Periodic Reporting for period 1 - BIOcean5D (MARINE BIODIVERSITY ASSESSMENT AND PREDICTION ACROSS SPATIAL, TEMPORAL AND HUMAN SCALES)
Période du rapport: 2022-12-01 au 2024-05-31
Marine biodiversity sustains ecosystem services for planetary and human health. Recent surveys of marine ecosystems have unveiled our ignorance of the richness and functioning of marine life, which is changing at a faster rate than terrestrial life in the Anthropocene. BIOcean5D (B5D) unites major EU centers in molecular/cell biology (EMBL), marine biology (EMBRC), and sequencing (Genoscope), together with 26 partners from 11 countries along the European coastline, to build a unique suite of technologies and protocols allowing holistic re-exploration of marine biodiversity, from viruses to mammals, from genomes to holobionts, across exceptional spatial and temporal scales from pre-industrial to modern time. A focus is given on understanding pan-European marine biodiversity in waters, sediments, and the air, across land-to-sea gradients, with notably the TREC expedition which deploys in 2023/24 mobile labs, research vessels including the schooner Tara, and innovative citizen science tools, through 21 European coastal countries and 35 marine labs from the Baltic to the Mediterranean seas. The new data is harmonized with existing ones into a B5D data hub leveraging international infrastructures, and generating transformative, cross-technologies/cross-scales standard marine biodiversity knowledge at socio-ecosystem level. Knowledge will inform and constrain (i) new theories and models of marine biodiversity ecological and evolutionary dynamics and drivers, at both taxonomic and functional scales, (ii) a portfolio of novel holistic indicators of marine ecosystem health, (iii) innovative methods and protocols for economic and legal valuations of marine biodiversity and services integrating the dynamical and functional complexity of marine life. Overall, B5D has been thought as a powerful aggregator, bridging molecular/subcellular to organismal biology, theoretical ecology and econometrics, and marine complex systems to social sciences, toward sustainable preservation of our oceans and seas.
Toward our first objective to ‘close the marine biodiversity and ecosystem knowledge gap’, we have generated, during the first 18 months of the project, arguably the most complete set of biological samples and contextual data across marine ecosystems and biomes to date. In May 2023, the TREC/Tara EUROPA expedition had holistically sampled marine waters, sediments, aerosols, and holobionts across >100 Land-Sea transects along the European coastline from Finland to Italy. >150 standard protocols were systematically applied to sample life, from viruses to animals, across biocomplexity scales (molecular, subcellular, to organismal and community) together with key contextual parameters including pollutants. This has generated >35,000 samples stored and registered at the EMBL Planetary Biology Biobank. Furthermore, 60 1m-sediment cores were collected at 12 sites along the way, covering time periods ranging from the early 20th century to the 18th century, and providing >10,000 samples for various chemical and paleoecological analyses including paleo-DNA sequencing. Data and biomass samples from weekly or bi-weekly ecosystem time series performed in Naples, Banyuls, Blanes, Azti, Roscoff and Plymouth over the last 2-3 decades, were assembled and partly re-sequenced for cross time-series comparisons. Marine waters and sediments across land-sea transects were also sampled along seasons in Roscoff and Naples, using TREC-compatible protocols, with 10 sampling campaigns achieved since April 2023. Finally, 80% of the planned samples from 15 keystone holobionts were collected across critical ecological dimensions of their habitats, including plankton, kelp forests, seagrasses, shallow and deep sea reefs.
To understand the drivers and mechanisms of marine biodiversity structure and dynamics, and determine which element of biodiversity are key for marine ecosystems functions and services, the first 18 months of the project were mainly spent on developing new theoretical models, assembling large-scale meta-datasets to develop statistical indicators and models to monitor and predict marine biodiversity changes, and building associated softwares. On the one hand, we have explored various novel ways of modeling marine biodiversity across levels of biological organization: (i) based on biological and physiological traits, (ii) integrating population drift, neutral heritable variation, and dispersal across the seascape, (iii) assembling comprehensive metabolic knowledge from metagenomes and metatranscriptomes, (iv) linking eco-evolutionary mechanisms of species interactions to ecosystem functions. On the other hand, we have compiled and completed large datasets - e.g. eDNA metabarcoding, fish-catch, phytoplankton microscopy, soundscapes, etc., together with environmental metadata - to build up statistical indicators and models of marine ecosystems status and health. Integrating across inclusive spatial, temporal, and/or organismal/biological dimensions, these data-driven models are used as new tools to quantify the impact of local (aquacultures, fisheries, invasive species) and global (natural versus anthropogenic climate and environmental changes) drivers on marine biodiversity and ecosystem functions.
To understand the drivers and mechanisms of marine biodiversity structure and dynamics, and determine which element of biodiversity are key for marine ecosystems functions and services, the first 18 months of the project were mainly spent on developing new theoretical models, assembling large-scale meta-datasets to develop statistical indicators and models to monitor and predict marine biodiversity changes, and building associated softwares. On the one hand, we have explored various novel ways of modeling marine biodiversity across levels of biological organization: (i) based on biological and physiological traits, (ii) integrating population drift, neutral heritable variation, and dispersal across the seascape, (iii) assembling comprehensive metabolic knowledge from metagenomes and metatranscriptomes, (iv) linking eco-evolutionary mechanisms of species interactions to ecosystem functions. On the other hand, we have compiled and completed large datasets - e.g. eDNA metabarcoding, fish-catch, phytoplankton microscopy, soundscapes, etc., together with environmental metadata - to build up statistical indicators and models of marine ecosystems status and health. Integrating across inclusive spatial, temporal, and/or organismal/biological dimensions, these data-driven models are used as new tools to quantify the impact of local (aquacultures, fisheries, invasive species) and global (natural versus anthropogenic climate and environmental changes) drivers on marine biodiversity and ecosystem functions.
The B5D sampling strategy and standardized protocols was published in a 273 pp. ‘Handbook’ that will serve as a reference for future holistic explorations of marine ecosystems in other parts of the world. The collection of thousands of consistent samples across taxa and biological organization, ecosystems, and natural and anthropogenic environmental variations, represent the most complete and consistent new source of information to assess the structure and dynamics of marine biodiversity across space, time, and the environment - 5D. It will not only feed B5D developments of theoretical and data-driven models, but will also generate the most comprehensive multiscale data baseline allowing integration of marine ecosystems into the emerging field of ‘planetary systems biology’. Together with the recruitment of already 44 ECRs in the project, contributing to the future EU task force in marine science, the B5D biobank and datahub will generate new knowledge and understanding for many years beyond the duration of the project.