The Mediterranean Sea is shaped by gradients, measurable spatial changes in environmental conditions such as temperature, salinity, nutrients, and oxygen. These variations form a dynamic three-dimensional structure in the water column, which modern tools can increasingly map at high resolution.
But gradients are not only physical and chemical. Living communities add complexity, especially in the microbial world, where microorganisms both respond to environmental change and actively create chemical gradients through their metabolism.
Understanding this 3D mosaic of interacting physical, chemical, and biological processes is one of today’s major scientific challenges.
In Workshop Monograph No. 53, CIESM brings together experts from 16 countries to advance new approaches for mapping and visualizing high-resolution marine data opening the way to a more integrated view of the Mediterranean Sea.
Revolutionary 3D visualization technology
A central component of the workshop was the further development of the pilot CIESM 3D visualization tool, a versatile platform designed to integrate and explore diverse datasets (biological, physical, chemical, and genetic parameters) within realistic 3D bathymetric environments. While the workshop addressed broader scientific questions on marine gradients, it also provided a unique opportunity to advance dedicated prototypes for visualizing complex spatial variability.
The tool enables volumetric representations of nutrient hotspots and biogeochemical structures, facilitating the interpretation of variations across depth and across the basin.
Key demonstrations included:
• Basin-scale variability in the Mediterranean: large temperature contrasts between the western and eastern sub-basins, and nitrate distributions linked to Atlantic water inflow, illustrating how water masses can be tracked through physical and chemical signatures.
• MetaCube prototype: extending 3D visualization to microbial metabolic networks, from marine systems to the human gut, highlighting how environmental or dietary factors shape community function.
• Extreme-environment sampling: advanced methodologies to resolve sharp physicochemical gradients at deep hypersaline interfaces (>3,400 m depth), including investigations of the Hephaestus brine lake.
Advanced data integration
The CIESM 3D tool is designed to handle a wide diversity of datasets, from classical gridded geological and oceanographic fields to more heterogeneous chemical, biological, and molecular observations that require specific structuring to be effectively explored. By organizing these data types within a coherent 3D framework, the platform helps users address targeted scientific questions and generate new hypotheses.
The system can incorporate data from major international repositories, including GEBCO, EMODnet, MGnify, Tara Oceans, ODATIS, and GEOTRACES.
Complementary analytical approaches were also discussed. Environmental niche clustering supports the identification of coherent ecological patterns. MetaDAG helps simplify and interpret metabolic pathway networks. The Microbiome MetaCube focuses on comparing molecular datasets such as metabolic pathways or taxonomic composition supporting the exploration of similarities and differences between samples, including across natural microbial communities distributed along physical or chemical transitions.
Data governance framework
Beyond technical innovation, the workshop also considered broader challenges related to ocean data governance. Discussions addressed legal and ethical aspects linked to international frameworks such as UNCLOS, as well as emerging questions associated with AI-based tools, including data ownership, traceability, and responsibility in data use.
Future perspectives
Developed with an emphasis on open access, the pilot CIESM 3D visualization tool represents a transformative approach to marine data science. By unifying geological, physicochemical, and biological data in a coherent 3D environment, CIESM positions the Mediterranean region at the forefront of addressing biodiversity loss, climate change, and pollution through science-based cooperation.
This monograph is an essential reference for researchers, data scientists, policymakers, and legal experts working to unlock the full potential of high-resolution ocean data.
The CIESM 3D visualization tool will be made available online soon
🔗 Access WM No. 53 here: https://ciesm.org/online/monographs/full/CIESM_Workshop_Monograph_53.pdf