In the frame of the circum-global bio-oceanographic project TARA-OCEANS (http://oceans.taraexpeditions.org/ ), the Station Biologique de Roscoff and the Génoscope (Genomic Institute from CEA, France) are collaborating for the production and analyses of large sets of marine environmental sequencing data.

The ANR project PROMETHEUS (PROject on METagenomics/transcriptomics of tHe global ocean unicellular EUkaryoteS) will produce, describe, and compare the genetic and transcriptomic diversity of several populations and size fractions of planktonic unicellular eukaryotes (protists). New-generation sequencing machines will be used to generate massive amount of nucleotide sequences out of total DNA and RNA extractions from worldwide protistan populations samples. Physical, chemical, and imaging metadata collected from the same water samples will complement the sequencing data.

Job offer: TARA OCEANS Onboard Biological Engineer.

TaraOceans is a 3 year international scientific expedition aboard the schooner "Tara", aiming to study the composition and dynamics of planktonic ecosystems and certain unexplored coral reefs around the globe. Several French and international laboratories are involved in TaraOceans, including the EMBL, EBI and MIT, and the CNRS which strongly supports the project. A wide-ranging program of communication, including audiovisual and multimedia productions, and educational outreach actions, is conducted in parallel to the scientific project.

The TaraOceans project is seeking an Onboard Biological Engineer who will ensure the smooth and efficient running and the continuity of the onboard scientific protocol, as well as being responsible for onboard sampling logistics, including tracking of samples and inventories of chemicals and consumables. The successful candidate will work in close collaboration with two land-based engineers responsible for preparatory and follow-up logistical organization (orders, shipment of material to/from the boat, transfer of biological samples to partner laboratories, etc.)..

The BIOSOPE cruise in 2004 crossed the most oligotrophic region of the world oceans.  On board flow cytometry allowed to sort specific picoplankton populations in order to perform genetic analyses.

Two papers just came out presenting some of these data.  In the first paper (Shi et al. PloS One, 2009) we use flow cytometry to sort picoeukaryotes and construct 18S rRNA gene clone library, revealing novel groups of uncultivated photosynthetic eukaryotes in particular among Prasinophyceae, Chrysophyceae and Haptophyta. In the second one (Lepère et al. EM 2009), the use of probes targeted agains 16S plastid rRNA confirms the importance of groups such as Chrysophyceae and Haptophyta.

• Shi, X. L., Marie, D., Jardillier, L., Scanlan, D. J. & Vaulot, D. 2009. Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PLoS ONE 4:e7657 - pdf
• Lepère, C., Vaulot, D. & Scanlan, D. J. 2009. Photosynthetic picoeukaryote community structure in the South East Pacific Ocean encompassing the most oligotrophic waters on Earth. Environmental Microbiology 11:3105–3117. - pdf

• Press release on the CNRS web site .

Sharon and coworkers (with F. Partensky as coauthor) just reported in the 10 September issue of Nature the discovery of a set of seven photosystem I (PSI) genes in the Global Ocean Survey (GOS) and other marine viriome databanks. This was confirmed by long PCR on environmental DNA from the Northern Line islands area (equatorial Pacific Ocean). One of the genes is actually a unique fusion of two PSI genes (psaF and J) that is never found in cyanobacteria and that may allow the 'viral' PSI to accept other electron carriers than do typical cyanobacterial PSI. So it is a remarkable example of bioengineering. Furthermore, only psaA/B and psaF/J are found associated in cyanobacteria genomes while all other PSI genes are isolated. So this organization in cluster of seven genes is also unique. At last, although the lack of genes is not a proof of absence, it seems that these viral PSI may not include PsaI, L and M and I, three proteins that are involved in PSI trimerization. So this viral PSI cluster would encode a monomeric PSI (like in plants) and not a trimeric one (like in cyanobacteria).

•  Comment in New Scientist
•  News sur le site web de l'INEE (En direct des laboratoires )

Three members of the team, Christian Jeanthon and Daniel Vaulot are currently participating in the MALINA research cruise on board the Canadian ice breaker Amundsen in the Beaufort Sea.

The cruise aims among other goals at accumulating data on the microbial foodweb in this arctic region which is very much affected by global warming.

Working in such remote and hostile region is quite challenging logistically but after a bit more than two weeks of cruise many of the objectives have already been met.  Moreover we have seen many fanstastic sights such as polar bears, ringed seal and thewonderful arctic light, ever changing.

The logistics of the cruise where quite challenging. 
For exemple at the end of our leg our flow cytometer was flown by helicopter from teh ship to Paulatuk in the extreme North of Canada to be loaded into a DC3 to get to Invuk where actually it got stranded, because the planed taking the crew from Inuvik to Québec lacked proper cargo space...Hopefully, it will makeit back to Roscoff.

The flow cytometer ready to leave in its box	Attaching it to the helicopter
A flying flow cytometer over the Beaufort Sea	The final loading into a 1935 DC3

More pictures from the cruise can be seen here.