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Uncultured planktonic eukaryotes finally reveal their secrets

With massively parallel sequencing of DNA collected from the surfaces of the earth's oceans and seas (Tara Oceans expeditions) and more than ten years of analysis, an international team piloted by researchers from Genoscope (CEA-Jacob) and the CNRS has solved one of environmental biology's greatest puzzles. The team successfully united close to 300 billion small planktonic DNA fragments and reconstructed hundreds of eukaryotic genomes having evaded conventional in vitro culturing techniques. The work, published in Cell Genomics, has revealed the complex associations between evolution and functional capacity in numerous unicellular eukaryotes indispensable for the global oceanic ecosystem. 

Published on 29 April 2022

Eukaryotic microorganisms are abundant on ocean surfaces, where they have a considerable influence on biogeochemical cycles and the global climate. Although some of these organisms, like various green algae and diatoms, are well known, most have yet to be described. Indeed, the majority of this enormous diversity of eukaryotic plankton does not lend itself to laboratory culturing, which greatly limits science's functional understanding of it. The genomic characterization of these organisms would yield great insights into their evolution and functional traits, the roles they play in biogeochemical cycles and their ability to adapt to climate change. To achieve that goal, scientists had to find a way to solve one of today's largest environmental genomics puzzles: how to reconstruct the sizable genomes of eukaryotes from the millions of DNA fragments obtained by planktonic metagenome sequencing. To date, the scientific community had used metagenome sequencing only on much more genetically-simple organisms such as bacteria and viruses.

An article published in Cell Genomics  has described a notable initial success in the large-scale genomic characterization of eukaryotes without using in vitro culturing. For that study, revealing the surprising functional capacities of these microorganisms, the authoring researchers used close to 300 billion short DNA sequences—equivalent to 10,000 human genomes—produced over the years by Genoscope from ocean surface samples collected across the globe by the Tara Oceans expeditions. The team was able to reconstruct genomes corresponding to hundreds of eukaryotic species abundant in plankton. The resulting resource includes notably the largest planktonic genome described to date (more than a billion nucleotides) and numerous, formerly unknown taxonomic branches.

The researchers went on to analyze the distribution of these novel genomes across ocean surfaces. Some were only present in the Southern Ocean, others only in the Indian Ocean, etc., revealing a sort-of reconstructed-genome-based atlas.

They then identified 10 million genes within the genomes, and defined four eukaryotic groups based on their genetic profiles. Surprisingly, this tactic shed light on functional convergences between evolutionarily distant species. In other words, large-scale environmental genomics was able to show that eukaryotes not sharing any recent ancestors, such as green algae and diatoms, have nonetheless numerous, similar genetic functions. Unicellular marine eukaryotes thus appear to have evolved in a complex, non-linear manner.

The study's data and results represent a pioneering advance and will serve as a base reference, but they only cover a small part of the planktonic world. The coming decade will surely see a revolution in our understanding of environmental eukaryotic organisms driven by genomic approaches instead of laboratory culturing. 

Figure : Illustration of the genomic resource of abundant eukaryotic plankton at the ocean surface (evolutive tree: Tom Delmont and Morgan Gaia; plankton picture : Noan Le Bescot).

Contact : Tom Delmont |

Sustainable development objectives: 3 (good health and well-being), 6 (clean water and sanitation), 13 (climate action), 14 (life below water) 
This study supplies base knowledge on the genomics of plankton abundant on the oceans' surfaces. That plankton is a marker of marine water quality and health and a powerful climate regulator. It thus contributes to the well-being and good health of humanity.
Discover all of the involved CNRS laboratories at the CNRS's INEE website.

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