Occurrence

eDNA from water column to characterise fish and invertebrate communities from 30 sites in the Belgian Part of the North Sea -COI

Latest version published by Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) on 28 March 2024 Flanders Research Institute for Agriculture, Fisheries and Food (ILVO)

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 171,746 records in English (15 MB) - Update frequency: unknown
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Description

This dataset contains eDNA metabarcoding data of fish species detected in 30 locations in the Belgian Part of the North Sea (BPNS). The seawater samples were collected during two different field campaigns in September and November 2021. The invertebrate species were identified using COI eDNA metabarcoding. The dataset includes amplicon sequence variants and their associated metadata.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 171,746 records.

1 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.

Occurrence (core)
171746
dnaDerivedData 
171746

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Cornelis I, Brosens D, Derycke S (2024). eDNA from water column to characterise fish and invertebrate communities from 30 sites in the Belgian Part of the North Sea -COI. Version 1.2. Flanders Research Institute for Agriculture, Fisheries and Food (ILVO). Occurrence dataset. https://ipt.inbo.be/resource?r=ilvo-metabarcoding-coi-bpns&v=1.2

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is Flanders Research Institute for Agriculture, Fisheries and Food (ILVO). This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 652ac1af-3907-4fd3-a509-2151a00bccc2.  Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Ocean Biodiversity Information System.

Keywords

Marine Invertebrates; Belgian Part of the North Sea; COI eDNA metabarcoding; Offshore Wind Farms; Occurrence

Contacts

Isolde Cornelis
  • Metadata Provider
  • Point Of Contact
Scientist Marine Genomics Lab
ILVO
Jacobsenstraat 1
Oostende
Oost-Vlaanderen
BE
Dimitri Brosens
  • Originator
Research Institute for Nature and Forest/ Belgian Biodiversity Platform
BE
Sofie Derycke
  • Originator
  • Point Of Contact
ILVO
BE
Isolde Cornelis

Geographic Coverage

Belgian part of the North Sea

Bounding Coordinates South West [-90, -180], North East [90, 180]

Temporal Coverage

Start Date / End Date 2021-09-01 / 2021-11-30

Project Data

As part of the Zeroimpact project, we aim to develop an innovative, sustainable and automatic method to detect marine species using environmental DNA (eDNA) and metabarcoding.

Title Seawater from the North Sea
Identifier PRJNA1032405
Funding ILVO
Study Area Description ZERO-IMPACT will map the spatial and temporal patterns of eDNA in the North Sea to efficiently carry out the monitoring of the good state of the environment (WP1 and WP2). In addition, the potential of eDNA for the fisheries sector will be fully explored by focusing on automation (WP4) and by carrying out targeted case studies to identify fish spawning (WP3), shellfish spat (WP5) and the presence of toxic algae and harmful parasites near shellfish culture facilities (WP5).
Design Description The study of different organisms (fish, invertebrates, plankton) can be done based on only one sampling method, and continuous time series for marine biodiversity and fish populations can be obtained through automatic sampling of seawater.

The personnel involved in the project:

Sampling Methods

Sampling: During two different field campaigns in September and November 2021, a total of 12 coastal and 18 offshore locations, situated inside and outside the OWFs C-power (transition zone) and Belwind (offshore zone), were samples. The coastal locations were sampled in triplicate during the September field campaign with the research vessel Simon Stevin using a Niskin carousel. The offshore locations and one coastal location (ft230) were sampled in November 2021 with the research vessel GeoOcean V. During this campaign five biological replicates were taken by successively lowering one Niskin bottle five times. One exception was the coastal site ft230, where only three biological replicates were taken. At each location, seawater was collected at 1 m above the seafloor using a 10 L Niskin bottle. From each 10 L Niskin bottle, a subsample of 2 L was collected in clean commercial plastic drinking water bottles, using a sterilized 200 µm mesh nylon prefilter to remove bigger pieces of debris. Between locations, the Niskin bottles were thoroughly rinsed with commercial source water. The water samples were either immediately filtered on board (GeoOcean V) or stored in the dark at -20 °C (Simon Stevin) until further processing. Each sample was filtered over a 0.45 µm Sterivex polyvinylidene fluoride (PVDF) filter until the filter was nearly clogged or until 1 L was filtered. The filters were stored at -20 °C until eDNA extraction.

Study Extent The construction of offshore wind farms may affect local soft-sediment fauna. Hence, an efficient monitoring technique is needed to monitor the potential effects on the marine ecosystem. Here, we assess whether eDNA metabarcoding is a suitable alternative to monitor fish and epibenthos biodiversity in these difficult to access marine habitats. Water sampling and trawl surveys were conducted in parallel in 12 coastal and 18 offshore sites, the latter located inside and outside two offshore wind farms in the Belgian part of the North Sea.
Quality Control Negative control samples were collected in the field and laboratory environments. Negative field controls were taken by collecting commercial source water from the Niskin bottles after they were carefully rinsed using commercial source water, also using the prefilter. Negative filter controls were included by filtering source water over a blanco 0.45 µm Sterivex filter. Negative extraction controls were included by applying the extraction protocol on blanco 0.45 µM Sterivex filters. Negative PCR controls were included by replace the extracted eDNA with 3 µl of UltraPure™ water.

Method step description:

  1. eDNA extraction: After overnight incubation with the lysisbuffer at 56°C, the eDNA was extracted using the DNeasy Blood and Tissue kit (Qiagen).
  2. Library preparation: The genetic analysis was based on two molecular markers (12S for the fish species, and COI for the invertebrate species). A one-step amplification protocol was used in triplicate using fusion primers (Sigma Aldrich), which contained the template specific primer sequence and a unique barcode tag of 6 to 10 nucleotides. After amplification, the PCR replicates were pooled and purified using magnetic CleanNGS beads (CleanNA). After purification, the COI pools were quality checked on the BioAnalyzer. The eDNA libraries were sequenced with Illumina MiSeq, 2 x 300 bp.
  3. Bioinformatic processing: The quality of the raw Illumina MiSeq sequencing reads was verified with FASTQC v0.11.9. The paired-end reads were then reorientated, demultiplexed and trimmed by using cutadapt. After demultiplexing, DADA2 was used for denoising, dereplication, merging, and removing of chimeric reads from the demultiplexed sequences. The taxonomic assignment of the resulting ASV sequences was performed against a custom made reference database using RDP classifier in DADA2 with a minimum bootstrapping support of 80. ASVs that remained unassigned at species level with RDP were successively run with BLASTn v2.12.0 against the custom made reference databases and the GenBank nucleotide database (from October 2022). After taxonomic assignment, the count table was cleaned by removing all the ASVs identified as contaminant by the prevalence method in Decontam using the field, filter, DNA extraction and PCR negative control samples.

Bibliographic Citations

  1. Maes, S. M., Desmet, S., Brys, R., Sys, K., Ruttink, T., Maes, S., … Derycke, S. (2024). Detection and quantification of two commercial flatfishes (Solea solea and Pleuronectes platessa) in the North Sea using environmental DNA. Environmental DNA, 6(1). https://doi.org/10.1002/edn3.426 DOI: 10.1002/edn3.426

Additional Metadata