La formation de méthylmercure, la forme la plus toxique du mercure, est due à l’activité bactérienne anaérobie. Afin de connaître la contribution des compartiments microbiens (biofilms, eaux brutes, sédiments) dans la méthylation du mercure, nous avons évalué les vitesses de méthylation d’échantillons de mares de région tempérée (Lorraine) et subarctique (Québec, Canada). Si les bactéries des biofilms ne semblent pas plus méthylantes que d’autres, le sédiment apparait comme le compartiment le plus méthylant en lien avec la concentration en nutriments ainsi qu’avec la température. Ainsi, les changements climatiques actuels, en augmentant la température de l’eau et en favorisant l’activité biologique, peuvent faire de ces mares des sites préférentiels de la méthylation du mercure en milieu subarctique. Enfin, l’activité des biofilms a mené à la formation de rouille verte, un minéral capable de réduire HgII en mercure élémentaire, concurrençant ainsi la méthylation bactérienne / Monomethylmercury formation, the neurotoxic form of mercury, is mainly linked to anaerobic microbial activity. In order to assess the relative contribution of several microbial compartments (biofilms, raw water and sediment) we evaluated methylation of samples from ponds of temperate area (Lorraine, France) and from subarctic ponds (Nunavik, Quebec). Biofilms were not found to specifically promote mercury methylation, whereas sediment emerges as the main compartment involved in mercury methylation. The formation of methylmercury is positively linked to the temperature and to nutrients. Thus, by increasing the open water period, the water temperature and of the microbial activity, current climate changes may turn these ponds in preferential location for mercury methylation in the subarctic ecosystem. Finally, the reactivity of green rust, a mineral which can be produced by bacterial activity of environmental biofilms, may compete with mercury methylation by reducing HgII into Hg0

Reconnu par leur effet toxique, inhibiteur et corrosif, les sulfures (S2-, SH-, SH2) sont un sous-produit indésirable de la digestion anaérobie des boues de station de traitement des eaux domestiques de la ville de Marrakech, Maroc (STEP). Ils proviennent essentiellement de la réduction "dissimilatrice" des composés soufrés (SO4 2-, SO3 2-, S2O4 2- ..) contenus dans ces boues. Ce processus est réalisé par un groupe bactérien anaérobie appelé bactéries sulfatoréductrices (BSR). Une fois dans le biogaz, les sulfures sous forme gazeuse réduisent en plus la durée de vie des installations et des équipements de la STEP. Elle est ainsi dotée d’installations biologiques et physico-chimiques lui permettant d’éliminer ces sulfures avant la transformation du biogaz en énergie électrique. Cependant, ces procédés sont onéreuses et grandes consommatrices d’énergies. D’où l’idée de minimiser la production des sulfures au sein même des digesteurs anaérobies. Pour cela, il était nécessaire d’abord de connaître les microorganismes à l'origine de la production des sulfures (BSR), ceux potentiellement impliqués dans leur élimination (bactéries sulfo-oxydantes), et d’un groupe de microorganismes fermentaires (Synergistetes) intervenant dans le bon fonctionnement de la digestion anaérobie. Ces études ont été menées à la fois sur des d'approches moléculaires et culturales. Les résultats obtenus, ont permis de comprendre comment ces groupes bactériens, d’intérêts écologique et économique importants, interviennent dans la digestion anaérobie des boues de la STEP permettant à la fois d’accélérer les processus d’oxydation de la matière organique combinée à la réduction des composés soufrés et de minimiser la concentration des en sulfure dans le biogaz. / Recognized by their toxic, inhibitory and corrosive effect, sulfides (S2-, SH-, H2S) are an undesirable by-product of the anaerobic digestion of from domestic wastewater treatment plants sludge in the city of Marrakech, Morocco (WWTP). They produced mainly by the dissimilatory reduction of sulfur compounds (SO42-, SO32-, S2O42-) contained in these sludges. This process is performed by an anaerobic bacterial group called sulfate reducing bacteria (SRB). Once in the biogas, the sulfides in gaseous form shorten in addition the lifetime of the installations and equipments of the WWTP. It is thus equipped with biological and physicochemical installations allowing it to eliminate these sulfides before the transformation of biogas into electrical energy. However, these processes are expensive and consume large amounts of energy. Hence the idea of minimizing the production of sulfides within anaerobic digesters. For this, it was first necessary to know the microorganisms originating of the production of sulfides (SRB), those potentially involved in their elimination (sulfur oxidizing bacteria), and a group of fermentative microorganisms (Synergistetes) involved in the good functioning of the anaerobic digestion. These studies were conducted on both molecular and cultural approaches. The results obtained allowed to understand how these bacterial groups, of great ecological and economic interest, are involved in the anaerobic digestion of sludge from the WWTP, which both accelerates the oxidation processes of the organic matter combined with the reduction of sulfur compounds and to minimize the concentration of sulfide in biogas.

Ubiquitaires et très anciens, les communautés des tapis microbiens font preuve de capacités métaboliques et adaptatives très importantes. Situés en zone côtières, ces écosystèmes peuvent être soumis à des contaminations pétrolières. Dans ce contexte, cette étude vise d’une part à décrire la structure et le fonctionnement de tapis microbiens et d’autre part à comprendre l’impact d’une contamination pétrolière sur ces écosystèmes. Cette étude porte sur deux tapis microbiens de l’étang de Berre aux paramètres physico-Chimiques proches mais présentant des contaminations pétrolières contrastées. Le fonctionnement du système étant tributaire d’autres facteurs tels que la lumière et les saisons, les variations saisonnières et nycthémérales ont été prises en compte dans cette étude. Un accent particulier a également été porté sur le cycle du soufre de par son importance en milieu marin. Les résultats de cette étude mettent en évidence des structures de communautés différentes entre les deux tapis au niveau global, la séparation spatiale prévalant sur la séparation saisonnière. La fraction active de la communauté du site contaminé présente une évolution linéaire tandis que celle du site témoins suit pour sa part les variations saisonnières. Au niveau du site contaminé une augmentation de l’expression des gènes impliqués dans la dégradation des hydrocarbures couplée à une biodégradation des hydrocarbures suggère que le tapis contaminé est adapté à la contamination pétrolière. Malgré les différences de structures et d’activités de dégradation, des profils métaboliques très semblables sont cependant observables entre les deux tapis, avec des fonctions similaires laissant supposer une redondance fonctionnelle. Des variations saisonnières et nycthémérales ont également été observées avec notamment des Desulfobulbaceae plus abondantes au printemps et plus actives en journée. Des études culturales ont été réalisées en parallèle. Elles permettront d’appréhender de manière complémentaire la dynamique des communautés des sulfato-Réducteurs au sein du tapis et de mieux comprendre les variations mises en évidence dans cette étude. / Ubiquist and very ancient, the microbial mats communities demonstrate very important metabolic and adaptive capacities. Located in the coastal area, these ecosystems may be subject to oil contamination. In this context, the aim of this study is on one hand to describe the structure and functioning of microbial mats and on the other to understand the impact of oil contamination on these ecosystems. This study focused on two microbial mats from the Berre lagoon with close physical chemical parameters but with contrasted hydrocarbon contamination levels. The functioning of the system is dependent on other factors such as light and seasons, diurnal and seasonal variations were taken into account in this study. Special emphasis was placed on the sulfur cycle due to its importance in the marine environments. The results of this study highlighted different communities’ structures at the global level between both mats, the spatial variation prevailed on seasonal variation. The active part of the community from the contaminated site shows a linear trend while that one of the uncontaminated site follows the seasonal variations. The contaminated site shows genes involved in hydrocarbon degradation more expressed coupled to a hydrocarbon biodegradation suggesting that the contaminated mat is adapted to the petroleum contamination. Despite these differences in the structure and the degradation capacities, very similar metabolic profiles are observed between the two mats with similar functions, suggesting functional redundancy. Seasonal and diurnal variation was also observed, the Desulfobulbaceae were particularly more abundant in spring and more active during the day. A complementary cultural approach will allow to better understanding the dynamics of sulfate-Reducers communities in the mat and comprehending these variations.

Les écosystèmes côtiers sont des milieux complexes au sein desquels les communautés microbiennes, jouant un rôle majeur dans leur fonctionnement et leur maintien, s’adaptent et sont tolérantes à des conditions environnementales fluctuantes. En effet, au rythme des marées et de l'activité de la macrofaune, des oscillations oxie/anoxie influencent la composition et la dynamique des communautés microbiennes et par conséquent leur implication métabolique. Afin d’appréhender le devenir du pétrole dans ces écosystèmes, il est donc indispensable d’apporter des connaissances sur l’écologie des microorganismes intervenant dans son élimination, notamment dans des conditions oscillantes anoxie/oxie. Ainsi, ce travail de thèse a eu pour objectif de décrypter l’assemblage de communautés microbiennes hydrocarbonoclastesde sédiments intertidaux soumises à des oscillations anoxie/oxie en présence de pétrole lors d’une expérience en bioréacteurs. Les réponses écologiques des communautés bactériennes globales et de micro-organismes sulfato-réducteurs en conditions oscillantes ont pu être décrites en comparaison avec celles obtenues en conditions d’oxie ou d’anoxie permanentes, par l’analyse des données obtenues par séquençage haut-débit des gènes de l’ARN 16S et dsrB au niveau transcriptionnel. Ces études comparatives ont mis en évidence des profils écologiques en réponseaux conditions oscillantes, pouvant être répandus dans différents environnements marins côtiers. En réponse à ces conditions particulières, de nombreux microorganismes semblent avoir le potentiel à tolérer et/ou s’adapter aux différentes conditions d'oxygénation. Cette capacité d’acclimatation rapide des communautés bactériennes aux conditions oscillantes se sont accompagnées de capacités de dégradation équivalentes ou supérieures dans ces conditions par rapport à la condition d’oxie permanente montrant l’influence des oscillations anoxie/oxie sur le devenir du polluant dans les environnements pollués soumis à ces conditions. / Coastal ecosystems are complex environments in which microbial communities, playing a major role in their functioning and maintain, are tolerant and adapt to changing environmental conditions. Indeed, the tides and the macrofauna’s activity generate oxic/anoxic oscillations which influence the composition and dynamics of microbial communities and consequently their metabolic in volvement. To understand the fate of oil in these ecosystems, it is essential to provide knowledge on the ecology of microorganisms involved in these systems, taking into account anoxic/oxicoscillating conditions. Thus, this thesis aimed to decipher the organization of hydrocarbonoclastic microbial communities inhabiting intertidal sediments, when they are subjected to anoxic/oxic oscillations in an experiment in bioreactors with oil addition. Ecological responses of bacterial communities and sulfate-reducing microorganisms in oscillating conditions have been described comparing with those obtained with permanent oxic or anoxic conditions, using high-throughputsequencing analyses of the 16S rRNA and dsrB genes at the transcriptional level. These comparatives studies have highlighted ecological profiles in response to the oscillating conditions, which can be prevalent in different coastal marine environments. In response to these particular conditions, many organisms seem to have the potential to tolerate and / or adapt to the different conditions of oxygenation. This rapid acclimation capacity of bacterial communities tothese changing conditions have been accompanied by equivalent or greater degradation capacity under these conditions compared to the permanent oxic condition, showing the influence of the anoxic/oxic oscillations on the fate of pollutant in environments subjected tothese conditions.

Os micro-organismos constituem um grande problema em termos econômicos para a indústria petrolífera. Estes são responsáveis pela produção de substâncias corrosivas e a formação de biofilmes, que causam deterioração dos materiais metálicos. Os principais grupos microbianos presentes em amostras ambientais da indústria do petróleo são as bactérias anaeróbias heterotróficas totais (BANHT) e as bactérias redutoras de sulfato (BRS). Atualmente, a quantificação desses grupos microbianos é realizada através da técnica do Número Mais Provável (NMP) que estima o resultado em aproximadamente 28 dias. Neste trabalho foi otimizada uma metodologia para a microscopia de fluorescência de amostras salinas provenientes de tanques de armazenamento de água/óleo. As condições testadas foram o tipo de óleo de imersão, o tipo de diluente, o volume do corante, o volume da amostra corada e a concentração do fixador (glutaraldeído) numa tentativa de correlacionar com resultados de quantificação de BANHT e BRS através da técnica convencional do NMP. Nesse caso, as células totais foram quantificadas por microscopia de fluorescência utilizando o corante fluorescente laranja de acridina (AO). Verificou-se que houve uma correlação entre os resultados da quantificação de células totais por microscopia de fluorescência e os resultados de BANHT pela técnica do NMP, devido a pouca variação de valores expressos em ambas as quantificações. Entretanto, não foi possível correlacionar os resultados da quantificação de células totais com os resultados de BRS por NMP devido à grande variação dos valores de quantificação de BRS. Na microscopia de fluorescência, foi possível, quantificar os micro-organismos em aproximadamente 30 minutos e através das fotografias, verificou-se ainda que as amostras apresentaram-se nítidas e os micro-organismos com uma boa fluorescência / Microbial cells constitute a severe problem, from the economic point of view, for the petroleum industry. They are responsible for the production of corrosive metabolites and for the formation of biofilms, causing deterioration in the surface of metallic materials. The main microbial groups present in environmental samples from the petroleum industry include total anaerobic heterothrophic bacteria (TANHB) and sulfate-reducing bacteria (SRB). Nowadays, the quantification of those microbial groups is performed through the use of the most probable number technique (MPN), providing the final quantification after 28 days. In the present work a new methodology, based on fluorescence microscopy, was optimized on saline samples from water/oil storage tanks. The conditions tested were the type of immersion oil, type of diluent, the volume of the dye, the stained sample volume and concentration of fixative (glutaraldehyde) in order to quantify total cells, in an attempt to correlate with TANHB and SRB quantification through MPN. In that case, total cells were quantified with the help of acrydine orange as fluorescent dye. It could be observed a clear correlation between the results obtained for total cells quantification by fluorescence microscopy and the results obtained for TANHB through MPN technique, due to the negligible differences observed in both quantifications. However, when a correlation with SRB cells was tried results of total cells through fluorescence microscopy did not fit entirely. With the use of fluorescence microscopy, it was possible to quantify microbial cells in around 30 minutes and with the help of photographic reports obtained, it could be observed that the samples were clearly observed and the microbial cells indicated a good fluorescence

Solid wastes containing sulfate, such as construction and demolition debris (CDD), are an important source of pollution, which can create a lot of environmental problems. It is suggested that these wastes have to be separated from other wastes, especially organic waste, and place it in a specific area of the landfill. This results in the rapid rise of the disposal costs of these gypsum wastes. Although these wastes can be reused as soil amendment or to make building materials, a concern has been raised by regulators regarding the chemical characteristics of the material and the potential risks to human health and the environment due to CDD containing heavy metals and a high sulfate content. Soils containing gypsum, namely gypsiferous soils, also have several problems during agricultural development such as low water retention capacity, shallow depth to a hardpan and vertical crusting. In some mining areas, gypsiferous soil problems occur, coupled with acid mine drainage (AMD) problems which cause a significant environmental threat. Reduction of the sulfate content of these wastes and soils is an option to overcome the above mentioned problems. This study aimed to develop sulfate removal systems to reduce the sulfate content of CDD and gypsiferous soils in order to decrease the amount of solid wastes as well as to improve the quality of wastes and soils for recycling purposes or agricultural applications. The treatment concept leaches the gypsum contained in the CDD by water in a leaching step. The sulfate containing leachate is further treated in biotic or abiotic systems. Biological sulfate reduction systems used in this research were the Upflow Anaerobic Sludge Blanket (UASB) reactor, Inverse Fluidized Bed (IFB) Reactor and Gas Lift Anaerobic Membrane Bioreactor (GL-AnMBR). The highest sulfate removal efficiency achieved from these three systems ranges from 75 to 95%. The treated water from the bioreactor can then be reused in the leaching column. Chemical sulfate removal (abiotic system) is an alternative option to treat the CDD leachate. Several chemicals were tested including barium chloride, lead(II) nitrate, calcium chloride, calcium carbonate, calcium oxide, aluminium oxide and iron oxide coated sand. A sulfate removal efficiency of 99.9% was achieved with barium chloride and lead(II) nitrate.For AMD and gypsiferous soils treatment, five types of organic substrate including bamboo chips (BC), municipal wastewater treatment sludge (MWTS), rice husk (RH), coconut husk chip (CHC) and pig farm wastewater treatment sludge (PWTS) were tested as electron donors for biological sulfate reduction treating AMD. The highest sulfate reduction efficiency (84%) was achieved when using the combination of PWTS, RH and CHC as electron donors. Then, this organic mixture was further used for treatment of the gypsiferous soils. The gypsum mine soil (overburden) was mixed with an organic mixture in different amounts including 10, 20, 30 and 40% of soil. The highest sulfate removal efficiency of 59% was achieved in the soil mixture which contained 40% organic material.The removal of sulfide from the effluent of the biological sulfate reduction process is required as sulfide can cause several environmental impacts or be re-oxidized to sulfate if directly discharged to the environment. Electrochemical treatment is one of the alternatives for sulfur recovery from aqueous sulfide. A non-catalyzed graphite electrode was tested as electrode for the electrochemical sulfide oxidation. A high surface area of the graphite electrode is required in order to have less internal resistance as much as possible. The highest sulfide oxidation rate was achieved when using the external resistance at 30 Ω at a sulfide concentration of 250 mg L-1

Os micro-organismos constituem um grande problema em termos econômicos para a indústria petrolífera. Estes são responsáveis pela produção de substâncias corrosivas e a formação de biofilmes, que causam deterioração dos materiais metálicos. Os principais grupos microbianos presentes em amostras ambientais da indústria do petróleo são as bactérias anaeróbias heterotróficas totais (BANHT) e as bactérias redutoras de sulfato (BRS). Atualmente, a quantificação desses grupos microbianos é realizada através da técnica do Número Mais Provável (NMP) que estima o resultado em aproximadamente 28 dias. Neste trabalho foi otimizada uma metodologia para a microscopia de fluorescência de amostras salinas provenientes de tanques de armazenamento de água/óleo. As condições testadas foram o tipo de óleo de imersão, o tipo de diluente, o volume do corante, o volume da amostra corada e a concentração do fixador (glutaraldeído) numa tentativa de correlacionar com resultados de quantificação de BANHT e BRS através da técnica convencional do NMP. Nesse caso, as células totais foram quantificadas por microscopia de fluorescência utilizando o corante fluorescente laranja de acridina (AO). Verificou-se que houve uma correlação entre os resultados da quantificação de células totais por microscopia de fluorescência e os resultados de BANHT pela técnica do NMP, devido a pouca variação de valores expressos em ambas as quantificações. Entretanto, não foi possível correlacionar os resultados da quantificação de células totais com os resultados de BRS por NMP devido à grande variação dos valores de quantificação de BRS. Na microscopia de fluorescência, foi possível, quantificar os micro-organismos em aproximadamente 30 minutos e através das fotografias, verificou-se ainda que as amostras apresentaram-se nítidas e os micro-organismos com uma boa fluorescência / Microbial cells constitute a severe problem, from the economic point of view, for the petroleum industry. They are responsible for the production of corrosive metabolites and for the formation of biofilms, causing deterioration in the surface of metallic materials. The main microbial groups present in environmental samples from the petroleum industry include total anaerobic heterothrophic bacteria (TANHB) and sulfate-reducing bacteria (SRB). Nowadays, the quantification of those microbial groups is performed through the use of the most probable number technique (MPN), providing the final quantification after 28 days. In the present work a new methodology, based on fluorescence microscopy, was optimized on saline samples from water/oil storage tanks. The conditions tested were the type of immersion oil, type of diluent, the volume of the dye, the stained sample volume and concentration of fixative (glutaraldehyde) in order to quantify total cells, in an attempt to correlate with TANHB and SRB quantification through MPN. In that case, total cells were quantified with the help of acrydine orange as fluorescent dye. It could be observed a clear correlation between the results obtained for total cells quantification by fluorescence microscopy and the results obtained for TANHB through MPN technique, due to the negligible differences observed in both quantifications. However, when a correlation with SRB cells was tried results of total cells through fluorescence microscopy did not fit entirely. With the use of fluorescence microscopy, it was possible to quantify microbial cells in around 30 minutes and with the help of photographic reports obtained, it could be observed that the samples were clearly observed and the microbial cells indicated a good fluorescence

Les effondrements miniers en Lorraine (France) ont pour origine la rupture des piliers de soutien constitués de minerai de fer. Leur rupture n'est pas seulement due aux seules contraintes mécaniques qu’exerce le recouvrement mais également aux différentes transformations minéralogiques du minerai de fer, compromettant sa cohésion et sa résistance et par conséquent, la stabilité des piliers. On parle alors d’altération/vieillissement minéralogique du minerai de fer. Les mécanismes chimiques qui entrainent ces transformations minéralogiques sont désormais bien connus mais l’influence de l’activité bactérienne n’est pas encore bien comprise. Des travaux préliminaires ayant soulevé le rôle possible des activités microbiennes, ce travail de thèse s'est alors appliqué à identifier les métabolismes bactériens susceptibles de réagir avec le minerai de fer en conditions aérobie et anaérobie, et à en caractériser les effets physico-chimiques, minéralogiques et mécaniques. Les groupes métaboliques bactériens suspectés d’être impliqués dans ces réactions (activités ferri-réductrices, ferro-oxydantes et sulfato-réductrices) ont été identifiés dans les eaux de mine et incubés en présence du minerai de fer, en souche pure ou avec un consortium issu de l’eau de mine. Les bactéries ferri-réductrices (IRB), sulfato-réductrices (BSR) et acidophiles ferro-oxydantes ont été les seules qui, dans les conditions de laboratoire, ont impacté significativement le minerai en modifiant le ratio Fe(II)/Fe(III). Une phase ferro-carbonatée et de la pyrite se sont formées respectivement au cours des incubations avec les IRB et BSR, et ont été caractérisées par analyse du solide (spectroscopies infrarouge en réflexion diffuse (DRIFTS) et Mössbauer et par diffraction aux rayons X). Des bactéries nitrate-réductrices ont aussi été testées et aucune modification significative du ratio Fe(II)/Fe(III) du minerai de fer n’a été observée. Enfin, les propriétés mécaniques du minerai de fer ont été mesurées après les réactions d’oxydo-réduction biologiques et purement chimiques. Des modifications sensibles de ces propriétés mécaniques par rapport à l’état initial ont ainsi pu être mises en évidence. Sur la base de ces résultats, l’hypothèse de l’altération mécanique du minerai de fer par des activités microbiennes est donc tout à fait réaliste. / Mine collapses occurred in Lorraine (France) because of the failure of safety pillars made of iron ore. Their failure is not only due to the mechanic stresses applied by the overburden, but also due to the various mineralogical transformations in iron ore which decrease material cohesion and resistance and thus stability of pillars. This is called mineralogical alteration/ageing of iron ore. Chemical mechanisms inducing these mineralogical transformations are now well known but the influence of microbial activity is not well understood yet. Preliminary works have raised the possible role of microbial activity, then the focus of this work was to identify the various bacterial metabolisms capable of reacting with iron ore and to characterize the physico-chemical, mineralogical and mechanical effects. The bacterial metabolism groups possibly implied in these reactions (iron-reducing (IRB), iron-oxidizing and sulfate-reducing bacteria (SRB)) were identified from the mine water. As pure strain or as consortium, these bacteria were incubated with iron ore. Under laboratory conditions, only iron-reducing, sulfate-reducing and acidophilic iron-oxidizing bacteria impacted iron ore samples by modifying the Fe(II)/Fe(III) ratio. A ferrous-carbonate phase and pyrite were formed during incubations with IRB and SRB, respectively. These minerals were characterized from analysis of the solid phase (Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS), Mössbauer spectroscopy and X-ray diffraction). The impact nitrate-reducing bacteria was also tested but the Fe(II)/Fe(III) ratio of iron ore was not modified significantly. Finally, mechanical properties of iron ore were measured after microbial and purely chemical redox reactions. Discernible modifications of these mechanical properties were observed. From these results, the alteration of iron ore mechanical properties by bacterial activities is a realistic assumption.

No description available.

No description available.