Microbial communities in Ile de France Lakes: taxonomic and functional diversity – COM2LIFE

The project will 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.

Sampling sessions have started in June 2021 and are currently ongoing.

The first results show significant differences between lakes and over time both in the physico-chemical characteristics and in the composition of the communities. The in-depth analysis will make it possible to test the significance of the variations and to identify the driving factors and variables.

At this stage, three ESRs have worked on the project:
- Pierre Foucault (PhD, MNHN; started jan 2022, supervised by S. Duperron and J. Leloup) Diversité fonctionnelle des communautés microbiennes des lacs péri-urbains d’Ile-de-France : saisonnalité et influence du niveau d’eutrophisation
- Maïa Henry (M2, MNHN; jan-june 2022, supervised by S. Halary) Etude de l’impact de l’eutrophisation sur les communautés virales et microbiennes des lacs d’Île-de-France
- Alicia Dussol (M1, Univ. Paris-Saclay ; apr-jun 2022, supervised by S. Duperron and M. Goto) Impact de l’eutrophisation sur les communautés bactériennes photoautotrophes dans les lacs péri-urbains d’Ile-de-France

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.