How Eric Karsenti's quest to understand the cell launched a trip around the world. The project, called Tara Oceans, set sail from Lorient, France, in September 2009 for a 115,000-kilometre voyage to collect plankton — microscopic marine organisms — at 154 distinct sites around the world. Findings from the expedition are now starting to be published, and the bulk of the data will soon be made publicly available.
Although other surveys, such as the 2004–06 Global Ocean Sampling Expedition, piloted by genomics impresario Craig Venter, have sampled microscopic life in the seas, the Tara Oceans project is taking a broader approach — to “study it all”. Instead of focusing only on microbes, the scientists collected billions of organisms, from millimetre-scale zooplankton down to viruses 100,000 times smaller.
These marine organisms exert tremendous power over the planet, collectively forming a giant engine that drives the cycling of elements such as carbon, nitrogen and oxygen. Photosynthetic marine microbes produce about as much of the world's oxygen as do land plants. Ocean ecosystems are also hives of evolutionary activity in which countless viruses shuttle genes between organisms.
Understanding how these complex marine ecosystems work requires a holistic approach, says Karsenti. Tara Oceans scientists are identifying the plankton through a range of techniques including genomics, proteomics and automated high-throughput imaging. To link the organisms to their environments, the researchers also measured properties such as the temperature, pH and salinity of the water around each sample, which they plan to cross-reference with the biological data.
Although the project is limited by its ability to sample areas at only one time, “the data they collect could be used in revolutionary ways”, says Jack Gilbert, a microbial ecologist at Argonne National Laboratory in Illinois. By working out how the different plankton species interact with each other and the environment, the Tara Oceans project members hope to understand how ecosystems emerge from the sum of the interactions between their parts. This huge data set, they say, will help researchers to tackle big issues, such as calculating the biodiversity in the oceans, predicting how marine organisms will respond to environmental shifts and, perhaps, gaining insight into how evolution acts on networks of organisms in ecosystems or of molecules in cells.
Beyond the big numbers, the team is working to deduce potential ecological relationships. Seeing which organisms occur alongside others in samples, for example, can suggest possible interactions. Hiroyuki Ogata, a Tara Project collaborator and microbiologist at the Mediterranean Institute of Microbiology in Marseille, France, and his team dug through Tara Oceans data and found that a family of giant viruses called Megaviridae occurred alongside filamentous organisms known as oomycetes. Evidence of gene transfer between the two organisms gives the first hints, say the researchers, that oomycetes might be hosts for giant viruses. Karsenti says that such discoveries show how Tara Oceans data could help to unpick the parasitic and symbiotic relationships that have shaped evolution in the ocean.
Tara Oceans is now taking part in an arctic sampling mission, and scientists around the world will be able to access data from its first global circuit later this year, when the raw sequences, together with the environmental measurements, will be released in an open-access database hosted by the EMBL European Bioinformatics Institute in Hinxton, UK.
Researchers will then be able to compare the Tara Oceans data with results from other large marine surveys, such as Venter's Global Ocean Sampling Expedition and Spain's 2010–11 Malaspina project, which focused on samples from deep marine ecosystems. They can also compare the data with the plethora of smaller, more local marine-ecological studies that sample the same area over time so that scientists can see how the ecosystems change. Gilbert says that it is crucial that the data from Tara Oceans be viewed in the context of other longitudinal studies, because the static view from a single voyage is limited. “This has always been the criticism of these kinds of biogeographic surveys,” he says.
Robert Friedman, chief operating officer at the J. Craig Venter Institute in San Diego, California, agrees: “For us to truly understand the oceans, one was not sufficient; two is probably not sufficient. We're going to need many more.”
Karsenti hopes other researchers will take up that challenge and that some of them will, as he did, step outside their comfort zones to do so. Today's cell and developmental biologists, he suggests, should look beyond their yeasts, fruitflies and mice, and observe the extraordinary creatures inhabiting the seas. Perhaps future cell biologists will look first to the oceans, inspired by the tale of a sailor who peered into the heart of a single cell and caught a glimpse of the world.