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

Данные в формате DwC-A	Скачать 662 Записи в English (83 KB) - Частота обновления: неизвестно
Метаданные в формате EML	Скачать в English (29 KB)
Метаданные в формате RTF	Скачать в English (15 KB)

Описание

This dataset contains genetic observations of marine species in the port of Wallhamn between June and September 2022. The observations were made using water and plankton samples, as well as samples from Autonomous Reef Monitoring Structures (ARMS) units. Species were identified using COI metabarcoding. The dataset includes ASVs (amplicon sequence variants) and their associated metadata. This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/).

Записи данных

Данные этого occurrence ресурса были опубликованы в виде Darwin Core Archive (DwC-A), который является стандартным форматом для обмена данными о биоразнообразии в виде набора из одной или нескольких таблиц. Основная таблица данных содержит 662 записей.

Также в наличии 1 таблиц с данными расширений. Записи расширений содержат дополнительную информацию об основной записи. Число записей в каждой таблице данных расширения показано ниже.

662

Данный экземпляр IPT архивирует данные и таким образом служит хранилищем данных. Данные и метаданные ресурсов доступны для скачивания в разделе Загрузки. В таблице версий перечислены другие версии ресурса, которые были доступны публично, что позволяет отслеживать изменения, внесенные в ресурс с течением времени.

Версии

В таблице ниже указаны только опубликованные версии ресурса, которые доступны для свободного скачивания.

Как оформить ссылку

Исследователи должны дать ссылку на эту работу следующим образом:

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

Права

Исследователи должны соблюдать следующие права:

Публикующей организацией и владельцем прав на данную работу является University of Gothenburg. Эта работа находится под лицензией Creative Commons Attribution (CC-BY 4.0).

Регистрация в GBIF

Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: 37115f2e-a550-40c7-bc2c-f6b697fa7aca. University of Gothenburg отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке GBIF Sweden.

Ключевые слова

Occurrence; Observation

Контакты

Matthias Obst

Metadata Provider ●
Originator ●
Point Of Contact

Project Leader

Gothenburg University

matthias.obst@marine.gu.se

Географический охват

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

Ограничивающие координаты	Юг Запад [58,004, 11,697], Север Восток [58,011, 11,703]

Таксономический охват

N/A

Kingdom	Chromista, Animalia, Unassigned
Phylum	Mollusca, Arthropoda, Annelida, Chordata, Myzozoa, Phoronida, Cnidaria
Class	Hydrozoa, Dinophyceae, Polychaeta, Phoronida_X, Insecta, Bivalvia, Copepoda, Mammalia, Gastropoda
Order	Diptera, Calanoida, Ostreida, Gonyaulacales, Polychaeta_X, Cephalaspidea, Phyllodocida, Gastropoda_X, Venerida, Littorinimorpha, Carnivora, Phoronida_XX, Cyclopoida, Leptothecata
Family	Pectinariidae, Campanulariidae, Canidae, Gonyaulacales_X, Veneridae, Cerithiidae, Phoronidae, Oithonidae, Chironomidae, Philinidae, Spionidae, Ostreidae, Hydrobiidae, Nereididae, Centropagidae, Acartiidae

Временной охват

Дата начала / Дата окончания	2022-06-23 / 2022-09-09

Данные проекта

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.

Название	Övervakning främmande arter: jämförelse eRAS och DNA-baserad inventering Wallhamn (Tjörn)
Финансирование	This project was funded by the Swedish Agency for Marine and Water Management
Описание района исследования	The port of Wallhamn (Sweden), located in a bay, has both a commercial/industrial part in the North and a marina in the South that are separated by a few hundred meters.
Описание плана выполнения исследований	eRAS includes growth plates, artificial habitats, scraping on existing structures, and visual observations of non-native species. The DNA-based identification is based on settling panels (ARMS), plankton samples, and eDNA from filtered water samples. The outputs of both methods were then compared to estimate their abilities to identify species and detect potential invasive species.

Методы сбора

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.

Охват исследования	The different sampling methods had different timings over the summer 2022: The eRAS panels were put out on the 23rd of June and taken back on the 9th of September, one was in the industrial port, three were in the marina. The artificial habitats were put out on the 23rd of June and taken back on the 4th of August, one in each area. The ARMS were put out on the 23rd of June and taken back on the 9th of September, one in the industrial port and two in the marina. In the marina, three plankton samplings occurred on the 23rd of June, the 4th of August and the 9th of September (9 plankton samples in total). Similarly, in the marina, three eDNA samplings occurred on the 23rd of June, the 4th of August and the 9th of September (9 eDNA samples in total). Three scraping/RAS samplings occured on the 9th of September in the marina.
Контроль качества	Negative controls (blank samples) were created by the same extraction procedure but without the sampled material. No DNA could be detected in these samples, with neither Nanodrop nor Qubit. The blank samples were included in the preparation of libraries (below) as a further control for contamination during the extraction of DNA. Another negative control was performed during PCR.

Охват исследования

The different sampling methods had different timings over the summer 2022: The eRAS panels were put out on the 23rd of June and taken back on the 9th of September, one was in the industrial port, three were in the marina. The artificial habitats were put out on the 23rd of June and taken back on the 4th of August, one in each area. The ARMS were put out on the 23rd of June and taken back on the 9th of September, one in the industrial port and two in the marina. In the marina, three plankton samplings occurred on the 23rd of June, the 4th of August and the 9th of September (9 plankton samples in total). Similarly, in the marina, three eDNA samplings occurred on the 23rd of June, the 4th of August and the 9th of September (9 eDNA samples in total). Three scraping/RAS samplings occured on the 9th of September in the marina.

Контроль качества

Negative controls (blank samples) were created by the same extraction procedure but without the sampled material. No DNA could be detected in these samples, with neither Nanodrop nor Qubit. The blank samples were included in the preparation of libraries (below) as a further control for contamination during the extraction of DNA. Another negative control was performed during PCR.

Описание этапа методики:

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.
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.
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.
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.

Дополнительные метаданные

Альтернативные идентификаторы	37115f2e-a550-40c7-bc2c-f6b697fa7aca
	https://www.gbif.se/ipt/resource?r=gu-2022-wallhamn-coi