Key Expoitable Results (KERs)

Marine planktonic communities carry out almost half of the net primary production on our planet, keep atmospheric CO2 levels at roughly half of what they would be otherwise, form the base of food webs and produce more than half of the oxygen we breathe. Considering the wealth and economic importance of ecosystem services and climate regulation provided by our oceans fuelled from the very base of its food web, impacts of climate change on marine plankton are still poorly investigated. Within this project we aim to overcome disciplinary boundaries that contribute to impeding exchanges of scientific results between the research community and policy makers. We aim to build an interactive web tool for policy makers to help visualise future projections of climate change impact on global plankton ecosystems as a function of societal decisions. We continue the effort made by the ETH Environmental Physics (UP) Group (Zürich, Switzerland) that has mapped the biogeography of hundreds of plankton species and use this knowledge to define biomes for the surface ocean and identify hotspots of plankton diversity changes under global warming. We aim to include three fully coupled Earth System Models from the Coupled Model Intercomparison Project Phase CMIP5 using three different representative concentration pathways (RCP 2.6, RCP 4.5, RCP 8.5) covering the period from 2012 until 2100. We will translate projections into quantitative global impact metrics targeted at policy makers and characterize ecosystem impacts as a function of carbon emissions and global warming. International decision-makers are informed on potential future changes in global marine plankton and can start addressing challenges to marine conservation.

This latest release (v2.0) of the marine catalogue contains data from 1628 studies, including genomes from major sampling expeditions such as Tara Oceans, Malaspina, GO-Ship, and Geotraces, amongst others. An important advancement in this version of the catalogue is that it is representative of the marine genomes available in the public archives at the time of generation. It includes not only those generated and submitted by MGnify, but also MAGs generated by other groups and submitted to the INSDC, as well as isolate genomes (and MAGs) from marine data as curated by MarDB. All genomes undergo the same filtering for a quality score of QS50 (QS, quality score, defined as completeness - 5 x contamination) resulting in a total of 50,866 genomes (50,634 MAGs and 232 isolates) included in v2.0 of the MGnify Genomes marine catalogue. This catalogue was generated using v2.3.0 of the MGnify Genomes catalogue pipeline which is available on GitHub and WorkflowHub. Genomes are clustered into 13,223 species-level clusters, with a cluster representative genome defined for each. GTDB-Tk (Genome Taxonomy DataBase Toolkit) is used to assign a taxonomic rank to the clusters, allowing us to also understand the proportion of genomes within the catalogue which can be considered novel with respect to the current release of GTDB. As with all MGnify Genomes catalogues, the data is available to access and query both through the MGnify website as well as via the MGnify API. The catalogue can be browsed as a list of genomes, with the ability to filter on metadata fields, or a taxonomic tree providing access to individual cluster representative genome records. Within the individual genome records there are comprehensive genome statistics, summaries of annotations, and an interactive genome browser allowing interrogation of the various annotation tracks and their genomic context. All results files can be downloaded via HTTP or FTP from the catalogue directory. There are also two sequence-based search options that can be carried out via the website or API. The first is a COBS (COmpact Bit-sliced Signature index)-based query for searching gene sequences against the catalogues. The second is a kmer-based search using Sourmash to allow querying of whole genomes or sets of genomes against the catalogues.

Every few years, juvenile Kemp’s ridley turtles (Lepidochelys kempii) are stranded on the Dutch coasts. The main population distribution of this critically endangered species primarily inhabits the Gulf of Mexico and the east coast of the United States. This study focuses on five reports from the Netherlands between 2007 and 2022, where juvenile turtles were reported to strand alive during the winter, albeit in a hypothermic state. At ambient ocean temperatures between 10°C and 13°C, Kemp’s ridley turtles begin to show an inability to actively swim and remain afloat on the ocean’s surface, a condition termed ‘cold stunning’. Understanding their transport in cold-stunned state can help improve the rehabilitation process of stranded turtles. Cold-stunned turtles are back-tracked as passive, virtual particles from their stranding location using Lagrangian flow modelling. This study investigates when and where these juvenile turtles cross the threshold temperatures between 10° C and 14° C before stranding by tracking the temperature along the trajectories. As expected, the simulations show the transport of the cold-stunned turtles via the English Channel. More surprisingly, the analysis suggests they likely experience cold-stunning in the southern North Sea region and encounter temperatures below 10°C for only a few days to up to three weeks, and below 12°C for up to a month before stranding. The estimate of cold-stunned drift duration of the turtles provides additional knowledge about their health status at the time of stranding. Adherence to rehabilitation protocols for Kemp’s ridley and post-release monitoring are recommended to improve their long-term survival.

The present deliverable (D4.2) constitutes version 2 of the Handbook of Standards and Best Practices regarding AtlantECO's augmented observations and technological innovations as described in Work Package 4. The Handbook will be developed throughout the project and will be delivered progressively as four revised and augmented deliverables (D4.1-D4.4). The Handbook will address standards and best practices with respect to: Sample collection, Sample biobanking, Sample analysis, Access and Benefits Sharing, Provenance reporting, and Environmental context reporting. AtlantECO will generate new observations as part of the activities described in its Grant Agreement and also via a number of synergies with other European and International projects. The Handbook aims to harmonise as much as possible the methodologies used across these projects on some key types of observations, while allowing enough flexibility to adapt methodologies to the different observation programmes, therefore maximising the adoption of the standards and best practices.