Environmental Microbiology and Biotechnology (MEB)



Headers : Patricia Bonin, Alain Dolla



The research interest of the « Environmental Microbiology and Biotechnology » team focuses on understanding the role of the bacterial component in marine ecosystems. Our goal is to integrate metabolisms from microorganisms into the functioning of the biogeochemical cycles within natural and anthropically disturbed marine ecosystems by either organic and metallic contaminations or global climate change-induced perturbations. Special focus is given to microorganism relationships and these perturbations.

  • Characterization of the microbial biodiversity in marine ecosystems
  • Identification of the metabolic pathways and molecular mechanisms that allow microorganisms to adapt to specific environmental conditions, including extreme and contaminated conditions
  • Understanding their role and effects on ecosystem functions
  • Characterization of microbial metabolism diversity to develop monitoring biomarkers and biotechnological processes for bioenergy and the bioremediation of contaminated environments.

To achieve these goals, we develop a multidisciplinary approach that includes microbial ecology, genomics and post-genomics, genetics and biochemistry. Studies are conducted on both environmental samples and model microorganisms. Our team is participating in several oceanology campaigns (Tara Oceans, HYDROPRONIE, HIPPOCAMPE, PEACETIME, SARGASSES, MOMARSAT, etc.) to collect samples and conduct long-term and large-scale environmental monitoring. We are also developing bioinformatic tools for the entire scientific community (Ocean Gene Atlas).

Our main areas of study are within the Mediterranean Sea (MOOSE program, Antares), Pacific Ocean (SPOT program, Micro-Prony), North Atlantic Ocean (EMSO-Azores) and Artic Ocean (Green Edge Project). A strong partnership has been developed with Tunisian research institutes and laboratories, especially through the international joint research unit COSYS-MED, and southwestern Pacific institutes and civil societies through the ADCK-IRD collaboration agreement. Members of this team are associated with the Tara Oceans consortium and the GO-SEE (Global Oceans Systems Ecology & Evolution) project.


See the team's publications

The research performed at the MEB team is organized in five topics

Dynamics in complex microbial systems: relationships and interactions between organisms

Interactions among community members (including symbionts) could produce endogenous dynamics in composition and activities, even in the absence of environmental changes.


Read more

Microbial metabolisms that are involved in the functioning and coupling of biogeochemical cycles in the context of climate change

The team has great expertise in the microbial ecology of anaerobic environments, especially the carbon, nitrogen and sulfur biogeochemical cycles. Our goal is to focus on these elements’ coupling with respect to global climate change and related episodes of hypoxia.


Read more

Ecology and physiology of microorganisms in extreme conditions

We are interested in prokaryotes that are referred to extremophiles because they proliferate under physico-chemical (temperature, pH, salinity, pressure, and ionizing radiation) or biological (energy source) conditions that are close to the limits of life on Earth.


Read more

Interplay between microorganisms and contaminants

Our goal is to understand the mutual influences between contaminants and marine microorganisms at both the population and molecular levels. Historically, a solid expertise has been acquired in the team regarding organic contaminants (such as hydrocarbons), which has been supplemented in recent years by an expertise on inorganic contaminants such as metallic trace elements.


Read more

Biotechnology and instrumentation

This research aims to develop biotechnological processes involving marine microorganisms that are dedicated to both the production of green energy and highly valuable molecules and the bioremediation of environments that are contaminated by metals.


Read more

Protocol & Quality Approach