Search

University of Victoria Dataverse Logo
Data from: Multiple human activities in coastal benthic ecosystems: introducing a metric of cumulative exposure
Borealis
Dreujou, Elliot; Beauchesne, David; Daigle, Rémi M; Carrière, Julie; Noisette, Fanny; McKindsey, Christopher W; Archambault, Philippe — 2023-09-14 <h3>General presentation</h3> This repository presents the R code and associated data used in the article <em>Multiple human activities in coastal benthic ecosystems: introducing a metric of cumulative exposure</em>.<br><br> Datasets include information about the stations sampled at Sept-Îles (Québec, Canada) in 2017 and exposure indices. Data includes species biomass, density and taxonomy of benthic macrofaunal species, with physico-chemical parameters at the sediment surface, biotic indicators and exposure indices.<br><br> The main research questions were to: <ol> <li>model the exposure of benthic ecosystems to anthropogenic activities locally</li> <li>explore the links between benthic community diversity and anthropogenic exposure</li> </ol> <hr> <h3> Specific details</h3> <ul> <li>Variables, units and files are explained in files <strong>README.yml</strong> (this file is a basic text file formatted with a YAML language) and <strong>README.txt</strong>.</li> <li>Language and software used for the analyses: R (4.2), PRIMER-E (6)</li> </ul> <hr>
Dryad Logo
Data from: Ocean deoxygenation caused non-linear responses in the structure and functioning of benthic ecosystems
Pascal, Ludovic; Cool, Joannie; Archambault, Philippe; Calosi, Piero; Cuenca, André L. R.; Mucci, Alfonso O.; Chaillou, Gwénaëlle — 2023-10-18 <p><span lang="EN-CA">The O<sub>2 </sub>content of the global ocean has been declining progressively over the past decades, mainly because of human activities and global warming. Nevertheless, how long-term deoxygenation affects macrobenthic communities, sediment biogeochemistry and their mutual feedback remains poorly understood. Here, we evaluate the response of the benthic assemblages and biogeochemical functioning to decreasing O<sub>2 </sub>concentrations along the persistent bottom-water dissolved O<sub>2</sub> gradient of the Estuary and Gulf of St. Lawrence (QC, Canada). We report several of non-linear biodiversity and functional responses to decreasing O<sub>2</sub> concentrations, and identify an O<sub>2</sub> threshold that occurs at approximately at 63 µM. Below this threshold, macrobenthic community assemblages change, and bioturbation rates drastically decrease to near zero. Consequently, the sequence of electron acceptors used to metabolize the sedimentary organic matter is squeezed towards the sediment surface while reduced compounds accumulate closer (as much as 0.5 to 2.5 cm depending on the compound) to the sediment-water interface. Our results illustrate the capacity of bioturbating species to compensate for the biogeochemical consequences of hypoxia and can help to predict future changes in benthic ecosystems.</span></p>
University of Victoria Dataverse Logo
Data from: Determining the ecological status of benthic coastal communities: a case in an anthropized sub-Arctic area
Borealis
Dreujou, Elliot; Desroy, Nicolas; Carrière, Julie; Tréau de Coeli, Lisa; McKindsey, Christopher W; Archambault, Philippe — 2021-03-23 <h3>General presentation</h3> This repository presents the R code and associated data used in the article <em>Determining the ecological status of benthic coastal communities: a case study in an anthropized sub-Arctic area</em>.<br><br> Datasets include information about the stations sampled at Sept-Îles (Québec, Canada) in 2017. Data includes species biomass, density, taxonomy and traits of benthic macrofaunal species, with physico-chemical parameters at the sediment surface.<br><br> The main research questions were to: <ol> <li>compare outcomes of various benthic environmental indicators</li> <li>understand how these indicators relate to habitat parameters for validation and to select appropriate applications</li> </ol> <hr> <h3> Specific details</h3> <ul> <li>Variables, units and files are explained in files <strong>README.yml</strong> (this file is a basic text file formatted with a YAML language) and <strong>README.txt</strong>.</li> <li>Language and software used for the analyses: R (4.0.3)</li> </ul> <hr>
University of Victoria Dataverse Logo
Data from: Environmental stressors, complex interactions and marine benthic communities’ responses
Borealis
Carrier-Belleau, Charlotte; Drolet, David; McKindsey, Christopher W.; Archambault, Philippe — 2021-03-16 This dataset includes the data collected from a laboratory experiment between August 1 and October 23, 2018 to investigate the individual and combined effect of freshwater input, increased temperature and nutrient enrichment after two-exposure time on <i>Mytilus</i> sp, <i>Limecola balthica</i> and microphytobenthos biomass.
University of Victoria Dataverse Logo
Data from: Sea ice increases benthic community heterogeneity in a seagrass landscape
Borealis
Pascal, Ludovic; Bernatchez, Pascal; Chaillou, Gwénaëlle; Nozais, Christian; Lapointe Saint-Pierre, Mathilde; Archambault, Philippe — 2020-01-23 These data include macrofaunal (i.e. > 0.5 mm) densities and biomasses and environmental data from the monitoring of a seagrass meadow located at the Manicouagan peninsula, Quebec, Canada. Sampling occurred during the year 2018 (April, June, August and October). Sample were collected in vegetated areas (V) and in artificial (aTP) and natural (nTP) tidal pools.<br/> Data are organized in five tabular data files (.txt files; separator = tab, decimal = .)<br/> (1) Manicouagan_biomasses.txt includes biomasses (g blotted wet weight/m<sup>2</sup>) of sampled macrofaunal species<br/> (2) Manicouagan_densities.txt includes densities (individuals/m<sup>2</sup>) of sampled macrofaunal species<br/> (3) Manicouagan_porewater_profiles.txt include depth profile of nutrient (NH<sub>4</sub><sup>+</sup>, NO<sub>2</sub> + NO<sub>3</sub><sup>-</sup> and PO<sub>4</sub><sup>3-</sup>) concentrations (µM)<br/> (4) Manicouagan_Sediment_characteristics.txt includes median sediment grain size (D50; µm) sediment porosity (volume ration), particulate organic carbon content (OC; % Dry Weight), particulate total nitrogen content (TN; % DW), sediment chlorophyll a content (chla; µg/g), sediment phaeopigment content (µg/g), Total (Seagrass), above ground (AboGround) and below ground (BelGround) seagrass biomass (g/m<sup>2</sup>) and nutrients (NH<sub>4</sub><sup>+</sup>, NO<sub>2</sub> + NO<sub>3</sub><sup>-</sup> and PO<sub>4</sub><sup>3-</sup>) stock (µmol/m<sup>2</sup>) in the first 8 cm of the sediment column. (5) Manicouagan_Bacteria.txt include extractible bacteria count (Abundance in number of cells per mL of sediment) and fluorescence (green fluorescence, relative unit) in the sediment.
University of Victoria Dataverse Logo
Data for: Ecosystem-Based Quality Index at the bay scale: assessing the status of a heterogeneous system in a functional framework.
Borealis
Ferrario, Filippo; Archambault, Philippe; Johnson, Ladd Erik; McKindsey, Christopher W. — 2021-10-06 This dataset provides scripts and data used to produce the study "Ecosystem-Based Quality Index at the bay scale: assessing the status of a heterogeneous system in a functional framework." https://doi.org/10.1016/j.ecolind.2021.108260 . The Ecosystem-Based Quality Index (EBQI), developed for the Mediterranean Sea, may be adaptable to other ecosystems due to its functional approach being closer to a methodological framework than a specialized index. This work implement the shGSL-EBQI (shallow heterogeneous Gulf of St. Lawrence-EBQI) Data provided here include: - field data on macro-epibenthic invertebrates, algal community, infauna, bioturbation, Organic matter and photosynthetic pigments content in sediment in the Baie des Sept Îles (Québec, Canada). - potential environmental and anthropogenic drivers in the area - Scoring criteria, box scores, weighting schemes and model description datasets used to caculate the shGSL-EBQI. Methodological Information: - Macro epibentic Invertebrates, Macroalgal and Bioturbation data have been ectracted from georeferenced photomosaics realized using underwater imagery acquired by Filippo Ferrario using SCUBA (see paper for details). Data have been gathered in 2018 in the Bay of Sept-Îles (Québec, Canada) - Organic matter and Photosynthetic pigments (chlorophyll-a and pheopigments) were quantified from sediment collected in SCUBA (see paper for details). Data have been gathered in 2018 in the Bay of Sept-Îles (Québec, Canada) - Fishery data have been provided by David Beauchesne (CHONe). More information on data can be found in: Beauchesne et al 2020 (https://doi.org/10.3389/fmars.2020.00383) - Infauna data have been provided by Elliot Dreujou (CHONe). More information on data can be found in: Dreujou et al 2020 (https://doi.org/10.3390/w12092424).
Dryad Logo
Data from: Meiofauna affect the macrobenthic biodiversity-ecosystem functioning relationship
Dryad
Piot, Adeline; Nozais, Christian; Archambault, Philippe — 2014-05-13 The biodiversity–ecosystem functioning (B–EF) relationship has become of main interest in the last few decades, mostly because of the worldwide increase in species extinctions. However, most of these studies only consider species within single size-class or trophic level, thereby most likely underestimating ecosystem complexity. To reach more realistic scenarios, we assessed the role of meiofauna (lower size-class level) on the relationship between macrofaunal biodiversity and multiple benthic ecosystem properties. Experiments took place under controlled conditions using three macrofaunal species (Alitta (formerly Nereis) virens, Macoma balthica and Mya arenaria). A total of eight combinations of zero to three functionally different macrofaunal species were maintained in microcosms for 34 days in either the presence or absence of a different size-class grouping (a meiofaunal mixture). The organic matter content and bacterial abundance in sediments and the oxygen and nutrient (NH4+, NOx-, PO4 3-) fluxes across the sediment-water interface were measured and used as proxies of ecosystem properties. Overall, macrofaunal species richness did not modify any of the measured properties; however, we observed changes associated to the presence of A. virens and M. balthica. This study also revealed a strong impact of the presence of meiofauna on ecosystem properties. They changed interactions between macrofaunal species, which led to modifications in the ecosystem properties. Thus, even if this size-class group has been poorly considered in previous studies, this experiment suggests that future studies should consider the meiofauna with greater attention, particularly in the context of B–EF.
University of Victoria Dataverse Logo
Data from: Benthos response to nutrient enrichment and functional consequences in coastal ecosystems
Borealis
Pascal, Ludovic; Chaillou, Gwénaëlle; Nozais, Christian; Cool, Joannie; Bernatchez, Pascal; Letourneux, Kevin; Archambault, Philippe — 2022-02-15 <h1>General description</h1> <p>This dataset include the data collected during two experiments carried out in May and August 2019 to investigate the mechanisms involved in the benthic response to nutrient enrichment in coastal ecosystems.</p> <p>Sample were collected in an intertidal mudflat in Isle-Verte Bay (48° 2’ 36.76” N; 69° 21’ 3.736” W, St. Lawrence estuary, QC, Canada) in vegetated areas (Veg) and ice made-tidal pools (UnV). They were then exposed, in a well-controlled laboratory experiment, to three intensities of nutrient enrichment (N0, N1 and N2) during 30 days.</p> <hr> <h1>Description of the dataset</h1> <p><em>Data are organized in five tabular data files (.txt files; separator = tab, decimal = ., missing data = NA)</em>. Please refer to related publication for experimental design and analytical methods</p> <h3>Sediment_characteristics.txt</h3> <p>This file includes median sediment grain size (D<sub>50</sub>; µm), sediment porosity (volume ratio), Sediment organic matter (SOM; %Loss on ignition), Chlorophyll <em>a</em> content (Chl <em>a</em>; µg g<sup>-1</sup>), phaeopigments (µg g<sup>-1</sup>), Seagrass leaf biomasse (g) and Seagrass leaf elongation (cm day<sup>-1</sup>)</p> <h3>Macrofauna_density.txt</h3> <p>This file includes densities (individuals m<sup>-2</sup>) of sampled macrofaunal species</p> <h3>Bioturbation.txt</h3> <p>This files includes bioturbation metrics such as maximum penetration depth of luminophores (MPD; cm), Biodiffusion coefficient (D<sub>b</sub>; cm<sup>2</sup> y<sup>-1</sup>) and porewater exchange rate (Q; mL m<sup>-2</sup> h<sup>-1</sup>)</p> <h3>Oxygen_dynamics.txt</h3> <p>This file includes diffusive oxygen uptake (J; mmol m<sup>-2</sup> d<sup>-1</sup>) and oxygen penetration depth (Z; µm)</p> <h3>Nutrient_profiles.txt</h3> <p>This file includes porewater nutrient (NH<sub>4</sub><sup>+</sup>, NO<sub>3</sub><sup>-</sup> and PO<sub>4</sub><sup>3-</sup>; µM) profiles within the sediment column (depth; cm)</p> <h3>Benthic_fluxes.txt</h3> <p>This file includes oxygen (TOU) and nutrients ((NH<sub>4</sub><sup>+</sup>, NO<sub>3</sub><sup>-</sup>) benthic fluxes (mmol m<sup>-2</sup> h<sup>-1</sup>)</p>
Zenodo Logo
Interactions amplify cumulative effects in marine food webs - Data Input
Zenodo
Beauchesne, David; Cazelles, Kevin; Daigle, Remi; Gravel, Dominique; Archambault, Philippe — 2024-12-20 README for Input Data Archive Overview This README describes the input datasets prepared for the analyses for the manuscript titled "Interactions amplify cumulative effects in marine food webs", presenting a cumulative effects assessment on food webs in the Estuary and Gulf of St. Lawrence. The code to replicate the analyses is available on GitHub: https://github.com/Ecosystem-Assessments/nceastl and the input data is described here. The data has been processed and formatted into tabular format (i.e., CSV files) and geospatial raster files (i.e., GeoTIFFs). Below is a detailed description of the datasets included in the archive. Included Data 1. Species List   - Description: A comprehensive list of species used in the assessment, with species names formatted to remove extra characters or spaces for consistency.   - File:     - `SpeciesList.csv`: Tabular format of species list.   - **Column description**:     - `species`: Full scientific name of the species, including genus and species.     - `Count`: Total count or frequency of the species in the dataset.     - `sp`: Simplified representation of the species name (genus and species separated by a space).     - `sp.`: Simplified representation of the species name (genus and species separated by a period).     - `species`.: Fully concatenated scientific name with genus and species joined by a period. 2. Simulated Trophic Sensitivities   - Description: Sensitivities of species to various trophic drivers, adapted from a study by Beauchesne et al. (2021; Ecology Letters, 10.1111/ele.13841).   - File:     - `TrophicSensitivity.csv`: Tabular format of trophic sensitivities.   - Column description:     - `pathID`: Identifier for the specific pathway of effect analyzed.     - `SpeciesID`: Unique identifier for the species involved in the motif.     - `motifID`: Identifier for the motif within the trophic network.     - `Species`: Label or shorthand representation of the species in the pathway.     - `pi`: Indicator of the species' presence in position "i" within the pathway (Boolean: True/False).     - `pj`: Indicator of the species' presence in position "j" within the pathway (Boolean: True/False).     - `pk`: Indicator of the species' presence in position "k" within the pathway (Boolean: True/False).     - `sensitivity_original`: Original sensitivity value for the species within the trophic pathway.     - `sensitivity_scaled`: Scaled sensitivity value, normalized for comparison across pathways.     - `sensitivity_1`: Sensitivity value adjusted for a specific analysis or scenario. 3. Biotic Data   - Description: Species presence data transformed into logical matrices and geospatial rasters. Assumes phytoplankton and zooplankton are ubiquitous in the study area.   - Files:     - `txNames.csv`: String of names of taxa included in the biotic dataset.     - `bt.csv`: Logical matrix of species presence with one row per raster cell and one column per species.      - `idBiotic.csv`: Logical string identifying cells with biotic data.     - `r.tif`: Empty raster file for reference.     - `biotic/`: Folder containing GeoTIFF files for each species. 4. Metaweb   - Description: Interaction matrix representing trophic links between species. Includes only species present in the biotic dataset.   - File:     - `metaweb.csv`: Interaction matrix in tabular format, with species names as column and row names. 5. Species-Specific Sensitivities   - Description: Sensitivities of species to different drivers, with added records for phytoplankton and zooplankton (assumed insensitive to all drivers).   - File:     - `species_sensitivity.csv`: Tabular format of species sensitivities to all environmental drivers considered, with driver names as columns and taxa names as row names.  6. Drivers Data   - Description: Environmental drivers affecting species, aligned with vulnerability assessments. Data is provided in matrix and raster formats.   - Files:     - `dr.csv`: Matrix of drivers intensity with one row per raster cell and one column per driver.     - `drivers/`: Folder containing GeoTIFF files for each driver. Contact For questions or clarifications about the dataset, please contact [David Beauchesne] at [david.beauchesne@insileco.io]. https://creativecommons.org/licenses/by/4.0/legalcode
PANGAEA Logo
Measured values of Ba/Ca in coral and coralline algae for seawater barium calibrations
PANGAEA
Williams, Thomas J; Standish, Christopher D; Archambault, Philippe; Godbold, Jasmin A; Solan, Martin; Katsamenis, Orestis; Basford, Philip; Foster, Gavin L — 2023 A comprehensive georeferenced database of measured values of Ba/Ca in coral and coralline algae compiled from the scientific literature (1950-2021; http://www.webofknowledge.com, accessed 2022-09-30). https://creativecommons.org/licenses/by/4.0/legalcode
PANGAEA Logo
Measured values of Li/Mg, Mg/Ca, Sr/Ca, Ba/Ca, U/Ca and Sr-U for coral and coralline algae paleothermometer calibrations
PANGAEA
Williams, Thomas J; Standish, Christopher D; Archambault, Philippe; Godbold, Jasmin A; Solan, Martin; Katsamenis, Orestis; Basford, Philip; Foster, Gavin L — 2023 A comprehensive georeferenced database of measured values of Li/Mg, Mg/Ca, Sr/Ca, Ba/Ca, U/Ca and Sr-U in coral and coralline algae compiled from the scientific literature (1950-2021; http://www.webofknowledge.com, accessed 2022-09-30). https://creativecommons.org/licenses/by/4.0/legalcode

Map search instructions

1.Turn on the map filter by clicking the “Limit by map area” toggle.
2.Move the map to display your area of interest. Holding the shift key and clicking to draw a box allows for zooming in on a specific area. Search results change as the map moves.
3.Access a record by clicking on an item in the search results or by clicking on a location pin and the linked record title.
Note: Clusters are intended to provide a visual preview of data location. Because there is a maximum of 50 records displayed on the map, they may not be a completely accurate reflection of the total number of search results.

(Author: Archambault, Philippe)

Limit by:

Clear all

to