COI Metabarcoding Genetic Observations of Marine Species in the Port of Wallhamn, Sweden (2022)

Enregistrements de données

Les données de cette ressource occurrence ont été publiées sous forme d'une Archive Darwin Core (Darwin Core Archive ou DwC-A), le format standard pour partager des données de biodiversité en tant qu'ensemble d'un ou plusieurs tableurs de données. Le tableur de données du cœur de standard (core) contient 662 enregistrements.

1 tableurs de données d'extension existent également. Un enregistrement d'extension fournit des informations supplémentaires sur un enregistrement du cœur de standard (core). Le nombre d'enregistrements dans chaque tableur de données d'extension est illustré ci-dessous.

Cet IPT archive les données et sert donc de dépôt de données. Les données et métadonnées de la ressource sont disponibles pour téléchargement dans la section téléchargements. Le tableau des versions liste les autres versions de chaque ressource rendues disponibles de façon publique et permet de tracer les modifications apportées à la ressource au fil du temps.

Versions

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Obst M (2023). COI Metabarcoding Genetic Observations of Marine Species in the Port of Wallhamn, Sweden (2022). Version 1.4. University of Gothenburg. Occurrence dataset. https://www.gbif.se/ipt/resource?r=gu-2022-wallhamn-coi&v=1.4

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est University of Gothenburg. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 37115f2e-a550-40c7-bc2c-f6b697fa7aca.  University of Gothenburg publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du GBIF Sweden.

Mots-clé

Occurrence; Observation

Contacts

Couverture géographique

This dataset covers the port of Wallhamn (Sweden) which has both a commercial/industrial part in the North and a marina in the South.

Couverture taxonomique

N/A

Couverture temporelle

Données sur le projet

A comparison between eRAS (extended rapid assessment) and DNA-based identification of native and invasive species has been performed based on sampling in the port of Wallhamn. Wallhamn has been chosen out of five harbours (Strömstad, Smögen, Kungshamn, Oxelösund, Wallhamn) based on its proximity to Gothenburg and the fact that it is an established harbour with a large number of ships calling every year.

Méthodes d'échantillonnage

Artificial habitats are plastic trays filled with pottery shards, a weight at the bottom to hold the trays down and a net above to keep the shards in place. On two sides, larger holes were cut to allow fish to move freely in and out of the habitat Plankton samples were taken as vertical hauls from the bottom (5-10 m) up to the surface with a 90 µm plankton bucket. The samples were fixed in 95% ethanol directly in place with an amount of alcohol that was judged to result in a sample with at least 70% ethanol. Upon return to the lab, the plankton samples were decanted and new alcohol was added to ensure that the ethanol content was sufficiently high. The samples were then stored in a freezer (-20°C) until extraction. Water samples for eDNA were taken with Ruttner retrievers at slightly different depths on the premises and pooled in a 1 litre vessel. Water was filtered on site and fixed with 95% ethanol.The filters were stored in a freezer (-20°C) until extraction.

Description des étapes de la méthode:

1. DNA was extracted from the filters with the Nucleospin eDNA water kit (Macherey-Nagel) using the Nagel) using the technique and standard developed in the laboratory. Concentration of DNA in the extracts was measured with the Qubit® fluorometer. Note that this measures concentration of all DNA in the sample and not specific DNA from the target species. This is done to ensure that the extractions have worked.
2. The genetic analysis and comparison was based on two molecular markers (COI and 18S). These markers were amplified for each sample. Same PCR protocols were used for metabarcoding of the ARMS, eDNA and plankton samples The DNA libraries were sequenced with Illumina MiSeq, 2 x 300 bp.
3. The analysis was performed in the R-environment with a DADA2 package. After initial quality control, the sequences were filtered for low quality, as well as adapters and primers were removed. Sequencing errors were corrected by calculating an error model; and after that singletons and chimeras were removed using the “pseudo-pooling” function in DADA2.
4. The filtered and quality-controlled COI sequences were matched against the BOLD database with the python package BOLDigger. The 18S sequences were matched against the PR2 database. All subsequent analysis was performed with customized R scripts where identified species were matched against different NIS and IAS species reference lists.

Métadonnées additionnelles