Marine genetic resources (MGRs) are crucial for understanding marine biodiversity and tracking changes in ecosystems, while also providing a valuable foundation for biotechnological innovation. The recent adoption of the UN Treaty on Biodiversity Beyond National Jurisdiction (BBNJ Treaty) and the inclusion of digital sequence information in this legally binding agreement open new opportunities for protecting biodiversity in the high seas, including the deep sea. However, a significant knowledge gap exists in fully understanding current and potential future applications of MGRs in biotechnological innovation, creating uncertainties around the Treaty's implementation. Classifying MGR functions for specific technological uses - such as antibiotic resistance, bioremediation, and biofuels - can significantly increase our understanding of the economic value of marine ecosystems and help discover new genes and enzymes with practical applications that hold great potential for sustainable development.

Here, we analyzed the Marine Bioprospecting Patent Database (https://mabpat.shinyapps.io/main/), a global catalogue of marine genes used in innovation, that includes 104,467 nucleotide sequences from 1,639 marine species across 4,779 unique patents. We used technological codes, structured topic modeling, and a suite of knowledge diversity indices to evaluate the unique contributions of marine sequences to the biotechnology sector and other global economic areas. Our findings show that most MGRs are used in molecular biology to develop new enzymes and fluorescence methods, as well as in public health to create new therapeutic and diagnostic products. Additionally, we encounter various connections between marine bioprospecting inventions and the Sustainable Development Goals, emphasizing the potential of MGR utilization to promote sustainable development. Our study provides policymakers with new insight into the scope and scale of innovation based on MGR, enabling science-based decision-making related to the conservation and sustainable use of marine ecosystems.

How to cite: Zhivkoplias, E., Dunshirn, P., Jouffray, J.-B., and Blasiak, R.: From genes to innovation: exploring the use of marine genetic resources in biotechnology, One Ocean Science Congress 2025, Nice, France, 3–6 Jun 2025, OOS2025-498, https://doi.org/10.5194/oos2025-498, 2025.

Interactions between phytoplankton and heterotrophic bacteria play major roles at the basis of marine food webs. Through the balance between photosynthesis and respiration as well as nutrient recycling, they impact marine biochemistry via global carbon, oxygen, nitrogen and other nutrient cycles. By analogy to the terrestrial rhizosphere, phytoplankton and bacteria are known to interact at a microscale, in the microenvironment surrounding phytoplankton cells called the “phycosphere”. Despite its ecological significance, the diversity of bacterial species within the phycosphere, along with their nutritive and/or chemical communication with phytoplankton cells, remain poorly understood. 

We aim to characterize these mutualistic interactions by investigating long-term stable associations between bacteria and phytoplankton, cultured in our laboratory - where phytoplankton cells have been surprisingly surviving for over 3 years without any addition of fresh medium. Using genomic and metagenomic analyses, we assess the bacterial diversity within these phytoplankton-associated microbiomes and explore the metabolic pathways involved in these mutualistic interactions. Co-culture experiments will allow us to identify specific phytoplankton-bacteria symbioses. Microbiome transplant experiments across various phylogenetically diverse phytoplankton strains are performed to test the hypothesis of a universal core microbiome. 

Our findings may reveal key bacteria for phytoplankton survival, providing new insights into marine symbiosis as well as new marine genetic resources paving the way for improving high-biomass algal production in bioreactors, biofuels and algal growth for biotechnology.

How to cite: Fiorile, C., Sanchez-Brosseau, S., Suzuki, M., and Piganeau, G.: Genomics of mutualistic interactions between phytoplankton and bacteria : to a better understanding of marine symbiosis , One Ocean Science Congress 2025, Nice, France, 3–6 Jun 2025, OOS2025-538, https://doi.org/10.5194/oos2025-538, 2025.

The research, development and commercialisation pipeline for accessing, using and sharing marine genetic resources (MGR) of areas beyond national jurisdiction (ABNJ) is highly varied and complex. Equally complex is the governance framework under the 2023 agreement on the conservation and sustainable use of marine biological diversity of ABNJ (the ‘BBNJ’ Agreement), for which many practical details, including procedures, are yet to be decided by treaty Parties.

In general terms, all actors involved in acquiring, storing and utilizing MGR or associated Digital Sequence Information (DSI) and Traditional Knowledge (TK), including academia, government and industry, need to understand BBNJ Agreement obligations and comply with the laws of the Parties that implement them. Given that there are practical aspects of the framework that are yet to be determined by the Conference of the Parties (CoP), this will require proactive development of procedures and systems to compile, curate and provide necessary information to Parties, including data management plans and the BBNJ Identifier, when undertaking activities regulated under Part II. It is likely that this information will be provided at the first instance to the Party that has jurisdiction or control over the relevant activity, but there may be opportunities for directly sharing information with the Clearing House mechanism (CHM).

This presentation draws from real world examples to analyse ways in which current scientific practice is supported or challenged by framework elements, including notification, monitoring and benefit sharing systems and associated infrastructure such as the BBNJ Standardised Batch Identifier and data management plans. It compares how the elements and infrastructure may work in practice using realistic research and development (R&D) scenarios ranging from an idealised linear pathway to more complex pathways involving automation, sequence information and traditional knowledge associated with MGR in different geographical and temporal scales. For an efficient and ‘future proofed’ framework that supports innovation and fulfils treaty objectives, it is proposed that treaty bodies and policy makers need to look beyond the idealised R&D pathways envisaged in the treaty and engage directly with scientists and commercial end users when designing the practical details of implementation.

The BBNJ Agreement presents a linear vision of science which belies many inherent complexities. It is crucial that the R&D process for MGR is not imagined as a linear progression where such work would automatically result in commercialisation. Most R&D pathways are non-linear with many side branches that may be abandoned or pursued, iterative loops and long breaks in the process. Often several research threads are pursued in parallel, and the intended application is completely changed between the start and end of the process. Although many existing research practices are consistent with the notification and information sharing requirements, many challenges arise for non-linear scenarios, including utilizing MGR and DSI from collections prior to the BBNJ Agreement, complex uses of multiple DSI, automation in collection and use, change of use from harvest fisheries to R&D and access and use of TK associated with MGR of ABNJ.

How to cite: Jaspars, M., Rabone, M., Horton, T., Humphries, F., Lyal, C., Muraki Gottlieb, H., Scholz, A., and Vanagt, T.: BBNJ Agreement: Considerations for Scientists and Commercial End Users of MGR at Research, Development and Commercialisation Stages, One Ocean Science Congress 2025, Nice, France, 3–6 Jun 2025, OOS2025-567, https://doi.org/10.5194/oos2025-567, 2025.

NewAtlantis Labs (NAL) utilizes advanced science and meta-omics data processing to transform molecular insights into a comprehensive understanding of marine ecosystems, enabling us to assess their health and resilience while informing conservation strategies. Our innovative approach can also provide the foundation for the creation of new financial products, such as ecosystem service bonds and biodiversity credits, which can generate revenue to support local conservation efforts through a benefit-sharing model compliant with the Nagoya Protocol. To achieve this, NAL is building a scientific platform optimized for marine microbes, protists, and fungi that leverages a highly interoperable toolkit ecosystem with curated structured genomics databases. Our platform is designed not only as a resource for processing metagenomics and metatranscriptomics data, but also as a contextualized knowledge base for exploring specific research areas such as predictive ecological modeling, bioprospecting for natural products, pathogenicity screening, and examining links between environmental conditions and genes, metabolic pathways, and genomes of interest. Key components of our interoperable platform include: 1) VEBA, our open-source modular end-to-end multi-omics software suite; 2) Leviathan, our open-source taxonomic and functional profiling software; 3) the Metabolic Niche Space, our open-source framework for data-driven analysis of metabolic/ecological niches; 4) our genome-resolved NAL Genomics Database, which includes >70k well-curated bacterial, protist, and fungal genomes representing over 250M proteins; 5) Clairvoyance, our open source AutoML biomarker discovery algorithm; and 6) our marine biodiversity Knowledge Graph, which integrates and contextualizes outputs from our toolkits. To demonstrate the platform's utility, here we present a case study analyzing time-series multi-omics data collected during an algal bloom event in Monterey Bay. This application illustrates how our integrated approach can reveal complex ecological dynamics and functional interactions within marine microbial communities, which provide advanced marine ecosystem analytics that can support policy making, coastal protection and conservation efforts.

How to cite: Espinoza, J., Gutierrez, J., and Robaina, S.: An Integrated Multi-omics Platform for Marine Microbial Discovery and Ecosystem Analysis, One Ocean Science Congress 2025, Nice, France, 3–6 Jun 2025, OOS2025-703, https://doi.org/10.5194/oos2025-703, 2025.

The rapid advancements in genome sequencing technologies over the past two decades have unlocked unprecedented opportunities to understand and protect life in all its diversity. Genomes largely control biological development, physiology and the production of essential biomolecules, but they also connect all species within the tree of life. Genomes are invaluable tools for monitoring genetic diversity, providing insights into the resilience of populations and species facing environmental changes.

The ATLASea program (https://www.atlasea.fr) is dedicated to decoding this immense wealth of genomic information by conducting extensive sampling campaigns across the French Exclusive Economic Zone (EEZ) to collect specimens of eukaryotic marine species, sequence their genomes to high-quality standards, and make the data publicly available to the scientific community for research and analysis. Funded by the French government for an eight-year period, ATLASea has been already active for 18 months. During this time, the program has established key protocols, developed an informatics infrastructure, and forged international collaborations, including affiliations with the Ocean Decade Initiative and the Earth BioGenome Project. Genomes from diverse taxonomic groups have already been sequenced, with throughput progressively scaling up. Sampling efforts have spanned six locations on the coasts of metropolitan France, as well as sites in the Pacific Ocean and the Caribbean, covering over 1,000 species.

Ultimately, ATLASea aims to sequence the genomes of several thousand species, focusing on those of ecological and scientific importance, economic value, and cultural significance. ATLASea is also committed to training the next generation of scientists. Summer and winter schools, scheduled for 2025 and 2026, will welcome international participants, providing PhD students and early-career researchers with training in sampling and taxonomic identification, genome sequencing and assembly, genome annotation, and comparative and evolutionary genomics. Additionally, ATLASea will support private-public partnerships, driving innovation through workshops, funding opportunities, and collaborations with small and medium enterprises (SMEs) that could benefit from advances in marine genomics.

The oceans, home to millions of species threatened by human activity and climate change, harbor essential species that support the planet’s most efficient carbon pump, hold vast potential to feed a growing global population, and offer countless biological innovations shaped through evolution. Studying and monitoring ocean biodiversity must remain central to international efforts to deepen our understanding, preservation and sustainable use of the oceans.

How to cite: Roest Crollius, H., Aury, J.-M., Corre, E., Le Gall, L., and Wincker, P.: ATLASea: reference genomes to understand and monitor marine biodiversity worldwide, One Ocean Science Congress 2025, Nice, France, 3–6 Jun 2025, OOS2025-992, https://doi.org/10.5194/oos2025-992, 2025.

The Biocode 2.0 project represents an advancement in marine genetic research. The project is based in French Polynesia, already one of the world’s best-studied tropical marine systems. Building on the pioneering Moorea Biocode Project (2007-2010), Biocode 2.0 aims to uncover the unseen biodiversity of coral reefs, notably host-associated microbiomes and viromes. These data will help researchers understand how biodiversity at the molecular scale responds to and recovers from disturbances. Biocode 2.0 seeks to do this through a co-designed process with the local community, implementing access and benefit-sharing (ABS) agreements, while providing unprecedented transparency and provenance tracking. The project implements novel data infrastructure to effectively monitor and ensure compliance with biodiversity data governance, including the Convention of Biological Diversity (CBD) and, in high-seas contexts, the BBNJ Agreement under the United Nations Convention on the Law of the Sea - designing new ways to respond to compliance challenges associated with these international biodiversity governance frameworks. Biocode 2.0 is developing a robust sociotechnical infrastructure for compliance called iPlaces, which leverages the GEOME Field Information Management System. GEOME facilitates the tracking of key metadata about sampling events and the resulting specimens collected, linking these data to project permits (legal) and Indigenous community consent (extra legal) as documented through Local Contexts notices and labels. This framework allows for connecting upstream sampling data to downstream genomic information and other outputs, ensuring the cultural and legal metadata are transmitted along with scientific metadata. By incorporating FAIR (Findable, Accessible, Interoperable, and Reusable) and CARE (Collective Benefit, Authority to Control, Responsibility, and Ethics) principles, Biocode 2.0 aligns scientific progress with ethical standards, creating a model for inclusive and compliant marine genetic research that advances global scientific understanding and valorizes local and Indigenous knowledge appropriately.

How to cite: Davies, N., Robinson, E., and White Davies, M.: Biocode 2.0 Moorea Coral Reef Hologenome Sequencing Project:  A model for legal and ethical marine genetic research, One Ocean Science Congress 2025, Nice, France, 3–6 Jun 2025, OOS2025-1034, https://doi.org/10.5194/oos2025-1034, 2025.

Populations’ persistence relies on their demography in the short-term and their adaptive capacity in the long-run. The former is known to depend on species’ functional traits whereas the latter is determined by species’ intraspecific genetic diversity (IGD). However, several empirical and theoretical studies have shown that species’ life-history traits and IGD are related thus linking species’ demography and evolution. Such link is critical to understand the eco-evolutionary response of species to short-term pressures, notably climate change. In marine fish, small-bodied short-lived pelagic species are for instance known to be more sensitive to climate whereas large-bodied long-lived demersal species are more vulnerable to fishing. The interplay between species’ IGD and functional traits will therefore determine the eco-evolutionary resilience of populations to natural and anthropogenic pressures.

Here, we model fish’ functional traits and genetic diversity with Ev-OSMOSE, a new individual-based eco-evolutionary ecosystem model representing fish communities. From these simulations we deduce how fish species’ IGD is affected by their functional traits. As the mechanisms linking functional traits and IGD might be affected by external pressures, we forecast fish community eco-evolutionary pathways and distribution shift under climate change and fishing.

Our results confirm that life-history traits affect genetic diversity and show how functional traits such as the trophic level or habitat influence fish IGD. This work provides insights for evolutionarily-enlightened fish stocks management under climate change.

How to cite: Beneat, M., Ernande, B., Shin, Y.-J., Morell, A., and Moullec, F.: The Interplay of Functional Traits and Genetic Diversity in Fish Population Resilience Under Climate Change, One Ocean Science Congress 2025, Nice, France, 3–6 Jun 2025, OOS2025-1114, https://doi.org/10.5194/oos2025-1114, 2025.

Our contribution will present the methods and results of the first international project (POLYCONE, supported by the Belmont Forum, CRA Ocean) in sustainability science, aimed at establishing a sustainable, fair and ethical management plan for marine cones in French Polynesia. After four years of interdisciplinary work and dialogue with local communities and authorities, we will present the levers and obstacles to the sustainable use and fair retribution of genetic resources, focusing on socio-ecological governance as a transformative and effective solution for ecosystems, non-human populations and the human societies that depend on them.

This analytical feedback could enlighten other territories and communities, particularly island ones, on the front line of global change, where the sciences of sustainability and transformation have much to contribute by linking nature and culture through the thread of knowledge and enlightened, ethical public decision-making and collective action around the commons.

The question of how to define communities, their political role and the legal and ethical pluralism between local, national and international statutes (Nagoya Protocol and The Access and Benefit-sharing on Genetic Resources) will be particularly discussed in the case of French over-seas territories. This contribution reports on the international collaboration within the POLYCONE project and interactions with the International Research Netwok APOLMER on Ocean governance and resource management (CNRS-Sciences Po, Univ. Hawaii and Ottawa, CNRS research units) in strong interaction with the Chaire Outre-mer (Sciences Po - CEVIPOF), while itself questioning the role of science and scientists in (post)colonial territories subject facing the impacts of global change in marine ans coastal environments.

How to cite: Maze, C., Mawyer, A., Burelli, T., and Bambridge, T.: Towards an integrated approach with local communities to ensure sustainable and ethical use of marine genetic resources - The case of cone snails in French Polynesia, One Ocean Science Congress 2025, Nice, France, 3–6 Jun 2025, OOS2025-1139, https://doi.org/10.5194/oos2025-1139, 2025.

The Arctic is being heavily impacted by climate change. The air temperature is rising more than 2 times faster than the rest of the globe, sea ice cover is shrinking every year and we are observing increased freshwater inputs from melting coastal glaciers (Ardyna & Arrigo, 2020).

We attempt to quantify the impact of these evolving parameters on the Arctic marine microbiome, which is at the base of the marine food web and ecosystems. In particular, we develop meta-omics-based bioindicators, targeting bacterial plankton, and investigating community growth rates as a key ecological trait to study the global plankton response to environmental changes. This adaptive phenotypic trait, which has been shown to consistently vary with water temperature in non-Arctic bacteria (Abreu et al., 2023), can be estimated for single organisms and can also be averaged to capture the evolution of an entire community.

Here, we compare multiple methods linking omics data to growth rate and explore how the relationship between growth and temperature behaves in Arctic waters. We demonstrate its robustness by quantifying the impact of nutrients on the temperature-growth rate relationship. Finally, we integrate data from ocean and sea ice ecosystems collected during large-scale Arctic campaigns (i.e., TOPC, FRAM, MOSAIC, Refuge-Arctic) in order to decipher the spatiotemporal distribution of this relationship in the Arctic.

Altogether, this work will be instrumental to understand the various local responses of the Arctic microbiome ecosystems to contrasted perturbations.

How to cite: Gouzien, C., Joux, F., Chaffron, S., and Ardyna, M.: Towards marine microbiome community bioindicators for monitoring Arctic plankton in response to climate change, One Ocean Science Congress 2025, Nice, France, 3–6 Jun 2025, OOS2025-1144, https://doi.org/10.5194/oos2025-1144, 2025.

How to cite: Durand, P., Auffret, P., Goudenege, D., Noel, C., Leroi, L., and Cormier, A.: athENA and SAMBA: the Global Marine Biodiversity Data Management and Analysis Framework, One Ocean Science Congress 2025, Nice, France, 3–6 Jun 2025, OOS2025-1428, https://doi.org/10.5194/oos2025-1428, 2025.