Tara Pacific samples are being sequenced at the Genoscope – Interview with Quentin Carradec

© Noëlie Pansiot / Fondation Tara Océan

The 36,000 samples of coral, plankton and fish from the Tara Pacific 2016-2018 expedition are now being carefully examined and their genetic sequencing is underway at the Genoscope in Evry (CEA), France. We met Quentin Carradec, researcher/bioinformatician in charge of analyzing the sequencing results. Coral’s mysteries are being revealed!

How is the Genoscope involved in the Tara Pacific expedition and what is your role?

The Genoscope manages all of the genomic aspects of Tara Pacific, as it does for Tara Oceans. Engineers and technicians at the Genoscope platform receive the samples and make an inventory before sequencing. The resulting data is then analyzed by researchers. For Tara Pacific, the samples come from various marine organisms: 3 different species of coral and 2 species of fish, but also water samples and all the plankton they contain. Our role is to extract the DNA from these samples and use it to better understand the functioning of the organisms in the face of various environmental threats like warming, pollution, etc. With Tara Pacific, we are trying to find out if a coral species will adapt or acclimatize to its new environment or if, on the contrary, it will die out permanently.

Why is it crucial to study coral DNA?

The DNA of each organism is unique, like the passport of a living being. Sequencing the DNA of a sample means identifying the sequence of nucleotides in a strand of DNA so that we can decode its genes. This gives us information, among other things, about the reproduction or survival capacities of an organism. Sequencing tells us 3 different things. First, it identifies the organism (in this case the species of coral) by sequencing a marker gene – a small piece of DNA which varies from one species to another. The DNA then gives us information about the life of this particular coral: how it grows and feeds; how it has evolved and dispersed over time. Finally, we can extract the RNA – molecules similar to those of DNA which are an intermediate for protein synthesis. This reveals the coral’s activity at the time of sampling. RNA provides information on the organism’s “biological” response at a specific time. For example, we can know if there was stress, or the impact of a particular pollutant.

Echantillon de corail Coral sample © Noëlie Pansiot / Tara Expeditions Foundation 

What are the different coral responses to different environmental changes?

There are 3 possibilities when coral faces a change in its environment: adaptation, acclimatization or extinction. We must differentiate between the first 2. When a coral acclimates to a new environment, its physiology changes so that it can survive in both the old and new environments. It will for example, modify its amount of protein to withstand water at 28° C and 32° C without bleaching. This acclimatization is reversible to cope with seasonal variations, for example. On the other hand, when a coral adapts to a new environment, it undergoes definitive mutations in its genome: once it has adapted to high temperatures, it may no longer be able to develop in lower temperatures. This phenomenon of adaptation is very slow, and if the coral can neither adapt nor acclimatize, then it becomes extinct.

Scientific results from Tara Pacific have not yet been published. Research and analysis of data take a long time. Can you tell us about the first trends?

First is the information we obtained from observations during the expedition. Since Tara‘s return, sequencing has advanced well in the laboratories. About half of the samples have already been sequenced and are being analyzed. Obviously, we are waiting for the complete results before presentation. However, we can already say that the 3 corals sampled present the 2 systems of response to environmental variations mentioned above, and that there are very important differences across the Pacific for the same species of coral. We will now study in detail the range of possibilities of corals in their response to differences in temperature, acidity and various pollutants in the Pacific Ocean.

As a researcher, do you think these results will help political, economic and/or social decision-making?

For the moment we are doing basic research – trying to understand how living organisms function. We are still very far from knowing everything about corals! They are extremely complex systems and it will take time to really understand how they work on this scale. Tara Pacific has provided us with a global view of these 3 coral species throughout the Pacific Ocean. This overview allows us to draw conclusions about what most affects the corals, and to make hypotheses about the zones where the corals will survive or on the contrary, disappear. Of course, we can already take steps to limit the threats to these species: protect shorelines, limit the discharge of pollutants into the ocean, and limit overfishing.

How would you summarize Tara Pacific?

Tara Pacific is a unique expedition in terms of the amount of data collected. Very few scientific projects allow researchers to have such a global and almost simultaneous view of the functioning of an ecosystem and its capacity for adaptation and acclimatization. Of course, there is also the pleasure of being on board Tara to work on these samples. Laboratory work is essential but the protocols carried out on board make it possible to understand the functioning of organisms.

Corail graine Focus on a coral seed  © François Aurat / Tara Expeditions Foundation 

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