La préservation de la qualité des eaux marines et la lutte contre les pollutions liées à l'activité humaine sont devenues des enjeux mondiaux. De nombreux contaminants biologiques et polluants chimiques se retrouvent dans l’eau de mer, par conséquent dans les produits aquacoles. Ce contexte fait qu’aujourd’hui, les professionnels de la mer sont à la recherche de solutions pour préserver voire améliorer la qualité de leurs eaux. Au sein de notre biodiversité, les éponges marines sont des animaux capables de filtrer 10 000 fois leur volume en eau par jour et de retenir 80% des particules en suspension comme la matière organique, les minéraux, les bactéries et les virus. Par la même occasion, elles accumulent certains éléments traces métalliques comme le plomb, le cadmium ou le cuivre. En collaboration avec le Comité Régional de Conchyliculture de Bretagne Sud, le projet REMEDBIO dans lequel s’inscrit cette thèse se propose d'exploiter le potentiel de filtration des éponges marines du littoral breton. Les objectifs sont de contrôler le développement de bactéries pathogènes et de réduire la présence de polluants chimiques. L’éponge marine Hymeniacidon perlevis (Demospongiae) a été choisie comme modèle pour cette étude. Après avoir mis en évidence la faisabilité de la culture d’éponges marines sur l’estran, notre travail a montré, lors d’essais in vitro, une diminution de la contamination des huîtres par deux bactéries, Escherichia coli et Vibrio aestuarianus, et par le plomb, un élément trace métallique, en présence d’éponges. La dernière phase de ce travail a consisté à valoriser les résultats obtenus. Le projet d’entreprise LECOMER a débuté par le concours START’UBS (lauréat) proposé par l’Université de Bretagne Sud en 2014. Par la suite, LECOMER a été élu lauréat des Trophées de l’Innovation du Morbihan 2014. / The conservation of waters quality and the fight against pollution due to human activities havebecome global issues. Many biological contaminants and chemical pollutants are found in sea water, therefore in aquaculture products. This context fact sea professional are looking for solutions to preserve or even improve the quality of their waters. Among marine biodiversity, marine sponges filter 10 000 times their volume of water per day and retain 80 % of suspended particles such as organic matter, minerals, bacteria and viruses. In addition, sponges are therefore considered as bio-accumulators of metallic trace element such as lead, cadmium or copper. In collaboration with the Comité Régional de Conchyliculture de Bretagne Sud, REMEDBIO project proposes to exploite potential of marine sponges of the Brittany coast. One of the main priorities of this project is to reduce the impact of chemicals (heavy metals) and of biological contaminants (bacteria, viruses) on shellfish breeding. The marine sponges Hymeniacidon perlevis (Demospongiae) was chosen as the model for this study. Having demonstrated the feasibility of the culture of marine sponges on the foreshore, our work has shown, when tested in vitro, reduced contamination of oysters by two bacteria, Escherichia coli and Vibrio aestuarianus, and lead, a metal trace element, in the presence of sponges. The last phase of this work has been to enhance the results. The company LECOMER project began with the START'UBS contest (winner) proposed by the Université de Bretagne Sud in 2014. Thereafter, LECOMER was elected winner of the Innovation Awards of Morbihan in 2014.

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This thesis explores bio-mediated processes in geotechnical and petroleum engineering. Worldwide energy consumption is rapidly increasing as the world population and per-capita consumption rises. The US Energy Information Agency (EIA) predicts that hydrocarbons will remain the primary energy source to satisfy the surging energy demands in the near future. The three topics described in detail in this document aim to link microbiology with geotechnical engineering and the petroleum industry. Microorganisms have the potential to exploit residual hydrocarbons in depleted reservoirs in a technique known as microbial enhanced oil recovery, MEOR. The potential of biosurfactants was analyzed in detail with a literature review. Biosurfactant production is the most accepted MEOR technique, and has been successfully implemented in over 700 field cases. Temperature is the main limiting factor for these techniques. The dissolution of carbonates by microorganisms was investigated experimentally. We designed a simple, economical, and robust procedure to monitor diffusion through porous media. This technique determined the diffusion coefficient of H+ in 1.5% agar, 1.122 x 10-5 cm2 sec-1, by using bromothymol blue as a pH indicator and image processing. This robust technique allows for manipulation of the composition of the agar to identify the effect of specific compounds on diffusion. The Red Sea consists of multiple seeps; the nearby sediments are telltales of deeper hydrocarbon systems. Microbial communities associated with the sediments function as in-situ sensors that provide information about the presence of carbon sources, metabolites, and the remediation potential. Sediments seeps in the Red Sea revealed different levels of bioactivity. The more active seeps, from the southern site in the Red Sea, indicated larger pore sizes, higher levels of carbon, and bioactivity with both bacteria and archaeal species present.

Philosophiae Doctor - PhD / As a consequence of various cellar activities the wine industry produces copious volumes of potentially hazardous wastewater each year. South Africa is one of the top ten wine-producing countries, making the successful treatment of cellar effluent an important environmental obligation in this country. Constructed wetlands (CWs) are resilient to the seasonal input fluxes associated with agri-industrial waste and are ideal systems for the in-situ treatment of cellar effluent in small to medium-sized wineries not connected to municipal reticulation systems. In a project sponsored by the Water Research Commission of South Africa, a number of studies were undertaken to assess the remediation of winery wastewater and common components of winery wastewater in sand-filled pilot-scale constructed wetlands operated in batch mode. This thesis contains the results of three studies. The first study evaluated the temporal aspects of CW equilibration as a basis for future studies of system response to amendment. Microbial biomass and hydraulic conductivity values were monitored and microbial community fingerprints were obtained using denaturing gradient gel electrophoresis. The study showed that microbial community fingerprinting provides a valuable tool to assess the time-scales of microbial equilibration, which was found to be in the order of 100 days. In the second study, the biodegradation and mineralization of ethanol by acclimated and non-acclimated microbial populations in CWs were compared. By increasing the influent ethanol concentration at incremental intervals (incremental priming), the biodegradative capacity was significantly enhanced. At an influent COD concentration of 15 800 mg/L, no volatile fatty acids were detected in the effluent of an incrementally primed system and the maximum effluent COD measured was 180 mg/L. In contrast, an identical, unprimed system, amended with a lower concentration of COD (7587 mg/L), exhibited a maximum effluent COD concentration of 1 400 mg/L, with the metabolites butyrate and propionate accounting for up to 83% of the effluent COD. It was conclusively demonstrated that the use of incremental priming, together with the batch mode of operation enhanced long-term function of the CWs. In the third study, the removal of the phenolic component of winery wastewater was evaluated in CWs, as well as in sand columns and microcosms. It was found that at low influent phenolic concentrations in CWs, complete organic removal was accomplished, but at high concentrations, there was incomplete substrate removal and an accumulation of potentially toxic metabolites, including catechol. The sand provided a suitable substrate for the treatment of phenolic-laden waste, and both biotic (48%) and abiotic (52%) removal mechanisms effected the removal of model phenolics. Prior acclimation of microbial communities increased the biodegradation rate of phenolic acids significantly.

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Permeable reactive biobarrier (PRBB) is a flow-through zone where microorganisms degrade contaminants in groundwater. Discontinuous presence of contaminants in groundwater causes performance loss of a PRBB in removing the target contaminant. A novel enricher reactor (ER) - PRBB system was developed to treat groundwater with contaminants that reappear after an absence period. ER is an offline reactor for enriching contaminant degraders, which were used for augmenting PRBB to maintain its performance after a period of contaminant absence. The ER-PRBB concept was initially applied to remove benzene that reappeared after absence periods of 10 and 25 days. PRBBs without ER augmentation experienced performance losses of up to 15% higher than ER-PRBBs. The role of inducer compounds in the ER to enrich bacteria that can degrade a mixture of benzene, toluene, ethylbenzene, and xylene (BTEX) was investigated with an objective to minimize the use of toxic chemicals as inducers. Three inducer types were studied: individual BTEX compounds, BTEX mixture, and benzoate (a non toxic and a common intermediate for BTEX biodegradation). Complete BTEX removal was observed for degraders enriched on all three inducer types; however, the removal rates were dependent on the inducer type. Degraders enriched on toluene and BTEX had the highest degradation rates for BTEX of 0.006 to 0.014 day-1 and 0.006 to 0.012 day-1, respectively, while degraders enriched on benzoate showed the lowest degradation rates of 0.004 to 0.009 day-1. The ER-PRBB technique was finally applied to address the performance loss of a PRBB due to inhibition interactions among BTEX, when the mixture reappeared after a 10 day absence period. The ER-PRBBs experienced minimal to no performance loss, while PRBBs without ER augmentation experienced performance losses between 11% and 35%. Presence of ethanol during the BTEX absence period increased the performance loss of PRBB for benzene removal. PRBBs augmented with degraders enriched on toluene alone overcame the inhibition interaction between benzene and toluene indicating that toluene can be used as a single effective inducer in an ER. The ER-PRBB was demonstrated to be a promising remediation technique and has potential for applications to a wide range of organic contaminants.

Mining related activities are more expansive than ever before, with population growth data showing an exponential increase. These societies form part of the world consumer market in which people are constantly buying products with a short life-expectancy, such as consumer electronic devices. More often than not, these mining activities occur in developing countries or rural areas. A repercussion of mines located long distances from active communities is the formation of new communities based solely on the monetary system of a mine. Various precedents show the societal damage caused by the inevitable closure of mines. This eventuality is not the only societal concern associated with mining communities; communities with few social binding factors. These spaces are often made up of individuals from geographically and culturally disparate spaces who are brought together solely in their united search for monetary stability. This often leaves these communities rife with xenophobic tendencies and unsustainably weak community identities. Can a system be created in which community identity can act as a social catalyst preventing the disintegration of communities abandoned by mines? The close-out plans, drawn up by mines, leaves a lot to be desired. Based on outdated environmental data and environmental laws, these closure plans offer very little environmental protection or land rehabilitation options, and nearly no protection of any kind for communities involved in mining activities. There lies irreversible societal and environmental damage in our near future, not only for South Africa, but worldwide, if we do not start offering up innovative ideas and possible solutions for these mining communities. This dissertation will investigate architecturally based solutions for community stability, and environmental stability, through the formation of a strong communal identity which will be based on environmental rehabilitation as the catalyst for stability. The proposed site exists as a no-man’s-land between the Refilwe Community and Cullinan diamond mines' largest slime dam. The constant expansion of the Refilwe community has pushed property development to the absolute limit, in terms of proximity to the slime dam. This community currently borders on this slime dam, hazardous to the humans and animals that live there.The history of Refilwe exemplifies pre-Apartheid and Apartheid laws of segregation; a political system which still affects the identity of the residents and the community as a whole today. Recent community-directed architectural failures leads this dissertation to reconsider how architecture can rehabilitate or assist a community. As a point of departure, this dissertation examines utilizing existing potential within a damaged space and analyses the significant community requirements at hand. The architectural response will primarily be based on information collected from various sources, including but not limited to: sites studies, environmental analyses, precedents and historical information. The programme was developed to utilize architecture as a response method for remediation of both man and nature. / Myn gebasseerde aktiwiteite het 'n hoër produksie en verwagting as ooit tevore met die bevolking se eksponensiële toename. Hierdie gemeenskappe vorm deel van die wêreld se vebruikersmark. Die publiek koop aanhoudend produkte wat binne 'n paar jaar op die vullishoop beland, byvoorbeeld elektroniese objekte. Die meerderheid myne word gevind in onontwikkelde lande of in 'n plattelandse omgewing. Die nadeel van myne wat ver van stedelike gebiede is, is dat die nuwe gemeenskappe alleenlik gevorm word om die stigting van die myn. Dit is bewys dat die onvermydelike staking van produksie van myne veroorsaak sosiale verwoesting in sulke gemeenskappe. Dit is nie die enigste probleem nie. Hierdie gemeenskappe het geen sosiale groepseenheid nie en bestaan meestal van mense van verskillende agtergronde en plekke. Hulle is saamgegooi as gevolg van werksgeleenthede. Die gevolg daarvan is dat die gemeenskap se individuele identiteit swak is, en xenofobiese gevoelens ontstaan. Die vraag is, kan 'n sisteem ontwerp word om 'n gemeenskaplike identiteit te help vorm? Wat sal help om die gemeenskap bymekaar te hou en te ontwikkel na die myn toemaak? Die finale plan vir die toemaak van 'n myn is gewoonlik nie bevredigend genoeg nie. Gebaseer op verouderde omgewingsinformasie en omgewingswette word te min beskermings opsies aangebied vir die rehabilitasie van die gebied. Onomkeerbare sosiale en omgewingsvernietiging sal in die toekoms volg, nie net vir Suid-Afrika nie, maar wêreldwyd, indien ons nie begin kyk na nuwe kreatiewe idees, en moontlike oplossings vir hierdie myn gemeenskappe nie. Die verhandeling versoek en beoog 'n oplossing met argitektuur as basis en agtergrond, vir die gemeenskap en die omgewings stabiliteit, deur die vorming van 'n sterker gemeenskaps identiteit wat gebaseer word of omgewings rehabilitasie. Die voorgestelde terrein plan en ontwikkeling skep 'n buffer tussen die Refilwe gemeenskap en die Cullinan Diamant Myn se grootste slyk dam. Die aanhoudende populasie aanwas van die Refilwe gemeenskap het eindomsontwikkeling tot aan sy grense gestoot in terme van sy ligging tot die slyk dam. Huidiglik grens die gemeenskap aan die slyk dam wat 'n gesondheids risiko is vir mens en dier wat daar lewe. Die geskiedenis van Refilwe vertoonbeeld die tydperk van Apartheid en Apartheidswette van segregasie, 'n politiese sisteem wat tot vandag toe die identiteit van die inwoners en die gemeenskap negatief beinvloed. Onlangse gemeenskapsgedrewe argitektuur mislukkings, lei hierdie verhandeling na die heroorweging van hoe argitektuur 'n gemeenskap kan rehabiliteer. Ter afsluiting, ondersoek die verhandeling die moontlikheid om die huidige potensiaal te gebruik in 'n geaffekteerde ruimte en om die toepaslike gemeenskapbehoeftes te analiseer. Die argiteksgedrewe antwoord sal primêr gebaseer wees op data versamel van verskeie oorde, insluitende maar nie beperk tot: terreinstudies, omgewings analises, feite en historiese inligtig. Die projek was ontwikkel om argitektuur te gebruik as 'n moontlike antwoord vir die herstel van mens en die natuur en om 'n nuwe simbiose te skep. / Mini Dissertation MArch(Prof)--University of Pretoria, 2018. / Architecture / MArch (Prof) / Unrestricted

The objective of this study was to investigate the spatial and temporal trends of a phytoremediation system comprised of poplar trees designed to control groundwater flow and remove primarily polycyclic aromatic hydrocarbons (PAHs). Several lab and field studies have demonstrated the success of poplar trees in effectively decreasing concentrations of volatile hydrocarbons, but few have demonstrated effects on PAH concentrations. Thus, the focus of this report will be the response of the poplar trees in relation to hydrophobic, nonvolatile polycyclic aromatic hydrocarbons (acenapthene, acenapthylene, anthracene, chrysene, fluoranthene, naphthalene, phenanthrene, and pyrene) in a shallow, surficial aquifer. This field study was conducted on a 1.7-acre site in Oneida, Tennessee contaminated with creosote that was once used for railroad cross-tie treatment. Spatial analysis was used to divide the site into areas based on contaminant levels and a layer of coal that served as a layer of low permeability at an approximate depth of 2 feet. The semi-impermeable coal layer does have an adverse impact on tree growth, while the contamination does not appear to adversely affect tree growth. The rate of growth is also impacted by the age of the tree at planting where younger trees grow faster than the older trees. A steady decrease in PAH concentrations has occurred at the multi-level samplers surrounded by a root zone that has penetrated the contamination. PAH compounds present at relatively high concentrations in the soil and groundwater do not appear to affect tree growth to a greater or lesser extent than lower PAH concentrations. While further research is required to affirm the positive effects of poplar trees at this site, the tree stand has responded well to the high PAH levels. / Master of Science

Regulatory acceptance of monitored natural attenuation (MNA) requires demonstration that natural processes, such as sorption and biodegradation, attenuate specific contaminants of concern on a time scale that is comparable to other remediation options while concurrently preventing contaminant migration to site-specific points of contact. Two of the tools used to demonstrate the efficacy of MNA, microcosm experiments and numerical fate and transport modeling, were examined in this study. In the first phase of this work, laboratory microcosm studies were initiated as part of an overall MNA site assessment to determine whether a native microbial consortia collected with a soil sample from a petroleum-hydrocarbon contaminated site was capable of biodegrading specific polynuclear aromatic hydrocarbon (PAH) compounds. Results indicated that selected PAH compounds were biodegraded under simulated natural conditions using oxygen and sulfate as electron acceptors. In the second phase of this study, a numerical experiment was conducted using the three-dimensional, multiple substrate, multiple electron acceptor fate and transport model SEAM3D (Waddill and Widdowson, 1997) to evaluate the impact of including iron(III)-reducing conditions during numerical simulations of natural attenuation. Results for this phase of the study indicated that the mass of hydrocarbon simulated as biodegraded by the iron(III)-reducing population was significantly larger than hydrocarbon biodegradation under aerobic conditions. The final component of research used the SEAM3D model to interpret field observations recorded during a natural attenuation experiment where the fate and transport of selected hydrocarbon contaminants (BTEX and naphthalene) was tracked through an extremely heterogeneous, but well-instrumented test aquifer. Results from the calibrated model for the NATS experiment indicated that the majority of the contaminant remained in the non-aqueous phase during the first year of the experiment, and that aerobic biodegradation was the dominant natural attenuation process. Model results were particularly sensitive to the rate of contaminant release and the starting mass of electron acceptor. / Ph. D.