Micro-organisms and interactions with macro-organisms

, by Auguet Jean-Christophe, Villeger Sébastien

Representatives: Sébastien Villéger (CNRS) and Jean-Christophe Auguet (CNRS)


The knowledge of the diversity of organisms and their symbiotic, parasitic or commensal interactions is essential to explain the coexistence of species, their distribution, their productivity and their capacity for resistance and resilience. This concerns both the interactions between microorganisms (from viruses to meso-zooplankton) and the interactions between micro- and macro-organisms.

Today, they represent an emerging field of research that aims to assess the ecological role of micro-organisms on the host organism and in return the influence of the host organism on microbial communities.


  • To identify the taxonomic, genetic and functional diversity of microbial communities, in particular to highlight associations between species and identify rare species.

  • To understand the influence of the physicochemical and biotic environmental forcing on the structure, the distribution and the dynamics of microbial communities and their interactions.

  • To evaluate the effects of micro-organisms and their biodiversity on the condition and health of macro-organisms.

  • To quantify the role of macro-organisms on the structure and functioning of microbial communities whether related to the host or to the environment.


  • Study areas: the ecosystem model is the coastal system under strong anthropogenic pressure (including estuaries and lagoons) and located at temperate latitudes (northern and southern Mediterranean, Atlantic Ocean, North Sea and tropical seas (West Africa, Western Indian Ocean, South East Asia).

  • Biological models: micro-organisms (zoo- and phytoplankton, bacteria, and viruses) and macro- organisms (fish, corals, bivalves, gelatinous plankton).


  • Data Acquisition (1) by in situ observations (punctual or permanent) and (2) through in vitro and in situ experiments (crops, nano to macro scales).
• Methods: physicochemical characterization of the environment, biological / biochemical and isotopic characterizations (radioactive, stable tracers) of organisms and communities,
  • Molecular and metagenomics imprint method of inventory of taxonomic and functional diversity, 

  • Methods on cells or isolated individuals sorted by microscopy or flow cytometry, cell tagging techniques, development of non-invasive sensors for microbial activities.



MARBEC MARine Biodiversity, Exploitation and Conservation, is a research unit which includes the staff of 4 organizations: IRD, IFREMER, UM and CNRS. Its objective is the study of marine biodiversity in lagoon coastal and offshore ecosystems, at different integration levels, molecular, individual, population and community aspects and the way humans use this biodiversity.