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

Datos como un archivo DwC-A	descargar 662 registros en Inglés (83 KB) - Frecuencia de actualización: desconocido
Metadatos como un archivo EML	descargar en Inglés (29 KB)
Metadatos como un archivo RTF	descargar en Inglés (15 KB)

Descripción

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/).

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 662 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.

662

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:

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

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es University of Gothenburg. 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: 37115f2e-a550-40c7-bc2c-f6b697fa7aca. University of Gothenburg publica este recurso y está registrado en GBIF como un publicador de datos avalado por GBIF Sweden.

Palabras clave

Occurrence; Observation

Contactos

Matthias Obst

Proveedor De Los Metadatos ●
Originador ●
Punto De Contacto

Project Leader

Gothenburg University

matthias.obst@marine.gu.se

Cobertura geográfica

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

Coordenadas límite	Latitud Mínima Longitud Mínima [58,004, 11,697], Latitud Máxima Longitud Máxima [58,011, 11,703]

Cobertura taxonómica

N/A

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

Cobertura temporal

Fecha Inicial / Fecha Final	2022-06-23 / 2022-09-09

Datos del proyecto

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.

Título	Övervakning främmande arter: jämförelse eRAS och DNA-baserad inventering Wallhamn (Tjörn)
Fuentes de Financiación	This project was funded by the Swedish Agency for Marine and Water Management
Descripción del área de estudio	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.
Descripción del diseño	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.

Métodos de muestreo

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.

Área de Estudio	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.
Control de Calidad	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.

Área de Estudio

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.

Control de Calidad

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.

Descripción de la metodología paso a paso:

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.

Metadatos adicionales

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