Tara Oceans Expedition sequences the ocean
The Tara Oceans consortium recently published five scientific papers in the journal Science presenting the initial wave of scientific results from the first six years of the project.1-5 The findings show the extraordinary diversity of plankton in the world’s oceans, uncover many of the interactions between them, and reveal how plankton impact and are influenced by the environment. One of the papers1 describes an ocean microbial reference gene catalog containing 40 million genes from marine microbes (bacteria, viruses, Archaea and picoeukaryotes). Derived from samples of seawater collected from all over the world and at depths down to 1,000 metres the authors show that this publicly available DNA sequence dataset is more than 1,000 times larger than what was previously available and is likely to have captured all the abundant microbial genes present in the areas sampled.
The Tara Oceans project has grasped the attention and imagination of both scientists and the general public, with TV, film and radio presentations, as well as thousands of articles being written in the international press (http://oceans.taraexpeditions.org/en/). Starting as a grass-roots initiative by a group of academic scientists, the research-enabled 36 metre schooner Tara spent almost 4 years circumnavigating the globe and going around the Arctic Circle. Overall, Tara Oceans sampled plankton at more than 210 sites and at multiple depth layers in all the major oceanic regions. The 35,000 samples collected from the expedition now form the basis for extensive processing, analysis, and data integration on land. One of the wettest experiments ever has generated more than 7 terabytes of information, one of the largest contiguous sets of DNA sequence available to the scientific community.6-8
The enormous 40 million gene set described by Sunagawa et al.1 is shown to derive principally from around 35,000 species of marine bacteria. Around 80% of these sequences are novel, and most of the novelty is shown to derive from oceanic regions traditionally undersampled (such as the Southern Ocean), and from the twilight zone below the upper +/- 100 metres of the water column where sunlight can pass. The microbial communities are quite different from one location to another, and the authors found that temperature is the main factor determining their composition. In fact just by looking at the species content they could predict the temperature of the water with a high precision – quite a sophisticated thermometer! The implication of this finding is that temperature changes in a future ocean impacted by climate change are likely to affect the functioning of the whole marine ecosystem, impacting the food chain and the biogeochemical cycles that depend on this microbial world.
An interesting aspect of the work was to compare the ocean microbiome (the community of all microorganisms) with the human gut microbiome, on the premise that both represent single contiguous ecosystems. The 40 million genes in the global ocean compare to 10 million genes in the human gut microbiome, so the numbers are quite similar. Furthermore, in terms of abundance close to ¾ of ocean and gut genes are the same, in spite of them being very different ecosystems and containing different microbes. On the other hand, around 90% of these gut microbiome genes have putative functions assigned to them, which compares to less than 60% of the ocean microbiome. These striking differences reflect the priorities of funding biomedical research at the expense of environmental research, even though a healthy ecosystem promotes human health too. Another striking difference between the ocean and gut microbiomes is that whereas many gut microbiome genes are involved in signaling and cell-cell communication, the primary signal from the ocean microbiome is one of nutrient transport, energy utilization and basic metabolism.
Life evolved in the ocean, and the complex consortium of organisms that make us human is not unlike the organisms that co-evolved to adapt to life in marine plankton ecosystems. The striking similarities between the two ecosystems are food for thought to ponder about our origins and to remember the importance of marine plankton ecosystems for generating and maintaining planet Earth habitable for us. In spite of our anthropocentric focus on biomedical research related to human healthcare, we should not forget the microbial life support systems that made our planet habitable for us in the first place and that continue to do so. In today’s world of changing climate, the strong sensitivity of marine microbes to temperature should be a wake-up call to stop exploiting marine resources and treating the ocean as a garbage site for everything we want to get rid of.
Original Article:Sunagawa, S., Coelho, L., Chaffron, S., Kultima, J., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D., Alberti, A., Cornejo-Castillo, F., Costea, P., Cruaud, C., d'Ovidio, F., Engelen, S., Ferrera, I., Gasol, J., Guidi, L., Hildebrand, F., Kokoszka, F., Lepoivre, C., Lima-Mendez, G., Poulain, J., Poulos, B., Royo-Llonch, M., Sarmento, H., Vieira-Silva, S., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Bowler, C., de Vargas, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Jaillon, O., Not, F., Ogata, H., Pesant, S., Speich, S., Stemmann, L., Sullivan, M., Weissenbach, J., Wincker, P., Karsenti, E., Raes, J., Acinas, S., Bork, P., Boss, E., Bowler, C., Follows, M., Karp-Boss, L., Krzic, U., Reynaud, E., Sardet, C., Sieracki, M. and Velayoudon, D. (2015). Structure and function of the global ocean microbiome. Science, 348(6237), pp.1261359-1261359.
Dr. Tobias Preuten , Editorial Advisor - Review operation manager
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