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 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

This metadata corresponds to the EUNIS Littoral biogenic habitat (salt marshes) types, predicted distribution of habitat suitability dataset. Littoral habitats are those formed by animals such as worms and mussels or plants (salt marshes). The verified littoral biogenic 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 modelled suitability for EUNIS saltmarsh habitat types is an indication of where conditions are favourable for the habitat type based on sample plot data (Braun-Blanquet database) and the Maxent software package. The modelled suitability map may be used as a proxy for the geographical distribution of the habitat type. However, note that it is not representing the actual distribution of the habitat type. As predictors for the suitabilty modelling not only Climate and Soil parameters have been taken into account, but also so-called RS-EVB's, Remote Sensing-enabled Essential Biodiversity Variables like Landuse, Vegetation height, Phenology, LAI(Leave Area Index) and Population density. Because the EBV's are restricted by the extent of the Remote Sensing data (EEA38 countries and the United Kingdom) the modelling result does also not go beyond this boundary. The dataset is provided both in Geodatabase and Geopackage formats. The Training map files show the modelled suitable distribution, omitting the 10% of occurrence records in the least suitable environment under the assumption that they are not representative of the overall suitable habitat distribution. The 10 percentile training presence is an arbitrary threshold which omits all regions with habitat suitability lower than the suitability values for the lowest 10% of occurrence records.

This metadata corresponds to the EUNIS Coastal habitat types, predicted distribution of habitat suitability 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 modelled suitability for EUNIS coastal habitat types is an indication of where conditions are favourable for the habitat type based on sample plot data (Braun-Blanquet database) and the Maxent software package. The modelled suitability map may be used as a proxy for the geographical distribution of the habitat type. Note however that it is not representing the actual distribution of the habitat type. As predictors for the suitability modelling not only climate and soil parameters have been taken into account, but also so-called RS-EVB's, Remote Sensing-enabled Essential Biodiversity Variables, like land use, vegetation height, phenology, and LAI (Leaf Area Index). Because the EBV's are restricted by the extent of the remote sensing data (EEA38 countries and the United Kingdom) the modelling result does also not go beyond this boundary. The dataset is provided both in Geodatabase and Geopackage formats.

Gridded Distribution of Species as reported during the Article 17 of the Habitats Directive (92/43/EEC) covering the period 2001 to 2006. The data covers the EU 25. All Member States are requested by the Habitats Directive (92/43/EEC) to monitor habitat types and species considered to be of Community interest. Article 17 of the Habitats Directive 92/43/EEC requires that every 6 years Member States prepare reports to be sent to the European Commission on the implementation of the Directive. The Article 17 report for the period 2001-2006 for the first time includes assessments on the conservation status of the habitat types and species of Community interest. Information on the data quality of the 2001-2006 reporting round is available at http://bd.eionet.europa.eu/article17.