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

資料紀錄

此資源出現紀錄的資料已發佈為達爾文核心集檔案（DwC-A），其以一或多組資料表構成分享生物多樣性資料的標準格式。 核心資料表包含 662 筆紀錄。

亦存在 1 筆延伸集的資料表。延伸集中的紀錄補充核心集中紀錄的額外資訊。 每個延伸集資料表中資料筆數顯示如下。

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版本

以下的表格只顯示可公開存取資源的已發布版本。

如何引用

研究者應依照以下指示引用此資源。:

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

權利

研究者應尊重以下權利聲明。:

此資料的發布者及權利單位為 University of Gothenburg。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF 註冊

此資源已向GBIF註冊，並指定以下之GBIF UUID: 37115f2e-a550-40c7-bc2c-f6b697fa7aca。  University of Gothenburg 發佈此資源，並經由GBIF Sweden同意向GBIF註冊成為資料發佈者。

關鍵字

Occurrence; Observation

聯絡資訊

地理涵蓋範圍

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

分類群涵蓋範圍

N/A

時間涵蓋範圍

計畫資料

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.

取樣方法

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.

方法步驟描述:

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.

額外的詮釋資料