The ABYSS project aims at describing deep-sea benthic biodiversity spanning several branches of the tree of life with eDNA metabarcoding tools. To accommodate both micro- and macro biologists, we designed a bioinformatic pipeline based on Illumina read correction with Dada2 allowing analysing metabarcodes from prokaryotic and eukaryotic life compartments.

Combination MPAs and monitoring stations for biodiversity elements

RESOMAR is a national network whose main objective is to bring together studies and monitoring programmes conducted at the network’s stations and observatories (Wimereux, Luc/Mer, Dinard, Roscoff, Brest, Concarneau, Ile d'Yeu, La Rochelle, Arcachon, Anglet, Banyuls, Perpignan, Sète, Marseille, Villefranche / Mer). Based on benthic and plankton community monitoring programmes implemented by the stations, one of RESOMAR’s objectives is to use this biological information in order to answer scientific questions, for example concerning the factors which control the distribution and abundance of organisms on different spatial and temporal scales. This monitoring information, the characteristics of which vary depending on the station (number of sites, frequency, continuous monitoring or not, communities observed, taxonomic resolution, observation methods, etc.) is brought together in two databases (RESOMAR/BENTHOS and RESOMAR/PELAGOS), which are currently being developed. The RESOMAR-PELAGOS database hosts biological data obtained by the pelagic aspects of RESOMAR (around fifteen programmes as of September 2012): http://abims.sb- roscoff.fr/pelagos/ This database in particular brings together observation data (long-term series, inventories, spatial studies, etc.).

Upon building a new waste pool for waste from oyster farming, a zostera noltii seagrass meadow was destroyed by sediment deposits. This site is located in the Arcachon basin and has been monitored since 2005 in order to evaluate the impact this of this work and the recolonisation of the site by benthic macrofauna.

The EEA coastline for analysis is created for highly detailed analysis, e.g. 1:100 000, for geographical Europe. The coastline is a hybrid product obtained from projects using satellite imagery as data source: EUHYDRO (https://land.copernicus.eu/imagery-in-situ/eu-hydro) and GSHHG (http://www.soest.hawaii.edu/pwessel/gshhg/). The defining criteria was altitude level = 0 from EUDEM (https://land.copernicus.eu/pan-european/satellite-derived-products/eu-dem/view). Outside the coverage of the EUDEM, the coastline from GSHHG was used without modifications. A few manual amendments to the dataset were necessary to meet requirements from EU Nature Directives, Water Framework Directive and Marine Strategy Framework Directive. In 2015, several corrections were made in the Kalogeroi Islands (coordinates 38.169, 25.287) and two other Greek little islets (coordinates 36.766264, 23.604318), as well as in the peninsula of Porkkala (around coordinates 59.99, 24.42). In this revision (v3, 2017), 2 big lagoons have been removed from Baltic region, because, according to HELCOM, are freshwater lagoons.

The grid is based on proposal at the 1st European Workshop on Reference Grids in 2003 and later INSPIRE geographical grid systems. The sample grid available here is part of a set of three polygon grids in 1, 10 and 100 kilometres. The grids cover at least country borders and, where applicable, marine Exclusive Economic Zones v7.0, http://www.marineregions.org. Note that the extent of the grid into the marine area does not reflect the extent of the territorial waters.

The grid is based on proposal at the 1st European Workshop on Reference Grids in 2003 and later INSPIRE geographical grid systems. The sample grid available here is part of a set of three polygon grids in 1, 10 and 100 kilometres. The grids cover at least country borders and, where applicable, marine Exclusive Economic Zones v7.0, http://www.marineregions.org. Note that the extent of the grid into the marine area does not reflect the extent of the territorial waters.

Zooplankton monitoring (essentially metazoal) – mesozooplankton in the Gironde estuary (3 stations) since 1997 Locations : 3 Stations pK86 : 45°31’N, 01°57’W, pK52 : 45°14’80’’N, 0°43’50’’W pK30 : 45°04’10’’N, 0°38’30’’W

EVHOE surveys have been providing observational data on bentho-demersal communities on the continental shelves of the Bay of Biscay and the Celtic Sea for more than 30 years. The surveys operate a standardized fishing gear and are conducted on the continental shelves from 15 to 600 m depth, usually in the fourth quarter of the year, starting at the end of October. The main objectives are the monitoring of 22 stocks of benthic fish species and 10 cephalopods from the North-East Atlantic. The data also provide a description of regional diversity by including 250 taxa of fish and 45 taxa of cephalopods and others “commercial” invertebrates. The dataset is structured in 3 tables providing information on stations, numbers, biomass of observed species and size distributions for a selection of species. This dataset is of great interest for the long-term monitoring of the continental shelves of the Bay of Biscay and the Celtic Sea. Moreover, on a larger scale, by being integrated into a European network of bottom trawl surveys, these data play an essential role in studying the evolution of ecosystems from continental shelves to the scale of the eastern North Atlantic.

This metadata corresponds to the EUNIS Coastal habitat types, distribution based on vegetation plot data dataset. Coastal habitats are those above spring high tide limit (or above mean water level in non-tidal waters) occupying coastal features and characterised by their proximity to the sea, including coastal dunes and wooded coastal dunes, beaches and cliffs. Includes free-draining supralittoral habitats adjacent to marine habitats which are normally only very rarely subject to any type of salt water, in as much as they may be inhabited predominantly by terrestrial species, strandlines characterised by terrestrial invertebrates and moist and wet coastal dune slacks and dune-slack pools. Supralittoral sands and wracks may be found also in marine habitats (M). Excludes supralittoral rock pools and habitats, the splash zone immediately above the the mean water line, as well the spray zone and zone subject to sporadic inundation with salt water in as much as it may be inhabited predominantly by marine species, which are included in marine (M). The verified coastal habitat samples used are derived from the Braun-Blanquet database (http://www.sci.muni.cz/botany/vegsci/braun_blanquet.php?lang=en) which is a centralised database of vegetation plots and comprises copies of national and regional databases using a unified taxonomic reference database. The geographic extent of the distribution data are all European countries except Armenia and Azerbaijan. The dataset is provided both in Geodatabase and Geopackage formats.