Title: The effects of bioturbation on the diversity of the prokaryotic communities in the sediment, and study of bioirrigation in ecologically contrasted habitats.
Abstract
The Arcachon bay shelters a Zostera noltii meadow (marine phanerogam) which covers the majority of the shore (about 70 km² in the 80's), but which undergoes a drastic regression since 2005 (about 30 % of area less in 2007 compared with 1989). Recent studies have demonstrated the ecological and biogeochemical importance of these meadows. Bioturbation activity of benthic invertebrates generates both a particulate reworking and a transport of porewater (bioirrigation). Bioturbation modifies the physical, chemical and biological properties of the sediment-water interface and thus exert a control on sediment biogeochemistry, mainly via a modification of the specific and/or functional diversity of the benthic prokaryotic communities. In this context, this PhD has two main objectives: 1. To measure the spatio-temporal variations of the bioirrigation activity of the benthic fauna in the Arcachon Bay; 2. To study the influence of bioturbation on the diversity of the benthic prokaryotic communities (bacteria and archea) of the Arcachon Bay.
In the recent context of meadows regression in Arcachon Bay, the consequence of this regression on biogeochemical cycles needs to be addressed. In order to evaluate the impact of this regression on bioirrigation activity, the first objective of the thesis is to measure the bioirrigation activity of the benthic fauna in several habitats: naked sediments, sediments covered with a low density meadow (i.e. in the regression area) and sediments covered with a high density meadow. Bioirrigation has still never been measured in Arcachon Bay. To analyse the spatial variability, studies will be realised in three stations, localised on different levels of the confinement gradient of Arcachon Bay, with three sampling sites by station (three meadow densities). A seasonal follow-up will also be done in one of the three stations, to estimate the temporal variability. Measurements will be done using an ex-situ method developed at the laboratory and based on the monitoring of the decrease of fluorescent dissolved tracer in the water column with fluorimetric sensors.
The second objective of the thesis is to study the influence of bioturbation on the taxonomic and functional diversity of the benthic prokaryotic communities (bacteria and archea) of the Arcachon Bay. This research topic is emergent and important as most of the diagenetic processes are directly or indirectly controlled by prokaryotes, but it has been little studied in the Arcachon Bay. The effects of the various functional groups of bioturbation on the total number of prokaryotes (flow cytometry), on the taxonomic diversity of prokaryotic communities (ARISA for bacteria, tRFLP for archea), as well as on the functional prokaryotic diversity (cultural approaches and/or SIP-ARISA), will be analysed. Studies will be realised both in-situ and experimentally. In order to follow the spatio-temporal dynamic of the interactions between bioturbators and prokaryotic communities, sediment sampling for analyses will be done at different times, in different zones of the burrows belonging to different functional groups of bioturbation, and at various distance from the burrows.
This PhD thesis, based in Arcachon Marine station, is interdisciplinary between benthic ecology and microbiology. Studies will be developed both in the field and experimentally.
Scientific collaborations outside EPOC laboratory
-Franck Gilbert (UMR 5245 ECOLAB)
-Philippe Cuny (UMR 6117 LMGEM)
Contact
-Frédéric Garabétian: f.garabetian@epoc.u-bordeaux1.fr (director of the PhD, Pr. Univ. Bx1)
-Aurélie Ciutat: a.ciutat@epoc.u-bordeaux1.fr (co-director of the PhD, CR CNRS)
Laboratory
EPOC UMR 5805 - Team ECOBIOC - Arcachon Marine Station, France.
Application
This PhD thesis is for a graduate student highly motivated by doing research. The candidate will have to be either a microbiologist with a strong interest for benthic ecology, or a benthic ecologist with a strong interest for microbiology. As the funding for the PhD will be a ministerial grant awarded according to the merit of the candidate, the candidate needs good academic results.
If you are interested by this PhD thesis, please send a curriculum vitae and a cover letter detailing your research activities and your expertise, to the two directors of the thesis.
To apply to this position, please visit the web site of the Doctoral School "Sciences and Environnements" from Bordeaux 1 University: ici.. Deadline for application: 09/05/2011.
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