High-Resolution Digital Elevation Model (HRDEM) generated from LiDAR. This data collection includes a Digital Terrain Model (DTM) and a Digital Surface Model (DSM). The HRDEM product is referenced to the Canadian Geodetic Vertical Datum of 2013 (CGVD2013). Source data for HRDEM datasets is acquired through multiple projects with different partners. Since data is being acquired by project, there is no integration or edgematching done between projects. The data in this collection have been reprojected from the source reference system to the Canada Atlas Lambert projection (EPSG:3979). **This third party metadata element follows the Spatio Temporal Asset Catalog (STAC) specification.**

This data report provides information on temperature and salinity in the Godbout region of the St. Lawrence Estuary. Sampling was carried out from 2019 to 2021 over an area of <5 km2. The databases provide information on temperature and salinity at an hourly rate for 2 years. The aim of this project is to analyze telemetry data from sea urchins (Strongylocentrotus droebachiensis), snow crabs (Chionoecetes opilio), rock crabs (Cancer irroratus), spider crabs (Hyas spp.) and whelks (Buccinum undatum). This report focuses on the presentation of benthic environmental data collected throughout the study with high spatial and temporal resolution. All reported variables were collected at the seafloor, as the aim of the project was to study the movement of epibenthic species. Temperature data were collected from three devices: telemetry receivers with integrated temperature sensors (InnovaseaTM), HoboTM and Star-OddiTM probes. Temperature data processing involved cleaning up extreme values (below 2°C and above 20°C) and homogenizing the data to fit the bathymetry matrix (1m x 1m cells) of the study site. Temperature data are provided in a NetCDF file with a matrix of the entire study site, where there is a stratum for each hour between August 2019 and October 2021 and in each file, a temperature value for each pixel of the raster. Salinity data were collected from Star-OddiTM probes only. Salinity values were averaged hourly for the entire study area. Salinity data is provided as a CSV file with one salinity value per hour for the entire study area.

High-Resolution Digital Elevation Model (HRDEM) generated from LiDAR. This data collection includes a Digital Terrain Model (DTM) and a Digital Surface Model (DSM). The HRDEM product is referenced to the Canadian Geodetic Vertical Datum of 2013 (CGVD2013). Source data for HRDEM datasets is acquired through multiple projects with different partners. Since data is being acquired by project, there is no integration or edgematching done between projects. The data in this collection have been reprojected from the source reference system to the Canada Atlas Lambert projection (EPSG:3979). **This third party metadata element follows the Spatio Temporal Asset Catalog (STAC) specification.**

High-Resolution Digital Elevation Model (HRDEM) generated from LiDAR. This data collection includes a Digital Terrain Model (DTM) and a Digital Surface Model (DSM). The HRDEM product is referenced to the Canadian Geodetic Vertical Datum of 2013 (CGVD2013). Source data for HRDEM datasets is acquired through multiple projects with different partners. Since data is being acquired by project, there is no integration or edgematching done between projects. The data in this collection have been reprojected from the source reference system to the Canada Atlas Lambert projection (EPSG:3979). **This third party metadata element follows the Spatio Temporal Asset Catalog (STAC) specification.**

High-Resolution Digital Elevation Model (HRDEM) generated from LiDAR. This data collection includes a Digital Terrain Model (DTM) and a Digital Surface Model (DSM). The HRDEM product is referenced to the Canadian Geodetic Vertical Datum of 2013 (CGVD2013). Source data for HRDEM datasets is acquired through multiple projects with different partners. Since data is being acquired by project, there is no integration or edgematching done between projects. The data in this collection have been reprojected from the source reference system to the Canada Atlas Lambert projection (EPSG:3979). **This third party metadata element follows the Spatio Temporal Asset Catalog (STAC) specification.**

High-Resolution Digital Elevation Model (HRDEM) generated from LiDAR. This data collection includes a Digital Terrain Model (DTM) and a Digital Surface Model (DSM). The HRDEM product is referenced to the Canadian Geodetic Vertical Datum of 2013 (CGVD2013). Source data for HRDEM datasets is acquired through multiple projects with different partners. Since data is being acquired by project, there is no integration or edgematching done between projects. The data in this collection have been reprojected from the source reference system to the Canada Atlas Lambert projection (EPSG:3979). **This third party metadata element follows the Spatio Temporal Asset Catalog (STAC) specification.**

The North Shore of the Lower Estuary (Upper North Shore, Quebec) is a productive coastal system where many commercial species of benthic invertebrates are fished in the infralittoral (10-20 m) and circalittoral (20-50 m) zone. However, little data exist on the biodiversity of non-commercial species and the environmental characteristics of the benthic habitat in this area. Two scientific surveys were conducted in 2018 and 2019 to address this knowledge gap by developing a framework of biodiversity and environmental (water column and seafloor) data taking that will be used to determine the baseline state of the benthic ecosystem in this region.Surveys were conducted in 2018 (August 11-14) and 2019 (July 30-August 5) in the Upper North Shore region (between the towns of Forestville and Godbout). Surveys followed a fixed sampling design of eight transects perpendicular to bathymetry with stations at 10 m depth intervals in a bathymetry range of 10-50 m for a total of approximately 40 stations per survey. Specimens were collected with a beam trawl with an opening of 2.8 m. The hauls were made at a target speed of 2 knots and a target duration of 7 minutes. Start and end positions were recorded to calculate the distance traveled on each tow using the geosphere library of R. The average tow distance was approximately 425 m. The area covered at each tow was the product of the trawl opening and the distance traveled. The three files provided (DarwinCore format) are complementary and are linked by the "eventID" key. The "event_information" file includes generic event information, including date and location. The "additional_information_event_and_occurrence" file includes sample size, sampling protocol and sampling effort, among others. The "taxon_occurrence" file includes the taxonomy of the species observed, identified to the species or lowest possible taxonomic level. For abundance and biomass estimates, contact Virginie Roy (virginie.roy@dfo-mpo.gc.ca). For quality controls, all taxonomic names were checked against the World Register of Marine Species (WoRMS) to match recognized standards. The WoRMS match was placed in the "scientificNameID" field of the occurrence file. Special cases were noted in "identificationRemarks" and selected specimens were confirmed using field photos. Data quality checks were performed using the R obistools and worrms libraries. All sampling locations were spatially validated.This project was funded by DFO Coastal Environmental Baseline Program under Canada’s Oceans Protection Plan. This initiative aims to acquire environmental baseline data contributing to the characterization of important coastal areas and to support evidence-based assessments and management decisions for preserving marine ecosystems.

Species characterization by environmental DNA (eDNA) is a method that allows the use of DNA released into the environment by organisms from various sources (secretions, faeces, gametes, tissues, etc.). It is a complementary tool to standard sampling methods for the identification of biodiversity. This project provides a list of invertebrates species whose DNA has been detected in water samples collected at 2018 using the marker COI.The surveys were carried out in the summer of 2018 from August 11 to 14, between Forestville and Godbout (Haute-Côte-Nord). Sampling was carried out between 9-52 meters depth in 40 stations with one sample par station. Two liters of water were filtered through a 1.2 µm fiberglass filter. DNA extractions were performed with the DNeasy Blood and Tissue extraction kit (Qiagen). Negative field, extraction and PCR controls were added at the different stages of the protocol. Libraries at the COI locus were prepared by Genome Quebec and sequenced on an Illumina MiSeq PE250 system. The bioinformatics analysis of the sequences obtained was carried out using an in-house analysis pipeline as reported in Bourret et al. 2022. A first step made it possible to obtain a molecular operational taxonomic unit table (MOTU) using the cutadapt software for the removal of the adapters and the DADA2 R package for the filtration, fusion, chimera removal and data compilation. The MOTUs table was subsequently corrected by taking into account the negative controls, where the number of observations in the latter was removed from the linked samples. Singleton MOTUs have also been removed. Finally, the taxonomic assignments were carried out on the MOTUs using the IDTAXA classifier (present in the DECIPHIER R package) using a training set trained on the COI reference bank for Golf St-Laurent (GSL-rl v1.0, https://github.com/GenomicsMLI-DFO/MLI_GSL-rl) and a threshold of 40. Detections with an “Unreliable due to gaps” category were reported at the genus level only.The file provided includes generic activity information, including site, station name, date, marker type, assignment types used for taxa identification, and a list of taxa or species. The list of taxa has been verified by a biodiversity expert from the Maurice-Lamontagne Institute.This project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline Data Program under the Oceans Protection Plan. This initiative aims to acquire baseline environmental data that contributes to the characterization of significant coastal areas and supports evidence-based assessments and management decisions to preserve marine ecosystems.Data are also available on SLGO platform : https://doi.org/10.26071/ogsl-cd4c205b-f63b

Species characterization by environmental DNA (eDNA) is a method that allows the use of DNA released into the environment by organisms from various sources (secretions, faeces, gametes, tissues, etc.). It is a complementary tool to standard sampling methods for the identification of biodiversity. This project provides a list of fish and marine mammal species whose DNA has been detected in water samples collected between 2019 and 2021 using the mitochondrial marker MiFish (12S).The surveys were carried out in the summer of 2019 (July 14-18) and (July 30 - August 5), in the fall of 2020 (October 27-28) and in the summer-fall of 2021 (May 31 - June 3 ) and (August 24-25) between Forestville and Godbout (Haute-Côte-Nord). Sampling was carried out between 1-50 meters depth in 91 stations, with 1 to 3 replicates per station. Two liters of water were filtered through a 1.2 µm fiberglass filter. DNA extractions were performed with the DNeasy Blood and Tissues or PowerWater extraction kit (Qiagen). Negative field, extraction and PCR controls were added at the different stages of the protocol. The libraries were prepared either by Génome Québec (2019, 2020) or by the Genomics Laboratory of the Maurice-Lamontagne Institute (2021), then sequenced on a NovaSeq 4000 PE250 system by Génome Québec. The bioinformatics analysis of the sequences obtained was carried out using an analysis pipeline developed in the genomics laboratory. A first step made it possible to obtain a table of molecular operational taxonomic units (MOTU) using the cutadapt software for the removal of the adapters and the R package DADA2 for the filtration, the fusion, removal of chimeras and compilation of data. The MOTUs table was then corrected using the R package metabaR to eliminate the tag-jumping and take contaminants into consideration. Samples showing a strong presence of contaminating MOTUs were removed from the dataset. The MOTUs were also filtered to remove all remaining adapter sequences and also retain only those of the expected size (around 170 bp). Finally, taxonomic assignments were made on the MOTUs using the BLAST+ program and the NCBI-nt database. Taxonomic levels (species, genus or family) were assigned using a best match method (Top hit), with a threshold of 95%. Only assignments at the level of fish and marine mammals were considered, and the taxa detected were compared to a list of regional species, and corrected if necessary. The species detections of the different replicas have been combined.The file provided includes generic activity information, including site, station name, date, marker type, assignment types used for taxa identification, and a list of taxa or species. The list of taxa has been verified by a biodiversity expert from the Maurice-Lamontagne Institute.This project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline Data Program under the Oceans Protection Plan. This initiative aims to acquire baseline environmental data that contributes to the characterization of significant coastal areas and supports evidence-based assessments and management decisions to preserve marine ecosystems.Data were also published on SLGO platform : https://doi.org/10.26071/ogsl-2239bca5-c24a

This dataset derives from a series of beam trawl tows conducted during several research surveys in coastal areas of the St. Lawrence Estuary, between Portneuf-sur-Mer and Pointe-des-Monts, and between June and October of 2019, 2020, 2021 and 2022. It contains catch data for fish and invertebrates (occurrence and catch weights by species), in trawl tows conducted at depths ranging from 10 to 50 meters. Data were collected in various cruises:• June 28th to July 5th 2019 (NGCC Leim)• September 30th to October 9th 2019 (NGCC Leim)• October 1st to October 10th 2020 (NGCC Leim)• April 22nd to May 5th 2021 (NGCC Perley)• October 15th to October 24th 2021 (NGCC Perley)• June 24th to July 15th 2022 (NGCC LEIM)The beam trawl used to generate this data set consists of a frame (width of 2.8 m, height of 0.8 m) equipped with a 6.5 m long net with 40 mm diamond mesh, which is lined with a net (skirt) of square mesh (5 mm) at the cod-end (length 2 m) and a protective apron (75 mm mesh) on the ventral portion. Three skid chains are linked at the base of the skates. Each station corresponds to a 5 to 10 minutes tow along an isobath at a speed of about 2 knots. At each haul, the trawl catch was placed on a sorting table on the deck and the organisms were sorted and identified at the best possible taxonomic resolution. Most taxa were independently weighed. Some invertebrates taxa were subsampled, counted and weighted in order to estimate their contribution (weight and number) to the total catch. Additionally, the first 30 fish of each species were measured and weighed individually.Taxonomic names were verified on the World Register of Marine Species (WoRMS) to match recognized standards. The WoRMS match has been put in the scientificNameID field in the occurrence file. Data quality control was performed using the R packages obistools and worrms. All sampling locations were plotted on a map to perform a visual check confirming that the latitude and longitude coordinates were within the described sampling area. Data acquired during the research surveys additionally included: 1) occurrence data on epibenthic invertebrates and submerged aquatic vegetation in photo samples from a drop camera system, 2) occurrence data on fish and invertebrate taxa in video samples collected using a baited underwater video system (BUV), 3) substrate classification based on drop camera photo samples, 4) oceanographic measurements of the water column from Seabird 19plus V2 profiling CTD (conductivity, temperature, depth, photosynthetic active radiation, pH, dissolved oxygen), 5) nutrients (NO2, NO3, NH4, PO4, SiO3) and dissolve organic carbon (DOC) concentrations, and 6) current speed and direction from tilt meters. The first two items are available as independent data on the OBIS portal. To obtain data from items 3-6 and/or biological data collected on fish and invertebrate taxa, please contact David Lévesque or Marie-Julie Roux.The research surveys were undertaken by the Department of Fisheries and Oceans Canada as part of the baseline program of the Ocean Protection Plan. This initiative aimed to acquire environmental baseline data contributing to the characterization of important coastal areas and in support of evidence-based assessments and management decision-making for preserving marine ecosystems.Which contribute to the elaboration of conservation objectives based on an ecosystem assessment approach for fishery stock assessment requires the development of sampling methods to maximize the data collection on the ecosystem, while minimizing the impact on organisms and the marine environment. This project aims at characterising the coastal ecosystem of the St. Lawrence Estuary between Portneuf-sur-Mer and Godbout (QC), including the physico-chemistry of water, phytoplankton, zooplankton, submerged vegetation, benthic habitats as well as assemblages of fish and invertebrates. Sampling was performed by combining conventional methods such as CTD profiling, zooplankton nets, and beam trawl, with non-extractive methods such as dropped photo cameras and stereoscopic baited video camera systems. The data collected will help define baseline ecosystem conditions in the study area; explore the links between environmental conditions, habitat structure and biological assemblages; identify important habitats for marine species; as well as the evaluation of the performance of visual sampling methods compared to conventional methods. The results will make it possible to optimize the seasonal or annual monitoring in order to better understand the direct and indirect effects of human activities in coastal environments.This project was funded by the Department of Fisheries and Oceans Canada as part of the baseline program of the Ocean Protection Plan.