The international expedition Tara Oceans took place between 2009 and 2013, with more than a hundred scientists from 31 countries and laboratories, and an ambitious task: studying the plankton from marine ecosystems, not only to identify the microorganisms that compose the plankton but to understand how these microorganisms interact with each other and with the environment. The expedition team circumnavigated the planet and collected near 35.000 samples in different oceans at different seasons.
The international expedition Tara Oceans took place between 2009 and 2013, with more than a hundred scientists from 31 countries and laboratories, and an ambitious task: studying the plankton from marine ecosystems, not only to identify the microorganisms that compose the plankton but to understand how these microorganisms interact with each other and with the environment. The expedition team circumnavigated the planet and collected near 35.000 samples in different oceans at different seasons. Now, the results are published in a special issue of the Science journal, in five different articles.
One of the scientific coordinators of the Tara Oceans project is Silvia G. Acinas, a researcher at the Institute of Marine Sciences (ICM) of the CSIC. She has led the study of the Oceanic Microbioma together with scientists at the European Molecular Biology Lab (EMBL) in Germany (Shinichi Sunagawa, Peer Bork y Eric Karsenti) and at the Vlaams Institute of Biotechnology (VIB) in Belgium (Jeroen Raes). Besides, several scientists from the ICM-CSIC have been involved in the project.
“One of the achievements of Tara Oceans has been to describe the microbial diversity (viruses, bacteria, archaea and protists) at a global scale and at an extraordinary resolution level thanks to the massive sequencing of the DNA and RNA”, says Silvia G.Acinas. Besides the impact of the environment on the plankton, scientists have also studied how oceanic eddies affect the structure of planktonic communities.
The oceanic plankton is essential for our planet: produces half of the oxygen, acts as a carbon sink, influences the weather, and forms the base of the food web that sustains the larger fish and marine mammals.
“Beyond the cutting-edge science that was developed thanks to our collaborative work with the Tara Expéditions Foundation, this adventure is also about showing people all over the world how important the ocean is for our own well-being,” says Eric Karsenti, director of Tara Oceans, from EMBL and CNRS.
A legacy for future generations
During the expedition, 35.000 samples were collected at different depths in different oceans and seas, covering all the major oceanic regions of the planet, except for the Artic. The pioneering research of Tara Oceans has focused on the study of the "ocean dermis", from epipelagic waters down to 900 meters deep (mesopelagic zone). Every sample was taken duplicated, therefore scientists can preserve one of the samples for being analyzed in the future when more advanced technologies will be developed.
The article Structure and Function of the Global Ocean Microbiome, led by Silvia G. Acinas, scientist at the ICM-CSIC, shows the results of the analysis of 243 samples from 68 locations. The metagenomic analysis has resulted in 7,2 trillion of DNA base pairs from the microbial communities. This is 1,000 times more DNA sequences than any other previous study of marine diversity, more than any other sequencing study of other environmental microbiomes, and even surpasses the sequencing of the human microbiome of more than a thousand people together.
This extraordinary amount of sequences contained 111 million of genes. But once the redundant sequences were discarded, the result is a microbial genetic catalogue of 40 million genes, 80% of which being totally new to science.
“This database and the collection of samples is a legacy for the scientific community and for future generations”, says Acinas. This genetic catalog will be a base for future development of models related to global change and the functioning of our marine ecosystems.
“We are excited about the fact that 80% of the identified genes are new, which means they have not been previously deposited in the public genetic databases”, highlights Josep M. Gasol, research professor at the ICM-CSIC. Of the 40 million genes, more than half belong to bacteria (58.8%), and the others belong to viruses (5-4%), archaea (2%) and small unicellular and multicellular eukaryotes (3.3%). For the rest of the genes, approximately 28%, we do not yet know to what group they belong.
More differences due to temperature than to geographical distance
The group of Dr. Acinas has focused on the study of marine bacteria and archaea, the marine bacterioplankton, which shows massive abundances: around 10^29 cells in the ocean or one million cells in a drop of seawater (1 milliliter). “We have analyzed 243 samples, which has enabled us to describe the diversity of these microorganisms in the global ocean. We estimate that there is a minimum of 35,000 taxa or possible species of prokaryotes (bacteria and archaea)”, comments Gulliem Salazar, PhD student.
Another questions that scientists had in mind was if there are large differences in the taxonomic composition of microbial communities from different oceanic regions. Francisco M. Cornejo, PhD student at the ICM-CSIC, explains that an interesting finding has been to discover that what mostly shapes which species are present is not geographical location but temperature and depth. “Microbial communities separated by thousands of kilometers are more similar between them than communities which are nearby but at different temperatures”, he says.
“Previous studies at local scale had shown that temperature had an essential role in shaping microbial distribution. Now we have shown this pattern at a global scale. This is especially important in a climate change context, because small variations in temperature can have an effect on the structure and biodiversity on these microbial communities”, remarks Silvia G. Acinas.
Functional genes
Another of the questions scientists wondered was understand the key functions of the ocean microbiome and the differences between marine ecosystems. Here, one of the most striking things we have seen, says Silvia G. Acinas, is that “67% of the oceanic microbioma genes already known are shared by all bacteria and archaea, which supposes a high functional redundance”. This implies, says Acinas, that “these genes are related to functions which are common to many organisms in functions highly preserved such as cellular replication, DNA transcription or protein shynthesis”.
On the contrary, only a small part of the genes (4%) has a high variability between the samples and between different taxa, encoding those functions related to local adaptations such as being adaptated to life on aggregates or in association to other organisms. It is in this small pool of the genes is where the potential for adaptation resides and this explains the resilience of the microbial communities.
From viruses to protists: looking at the whole spectrum of the plankton
The analyses performed during the Tara Oceans expedition and later in the lab, have led to an important development of experimental techniques. Through the use of different filters and meshes, plankton was divided into seven fractions, which correspond, from smaller to larger sizes, to viruses, giant viruses, bacteria, protists -a large group of eukaryotic microorganisms that includes from single-cells to multicellular organisms-, and zooplankton. This methodology has allowed to analyze the whole spectrum of the plankton.
Together with conventional technologies, such as flow cytometry or microscopy, the scientists have used methods to automatically detect and recognize images in order to morphologically identify the organisms. For the genomic analyses (DNA and RNA) the latest improvements in massive sequencing have been applied, remarks Isabel Ferrera.
Another of the articles of Tara Oceans, published in this Science issue, is focused on virus diversity. It has been led by Matthew B. Sullivan with the participation of Silvia G. Acinas and Josep M. Gasol. The viruses have an essential role in maintaining microbial diversity. In this work, the scientists have used a methodology that allowed them to recover and analyze up to the 90% of the planktonic viruses. This is an outstanding improvement compared to the previously used techniques that missed a large part of the viruses. This is the first global study on diversity of ocean viral communities and as a result, more tan 5000 virus populations in 43 locations have been detected.
Another of the articles focuses on the diversity of unicellular eukaryotic protists. It has been led by CNRS researcher Colomban de Vargas. In this work, the scientists have obtained 766 million sequences of the 18 rRNA gene and have concluded that the diversity of these microorganisms is much larger than previously thought. From these microorganisms, which have been forgotten for a long time, all superior organisms have evolved. “These eukaryotes are surprisingly diverse and important for the ocean ecosystem performance. We have identified at least 150,000 taxons of protists”, adds Ramiro Logares, scientists at the ICM-CSIC.
Who interact with whom
Thanks to novel computer models, the researchers were able to predict how these diverse planktonic organisms interact. Later, some of these predictions were confirmed through selective microscopy observations.
This work lead by Jeroen Raes from VIB, KU Leuven, and Vrije Universiteit Brussel hints to unexpected discoveries. “When we mapped how planktonic organisms – from viruses to small animal larvae – interact with each other, we discovered that most of those interactions are parasitic, recycling nutrients back down the food chain,” says Dr. Raes. This map is a first step towards a better understanding of the dynamics and structure of the global marine ecosystem.
Many scientists of the Institute of Marine Sciences (ICM-CSIC) have been involved in the Tara Oceans research. On one hand, the team led by Silvia G. Acinas, with Francisco M. Cornejo, Marta Royo-Llonch y Guillem Salazar. Also, the scientists Ana M. Cabello, Isabel Ferrera, Elena Lara, Ramiro Logares, Pablo Sánchez, Hugo Sarmento, Marta Sebastián and the professor Josep M Gasol.
Besides, the ICM-CSIC acts as a repository for the Tara Ocean expedition samples, storing ca. 4,600 samples of bacteria and archaea, for future research.
The Tara Oceans expedition has been funded by the Centre National de la Recherche Scientifique (France); the European Molecular Biology Laboratory (Germany), and the Commissariat à l'Énergie Atomique et aux Énergies alternatives (France). The project had also the support of several public and private institutions. The research at the ICM-CSIC has been partially funded by one AACC from MICINN and a grant of AGAUR from the Generalitat of Catalunya.
Tara Oceans Articles
Sunagawa, Coelho, Chaffron, et al. Structure and Function of the Global Ocean Microbiome. DOI: 10.1126/science.1261359
De Vargas, Audic, Henry, et al. Eukaryotic plankton diversity in the sunlit global ocean. DOI: 10.1126/science.1261605
Lima-Mendez, Faust, Henry et al. Determinants of community structure in the global plankton interactome. DOI: 10.1126/science.1262073
Villar, Farrant, Follows et al. Environmental characteristics of Agulhas rings affect inter-ocean plankton transport. DOI: 10.1126/science.1261447
Brum, Ignacio-Espinosa, Roux et al. Global patterns and ecological drivers of ocean viral communities. DOI: 10.1126/science.1261498