La France est dépendante en gaz naturel dont elle importe 98% de sa consommation. Comme pour plusieurs autres pays (Etats-Unis, Canada, Grande Bretagne, Autriche, Allemagne, etc.), le stockage de gaz est principalement réalisé afin de pallier aux variations saisonnières de consommation. Grâce aux spécificités géologiques de notre territoire, ce stockage se fait essentiellement aux niveaux d’aquifères très profonds (-500 à 1000 mètres). Le gaz naturel contient en majorité du méthane mais également des traces d’autres composés tels que les BTEX (Benzène, Toluène, Ethylbenzène et les trois isomères du Xylène) qui sont connus pour leur toxicité. Ces hydrocarbures monoaromatiques peuvent se solubiliser dans l’eau de formation aux niveaux des interfaces eau/gaz. Leur biodégradation est bien moins rapide en anaérobiose qu’en aérobiose mais un potentiel d’atténuation naturelle des BTEX par les communautés microbiennes indigènes a déjà pu être démontré lors de travaux antérieurs. Cependant, bien que de nombreuses études aient été réalisées sur le sujet, les voies de dégradation anaérobie ne sont que partiellement connues et les connaissances concernant les microorganismes impliqués sont réduites, voire inexistantes. Le développement de biomarqueurs moléculaires in situ doit permettre d’évaluer rapidement le potentiel de dégradation des microorganismes d’un aquifère. Pour atteindre cet objectif, il est indispensable d’acquérir une meilleure compréhension des mécanismes de dégradation et donc, d’isoler les microorganismes impliqués dans la dégradation de ces composés. Au cours de cette étude, des communautés microbiennes provenant d’échantillons d’eau de formation issue de trois aquifères distincts (nommés dans ce travail A, C et D) ont été étudiées à l’aide de trois approches différentes de microbiologie environnementale. L’ensemble de ces résultats ainsi que ceux de la littérature suggèrent l’ubiquité des bactéries sulfato-réductrices à Gram positif tels que les Desulfotomaculum dans les environnements profonds. Les résultats obtenus lors de ce travail de doctorat suggèrent le rôle prépondérant de microorganismes affiliés au genre Desulfotomaculum dans la dégradation des BTEX en aquifères très profonds et représentent une avancée dans la compréhension des phénomènes d’atténuation naturelle des BTEX dans ce type d’environnement. / France is dependent on natural gas and imports 98% of its consumption. Like in many other countries (The United States of America, Canada, Great Britain, Austria, Germany, etc.), gas storage is primarily performed to compensate for seasonal variations in consumption. Geological characteristics of our territory allow to store essentially natural gas into deep aquifers (-500 to 1000 meters). Natural gas contains mostly methane, but also traces of other compounds such as BTEX (Benzene, Toluene, Ethylbenzene and the three isomers of Xylene) which are known to be toxic. These mono-aromatic hydrocarbons are soluble in water. Anaerobic biodegradation is much slower than aerobic processes however potential for anaerobic BTEX natural attenuation by indigenous microbial communities has already been shown previously. Although many studies have been done on the topic, the anaerobic degradation pathways are only partially known and the knowledge of microorganisms involved is low or nonexistent. The development of in situ molecular biomarkers will allow rapid evaluation of the potential degradation of aquifer microorganisms. To achieve this goal, a better understanding of the mechanisms of degradation is crucial and requires isolation of microorganisms involved in the degradation of these compounds. In this study, microbial communities sampled from formation waters of three distinct aquifers (named in this work A, C and D) were studied using three different environmental microbiology approaches. All these results and those from the literature suggest the ubiquity of sulfate-reducing bacteria such as Gram positive Desulfotomaculum in deep environments. The results obtained during this PhD suggest the importance of microorganisms related to the genus Desulfotomaculum in BTEX degradation in deep aquifers. This work represents a step forward in understanding the phenomenon of natural attenuation of BTEX in this kind of environment.

Les procaryotes sulfato-réducteurs (PSRs)jouent un rôle majeur dans les cycles biogéochimiques de la matière et interviennentnotamment dans la dégradation de la matière organique récalcitrante (e.g. hydrocarbures) mais également dans les processus d’oxydo-réduction de métaux et/ou métalloïdes.L’objet de ce travail a consisté à approfondir certain de ces aspects de la physiologie des PSRs. La dégradation d’hydrocarbures a été étudiée en mésophilie, avec la caractérisation d’une souche bactérienne issue d’un site pollué. Cette souche décrite comme une nouvelle espèce,Desulfatiferulaberrensis BE2801, est capable de dégrader les n-alcènes. La dégradation d’hydrocarbures a également été étudiée à très haute température chez une archée,Archaeoglobus fulgidus. Cette souche oxyde les n-alcanes, l’oxydation étant vraisemblablement catalysée par la protéine PflD.L’ensemble des travaux réalisés montre que PflDserait une alkylsuccinate synthase qui permettrait l’activation de l’hydrocarbure par addition au fumarate. Outre ses capacités hydrocarbonoclastes à haute température, A. fulgidusest également capable de corroder le fer, de manière indirecte par la production de sulfures, et directement, en oxydant le fer de manière originale avec la formation de « micro-cheminées ». Outre l’oxydation de matière organique et de métaux, les PSRs sont également capables de réduire un grand nombre d’éléments, notamment les métaux et métalloïdes. C’est le cas de Desulfotomaculum hydrothermale, connue pour réduire à haute température l’arsenic, métalloïde hautement toxique. L’analyse de la séquence du génome de cette souche a confirmé ses capacités de détoxication. / Sulfate-reducing prokaryotes (SRPs) play a significant role in the biogeochemical cycles of matter, in particular in the degradation of recalcitrant organic compounds (e.g. hydrocarbons) but also in oxido-reduction of metals and/or metalloids. The aim of this work was to deepen some of these aspects of SRPs physiology. Hydrocarbon degradation was studied with a mesophilic bacterial strain isolated from a polluted site.This strain, described as a new species, Desulfatiferula berrensis BE2801, is able to degrade n-alkenes. Degradation of hydrocarbons has also been studied at high temperatures with an archaeon, Archaeoglobus fulgidus. This archaeon oxidize n-alkanes with most likely involvement of the PflD protein. All our experiments showed that PflD would be an alkylsuccinate synthase allowing hydrocarbon activation by addition to fumarate. Moreover, A. fulgidus was shown to corrode iron at high temperature, through the production of sulfide and also by directly oxidizing iron with formation of unusual "micro-chimneys". In addition to organic matter oxidation, SRPs are known to reduce a large number of elements, including metals and metalloids. This is the case for Desulfotomaculum hydrothermale reported to reduce arsenic at high temperature. Analyses of the genome sequence of this bacterium confirmed its ability to detoxify this mineral.

No description available.

Acid mine drainage (AMD) is a worldwide environmental problem associated with the mining wastes, generated from active and inactive mining sites from mineral processing activities. AMD is defined as the drainage that occurs as a result of oxidation of sulphide minerals/wastes/tailings when exposed to air and water in the presence of chemolithotrophs namely the Acidithiobacillus sp. AMD is characterised by low pH and increased acidity due to elevated heavy metals and sulphate concentration. The acid production potential was carried out for sulphide minerals such as pyrite and chalcopyrite and copper tailings sample in the absence and presence of bacteria namely Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. Acidity was generated in all the cases due to the oxidation of the mineral samples. The oxidation was found to occur at a higher rate in the presence of the bacteria compared to the control samples. Bioremediation experiments were conducted on acid mine water collected from the Ingaldahl Mines, Chitradurga, Karnataka, India, using organic and inorganic substrates. In the experiments with rice husk, complete removal of metal ions from the acid mine water was achieved with an attendant increase in the pH of the acid mine water from 2.3 to 5.5. About 21% of sulphate could be removed using Dsm. nigrificans from acid mine water pretreated with rice husk at pH 5.5 and this was further increased to 40% by the supplementation of organic components. The rice husk filtrate was found to serve as a good growth medium for Dsm. nigrificans. About 96 % of Fe, 75 % of Zn, 92 % of Cu and 41 % of sulphate removal was achieved from the acid mine water of pH 2.4 with a concomitant increase in the pH value by two units after interaction with the tree bark. About 56 % and 71 % of sulphate reduction could be achieved at initial pH values of 4.1 and 5.5 respectively of the acid mine water pretreated with E. tereticornis (Sm) bark, after inoculation with Dsm. nigrificans. The complete removal of Fe2+ and Fe3+, 80% of Zn, 83% of Cu and 62% of sulphate could be removed from acid mine water using fly ash as the substrate with an increase in pH of acid mine water from 2.3 to 7. About 68% of sulphate reduction at pH 6.8 could be achieved in acid mine water pretreated with fly ash in the presence of Dsm. nigrificans. With red mud as the substrate, complete removal of all the metal ions namely Fe2+, Fe3+, Zn, and Cu from acid mine water was achieved with a concomitant increase in the pH from 2.3 to 8. The sulphate reduction was increased to about 51% at pH 7.2 when the acid mine water pretreated with red mud was inoculated with Dsm. nigrificans. The adsorption experiments carried out on the acid mine water using either organic or inorganic substrates indicated that the free energy of adsorption was negative for all the chosen metal ions attesting to favorable interaction. The adsorption isotherms of the metal ions for rice husk exhibited Langmuirian behaviour, while those for the other substrates adhered to both Langmuir and Freundlich relationships. The adsorption process was found to be endothermic in nature for rice husk, fly ash and red mud. On the contrary, the adsorption onto tree bark showed exothermic behaviour. The adsorption kinetics of the metal ions onto the various substrates adhered to the first order Lagergren equation. The metal uptake processes by the organic and inorganic substrates chosen for this study involve ionic, chemical and physical forces of adsorption. The different types of functional groups present on the surface of the substrates such as carboxyl, hydroxyl and carbonyl, as revealed by FTIR spectroscopic studies, partake in metal binding. The metal ions will also be adsorbed by complexing with the negatively charged reaction sites on the substrate surfaces. Furthermore, the complex solution chemistry of the metals as a function of pH has also to be taken into consideration. The mechanism of sulphate reduction by Dsm. nigrificans in the presence of organic carbon can be illustrated as: 2CH2O + SO42- + 2H+  2CO2 + 2H2O + H2S M2 + H2S  MS  + 2H+ where, CH2O represents the organic matter and M represents the metal ion.