Stromatolites are organosedimentary structures resulting from the activity of microbes. Fossil stromatolites are considered to be among the oldest traces of life on Earth, their oldest occurrence being at 3.5Ga. Although stromatolites dominate the Precambrian geological record, the abiotic and biological processes leading to their formation and thus the exact information that can be retrieved from them are still poorly understood. The main objective of this work was to study the formation of modern microbialites in order to better constrain the interpretation of the fossil ones. With this aim, we studied living microbialites from the alkaline Lake Alchichica in Mexico as a model system. The first part of this work has been devoted to the description of Alchichica microbialites including mineral phases and the associated microbial diversity. Alchichica microbialites are composed of aragonite [CaCO3] and hydromagnesite [Mg5(CO3)4(OH)2*4(H2O)]. Cultivation-independent molecular methods revealed a high diversity of bacteria (344 phylotypes distributed in 21 phyla) and microbial eukaryotes (58 phylotypes distributed in 9 phyla) in contrast with a low diversity of archaea (2 phylotypes). Molecular phylogenetic analyses allowed us to identify the closest cultivated members of the different phylotypes retrieved. This information was used to predict which metabolisms are putatively important in Alchichica microbialites. Oxygenic photosynthesizers were dominated by cyanobacteria, green algae and diatoms. Anoxygenic photosynthesizers were also diverse, comprising members of Alphaproteobacteria and Chloroflexi. Although photosynthetic microorganisms dominated the biomass, heterotrophic lineages were more diverse. We found sulphate-reducing lineages among Deltaproteobacteria and Firmicutes and very diverse taxa likely able to degrade complex polymeric substances, such as Planctomycetales, Bacteroidetes and Verrucomicrobia. Based on this, we build a hypothetical model of metabolic-geochemical reactions leading to carbonate precipitation or dissolution in Alchichica microbialites. In a second chapter, we describe a combination of microscopic and spectroscopic studies to study cyanobacteria-carbonate phase assemblages. We showed a preferential association between cyanobacterial colonies belonging to the order Pleurocapsales and aragonite. We described the early stages of fossilization of Pleurocapsales cells within aragonite down to the nanoscale. This reveals that microfossils of these cyanobacteria can be recognized even if the cells are totally encrusted. The mineralization sequence produces successive layers of aragonite whose textural organization points out the initial cells ultrastructures. This study opens new perspectives in the research of calcified cyanobacteria in ancient rocks. The third part reports the discovery of a cyanobacterium capable of performing controlled intracellular carbonate biomineralization. This strain, that we tentatively called Candidatus Gloeomargarita lithophora belongs to the basal cyanobacterial order of the Gloeobacterales. Intracellular inclusions formed by Ca. G. lithophora are amorphous Ba-Sr-Ca-Mg carbonates. The discovery of this new pattern of biomineralization in a basal order of cyanobacteria opens new perspectives for the interpretation of ancient fossil record.
