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Lab:    UMR CARRTEL – Alpine Center for Research on Lake Ecosystems and Food Webs
           Domaine Universitaire
           73376 Le Bourget-du-Lac, France

Title:   Application of microbial diversity based approaches in paleolimnology to characterize the historical evolution of local pressures on lake ecosystems

Supervisor:                 Isabelle Domaizon, INRAE, CARRTEL
Co-supervisors:          David Etienne, University Savoie Mont Blanc, CARRTEL
                                     Emilie Lyautey, University Savoie Mont Blanc, CARRTEL

Subject: Long‐term understanding of past environmental conditions and past biological communities is a key challenge to predict how future environmental changes will affect ecosystem properties and biological diversity. Lake sediments are particularly relevant archives because of their ability to record both local and global environmental conditions, and to reconstruct temporal evolutions over the last millennia. In lake ecosystems, understanding the impact of anthropogenic stresses on microbial communities is a major challenge for current and future scientific research. Changes in microorganism diversity are likely to affect associated functions and will theoretically impact the resilience of these environments. As a consequence, lake ecosystems might be affected and less prone to resist to current and future environmental changes. Although multiple paleolimnological studies have already been developed on several lake ecosystems around the world, the analysis of subfossil DNA preserved in lake sediments is currently identified as one of the most promising developments in paleoecology, expanding the range of biological data that can be extracted from lacustrine sediments. While the use of genomic approaches has been successfully developed and applied for reconstructing long‐term dynamics of microbial eukaryotes, few similar application has yet been applied on microorganisms (micro‐eukaryotes, bacteria and archaea), although they may represent valuable indicators of global and local environmental changes affecting the lake ecosystem. This thesis aims to develop an integrative and holistic approach to understand the in natura complexity of microbial communities in the three domains of life within lake ecosystems. In this project, the strategy is to simultaneous study archaea, bacteria and micro‐eukaryotes, considering both the present and active microbial fractions, to understand microbiomes and their dynamics on large time and space scales. This will integrate questions relevant of microbial ecology and paleogenomic centered both on the aquatic and terrestrial communities archived in the sedimentary compartment.

Keywords: Bacteria • Archaea • Eukaryotes • SedDNA • Past and actual communities