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A feat in the study of planktonic life

A Genoscope research team was part of a pioneering study in environmental genomics. From 280 billion small planktonic-DNA sequences harvested across the Earth’s oceans, the researchers were able to at least partially reconstitute the genomes of close to 700 eukaryote species. That work represents a tour de force for the large and complex genomes of these species, furthermore impossible to isolate and cultivate in the laboratory. The study, which made the cover of the 11 May 2022 edition of Cell Genomics, revealed a treasure trove of planktonic life.
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Couverture de la revue Cell Genomics - Le plancton Couverture de la revue Cell Genomics - Le plancton

For more than 10 years now, the plankton samples collected from across the globe by the Tara Oceans expeditions have been continuously delivering new discoveries on this vital ecosystem for the planet and humankind. For this grand scientific adventure, Genoscope sequences and analyzes the DNA found within the water samples collected from more than 150 oceanic sites and at a variety of water depths. The method used by the laboratory, called “metagenomics, has shown its potential by delivering the DNA sequences of all of the organisms present in each water sample.

Making up a large part of the many species present in plankton, eukaryotes are complex, nucleated organisms that live mainly near the ocean surface. They comprise unicellular organisms, microscopic animals and photosynthetic algae among others. By contributing greatly to the flux of matter, energy and oxygen in the ocean, eukaryotic plankton plays a key role in the stability of the entire marine ecosystem.

Compared to those of prokaryotes, the genomes of eukaryotes are larger, more complex, divided into chromosomes and marked by numerous non-coding and repetitive sequences. Because of that complexity, reconstructing individual eukaryote genomes from the global metagenome derived from oceanic water samples had remained out of science’s reach. Until now. Indeed, an international team piloted by the CNRS and Genoscope (CEA/CNRS/University of Évry-Paris Saclay) has finally touched that goal. Benefiting from the partial exclusion of prokaryotes via the size fractionation methodology available on the schooner Tara, the researchers worked on the massive amount of sequencing data from close to 800 metagenomics samples, representing 280 billion short DNA sequences. Their unprecedented results earned the cover of the 11 May 2022 edition of Cell Genomics.

From Tara Oceans to Euckaryotic plankton genomicsThe work reconstructed, at least partially, close to 700 planktonic eukaryote species genomes, and in so doing, established the most precise representation of the diversity of those species available today. The researchers were able to place the organisms into five groups sharing biological functions, one comprising multicellular species and the four others unicellular species. Surprisingly, two groups brought together taxonomically-distant organisms, demonstrating functional convergence (developing the same adaptive strategies) among species sharing a same oceanic ecosystem for millions of years. For example, similar sugar transport and metabolism functions were found in a diverse group of large eukaryotes, perhaps associated with a shared prey.

This study is a threshold-crossing first step.

Novel sequencing approaches and improved bioinformatics tools will bring even greater progress to the assembly of genomes for planktonic eukaryotes and the exploration of their genetic diversity and functions, all contributing to a better understanding of the oceans’ role in the global ecosystem.

  • What is plankton?

    Placton - Tara Océans

    The term plankton describes the collection of aquatic organisms that float passively with ocean currents, having little or no ability to swim against them. Therein are millions of different species, including viruses, bacteria, single-celled eukaryotes, microscopic algae, small crustaceans, and fish eggs and larvae among others. They constitute the first links of the oceanic food chain, produce half of the earth’s oxygen and contribute to climate stability.

  • What is metagenomics?

    The term metagenomics describes the application of genomics to the community of organisms living in a natural environment. The approach unveils the entire ecosystem in all its complexity. Metagenomics enables the single-analysis study of the collective DNA of all the microorganisms in, for example, an area of soil, the intestinal flora, human skin, or, in the present case, the oceanic plankton collected by the Tara Oceans expeditions.
    Uniting high throughput sequencing and bioinformatics, the method enables the discovery of thousands of novel genes, their functions, and even heretofore unknown species. Within the Tara Oceans expeditions, metagenomics enabled the discovery of the complex world of plankton by analyzing the DNA fragments from the community of organisms present in each sample of oceanic water.
    However, the global analysis of an environment’s DNA in this manner makes it difficult to identify and study the individual species present there, notably for large, complex genomes like those of eukaryotes.


Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Article posted on 8 June 2022


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