Diversity, Ecology and Evolution of Microbes


(PI Sébastien Duperron, 2021-2024)

Peri-urban lakes are of major significance to urban ecology and to the public. Apart from the phytoplankton, investigated because of their importance, our knowledge of the microbial communities they host and their functions is still limited. Understanding the effect of eutrophication, an indicator of anthropization, on freshwater bodies is an archetypal “One Health” problem. Indeed, the interdependencies between ecosystem, animal and human health are so strong, particularly in peri- urban areas, that holistic approaches must be adopted to adequately and simultaneously address the issues of environmental health and human well-being. However, larger-scale evaluation of eutrophication effect on lakes microbiome is currently mostly lacking. In COM2LIFE, we propose to evaluate the effect of eutrophication on the biodiversity of microbial communities occurring in peri-urban lakes in the very densely populated Île-de-France region. Specifically, it will investigate the taxonomic and functional diversity of Archaea, Bacteria, Eukarya, and viruses in the water, sediment and fishes microbial communities along a eutrophication gradient. COM2LIFE will test two hypotheses. First, we expect that the spatial and temporal heterogeneity of environmental factors related to anthropic pressure at the regional scale will result in differences in the taxonomic and functional diversity of lakes microbial communities. Second, we expect that the microbial communities observed in the water column, sediment, and fish compartments may vary in space and time, but that the functions they provide will be conserved due to functional redundancy among organisms and compartments. To test these hypotheses, we will perform time-series monitoring of microbial communities composition, structure, and metabolic potential by applying state- of-the-art next generation sequencing technologies, coupled with physico-chemical characterization of the compartments. The spatio-temporal heterogeneity of environmental factors related to anthropic pressure and their influence on the taxonomic composition and functional potential of microbial communities, as well as their interactions, will be deciphered using the most recent data analyses tools and modeling approaches. This will allow us to identify the key factors governing microbial community dynamics at the regional scale. The project will thus identify the biotic and abiotic parameters that constrain community compositions and functions at the lake and regional scales and the influence of eutrophication levels. This approach has the potential to provide new candidate bioindicators for evaluating anthropic pressures and water/ecosystem quality.