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First scientific results from the Tara Oceans expedition

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On May 22, in a special issue of Science, an international, interdisciplinary, team of scientists maps the biodiversity of a wide range of planktonic organisms, exploring their interactions - mainly parasitic, and how they impact and are affected by their environment, primarily the temperature.
Friday, May 29, 2015 - 10:30

Science

© N. Le Bescot ; S. Colin ; J. Decelle / EPEP UMR7144
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The special issue reports on the detailed mapping of the planktonic biodiversity in the world's oceans by an international interdisciplinary team of scientists during the 2009 - 2013 expedition of the schooner TARA. The papers explore interactions among the various organisms and their environment in detail. The massive amount of material and data collected during this expedition will provide the scientific community at large with unprecedented resources, including a catalogue of several million new genes, which will transform how we study the oceans and assess climate change.

EMBRC provided facilities and infrastructure in support of this effort via its French and Italian nodes in CNRS-UPMC Station Biologique de Roscoff & Observatoire Océanologique de Villefranche-sur-Mer and in the Stazione Zoologica Anton Dohrn.

It is great to see marine biology on the cover of a high impact scientific journal and highlights the important role that marine biology can play in the life sciences. These are the first results from the TARA Oceans program, published in a prominent journal, and we are likely to see more exciting results as scientists drill further down into the collected material.

 

 

Scientific contact : Colomban de Vargas, equipe EPEP, UMR 7144, vargas@sb-roscoff.fr.

Uncovering hidden worlds of ocean biodiversity; E. Virginia Armbrust and Stephen R. Palumbi ; Science ; 22 mai 2015.
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Tara Oceans studies plankton at planetary scale ; Bork et al ; Science ; 22 mai 2015.
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Eukaryotic plankton diversity in the sunlit ocean ; De Vargas, Audic, Henry, et al ; Science ; 22 mai 2015.
DOI: 10.1126/science.1261605

Structure and function of the global ocean microbiome ; Sunagawa, Coelho, Chaffron, et al ; Science ; 22 mai 2015.
DOI: 10.1126/science.1261359

Patterns and ecological drivers of ocean viral communities ; Brum, Ignacio-Espinosa, Roux et al ; Science ; 22 mai 2015.
DOI: 10.1126/science.1261498

Determinants of community structure in the global plankton interactome ; Lima-Mendez, Faust, Henry et al ; Science ; 22 mai 2015.
DOI: 10.1126/science.1262073

Environmental characteristics of Agulhas rings affect inter-ocean plankton transport ; Villar, Farrant, Follows et al ; Science ; 22 mai 2015.
DOI: 10.1126/science.1261447

 

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Evolution of Plankton and pelagic ecosystems
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Research news

an analysis of 243 metagenomes collected by the TARA Oceans projects

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Friday, July 3, 2015 - 13:30

Science

© N. Le Bescot ; S. Colin ; J. Decelle / EPEP UMR7144
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Adaptation and Diversity in the Marine Environment
Station Biologique de Roscoff - Salle de conférence
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ABSTRACT

 

I present an analysis of 243 metagenomes collected by the TARA Oceans projects. These metagenomes sum to over 7 Terabasepairs from 68 stations covering all non-Artic ocean basins at three depths (surface, deep chlorophyll maximum, and mesopelagic). From this dataset in conjunction with publicly available data, we have assembled gene catalog comprised of 40 million non-redundant genes, the majority of which had not been previously available. When considering only the prokaryotic-enriched fraction, we determined that structure was, as expected, mainly determined by depth (particularly, photic vs non-photic). Within the photic zone, temperature was the main determinant of community structure). When analysing the data at the level orthologous groups (OGs), we observed that the majority of the gene abundance stems from a small number of core OGs (i.e., OGs present in every sample), which surprisingly is shared with the core of the human gut microbiome, a very different environment.


About Dr Coelho:

Luis Pedro Coelho is a postdoctoral researcher in Peer Bork's group at
the European Molecular Biology Laboratory (EMBL). He has a PhD from
Carnegie Mellon University where he worked under the supervision of
Prof. Bob Murphy. He currently works on the analysis of microbial
communities in different environments,

such as the marine environment
[http://www.sciencemag.org/content/348/6237/1261359.full]
or the human gut
[http://onlinelibrary.wiley.com/doi/10.1002/bies.201300143/full]
using computational methods, namely metagenomic analysis
[http://www.nature.com/nmeth/journal/v10/n12/abs/nmeth.2693.html]
and fluorescence microscopy analysis
[http://bioinformatics.oxfordjournals.org/content/early/2015/03/19/bioinf...

Luis Pedro Coelho
European Molecular Biology Laboratory (EMBL)
News type: 
Seminar

New publication / Marine Protists : Diversity and Dynamics

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This comprehensive book provides a unique overview of advances in the biology and ecology of marine protists. Nowadays marine protistology is a hot spot in science to disclose life phenomena using the latest techniques.
Wednesday, October 28, 2015 - 13:30

Acanthaires

© Johan Decelle
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livre marine protistsAlthough many protistological textbooks deal with the cytology, genetics, ecology, and pathology of specific organisms, none keeps up with the quick pace of new discoveries on the diversity and dynamics of marine protists in general. The book Marine Protists: Diversity and Dynamics gives an overview of current research on the phylogeny, cytology, genomics, biology, ecology, fisheries, applied sciences, geology and pathology of marine free-living and symbiotic protists. Poorly known but ecologically important protists such as labyrinthulids and apostome ciliates are also presented in detail. Special attention is paid to complex interactions between marine protists and other organisms including human beings. An understanding of the ecological roles of marine protists is essential for conservation of nature and human welfare. This book will be of great interest not only to scientists and students but also to a larger audience, to give a better understanding of protists’ diverse roles in marine ecosystems.

Editors  : Ohtsuka, S., Suzaki, T., Horiguchi, T., Suzuki, N., Not, F.

Buy the book

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Research news

Seminar/ Experimental evolution meets marine phytoplankton

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1.30 pm / Station biologique de Roscoff / conferences room
Experimental evolution meets marine phytoplankton
Friday, November 13, 2015 - 13:30

coccolithophore

© EPPEP / SBR
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Station Biologique de Roscoff
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Global climate change in the oceans is associated with the simultaneous change of several environmental parameters such as warming, acidification and nutrient supply. It thus has the potential to dramatically change physiology and community composition of marine species. As a third response, there is a rapidly increasing interest in evolutionary adaptation as one possible response to environmental change. My talk focuses on photoautotrophic microbes (phytoplankton) which are responsible for ~50% of global primary productivity. Their large population sizes, standing genetic variation and rapid turnover time should promote swift evolutionary change. Hence, marine biologists have recently begun to address the possibility of evolutionary adaptation. I present recent case studies from coccolithophore species where experimental evolution revealed adaptation to temperature stress and enhanced partial pressure of CO2 via lineage sorting (clonal selection) and de novo mutations. I then discuss challenges for the future. How can evolution-in-a-bottle experiments be scaled-up to the real ocean? How will species interactions co-evolve? What are the relative responses of species sorting vs adaptive evolution within species in the face of global change?

Prof. Dr. Thorsten Reusch
GEOMAR Helmholtz Centre for Ocean Research Kiel
News type: 
Seminar

Seminar / Mollusk larval shell ultrastructure and proteomics: integrating analytical tools

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Station Biologique de Roscoff / 13H30 / Conference room
EU Newfelpro project „MARSUPIAL“ “Mollusk larval shell ultrastructure and proteomics: integrating analytical tools”
Monday, November 9, 2015 - 13:30

Salle de conférence de la Station Biologique

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The main objective of Marsupial project is to explore and describe the fabrication of the mollusk shell during embryos and the larval development, in a set of selected mollusks, including marine bivalves and gastropods (oysters, Ostrea edulis and Crassostrea gigas; mussels, Mytilus edulis M. galloprovincialis; gastropods, Aplysia punctata and A.californica), and terrestrial gastropods (land snails, Helix aspersa and H.pomatia). Ultimately, goal will be to propose a general model of larval shell formation in mollusks and to provide a platform for subsequent studies on the impact of ocean acidification on mollusk shell calcification.

To this aim, two approaches will be used: ultrastructural and molecular. The first approach will allow a precise description of the different steps of formation of the larval shell. Another point is to understand how the shell microstructures are set up, by observing at different growth stages the microstructures of the larval shell on transverse sections.

This ultrastructural work would only be descriptive if it was not combined with a molecular approach, the aim of which is to correlate the expression of protein markers with transition steps in the larval shell development. It will be of particular significance the expression of key-enzymes, such as carbonic anhydrase, alkaline phosphatase, tyrosinase, and the expression of specific shell matrix proteins. This approach will be tackled by proteomics, combined with immuno-histological localization.

In this talk collaboration with scientists from CNRS-UPMC, Biological Station in Roscoff, in production of the embryos and larval stages of mussels Mytilus edulis under EMBRC France project: CAPRA “Carbonic Anhydrase and Protein Activity” will be presented.

Dr.Davorin Medaković,
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Seminar

Registration for the UE Schmid Training Course : deadline 10 december

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EU Schmid Training Course "Established and emerging model organisms for Marine Science" : deadline for registration 10 december 2015
Thursday, December 10, 2015 - 11:00

embryons d'amphioxus

© A. Boutet / embryons d'amphioxus / amphioxus embryos
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7 - 18 march 2016  / Station Biologique de Roscoff

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Training

PhD Position at the interface of mathematics (models) and biology (applications)

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The Laboratory of Integrative Biology of Marine Models invites applications for one fully funded PhD studentship.
Wednesday, November 18, 2015 - 15:00
Laboratory of Integrative Biology of Marine Models
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Document(s)

Thesis project
pdf 170.63 KB

The topic lies at the interface of mathematics (models) and biology (applications). It involves researchers of "Laboratoire Jacques-Louis Lions" in Paris and "Laboratoire de Biologie Intégrative des Modèles Marins" in the Roscoff marine station in Brittany. The PhD project aims to build a spatio-temporal model for the dynamics of the translation repressor 4E-BP regulation network following fertilization of the sea urchin egg.

patrick.cormier@sb-roscoff.frand benoit.sarels@ljll.math.upmc.fr

Please send in a CV, a student certificate, a transcript with the grades obtained during the current and the last years and a cover letter.

News type: 
Training

Towards deciphering the N-glycosylation pathways in microalgae

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13h30 / StationBiologique de Roscoff / Conférence Room
Towards deciphering the N-glycosylation pathways in microalgae
Friday, November 27, 2015 - 13:30
Laboratory of Integrative Biology of Marine Models
Station Biologique de Roscoff - Salle de conférence
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Professeure Muriel BARDOR
Université de Caen
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Seminar

Publication : "Genome of the flowering plant that returned to the sea'

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An international consortium of 35 laboratories led by University of Groningen, Netherlands, professor Jeanine Olsen, and with four co-authors from the Station Biologique de Roscoff has published the genome of the seagrass Zostera marina in the scientific journal Nature on 18 february. Seagrasses are flowering plants that have returned to the sea and provide a unique possibility to study the adaptations involved in this important transition. The Z. marina genome represents a valuable resource supporting a wide range of research themes, from adaptation of marine ecosystems under climate warming and its role in carbon burial to unravelling the mechanisms of salinity tolerance that may further inform assisted breeding of crop plants.
Wednesday, February 10, 2016 - 14:15

Genome of the flowering plant that returned to the

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Seagrasses meadows are one of the most productive and biodiverse ecosystems on Earth, rivaling coral reefs and rain forests in terms of the ecosystem services they provide to humans. Seagrass meadows are part of soft-sediment, coastal ecosystems of all continents, with the exception of Antarctica. They form a nursery for young fish and other organisms, but also protect the coastline from erosion and maintain water clarity.

Zostera marina, also called eelgrass, is the most widely distributed seagrass species and can be found throughout the northern hemisphere, ranging from the warm waters of Southern Portugal to the Arctic waters of Northern Norway. The ancestor of eelgrass lived on land and modern seagrasses has thus adapted to seawater and as an additional twist to the story, the ancestor of terrestrial plants was a green alga possibly living in the sea. This makes seagrass interesting for the study of temperature tolerance, like climate warming, and the mechanisms of salt tolerance.

The necessary first step in order to efficiently study genes, genetic networks and the interaction of ecology and evolution in these plants is a high quality genome sequence with an analysis of which genes are present and absent. Going back to the sea made seagrasses look more like algae. For example, eelgrass has not only lost its stomata (which let air into the leaves and let oxygen leave) but also all of the genes involved in stomatal differentiation and have an uptake of carbon dioxide more like algae. Their cell walls are also now more like algal cell walls, with sulphated polysaccharides, than the cell walls of terrestrial plants. The Zostera genome thus allows for comparisons with marine algae- how do organisms with different evolutionary histories solve similar biological problems?

Plant signalling and defence are also different. Genes that produce volatile compounds in land plants have disappeared from the Z. marina genome. Of course, there are no insects in the sea to pollinate their flowers. Sex is entirely underwater involving naked and long sperm filaments especially adapted for underwater fertilization of the tiny flowers. As for predators and pathogens, there are still plenty of  small ‘grazers’ that scrape algae off the leaves and little is known about seagrass pathogens. These are just a few of the adaptations to the marine life described in the Nature paper.

Learning more about eco-evolutionary interactions is relevant to the development of genomics-based, early-warning indicators that may foreshadow seagrass ecosystem shifts and tipping points. This is urgent because seagrass meadows are threatened worldwide. There are many initiatives working to try and restore degraded meadows but with limited success. Studying the adaptive capacity of seagrass in detail may help conservation efforts.

Reference

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea
Nature (2016), doi:10.1038/nature16548

News type: 
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Plankton network linked to ocean's biological carbon pump revealed

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Authors : Lionel Guidi, Samuel Chaffron, Lucie Bittner, Damien Eveillard, Abdelhalim Larhlimi, Simon Roux, Youssef Darzi, Stephane Audic, Léo Berline, Jennifer Brum, Luis Pedro Coelho, Julio Cesar Ignacio Espinoza, Shruti Malviya, Shinichi Sunagawa, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Julie Poulain, Sarah Searson, Tara Oceans coordinators, Lars Stemmann, Fabrice Not, Pascal Hingamp, Sabrina Speich, Mick Follows, Lee Karp-Boss, Emmanuel Boss, Hiroyuki Ogata, Stephane Pesant, Jean Weissenbach, Patrick Wincker, Silvia G. Acinas, Peer Bork, Colomban de Vargas, Daniele Iudicone, Matthew B. Sullivan, Jeroen Raes, Eric Karsenti, Chris Bowler, Gabriel Gorsky. Published on 10 February 2016 on the Nature website. DOI: 10.1038/nature16942
Plankton networks driving carbon export in the oligotrophic ocean. <br><i>ublished on 10 February 2016 on the website of the journal Nature, this work highlights the important role played by plankton in the climate system. DOI: 10.1038/nature16942</i>
Thursday, February 11, 2016 - 11:45

plancton

© Christian SARDET/Tara Océans/CNRS Photothèque
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The ocean is the largest carbon sink on the planet. The community of planktonic organisms involved in the removal of carbon from the upper layers of the ocean has now been described by an interdisciplinary team bringing together oceanographers, biologists and computer scientists, principally from the CNRS, UPMC, Nantes University, VIB, EMBL and CEA. This first overview of the network of species linked to the oceanic biological pump has revealed some new players as well as the main bacterial functions participating in the process. It was obtained by analyzing samples collected by the Tara Oceans expedition in the nutrient-poor regions that cover most of the oceans. The scientists have also shown that the presence of a small number of bacterial and viral genes predicts variation in carbon export from the upper layers of the ocean. These findings should enable researchers to better understand the sensitivity of this network to a changing ocean and to better predict the effects that climate change will have on the functioning of the biological carbon pump, which is a key process for sequestering carbon at global scale. Published on 10 February 2016 on the website of the journal Nature, this work highlights the important role played by plankton in the climate system.

Teams: 
Evolution of Plankton and pelagic ecosystems
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Research news

Open PhD position at Roscoff (France) / DIPO team

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PHD position : "The paradox of being a specialist for a parasite of marine blooming dinoflagellates"
Thursday, March 17, 2016 - 14:15

dipo

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The student will work at the Station Biologique of Roscoff (UMR7144, France) under the supervision of L. Guillou (Team Diversity and Interactions in oceanic plankton)
An interview will be done in Paris during June. Applicant, if successful, will start the 1rst of October 2016. The duration of a PhD in France is 3 years.
Applications should be sent to Laure Guillou (lguillou@sb-roscoff.fr) before middle of April 2016.

 

 

Document(s)
Teams: 
Diversity and Interactions in Oceanic Plankton
News type: 
Research news

2 PhD positions available in the EPEP team (Groupe Plancton, Roscoff)

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2 PhD positions available in the EPEP team (Groupe Plancton, Roscoff) and starting next September
Friday, March 25, 2016 - 17:45

plancton

© Christian SARDET/Tara Océans/CNRS Photothèque
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Adaptation and Diversity in the Marine Environment
2 PhD positions available in the EPEP team (Groupe Plancton, Roscoff)
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Document(s)
  • SYMBIOME: an eco-systemic approach to eukaryotic symbioses in global photic plankton
     
  • Exploring the Ocean’s biological dark matter using single eukaryotic cell genomics & transcriptomics applied to world meta-omics datasets.

     

The two  projects aims at further exploring the symbiotic/mixotrophic structure of protistan diversity across Life’s kingdoms and global oceans biogeography and hydrography, as well as understanding the acclimation and adaptation patterns of the key protist players in these ecosystems which cover 71% of our planet and generate half its oxygen. Both students will apply innovative protocols combining eco-bioinformatics, single-cell -omics, and advanced imaging on Tara Oceans datasets and samples. They will integrate the Tara Oceans/Oceanomics international consortium (http://oceans.taraexpeditions.org/en/http://www.oceanomics.eu/), and benefit from the great and long-standing pluridisciplinary expertise developed over the last 7 years in the collaborative network.

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Post-doctoral position – 33 months - Phytoplankton survival during Polar winter

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We are offering a 33 months post-doctoral position to study phytoplankton survival position in the winter (cultures, physiology, transcriptomics).
Wednesday, March 30, 2016 - 10:30 to Monday, June 13, 2016 - 10:30

The Arctic winter off Svalbard - MicroPolar projec

© MicroPolar
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Adaptation and Diversity in the Marine Environment
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Phytoplankton is responsible for nearly half of the photosynthesis on the planet. In polar regions, phototrophic organisms need to survive during long periods of darkness occurring in winter. However survival mechanisms remain mysterious and elucidating them would provide a key to understanding how primary production is sustained in polar ecosystems, which are among the highest productive areas on the planet. Until now, studies have been hampered by the difficulty to access these environments, especially in winter. The Norwegian project “MicroPolar” to which the Roscoff team is associated has offered a unique opportunity to sample polar waters every two months for one year, including during winter (January, March, May, August and November 2014). Another French-Canadian project called “Green Edge” focuses on the development of the spring bloom that takes place at the ice edge in the Arctic.  A first field campaign has been conducted in 2015 and another one is planned for 2016 along with a 60-day oceanographic cruise.

The ANR project PHYTOPOL is taking advantage of these opportunities to address the question of the survival of phytoplankton during extended periods of darkness. The project is structured in three tasks: i) characterize dominant Arctic photosynthetic pico- and nano-phytoplankton strains, ii) determine the physiological mechanism(s) used to survive long periods in the dark, and iii) elucidate the molecular mechanisms of these adaptations.  The project associates the Roscoff DIPO team (D. Vaulot and F. Not) and the Banyuls laboratory (H. Moreau)

 

The post-doctoral fellow is expected to :

  • Perform experiments on a set of Arctic and Antarctic microalgal strains (green algae, diatoms etc..) from the Roscoff Culture Collection to test their long term survival strategy under darkness (mixotrophy, phagotrophy, resting stage) and their capacity to recover once light is provided again.
  • Acquire and analyze transcriptomes for a limited number of strains to assess differences in gene expression in response to dark conditions and return to light.
  • Data mine environmental meta-transcriptomes acquired in polar regions (e.g. from the Tara Oceans expedition) to search for genes involved in adaptation to dark conditions.

The candidates must have defended their PhD within two-years of their application.  They must have a good background knowledge of algal taxonomy and physiology and have practical experience in algal culture, molecular methods (DNA extraction, PCR, cloning, Sanger sequencing), Illumina sequencing, and transcriptome and meta-transcriptome data analysis.


 

The Plankton Group in Roscoff is composed 40 people (researchers, technicians, students) working on various aspects of plankton taxonomy and ecology (picoplankton, viruses, cyanobacteria, symbioses, parasitism).  The Station Biologique is well equipped for microbial diversity studies with microscopes, flow cytometers, culture chambers, Illumina sequencer, and large bioinformatics clusters.

Duration: 33 months starting in summer/fall of 2016.

Salary : about 1600 € per month

Deadline for applications: May 30, 2016

 

In order to apply please send by email to : vaulot@sb-roscoff.fr

  • Motivation letter
  • Detailed CV limited to 2 pages
  • One recommendation letter
  • A copy of what you estimate your paper most relevant to your application

 

Contact : Daniel Vaulot (vaulot@sb-roscoff.fr) and Fabrice Not ( ), UMR 7144, Station Biologique de Roscoff
F29680 Roscoff  France

 

More information :

 

Papers relevant to the project :

  • Mitra, A., Flynn, K.J., Tillmann, U., Raven, J.A., Caron, D., Stoecker, D.K., Not, F. et al. 2016. Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition; Incorporation of Diverse Mixotrophic Strategies. Protist. 167:106–20.
  • Berge, J., Renaud, P.E., Darnis, G., Cottier, F., Last, K., Gabrielsen, T.M., Johnsen, G. et al. 2015. In the dark: A review of ecosystem processes during the Arctic polar night. Prog. Oceanogr. in press
  • McKie-Krisberg, Z.M. & Sanders, R.W. 2014. Phagotrophy by the picoeukaryotic green alga Micromonas: implications for Arctic Oceans. Isme J. 10 : 1953-1961
Teams: 
Diversity and Interactions in Oceanic Plankton
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an analysis of 243 metagenomes collected by the TARA Oceans projects

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English
Friday, July 3, 2015 - 13:30

Science

© N. Le Bescot ; S. Colin ; J. Decelle / EPEP UMR7144
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Adaptation and Diversity in the Marine Environment
Station Biologique de Roscoff - Salle de conférence
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ABSTRACT

 

I present an analysis of 243 metagenomes collected by the TARA Oceans projects. These metagenomes sum to over 7 Terabasepairs from 68 stations covering all non-Artic ocean basins at three depths (surface, deep chlorophyll maximum, and mesopelagic). From this dataset in conjunction with publicly available data, we have assembled gene catalog comprised of 40 million non-redundant genes, the majority of which had not been previously available. When considering only the prokaryotic-enriched fraction, we determined that structure was, as expected, mainly determined by depth (particularly, photic vs non-photic). Within the photic zone, temperature was the main determinant of community structure). When analysing the data at the level orthologous groups (OGs), we observed that the majority of the gene abundance stems from a small number of core OGs (i.e., OGs present in every sample), which surprisingly is shared with the core of the human gut microbiome, a very different environment.


About Dr Coelho:

Luis Pedro Coelho is a postdoctoral researcher in Peer Bork's group at
the European Molecular Biology Laboratory (EMBL). He has a PhD from
Carnegie Mellon University where he worked under the supervision of
Prof. Bob Murphy. He currently works on the analysis of microbial
communities in different environments,

such as the marine environment
[http://www.sciencemag.org/content/348/6237/1261359.full]
or the human gut
[http://onlinelibrary.wiley.com/doi/10.1002/bies.201300143/full]
using computational methods, namely metagenomic analysis
[http://www.nature.com/nmeth/journal/v10/n12/abs/nmeth.2693.html]
and fluorescence microscopy analysis
[http://bioinformatics.oxfordjournals.org/content/early/2015/03/19/bioinf...

Luis Pedro Coelho
European Molecular Biology Laboratory (EMBL)
News type: 
Seminar

New publication / Mutant swarms of a totivirus-like entities are present in...

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Authors : Sylvie Rousvoal ; Betty Bouyer ; Camilo López-Cristoffanini ; Catherine Boyen ; Jonas Collén <br><i>DOI : Journal of Phycology, Wiley, 2016, <10.1111/jpy.12427></i>
Mutant swarms of a totivirus-like entities are present in the red macroalga Chondrus crispus and have been partially transferred to the nuclear genome.
Friday, August 26, 2016 - 14:15

chondrus

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Abstract : Chondrus crispus Stackhouse (Gigartinales) is a red seaweed found on North Atlantic rocky shores. Electrophoresis of RNA extracts showed a prominent band with a size of around 6,000 bp. Sequencing of the band revealed several sequences with similarity to totiviruses, double-stranded RNA viruses that normally infect fungi. This virus-like entity was named CcV. It should probably be regarded as an extreme viral quasispecies or a mutant swarm since low identity (<65%) was found between sequences. Totiviruses typically code for two genes: one capsid gene (gag) and one RNA-dependent RNA polymerase gene (pol) with a pseudoknot structure between the genes. Both the genes and the intergenic structures were found in the CcV sequences. A non-identical gag gene was also found in the nuclear genome of C. crispus, with associated EST and upstream regulatory features. The gene was presumably horizontally transferred from the virus to the alga. Similar dsRNA bands were seen in extracts from different life cycle stages of C. crispus and from all geographical locations tested. In addition, similar bands were also observed in RNA extractions from other red algae; however, the significance of this apparently widespread phenomenon is unknown. No phenotype caused by the infection nor any virus particles, or capsid proteins were identified; thus, the presence of viral particles has not been validated. These findings increase the known host range of totiviruses to include marine red algae.

https://hal.archives-ouvertes.fr/hal-01320013

related content
Opening the door to new virus interactions in the aquatic world
http://onlinelibrary.wiley.com/doi/10.1111/jpy.12429/full

 

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Research news

Position available : Research assistant position

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We are looking for candidates to fill a Research Assistant position available in the Algal Genetics Group at the Station Biologique in Roscoff (CNRS UPMC)
Friday, September 2, 2016 - 14:15

Fonds marins / Marine underwater

© Y.FONTANA
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The successful candidate will conduct research leading to the development of a genetic transformation protocol for the brown algal model Ectocarpus. Experience with molecular and cell biology techniques is essential. Experience with Agrobacterium-mediated plant transformation and algal manipulation would also be useful. Excellent written and oral communication skills and the ability to participate in writing reports and manuscripts are required.

Required Skills:

- MS in Biology, Molecular Biology, Biotechnology, Plant Science or related area preferred (other degrees could be considered depending on skills);

- Technical proficiency, scientific creativity, and ability to collaborate with others;

- Ability to work and think independently;

- Experience in DNA and RNA extraction, molecular analysis of transgenic organisms; transgenesis protocols; RNA interference

- Statistical data collection and interpretation;

- Excellent time management skills 

Initial appointment is for 12 months and could be renewed depending on satisfactory performance and funding availability. Interested applicants should send via email a cover letter describing previous experience, CV, and names, telephone numbers and e-mail addresses of three references to coelho@sb-roscoff.fr and cock@sb-roscoff.fr.

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Job opportunities

SulfAtlas, a general classification database for sulfatases

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Sulfated biomolecules are widespread in Nature and highly diverse in chemical structure and biological function. in marine environment, all marine animals, plants and algae synthesize sulfated polysaccharides as major compounds of their extracellular matrix. In the context of the explosion of genomic data, the prediction of the function of new sulfatases is therefore particularly prone to misinterpretations. To answer this issue the Marine Glycobiology group, in close collaboration with the bioinformatics platform ABIMS, has created a general database, SulfAtlas, to classify all available sulfatases based on sequence homology. The details of this collaborative work has been published in the journal PLOS One the 17th of October 2016 (link). The SulfAtlas database will be regularly updated and is in free access at the following address <a href="http://abims.sb-roscoff.fr/sulfatlas/"> http://abims.sb-roscoff.fr/sulfatlas/</a>
Monday, October 17, 2016 - 10:30

database SulfAtlas

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Sulfated biomolecules are widespread in Nature and highly diverse in chemical structure and biological function. For instance steroid sulfate, cerebroside sulfate or heparin play vital roles in human and animals. Plants produce numerous sulfated secondary metabolites acting as defense or communication molecules. Sulfated biomolecules are also ubiquitous in marine environment. Indeed all marine animals, plants and algae synthesize sulfated polysaccharides as major compounds of their extracellular matrix.

Sulfatases catalyze the cleavage of sulfate groups from such molecules and are thus essential enzymes in the biomedical field, but also in general biology, in environmental processes and in biotechnology. These proteins have been essentially studied in the context of severe genetic diseases in human and the number of characterized sulfatases is thus limited in comparison to the huge diversity of sulfated compounds. In the context of the explosion of genomic data, the prediction of the function of new sulfatases is therefore particularly prone to misinterpretations. A classification system allowing a better prediction of substrate specificity and for setting the limit of functional annotations is therefore urgently needed for sulfatases.

To answer this issue the Marine Glycobiology group, in close collaboration with the bioinformatics platform ABIMS, has created a general database, SulfAtlas, to classify all available sulfatases based on sequence homology. The details of this collaborative work has been published in the journal PLOS One the 17th of October 2016. The SulfAtlas database will be regularly updated and is in free access at the following address: http://abims.sb-roscoff.fr/sulfatlas/.

Reference: Tristan BARBEYRON, Loraine BRILLET-GUÉGUEN, Wilfrid CARRÉ, Cathelène CARRIÈRE, Christophe CARON, Mirjam CZJZEK, Mark HOEBEKE and Gurvan MICHEL. (2016) Matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity (2016) PLOS One, in the press.

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Genome sequencing of Zobellia galactanivorans, a model algae-associated bacterium

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In collaboration with Genoscope and the Max Planck Institute of Bremen, the Marine Glycobiology group (CNRS/UPMC) has published in Environmental Microbiology an extensive genomic and physiological analysis of Z. galactanivorans.
Genome sequencing of Zobellia galactanivorans, a model marine bacterium for the study of algae-bacteria interactions and for blue biotechnology
Monday, October 24, 2016 - 13:45

zobellia algae interactions

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Laboratory of Integrative Biology of Marine Models
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Algae constitute a huge biomass composed at least by 50% of polysaccharides. These complex polymers essentially differ from the polysaccharides of land plants and the enzymes involved in their degradation remain largely uncharacterized. In the last 20 years the marine bacterium Zobellia galactanivorans has emerged as the main model for the discovery of enzymes specific for the bioconversion of algal polysaccharides.The characterization of these new enzymes is a key issue to understand the marine carbon cycle. These enzymes are also essential for the valorization of algal biomass and for blue biotechnology.

In collaboration with Genoscope and the Max Planck Institute of Bremen, the Marine Glycobiology group (CNRS/UPMC) has published in Environmental Microbiology an extensive genomic and physiological analysis of Z. galactanivorans. Notably a comparison with more than 100 genomes of marine heterotrophic bacteria confirms that Z. galactanivorans is currently the microorganism with the largest capacities for the bioconversion of algal polysaccharides. This microbe also possesses numerous adaptive traits for algae-associated life (consumption of algal exudates, iodine metabolism, methylotrophy, etc). Therefore, Z. galactanivorans is also a suitable model for the study of algae-bacteria interactions. Finally on a more holistic level this comparative genomic study demonstrates that habitat and taxon are two major forces driving the carbohydrate catabolism of marine bacteria.

 

Reference:

Barbeyron T, Thomas F, Barbe V, Teeling H, Schenowitz C, Dossat C, Goesmann A, Leblanc C, Glöckner FO, Czjzek M, Amann R and Michel G. (2016) Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans. Environmental Microbiology, doi: 10.1111/1462-2920.1358

 

 

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New publication / Evidence for parasite-mediated selection during short-lasting ....

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François Blanquart, Myriam Valero, Catharina Alves-de-Souza, Aliou Dia, Frédéric Lepelletier, Estelle Bigeard, Christian Jeanthon, Christophe Destombe, Laure Guillou <br> Proc.R.Soc.B283:20161870.http://dx.doi.org/10.1098/rspb.2016.1870
Evidence for parasite-mediated selection during short-lasting toxic algal blooms
Friday, October 28, 2016 - 15:45

Evidence for parasite-mediated selection

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Adaptation and Diversity in the Marine Environment
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ABSTRACT

Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellate Alexandrium minutum and two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily reduction in relative A. minutum abundances, demonstrating strong parasite-mediated selection. There was genetic variability in infectivity in both parasite species, and in resistance in the host. We found no evidence for coevolution in one estuary; however, in the other estuary, we found high genetic diversity in the two parasite species, fluctuations in infectivity and suggestion that the two parasites are well adapted to their host, as in ‘Red Queen’ dynamics. Thus, coevolution is possible over the short time span of a bloom, but geographically variable, and may feedback on community dynamics.

Evidence for parasite-mediated selection during short-lasting toxic algal blooms

François Blanquart, Myriam Valero, Catharina Alves-de-Souza, Aliou Dia, Frédéric Lepelletier, Estelle Bigeard, Christian Jeanthon, Christophe Destombe, Laure Guillou

Proc.R.Soc.B283:20161870.http://dx.doi.org/10.1098/rspb.2016.1870

Published 26 October 2016.DOI: 10.1098/rspb.2016.1870

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Proposal of Master 2 thesis

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Proposal of Master 2 thesis at the Station Biologique de Roscoff
Thursday, November 3, 2016 - 11:15

fête de la science

© L. Ardhuin / UPMC
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Roscoff Marine Station
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Kelpadapt : Environmental changes, gene flow and local adaptation in kelps

Document(s)

Hosting laboratory:

UMI3614 Evolutionary Biology and Ecology of Algae
Station Biologique de Roscoff, Place George Tessier, Roscoff, France

Supervisors :
Myriam Valero (co-supervision with the Post-Doc : Bertrand Jacquemin)
Tel : +33 (0)298292328
Email : myriam.valero@sb-roscoff.fr ; bertrand.jacquemin@sb-roscoff.fr

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