説明
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. [This dataset was processed using the GBIF eDNA converter tool.]
データ レコード
この オカレンス（観察データと標本) リソース内のデータは、1 つまたは複数のデータ テーブルとして生物多様性データを共有するための標準化された形式であるダーウィン コア アーカイブ (DwC-A) として公開されています。 コア データ テーブルには、171,746 レコードが含まれています。
拡張データ テーブルは1 件存在しています。拡張レコードは、コアのレコードについての追加情報を提供するものです。 各拡張データ テーブル内のレコード数を以下に示します。
この IPT はデータをアーカイブし、データ リポジトリとして機能します。データとリソースのメタデータは、 ダウンロード セクションからダウンロードできます。 バージョン テーブルから公開可能な他のバージョンを閲覧でき、リソースに加えられた変更を知ることができます。
バージョン
次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。
引用方法
研究者はこの研究内容を以下のように引用する必要があります。:
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 1.8. Flanders Research Institute for Agriculture, Fisheries and Food (ILVO). Occurrence dataset. https://ipt.inbo.be/resource?r=ilvo-metabarcoding-coi-bpns&v=1.8
権利
研究者は権利に関する下記ステートメントを尊重する必要があります。:
パブリッシャーとライセンス保持者権利者は Flanders Research Institute for Agriculture, Fisheries and Food (ILVO)。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF登録
このリソースをはGBIF と登録されており GBIF UUID: 652ac1af-3907-4fd3-a509-2151a00bccc2が割り当てられています。 Ocean Biodiversity Information System によって承認されたデータ パブリッシャーとして GBIF に登録されているFlanders Research Institute for Agriculture, Fisheries and Food (ILVO) が、このリソースをパブリッシュしました。
キーワード
Marine Invertebrates; Belgian Part of the North Sea; COI eDNA metabarcoding; Offshore Wind Farms; Occurrence
連絡先
- メタデータ提供者 ●
- 最初のデータ採集者 ●
- 連絡先
https://orcid.org/0009-0006-0636-2477
- 最初のデータ採集者
地理的範囲
Belgian part of the North Sea
| 座標（緯度経度） | 南 西 [51.147, 2.586], 北 東 [51.676, 3.255] |
|---|
時間的範囲
| 開始日 / 終了日 | 2021-09-01 / 2021-11-30 |
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プロジェクトデータ
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.
| タイトル | Seawater from the North Sea |
|---|---|
| 識別子 | PRJNA1032405 |
| ファンデイング | 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). |
| 研究の意図、目的、背景など（デザイン） | 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. |
プロジェクトに携わる要員:
収集方法
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:
- eDNA extraction: After overnight incubation with the lysisbuffer at 56°C, the eDNA was extracted using the DNeasy Blood and Tissue kit (Qiagen).
- 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.
- 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.
書誌情報の引用
- 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
追加のメタデータ
| 代替識別子 | 652ac1af-3907-4fd3-a509-2151a00bccc2 |
|---|---|
| https://ipt.inbo.be/resource?r=ilvo-metabarcoding-coi-bpns |