Conchas do molusco Physa sp., um gastrópode (caracol) comum de aquários de água doce, serviram como modelo para o estudo de alguns aspectos envolvidos na biomineralização. A concha calcária é constituída por cristais de carbonato de cálcio depositados em associação com uma matriz orgânica. Os componentes cristalinos e a matriz, foram estudados por microscopia eletrônica de transmissão e de varredura, e caracterizados por métodos espectroscópicos e analíticos. A constituição cristalina, em geral, assemelha-se àquela existente na maioria dos moluscos, enquanto a camada nacarada, interna da concha, apresenta comparativamente maiores variações. A matriz orgânica consta de um componente insolúvel, essencialmente constituído por polissacarídeos, enxofre e fósforo; e outro componente solúvel, com predominância de serina, glicina, ácido aspártico e ácido glutâmico. A análise feita por ativação de nêutrons demonstrou maior concentração de cálcio, sódio e estrôncio; estes elementos estão geralmente relacionados à presença de aragonita, em outras conchas de moluscos. O estudo qualitativo da fase cristalina foi realizado por difração eletrônica e por espectroscopia de infravermelho. Para análise quantitativa, usou-se a difração de raios-X, sendo os dados refinados pelo método de Rietveld. Os resultados obtidos demonstram a existência de dois polimorfos do carbonato de cálcio, aragonita e calcita, na concha da Physa. A caracterização qualitativa dos componentes inorgânico e orgânico do material estudado, mostrou semelhanças com relação a outros gêneros de moluscos. Experimentos de cristalização do carbonato de cálcio in vitro produziram aragonita e vaterita em presença de ácido aspártico ou glutâmico. Sob ação de glicina, serina ou quitina, houve formação de calcita. Em presença da matriz orgânica insolúvel, houve cristalização de calcita, enquanto a matriz solúvel induziu a cristalização da aragonita. Analisou-se quantitativamente todas as fases cristalinas obtidas nestes experimentos e estudou-se a morfologia dos cristais formados através da MEV e por MO luz. O resultado comparativo das investigações usando a concha natural, e dos cristais sintetizados, permitiu confirmar o papel fundamental da matriz orgânica no processo de cristalização do carbonato de cálcio. / Shells of Physa sp., a common freshwater gastropod snail, were used as a model for mineralization studies of calcium carbonate. The shell is a biomineral that consists of organized crystalline deposits associated to an organic matrix, both of which were studied by transmission and scanning electron microscopy; they were further characterized by means of pectroscopic and analytical methods. As a whole, its structural organization does not differ greatly from that found in other mollusc shells, except for the innermost, nacreous layer, that lines the shell. The organic matrix in Physa was found to consist of an insoluble fraction, essentially containing a polysaccharide, sulphur and phosphor. In addition, another (soluble) fraction is present, in which serine, glycine, aspartic acid and glutamic acid residues prevail. Neutronic activation analysis demonstrates a high concentration of calcium, sodium and strontium, elements known to be related to the presence of aragonite in other molluscan shells. A qualitative study of the crystalline phase was obtained through use of electron diffraction and FTIR spectroscopy. For quantitative analysis X-ray diffraction was used, as refined by the Rietveld method. Results obtained demonstrate the existence of two calcium carbonate polymorphs, aragonite and calcite in the shell of Physa, Qualitative evaluation of both organic and inorganic material from Physa showed similarities to those found in other mollusk shells. In vitro experiments performed at similar-to-natural conditions, on crystallization of calcium carbonate, did also crystallize aragonite and vaterite, provided aspartic acid or glutamic acid were present; whereas calcite was formed in solutions containing glycine, serine or chitin. Aragonite did crystallize when the soluble organic matrix was added to the solution. All these crystalline phases obtained were quantitatively evaluated, their morphologies being studied through light and electron microscopies. A comparative study of the natural crystals from the shell, and those obtained in laboratory experiments, stresses the fundamental role of the organic matrix on calcium carbonate crystallization

Dentre os diversos processos de formação de mineral em organismos vivos, a formação do tecido ósseo é um exemplo particular, uma vez que fosfatos de cálcio, na forma de hidroxiapatita, são produzidos em meio a fibrilas de colágeno na matriz extracelular de células osteogênicas; processo este regulado por um complexo enzimático. A fosfatase alcalina tecido não-específico (TNAP) desempenha um papel fundamental na histogênese óssea, responsável principalmente pela produção de fosfato inorgânico necessário para a formação dos minerais. Diversas abordagens experimentais permitem a reconstituição desta enzima em sistemas miméticos de membrana celular, dentre os quais, os filmes Langmuir-Blodgett (LB), que possibilitam a formação de materiais com propriedades osteoindutoras. No presente estudo, foi investigada a imobilização desta enzima em filmes LB sobre suportes de Ti. O ácido dimiristoil fosfatídico foi o fosfolipídeo utilizado na confecção dos filmes LB, obtendo um regime de deposição linear de massa em função do número de camadas depositadas em subfases de CaCl2. A TNAP foi imobilizada nos filmes através de duas metodologias: a partir da adsorção física da enzima aos filmes LB pré-transferidos a um suporte sólido, ou ainda por meio da construção do filme a partir de uma monocamada mista de DMPA/Ca2+/TNAP. Em ambas as metodologias adotadas, foi obtida uma diminuição drástica da atividade fosfohidrolítica da forma imobilizada da enzima, em relação à sua atividade obtida em meio homogêneo. Ao expor suportes de Ti modificados com os filmes LB em uma solução contendo íons Ca2+ e ATP como fonte de fosfato inorgânico, foi observada a formação de uma maior quantidade de mineral para as amostras contendo a TNAP imobilizada; atribuída a uma maior supersaturação local de íons fosfato devido a maior hidrólise de ATP na presença da enzima, demonstrando a capacidade desta em conferir à superfície modificada uma maior capacidade na indução de formação de mineral. Após este ensaio de mineralização in vitro, foi obtida uma maior hidrofilicidade das superfícies recobertas com os filmes LB na presença da TNAP, tornando estas superfícies modificadas mais bioativas. A presença dos filmes LB mistos de lipídeo/TNAP nas superfícies permitiram a adesão, proliferação e recobrimento homogêneo de células osteogênicas, que posteriormente promoveram o extravasamento de fibrilas proteicas e a formação de nódulos de mineralização. Estes resultados são importantes na confecção de materiais que acelerem o processo de osteoindução. / Among all the processes of mineral formation in living organisms, the osseous tissue formation is a particular example, since that calcium phosphates as hydroxyapatite are produced among collagen fibrils at the extracellular matrix of osteogenic cells, being this process regulated by an enzymatic complex. The tissue nonspecific alkaline phosphatase (TNAP) plays a central role on the osseous histogenesis, responsible mainly for the inorganic phosphate production necessary for mineral formation. Various experimental approaches allows this enzyme reconstitution in cellular membrane mimetic systems, among which, the Langmuir-Blodgett films (LB), that allows the formation of materials with osteoinductive properties. With that in mind, the immobilization of that enzyme in titanium supports modified with LB films was investigated. The dimyristoyl phosphatidic acid was the phospholipid used in the LB film construction, obtaining a linear deposition-layer numbers relation in CaCl2 subphases. The TNAP was immobilized at the films through two main methodologies: from the physical adsorption of the enzyme to the LB film pre-constructed on a solid support, or through the film construction from the mixed DMPA/Ca2+/TNAP monolayer. At both the adopted methodologies, it was obtained a diminishment at the phosphohidrolytic activity of the immobilized enzyme, comparing to its activity at homogeneous media. Exposing the Ti supports with the LB films in a solution containing Ca2+ ions and ATP as a phosphate source, it was observed a higeher mineral formation to the samples containing the immobilized TNAP, possibly due to a higher phosphate ions supersaturation from the higher ATP hydrolysis at the presence of the enzyme, demonstrating the capacity of the TNAP in promoting a higher mineral formation induction to the modified surface. After this in vitro mineralization assay, it was obtained surfaces more hydrophilic at presence of the LB films containing TNAP, making those modified surfaces more bioactive. The mixed LB films presence at the surfaces allowed the adhesion, proliferation and homogeneous covering of osteogenic cells, that posteriorly promoted the production of proteic fibrils and mineralization nodules. Those results are important in order to construct materials more osteointegrative.

De nombreux organismes marins précipitent des squelettes en calcite magnésienne. Depuis près d’un siècle, il est connu que les concentrations en magnésium de ces squelettes sont influencées par les conditions environnementales, telle la température, régnant au moment de leur dépôt. Dans le contexte actuel de changement climatique, cette propriété a promu l’usage de plusieurs taxons en tant qu’archive naturelle des conditions environnementales du passé. Cependant, les squelettes d’espèces sympatriques, voire d’individus de la même espèce, peuvent présenter des concentrations en magnésium très différentes, attestant de l’influence de facteurs biologiques sur la détermination de la concentration squelettique en cet élément. Une parfaite compréhension des mécanismes d’incorporation du magnésium dans les squelettes est donc requise pour valider l’usage de ce paléotraceur. De plus, la solubilité des calcites augmentant avec leur concentration en magnésium, l’incorporation de cet élément conditionne en partie la stabilité des squelettes calcitiques dans un océan en cours d’acidification.<p>Le présent travail contribue à l’étude des différents facteurs, tant environnementaux que physiologiques et minéralogiques, susceptibles d’affecter l’incorporation du magnésium dans les squelettes en calcite de trois taxons présentant des concentrations en cet élément particulièrement élevées, une éponge hypercalcifiée, Petrobiona massiliana, et deux échinodermes, Paracentrotus lividus et Asterias rubens.<p>Dans une première partie, les effets de plusieurs facteurs environnementaux ont été étudiés, en milieu naturel dans le cas de l’éponge, étant donné son incapacité à survivre en aquarium, et en conditions contrôlées d’aquarium dans le cas des deux échinodermes. Une influence environnementale prépondérante de la température sur la concentration en magnésium squelettique a été mise en évidence dans les 3 modèles biologiques étudiés. Une fois les facteurs génétiques (espèce) et structurels (élément squelettique) fixés, une relation positive liant la température à la concentration en magnésium squelettique a été caractérisée en milieu naturel chez l’éponge hypercalcifiée P. massiliana et en conditions contrôlées chez l’oursin P. lividus. Chez ce dernier, cette relation, non linéaire, se stabilise aux plus hautes températures envisagées, probablement suite à la saturation d’un processus biologique intervenant dans l’incorporation de cet élément. La salinité, un autre facteur environnemental majeur en milieu marin, influence elle aussi positivement la concentration en magnésium dans le squelette de l’étoile de mer A. rubens. A nouveau, il est proposé que cette influence de l’environnement soit modulée par un processus biologique: chez les échinodermes, la concentration en magnésium, contrairement à celle du calcium, n’est pas régulée dans le liquide coelomique. Elle est donc directement influencée par la salinité, et affecte probablement la concentration en cet élément dans le squelette formé. La diffusion depuis l’eau de mer jusqu’au site de calcification par l’intermédiaire des fluides internes a en effet été suggérée sur base du fait que le rapport Mg/Ca de l’eau de mer influence celui des squelettes calcaires<p>Une fois l’influence, directe ou indirecte, des facteurs environnementaux exclue, 44% de la variabilité du rapport Mg/Ca du squelette des échinodermes restent à expliquer. Les expériences de croissance d’échinodermes réalisées en conditions contrôlées indiquent que ce rapport est indépendant de la vitesse de croissance dans ce groupe, contrairement aux hypothèses émises dans la littérature.<p>Dans la seconde partie, la modulation des facteurs minéralogiques par les facteurs biologiques a été investiguée. Pour ce faire, d’une part, les interactions entre rapport Mg/Ca en solution et matrice organique de minéralisation ont été étudiées dans un modèle in vitro. D’autre part, les relations entre soufre et magnésium dans le squelette ont été décryptées.<p>Le rapport Mg/Ca de la solution de précipitation a une influence prépondérante sur la concentration en magnésium du carbonate de calcium précipité in vitro, attestant de l’importance de la régulation de la composition du fluide de calcification et des mécanismes de transport la contrôlant. Deux mécanismes biologiques complémentaires permettent de favoriser l’incorporation, dans les calcites biogéniques, de quantités de magnésium largement supérieures à celles observées dans les calcites inorganiques, et ce, malgré la forte hydratation de ce cation :l’intervention d’agents chélateurs du magnésium et le passage par une phase de carbonate de calcium amorphe (CCA). Les molécules de la matrice organique de minéralisation jouent entre autres le rôle de chélateur du magnésium, réduisant son état d’hydratation et facilitant ainsi son incorporation dans le minéral. Un rôle similaire a été suggéré pour les sulfates en solution, au vu de la corrélation observée dans ce travail entre les rapports Mg/Ca et S/Ca dans la phase minérale des calcites biogéniques étudiées. La matrice organique affecte elle aussi la concentration en magnésium dans le cristal, probablement via la stabilisation de la phase de CCA nécessaire à l’incorporation de concentrations élevées de cet élément: ainsi, les macromolécules de la matrice organique du test d’oursin induisent in vitro la formation de calcites plus riches en magnésium que celles formées en présence de matrice de piquant, un résultat concordant avec le fait que, in vivo, le test contient des concentrations en magnésium plus élevées que les piquants.<p>Cette thèse de doctorat a donc soulevé l’importance des effets biologiques dans la détermination du rapport Mg/Ca dans les calcites biogéniques. Les résultats obtenus montrent que le décryptage des mécanismes impliqués dans l’incorporation du magnésium se doit de considérer la phase amorphe transitoire qui précède la cristallisation. Des effets environnementaux affectent eux aussi la concentration squelettique en magnésium, mais nos résultats suggèrent qu’ils agissent au travers d’une modulation des effets biologiques, et non par une influence thermodynamique directe. Cette hypothèse, si elle est confirmée, impose la plus grande prudence lors de l’utilisation des squelettes en calcite en tant que paléotraceurs.<p><p><p>SUMMARY<p>The magnesium concentration in calcite skeletons produced by marine invertebrates is known to be dependent on several environmental parameters, including temperature, salinity and seawater Mg/Ca ratio. This property prompted the use of this concentration as a proxy of the considered parameters. However, skeletal magnesium contents in sympatric species and even in individuals of the same species may be rather different. These inter and intra-individual variabilities indicate that biological factors also affect magnesium incorporation into biogenic calcites. Magnesium incorporation mechanisms are still unknown in calcifying invertebrates, a fact that questions the validity of this element as a paleoproxy. Moreover, higher magnesium contents increase calcite solubility and could therefore worsen the case of calcifying organisms facing ocean acidification linked to global change.<p>The present thesis is a contribution to the study of the environmental, biological and mineralogical factors affecting magnesium incorporation into the calcitic skeletons of 3 taxa, i.e. one hypercalcified sponge, Petrobiona massiliana, and two echinoderms, Paracentrotus lividus and Asterias rubens.<p>The first part of this work was dedicated to the study of several environmental factors affecting the magnesium concentration in the calcite skeleton of the 3 studied organisms. Consequently to its low survival in aquarium, the sponge was studied using field specimens collected along an environmental gradient. Echinoderms were grown in controlled conditions in aquarium. Once the genetic (species) and structural (skeletal element) factors were fixed, skeletal magnesium concentration was positively related to temperature in the 3 studied species. The Mg/Ca ratio of the test of aquarium-grown P. lividus increased with temperature until a plateau which was probably due to the saturation of a biological process involved in magnesium incorporation. A positive effect of salinity, an other major environmental parameter, on skeletal Mg/Ca was demonstrated in aquarium-grown A. rubens. This influence can also be linked to a biological process: contrary to magnesium, calcium concentration is controlled in the coelomic fluid, from which ions probably diffuse through the living tissues to the calcification site. Thus, the observed positive relation can be explained by the fact that a salinity increase raises the coelomic Mg/Ca ratio, which, according to previous studies, affected the Mg/Ca ratio of the precipitated skeleton.<p>In addition to the reported environmental influences, 44% of the skeletal Mg/Ca ratio variation remained unexplained in echinoderms. The absence of growth rate effect on magnesium incorporation into the echinoderm skeleton was demonstrated in aquarium experiments, contrary to previous literature statements. Other biological factors must therefore affect the incorporation of this element.<p>In the second part of this work, the modulation of mineralogical factors by biological factors was investigated. The interaction between Mg/Ca ratio in the precipitation solution and organic matrix was studied in an in vitro precipitation experiment. In addition, the relation between skeletal Mg/Ca and S/Ca ratios was investigated.<p>A major influence of the precipitation solution Mg/Ca ratio on the magnesium concentration of in vitro precipitated minerals was evidenced, highlighting the importance of transport mechanisms which determine the composition of the calcifying solution. The<p>higher magnesium concentrations presented in some biogenic calcites in comparison to inorganic calcites can be attributed to the action of chelating molecules and to the transition trough an amorphous phase. The strong tendency of magnesium towards hydration can be overcome by the involvement of molecules that can function as magnesium chelators and, therefore, favour the formation of calcite with a high magnesium content. Organic matrix macromolecules have been suggested to proceed as magnesium chelators, reducing the hydration of this ion and facilitating its incorporation into calcite. A similar function was suggested for sulphates that were measured in the echinoderm skeleton. This would explain the positive correlation between skeletal Mg/Ca and S/Ca ratios observed in the studied species. Organic matrix macromolecules also increased the magnesium concentration of minerals precipitated in vitro, probably stabilizing the transient phase of amorphous calcium carbonate, which can incorporate high quantities of magnesium in its structure. The enhancement of magnesium incorporation was more pronounced with the organic matrix extracted from the test of sea urchin than with that extracted from their spines. This result was in agreement with the in vivo skeletal Mg/Ca ratios in P. lividus skeleton that were higher in the test than in the spines.<p>This study demonstrated the importance of the biological effects in the determination of Mg/Ca ratios in biogenic calcites. According to the suggested hypotheses, the understanding of mechanisms involved in magnesium incorporation should take the transient amorphous phase into account. Magnesium concentration in biogenic calcite was also affected by environmental parameters, but these influences could proceed through the indirect modulation of biological rather than a direct thermodynamic control. This hypothesis, if proved correct, would have deep implications for the use of magnesium in calcite skeletons as a paleoproxy. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

A natural arsenic anomaly at Mokrsko is a site of biogenic precipitation of realgar (As4S4) in stream sediment. The extent of the phenomenon in Mokrsko is globally unique. A previous study showed the ability of microorganisms to solubilize arsenic from its secondary minerals and to produce realgar precursors, i.e. sulfides and arsenites, by anaerobic respiration. The study also raised questions about the mechanism of realgar precipitation since physicochemical conditions favoring this reaction were never detected despite significant sampling efforts. We chemically and microbiologically analyzed sedimentary profiles to the depth of ca. 120 cm in order to understand the functioning of the biogeochemical system. The profiles comprised both the unsaturated and the saturated zone. We distinguished six different domains representing environments from the surface soil to anoxic sedimnent containing realgar-encrusted wood. An analysis of phylogenetic dissimilarity revealed that microbial communities from the various domains form distinct clusters. This suggests that different conditions prevail in the various domains, and that different biogeochemical processes take place there. Incubation (microcosm) experiments showed that bioprecipitation of realgar can be conducted in vitro. It requires a suppression...

Cette thèse vise à avancer dans la compréhension de la formation récemment découverte de carbonates amorphes intracellulaires par des cyanobactéries. Des synthèses abiotiques ont permis de produire des carbonates similaires aux inclusions intracellulaires en termes de morphologie, structure et composition chimique. Ceci a permis notamment de discuter les conditions chimiques présentes dans le milieu intracellulaire de ces bactéries, qui semblent incompatibles avec les connaissances actuelles de l’intérieur des cyanobactéries. Plusieurs souches de cyanobactéries formant ou non des carbonates intracellulaires ont été cultivées en laboratoire. Des études de chimie des solutions sur le milieu extracellulaire ont montré que la précipitation intracellulaire est un processus actif pour la cellule, c’est-à-dire nécessitant de l’énergie. De plus, les cyanobactéries formant des carbonates de calcium intracellulaires imposent de faibles concentrations en calcium dans leur milieu de vie. Le suivi de la formation de carbonates intracellulaires dans des milieux contrôlés a aussi permis de démontrer qu’une espèce formait spécifiquement des carbonates de baryum et de strontium grâce à une affinité pour le baryum supérieure à celle pour le strontium, elle-même supérieure à celle pour le calcium. Ceci ouvre des perspectives intéressantes pour la dépollution et questionne l’utilisation des rapports Sr/Ca comme proxy des paléo-environnements. / In this thesis we study the recently discovered formation of intracellular amorphous carbonates by cyanobacteria. Abiotic syntheses produced carbonates with a morphology, structure and composition similar as intracellular inclusions. The intracellular chemical conditions in the cyanobacteria can be discussed; they seem inconsistent with our current knowledge about cyanobacteria. Several cyanobacterial strains, forming intracellular carbonates or not, were cultured in the laboratory. Analyses of the chemical composition of extracellular solutions showed that intracellular precipitation is an active process, i.e., it needs energy. Also, cyanobacteria forming intracellular calcium carbonates imposed low concentrations in calcium in their living environment. Monitoring the formation of intracellular carbonates in controlled environments also demonstrated that one species formed carbonates of barium and strontium owing to an affinity for barium higher than for strontium and higher for strontium than calcium. This feature opens interesting perspectives on bioremediation and questions the use of Sr/Ca ratios as a proxy for paleo-environments.

Please read the abstract in the section 00front of this document / Thesis (DSc (Oral Pathology))--University of Pretoria, 2005. / Community Dentistry / unrestricted

Biomining technologies have been developed to use acidophilic microorganisms and the reactions that they catalyze to extract metals from ores in the mining industry. This biological processing through hydrometallurgy is responsible for the production of a significant portion of the world’s copper and gold supplies. Acidithiobacillus ferrooxidans is one of the better-studied and important chemolithotrophic bacterial species that is a part of the natural consortia found in mines across the world. This acidophile is unique in the array of redox reactions it participates in as it is capable of oxidizing both iron and reduced inorganic sulfur species, enabling dissolution of metal from minerals. As the transition to renewable energy continues and the demand for electronic devices grows, more copper and other valuable metals will need to be extracted from increasingly low-grade ores, such as chalcopyrite. Additionally, there has been a growing interest in further developing this biotechnology for the leaching and the recovery of valuable metals from scrap alloys and electronic waste as these feedstock streams can contain rare metals at concentrations above those found in the earth. However, the challenge in deploying biomining to these applications involves understanding the interactions that can potentially inhibit the extraction of these metals. In this dissertation, we expanded the genetic toolbox for A. ferrooxidans by using a transposition technique for the chromosomal integration of exogenous genes. The ability to permanently modify the genome enables engineering of strains that can be used in industry without the need of maintaining selective pressure for plasmid-based expression. Next, we investigated the potential role of A. ferrooxidans in microbially influenced corrosion. We focused on finding conditions that would enable the corrosion of stainless steel, which is resistant to the medium typically used for the growth of the bacterium. Additionally, the further optimization of the corrosive environment and the introduction of genetically engineered cells led to additional corrosion of a higher-grade stainless steel. Then, we explored how altering the bioavailability of sulfur in different formulations could shift the population phenotypes in A. ferrooxidans. We found that a unified description with a few parameters could describe the wide range of behaviors observed in the presence of iron and sulfur. Thus, using this improved understanding of A. ferrooxidans, we are able to engineer phenotypes of interest to generate robust strains that can modulate leaching conditions.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第21583号 / 理博第4490号 / 新制||理||1645(附属図書館) / 京都大学大学院理学研究科地球惑星科学専攻 / (主査)准教授 伊藤 正一, 教授 生形 貴男, 教授 山路 敦 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Les tapis microbiens sont des communautés benthiques, calcifiées (i.e. microbialites) ou non, diverses à la fois phylogénétiquement et métaboliquement. Les tapis microbiens fossiles constituent les plus anciennes traces de vie sur Terre et leurs représentants modernes peuvent donc être utilisés pour comprendre le fonctionnement de ces écosystèmes anciens. J'ai étudié les communautés microbiennes (archées, bactéries et eucaryotes) de plusieurs microbialites (lac Alchichica, Mexique) et tapis microbiens (dans une mare du salar de Llamara, Chili) afin de caractériser finement leur structure phylogénétique et d'améliorer notre compréhension de leur fonctionnement. J'ai pour cela utilisé une approche combinant des outils moléculaires (métabarcoding, métagénomique) à des données environnementales (paramètres physico-chimiques de la colonne d'eau ou composition minérale des microbialites). Mon travail de thèse a permis d'affiner le modèle de formation des microbialites d'Alchichica, en montrant notamment que, en plus de la photosynthèse oxygénique cyanobactérienne, le potentiel à précipiter des carbonates de la photosynthèse eucaryote et, surtout, de la photosynthèse anoxygénique est important. Les communautés des tapis de Llamara étaient quant à elles caractérisées par la présence de nombreuses lignées d'archées et de bactéries très divergentes, dont certaines ont été identifiées pour la première fois dans ce travail. Nos analyses ont aussi souligné la diversité des organismes impliqués dans les cycles du soufre et de l'azote au sein de ces systèmes et permis d'identifier de potentielles interactions biotiques entre des lignées procaryotes dont l'écologie est peu connue. Enfin, nous avons mis en évidence que les paramètres environnementaux influencent fortement la composition des communautés associées à ces microbialites et à ces tapis microbiens. L'ensemble de ces résultats permet de mieux comprendre le fonctionnement de ces systèmes ainsi que les facteurs qui influencent leur structure phylogénétique et fonctionnelle. / Microbial mats are phylogenetically and functionally diverse benthic microbial communities, which can be sometimes calcified (i.e. microbialites). Fossil microbial mats constitute the oldest traces of life on Earth and their modern representatives are thus used as analogues of those primordial ecosystems to gain insights into their functioning. I have studied the microbial communities (archaea, bacteria and eukaryotes) of several microbialites (lake Alchichica, Mexico) and microbial mats (in a small pond in the salar de Llamara, Chile). The main objectives of my PhD were to finely characterize their phylogenetic structure and to improve our understanding of the functioning of these complex ecosystems. To do so, I have applied a multi-disciplinary approach combining molecular approaches (metabarcoding, metagenomics) to environmental data (physico-chemical parameters of the water column or mineral composition of the microbialites).The results presented in this thesis allowed refining our model of microbialite formation in Lake Alchichica. We showed that, in addition to cyanobacterial photosynthesis, both eukaryotic and, particularly, anoxygenic photosyntheses were potentially important to promote carbonate precipitation. Llamara mat communities were characterised by the presence of numerous novel archaeal and bacterial lineages, some of which were identified for the first time in this work. Our analyses have also highlighted the diversity of organisms involved in both sulphur and nitrogen cycles in these mats and identified potential biotic interactions between poorly known prokaryotic lineages. Finally, we showed that the composition of the microbial communities associated to these microbialites and microbial mats was strongly influenced by environmental parameters. Overall, these results represent a substantial contribution to our understanding of the ecology of these systems as well as of the factors that influence their phylogenetic and functional structures.

Iron is a common cation in biomineral sand; it is present for example in magnetite produced by magnetotactic bacteria and in iron sulfides produced by sulfate reducing microorganisms. The work presented in this thesis focused on two types of microorganisms capable of forming iron biominerals. In the first project I have studied the effect of O2 on the respiratory physiology and the formation of magnetosomes by Magnetospirillum magneticum AMB-1. In the second project I have studied the relationship between olivine and the activity of dissimilatory sulfate reducing (DSR) microorganisms. For the first project, I grew cells of AMB-1 in cultures with various concentrations of O2 and monitored growth and the formation of magnetic mineral particles (MMP). Results have shown that AMB-1 cells grew better at 100-225 uMO2(aq) than at lower [O2], yet the formation of MMP was repressed at ~45 uM O2(aq) and strongly inhibited at >100 uM O2(aq).These results have helped better understand the dissimilarity between the optimal growth conditions of magnetotactic bacteria and the conditions needed for the formation of MMPs. My results have also shown that the reaction between H2S produced by DSRs and olivine is abiotic, not catalyzed and exergonic. The pH did not vary significantly during this reaction and pH variation (in the 5-9 range) did not significantly influence this chemical reaction. Bicarbonate inhibited the reaction between H2S and olivine, but not the chemical equilibrium. Phosphate, a weak iron chelator, influenced the equilibrium of the reaction and it is assumed to help increase the rate of olivine weathering in the presence of DSRs. The activity of DSRs was positively influenced by the presence and abundance of olivine. Based on my results I propose that olivine help DSR obtain energy more efficiently, but does not represent a source of energy or nutrients for the cells. These results helped better understand the formation of iron biominerals and signatures of this activity.