Submitted by GÉSSICA APARECIDA SILVEIRA (gessicasilveira100@hotmail.com) on 2016-01-22T12:21:41Z No. of bitstreams: 1 Dissertação_Gessica_Aparecida_Silveira.pdf: 2697973 bytes, checksum: 0379873e1b58dd16332e3d3e730d4b7b (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-01-25T13:46:57Z (GMT) No. of bitstreams: 1 silveira_ga_me_jabo.pdf: 2697973 bytes, checksum: 0379873e1b58dd16332e3d3e730d4b7b (MD5) / Made available in DSpace on 2016-01-25T13:46:57Z (GMT). No. of bitstreams: 1 silveira_ga_me_jabo.pdf: 2697973 bytes, checksum: 0379873e1b58dd16332e3d3e730d4b7b (MD5) Previous issue date: 2015-12-14 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Atividades agropecuárias contribuem para a degradação das águas, alterando processos físico-químicos e biológicos, principalmente pela ocupação e uso do solo, por processos de lixiviação e/ou erosão. Os objetivos do presente trabalho foram: avaliar a influência do uso do solo na qualidade da água dos córregos Jaboticabal e Cerradinho e estudar o perfil metabólico da população microbiana da água. As coletas (C1 a C6) foram realizadas bimestralmente (Fev a Dez/2014) em oito pontos (P1 a P8), um deles situado na entrada do município de Jaboticabal, no córrego Cerradinho; outro, próximo à nascente do Córrego Jaboticabal; três pontos localizados em área urbana e os demais, em área rural. Foram determinadas variáveis físicas e químicas e a comparação metabólica da população microbiana das amostras de água foi realizada pela avaliação da capacidade de metabolização de diversas fontes de carbono pelo método EcoPlate (Biolog). Os resultados para oxigênio dissolvido, cloreto, nitrito, nitrato, sólidos totais dissolvidos e turbidez, estão de acordo com os valores estabelecidos na resolução 357/2005 do Conselho Nacional do Meio Ambiente (CONAMA), para corpos d´água classe 2. Em todos os pontos e coletas, o teor de fósforo total (Ptotal) excedeu o limite estabelecido pelo CONAMA. Em pontos próximos de atividades agrícolas ocorreram alterações nos valores de variáveis físicas e de variáveis químicas, observando-se resultados elevados para Ptotal e demanda química de oxigênio. A estatística multivariada auxiliou na interpretação dos resultados, mostrando que as atividades antropogênicas afetam a qualidade da água. O estudo de comparação das populações microbianas pela análise da capacidade de metabolização de diferentes fontes de carbono mostrou que a população microbiana da água parece não estar sendo alterada pelas atividades agrícolas. O perfil metabólico da população bacteriana das amostras não apresentou correlação com a presença das atividades agrícolas, os resultados mostram diferenças entre as coletas, mas não entre os pontos de amostragem. Atividades agropecuárias contribuem para a degradação das águas. Metais incorporados no solo, devido a diferentes manejos, podem ser transportados para as águas superficiais por processos de lixiviação e/ou erosão contaminando-as. Bactérias resistentes a metais podem ser utilizadas em processos de biorremediação. Objetivos: determinar as concentrações de metais traço em dois corpos d´água e no seu sedimento e isolar micro-organismos presentes na água para testes de resistência aos metais. As coletas de água (C1 a C6) foram realizadas bimestralmente (fevereiro a dezembro/2014) em oito pontos (P1 a P8). Um deles situado na entrada do município de Jaboticabal, no córrego Cerradinho; outro, próximo à nascente do Córrego Jaboticabal; três pontos localizados em área urbana e os demais, em área rural. O sedimento foi coletado na C6 nos pontos P3, P4, P6, P7 e P8. Nas amostras de água e sedimento foram determinadas as concentrações de cobre, cádmio, zinco, chumbo, níquel e cromo. Visando relacionar os teores de metais encontrados na água com os presentes no solo do entorno, foram coletadas (em fevereiro e agosto/2014), amostras de solo, em doze pontos (PS1 a PS12): PS1, PS2 e PS3, distantes do córrego Jaboticabal; PS4, PS5 e PS6 em área de plantação; PS7, PS8, PS9, PS10, PS11 e PS12, nas matas ciliares presentes nas imediações do córrego Jaboticabal. Foram isolados 182 micro-organismos das amostras de água e submetidos a testes de resistência aos metais estudados em meio de cultivo contendo diferentes concentrações (1, 2, 3, 4 e 5 mmol L-1) dos metais. Em pontos próximos ao córrego Jaboticabal foi possível observar maiores concentrações de metais no solo que, portanto, pode afetar a qualidade da água por meio de processos de erosão e/ou lixiviação, promovendo aumento da concentração de metais no corpo d’ água. Para a água observou-se reta de tendência com aumento nas concentrações de cádmio, cobre e cromo nos pontos da área agrícola (P6, P7 e P8). No sedimento, as maiores concentrações de metais foram encontradas em área agrícola evidenciando que o córrego está sendo impactado. Os micro-organismos isolados mostraram capacidade de se desenvolver mesmo na maior concentração estudada (5 mmol L-1) em proporções diferentes: para Zn (62,1%) e Pb (92,9%), Cd (32,4%) e Ni (29,7%), Cu (0,5%) e Cr (0%). Dos isolados resistentes 35 se desenvolveram em meio com quatro metais (Cd, Zn, Pb e Ni), mas apenas 1 isolado apresentou resistência aos cinco metais (Cu, Cd, Zn, Pb e Ni). Os microrganismos isolados precisam ser identificados e poderão ser utilizados em processos de biorremediação. / Farming activities contribute significantly to water degradation through alterations in physico-chemical and biological properties, which are mainly derived from land use and occupation as well as processes such as leaching and/ or erosion. This paper focused on assessing the influence of soil use on the water quality of surface waters of Jaboticabal and Cerradinho streams and study the metabolic profile of microbial communities found in this water body. Sampling dates (C1 to C6) were carried out bimonthly (from February to December of 2014) at eight different points (P1 to P8). One of these areas was set at the entrance of Jaboticabal city in Cerradinho stream. Another point lies near the source of the Jaboticabal stream. Three points were set within the urban area and the others within the rural area of Jaboticabal. Water physical and chemical variables were assessed. Moreover, we compared the ability of microorganisms to metabolize different sources of carbon using the Ecoplate method (Biolog). The results on dissolved oxygen, chloride, nitrite, nitrate, total dissolved solids and turbidity are in accordance with standards established by resolution number 357/ 2005 of the National Council on the Environment (CONAMA) for class 2 water bodies. The concentration of total phosphorus (TP) exceeded the limit value set by the CONAMA. We also noted significant changes on physical and chemical variables in areas near agricultural activities such as alterations of TP and chemical oxygen demand. Multivariate statistics assisted on data interpretation and showed the influence of human activities on water quality. Furthermore, the comparisons among microbial communities via study of metabolization of various carbon sources proved that farming activities have not affected the population structures. Therefore, the bacterial metabolic profile had no association with farming practices; however, the results showed differences among sampling dates, but not referring to the sampling points. Agricultural activities contribute to the degradation of the water bodies. Metals incorporated into the soil, due to different management, can be transported to the surface waters through the processes of lixiviation and / or erosion, contaminating them. Bacteria which are resistant to metals can be used in the bioremediation processes. Objectives: To determine the concentrations of trace metals in two a bodies of water and its sediment and isolate micro-organisms present in the water for testing their resistance to metals. The water sampling dates (C1 to C6) were carried out bimonthly (from february to december of 2014) at eight different points (P1 to P8). One of these areas was set at the entrance of Jaboticabal city in Cerradinho stream. Another point lies near the source of the Jaboticabal stream. Three points were set within the urban area and the others within the rural area of Jaboticabal. The sediment was sampling dates in C6 in the points P3, P4, P6, P7 and P8. For the water and sediment samples were determined the concentrations of copper, cadmium, zinc, lead, nickel and chromium. Aiming to relate the the levels of metals found in water with the ones present in the soil from the surroundings, were collected (in february and august / 2014), samples of the soil in twelve points (PS1 to PS12): PS1, PS2 and PS3, far from the stream Jaboticabal; PS4, PS5 and PS6 in plantation areas; PS7, PS8, PS9, PS10, PS11 and PS12,in riparian forests present in the stream nearby. 182 micro-organisms from the samples were isolated in the water samples and tested for resistance to the metals in culture media containing different concentrations(1, 2, 3, 4 and 5 mmol L-1) of metals. At points near the stream it was possible to observe higher metal concentrations in soil, therefore, may affect the quality of water through erosion and / or leaching, promoting increased concentration of metals in the body of water. For the water, the trend was observed with the increase in the concentrations of cadmium, copper and chromium in points of the agricultural area (P6, P7 and P8). In the sediment, the highest concentrations of metals were found in agricultural areas, showing that the stream is being impacted. The micro-organisms isolated showed the same ability to grow even in the highest concentration studied (5 mmol L-1) in different proportions: for Zn(62.1%) and Pb (92.9%), Cd (32.4%) and Ni (29.7%), Cu (0.5%) and Cr (0%). From the 35 isolated resistant organisms developed in medium with four metals (Cd, Zn,Pb and Ni), but only one isolate was resistant to the five metals (Cu,Cd, Zn, Pb and Ni). The microorganisms need to be identified and will be able to be used in bioremediation processes.

Submitted by MILENA TAVARES LIMA null (milena.tavares@hotmail.com) on 2018-02-22T20:53:15Z No. of bitstreams: 1 tese.docx: 10715432 bytes, checksum: 43d05c474d46b9a07105fe43fdc08920 (MD5) / Rejected by Alexandra Maria Donadon Lusser Segali null (alexmar@fcav.unesp.br), reason: Solicitamos que realize correções na submissão seguindo as orientações abaixo: O arquivo para ser submetido no repositório deve ser em formato pdf como descrito no item 13 do tutorial do repositório: 13. Para enviar o arquivo contendo sua dissertação ou tese é necessário que:  o arquivo esteja no formato Portable Document Format (PDF);  o arquivo não esteja protegido;  o trabalho (dissertação ou tese) esteja reunido em um único arquivo, inclusive os apêndices e anexos. Agradecemos a compreensão on 2018-02-23T13:51:33Z (GMT) / Submitted by MILENA TAVARES LIMA null (milena.tavares@hotmail.com) on 2018-02-23T13:57:19Z No. of bitstreams: 1 Tese_Milena_Tavares_Lima_Constancio.pdf: 2839426 bytes, checksum: 0aaadc8cdfe45a78b2777dd26109dea2 (MD5) / Approved for entry into archive by Alexandra Maria Donadon Lusser Segali null (alexmar@fcav.unesp.br) on 2018-02-23T17:32:08Z (GMT) No. of bitstreams: 1 constancio_mtl_dr_jabo.pdf: 2839426 bytes, checksum: 0aaadc8cdfe45a78b2777dd26109dea2 (MD5) / Made available in DSpace on 2018-02-23T17:32:08Z (GMT). No. of bitstreams: 1 constancio_mtl_dr_jabo.pdf: 2839426 bytes, checksum: 0aaadc8cdfe45a78b2777dd26109dea2 (MD5) Previous issue date: 2018-01-29 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O interesse no estudo de comunidades microbianas de ambientes pouco avaliados, impactados e/ou extremos tem aumentado significativamente. Dentre os ambientes estudados, encontram-se as águas residuais de áreas de mineração. Com o grande número de cavas e lagoas de rejeitos gerados através da atividade mineradora e o pouco estudo deste tema no Brasil, foi desenvolvido este trabalho, onde avaliamos a taxonomia e capacidade funcional da comunidade microbiana. As amostras de água foram coletadas de uma cava de mineração e uma lagoa de rejeitos de uma região anteriormente utilizada para extração de minério de ferro no Centro de Biodiversidade (CeBio) da empresa VALE/SA, em Sabará/MG. Análises do perfil de atividade metabólica indicaram um excelente desempenho quanto à degradação de diferentes compostos. Além disso, o isolamento com métodos tradicionais de cultivo mostrou que algumas bactérias apresentam capacidade em produzir diferentes enzimas de interesse biotecnológico. O DNA foi extraído e sequenciado através de técnicas metagenômicas, o sequenciamento do gene de 16S rRNA foi realizado na plataforma Ion PGM™. Esta análise, além de revelar a taxonomia da comunidade presente na água da cava e lagoa, identificou o perfil funcional indicando enriquecimento de subsistemas importantes para ambas as amostras. Adicionalmente para a água da cava de mineração, foi realizado o sequenciamento do DNA total na plataforma Ion Proton™, que através de análises com o banco de dados SEED revelou genes associados à manutenção celular e ao ciclo do nitrogênio, sugerindo que a comunidade microbiana está bem adaptada ao processo de recuperação da área. Além disso, as ORfs preditas do metagenoma foram utilizadas para uma análise no banco de dados BacMet, que revelou uma abundância de genes relacionados a resistência a metais. Assim, nossos dados expandem os conhecimentos sobre a estrutura e capacidade funcional das comunidades microbianas de ambientes aquáticos impactados, fornecendo uma melhor compreensão do papel dos micro-organismos em processos de remediação natural. / The interest in the study of microbial communities of low evaluated, impacted or extreme environments has increased significantly. Among the studied environments, there is the wastewater from mining areas. Due to the large number of reject pits and lagoons generated by the mining activity and the lack of study of this theme in Brazil, this study was developed to evaluate the taxonomy and functional capacity of the microbial community. The water samples were collected from a mining pit and a reject lagoon from a region formerly used for iron extraction at the Biodiversity Center (CeBio) from VALE/SA, in Sabará/MG. Analyzes of the metabolic activity profile indicated an excellent performance regarding the degradation of different compounds. Moreover, the isolation with traditional methods of culture showed that some bacteria have the capacity to produce different enzymes of biotechnological interest. The DNA was extracted and sequenced using metagenomic techniques, the 16S rRNA gene sequencing was performed on the Ion PGM™ platform. This analysis, in addition to revealing the taxonomy of the community present in the water of the pit and the lagoon, identified the functional profile indicating enrichment of important subsystems for the studied samples. In addition to the water from the mining pit, the total DNA sequencing was carried out on the ION Proton™ platform, which, through analysis with the SEED database, revealed genes associated with cell maintenance and the nitrogen cycle, suggesting that the microbial community is well adapted to the recovery process of the area. Also, the predicted ORfs from metagenomic were used for an analysis in the BacMet database that revealed an abundance of genes related to resistance to metals. Thus, our data expand the knowledge about the structure and functional capacity of microbial communities in impacted aquatic environments, providing a better understanding of the role of microorganisms in natural remediation processes. / FAPESP: 2014/07592-3

The need for new antibiotics has been highlighted recently with the increasing pace of emergence of drug resistant pathogens (MRSA, XDR-TB, etc.). Modification of existing antibiotics with the additions of side chains or other chemical groups and genomics based drug targeting have been the preferred method of drug development at the corporate level in recent years. These approaches have yielded few viable antibiotics and natural products are once again becoming an area of interest for drug discovery. We examined the antimicrobial "Red Soils" of the Hashemite Kingdom of Jordan that have historically been used to prevent infection and cure rashes by the native peoples. Antimicrobial producing bacteria were present in these soils and found to be the reason for their antibiotic activity. After isolation, these bacteria were found to excrete their antimicrobials into the liquid culture media which we could then attempt to isolate for further study. Adsorbent resins were employed to capture the antimicrobial compounds and then elute them in a more concentrated solution. As part of a drug discovery program, we sought a way to quickly characterize other soils for potential antibiotic producing bacteria. The community level physiologic profile was examined to determine if this approach would allow for a rapid categorizing of soils based on their probability of containing antimicrobial producing microorganisms. This method proved to have a high level of variability that could not be overcome even after mixing using a commercial blender. The role of these antimicrobial producing bacteria within their natural microbial community has largely been confined to microbe-plant interactions. The role of antimicrobial-producing microorganisms in driving the diversity of their community has not been a focus of considerable study. The potential of an antimicrobial-producing bacterium to act as a driver of diversity was examined using an artificial microbial community based in a sand microcosm. The changes in the microbial assemblage indicate that antimicrobial-producing bacteria may act in an allelopathic manner rather than in a predatory role. / Ph. D.

Tese(doutorado) - Universidade Federal do Rio Grande, Programa de Pós–Graduação em Oceanografia Biológica, Instituto de Oceanografia, 2013. / Submitted by Cristiane Gomides (cristiane_gomides@hotmail.com) on 2013-10-15T11:55:34Z No. of bitstreams: 1 NG.pdf: 3593852 bytes, checksum: 4c20bdc4282f3f36ffe2b4772a93b1cb (MD5) / Approved for entry into archive by Sabrina Andrade (sabrinabeatriz@ibest.com.br) on 2013-10-17T17:34:15Z (GMT) No. of bitstreams: 1 NG.pdf: 3593852 bytes, checksum: 4c20bdc4282f3f36ffe2b4772a93b1cb (MD5) / Made available in DSpace on 2013-10-17T17:34:15Z (GMT). No. of bitstreams: 1 NG.pdf: 3593852 bytes, checksum: 4c20bdc4282f3f36ffe2b4772a93b1cb (MD5) Previous issue date: 2013 / A composição (CCB) e a atividade (perfil fisiológico - PFCB) da comunidade bacteriana foram investigadas no estuário da Lagoa dos Patos e região costeira adjacente através de amostragem tipo-Lagrangiana, Euleriana e ao longo de um transecto para responder três perguntas: i) existe um padrão de recorrência (estabilidade) da CCB e PFCB em diferentes faixas de salinidade? ii) a CCB e PFCB respondem a diferentes escalas temporais e espaciais, inclusive a fenômenos climáticos globais que afetam a hidrodinâmica do estuário, tais como o “El Niño Southern Oscillation” (ENSO) ? iii) que fatores, além da salinidade, afetam a CCB e a PFCB? A CCB e a PFCB estiveram associadas à hidrodinâmica do estuário, tanto em escalas curtas (entrada de cunha salina), médias (sazonal) e largas (ENSO). Isto porquê a hidrodinâmica condiciona a variabilidade da salinidade e secundariamente o seston, nutrientes inorgânicos dissolvidos e substratos orgânicos, que afetam as bactérias. A CCB foi primariamente estruturada pela salinidade, seguindo o padrão normalmente encontrado na literatura para estuários, com comunidades características de água salgada e doce. Já a PFCB teve maior influência da quantidade de nutrientes e substratos e de maneira indireta da salinidade. De maneira geral, a atividade bacteriana foi menor em águas salgadas mais oligotróficas. Entretanto, grande atividade bacteriana foi observada em água salgada rica em nutrientes que penetrava no estuário. A maior concentração de nutrientes na água salgada pode ter sido resultado de ressuspensão de sedimento, ou ingresso de água costeira previamente enriquecida com água estuarina. / The composition (BCC) and activity (community level physiological profiles, CLPP) of the bacterial community were investigated in the Patos Lagoon estuary and adjacent coastal region through Lagrangian-like, Eulerian and transect samplings in order to answer three questions: i) is there a pattern of recurrence (stability) of the BCC and CLPP in different salinity ranges? ii) does the BCC and CLPP respond to different temporal and spatial scales, including global climate phenomena that affect the estuary hydrodynamics like El Niño Southern Oscillation (ENSO)? iii) which factors apart from salinity affect the BCC and CLPP? The BCC and CLPP were associated to the estuary hydrodynamics, at short- (salt wedge entrance), meso- (seasonal) and largescales (ENSO). This is because the hydrodynamics conditions the variability of salinity and secondarily the seston, dissolved inorganic nutrients and organic substrates, which in turn affect bacteria. The BCC was primarily structured by salinity, following the pattern commonly found in the literature for estuaries, with characteristic fresh- and saltwater communities. The CLPP had higher influence of the amount of nutrients and substrates and indirectly of salinity. In general the bacterial activity was lower in oligotrophic, saltier waters. However, high bacterial activity was observed in nutrient-rich saltwater that entered the estuary. The higher concentration of nutrients in saltwater is likely the result of ressuspension of the sediment or ingress of coastal water previously enriched with estuarine water.

The objective of this work was to understand microbial population density and diversity, both spatially and temporally, in wetland mesocosms to gain a better fundamental understanding for use in the optimization and design of constructed wetlands (CWs). A standardized community level physiological profiling (CLPP) data analysis protocol was adapted and utilized for CW mesocosms. A new one-dimensional metric was developed to track community divergence using BIOLOGTM ECO plate data. The method proved easy to use, did not require a background in multivariate statistics, and accurately described community divergence in mesocosm systems. To study mesocosm biofilm-bound bacterial communities an appropriate detachment protocol was required. Various shaking protocols were evaluated for their effectiveness in the detachment of bacteria from mesocosm pea gravel, with a focus on detachment of viable and representative bacterial communities. A protocol based on mechanical shaking with buffer and enzymes was identified as an optimal approach and used further in this study. The bacterial communities associated with the interstitial water, pea gravel media, and rhizospheric regions from both planted and unplanted CW mesocosms were profiled using the CLPP method and compared. Vertical community stratification was observed for all mesocosm systems. Rhizospheric communities were found to be significantly more active than their gravel-associated counterparts, suggesting that although rhizospheric bacteria were less abundant in the mesocosms they may play a more significant role in the removal and fate of water born contaminants. The start-up dynamics of CW mesocosms was investigated using the CLPP and standard CW characterization methods over an eight month period. All mesocosms showed a steep increase in interstitial community divergence until day 75-100, at which point a steady-state was reached. The interstitial communities were also characterized in terms of similarity based on experimental design treatments (planted/unplanted and origin of seeding inoculum). Four stages were identified during the start-up consisting of an initial stage where mesocosm communities were differentiated based on origin of the inoculum, a period where adjustments and shifts occurred in all mesocosm, a time where all mesocosm communities were quite similar, and a final state where community differentiations were made based plant presence in the mesocosms.

The objective of this work was to understand microbial population density and diversity, both spatially and temporally, in wetland mesocosms to gain a better fundamental understanding for use in the optimization and design of constructed wetlands (CWs). A standardized community level physiological profiling (CLPP) data analysis protocol was adapted and utilized for CW mesocosms. A new one-dimensional metric was developed to track community divergence using BIOLOGTM ECO plate data. The method proved easy to use, did not require a background in multivariate statistics, and accurately described community divergence in mesocosm systems. To study mesocosm biofilm-bound bacterial communities an appropriate detachment protocol was required. Various shaking protocols were evaluated for their effectiveness in the detachment of bacteria from mesocosm pea gravel, with a focus on detachment of viable and representative bacterial communities. A protocol based on mechanical shaking with buffer and enzymes was identified as an optimal approach and used further in this study. The bacterial communities associated with the interstitial water, pea gravel media, and rhizospheric regions from both planted and unplanted CW mesocosms were profiled using the CLPP method and compared. Vertical community stratification was observed for all mesocosm systems. Rhizospheric communities were found to be significantly more active than their gravel-associated counterparts, suggesting that although rhizospheric bacteria were less abundant in the mesocosms they may play a more significant role in the removal and fate of water born contaminants. The start-up dynamics of CW mesocosms was investigated using the CLPP and standard CW characterization methods over an eight month period. All mesocosms showed a steep increase in interstitial community divergence until day 75-100, at which point a steady-state was reached. The interstitial communities were also characterized in terms of similarity based on experimental design treatments (planted/unplanted and origin of seeding inoculum). Four stages were identified during the start-up consisting of an initial stage where mesocosm communities were differentiated based on origin of the inoculum, a period where adjustments and shifts occurred in all mesocosm, a time where all mesocosm communities were quite similar, and a final state where community differentiations were made based plant presence in the mesocosms.