Descripción
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.]
Registros
Los datos en este recurso de registros biológicos han sido publicados como Archivo Darwin Core(DwC-A), el cual es un formato estándar para compartir datos de biodiversidad como un conjunto de una o más tablas de datos. La tabla de datos del core contiene 171.746 registros.
también existen 1 tablas de datos de extensiones. Un registro en una extensión provee información adicional sobre un registro en el core. El número de registros en cada tabla de datos de la extensión se ilustra a continuación.
Este IPT archiva los datos y, por lo tanto, sirve como repositorio de datos. Los datos y los metadatos del recurso están disponibles para su descarga en la sección descargas. La tabla versiones enumera otras versiones del recurso que se han puesto a disposición del público y permite seguir los cambios realizados en el recurso a lo largo del tiempo.
Versiones
La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.
¿Cómo referenciar?
Los usuarios deben citar este trabajo de la siguiente manera:
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
Derechos
Los usuarios deben respetar los siguientes derechos de uso:
El publicador y propietario de los derechos de este trabajo es Flanders Research Institute for Agriculture, Fisheries and Food (ILVO). Esta obra está bajo una licencia Creative Commons de Atribución/Reconocimiento (CC-BY 4.0).
Registro GBIF
Este recurso ha sido registrado en GBIF con el siguiente UUID: 652ac1af-3907-4fd3-a509-2151a00bccc2. Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) publica este recurso y está registrado en GBIF como un publicador de datos avalado por Ocean Biodiversity Information System.
Palabras clave
Marine Invertebrates; Belgian Part of the North Sea; COI eDNA metabarcoding; Offshore Wind Farms; Occurrence
Contactos
- Proveedor De Los Metadatos ●
- Originador ●
- Punto De Contacto
https://orcid.org/0009-0006-0636-2477
- Originador
Cobertura geográfica
Belgian part of the North Sea
| Coordenadas límite | Latitud Mínima Longitud Mínima [51,147, 2,586], Latitud Máxima Longitud Máxima [51,676, 3,255] |
|---|
Cobertura temporal
| Fecha Inicial / Fecha Final | 2021-09-01 / 2021-11-30 |
|---|
Datos del proyecto
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.
| Título | Seawater from the North Sea |
|---|---|
| Identificador | PRJNA1032405 |
| Fuentes de Financiación | ILVO |
| Descripción del área de estudio | 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). |
| Descripción del diseño | 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. |
Personas asociadas al proyecto:
Métodos de muestreo
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.
| Área de Estudio | 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. |
|---|---|
| Control de Calidad | 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. |
Descripción de la metodología paso a paso:
- 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.
Referencias bibliográficas
- 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
Metadatos adicionales
| Identificadores alternativos | 652ac1af-3907-4fd3-a509-2151a00bccc2 |
|---|---|
| https://ipt.inbo.be/resource?r=ilvo-metabarcoding-coi-bpns |