Leonardo da Vinci's art and science have a dynamic relationship that can be used to better understand the role of the individual and the human body within his art. Leonardo believed that movements of the body were expressions of the soul. He also thought that the body was as a microcosm of the physical world. The theories, based in ancient tradition, would be challenged by his work with the human anatomy. By studying his notebooks it becomes evident that Leonardo held nature to be the highest creator of the world but as he worked to understand the human body and through extension the physical world, his ideas about nature and the divine became more incomprehensible. Leonardo's art reflects this turn of perspective as he becomes unable to define the physical world through the human body.

Cette étude vise à développer un système de dépollution d'eau et de sédiments viticoles. Le glyphosate, diuron et 3,4-dichloroaniline (3,4-DCA) sont considérés, en tenant compte de la charge en cuivre. L'augmentation du temps de séjour des polluants dans le système et le choix de la bioaugmentation couplée à la phytoremédiation est la stratégie retenue. Chaque composante d'un triplet « sorbant-inoculum bactérien-plante » a été sélectionnée en laboratoire et le triplet mis en oeuvre en microcosmes en conditions partiellement contrôlées.La sélection de matériaux sorbants dans différentes matrices liquides en présence des polluants seuls ou en mélange montre que les capacités de sorption des différents matériaux testés varient selon le polluant, sa formulation (seul ou en mélange) et la matrice liquide. Le sédiment se révèle être le meilleur sorbant pour le glyphosate ; le sable pour le diuron et le 3,4-DCA.Les performances de dissipation des colonies tolérantes isolées varient fortement selon le polluant. Le consortium sélectionné pour le procédé dissipe le glyphosate, le diuron et le 3,4-DCA en milieu liquide et complexe par ailleurs le cuivre.L'expérience en microcosmes montre que le temps de rétention hydraulique influe sur l'efficacité du système et que les matériaux sorbants sont efficaces. De plus les performances de dissipation atteintes sont bonnes. L'effet de la bioaugmentation sur les performances de dissipation n'est pas significatif pour le glyphosate et le 3,4-DCA, mais améliore en moyenne la dissipation du diuron. Un temps d'action prolongé dans la matrice solide s'avère nécessaire pour obtenir une bonne efficacité du procédé. / This study aims at developing a depollution system for vineyard sediments and passing water. Glyphosate, diuron and 3,4-dichloroaniline (3,4-DCA) have been chosen, taking a copper load into account. Strategical choices are increased pollutant hydraulic retention time and the use of bioaugmentation together with phytoextraction. Each item on this « sorbent-bacterial inoculum-plant » triplet has been beforehand selected in the laboratory and implemented in microcosm experiments under semi-controlled conditions.Sorbent material selection in different liquid matrices with pollutants alone or in combination shows that material sorption capacities change with the type of pollutant. It has also been shown that these capacities vary with formulation (alone or in combination) and liquid matrix chosen. Sediment is awarded the best sorbent for glyphosate, sand the best sorbent for diuron and 3,4-DCA.Dissipation performances from isolated colonies are strongly related to the nature of the compound. Elected consortium degrades glyphosate, diuron and 3,4-dichloroaniline (3,4-DCA) in liquid culture as well as it complexes copper.Microcosm experiments show that hydraulic retention time weighs on pollutant concentration in water at the system outlet. Sorbents prove to be efficient. Dissipation performances are satisfactory. Bioaugmentation does not impact on glyphosate and 3,4-DCA dissipation performances significantly, but enhances diuron dissipation in average. Suitable process efficiency requires increased action time within the solid matrix.

To improve biogas production from lignocellulosics, methanogenic microbial enrichments were prepared from moose rumen fluid, beaver droppings, and internal circulation (IC) reactor granules amended with cellulose, pine needles, lignosulphonate, tannic acid, and poplar hydrolysate. Tannic acid delayed methanogenesis compared to cellulose only enrichments, both by reducing initial rates (up to 50% in beaver dropping cultures) and increasing lag times (up to 50 days in moose rumen cultures). Biogas yields from poplar hydrolysate were 56 % by beaver droppings, 51% % by IC granules, and 31 % by moose rumen enrichments. Bacterial community profiles, determined via denaturing gradient gel electrophoresis (DGGE) showed divergent populations between enrichments. Enrichment on pine needles or poplar hydrolysate promoted bioconversion of post extraction wash (PEW), and beaver dropping enrichments fed pine needles equaled the yield (about 23%) from IC granules. Together, the DGGE and PEW results provide evidence of acclimatization to previously recalcitrant feeds.

To improve biogas production from lignocellulosics, methanogenic microbial enrichments were prepared from moose rumen fluid, beaver droppings, and internal circulation (IC) reactor granules amended with cellulose, pine needles, lignosulphonate, tannic acid, and poplar hydrolysate. Tannic acid delayed methanogenesis compared to cellulose only enrichments, both by reducing initial rates (up to 50% in beaver dropping cultures) and increasing lag times (up to 50 days in moose rumen cultures). Biogas yields from poplar hydrolysate were 56 % by beaver droppings, 51% % by IC granules, and 31 % by moose rumen enrichments. Bacterial community profiles, determined via denaturing gradient gel electrophoresis (DGGE) showed divergent populations between enrichments. Enrichment on pine needles or poplar hydrolysate promoted bioconversion of post extraction wash (PEW), and beaver dropping enrichments fed pine needles equaled the yield (about 23%) from IC granules. Together, the DGGE and PEW results provide evidence of acclimatization to previously recalcitrant feeds.

Contamination of groundwater supplies by gasoline and other petroleum-derived hydrocarbons released from underground or aboveground storage tanks is a serious and widespread environmental problem. Corrosion, ground movement, and poor sealing can cause leaks in tanks and associated piping. Petroleum hydrocarbons contain methyl tertiary-butyl ether (MTBE) (a fuel oxygenate), benzene, toluene, ethylbenzene, and xylene isomers (BTEX), the major components of gasoline, which are hazardous substances regulated by many nations. MTBE possesses all the characteristics of a persistent compound in the subsurface: high solubility, low volatility, low sediment sorption, and resistance to biodegradation. The objectives of this study were to (1) evaluate the biodegradibility of MTBE under aerobic conditions, and (2) assess the potential of using the aerobic bioremediation technique to clean up aquifers contaminated by MTBE. In this study, microcosms were constructed to determine the feasibility of biodegrading MTBE by intrinsic microbial consortia (aquifer sediments) under aerobic and aerobic cometabolic conditions. In the cometabolic microcosms, propane, ethanol, and BTEX were applied as the primary substracts to enhance the biodegradation of MTBE. The inocula used in this microcosm study were aquifer sediments collected from the contaminated-zones of a petroleum-hydrocarbon (including MTBE) contaminated site. Microcosms were constructed with nutrient medium (or site groundwater), sediments, and MTBE solution in 70-mL serum bottles sealed with Teflon-lined rubber septa. MTBE was analyzed using purge-and-trap instrument following gas chromatography (GC)/flame ionization detector (FID). Results show that the indigenous microorganisms were able to biodegrade MTBE under aerobic conditions using MTBE as the sole primary substrate. Microcosms with site groundwater as the medium solution show higher MTBE biodegradation rate. This indicates that site groundwater might contain some trace minerals or organics, which could enhance the MTBE biodegradation rate. Results show that the addition of BTEX would also enhance the MTBE removal. However, no significant MTBE biodegradation was observed in microcosms with propane and ethanol as the primary substrates. This reveals that the supplement of the second carbon source might inhibit the degradation of MTBE due to the preferential removal of some organics over MTBE. Results from the microcosm study suggest that aerobic biodegradation plays an important role on the MTBE removal. Intrinsic bioremediation is a feasible technology to remediate the studied MTBE-contaminated site.

The current rate of species extinction is higher than at any other time in Earth’s history. Despite our understanding of the causes and consequences of extinction and the development of numerous species conservation plans, it is surprising how little we know about the dynamics of extinction and recovery. Here, I explore the dynamics of population extinction and recovery across a range of meio-invertebrate species embedded in aquatic multi-trophic communities under external pressure. My results indicate that external mortality frequency has a negative impact on the dynamics of population extinction and recovery and suggest that it may be possible to predict patterns of population extinction from patterns of population growth as well as patterns of recovery from patterns of population collapse. My findings provide a valuable empirical basis from which we may increase our understanding of the factors influencing extinction risk and recovery potential to develop sustainable management strategies.

Submitted by Vasti Diniz (vastijpa@hotmail.com) on 2017-09-04T13:42:04Z No. of bitstreams: 1 arquivototal.pdf: 1325395 bytes, checksum: 78cd9c8200516699f0b0083ff622ab87 (MD5) / Made available in DSpace on 2017-09-04T13:42:04Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 1325395 bytes, checksum: 78cd9c8200516699f0b0083ff622ab87 (MD5) Previous issue date: 2017-06-08 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Several microorganisms have the capacity to produce biosurfactants and to degrade petroleum hydrocarbons, which can be used in the bioremediation strategies for the recovery of environments polluted by petroleum and its derivatives. The present work aimed to evaluate the potential of biosurfactants production and degradation of diesel oil by bacteria isolates, as well as to evaluate the growth dynamics of bacteria introduced into seawater and soil with addition of diesel oil in laboratory conditions (microcosm experiment). Phylogenetic analysis of the isolates was performed on the basis of 16S rRNA sequences. The biosurfactant production capacity was analyzed by diesel oil emulsification, hemolysis and rhamnolipid production tests on the medium with cetyltrimethyl ammonium bromide (CTAB) and methylene blue. The presence of the genes rhlAB, involved in the synthesis of rhamnolipids and alkB, involved in the degradation of alkanes of diesel oil was evaluated by Polymerase Chain Reaction (PCR). The microcosm experiments were carried out using soil and seawater contaminated by diesel oil. Phylogenetic analysis of ten isolates of bacteria revealed that five isolates belonged to the genus Bacillus and five to the genus Pseudomonas. Emulsification of diesel oil was observed in four isolates in the Bushnell and Haas medium and in the nutrient broth. All isolates showed hemolytic activity and eight isolates produced rhamnolipids in medium with CTAB and methylene blue. The rhlAB gene was detected in four isolates, all belonging to the genus Pseudomonas, and the alkB gene in nine isolates. The results of the microcosm experiment with two isolates of P. aeruginosa introduced into soil and seawater containing 1% of diesel oil showed that their density increased from the fifth day of incubation indicating that the presence of diesel oil stimulated the growth of bacteria tested. The bacterial isolates analyzed in this study showed potential of application in bioremediation processes of environments contaminated by petroleum. / Vários microrganismos possuem a capacidade de produzir biossurfactantes e de degradar hidrocarbonetos do petróleo, os quais podem ser utilizados em estratégias de biorremediação para recuperação de ambientes poluídos pelo petróleo e seus derivados. No presente trabalho objetivou-se avaliar a produção de biossurfactantes e potencial de degradação do óleo diesel por bactérias, bem como a dinâmica de crescimento de bactérias introduzidas em água do mar e no solo com adição do óleo diesel em condições laboratoriais (experimento microcosmo). A análise filogenética dos isolados foi realizada com base de sequencias de RNAr 16S. A capacidade de produção de biossurfactantes foi analisada através dos testes de emulsificação do óleo diesel, hemólise e teste de produção de ramnolipídeos no meio com brometo de cetiltrimeltilamônio (CTAB) e azul de metileno. A presença do gene rhlAB, envolvido na síntese de ramnolipídeos e do gene alkB, envolvido na degradação de alcanos do óleo diesel foi avaliada pela Reação de Polimerase em Cadeia (PCR). Os experimentos microcosmo foram realizados utilizando solo e água do mar com adição do óleo diesel. Analise filogenética de dez isolados de bactérias revelou que cinco isolados pertenceram ao gênero Bacillus e cinco ao gênero Pseudomonas. A emulsificação do óleo diesel foi observada em quatro isolados no meio de Bushnell e Haas e no caldo nutriente. Todos os isolados apresentaram atividade hemolítica e oito isolados produziram ramnolipídeos em meio com CTAB e azul de metileno. O gene rhlAB foi detectado em quatro isolados, todos pertencentes ao gênero Pseudomonas, e gene alkB em nove isolados. Os resultados do experimento microcosmo mostraram que os dois isolados de P. aeruginosa introduzidos no solo e na água do mar contendo 1% de óleo diesel apresentaram aumento de densidade a partir do quinto dia de incubação indicando que a presença de óleo diesel estimulou o crescimento das bactérias testadas. Os isolados de bactérias analisados neste estudo exibiram potencial de aplicação em processos de biorremediação de ambientes contaminados por petróleo.

Dans un contexte de réchauffement climatique et d'anthropisation, les organismes colonisant les espaces côtiers sont, et seront soumis, à des variations importantes de leur milieu de vie. Parmi ces organismes, la moule bleue Mytilus edulis constitue une espèce clé des écosystèmes intertidaux et est utilisée comme sentinelle. Au cours de cette thèse, des moules collectées sur des sites présentant des niveaux de contamination contrastés ont été conditionnées à deux niveaux de température différents avant une exposition à un stress thermique aigu. Des analyses protéomiques ont été réalisées pour explorer les effets de ces stress sur l'homéostasie des protéines. Une forte mortalité est observée exclusivement pour les individus issus du site pollué et conditionnés à des températures modérées. Chez les individus issus du site propre, une abondance de protéines de stress thermique et une sur-expression d'acteurs indiquant la mise en place d'un métabolisme anaérobie est observée. Les individus conditionnés à des températures plus élevées ont une meilleure réponse vis-à-vis des individus conditionnés aux températures modérées. Pour les moules provenant du site contaminé les réponses protéiques sont bien moins nettes et tendent à démontrer un effet additif délétère de la contamination et de la température. Là encore, les individus conditionnés aux températures les plus élevées répondent mieux. En conclusion, les individus au trait de vie non contaminés affichent de meilleures réponses physiologiques que les individus contaminés. De plus, les organismes dont l'historique thermique est favorable, i.e. conditionnés à des températures plus élevées, ont également des réponses améliorées. / Intertidal organisms live in a fluctuating environment. The blue mussel Mytilus edulis is a key species of those ecosystems and are largely use as sentinel species. Global warming associated with anthropization will expose mussels to contaminations together with increased temperatures. In addition, more frequent heatwaves are expected. In this work, mussels were collected at two sites depicting contrasted levels of contamination and thermal exposure in microcosm were conducted. Two acclimation scenarios were set up prior to exposure to an identical acute thermal stress. In order to decipher joint effects of acclimation and contamination on protein homeostasis, gill proteome comparisons were performed. High mortality was observed only for mussels collected at the contaminated site and acclimated to current temperatures. Concerning gill proteome analysis, organisms from the pristine site exhibit high abundance of thermal stress proteins. Proteoforms involved in anaerobic metabolism were also up-regulated. Interestingly, mussels acclimated to the higher temperatures show an enhanced response compare to the one acclimated to current temperatures. Concerning mussels from the contaminated site, the response appears more confusing, excepted for heat stress protein response. This may indicate deleterious effects of combined contamination and heat stress. Therefore, organisms acclimated to higher temperature display improved responses. In conclusion, mussels with a clean life history show better physiological abilities than individuals with contaminated life history. Moreover, organisms prepared to heat stress by higher acclimation temperatures also develop a more effective response.

Biological remediation of Cr(VI) contaminated soil and groundwater is an emerging field. In this study, the in situ bioremediation technology for treating Cr(VI) contaminated groundwater aquifers was evaluated using a laboratory microcosm system. The study was conducted using columns with five equally spaced intermediate sampling ports along the length to facilitate finite difference modelling of the Cr(VI) concentration profile within the column. Cr(VI) concentration was continuously measured in the influent, in five equally spaced intermediate ports within the column and in the effluent port. The change or the shift in microbial community within the inoculated column was also monitored due to exposure to toxic conditions after seven weeks of operation using the 16S rRNA genotype fingerprinting method. The effect of introducing a natural carbon source (sawdust) in inoculated columns in comparison with the performance of sterile controls under various loading conditions was also evaluated. Near complete Cr(VI) removal was achieved in an inoculated carbon source reactor, whereas only 69.5% of Cr(VI) removal was achieved in an inoculated column without an added carbon source after 4 days of operation at 20 mg/L. In a sterile control reactor less than 2% of Cr(VI) was removed after 4 days of operation at 20 mg/L. Experimental cores demonstrated a successful Cr(VI) reduction process in the simulated microbial barrier system that was evaluated internally. The model that simulates Cr(VI) removal and transport in the subsoil environment was developed. The Cr(VI) mass balance model across the reactor that accounts for the flow characteristics and biological removal mechanism successfully captured the trends of Cr(VI) response profiles under quasi-steady state conditions for different loading conditions. This study demonstrate the potential of applying effective Cr(VI) reducers in the reactive barrier systems to contain or attenuate the spread of Cr(VI) contaminant in groundwater aquifer systems. The finite difference model developed in this study to evaluate the behaviour of Cr(VI) in the reactor could contribute towards improved designs of future in situ bioremediation systems that can be implemented for remediation of Cr(VI) on site. / Dissertation (MSc)--University of Pretoria, 2011. / Chemical Engineering / unrestricted

The feasibility of in situ bioremediation of Cr(VI) in groundwater and aquifer media was investigated using microcosm and mesocosm reactors inoculated with indigenous species of bacteria from dry sludge. Microcosm cores were used to simulate contaminant movement in the vadose and aquifer zones of the aquifer system. Cr(VI) breakthrough analysis through the experimental cores demonstrated successful Cr(VI) immobilisation in simulated barrier systems. Cr(VI) reduction was continuously monitored and microbial culture dynamics were evaluated using 16S rRNA genomic fingerprinting. A culture shift was observed in the microcosm cores with the emerging predominance of known Cr(VI) reducers - Enterococci from soil and Lysinibacilli from sludge - after operation for 45 days. The Cr(VI) reduction process in the columns was determined to be enzyme mediated and non-competitively inhibited by Cr(VI). The microbial cultures under microaerobic conditions depicted a threshold Cr(VI) concentration (Cr) of approximately 100 mg/L which was much higher than the target operation concentration of 40 mg/L at the proposed remediation sites. Using the Computer Program for the Identification and Simulation of Aquatic Systems (Aquasim), it was possible to predict Cr(VI) removal efficiency and the impact of Cr(VI) toxicity on culture dynamics in the barrier. The study demonstrates the potential of applying selected Cr(VI) reducing bacteria in biological permeable reactive barrier systems in preventing the spread of the pollutant into adjacent water supply aquifers. The impact of the presence of natural carbon sources was also evaluated by filtering the feed water through a saw dust bed. Reactors without added carbon source removed up to 70% Cr(VI), and no removal was observed in sterile controls. In the packed mesocosm reactor, the areas before the reactive barrier had no chromium reduction whereas most of the areas after the barrier achieved near 100% reduction. The microbial dynamics were monitored by the 16S rRNA fingerprinting after exposure to Cr(VI). After operating the microcosm reactors under oxygen stressed conditions in the presence of other soil bacteria, a community shift was expected. The soil from inoculated reactors contained a wide range of soil dwelling species of bacteria as well as the newly introduced bacteria from the dried sludge. There was a noted presence of Cr(VI) reducing bacteria, Microbacterium, Acinetobacter, Arthrobacter, Brevibacterium, Rumen bacteria, and several Enterococci in the sludge culture and Arthrobacter spp., Clostridium spp., and Klebsella spp. were amongst the evident among identified species. A non-competitive inhibition model was used for the evaluation of aerobic performances in batch experimental studies, whereas the inhibition threshold term C0-Cr/C0, was introduced for the anaerobic model performance for the reduction of chromium in batch studies. In sterile packed soil columns a model for saturated soil column with dispersion was adopted from AQUASIM 2.0. This model was used in combination with the chromium reduction rate adopted from the anaerobic batch modelling for most non sterile reactors in the microcosm performance. The study demonstrates the potential of applying selected Cr(VI) reducing bacteria in biological permeable reactive barrier systems in restraining the spread of the pollutant into adjacent water supply aquifers. The outcome of this exercise could be useful in the formulation of biological permeable barriers for protection against the spread of the pollutant from hot spots in the area. This is serves as a significant step towards a pilot study. / Thesis (PhD)--University of Pretoria, 2010. / Chemical Engineering / unrestricted