oih/oih-wis2 huggingface dataset:
Use of the COI Marker for the Development of an Approach for Characterizing Coastal Species Using Environmental DNA (eDNA)

Keywords: production, ckan
Temporal coverage: 2018-08-11/2018-08-14

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 invertebrate species whose DNA has been detected in water samples collected in 2018 using the mitochondrial marker COI.

The surveys were carried out in the summer of 2018 from August 11 to 14, between Forestville and Godbout (Haute-Côte-Nord) from the vessel CCGC Leim. 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 Gulf of St. Lawrence](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 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.
Coastal development, Driver of Environmental Change: eDrivers Project for the St.Lawrence System

Keywords: production, ckan
Temporal coverage: 2015-01-01T00:00:00

Terrestrial stable lights at night mostly represent light from human settlements and industrial sites with electricity. We thus used lights at night as a proxy of coastal infrastructure development.

The data come from the Nighttime Lights Time Series. Nighttime light products are compiled by the Earth Observation Group at the National Oceanic and Atmospheric Administration’s (NOAA) National Centers for Environmental Information (NCEI). They use globally available nighttime data obtained from the Visible Infrared Imaging Radiometer Suite (VIIRS) Day/Night Band (DNB) of the Defense Meteorological Satellite Program (DMSP) to characterize global average radiance composite images at a 15 arc-second (~200 m) resolution.

We used the annual Version 1 Nighttime VIIRS DNB composites between 2015 and 2016 to characterize coastal development in coastal areas of the St. Lawrence.

It is possible to consult the scientific report of the **eDrivers** project: [Characterizing Exposure to and Sharing Knowledge of Drivers of Environmental Change in the St. Lawrence System in Canada](https://www.frontiersin.org/articles/10.3389/fmars .2020.00383/full) and the [additional data](https://www.frontiersin.org/articles/10.3389/fmars.2020.00383/full#supplementary-material). It is possible to consult the application [eDrivers](https://catalogue.ogsl.ca/dataset/ca-cioos_7c51ad5f-c2a9-4f4a-a78c-0b652e630825).

**REFERENCE:**

[Christopher D Elvidge, Kimberly Baugh, Mikhail Zhizhin, Feng Chi Hsu & Tilottama Ghosh (2017) VIIRS night-time lights, International Journal of Remote Sensing, 38:21, 5860-5879, DOI: 10.1080/01431161.2017.1342050](https://www.tandfonline.com/doi/full/10.1080/01431161.2017.1342050)
Distribution and relative abundance of diadromous fishes in Placentia Bay, Newfoundland and Labrador in 2020

Keywords: oceans, abundance-and-biomass, abondance-et-distribution-de-poissons, abondance-et-biomasse, invasive-species, seasurfacetemperature, ckan, fish-inventory, especes-envahissante, temperature-sous-la-surface, habitat-characterization, temperature-de-surface, potential-temperature, poisson, temperature-potentielle, caracterisation-des-habitats, inventaire-poisson, subsurfacetemperature, fishabundanceanddistribution, fish, production
Temporal coverage: 2020-07-07T00:00:00

Data on the abundance of diadromous fish and their habitats. Data were collected from July 7 to October 12, 2020, in streams around Placentia Bay, Newfoundland and Labrador. Human observations and electrofishing were used as the method of sampling fish. These data are intended to provide baseline information on diadromous fishes and their habitat prior to the influence of significant human activity.


The project was carried out by Kelly MacDonald, Gary McKeown, Tyler Lanteigne, Madisson Philips, Shawn Leroux, Craig Buy in collaboration with Memorial University of Newfoundland. This project is an integral part of Fisheries and Oceans Canada's Coastal Environmental Baseline Program.
WISE-Man Project (WaterSat Imaging Spectrometer Experiment), characterization of shallow inland and coastal waters: optical data

Keywords: reflectance, teledetection, couleur-de-leau, ckan, autre, oceans, optics, optique, water-color, couleur-des-oceans, manicouagan, production, oceancolour, other, remote-sensing
Temporal coverage: 2019-08-17/2019-08-25

This dataset includes water optical parameters sampled in situ such as reflectance at sea surface and bottom, diffuse attenuation coefficient, downwelling irradiance and more.

- Biogeochemical data are available via the following dataset: https://catalogue.ogsl.ca/en/dataset/ca-cioos_dbc63b41-b1ab-46be-a1a2-388d07c70cbb

- Data on the intertidal environment are available via the following dataset: https://catalogue.ogsl.ca/en/dataset/a90987aa-61a3-4c0a-900f-3c97dfb2cca1

The WaterSat Imaging Spectrometer Experiment (WISE) is developed for optically shallow inland and coastal waters assessment. The WISE-Man project objective was to demonstrate the potential of hyperspectral imagery for mapping bathymetry, water column quality (or inherent optical properties) and retrieve bottom properties; this in order to respond to the pressing needs of science (e.g. ecology, geomorphology, coastal risk), resource management and defense operation. Within the framework of WISE-Man, an intensive fieldwork campaign was conducted in the Manicouagan; Baie-Comeau region in August 2019.

This project is part of the Coastal Environmental Baseline Program Initiative under the Oceans Protection Plan of Fisheries and Oceans Canada.
WISE-Man Project (WaterSat Imaging Spectrometer Experiment), characterization of shallow inland and coastal waters: biogeochemistry data

Keywords: chlorophylle-a, nutriment, salinite-de-surface, seasurfacetemperature, nutriments, phytoplancton, teledetection, temperature-de-surface, water-temperature, oceans, physico-chimie, water-color, couleur-des-oceans, manicouagan, production, particulatematter, salinite-sous-la-surface, seasurfacesalinity, nutrient, nutrients, oceancolour, remote-sensing, salinity, physical-chemical, subsurfacetemperature, couleur-de-leau, salinite, temperature-de-leau, chlorophyll-a, ckan, phytoplankton, temperature-sous-la-surface, dissolvedorganiccarbon, subsurfacesalinity, matiere-particulaire, carbone-organique-dissous
Temporal coverage: 2019-08-17/2019-08-25

This dataset includes biogeochemical parameters analyzed in the laboratory from water samples, including water temperature, salinity, chlorophyll a, dissolved organic carbon, total organic carbon, nutrients, suspended particulate matter, phytoplankton, CDOM absorption, and more.

- Optical data are available via the following dataset: https://catalogue.ogsl.ca/en/dataset/ca-cioos_d624c859-5b72-4ee9-a832-d532582b1d3f

- Data on the intertidal environment are available via the following dataset: https://catalogue.ogsl.ca/en/dataset/a90987aa-61a3-4c0a-900f-3c97dfb2cca1

The WaterSat Imaging Spectrometer Experiment (WISE) is developed for optically shallow inland and coastal waters assessment. The WISE-Man project objective was to demonstrate the potential of hyperspectral imagery for mapping bathymetry, water column quality (or inherent optical properties) and retrieve bottom properties in order to respond to the pressing needs of science (e.g. ecology, geomorphology, coastal risk), resource management and defense operation. Within the framework of WISE-Man, an intensive fieldwork campaign was conducted in the Manicouagan; Baie-Comeau region in August 2019.

This project is part of the Coastal Environmental Baseline Program Initiative under the Oceans Protection Plan of Fisheries and Oceans Canada.
Analysis of the quality of life of the Betsiamites Estuary (2021-2022)

Keywords: nutriments, sediment-quality, oxygen, oxygene, betsiamites-estuary, ckan, estuaire-betsiamites, pollution-cotiere, qualite-eau, coastal-pollution, dissolvedorganiccarbon, matiere-particulaire, qualite-des-sediments, carbone-organique-dissous, autre, oceans, production, sediment, water-quality, particulatematter, nutrients, other
Temporal coverage: 2021-10-06/2022-03-28

Despite its many natural habitats housing a multitude of living organisms and offering various uses to the community, the Betsiamites River estuary undergoes anthropogenic actions that alter its quality of life.

In order to acquire data in order to better target habitat protection needs, AMIK commissioned an analysis on surface water and sediments. Although surface sediments do not indicate a danger to living organisms in the estuary, the results obtained for surface water appear to be more worrying. Therefore, it becomes urgent to take measures aimed at restoring or maintaining the state of health of the estuary.

This project was funded by the Coastal Environmental Baseline Program under Fisheries and Oceans Canada's Oceans Protection Plan (OPP).
Charlevoix Coastal Restoration Plan (2018)

Keywords: marineturtlesbirdsmammalsabundanceanddistribution, wetlands, coastal-characterization, autre, flore-cotiere, oceans, abondance-et-distribution-de-poissons, production, composition-et-couverture-des-herbiers-marins, other, abondance-et-distribution-de-tortues-marines-oiseaux-et-mammiferes, seagrasscoverandcomposition, inventaire-poisson, fishabundanceanddistribution, caracterisation-des-rives, ckan, fish-inventory, coastal-flora, milieux-humides
Temporal coverage: 2018-03-01/2018-08-31

Characterization of coastal marshes along the St. Lawrence River in the Charlevoix sector. The characterization carried out in 2018 includes the municipalities of Baie-Saint-Paul (BSP), Isle-aux-Coudres (IAC), Petite-Rivière-Saint-François (PRSF) and Les Éboulements (Saint-Joseph-de-la-Rive sector, SJDLR).

This dataset presents marshes characterization report that was produced with the aim of setting up future coastal restoration projects in the Charlevoix region. Vegetation data was collected in the different marshes and their influence (gain and loss) was also measured from historical maps from 1964 to 2012.
Acidification, Driver of Environmental Change: eDrivers Project for the St. Lawrence System

Keywords: production, ckan
Temporal coverage: 2017-08-01/2017-09-30

Oceans are the largest reservoirs and sinks of atmospheric carbon dioxide (CO2). Its uptake increases seawater acidity and lowers the saturation state of waters with respect to calcite (ΩC) and aragonite (ΩA), the two most common CaCO3 polymorphs that constitute the shells and skeletons of many marine organisms. Ocean acidification can have deleterious effects on carbonate-secreting organisms (e.g. mollusks and crustaceans) and certain physiological processes in non-calcifying organisms.

As part of the *eDrivers* project, we used ΩA to characterize ocean acidification in the bottom waters of the St. Lawrence. The data come from the Department of Fisheries and Oceans’ (DFO) Atlantic Zone Monitoring Program surveys and DFO’s multispecies surveys collected in August-September of 2017. ΩA, pH, and dissolved oxygen (O2) were measured at 117 stations in the Estuary and Gulf of St. Lawrence in the summer of 2018. The majority of sampling stations were located in the Southern Gulf (n = 84), the Estuary and Northern Gulf (n = 33).

It is possible to consult the scientific report of the **eDrivers** project: [Characterizing Exposure to and Sharing Knowledge of Drivers of Environmental Change in the St. Lawrence System in Canada](https://www.frontiersin.org/articles/10.3389/fmars .2020.00383/full) and the [additional data](https://www.frontiersin.org/articles/10.3389/fmars.2020.00383/full#supplementary-material). It is possible to consult the application [eDrivers](https://catalogue.ogsl.ca/dataset/ca-cioos_7c51ad5f-c2a9-4f4a-a78c-0b652e630825).
Water chemistry characteristics of two tributaries of Placentia Bay, Newfoundland, in 2019

Keywords: nutriments, coastal-characterization, stablecarbonisotopes, chlorophylle-a, caracterisation-des-rives, carbone-inorganique, chlorophyll-a, ckan, qualite-eau, isotopes-stables-du-carbone, dissolvedorganiccarbon, matiere-particulaire, carbone-organique-dissous, oceans, couleur-des-oceans, inorganiccarbon, production, water-quality, particulatematter, nutrients, oceancolour
Temporal coverage: 2019-02-18T00:00:00

This dataset includes surface water characteristics such as: dissolved organic carbon, total dissolved nitrogen, ammonium, nitrate, nitrite, phosphate, urea, silica, dissolved iron, dissolved aluminum, CDOM spectral slope, chlorophyll, particulate carbon, nitrogen particulate, delta 13C. These analyzes follow the estuarine gradient of two tributaries of Placentia Bay in Newfoundland, Canada. Samples were collected monthly from February to October 2019. The objective of this work is to provide critical baseline data for the Placentia Bay region.

This project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline Program under the Oceans Protection Plan.
Characterization of access to the St. Lawrence River in Charlevoix (2016)

Keywords: production, general-information, ckan, mise-en-valeur, sea-access, zone-cotiere, informations-generales, coastal-zone, other, acces-a-la-mer, autre, enhancement, oceans
Temporal coverage: 2016-09-01/2016-11-30

This study highlights the inventory and characterization of access to the river, as recorded during the late summer and fall of 2016. Characterized sites represent :


- Physical access;

- Visual access


The method adopted was to visit all the previously identified sites (map) and to take as many authorized roads in the direction of the river. The list of these sites was then submitted to the municipalities for advice, comments and additional information. In addition, a “general public” survey was proposed and disseminated via social media. This makes it possible to better understand tastes and needs in terms of access to the river.
CHONe II project (Canadian Healthy Oceans Network): baseline bio-optical data in the Bay of Sept-Îles, biogeochemistry data

Keywords: dissolvedorganiccarbon, subsurfacesalinity, matiere-particulaire, carbone-organique-dissous, nutrient, nutrients, oceancolour, remote-sensing, salinity, physical-chemical, baie-de-sept-iles, bay-of-sept-iles, subsurfacetemperature, production, particulatematter, salinite-sous-la-surface, seasurfacesalinity, oceans, physico-chimie, water-color, couleur-des-oceans, nutriments, phytoplancton, teledetection, temperature-de-surface, water-temperature, chlorophyll-a, ckan, phytoplankton, temperature-sous-la-surface, couleur-de-leau, salinite, temperature-de-leau, chlorophylle-a, nutriment, salinite-de-surface, seasurfacetemperature
Temporal coverage: 2016-08-23/2019-06-05

This dataset includes biogeochemical parameters analyzed in the laboratory from water samples, including water temperature, salinity, chlorophyll a, dissolved organic carbon, total organic carbon, nutrients, suspended particulate matter, phytoplankton, CDOM absorption, and more. Optical data are available via the following dataset:

- https://catalogue.ogsl.ca/en/dataset/ca-cioos_eb97522c-01fe-4216-b9fa-8578b6a6d73a

CHONe II’s research explores the characteristics that define how Canada’s oceans will respond to management strategies such as networks of Marine Protected Areas (MPAs), spatial closures, and restoration efforts. Our research also addresses how ocean stressors such as pollution, climate change, and fishing - individually and collectively - alter ocean life and how ocean environments work, including intensively used environments that provide food and other resources.

Under this research program, 10 field campaigns were conducted in the Bay of Sept-Îles area from 2016 to 2019 in order to establish baseline bio-optical information to promote and develop optical remote sensing tools for monitoring purposes.

The NSERC (Natural Sciences and Engineering Research Council of Canada) Canadian Healthy Oceans Network II (CHONe II), strategic partnership of Canadian university researchers and government scientists, brings together 39 researchers from universities and federal research labs from coast to coast in Canada. The Network trains many interdisciplinary undergraduate and graduate students, as well as postdoctoral researchers. CHONe II partners with the Department of Fisheries and Oceans Canada and INREST (Institut nordique de recherche en environnement et en santé au travail; representing the Port of Sept-Îles and the City of Sept-Îles).
CHONe II project (Canadian Healthy Oceans Network): baseline bio-optical data in the Bay of Sept-Îles, optical data

Keywords: oceancolour, other, remote-sensing, baie-de-sept-iles, bay-of-sept-iles, production, autre, oceans, optics, optique, water-color, couleur-des-oceans, reflectance, sept-iles, teledetection, ckan, couleur-de-leau
Temporal coverage: 2016-08-23/2019-06-05

This dataset includes water optical parameters sampled in situ such as reflectance at sea surface and bottom, diffuse attenuation coefficient, downwelling irradiance and more. Biogeochemical data are available via the following dataset:

- https://catalogue.ogsl.ca/en/dataset/ca-cioos_e5595db1-0684-4148-a322-6e9b68f52c4c

CHONe II’s research explores the characteristics that define how Canada’s oceans will respond to management strategies such as networks of Marine Protected Areas (MPAs), spatial closures, and restoration efforts. Our research also addresses how ocean stressors such as pollution, climate change, and fishing - individually and collectively - alter ocean life and how ocean environments work, including intensively used environments that provide food and other resources.

Under this research program, 10 field campaigns were conducted in the Bay of Sept-Îles area from 2016 to 2019 in order to establish baseline bio-optical information to promote and develop optical remote sensing tools for monitoring purposes.

The NSERC (Natural Sciences and Engineering Research Council of Canada) Canadian Healthy Oceans Network II (CHONe II), strategic partnership of Canadian university researchers and government scientists, brings together 39 researchers from universities and federal research labs from coast to coast in Canada. The Network trains many interdisciplinary undergraduate and graduate students, as well as postdoctoral researchers. CHONe II partners with the Department of Fisheries and Oceans Canada and INREST (Institut nordique de recherche en environnement et en santé au travail); representing the Port of Sept-Îles and the City of Sept-Îles).
Maricultural Monitoring in Support of Quebec Shellfish Aquaculture Industry from 2008 to 2015: Temperature Data

Keywords: subsurfacetemperature, ressources-maritimes, habitat-tracking, ckan, suivi-annuel, temperature-sous-la-surface, amelioration-des-connaissances, maritime-resources, temperature-de-leau, annual-follow-up, seasurfacetemperature, production, suivi-habitat, knowledge-improvement, oceans, temperature-de-surface, water-temperature
Temporal coverage: 2008-05-15/2015-12-17

From 2008 to 2015, a monitoring program in support of the Quebec mariculture industry was carried out by Merinov with the support of the Quebec Ministry of Agriculture, Fisheries and Food (French: Ministère de l’Agriculture, des Pêcheries et de l’Alimentation (MAPAQ)). The main objective was to compile and transmit relevant biological and environmental data to marine producers for the purpose of informed decision making during their commercial operations. Established for the three producing regions of maritime Quebec (Îles-de-la-Madeleine, Gaspésie and Côte-Nord), the mariculture monitoring program has made it possible to document in a synchronized manner some twenty mariculture sites (11 mussel farms, 7 pectin farms and 2 oyster farms). This was made possible through monitoring various biotic and abiotic parameters such as recruitment success (larvae and postlarvae) and collection performance of the cultivated species, proliferation of undesirable species (predators and epibionts) and the quality of the commercial product (meat yield).


This dataset contains a monitoring of water temperatures collected for the three regions: Îles-de-la-Madeleine, Côte-Nord and Gaspésie. For biotic monitoring data in support of the Quebec mariculture industry see [https://catalogue.ogsl.ca/fr/dataset/ca-cioos_8b0b9560-8621-4eeb-9cfd-bae5829b3849]. 


The reports are divided by year and sector of the mariculture industry.