Plankton screening for active compounds

Work-Package 7 description


This Working Group focuses on the applied research of the OCEANOMICS project. Its objectives are:

  • Streamline research of bioactive compounds from ocean plankton, based on analyses of Tara Oceans samples (Working Groups 2-5), especially regarding lipids and secondary metabolites through the study of metabolic pathways (Working Group No. 5).


  • Explore the diversity of excreted metabolites under controlled conditions and identify their biotechnological potential.


  • Characterize new molecules of interest in dermocosmetics and pharmaceuticals from purified compounds from selected strains.


  • Transfer technologies and imaging methods and high-throughput sequencing developed in OCEANOMICS to applied research, dedicated to the monitoring of water quality. In particular, characterizing the industrial value of biological materials concentrated in the early stages of the desalination process.


  • Develop a partnership between academic/technical platforms and  biotech companies to stimulate the transfer of knowledge and technology.


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Stéphane Bach and Chris Bowler are in charge of the Plankton screening for active compounds working group



This Working Group is coordinated by Stéphane Bach of the USR 3151 at the Roscoff Biological Station and Chris Bowler at the ENS Paris Institute of Biology. It also involves the UMR 7144 and FR 2424 of the Roscoff Biological Station, the Evry Genoscope,  the CEA Cell and Plant Physiology laboratory at Grenoble and private partners Greentech, Soliance and Veolia Environment Research and Innovation.



Plankton lipidomics - Task 7.1

The very complex fatty acid metabolism is undoubtedly one of the resources from biodiversity, microalgae and marine protists that is most easily applicable in the long term. Some of these fatty acids are characterized by an exceptional molecular diversity with variable lengths of even or odd numbers of carbon atoms (8 to more than 36 carbons), linear or branched with double bonds, oxidations, rings, etc.

These fatty acids are potential sources of biotechnology applications (hydrophobic polymers, microstructured materials), biomedical (anti-inflammatory, anti cell proliferation, anti-cancer) or in the domain of fuel substitutes (biofuels).

AcylUniverse, a database to screen and interpret the lipid diversity of the oceans.

The enormous amount of -omics and meta-omics data acquired by the working group on genetic data from Tara Oceans samples, as well as from reference organisms is being explored to reveal the presence of genes encoding enzymes or regulators of metabolic pathways potentially useful in the industrial sector. For this, a specific database, AcylUniverse has been improved and adapted to the extreme richness and complexity of fatty acid metabolism. Bioinformatics pipelines have been developed for high-speed scanning of the genes involved in the synthesis of these compounds. The knowledge generated will be used to select choice strains for research of bioactive compounds (Tasks 7.2 and 7.3).

High throughput phenotyping for identifying lipid producing strains.

In conjunction with the high-speed imaging platform set up in the framework of Working Group 3 (Production and primary analysis of imaging data), a protocol was developed for screening protist samples from the Tara Oceans expedition to identify cells with high lipid content. Based on the current use of the fluorescent dye Nile Red, this protocol has other screening characteristics allowing parallel acquisition of information about cell structures. Integrating the environmental and genetic data on these same samples (Working groups 2 and 4) will identify environmental conditions favoring the occurrence of planktonic cells with high lipid content.


Screening plankton strains for bioactive compounds for pharmaceutical and dermo-cosmetics - Task 7.2

To date, nearly 70% of active molecules on the market are natural substances, or molecules derived from them. These are from terrestrial plants, microorganisms, fungi and, more rarely, from animals. The objective of this section is to explore plankton as a potential source of new bioactive compounds. Before this working group proceeds, a selection of planktonic strains with high potential will be assessed. The strains will come from the planktonic culture collection of Roscoff (Roscoff Culture Collection - RCC) and choices will be made based on the knowledge developed by the working groups "Production and primary analyses of genetic data" and "Bioinformatics and modeling ecosystems ". Approximately 150 identified strains will be further analyzed for their metabolic profile. From these, 80 strains will be retained and extracted. Purification of the compounds will be carried out by our private partners Soliance and Greentech. The extracts and the purified molecules will then be identified by different chromatographic approaches.

Using dermocosmetic extracts.

This part of the project is to ensure the possibility of cultivating the identified species at a pilot scale, to obtain sufficient biomass for optimal extraction. The optimal growth  parameters will also be sought. Different extraction protocols will then be compared in order to obtain colorless and odorless extracts to meet the needs of cosmetics. The biological activity of compounds on the skin can then be evaluated using different in vitro cell types (keratinocytes, fibroblasts, adipocytes and melanocytes). Several aspects of cosmetic reactions will be covered, and toxicity of active compounds will also be tested to meet current standards before in vivo tests. Finally, a technical and economic study will be set up to assess the potential for marketing identified active compounds.

Pharmaceutical use.

The characterization of the active compounds from planktonic strains will be based on evaluating their role in inhibition and/or activation of mammalian cell migration in culture and their effects in vitro on growth of 5 mammalian cell lines. For each active extract, more than 20 sub-fractions and fractions will be studied and approaches to dermocosmetic use can also benefit from these protocols. In addition, protein kinase regulatory enzymes of many cellular mechanisms are often responsible for pathologies when deregulated and constitute a target of choice for this part of the project. Transcriptomic approaches will allow us to understand more precisely the mode of action of the identified active molecules.



High-throughput phenotyping of cultivable strains for exometabolomes - Task 7.3

The scientific literature shows that plankton, whether under stress or not, release into their environment a considerable amount of organic compounds among which are mostly sugars, compounds of major interest. Furthermore, other types of excreted molecules play a major ecological role and have strong biotechnological interest. This part of the OCEANOMICS project aims to explore protists selected again on morphogenetic criteria revealed by analyses of samples from Tara Oceans.


Evaluation and valorisation of pre-treatment steps in the desalination industry - Task 7.4

In 2015, 60 million m3 of drinking water will be produced per day by seawater desalination. The systems used to date involve filtration steps and reverse osmosis which retain impurities and salts respectively. One of the key issues to improve this process is to characterize the volume of water filtered and the biological agents causing clogging of filters. VEOLIA Research and Environment is also working on the possibility of returning to their natural habitats biological samples retained in the filter, and to reduce the environmental impact of filtration. The sequencing protocols and genetic metabolic and lipidomic analyses developed as part of OCEANOMICS will be utilized to assess the effectiveness of filtration steps and evaluate the industrial potential of biological material isolated during this process.