eDNA from water column to characterise fish and invertebrate communities from 30 sites in the Belgian Part of the North Sea -12S

Registros biológicos
Última versión publicado por Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) el jun. 21, 2024 Flanders Research Institute for Agriculture, Fisheries and Food (ILVO)

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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 fish species were identified using 12S eDNA metabarcoding. The dataset includes amplicon sequence variants and their associated metadata. Study extend: 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. project ID: Bioproject Accession - PRJNA1032405 (https://www.ncbi.nlm.nih.gov/bioproject/1032405) [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 77.591 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.

Occurrence (core)
77591
dnaDerivedData 
77591

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 -12S. Version 1.4. Flanders Research Institute for Agriculture, Fisheries and Food (ILVO). Occurrence dataset. https://ipt.inbo.be/resource?r=ilvo-metabarcoding-12s-bpns&v=1.4

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: 8fd84a4f-bbed-490b-9ca4-c0a3d0aea079.  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 Fish Diversity; Belgian Part of the North Sea; 12S eDNA metabarcoding; Offshore Wind Farms; Occurrence

Contactos

Isolde Cornelis
  • Proveedor De Los Metadatos
  • Punto De Contacto
  • Scientist Marine Genomics Lab
ILVO
  • Jacobsenstraat 1
Oostende
Oost-Vlaanderen (nl)
BE
Dimitri Brosens
  • Originador
Research Institute for Nature and Forest/ Belgian Biodiversity Platform
BE
Sofie Derycke
  • Punto De Contacto
ILVO
BE
Isolde Cornelis
  • Proveedor De Los Metadatos
  • Punto De Contacto
Sofie Derycke
  • Punto De Contacto
  • Senior scientist Marine Genomics Lab
ILVO
  • Jacobsenstraat 1
Oostende
Oost-Vlaanderen (nl)
BE

Cobertura temporal

Fecha Inicial / Fecha Final 2021-09-01 / 2021-11-30

Datos del proyecto

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. project ID: (https://www.ncbi.nlm.nih.gov/bioproject/1032405)

Título Automated biodiversity monitoring in the North Sea through eDNA ZERO-IMPACT
Identificador PRJNA1032405
Fuentes de Financiación ILVO
Descripción del 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.
Descripción del diseño Is it feasible to detect the presence of marine organisms based on “environmental” DNA (eDNA) in seawater? The ZERO impact project has answered this research question positively. The aim was to develop an innovative, sustainable and automatic method to detect marine species and marine biodiversity in a reliable and less invasive way. There are several advantages to this eDNA technique: 1/ because only seawater is collected to detect the presence of species, the organisms themselves are not disturbed or killed, 2/ only one sampling method is needed to identify different groups of organisms (fish, invertebrates, plankton), and 3/ by autonomous seawater collection, continuous time series for marine biodiversity and fish populations can be obtained.

Personas asociadas al proyecto:

Sofie Derycke

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 sampled.

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 eDNA

Descripción de la metodología paso a paso:

  1. 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
  2. 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.
  3. eDNA extraction After overnight incubation with the lysisbuffer at 56°C, the eDNA was extracted using the DNeasy Blood and Tissue kit (Qiagen).
  4. 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 three 12S were quality checked on the BioAnalyzer. The eDNA libraries were sequenced with Illumina MiSeq, 2 x 300 bp.
  5. 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

  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

Metadatos adicionales

Identificadores alternativos 8fd84a4f-bbed-490b-9ca4-c0a3d0aea079
https://ipt.inbo.be/resource?r=ilvo-metabarcoding-12s-bpns