Tara: transforming the way of studying the oceans

The first results of the “Tara Oceans” expedition (2009-2013) were the subject of a special issue of the periodical Science. In order to study and understand the impact of climate change and the ecological crisis on our oceans, the schooner has been sailing the seas since 2003, taking measurements in situ and collecting samples. Overview of the projects funded by ANR in connection with the Tara expeditions and the data that they made it possible to generate.

Very little is known about the marine ecosystem, and especially the plankton ecosystem, notwithstanding its considerable importance in climate and food chain regulation. The communities of organisms that make up plankton actually produce half of our oxygen and act like a carbon sink. They affect and are affected by the climate and constitute the basis of the ocean food chains that feed fish and marine mammals. The objective of the Tara Oceans expedition (2009-2013) was to promote our knowledge of this crucial ecosystem. In the course of the expedition, nearly 35,000 samples were collected from the planet’s oceans. These data constitute unprecedented resources for the international scientific community, including a catalog of several million new genes, which will transform the way in which oceans are studied and climate change is evaluated.

Genome analysis for a better understanding of the plankton system

With the objective of offering a first overview of this ecosystem, the Prometheus Project aimed to explore the genomes of all of the organisms present in the plankton samples collected, from the smallest (viruses) to the “largest” (organisms made up of several cells). The scope of the project was primarily linked to the technological difficulties that had to be overcome. In practical terms, the complexity of the environment to be analysed had kept it from ever being studied by means of broad-scale genomic approaches. Thanks to technological progress (sequencing methods, robotic automation and so forth), the partners in Prometheus were able to develop processing chains for molecular biology and bioinformatics, which enabled them to address the complexity of this ecosystem. In this way, it was possible to create a directory of 7 million genes, the majority of which were completely unlike anything known up to that point. This collection will constitute the starting point for efforts aimed at characterising unknown biological functions.

Giant viruses (also known as “giruses”) are an ancient line of viruses that infect various marine

microorganisms, from microalgae to plankton predators. By killing those organisms, they affect the food chain that depends on marine microbes; this, in turn, has implications for the carbon and nutrient cycles. Notwithstanding their ecological importance, the biology of these viruses is still largely unknown. In this context, the Tara-Girus Project aimed to provide a better characterisation of the genetic diversity of these marine pathogens and a better understanding of their ecological roles in plankton communities. The work performed in this project directly contributed to the implementation of onboard sampling strategies that made it possible to adapt to the limited space available on the Tara ship. In addition, it led to the production of sequence data through the use of extremely advanced technologies and to the development of new bioinformatics methods for analysing those data. More than 9 GB of genetic sequence data were produced in this way – that is, three times more than for the human genome, thereby increasing the total amount of genetic information now available to the public by 20%.

Getting around the limits of today’s information technology tools

Following the development of new sequencing methods, the mass of data to be processed proved to be so huge as to constitute a bottleneck for these new technologies. In order to remedy this situation, the Mappi Project developed new algorithms and software capable of handling these huge quantities of data. These tools, produced through the efforts of information technology research groups, were applied to data in the fields of metagenomics (DNA of the cells of a complete sample) and metatranscriptomics (RNA) originating in Tara Oceans – a total of more than 100 TB of data.
Similarly, the Hydrogen project aims to develop algorithmic and statistical tools that will enable the measurement and analysis of biodiversity by means of comparative metagenomics. This technology provides global environmental information on the basis of the DNA molecules of the environments studied. The work performed will be validated and scaled up to the level of algorithmic and statistical tools on the basis of the data resulting from the sequencing of the samples collected in the Tara Oceans expedition.

Oceanomics: exploiting the immense mass of data collected

As an extension of the Tara explorations and the Tara-Girus Project, the Oceanomics Project, financed in the framework of the “Biotechnologies and Bioresources” action of the Investments for the Future programme, is based on the thousands of samples and data collected during the Tara Oceans expedition. It will first explore this unique collection through the use of DNA sequencing and very high throughput imaging methods, in order to understand the nature of the plankton organisms, their genes and their genome, and how they organise themselves according to environmental parameters. All in all, this will add to the global understanding of how these ecosystems function and help to identify new and preferred species for research in the quest for high added value compounds.

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Thanks to the Tara ship, Tara Expeditions, a non-profit French initiative, has been active since 2003 for the benefit of the environment and research. This schooner sails the seas in order to take measurements in situ and collect samples intended for use in studying and understanding the impact of climate change and ecological crisis on our oceans.

See the joint press release issued by TaraExpeditions
The Prometheus Project is coordinated by Genoscope; its partners include teams from the Roscoff Biology Station and the Ecole Normale Supérieure de Paris. In the 2009 edition of the Genomics programme, it received funding from ANR in the amount of €678,000.
The Tara-Girus Project is coordinated by the Genomic and Structural Information department of the CNRS (French National Center for Scientific Research) in Marseilles. Its partners include the Banyuls Oceanology Observatory, the Roscoff Biology Station, Genoscope and ICM (Institute of Marine Sciences) / CSIC (Supreme Council of Scientific Investigations) in Spain. In the 2009 edition of the Genomics programme, it received funding from ANR in the amount of €583,000.
The MAPPI Project is coordinated by the Algorithmic Informatics Laboratory: Foundations and Applications in Jussieu. Its partners include the Basic Informatics Laboratory in Lille, the Institute for Research in IT and Random Systems (Rennes) and Genoscope. In the 2010 edition of the Cosinus programme, it received funding from ANR in the amount of €457,000.
The Hydrogen Project is coordinated by INRIA (National Institute of Research in Computer Sciences and Automation) in Rennes. Its partners include teams from INRA (National Institute of Agronomic Research), AgroParisTech and Genoscope. In the 2014 edition of the ANR generic call for proposals, it is receiving funding from ANR in the amount of €399,000.
The Oceanomics Project is coordinated by the Roscoff Biology Station.
It is funded by the State in the amount of €7 million over a period of eight years, in the framework of the “Biotechnologies and Bioresources” action of the Investments for the Future programme.

Last updated on 21 March 2019