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 compartment 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. A special focus is made on microorganism relationships as well as with these perturbations.

  • get a better characterization of the microbial biodiversity in marine ecosystems
  • identify metabolic pathways and molecular mechanisms allowing microorganisms to adapt to specific environmental conditions, including extreme and contaminated conditions.
  • Understand their role and impact on ecosystem functioning
  • Benefit from microbial metabolism diversity to develop monitoring biomarkers and biotechnological processes for bioenergy and bioremediation of contaminated environments.

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

Our main areas of study are within the Mediterranean Sea(programme MOOSE, Antares), Pacific (SPOT program, Micro-Prony), North Atlantic (EMSO-Açores) and Artic ocean (projet Green Edge). A strong partnership has been developed with Tunisian research institutes and laboratories, especially through the International Joint research Unit COSYS-MED as well as with South-West Pacific Institutes and civil societies through ADCK-IRD collaboration agreement. Members of team are associated with the Tara Oceans consortium and with 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.


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

The team has a great expertise in microbial ecology of anaerobic environments, specially concerning the Carbon, Nitrogen and Sufur biogeochemical cycles. Our goal is now to focus on their coupling with respect to the global climate change and related episodes of hypoxia.


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Ecology and physiology of microorganisms in extreme conditions

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


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Interplay between microorganisms and contaminants

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


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Biotechnology and Instrumentation

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


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Protocol & Quality Approach