Microbial communities

In the last years, the LM2E has been working on the description of microbial diversity of several extreme ecosystems and particularly on hydrothermal vents, continental margins around cold seeps and deep sea subsurface. As knowledge on the prokaryote diversity in these extreme environments is improving, functional studies on microbial communities in interaction with their biotope (both the mineral and the living ones) are starting.

Biogeochemical cycles

In the hydrothermal ecosystems, the carbon cycle will be mainly studied. Regarding the temperatures occurring in situ, aerobic and anaerobic conditions are successively encountered by microbial communities. In these areas, the relative importance of various metabolisms (aerobic and anaerobic oxidations, fermentative oxidations) which may co-occur, will be studied. Relationships between autotrophic and heterotrophic microbial communities will also be analysed.
Recent results obtained by our group in collaboration with the AMEX laboratory (UMR 7138) have shown that in the gill chamber, iron oxidation could be microbially promoted whereas in the digestive tract the iron reduction could occur. More work is needed on the iron cycle to confirm or not the importance of iron cycle in energetic pathways.
The last point would be the study of the anaerobic ammonium oxidation at high temperature (above 60°C) in the hydrothermal context. The anamox reaction is investigated through molecular and cultural approaches in collaboration with Pr M. Jetten (University of Nimègue, The Nederland).
In the context of the continental margin, the LM2E will focus on the methanogenic and methanotrophic pathways under aerobic and anaerobic conditions.

Interactions between prokaryotes and their environment

In deep sea ecosystems, as light does not penetrate, photosynthesis does not occur. Deep sea ecosystems are fed by the limited part of the surface primary production that sank to the bottom. Deep sea biomass is thus very limited, usually less than 1 g wet weight per m2 which corresponds more or less to a desert. On the contrary, at hydrothermal vent sites and close to cold seeps, life is very abundant and biomasses are high. Discovered in 1977 in the Galapagos, hydrothermal vent ecosystems are distributed along the East Pacific rise, Juan de Fuca ridge, Mid Atlantic ridge and the Back Arc Basins such as North Fiji. Colds seeps are generally encountered on continental margins. These ecosystems are linked to hydrothermal activity, consisting in reduced fluid emissions and high temperatures or to cold fluids emission generally methane and hydrogen sulfide. In these extreme environments, chemolithoautrophic microorganisms are the primary producers that allow the settlement of a rich and diverse fauna. This fauna could either feed on free living microorganisms or establish nutritional symbiotic relationships. Symbiosis in these environments are widespread and some examples are now well understood, such as the endosymbiosis of the giant vestimentiferan Riftia pachyptila or the bivalve Bathymlodiolus azoricus.

In other cases, the symbiotic relationship is not so obvious, as for the epibionts of the alvinellid tubeworm Alvinella pompejana or the caridean shrimp Rimicaris exoculata. Numerous hypotheses concerning the role of theses epibiotic microflora have still to be tested and we still have to confirm it is or not a real symbiosis (ie an interaction with reciprocal benefit for both partners). They may be (i) a feeding source, (ii) a detoxification role against mineral precipitates and emitted gases, (iii) a protection against other microorganisms that could be pathogens or (iv) a new pathogen form and a link in population control.

Our project will focus on the dominant megafaunal species found at the Mid-Atlantic Ridge, which currently remains poorly studied : the shrimp Rimicaris exoculata. During the course of the project, we intend to pursue and complete studies dealing with the interactions between Rimicaris exoculata and its epibiotic microbial community, both in the gill chamber and the digestive tract. We plan to focus on 4 main questions :


  • What is the carbon source of the shrimps : gill chamber epibionts, digestive tract epibionts and/or chimney wall microbial communities?
  • How shrimps gain their carbon from bacteria, and from which bacteria (digestive tract, gill chamber, or both)?
  • What are the metabolisms implicated in these interactions?
  • Does the bacterial diversity change in accordance to the chemical fluid conditions and the moulting stage?

Most studies to date on this epibiotic association are descriptives, for lack of technical means to have a functional approach. Our project aims to go further in the comprehension of the interactions between host and epibionts, by the use of in vivo under pressure experiments on board ship, in collaboration with the AMEX team of the unit UMR7138. As Rimicaris exoculata is able to survive decompression during ascent to the surface, perfecting of sampling and under pressure reconditioning techniques will allow in vivo experiments to test for the first time our hypotheses on the functioning of this symbiosis on several hydrothermal vent fields very different in term of fluid compositions.