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PhD thesis 2011/2014
Graduate School, University of La Rochelle (Gay Lussac)
Original training :
Master AIEL (Integrated approaches of coastal Ecosystems) 2010-2011

Keywords : Bacteria, Archaea, Functionnal Diversity,Nitrogen cycle, intertidal mudflat, microbial biofilm

PhD supervisor :
Christine DUPUY, Researcher Professor, University of La Rochelle, LIENSs UMR 7266
Team : DYFEA
Scientific supervisor :
Hélène AGOGUE, Researcher, CNRS, LIENSs UMR 7266
Funding : PhD grant of Conseil Général Charente Maritime (CG17)

Role (structure and fonction) of archaeal and bacterial communites in intertidal mudflat of the Pertuis Charentais : a multiscale study

Aim : Determine the functional role (distribution, diversity and activity) of each N-related prokaryotic community across a vertical gradient within the mudflat sediment itself and their temporal and seasonal variability.
Coastal areas show a large biodiversity, they are the seat of a strong biological productivity which is amongst the highest on Earth (up to 30% of the yearly total), and they play a major role in the biogeochemical cycles of many essential components. Tidal flats have been found to perform a number of important ecological functions including being both an important source and sink for nutrients, especially nitrogen. This nutrient is used by living organisms to produce several complex organic molecules like amino acids, proteins and nucleic acids and seems to limit biological productivity in many marine ecosystems.
In coastal ecosystems, both in the water column and in the sediment, many nitrogen transformations occurred thanks to the prokaryotic presence (Ward et al., 2007). The organic nitrogen can be converted in various form of inorganic nitrogen: ammonium (NH4+), nitrites (NO2-) and nitrates (NO3-). This process is named ammonification / mineralization. Conversely, the inorganic nitrogen can be converted in organic state thanks to the assimilation by microorganisms (nitrification). Others transformations can also occurred such as the nitrate reduction in ammonium or in nitrogen gas (denitrification). Recently, a new microbial process of ammonium transformation was deciphered in aquatic ecosystems (Strous et al., 1999; Schmid et al., 2000). Anaerobic bacteria can oxidize ammonium to nitrogen gas using nitrite instead of oxygen; these bacteria are called anammox (anaerobic ammonium oxidation) and belonged to the Planctomycetes division.
The functional role of prokaryotes will be assessed by detection, quantification and study of the functional genes diversity occurring in prokaryotic communities.