BlueRemediomics: harnessing marine microbes to promote a circular bioeconomy

Funding awarded for developing tools to harness marine microbiome data for biotechnological applications and ecosystem services

BlueRemediomics logo
BlueRemediomics funding. Credit: Karen Arnott/EMBL-EBI

The European Commission has funded the BlueRemediomics project, which will develop novel tools and approaches to catalogue marine microbiome data and marine culture collections. These tools will help facilitate the development of industrial processes that reduce waste, increase the reuse of natural products and by-products, and improve aquaculture – the farming of seafood.

The project simultaneously aims to ensure equitable access to and sharing of benefits derived from any new products, e.g. new medicines or cosmeceuticals, as well as gauge the wider society’s appetite for biobased solutions.

BlueRemediomics was awarded €7.65 million under the latest Horizon Europe Research and Innovation funding programme with an additional €1.54 million in Associated Partner funding provided by UK Research and Innovation (UKRI) and the Swiss State Secretariat for Education, Research and Innovation (SERI). BlueRemediomics is coordinated by EMBL’s European Bioinformatics Institute (EMBL-EBI) and the French National Centre for Scientific Research (CNRS). Together with 17 Beneficiaries and four Associated Partners, the project has wide participation across Europe, including the European Marine Biological Resource Centre – European Research Infrastructure Consortium (EMBRC-ERIC), the Tara Ocean Foundation, and several biotechnology, agritech, and aquaculture companies.

Leveraging data to protect oceans

The marine ecosystem is the largest ecosystem on Earth. Microorganisms make up around 65% of our ocean’s biomass and play vital roles in the food chain, oxygen production, and nutrient cycling. Marine microbiomes are also rapidly growing actors in the blue economy – the sustainable use of ocean resources while preserving the health of the ocean ecosystem. Their study is essential to advance the discovery, understanding, and protection of our oceans.

What is a microbiome? 

A microbiome is composed of diverse communities of microbes, including bacteria, fungi, algae, and viruses, which inhabit specific environments, such as oceans, soil, and human skin or gut. The precise microbial composition is dependent on the resources available to that community and many other factors. Recent studies are increasingly shining a spotlight on the pivotal role played by microbiomes in human health and disease, as well as in maintaining a healthy ocean.

BlueRemediomics addresses the European Commission’s European Green Deal and EU bioeconomy strategy by undertaking a collaborative effort to synergise marine microbiome data and biobank resources from across Europe. The project leverages microbiome data analysis experts from EMBL-EBI’s MGnify team as well as the rich datasets generated by Tara Oceans. One key aim of BlueRemediomics is to develop an open access biodiscovery platform to harmonise and integrate marine microbiome sequence data and to enrich this data with functional information to make it tractable for bioprospecting.

What is bioprospecting? 

Bioprospecting is the exploration of natural sources for biological products that could be developed for use in agriculture, bioremediation, pharmaceuticals, and more.

“Marine microbes have evolved to exploit and reuse both natural and artificial resources that they encounter in their relatively nutrient-poor environment. This can be as simple as a single enzyme, or involve a series of processes involving different species,” said Rob Finn, Coordinator of BlueRemediomics, Microbiome Informatics Team Leader and MGnify PI at EMBL-EBI. “The BlueRemediomics project will exploit existing data to help identify such processes and let us derive new biobased solutions for reducing waste or for bioremediation.”

Culturomics and bioprospecting

BlueRemediomics will also establish innovative culturomics approaches – high-throughput culturing techniques to isolate microorganisms from samples and grow different microorganisms together in co-cultures.  In addition, it will develop screening platforms to investigate the marine microbes’ functionalities. Scaling up and streamlining this process will help accelerate bioprospecting.

“Marine microbial communities represent a vast unexploited treasure trove of bioresources that have the potential to strengthen the European blue economy,” said Chris Bowler, Director of Research at CNRS, who is a co-coordinator of the project. “For example, to safely carry out aquaculture – the farming of our oceans – it is vital that we expand our understanding of the roles played by marine microbes for ocean health. The BlueRemediomics project will establish a Microbiome Health Index for monitoring marine environments, thus allowing us to promote healthy microbiome approaches and strategies in aquaculture in line with the ‘do no significant harm’ principle.”

BlueRemediomics also involves the participation of EMBL group leaders Michael Zimmerman, Maria Zimmerman-Kogadeeva, and Peer Bork. This work sits within the remit of the Microbial Ecosystems and Planetary Biology transversal themes introduced in EMBL’s ‘Molecules to Ecosystems’ Programme.

BlueRemediomics partners

  1. European Molecular Biology Laboratory (EMBL) (Germany)
  2. Centre National de la Recherche Scientifique (CNRS) (France)
  3. Sorbonne Université (France)
  4. Commissariat a l’énergie atomique et aux énergies alternatives (France)
  5. Institute Français de recherche pour l’exploitation de la mer (Ifremer) (France)
  6. European Marine Biological Resource Centre – European Research Infrastructure Consortium (EMBRC – ERIC) (France)
  7. Stazione Zoologica Anton Dohrn (Italy)
  8. Ústav organickéchemie a biochemie AV ČR (Czeck Republic)
  9. Norce Norwegian Research Centre AS (Norway)
  10. Acondicionamiento Tarrasense Associacion (Spain)
  11. Fondation Tara Ocean (France)
  12. University of the Western Cape (South Africa)
  13. ABS International (Belgium)
  14. ERINN Innovation (Ireland)
  15. Naicons SRL (Italy)
  16. Latvijas Biomedicinas Petijumu un Studiju Centrs (Latvia)
  17. Zilt (Belgium)
  18. Valagro SpA (Italy)
  19. Leroy Seafood Group ASA (Norway)
  20. Eidgenössische Technische Hochschule Zürich (Switzerland)
  21. University College London (UK)
  22. The Chancellors Masters and Scholars of the University of Cambridge (UK)
  23. University of Aberdeen (UK)

Tags: bioinformatics, embl-ebi, finn, funding, mgnify, microbiome, molecules to ecosystems, planetary biology, press release, sustainability, tara ocean foundation

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