Focus on our oceans’ microbiome

6 July 2015

​An international team of scientists, including Jeroen Raes, Gipsi Mendez, Karoline Faust and Samuel Chaffron (VIB/KU Leuven), has vastly increased our understanding of microscopic life in the oceans. The data from a three-year expedition across the world’s oceans on board the schooner Tara and several years of follow-up work, were recorded in 5 publications in a special issue of Science.

Why is it important to explore the microbiome of our oceans?
Jeroen: When you mention rich ecosystems that are vital for life on Earth, people tend to think of rainforests, but plankton is actually just as crucial. These tiny beings produce oxygen, act as carbon sinks, influence the weather, and sustain the larger fishes and whales. The resources we’ve generated will allow us to understand and predict the impact of climate change on the ocean systems and ultimately the earth.

Which part of this huge project did you focus on?
Gipsi: We studied the interactions between planktonic organisms – from viruses to small animal larvae. We discovered that many of their interactions are parasitic, recycling nutrients back to the base of the food chain. We proved that the impact of these biotic interactions is at least as important as the impact of the environment in the ocean ecosystem.
Karoline: The map was generated based on novel bioinformatics algorithms, months of computer calculations and finally confirmation through microscopy. It is amazing that we can actually predict the presence of organisms living inside other ones, just by using computer programs.

"It was a fantastic once in a lifetime experience!"
Samuel Chaffron

Samuel: In another paper we describe the huge untapped diversity of plankton species and associated functions and show how the environment affects them. At each sampling station we combined the collection of plankton samples with the measurement of environmental factors such as temperature, pH, and salinity, to investigate the influence of each factor on the structure of the ocean microbiome. We found that at depths where sunlight reaches, temperature rather than oxygen or geography was the main factor influencing the community composition. We also found that over 73 % of the core functionalities in the ocean are shared with the human gut, indicating common principles of microbial life in these very distinct ecosystems.

Gipsi and Sam, you spent some time on the schooner. How was it to work in a floating lab?
Gipsi: It was the first time I had been at sea longer than 3 hours… Leaving Savannah was very quiet, we saw dolphins, all seemed paradise but as soon as we entered the Atlantic we faced a very strong storm, it was quite dramatic. I had to collect the information about the sampling, the metadata. Sampling days were quite long, work started early morning and finished after midnight but scientists and crew were working together to make it happen. After 10 days at sea Tara sailed into New York harbor, where Tara docked at the foot of the freedom Tower and Tara received a visit from Ban Ki-moon (secretary general of the United Nations).
More info:

"For me that was one of the major take home messages – if you have a cool idea, don't give up!"
Jeroen Raes

Samuel: It was a fantastic once in a lifetime experience! I had the chance to be responsible for the zooplankton sampling during the of the 2nd part of the Tara Oceans expedition, around the North Pole. We spent one month onboard with a stop over in the Faeroe Islands. Overall we had good weather except a storm we had to cross; I still remember working in the wet lab filtering seawater on my knees! We crossed the polar circle and witnessed fantastic landscapes and animals. I am ready to leave again for the next expedition!

Jeroen, you were involved in the project from the very beginning, would you do it again?
Absolutely. From the very beginning all of the people involved in the Tara project wanted this adventure to be not just about cutting-edge science, but also about showing people all over the world how important the ocean is for life on our planet. This project started off as a rookie project with zero funding, but we kept on fighting with this amazing result in the end. For me that was one of the major take home messages – if you have a cool idea, don't give up!

Lima-Mendez, Faust, Henry et al.
Sunagawa, Coelho, Chaffron, et al.
Brum, Ignacio-Espinosa, Roux et al.
de Vargas, Audic, Henry, Decelle, Mahe et al.
Villar et al.


On the picture, from left to right:
Gipsi Lima Mendez, Jeroen Raes, Karoline Faust & Samuel Chaffron