Date : 31/10/2010

Laboratory
Molecular Plant Biology UMR 8197
Institut de Biologie de l'Ecole Normale Supérieure (IBENS)
46 rue d'Ulm
75005 Paris
Director : Antoine TRILLER

PhD Supervisor
Chris Bowler
email : Cet e-mail est protégé contre les robots collecteurs de mails, votre navigateur doit accepter le Javascript pour le voir
phone : +33 1 44 32 35 25

Subjects / Tools-Methodologies
1 : Diatom biology / Functional genomics
2 : Microbial oceanography / Comparative genomics
3 : Plankton biodiversity / Tara Oceans expedition

Summary of lab's interests

The laboratory currently consists of 10 persons that are highly knowledgable in diatom molecular and cellular biology, and is a world leader in diatom research. Numerous techniques have been developed for genome-enabled studies of diatom biology and ecology, including a diatom digital gene expression database (http://www.biologie.ens.fr/diatomics/EST3) and techniques for genetic transformation. In-house facilities are available for molecular and cellular biology, as well as bioinformatics and microarray hybridization and analysis facilities. The group is also one of the major participants in the Tara Oceans expedition.
Chris Bowler is widely recognized for his contributions in diatom research and in genome-enabled oceanography, and has published more than 80 scientific articles in peer-reviewed journals, including Nature, Science, Cell, and PNAS. He is editor of J Phycology and Plant Cell, the leading journals for diatom and plant research, and is a member of EMBO.

Summary of project

The Tara Oceans three year expedition is collecting information about oceanic plankton biodiversity around the world in an attempt to understand biodiversity in a functional context (wwwÖtaraexpeditions.org). During the expedition, a cytometer is continuously monitoring phytoplankton concentrations in surface waters. In addition, water samples are being collected that are enriched in phytoplankton of different sizes, both from surface waters and from the deep chlorophyll max (DCM). These samples are being used for microscopy observations, both onboard using live samples and onland using fixed samples, in order to characterize diatom populations at the genus and species level. To facilitate species identification Tara Oceans is using the fluorescent dye FITC-silane, which specifically labels the silicified cell walls of diatoms. Cells from water samples are also being collected on filters, stored in RNAlater, and DNA and RNA are being extracted by Genoscope, France. DNA and rRNA are being sequenced in order to quantify species abundance at the molecular level, and mRNA is being sequenced to reveal gene expression profiles in different oceanic contexts.
The Tara Oceans expedition is therefore generating a huge worldwide data set of phytoplankton abundance during its 3 year expedition that contains environmental metatransciptomics data linked to information about community composition and correlated physico-chemical data about the prevailing hydrological context at each sampling station. The PhD project will be based on extracting information about diatom functions in different oceanic environments from the Tara Oceans dataset. This project is of importance because diatoms are one of the most important components of marine phytoplankton and are the main players in the biological carbon pump.

Planned research activity:
The student will make use of the Tara Oceans dataset to extract information specifically related to diatom function. His/her tasks will be to associate information about diatom abundance and biodiversity with the expression of genes that can be ascribed to diatoms. Diatom gene calling will be feasible due to the availability of six genome sequences from diatoms. Furthermore, by reference to these whole genome sequences it will be possible in some cases to associate individual genes with pennate or centric diatoms, a process that will be further facilitated by the microscopic data generated by the Tara Oceans project. Once a diatom gene set has been defined, the student will explore the metabolic activities associated with their gene products, based on bioinformatics tools such as InterPro, KOG and KEGG, and will relate predicted metabolic pathway activities to the associated physico-chemical data at each sampling station.
Innovative aspects and relevance:
It is expected that diatom community activities will be defined in different oceanic environments, thus providing an ecological context to understand diatom community metabolism. Combination of these results with information about other phytoplankton groups, as well as Prochlorococcus and other bacteria, may provide sufficient information to develop models of diatom functional biodiversity. Key outcomes will be a global evaluation of diatom communities and diatom gene expression profiles in a range of different oceanic contexts. The results will provide a basis for understanding how diatoms will be affected by climate change-induced phenomena in the future.

Expected acquired skills:
functional and comparative genomics, bioinformatics.