18S Metabarcoding Genetic Observations of Marine Species in the Port of Wallhamn, Sweden (2022)

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、8,639 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。:

Obst M (2024). 18S Metabarcoding Genetic Observations of Marine Species in the Port of Wallhamn, Sweden (2022). Version 1.3. University of Gothenburg. Occurrence dataset. https://www.gbif.se/ipt/resource?r=gu-2022-wallhamn-18s&v=1.3

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 University of Gothenburg。 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: 456b2a82-cc89-4b68-9656-f67252d11b0aが割り当てられています。   GBIF Sweden 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University of Gothenburg が、このリソースをパブリッシュしました。

キーワード

Occurrence; Observation

連絡先

地理的範囲

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

生物分類学的範囲

N/A

時間的範囲

プロジェクトデータ

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.

収集方法

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.

Method step description:

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.

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