Oceanographic drivers of carbon storage in European seagrass beds: Environmental datasets

This repository contains all environmental datasets that were downloaded and used in the Gallo, Timmerman et al. manuscript on Oceanographic Drivers of Carbon Storage in European Seagrass Beds, for submission to Phil. Trans. Royal. Soc. B for the Royal Society Special Issue on Marine Biodiversity Loss, Fishing, and Climate Change. All code for the analysis is available through Github (https://github.com/orlando-code/Royal_Society_seagrass_carbon_remote_sensing), however, due to Github file storage size limitations, the environmental data need to be downloaded from here and added to the "data" folder in the downloaded Github repository in order to run the pipeline. The env_rasters zip contains a folder with all the environmental raster files for the oceanographic datasets downloaded from NASA, Copernicus, or GEBCO. The ICES_ecoregions and MEOW zip folders contain associated shapefiles to allow for regional grouping. 

Below is some additional details regarding the environmental rasters present in the env_rasters folder (additional information is provided in the manuscript). 

Six remote sensing data products were downloaded from the NASA Sentinel-3A Ocean and Land Color Instrument (OLCI) sensor. These were the diffuse attenuation coefficient at 490 nm (KD490), remote sensing reflectance at 620 nm (RRS620), remote sensing reflectance at 443 nm (RRS443), the chlorophyll-a concentration (Chla) proxy, particulate backscatter at 443 nm (PBS443), and absorption due to gelbstoff and detritus at 443 nm (CDOM). Composite data from the full mission period (2016–2025) was used. These data products were downloaded from https://oceandata.sci.gsfc.nasa.gov/l3/order/ on March 11, 2025.

From the Copernicus Marine Data Store, we selected seven data products covering physical, biogeochemical, and carbon-related parameters. These included the Global Ocean Physics Reanalysis (https://doi.org/10.48670/moi-00021), the Global Ocean Waves Reanalysis (https://doi.org/10.48670/moi-00022), the Ocean Biogeochemistry Hindcast (https://doi.org/10.48670/moi-00019), the Global Ocean OSTIA Sea Surface Temperature and Sea Ice Reprocessed product (https://doi.org/10.48670/moi-00168), the Surface Ocean Carbon Fields product (https://doi.org/10.48670/moi-00047), the Global Ocean Gridded L4 Sea Surface Heights And Derived Variables Reprocessed product (https://doi.org/10.48670/moi-00145), and the Global Ocean L4 Significant Wave Height From Nrt Satellite Measurements product (https://doi.org/10.48670/moi-00180). These data products were downloaded from the Copernicus Marine Data Store using the Copernicus Marine Toolbox v1 in R between May 12-27, 2025. From these seven data products, 22 proxy variables were extracted. In all cases, we downloaded the full data product and calculated the mean value, and also in certain cases an extreme representative value (e.g. 5th, 90th, 95th percentile). Copernicus data products differed in terms of their spatial resolution (ranging from 0.083 - 2 degrees), temporal resolution, and the time period the data product was available for.

Additionally, we downloaded bathymetry data from the General Bathymetric Chart of the Oceans (GEBCO) (https://doi.org/10.5285/37c52e96-24ea-67ce-e063-7086abc05f29).

Datafiles for the seagrass EOV were downloaded from the ICES metadata catalog (https://gis.ices.dk/geonetwork/srv/eng/catalog.search#/metadata/39746d9c-4220-425c-bc26-7cb3056c36a5) on March 26, 2026. Both the point and polygon files were downloaded and used. Seagrass species (relevant to seagrass species categories present in the EURO-CARBON database) were assigned based on seabedtype categories in the points datafile, and for the polygon file based on the habsubtype, eunis_code, and anxi_name. Locations for seagrass species not contained in the EURO-CARBON database (e.g. Ruppia maritima, Halodule spp., Syringodium filiforme, Thalassia testudinum) were removed. Seagrass beds with no species information provided were assigned to "Unspecified". "Zostera beds" were assigned to "Zostera marina" since this was the more abundant species in the EURO-CARBON database; however Eunis_code A2.61 was assigned to Zostera noltei because it is in the code section with other Zostera noltei entries. 

To calculate estimated carbon stock per country, EEZ shapefiles were downloaded from https://www.marineregions.org/downloads.php. Citation: Flanders Marine Institute (2023). Maritime Boundaries Geodatabase: Maritime Boundaries and Exclusive Economic Zones (200NM), version 12. https://doi.org/10.14284/632 There is a request not to provide the download elsewhere, so we refer users to the website for access instead of providing it here. (Maritime boundaries (latest version) -- World EEZ v12 (2023-10-25, 122 MB) -- Shapefile). 

This work was part of T5.3 and was funded by the European Union under the Horizon Europe Programme, Grant Agreement No. 101082021 (MARCO-BOLO). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency (REA). Neither the European Union nor the granting authority can be held responsible for them. UK participants in MARCO-BOLO are supported by the UKRI’s Horizon Europe Guarantee under Grant No. 10068180 (MS); No. 10063994 (MBA) and No. 10048178 (NOC).