MICROBIOMIQ - Multiomic approach to characterize the link between the structural biodiversity and the microbial activity along the natural evolution of periphytic biofilm

 This project is complete: see the results

In the context of global change, one of the major challenges for environmental and human health is to better understand how these communities respond to multiple pressures in terms of acclimation, adaptation, and resilience, in order to preserve the associated ecosystem functions and services. In particular, in the face of chemical contamination of these ecosystems, a current challenge is to determine how “natural” fluctuations in structural biodiversity and microbial functioning linked to environmental conditions modulate these communities’ response to chemical stress.

New so-called “omics” analytical methods and their combination open new perspectives in microbial eco(toxico)logy to address these knowledge gaps. For example, untargeted metagenomics simultaneously explores species diversity within a community and its functional potential (i.e., genes reservoir) while untargeted meta-metabolomics provides a global view of microbial activity in response to the environment by analysing all metabolites produced in a biological sample.

Objectives

MICROBIOMIQ aimed to better understand the link between microbial activity (i.e., metabolome), structural biodiversity (species and gene diversity via metagenomics), and sensitivity to chemical stress in periphytic biofilms, in relation to “natural” changes in community composition and functioning driven by environmental conditions. By implementing an approach combining metagenomics and meta-metabolomics on these biofilms, the project focused on the modulation of photosynthesis, a key function carried out by these communities and strongly involved in biogeochemical cycles and primary production.

These results will help improve our understanding of the adaptive mechanisms of ecosystem functions in response to chemical contamination and their temporal sequence. The data collected in this project may subsequently support the development of management tools within the framework of water quality biomonitoring.

Approaches

To achieve this, MICROBIOMIQ combined in situ investigations (longitudinal monitoring over 15 months) and laboratory experiments (monthly acute exposures) based on a multidisciplinary approach integrating metagenomics, meta-metabolomics, measurements of photosynthetic activity, and physicochemical characterization of the environments. The combination of these methods made it possible to assess in an innovative and precise way the interrelationships between changes in environmental factors, taxonomic diversity, microbial activity, and photosynthetic function, as well as their sensitivity to chemical pressure under natural and controlled conditions, supported by bioinformatic approaches.

Participants

INRAE units involved

• UR EABX - Unité de recherche Écosystèmes aquatiques et changements globaux
• UMR BIOGECO - Biodiversité, gènes et communautés