Research Projects

My main interest lies in understanding the synecology and autecology of microbes at different temporal and spatial scales in natural environments.

The main questions being addressed are:
- How much can we really understand from the gigantic world of tiny microbes?
- Are there ecological, functional or mathematical rules governing the community structure and abundance of microbes?
- What types of molecular tools can we use to cope with the huge microbial diversity in a high number of environmental samples?
- How can we make sense of microbial community patterns, their interactions, and their correlations when environmental, spatial or temporal parameters are available?
- Can we build a better understanding of microbial ecology by following a community ecology approach?

My current projects deal with the ecology of microbes at continental margins and at methane-driven ecosystems in marine sediments. My main approaches consist of using a combination of 1) molecular tools to study microbial communities in their environment, and 2) biostatistical analyses of environmental, spatial and temporal factors that may explain the observed patterns of diversity.

The identification of complex patterns and of their putative causes enables precise ecological and functional hypotheses to be formulated. Those hypotheses provide the basis for new experiments to be assessed in situ or under controlled conditions in the laboratory. This strategy defined as exploratory, quantitative microbial ecology tries to understand how communities evolve quantitatively and structurally as a response to their environment. An important part of the approach is also to determine how much of the variation in natural ecosystem can be predicted with the current methodologies. The next paragraphs provide examples of current projects that illustrate those points.

A) Spatial and temporal variations of bacterial activity and community structure are currently being examined using Automated ribosomal Intergenic Spacer Analysis (ARISA), and 454 high throughput tag sequencing in coastal sandy sediments. Using high throughput fingerprinting technologies it is now possible to assess the environmental variation of natural communities and to determine the relative importance of different factors such as space, time, and physico-chemical parameters of the water column or from the sediment (projects with A. Gobet and S. Boeer).

B) Continental margins are also investigated within the frame of the EU HERMES project (whose general aims are to study special ecosystems along the deep ocean margins) but targeting community structure and diversity of sulfide-oxidizing bacteria. Large sulfur oxidising bacteria belonging to Beggiatoa spp. or Thioploca spp. are being investigated to better understand the relationships between morphological differentiation, habitat structure and phylogeny (project with S. Grünke).

C) Targeted ecological questions are being addressed at Hydrate Ridge, off the coast of Oregon, Cascadia margin. Indeed, at about 700 m below surface level, high quantities of methane hydrates are deposited and the subsequent anaerobic oxidation of methane fuelled a great variety of eukaryotic and prokaryotic life forms. In such environments well-structured by specific advective fluxes of methane or energy sources from deeper in the sediments, the variation in diversity patterns microbial communities is being determined by ARISA and correlated with the complex environmental parameters at hand. Interestingly, environmental and spatial gradients have left a significantly signature in diversity patterns. The variation of functional groups, such as sulfate reducers, is also targeted in those sediments so as to obtain a more specific view of a given community know to be involved in the major processes occurring in those sediments (project with D. Santillano).

D) The diversity and specificity of bacteria associated with the cosmopolitan cold-water coral Lophelia pertusa is investigated by applying high-resolution molecular tools targeting differences in 16S-ITS rDNA sequences. We try to determine whether bacterial communities are specifically associated with microbial habitats such as coral skeleton surface, mucous exudates, tissue and proximal sediment when compared to those in ambient seawater. A combination of molecular diversity techniques, microscopy (FISH), and phylogenetic tools are used to provide insights into community composition and abundance of L. pertusa-associated bacteria (project with S. Schöttner).