Keywords:

interdisciplinary, computation, modeling, genomic, network, global ocean, arctic ocean, plankton, carbon pump, biodiversity.

Context:

Tara Oceans expedition (http://www.embl.de/tara-oceans/start/) produced and released a huge amount of genomics and environmental data enabling extensive studies of marine microbial planktonic communities [1-3]. Integrative and multi-domain analyses are now possible, and in this way a first study using genomic data from viruses, prokaryotes and eukaryotes, focused on revealing the entire planktonic community linked to carbon export in the ocean [4]. This study used a systems biology approach to reveal co-occuring sequences (modules) and to further link them by correlation analyses to abiotic and biotic factors.

Scientific goal:

As the Tara Oceans dataset continues currently to grow, we plan to apply the methodology used in Guidi et al. [4], to extended global, massive omics datasets which will be provided by the Tara Oceans consortium (metagenomics, metatranscriptomics). The dataset will include oligotrophic stations (as in Guidi et al. [4]) and also Arctic regions and nutrient-rich areas. We will then select module(s) (groups of co-occuring sequences) significantly correlated to carbon export and to net primary production (NPP) in order to highlight communities involved in the biological pump (carbon sequestration from the atmosphere to the deep-sea) in the global ocean. Members of these modules will be studied (taxonomic and functional biodiversity), and their dynamics (positive or negative interactions) will be revealed using co-occurence networks and confronted to environmental conditions.

The project will bring together a team of researchers from complementary fields (evolutionary and functional genomics, microbial ecologist, oceanography, bioinformatics, systems biology) with the overarching objective of developing an integrative methodology to study large omics datasets from marine ecosystems and to link them to principal functions in the ocean. The aim of the project is to provide a global and integrative view of the marine ecosystems with a specific focus on processes implied in the biological pump.

This project will principally takes place between two laboratories (team 1 on the Jussieu campus in Paris & team 2 in the Oceanographic Laboratory of Villefranche sur mer, close to Nice) and will rely on dynamic and collaborative work between the partners (team 1, 2 & 3).
Theoretically, the candidate will spend his/her first months of research in team 1, and will move to team 2 for the second part of the training.

Partners of the project:

Team 1:
Lucie Bittner (MCF UPMC, [email protected])
Evolution Paris Seine (UMR 7138), Université Pierre & Marie Curie (UPMC), Institut de Biologie Paris Seine, Paris, France
Team 2:
Lionel Guidi (CR1 CNRS, [email protected]) & Sakina-Dorothée Ayata (MCF UPMC,
[email protected])
Laboratoire d’Océanographie de Villefranche (UMR 7093), LOV, Villefranche sur mer, France
Team 3:
Chris Bowler (DR1 CNRS)
Ecology and Evolutionary Biology Section (UMR 8197), Institut de Biologie de l’Ecole Normale Supérieure (IBENS) IBENS, Paris, France

Qualifications:

The Master 2 candidate will work at the forefront of microbial ecology, evolution, marine biology & oceanography research using state-of-the-art technologies, within a motivating and cross-disciplinary scientific environment that should promote future career perspectives, such as PhD degree.
We are looking for a highly motivated Master 2 student who studied Bioinformatics, Ecology, Marine Biology, Oceanography and/or Physics.
He/She must have a strong interest in microbial ecology, evolution and computational biology, which is needed to perform the research and interpret results. The candidate must have proved fluency with at least one computer programming language (Python, R or Perl) and general Unix skills.
Extra aspects that will be evaluated positively are: motivation, communication skills, curiosity and autonomy as well as capability to work and collaborate in research teams.
A good command of English is required.
Depending on the candidate’s interests, research subject is flexible and can include more modeling, oceanographic and/or evolutionary aspects.

Salary:

As required, the student will receive about 600 euros / month (maximum of 6 months).

References:

Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d’Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J. Ocean plankton. Determinants of community structure in the global plankton interactome. Science. 2015 May 22;348(6237):1262073.
de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horák A, Jaillon O, Lima-Mendez G, Lukeš J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans Coordinators, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E. Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean. Science. 2015 May 22;348(6237):1261605.
Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d’Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans Coordinators, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D. Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science. 2015 May 22;348(6237):1261447.
Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum JR, Coelho LP, Ignacio-Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Coordinators TO, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss, E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, De Vargas C, Iudicone D, Sullivan JM, Raes J, Karsenti E, Bowler C, Gorsky G, In revision. Plankton networks driving carbon export in the oligotrophic ocean.

Contacts:

Please send a CV and motivation letter to:
[email protected], [email protected], [email protected]
And if you have any questions, don’t hesitate to contact us for further details.

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Pout toute autre question, vous pouvez contacter [email protected].