eDNA metabarcoding enriches traditional trawl survey data for monitoring biodiversity in the marine environment

Marine Protected Areas require comprehensive monitoring to ensure objectives are achieved; however, monitoring natural ecosystems at scale is challenged by the biodiversity it aims to measure. Environmental DNA (eDNA) metabarcoding holds promise to address this monitoring challenge. We conducted paired sampling at 54 sites for fish and invertebrate assemblages in the Northwest Atlantic using groundfish trawls and eDNA metabarcoding of benthic seawater using four genetic markers (12S rRNA, 16S rRNA, 18S rRNA, and CO1). Compared to trawling, eDNA detected similar patterns of species turnover, larger estimates of gamma diversity, and smaller estimates of alpha diversity. A total of 63.6% (42/66) of fish species captured by trawling were detected by eDNA, along with an additional 26 species. Of the 24 missed detections by eDNA, 12 were inevitable as they lacked reference sequences. Excluding taxa assigned to higher than species level and those without a species name, 23.6% (17/72) of invertebrate species captured by trawling were detected by CO1, which detected an additional 98 species. We demonstrate that eDNA is capable of detecting patterns of community assemblage and species turnover in an offshore environment, emphasizing its strong potential for a non-invasive, comprehensive, and scalable tool for biodiversity monitoring supporting marine conservation programmes.

Cite this data as: Jeffery, N., Rubidge, E., Abbott, C., Westfall, K., Stanley, R. (2024): Data of: eDNA metabarcoding enriches traditional trawl survey data for monitoring biodiversity in the marine environment.

Published: August 2024. Coastal Ecosystems Science Division, Fisheries and Oceans Canada, Dartmouth, N.S. https://open.canada.ca/data/en/dataset/43a91ba7-8025-4330-88db-db14022d729d

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Field	Value
Last Updated	October 22, 2024, 15:37 (UTC)
Created	October 1, 2024, 07:25 (UTC)
Domain / Topic Domain or topic of the dataset being cataloged.	Biota, Oceans
Description A description of the dataset.	Marine Protected Areas require comprehensive monitoring to ensure objectives are achieved; however, monitoring natural ecosystems at scale is challenged by the biodiversity it aims to measure. Environmental DNA (eDNA) metabarcoding holds promise to address this monitoring challenge. We conducted paired sampling at 54 sites for fish and invertebrate assemblages in the Northwest Atlantic using groundfish trawls and eDNA metabarcoding of benthic seawater using four genetic markers (12S rRNA, 16S rRNA, 18S rRNA, and CO1). Compared to trawling, eDNA detected similar patterns of species turnover, larger estimates of gamma diversity, and smaller estimates of alpha diversity. A total of 63.6% (42/66) of fish species captured by trawling were detected by eDNA, along with an additional 26 species. Of the 24 missed detections by eDNA, 12 were inevitable as they lacked reference sequences. Excluding taxa assigned to higher than species level and those without a species name, 23.6% (17/72) of invertebrate species captured by trawling were detected by CO1, which detected an additional 98 species. We demonstrate that eDNA is capable of detecting patterns of community assemblage and species turnover in an offshore environment, emphasizing its strong potential for a non-invasive, comprehensive, and scalable tool for biodiversity monitoring supporting marine conservation programmes. Cite this data as: Jeffery, N., Rubidge, E., Abbott, C., Westfall, K., Stanley, R. (2024): Data of: eDNA metabarcoding enriches traditional trawl survey data for monitoring biodiversity in the marine environment. Published: August 2024. Coastal Ecosystems Science Division, Fisheries and Oceans Canada, Dartmouth, N.S. https://open.canada.ca/data/en/dataset/43a91ba7-8025-4330-88db-db14022d729d
Tags Keywords/tags categorizing the dataset.	Nature and Environment Oceans Science and Technology eDNA
Format (CSV, XLS, TXT, PDF, etc) File format of the dataset.
Dataset Size Dataset size in megabytes.
Metadata Identifier Metadata identifier – can be used as the unique identifier for catalogue entry
Published Date Published date of the dataset.	2024-07-30
Time Period Data Span (start date) Start date of the data in the dataset.
Time Period Data Span (end date) End date of time data in the dataset.
GeoSpatial Area Data Span A spatial region or named place the dataset covers.

Field	Value
Access category Type of access granted for the dataset (open, closed, service, etc).
License License used to access the dataset.	Open Government Licence - Canada
Limits on use Limits on use of data.
Location Location of the dataset.
Data Service Data service for accessing a dataset.
Owner Owner of the dataset.	Fisheries and Oceans Canada \| Pêches et Océans Canada
Contact Point Who to contact regarding access?	Government of Canada; Fisheries and Oceans Canada, DFO.CESDDataRequest-DSECDemandededonnes.MPO@dfo-mpo.gc.ca
Contact Point Email The email to contact regarding access?
Publisher Publisher of the dataset.
Publisher Email Email of the publisher.	Nick.Jeffery@dfo-mpo.gc.ca
Accessed At Date the data and metadata was accessed.

Field	Value
Identifier Unique identifier for the dataset.
Language Language(s) of the dataset
Link to dataset description A URL to an external document describing the dataset.
Persistent Identifier Data is identified by a persistent identifier.
Globally Unique Identifier Data is identified by a persistent and globally unique identifier.
Contains data about individuals Does the data hold data about individuals?
Contains data about identifiable individuals Does the data hold identifiable data about individual?
Contains Indigenous Data Does the data hold data about Indigenous communities?

Field	Value
Source Source of the dataset.	https://open.canada.ca/data/en/dataset/43a91ba7-8025-4330-88db-db14022d729d
Version notes Version notes about the dataset.
Is version of another dataset Link to dataset that it is a version of.
Other versions Link to datasets that are versions of it.
Provenance Text Provenance Text of the data.
Provenance URL Provenance URL of the data.
Temporal resolution Describes how granular the date/time data in the dataset is.
GeoSpatial resolution in meters Describes how granular (in meters) geospatial data is in the dataset.
GeoSpatial resolution (in regions) Describes how granular (in regions) geospatial data is in the dataset.

Field	Value
Indigenous Community Permission Who holds the Indigenous Community Permission. Who to contact regarding access to a dataset that has data about Indigenous communities.
Community Permission Community permission (who gave permission).
The Indigenous communities the dataset is about Indigenous communities from which data is derived.

Field	Value
Number of data rows If tabular dataset, total number of rows.
Number of data columns If tabular dataset, total number of unique columns.
Number of data cells If tabular dataset, total number of cells with data.
Number of data relations If RDF dataset, total number of triples.
Number of entities If RDF dataset, total number of entities.
Number of data properties If RDF dataset, total number of unique properties used by the triples.
Data quality Describes the quality of the data in the dataset.
Metric for data quality A metric used to measure the quality of the data, such as missing values or invalid formats.

eDNA metabarcoding enriches traditional trawl survey data for monitoring biodiversity in the marine environment

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