Submitted by Roberta Alves Merguizo Chinellato null (robmerguizo@yahoo.com.br) on 2017-02-13T20:05:29Z No. of bitstreams: 1 DISSERTAÇÃO ROBERTA CORREÇÃO.pdf: 2087375 bytes, checksum: 1e6e52c04ff2049723f222505199bc2f (MD5) / Approved for entry into archive by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br) on 2017-02-15T18:25:56Z (GMT) No. of bitstreams: 1 chinellato_ram_me_svic.pdf: 2087375 bytes, checksum: 1e6e52c04ff2049723f222505199bc2f (MD5) / Made available in DSpace on 2017-02-15T18:25:56Z (GMT). No. of bitstreams: 1 chinellato_ram_me_svic.pdf: 2087375 bytes, checksum: 1e6e52c04ff2049723f222505199bc2f (MD5) Previous issue date: 2017-01-18 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Com o processo de expansão industrial, as regiões costeiras e estuarinas passaram a perceber a instalação de várias indústrias, devido à proximidade aos mercados consumidores e produtores, além da facilidade de escoamento de sua produção. Essas indústrias consomem uma grande quantidade de água, que é devolvida ao ambiente juntamente com uma série de substâncias tóxicas dissolvidas, incluindo hidrocarbonetos aromáticos, de biodegradabilidade intermediária e tendência à bioacumulação. Regiões estuarinas apresentam maior dificuldade de biorremediação, devido ao fato dos contaminantes ficarem aderidos ao sedimento. Além do descarte costeiro habitual, acidentes tendem a lançar uma quantidade maior e descontrolada de poluentes. A biorremediação é o processo de tratamento que utiliza os microrganismos encontrados tanto no ambiente terrestre como aquáticos contaminados para degradar substâncias toxicamente perigosas transformando-as em substâncias menos ou não tóxicas. As atividades para conter o incêndio no Terminal Químico Aratu S.A. (Ultracargo) lançou grande quantidade de hidrocarbonetos e líquido gerador de filme aquoso (AFFF) no estuário de Santos, modificando o perfil de contaminantes da região. As bactérias heterotróficas de ambientes marinhos apresentam grande potencial de biorremediação. O objetivo do presente trabalho foi avaliar, in vitro, a sucessão de espécies de bactérias heterotróficas em sedimentos do Estuário de Santos, afetados por hidrocarbonetos e AFFF e isolar espécies bacterianas com possível potencial uso em processos de biorremediação. Foram analisadas as densidades de bactérias heterotróficas e identificadas aquelas de maior relevância, por características morfológicas e identificação molecular. Após análise das amostras locais e Microcosmo, destacaram-se as bactérias do gênero Bacillus. A sucessão sugeriu três espécies como potenciais biorremediadoras, sendo elas Bacillus pumilus, Bacillus subtilis e Staphylococcus sp. / With the industrial expansion, coastal and estuarine regions began to perceive installation of several industries, due to the proximity to the consumer markets and producers, besides the ease of transportation of their production. These industries consume a large amount of water, which is returned to the environment with a series of dissolved toxic substances, which includes aromatic hydrocarbons, which are slightly biodegradable and have the tendency to bioaccumulate. Estuarine regions present higher difficulty of bioremediation, since the contaminants are adhered to the sediment. In addition to the usual coastal discard, accidents tend to release a larger and uncontrolled amount of pollutants. Bioremediation is the treatment process that uses microorganisms found in both the terrestrial and aquatic environments to degrade toxic substances by transforming them into less toxic or non-toxic substances. The fire at the Terminal Químico Aratu S.A. (Ultracargo) launched a large amount of hydrocarbons and aqueous film-forming foam (AFFF) in the Santos estuary, modifying the profile of contaminants in the region. The heterotrophic bacteria of marine environments present great bioremediation potential. The objective of the present work was to evaluate in vitro the succession of heterotrophic bacteria species in Santos Estuary sediments affected by hydrocarbons and AFFF and to isolate bacterial species with potential use in bioremediation processes. The densities of heterotrophic bacteria were analyzed and the most relevant ones were identified, by morphological characteristics and molecular identification, where the Bacillus genus deserved attention. The succession suggested three species as potential bioremediators, being Bacillus pumilus, Bacillus subtilis and Staphylococcus sp.

Orientador: Eliana Gertrudes de Macedo Lemos / Coorientador: Jackson Antonio Marcondes de Souza / Banca: Tsai Siu Mui / Banca: Hugo Miguel Preto de Morais Sarmento / Banca: Janete Aparecida Desiderio / Banca: Tereza Cristina Luque Castelane / Resumo: Os impactos ambientais causados por sucessivas extrações de minérios e compostos gerados dos resíduos tóxicos dessa atividade têm sido foco de preocupação dos ambientalistas, neste contexto há um grande esforço gerado para o desenvolvimento de metodologias eficientes e de baixo custo para remoção de metais pesados de solos e águas contaminadas. Os métodos biológicos surgem como uma alternativa aos métodos convencionais para o solo, um dos ecossistemas terrestre que apresentam uma infinidade de recursos naturais além da grande diversidade de microrganismos interagindo entre si. O mesmo constitui fonte de investimento para o isolamento de microrganismos e análises metagenômicas para prospecção de genes envolvidos em processos importantes para o equilíbrio metabólico e ecológico, pois, tanto de maneira isolada, como em interações, estes organismos desempenham papel importante no que diz respeito à produção de enzimas na biorremoção de metais e contaminantes do solo. Este trabalho teve como objetivo isolar, caracterizar e avaliar a biossorção e bioacumulação de metais por microrganismos originados de solos de ecossistemas de Sabará, uma região de mineradora desativada Minas Gerais. Adicionalmente buscou-se avaliar a diversidade metabólica funcional, para uma comparação da microbiota de, Sabará e Brumadinho, combinada com busca de genes que conferem resistência a cromo (crhA), cobre (copA, copB, cueO) e níquel (nixA). Os isolados obtidos foram classificados em gêneros como Burkolderia, Serratia, Bacillus, Stenotrophomonas e Artrobacter, que apresentam potencial para biorremediação de metais do solo e água. Entretanto, seis dos 32 isolados apresentaram resistência aos metais cobre, cromo e níquel, na concentração de 500 mgL-1. Destes isolados, dois deles, do gênero Burkolderia e Arthrobacter (CP15 e CR11) apresentaram capacidade metabólica de biossorver e interiorizar metais pesados em diferentes... / Abstract: The environmental impacts caused by successive extractions of minerals and compounds generated toxic waste of this activity have been the focus of concern for environmentalists in this context there is a great effort generated for the development of efficient methodologies and cost-effective to remove heavy metals from soils and contaminated water. Biological methods appear as an alternative to conventional methods for the ground of the earth's ecosystems have a multitude of natural resources beyond the great diversity of microorganisms interacting. The same is investment source for the isolation of microorganisms and metagenomic analyzes to search for genes involved in important processes for metabolic and ecological balance, since both in isolation, as in interactions, these organisms play an important role as regards the production of enzymes in biorremoção metal and soil contaminants. This study aimed to isolate, characterize and evaluate the biosorption and bioaccumulation of metals by microorganisms originating from Sabara ecosystems soil, a mining region of Minas Gerais disabled. In addition we sought to evaluate the functional metabolic diversity, for a comparison of the microbiota of Sabara and Brumadinho, combined with search of genes that confer resistance to chromium (CRHA), copper (copA, CopB, cueO) and nickel (Nixa). The isolates were classified into genres such as Burkolderia, Serratia, Bacillus, Stenotrophomonas and Artrobacter, which have the potential for bioremediation of metals from soil and water. However, six of the 32 isolates were resistant to metals copper, chromium and nickel, at a concentration of 500 mg L-1. Of these isolates, two of them, the genus Arthrobacter and Burkolderia (CP15 and CR11) had metabolic capacity to internalize biossorver and heavy metals at different stages of development. As metabolic activity, the microbial community of the perimeter of iron quadrangle soils (MG) has high activity ... / Doutor

No description available.

Difficulties associated with the study of microbial communities, such as low proportions of cultivable species, have been addressed in recent years with the advent of a range of sequencing technologies and bioinformatic tools. This is enabling previously unexplored communities to be characterised and utilised in a range of biotechnology applications. In this thesis bioinformatic methods were applied to two datasets of biotechnological interest: microbial communities found living with the oil-producing alga Botryococcus braunii and microbial communities in acid mine drainage (AMD). B. braunii is of high interest to the biofuel industry due to its ability to produce high amounts of oils, in the form of hydrocarbons. However, a number of factors, including low growth rates, have prevented its cultivation on an industrial scale. Studies show B. braunii lives in a consortium with numerous bacteria which may influence its growth. This thesis reports both whole genome analysis and 16S rRNA gene sequence analysis to gain a greater understanding of the B. braunii bacterial consortium. Bacteria have been identified, some of which had not previously been documented as living with B. braunii, and evidence is presented for ways in which they may influence growth of the alga, including B-vitamin synthesis and secretion systems. AMD is a worldwide problem, polluting the environment and negatively impacting on human health. This by-product of the mining industry is a problem in the South West of England, where disused metalliferous mines are now a source of AMD. Bioremediation of AMD is an active area of research; sulphur-reducing bacteria and other bacteria which can remove toxic metals from AMD can be utilised for this purpose. Identifying bacteria and archaea that are able to thrive in AMD and which also have these bioremediation properties is therefore of great importance. Metagenomic sequencing has been carried out on the microbial community living in AMD sediment at the Wheal Maid tailings lagoon near Penryn in Cornwall. From these data have been identified a diverse range of bacteria and archaea present at both the sediment surface level and at depth, including microorganisms closely related to taxa reported from metalliferous mines on other continents. Evidence has been found of sulphur-reducing bacteria and of pathways for various other bioremediation-linked processes.

Plastificantes podem ser definidos como aditivos de baixa volatilidade utilizados para aumentar a processabilidade, flexibilidade ou diminuir a dureza de materiais poliméricos. Os ftalatos e adipatos utilizados como plastificantes, por sua baixa solubilidade em água e pelo alto coeficiente de partição octanol/água, tendem a se acumular no solo e sedimentos. Estes compostos são considerados potencialmente carcinogênicos, teratogênicos e disruptores endócrinos. A presente pesquisa compreendeu a biorremediação ex-situ do solo contaminado com resíduos de uma unidade industrial de plastificantes, utilizando reatores aeróbios, com microrganismos indígenas e exógenos adaptados através da adição de inóculo retirado da Estação de Tratamento de Efluentes por Lodos Ativados desta indústria. Foram avaliados os plastificantes: DIBP (Di-isobutilftalato), DBP (Dibutilftalato), DOP (Dioctilftalato),DIDP (Di-isodecilftalato), DIAP (Di-isoamilftalato) e DOA (dioctiladipato). Após a caracterização geotécnica do solo da área de plastificantes em 10 diferentes pontos, foram retiradas as quantidades para a biorremediação em 8 diferentes pontos (100kg/ponto) com os teores totais de plastificantes compreendidos entre 17 mg/kg solo a 6222 mg/kg solo. Análises mineralógicas, físicas e químicas foram realizadas posteriormente e indicaram que possivelmente a capacidade de troca catiônica do solo era devida aos plastificantes. Na biorremediação, os teores iniciais de plastificantes no solo, variaram de 85 mg/kg a 1688 mg/kg e após 120 dias de biodegradação em reatores aeróbios, as eficiências de remoção foram de 75 a 97%. Conforme as análises de fingerprint da comunidade bacteriana, ao final do processo, as bactérias presentes no solo eram originárias do lodo e do solo inicial e as análises de CGMS identificaram os metabólitos MEHP e os sub-produtos finais da biodegradação. / Plasticizers are low volatility compounds that offer flexibility and processability to resins. The phthalates and adipates, used as plasticizers, have low water solubility e high partition octanol/water(Kow) and accumulate in soil and sediments. This compounds are considered teratogenics, carcinogenics and as endocrine disruptors. This study evaluated the bioremediation of tropical soil contaminated with plasticizers process wastes, in aerobic conditions, with and without introduction of acclimated bacteria. After geological analysis of soil, considering ten differents points on the factory area, it was selected the soil for biodegradation of eight points (100kg/point) representing 17mg total plasticizers/kg soil to 6222mg total plasticizers/kg soil. Mineralogical, physical and chemical analysis were done and the results showed that perhaps the cationic change capacity was due to plasticizers. The plasticizers contents in soil were 85-1688mg/kg and after 120 days of biodegradation in eight aerobic reactors, the removal efficiencies were 75-97%. The fingerprint analysis showed that the final bacteria present in reactors originated from soil and sludge and the CGMS analysis identified the metabolic MEHP, and showed the sub-products and final products of biodegradation.

Microbial biofilms are significant in a variety of settings including the human microbiome, infectious disease, industrial processes, and environmental remediation. Due to the ubiquitous nature of biofilms, there is a great interest in understanding cellular activities within the biofilm matrix. Biofilm cells are able to better withstand environmental stress, experience increased horizontal gene transfer, and live longer. The purpose of this research is to grow Pseudomonas sp. strain ADP as a biofilm and examine the chemical and physical characteristics the microbe undertakes in a sticky extracellular matrix. ADP is the organism of choice because of its ability to metabolize atrazine. Cells are grown in a drip biofilm reactor and flow cells under varying time lapse to gain insight to biofilm formation. Some cells are grown with atrazine as the sole nitrogen source, while others are grown in a nutrient-rich medium to compare cells response under nutrient-limited conditions with atrazine particles in the matrix. As a positive control, Escherichia coli are grown in a similar manner. Raman spectroscopy was the main analytical technique used to evaluate the chemical and molecular characteristics of this system. Scanning electron microscopy is used to examine cellular distribution, and several assays are performed for molecular composition analysis. Raman analysis in the fingerprint region revealed distinct differences between free cells and cells in biofilm. Soluble extracellular polymeric substances (EPS) were found to be more prevalent than tightly bound EPS and lightly bound EPS in the biofilm matrix. Comparison of relative peak intensity ratios suggests that it is possible to track atrazine degradation by means of intermediates using Raman spectroscopy. SEM micrographs revealed EPS role as an immobilizing agent when in contact with compounds, such as atrazine. Further research is needed to determine if atrazine can bind to EPS fractions outside the presence of cells and whether its affinity to EPS is mostly attributed to physical conditions, due to the architecture of biofilm, or chemical, based on functional groups presents. The results obtained from this research will contribute to the development of a less invasive microscale approach to address the acquisition and induction of biotransformation activity occurring in xenobiotic degrading systems. The extracellular interactions observed can be used to further characterize biofilm-mediated bioremediation. Results have contributed to the Raman spectra library for microorganisms and organic compounds. .

The extensive use of tetrachloroethene (PCE) and trichloroethene (TCE) as cleaning solvents has resulted in widespread contamination of groundwater systems with vinyl chloride (VC). VC, a known human carcinogen, is primarily formed in groundwater via incomplete anaerobic reductive dechlorination of PCE and TCE. Aerobic, methane-degrading bacteria (methanotrophs), which are capable of VC cometabolism while growing on methane, could be important in natural attenuation of VC plumes that escape anaerobic treatment. Real-time PCR (qPCR) represents an innovative approach for detecting and quantifying the presence and activity of these VC-degrading microbes. Immediate applications of this technique include use in a laboratory setting to help elucidate the potential bacterial-substrate interactions occurring in the subsurface environments at these contaminated sites; interactions that could ultimately affect the role of methanotrophs in VC degradation. This technique could also provide lines of evidence for natural attenuation of VC, thus support existing anaerobic bioremediation technologies that generate VC as a metabolic intermediate. In this work, we evaluated several PCR primer sets from the literature for use in methanotroph qPCR assays of groundwater samples. PCR primers targeting two functional genes involved in VC cometabolism, pmoA (sub-unit of particulate methane monooxygenase (pMMO)) and mmoX (sub-unit of soluble MMO (sMMO)), as well as 16S rRNA gene primers that targeted Bacteria, and Type I and Type II methanotrophs were tested. These assays were made quantitative by constructing standard curves with DNA from Methylococcus capsulatus (Type I) and Methylocystis sp. strain Rockwell (Type II). Primer sets were evaluated by comparing gene abundance estimated against known amounts of Type I and Type II methanotroph DNA. After primer validation, an effort to substantiate this methanotroph qPCR method was made by attempting to investigate methanotroph populations in groundwater samples from VC-contaminated sites. Some samples studied were also subjected to 16S rRNA gene pyrosequencing, allowing for relative abundance comparisons with qPCR analyses. Following our primer assessment experiments, effective primer sets were used to estimate the presence of methanotrophs at environmental sites in Soldotna, Alaska; Naval Air Station Oceana, Virginia Beach, Virginia; and Carver, Massachusetts. Results showed that methanotrophs were present in nearly all wells sampled from all environmental sites. Estimations of methanotroph relative abundance in environmental samples were determined by comparing the Type I and Type II primer estimates to those of the 16S universal primers. Methanotrophs in these groundwater samples ranged from 0.2% to 6.6% of the total bacterial population. Pyrosequencing analysis of the same samples showed methanotroph relative abundances that ranged from 1.7% to 54%. In groundwater samples where both DNA and RNA was extracted, the quantities of functional gene transcripts per gene copy was compared, revealing that the transcripts/gene ratio for both pmoA and mmoX was less than one, implying relatively low methanotroph activity. Analysis of mmoX environmental sample dissociation curves revealed a double peak, indicating possible non-specific PCR products. Our data suggests that most of the qPCR primer sets used in the environmental samples adequately detect methanotrophs, though the mmoX primers need to be further validated. These primer sets will be useful for supporting VC bioremediation strategies by providing a rapid, convincing, and cost effective alternative the enrichment culture technique currently employed. Comparison of qPCR and pyrosequencing analysis revealed biases in either one, or both techniques. Finally, our preliminary transcripts/gene data suggests that the methanotrophs at the Carver site are not actively expressing pMMO and sMMO genes above basal levels.

L'uranium est un toxique à la fois chimique et radiologique. C'est un élément que l'on retrouve à faible concentration dans l'environnement sauf lors de pollutions causées par les activités humaines. Du fait de sa forte réactivité, l'ion uranyle peut se complexer à de nombreux constituants du sol, qu'ils soient minéraux ou organiques. Ces différentes formes peuvent être ainsi plus ou moins biodisponibles pour les microorganismes et les plantes et peuvent ensuite rentrer dans la chaîne alimentaire de l'homme. La connaissance et la compréhension des mécanismes de transfert et du devenir d'éléments toxiques chimiques et radiologiques dans la biosphère constituent donc un enjeu capital pour permettre une bonne estimation des risques sanitaires et écologiques. La connaissance de la spéciation est capitale pour engager des processus de biorémédiation. Ici, c'est l'effet des microorganismes sur la spéciation de l'uranium dans l'environnement qui nous intéresse. Selon les formes initiales de l'uranium, les bactéries peuvent l'accumuler et/ou le transformer et ainsi modifier sa biodisponibilité. Les modèles utilisés dans cette étude sont Cupriavidus metallidurans CH34, bactérie tellurique résistante aux métaux lourds, Deinococcus radiodurans R1, bactérie connue pour être une des espèces les plus radiorésistantes et Rhodopseudomonas palustris, bactérie pourpre autotrophe capable de dégrader les composés aromatiques en anaérobie. Ces bactéries sont cultivées en présence de deux formes d'uranium retrouvées dans l'environnement : une forme minérale, le carbonate d'uranyle et une forme organique, le citrate d'uranyle. Ces formes ont d'abord été modélisées et les milieux de culture ont été modifiés pour pouvoir travailler avec ces espèces. La capacité des bactéries à résister, à transformer et/ou accumuler l'uranium a été étudiée. On observe une différence entre les concentrations minimales inhibitrices des deux spéciations mais celle-ci est en fait due à une différence de biodisponibilité des phosphates. Aucune accumulation ne semble être mise en évidence aux pH environnementaux par dosage de l'uranium et par observation au microscope électronique à transmission alors qu'une précipitation est observée à pH 1. La spéciation de l'uranium a été étudiée par spectroscopie d'absorption X (EXAFS). La spéciation est bien maitrisée dans les milieux de culture et les précipités observés aux pH très acide sont ces complexes de phosphates d'uranyle.

Graduation date: 1998

In situ bioremediation of pentachlorophenol-contaminated ground water in a sequential anaerobic-aerobic down borehole permeable barrier reactor requires a non-toxic primary substrate for dichlorophenol cometabolism. Serum bottle tests comparing the effectiveness of eight primary substrates for aerobic dichlorophenol degradation showed phenol to be the most effective followed by imitation vanilla flavoring, guaiacol, sodium benzoate, molasses, acetic acid, propylene glycol and ethyl vanillin in propylene glycol. As phenol is a pollutant, imitation vanilla flavoring is the recommended primary substrate for field use. In a second bottle test, 3,4,5-trichlorophenol was not sufficiently biotransformed, emphasizing the need for biotransformation to occur in the anaerobic zone of the reactor. / Graduation date: 1996