Bogengrabens nachgewiesen. Die Zusammensetzung der SRB in den Klonbanken variierte in Abhängigkeit der Parameter gelöster reaktiver Phosphor (SRP), organische Substanz, DOC und Nitrat. Mit T-RFLP und DGGE konnte eine sedimenttiefenabhängige Variabilität der SRB festgestellt werden, die sich zwischen den Proben Anglerteich und Bogengraben am meisten glich. Mit der DGGE erfolgte eine erste zeitabhängige Untersuchung, die deutlich verschiedene Biozönosen zwischen der Talsperre Saidenbach und den Proben des Nationalparks „Unteres Odertal“ zeigte. Das enorm hohe Bandenspektrum erschwerte die Analyse der zeitlichen Variabilität. Die Nitrat-Stickstoffkonzentrationen waren in den Sedimenten mit zunehmender Tiefe unverändert niedrig, was sich in einer mit T-RFLP untersuchten niedrigen Diversität der Denitrifikanten wiederspiegelte, die nur wenige vertikale oder zeitliche Varianzen zeigten. Die Anwendung von Kultivierungsversuchen ermöglichte die Isolation und eine erste Charakterisierung von Cyano- und Eisenbakterien. Insbesondere fädige Cyanobakterien der Gattungen Leptolyngbya, Nostoc und Pseudanabaena wiesen ein interessantes Sekundärmetabolitspektrum auf. Die Untersuchung erster Extrakte (Firma Cyano Biotech) wies auf biologisch aktive Substanzen hin. Die Untersuchung hygienisch relevanter Mikroorganismen zeigte ein höheres Vorkommen coliformer Bakterien im Sediment der Oder-Zollstation als im Anglerteich oder Bogengraben. Neben den Eubakterien wurde die Lebensgemeinschaft der Archaea durch Sequenzierung generierter Klonbanken identifiziert sowie die vertikale und temporale Variabilität ihrer Struktur untersucht (T-RFLP, DGGE). Die für aquatische Sedimente vergleichsweise hohe archaeale Diversität unterschied sich enorm zwischen den Klonbibliotheken. Die höchste Diversität wurde in der Klonbank der Probe Dornburgs festgestellt, die neben Vertretern des „Rice Clusters V“ (RC-V) überwiegend aus Crenarchaea bestand. RC-V Archaea dominierten, bis auf die Oder-Zollstation, alle generierten Bibliotheken. Methanogene Archaea waren besonders abundant in der Bibliothek der Oder-Zollstation (Methanomicrobiaceae, Methanosaetaceae) und des Haselbachs (Methanospirillaceae). Einflussnehmende Umweltfaktoren waren Sulfat (Dornburg), Nitrat (Entnahmestelle), DIC (Anglerteich), Sauerstoff (Haselbach) und Ammonium (Oder-Zollstation). Die T-RFLP Analyse zeigte die methanogenen Archaea Methanosarcinales/Methanomicrobiales (Msm) als besonders abundant an. Eine erwartete tiefenabhängige Varianz konnte mit T-RFLP gezeigt werden. Die Unterschiede zwischen den Probenahmestellen waren jedoch deutlicher und zeigten anhand der DGGE Analyse ein breiteres Msm Bandenspektrum für den Anglerteich und Bogengraben im Vergleich zur Oder-Zollstation und zum Haselbach. Die zeitabhängige Variabilität der Archaea und Msm konnte mit T-RFLP und DGGE gezeigt werden. Der Einfluss der Flutung war im Vergleich zu allen anderen Probenahmedaten nicht so ausschlaggebend wie erwartet. Insgesamt zeigen die Ergebnisse eine hohe Biodiversität der Mikroorganismen im Nationalpark Unteres Odertal. Die Flutung hatte insbesondere auf die Eubakterien einen großen Einfluss. Zeitliche Variabilität der Zusammensetzung der Lebensgemeinschaften der Prokaryoten lässt sich im Odertal nicht mit einer Jahreszeit in Zusammenhang bringen. Hingegen sind die mikrobiellen Biozönosen im Haselbach nachweislich von den wechselnden Zirkulationsphasen beeinflusst. Die hier verwendeten Methoden sind zur Charakterisierung mikrobieller Biozönosen in der Umweltmikrobiologie weit verbreitet. Die Anwendung der neuen Pyrosequenzierungsmethode ermöglichte trotz enormer Anzahl analysierter Sequenzen keine vollständige Erfassung der hohen Biodiversität, aber durch das Fehlen des Klonierungsschrittes wurde eine Fehlerursache in der Darstellung der realen Biozönose ausgeschlossen. Unstimmigkeiten in den Ergebnissen der verschiedenen Experimente beruhen meist auf methodischen Limitationen. Die DNA Isolationsmethode, die Vorauswahl von Primern, die bevorzugte Amplifikation, die allen PCR-basierten Methoden zu Grunde liegen, verschieben die reale Darstellung der Struktur einer Biozönose. Die fehlende Aussagekraft über die Aktivität der Mikroorganismen durch DNA basierte Analysen kann durch die Beobachtung der zeitlichen Änderungen ihrer Abundanz reduziert werden. Erste einflussnehmende Umweltparameter konnten ermittelt werden. Zusätzliche Analysen weiterer Elektronenakzeptoren über einen längeren Zeitraum sind jedoch nötig, um eine hinreichend sichere Aussage treffen zu können.

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Plassart, Pierre. "Pertinence des indicateurs microbiens dans l'évaluation de l'état des sols agricoles". Rouen, 2010. http://www.theses.fr/2010ROUES048.

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La plupart des sols du monde sont aujourd’hui modifiés par les activités humaines. Ainsi, pour de nombreux sols agricoles, les pratiques culturales intensives et l’apport chronique d’intrants chimiques ont conduit à une diminution de la fertilité de ces sols. Pourtant, alors même que ces sols sont en danger, il n’existe que peu d’outils d’évaluation pertinents de leur état. La composante biologique a longtemps été négligée, or le sol héberge une très forte diversité d’organismes impliquée dans les cycles biogéochimique dont les microorganismes susceptibles alors de constituer des bioindicateurs potentiels de l’état du sol. L'objectif de ce travail consiste donc à identifer des variables descriptives de la diversité bactérienne, sensibles à l’état du sol. La structure des communautés bactériennes (abondance, diversité génétique et fonctionnelle) a été appréhendée dans son ensemble mais également au travers de l’analyse des populations de Pseudomonas, genre bactérien largement représenté dans les sols et particulièrement sensible à ses perturbations. L’approche expérimentale, de la parcelle au microcosme, a consisté en l’évaluation comparée de l’effet (1) d’un apport de cuivre (dose agronomique x100) (2), de perturbations naturelles (spatiale, climatique), et (3) de perturbations anthropiques (pratiques culturales) sur les communautés bactériennes. La première partie de ce travail a été réalisée in situ sur sols de Prairie et de Grande culture afin de définir les bornes naturelles de la variation spatiale et temporelle de différents descripteurs bactériens de sols limoneux caractéristiques de Haute Normandie. Par ailleurs, cette partie a également permis d’appréhender les sensibilités relatives des différentes variables descriptives mesurées et de valider en conséquence les approches méthodologiques mises en oeuvre. Ainsi les variables mesurées peuvent être classées en deux catégories : les variables dont la mesure repose sur la culture des microorganismes reflèteraient les perturbations récentes du sol tandis que les variables basées sur une approche moléculaire reflèteraient l’historique cultural des parcelles. La seconde partie de ce travail a permis d’étudier en microcosmes l’impact d’une contamination métallique par le cuivre sur les descripteurs étudiés dans la première partie. Les résultats obtenus montrent que les variations de la structure des communautés bactériennes causées par une contamination cuprique ponctuelle, comparées à celles liées à la saison ou aux pratiques culturales, sont mineures. Parallèlement une analyse comparative des données obtenues en cosmes tamisés et non tamisés révèle que l'état du sol peut influencer la réponse des communautés bactériennes à une contamination métallique ; en effet la perturbation physique du sol par le tamisage a induit une réponse transitoire des communautés à la contamination métallique. Ce travail a permis (1) la constitution d’un référentiel de données microbiologiques de sols agricoles limoneux, intégrant les fluctuations spatiales et temporelles des variables mesurées, (2) de déterminer la sensibilité de variables descriptives aux effets naturels et anthropiques et d’identifier les limites et complémentarités des approches cellulaires et moléculaires, (3) de hierarchiser des facteurs déterminant la structure génétique et fonctionnelle des communautés bactériennes, (4) de valider la pertinence de l’utilisation des bactéries du genre Pseudomonas dans l’évaluation de l’impact du cuivre sur les sols
Most 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

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Gillespie, Jaimie. "The effects of saltwater intrusion on methanogen community abundance, structure, and activity". VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/3175.

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Tidal freshwater wetlands (TFW) are at significant risk of loss or alteration due to global climate change, and saltwater intrusion from sea level rise is of particular concern for these habitats due to their proximity to coastal areas. A space-for-time model was used to investigate the effects of saltwater intrusion on soil methanogen communities along naturally occurring salinity gradients on the Waccamaw, James, and Hudson Rivers. Amplification of the methyl coenzyme-M reductase (mcrA) functional gene was used in qPCR, reverse transcription qPCR, and T-RFLP to measure the abundance, activity, and community composition of soil methanogens. Both the abundance and activity of methanogens decreased with increasing salinity, and the both total and active methanogen community composition shifted in response to changes in salinity. This research demonstrates that saltwater intrusion will alter carbon cycling in TFWs, potentially altering their ability to sequester carbon and keep pace with rising sea level.

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Daniels, Camille Arian. "Microbial Landscapes of Corals and Ctenophores". Scholar Commons, 2011. http://scholarcommons.usf.edu/etd/3061.

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As technology and engineering allow mankind to survey nature at finer scales, the importance of bacteria has been elucidated in their metabolic diversity, ability to transfer genetic information, involvement in biogeochemical cycling, and sheer abundance. With an individual domain of life unto themselves, this diverse group of microorganisms plays an integral role in facilitating life on land and in the oceans, and is second only to viruses in abundance on Earth. They carve niches in a wide range of environments, including those inhospitable to other life forms, and reside in concert or to the detriment of other microbes and/or hosts they inhabit. Solely culturing microorganisms has proven to severely underestimate microbial numbers, capturing less than 1% of marine microbes. However, the advent of molecular methods has revealed the ubiquity, abundance, and diversity of bacteria. Higher organisms have evolved varying degrees of ecological relationships with bacteria, ranging from mutualism to parasitism. As the microbial players are elucidated, determining the specificity and functional roles of these bacteria is a critical and exciting scientific question. The microbiome of corals is an interesting model of complexity, with the animal host striving to maintain a delicate symbiosis, and using its microbiota to assist in nutrient cycling and protection. A contrasting example to the well-studied cnidarians are ctenophores, gelatinous organisms that are globally distributed in the world's oceans, yet the literature contains few studies on microbiota associated with this unique group of animals. Since ctenophores are one of the earliest diverging, extant multicellular animals, these unique organisms could prove to be a better model system than cnidarians. The first project in this dissertation examined spatial structure of bacteria across wild, healthy colonies of the coral Montastraea annularis. Microscale heterogeneity of the bacterial community was observed in coral mucus samples collected tens of centimeters apart on the same coral colony, which has implications for sampling strategies in microbiological studies, and impacts the application of the bacterial community as a proxy for determining coral condition in coral restoration projects. The second project looked at the linkages between coral bacterial community composition and zooxanthellae clade in Pocillopora damicornis, and results suggested that clade is not a major factor in influencing coral bacterial community composition. Sample location was also considered in the P. damicornis bacterial surveys and determined to be driving community structure. The third project is the first study to describe bacteria associated with ctenophores (Mnemiopsis leidyi and Beroe ovata). The ctenophores contained bacterial communities that were distinct from the surrounding water column, and temporal variability was exhibited by bacteria associated with the ctenophores. Exploring microbial landscapes in cnidarians and ctenophores to understand microbial roles in health and disease is the uniting theme of the three separate projects that will be discussed in this dissertation.

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Gumiere, 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/.

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A cana-de-açúcar é atualmente a cultura de maior importância agrícola do Estado de São Paulo, a partir da qual são gerados açúcar e etanol, além de vários outros subprodutos. No entanto, com a expansão das fronteiras agrícolas e alterações nas práticas de manejo, ocorre atualmente um momento de adequação de tal cultivo, que visa uma maior produtividade e sustentabilidade de produção. Para isto, dentre outros fatores, o papel da comunidade microbiana presente nos solos pode ter fundamental importância, auxiliando no melhor desenvolvimento da planta. No entanto, pouco se sabe sobre a comunidade microbiana existente nos solos cultivados com cana-de-açúcar. Dessa forma, este trabalho teve como objetivo avaliar a diversidade e a abundância de fungos em solos de cultivo de cana-deaçúcar no estado de São Paulo, em áreas sob diferentes atributos químicos, físicos e de manejo. Objetivou-se também, verificar a ocorrência de padrões biogeográficos na estruturação de tais comunidades. Para isso, foi realizada a análise da estrutura das comunidades fúngicas por polimorfismo de comprimento de fragmentos de restrição terminal (T-RFLP), juntamente com a quantificação destas comunidades por meio da PCR em tempo real (qPCR) em 476 amostras de solo, obtidas de 11 áreas de cultivo (usinas). Dentro deste conjunto de dados, temos que os atributos químicos, físicos e manejo explicam maiores valores de variância dentro de cada área amostra, mas pouco explicam da variância geral dos dados, sugerindo a ocorrência de padrões biogeográficos das comunidades de fungos neste ambiente. Tal ocorrência foi confirmada pela significância estatística da correlação entre distância e dissimilaridade das comunidades de fungos, dando suporte a geração dos primeiros mapas biogeográficos de fungos em tais solos. Adicionalmente, a abundância de fungos mostrou-se relacionada com a produtividade da cultura, indicando este ser um dos fatores que modulam a produtividade de cana-de-açúcar nas áreas avaliadas.
The 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.

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46

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.

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L'objectif de ce travail est d'analyser, au cours d'une cinétique de 24 mois, les effets de différents types de produits organiques (Boue de STEP, Fumier, Compost de fumier et Compost de boue) sur les communautés microbiennes telluriques, en tenant compte des conduites culturales. Les communautés ont été analysées d'un point de vue quantitatif (dénombrement des bactéries hétérotrophes aérobies cultivables, quantification de l'ADN et du carbone microbien) et par un suivi de l'activité métabolique potentielle (Biolog) et de la diversité génétique (T-RFLP ADNr 16S). Nous avons mis en évidence un impact spécifique transitoire au cours des trois premiers mois suivant l'épandage. L'évolution des communautés semble particulièrement influencée par la proportion de carbone minéralisable et de lignine (Van Soest) dans les produits organiques. L'influence du labour et des végétaux implantés est également révélée par l'évolution de la structure des communautés bactériennes au cours de la cinétique
The 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

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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.

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Le principal objectif de ce travail de recherche était l'étude de la dynamique des
communautés 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.

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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.

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Inflammatory bowel diseases, (IBD), are a group of chronic disorders of the gastro-intestinal tract, and include Crohn’s disease (CD) and Ulcerative Colitis (UC). The pathogenesis is not known, but involves at least in part a loss of tolerance towards the commensal colonic microbiota. In this thesis, we show in animal models of CD and UC that the colonic mucosal blood flow increased compared to healthy animals. This blood flow increase is due to an up regulation of endothelial nitric oxide synthase (NOS). Further, we show in the UC model that the thickness of the firmly adherent colonic mucus layer increased compared to healthy animals. This increase is due to an up regulation of inducible NOS in the epithelium. Both the blood flow and mucus thickness increase appear to be protective mechanisms. We demonstrate that the firmly adherent colonic mucus layer acts as a partial barrier towards luminal bacteria. In the UC model, this barrier is destroyed, causing increased bacterial translocation. The adhesion molecule P-selectin was up regulated in the UC model, leading to increased interactions between leukocytes and the endothelium, but also increased interactions between platelets and the endothelium. This indicates that not only leukocytes, but also platelets are involved in colonic inflammation. The addition of the probiotic bacterial strain Lactobacillus reuteri prevented disease by normalizing P-selectin levels and endothelial interactions with leukocytes and platelets. Lactobacillus reuteri also decreased bacterial translocation over the epithelium. In summary, this thesis highlights the importance of colonic barrier functions, and investigates the role of the microbiota in experimental IBD.

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Ormiston, 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.

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50

Lenz, 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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