DOI: 10.5061/dryad.gqnk98t0c
title: Data from: Applying eDNA Metabarcoding to assess invertebrate biodiversity of Eelgrass (Zostera marina) meadows across Nova Scotia

description: Eelgrass (Zostera marina) meadows are a common feature of Atlantic
 coastlines, forming productive marine communities that are valued for
 their ecosystem services. Long-term adaptive management of these sensitive
 ecosystems and effective conservation of the biodiversity they support
 requires tools to evaluate and monitor patterns of diversity.
 Environmental DNA (eDNA) metabarcoding is a relatively new approach for
 estimating aquatic biodiversity, with significant potential for
 broad-scale monitoring of complex habitats like seagrass communities. In
 this study, we utilized eDNA metabarcoding to characterize invertebrate
 biodiversity in eelgrass meadows along a latitudinal gradient in the
 Northwest Atlantic and compared results to historical surveys of eelgrass
 in the region. Across 17 sites, 138 metazoan invertebrate taxa were
 detected with a taxonomic probability assignment &gt; 95%. eDNA was
 successful at capturing regional patterns of community structure and
 detecting 20 of 26 common invertebrate taxa based on published records, as
 well as 80 species not historically recorded. These results emphasize the
 potential of eDNA to augment eelgrass ecosystem monitoring by enabling
 efficient, non-invasive cataloguing of biodiversity, including cryptic
 species that evade conventional sampling.
description: Seventeen sites were sampled across approximately 760 km (3.5° of
 latitude and 6° longitude) of coastline in Nova Scotia, selected based on
 the presence of eelgrass beds and accessibility. Ten of these sites were
 sampled from July to September 2019 as part of a study focusing on fish
 communities within eelgrass beds (He et al. 2022). These sites spanned
 approximately two degrees of latitude along the coast of mainland Nova
 Scotia with a focus on the Eastern Shore Islands Area of Interest, an area
 selected for potential marine conservation area designation (Jeffery et
 al. 2020). The geographic scope was expanded by additionally sampling six
 sites in Cape Breton and one on the south shore of Nova Scotia between
 June to October 2023. Cape Breton sites were sampled across approximately
 0.9° of latitude and were located in bays and estuaries on the east and
 west coasts of the island. Temporal comparisons were not undertaken
 because there was no overlap in sites between the two years and geographic
 regions sampled. Instead, data from 2019 and 2023 were combined to explore
 general geographic patterns in species richness and community composition
 over a broad latitudinal range.
description: # Data from: Applying eDNA Metabarcoding to assess invertebrate
 biodiversity of Eelgrass (Zostera marina) meadows across Nova Scotia
 Dataset DOI: [10.5061/dryad.gqnk98t0c](10.5061/dryad.gqnk98t0c) ##
 Description of the data and file structure # Marine invertebrate eDNA
 metabarcoding in Eelgrass Meadows Across Nova Scotia, Canada ## Contact
 Information Corresponding author:
 [Nick.Jeffery@dfo-mpo.gc.ca](mailto:Nick.Jeffery@dfo-mpo.gc.ca) Address:
 Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada, B2Y 4A2
 Project led by: Courtney Trask, Cape Breton University Submitted to
 Canadian Journal of Fisheries and Aquatic Sciences Alternate Contact:
 [Timothy_Rawlings@cbu.ca](mailto:Timothy_Rawlings@cbu.ca)  ### Dataset
 Overview The data files included her consist of data from eDNA
 metabarcoding samples from 17 locations across coastal Nova Scotia,
 sampled in 2019 and 2023. Included are an amplicon sequence variant (ASV)
 table for all samples, arranged as a matrix of the species detected with
 the number of sequence reads per site and sample. The ASV table was
 generated through the QIIME2 pipeline, where COI primers were trimmed and
 sequences merged and denoised in DADA2 (Callahan et al. 2016). Also
 included are two .fasta files which include the representative DNA
 sequences for each ASV detected from samples in 2019 and 2023. We also
 compare eDNA ASV results with species detected in coastal eelgrass meadows
 in Nova Scotia using 'traditional' methods, including sediment
 coring, snorkeling, and net-based methods.  ###### Date Range Samples for
 10 sites were collected between July and September 2019, while samples
 collected in Cape Breton were sampled between June and August 2023. 
 ###### eDNA Marker All samples were analyzed for a fragment of the COI
 gene amplified by the Leray et al. (2013) primer set. ### References
 Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J.
 A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference
 from Illumina amplicon data. *Nature methods*, *13*(7), 581-583. Leray M.,
 Yang J. Y., Meyer C. P., Mills S. C., Agudelo N., Ranwez V., et al.
 (2013). A new versatile primer set targeting a short fragment of the
 mitochondrial COI region for metabarcoding metazoan diversity: application
 for characterizing coral reef fish gut contents. *Front. Zoology* 10 (1),
 34. doi: 10.1186/1742-9994-10-34 ### Files and variables #### File:
 Final_ASVTable_withTaxonomy_Filtered.csv **Description:** A table of all
 amplicon sequence variants (ASVs) and associated taxonomy (species names)
 with read counts per taxon per sample.  ##### Variables * Phylum: The
 invertebrate phylum of the species listed * Class: The class of the
 species listed * Species: The species and genus name associated with a
 given ASV. * Probability: The probability (up to 100%) that the given
 species name belongs to the associated ASV * CAB-1: Sample replicate 1
 from Cable Island site * CAB-2: Sample replicate 2 from Cable Island site
 * CAB-3: Sample replicate 3 from Cable Island site * CON-1: Sample
 replicate 1 from Conrods Beach * CON-2: Sample replicate 2 from Conrods
 Beach * CON-3: Sample replicate 3 from Conrods Beach * FAI-1: Sample
 replicate 1 from Fifty Acre Island * FAI-2: Sample replicate 2 from Fifty
 Acre Island * FAI-3: Sample replicate 3 from Fifty Acre Island * FRK-1:
 Sample replicate 1 from Franks George Island * FRK-2: Sample replicate 2
 from Franks George Island * FRK-3: Sample replicate 3 from Franks George
 Island * MOS-1: Sample replicate 1 from Moosehead * MOS-2: Sample
 replicate 2 from Moosehead * MOS-3: Sample replicate 3 from Moosehead *
 PLS-1: Sample replicate 1 from Pleasant Point * PLS-2: Sample replicate 2
 from Pleasant Point * PLS-3: Sample replicate 3 from Pleasant Point *
 RSE-1: Sample replicate 1 from Rose Bay * RSE-2: Sample replicate 2 from
 Rose Bay * TAE-1: Sample replicate 1 from Taylor Head East * TAE-2: Sample
 replicate 2 from Taylor Head East * TAE-3: Sample replicate 3 from Taylor
 Head East * TAW-1: Sample replicate 1 from Taylor Head West * TAW-2:
 Sample replicate 2 from Taylor Head West * TAW-3: Sample replicate 3 from
 Taylor Head West * WRK02-1: Sample replicate 1 from Wreck Cove * WRK02-2:
 Sample replicate 2 from Wreck Cove * WRK02-3: Sample replicate 3 from
 Wreck Cove * ASB-1: Sample replicate 1 from Aspy Bay * ASB-2: Sample
 replicate 2 from Aspy Bay * ASB-3: Sample replicate 3 from Aspy Bay *
 CHB-1: Sample replicate 1 from Chebogue * CHB-2: Sample replicate 2 from
 Chebogue * CHB-3: Sample replicate 3 from Chebogue * LIN-1: Sample
 replicate 1 from Lingan Bay * LIN-2: Sample replicate 2 from Lingan Bay *
 LIN-3: Sample replicate 3 from Lingan Bay * MIR-1: Sample replicate 1 from
 Mira River * MIR-2: Sample replicate 2 from Mira River * MIR-3: Sample
 replicate 3 from Mira River * CHT-1: Sample replicate 1 from Cheticamp *
 CHT-2: Sample replicate 2 from Cheticamp * CHT-3: Sample replicate 3 from
 Cheticamp * NOR-1: Sample replicate 1 from North River * NOR-2: Sample
 replicate 2 from North River * NOR-3: Sample replicate 3 from North River
 * ESB-1: Sample replicate 1 from East Bay * ESB-2: Sample replicate 2 from
 East Bay * ESB-3: Sample replicate 3 from East Bay #### File:
 Site_coordinates.csv **Description:** A csv file with the GPS coordinates
 in WGS84 decimal degree format for each sample site ##### Variables *
 Site: The name of the sampling site * Latitude: The latitude of the
 sampling site in decimal degrees * Longitude: The longitude of the
 sampling site in decimal degrees * Code: A short code representing the
 sampling site name #### File: 2023_ASV_dna-sequences.fasta
 **Description:** A fasta file of representative DNA sequences of all
 amplicon sequence variants from the 2023 samples #### File:
 CO1_2019samples_9205ASVs_dna-sequences.fasta **Description:** A fasta file
 of representative DNA sequences of all amplicon sequence variants from the
 2019 samples #### File: comp_data_raw.csv **Description:** A csv file with
 taxa used for analysis in the manuscript. It contains the taxonomic ranks
 per species, any taxonomic issues noted (e.g., an outdated species name
 being used by a database), and whether it was detected by
 'traditional' methods (net-based capture, snorkeling, or
 sediment cores), or by eDNA metabarcoding. ##### Variables * Species: The
 species name  * Taxonomic issues: Any taxonomic issues when comparing
 species between previous publications and the eDNA metabarcoding data.
 These could include an outdated species or genus name being used in either
 the 'traditional' or eDNA taxonomic information.  * Phylum: The
 phylum of the species in question * Subphylum/Class: The subphylum/class
 of the species in question * Order: The order of the species in question *
 Family: The family of the species in question * Traditional: Whether the
 species was detected in previous publications using
 'traditional' methods, including net-based capture, snorkeling,
 or sediment cores * eDNA: whether the species was detected in eDNA data
 from 2019 and/or 2023 by Trask et al.  ## Code/software All raw eDNA fastq
 files were first analyzed with FastQC for quality checking, followed by
 the QIIME2 2024.5-amplicon version pipeline. All code for bioinformatics
 and analyses in R are available
 at [https://github.com/dfo-mar-mpas/coastal-invertebrate-metabarcoding](https://github.com/dfo-mar-mpas/coastal-invertebrate-metabarcoding).  The workflow for analyzing these data is as follows:  1\) FastQC - DNA sequence quality control  2\) Import into QIIME2 (2024.5-amplicon version) 3\) Remove forward and reverse COI primers with QIIME2 cutadapt plugin 4\) Denoise and merge sequences in QIIME2 dada2 plugin. An ASV table is produced at this step. 5\) Use COI RDP-classifier v5.0.0 to assign taxonomy to representative sequences for each ASV.  6\) In R 4.4.0, merge sample ASV table and taxonomy assignments for ecological analyses.  7\) R package *vegan* was primarily used to investigate species diversity and community structure (specaccum and nmds functions).  8\) All plots created using ggplot2 in R 4.4.0 ## Access information Other publicly accessible locations of the data: * Raw fastq files are available in NCBI **PRJNA1145319** * These data files will also be made available on the Government of Canada Open Data Platform