Thesis (doctoral)--Universität, Hamburg, 2006. / Includes bibliographical references (p. [215]-225) and index.

Thesis (M.S.) -- Mississippi State University. Department of Geosciences. / Title from title screen. Includes bibliographical references.

No description available.

This paper's objective is to determine the best approaches for clean-up of an underground oil leak using cost-benefit analysis. The background aspects of the leak, including a description and history of the oil plume, aspects of the site, and applicable Federal and local regulations, are discussed. Several remediation methods are chosen for examination. The costs associated with each method are estimated. An analysis of the area's property value data using the hedonic approach to benefits estimation is also conducted. Costs of the clean-up of the oil plume are compared to the benefits. It was determined that the amount of estimated benefits from restoration programs is $7.6 million. Based on this information and the cost data, the microbial fence / hydraulic containment method and the enhanced groundwater extraction / hydraulic containment method should be considered as remediation approaches. / Master of Arts

Les intégrons sont des éléments génétiques bactériens. Découverts récemment dans le contexte clinique, ils sont présents dans le génome d’un certain nombre de bactéries provenant d’environnements très variés. Ils sont composés d’un gène codant une intégrase et d’une succession de cassettes de gènes. L’activité de l’intégrase permet l’acquisition, la perte ou le réarrangement des cassettes. Par ailleurs un promoteur permet l’expression des cadres de lecture contenus dans les cassettes de gène. Ainsi les intégrons sont à la fois des réservoirs de gènes et des systèmes d'expression de ces gènes. Dans le contexte clinique, ils sont connus pour être impliqués dans l'adaptation des bactéries pathogènes. Ils sont en effet capables d'acquérir et de diffuser des gènes conférant un avantage sélectif face à la pression exercée par l’usage des antibiotiques et des biocides, et par ailleurs d’être mobilisés afin d’être transférés horizontalement. Quelques études ont porté sur les intégrons en dehors des environnements cliniques. Elles ont permis de caractériser de nombreuses cassettes de gènes, sans toutefois en atteindre toute la diversité, à partir de bactéries ou de communautés bactériennes issues d’environnements soumis à différents niveaux de contaminations. Cependant, la diversité de l'intégrase a été peu étudiée, car le plus souvent les études se sont limitées aux séquences d’intégrons cliniques. Ainsi, les intégrons environnementaux sont encore mal connus et mal caractérisés. Les objectifs de ma thèse étaient de caractériser la diversité des intégrons environnementaux, avec un focus particulier sur les intégrases, à partir d’environnements soumis à des contaminations chimiques variables, dans le but d’évaluer le rôle possible des intégrons dans l'adaptation des bactéries face à des perturbations environnementales. Au cours de ces travaux, environ 800 séquences d’intégrases différentes, pour la plupart encore inconnues, ont été obtenues à partir de différents sédiments d’eau douce et côtiers. Des études in situ et en microcosmes, d’environnements d’eau douce ou de milieux côtiers, et avec différents types et niveaux de polluants, ont permis de mettre en évidence un impact des contaminations du milieu sur la diversité des intégrons, sur l’intégrase comme sur les cassettes de gène, de manière indépendante à la structure de la communauté bactérienne. Enfin, lors de cette thèse a été réalisée la caractérisation d’un intégron potentiellement adaptatif face à une pollution pétrolière, porteur de la séquence intIOPS mise en évidence et nommée par Lionel Huang lors de sa thèse. Finalement, les résultats obtenus lors de cette thèse ont apporté de nouveaux éléments qui viennent soutenir notre hypothèse principale que les intégrons environnementaux seraient impliqués dans l’adaptation des communautés bactériennes en réponse à la présence de contaminants dans les milieux non cliniques. / Integrons are bacterial genetic elements. Recently discovered in the clinical context, they are present in the genome of a number of bacteria from a variety of environments. They are composed of a gene encoding an integrase and a succession of gene cassettes. The activity of integrase allows the acquisition, loss or rearrangement of cassettes. Furthermore, a promoter allows expression reading frames contained in the gene cassettes. Thus, integrons are both reservoirs of genes and these gene expression systems. In the clinical context, they are known to be involved in the adaptation of pathogenic bacteria. They are able to acquire and disseminate genes conferring a selective advantage over the pressure exerted by the use of antibiotics and biocides, and also being mobilized to be transferred horizontally. Some studies have focused on integrons outside of clinical environments. They have characterized many gene cassettes, without however reaching the diversity, from bacteria or bacterial communities coming from environments with different levels of contamination. However, the diversity of integrase has been little studied, because the majority of studies are limited to clinical integron sequences. Thus, environmental integrons are still poorly characterized and their diversity are little understood. The objectives of my thesis were to characterize the diversity of environmental integrate with a particular focus on integrase, from environments with varying chemical contamination, to evaluate the possible role of integrating in adapting bacteria face environmental disturbances. In this work, approximately 800 different integrase sequences, mostly unknown, were obtained from various freshwater and coastal water sediments. Field studies and microcosms of freshwater or coastal environments, with different types and levels of pollutants allowed to demonstrate an impact of environmental contaminations on the integron diversity, whether on the integrase or the gene cassettes, independently to the bacterial community structure. Finally, in this thesis the characterization of a potentially adaptive integron facing an oil pollution were performed. This integron carrying the intIOPS sequence highlighted and named by Lionel Huang during his thesis. Finally, the results obtained in this thesis provide further elements which support our main hypothesis that environmental integrons would be involved in the adaptation of bacterial communities in response to the presence of contaminants in non- clinical settings.

In 1970 the Arrow oil spill off Cape Breton contaminated 305 kilometres of shoreline. Aerial and land surveys have demonstrated that natural weathering has occurred throughout this period, but it was relatively slow, especially in sheltered areas like Black Duck Cove lagoon. This study analyzed the microbial hydrocarbon degradation potential in the lagoon sediments using direct and culture-based techniques. Mineralization of hydrocarbon substrates (hexadecane, octacosane and naphthalene) indicated the presence of an active degradative microbial community, however, genes from known bacterial hydrocarbon degradation pathways (alkB, ndoB, phnAc) were not detected by direct extraction of sediment DNA and PCR amplification. Sediment enrichment cultures had increased mineralization rates for naphthalene and hexadecane, and a hexadecane-degrading pure culture, Rhodococcus sp. BDC14, with a typical alkB gene was isolated. PCR analysis of total community DNA extracted directly from the enrichments indicated the presence of the Alcanivorax borkumensis alkB1 genotype. The results demonstrated that there were notable differences between culture-based and direct molecular analytical techniques in characterizing the contaminated sediments.

Alkane monooxygenases (encoded by the alkB gene) are a group of microbial enzymes that catalyze the first reaction of alkane degradation. Studies to determine the diversity and prevalence of alkB genotypes in the environment have focused on culturable organisms. The goal of this research was to use culture-independent methods (DGGE, clone library) to identify and characterize alkB genes, and to determine their prevalence in Arctic contaminated soils. General alkB PCR degenerate primers (alkB-Mc) were designed using the conserved nucleotide sequences of the Histidine I Box and Histidine III Box. General alkB-Mc and alkM (Acinetobacter spp. alkane monooxygenase genes) primers were used to screen the soils for the presence of alkane monooxygenase genotypes. A predominance of the Rhodococcus spp. alkB genotypes and the absence of alkM genotypes in these soils was found. alkB PCR fragments amplified from the soils were analyzed by DGGE (Denaturing Gradient Gel Electrophoresis). BlastN and blastX results of the DGGE bands sequences showed that they were similar to Rhodococcus spp. alkB genotypes (~80-90% DNA identity and ~80-90% amino acid homology). An alkB clone library was built using the general alkB-Mc primer set, screened by RFLP (Restriction Fragment Length Polymorphism) and characterized by sequencing of alkB clones. BlastN and blastX results of the alkB clone sequences showed the presence of divergent alkB genotypes (≤ 70% DNA identity and ≤ 67% of amino acid homology to data base sequences). The alignment of the clone-derived amino acid sequences to confirm functional alkane monooxygenase sequences revealed the presence of Histidine Box II and the HYG motif in all of the deduced amino acid clone sequences. These results indicate that the alkB sequences from the clone library represent novel alkB sequences. Both alkB DGGE and clone library techniques were independently able to identify alkB genotypes from High G+C microorganisms as predominant in the 1A03 soil sample. Nevertheless, only the clone library approach identified putative novel alkB sequences. Mineralization of hexadecane and naphthalene was clearly observed at subzero temperatures (-5ºC) in Arctic contaminated soils, proving that the indigenous microbial communities could mineralize these representative hydrocarbons at subzero temperatures in an environment that is predominantly frozen for most of the year.

The marine environment’s evolving discourse on oil pollution in the High Seas since the 1958 Convention on the High Seas and the Convention on Fishing and Conservation of the Living Resources of the High Seas is of great significance. This research aims to investigate the changes and developments in this discourse, shedding light on the importance of addressing oil pollution and its impact on the marine environment. By examining the changes in discourse, the study aims to highlight the difficulty of the problem and the potential implications of its resolution. The approach involves analyzing the 1958 Conventions, GESAMP reports, and the 1982 United Nations Convention on the Law of the Sea. The findings indicate that the 1982 treaty successfully addressed the semantic ambiguity of the terms ships and oil found in the 1958 Conventions. The inclusion of the term vessels in the treaty provided a more comprehensive definition, ensuring coverage of all types of ships. Furthermore, the discourse expanded beyond a singular focus on oil, encompassing a broader range of pollutants and environmental concerns. These results signify progress towards a more holistic approach to combat oil pollution in the high seas. The implications of these findings underscore the importance of ongoing efforts to protect and preserve the marine environment.

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No description available.