16S data from: Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea (Hu et al. 2016)

Registros de Dados

Os dados deste recurso de ocorrência foram publicados como um Darwin Core Archive (DwC-A), que é o formato padronizado para compartilhamento de dados de biodiversidade como um conjunto de uma ou mais tabelas de dados. A tabela de dados do núcleo contém 11.387 registros.

Também existem 2 tabelas de dados de extensão. Um registro de extensão fornece informações adicionais sobre um registro do núcleo. O número de registros em cada tabela de dados de extensão é ilustrado abaixo.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

Andersson A, Karlson B (2023). 16S data from: Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea (Hu et al. 2016). Version 1.10. KTH Royal Institute of Technology. Occurrence dataset. https://www.gbif.se/ipt/resource?r=sbdi-asv-3&v=1.10

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é KTH Royal Institute of Technology. To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: 9e29a2fe-d780-48a8-a93f-9ce041f9202f.  KTH Royal Institute of Technology publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por GBIF Sweden.

Palavras-chave

Occurrence; Observation

Contatos

Anders Andersson

• Provedor Dos Metadados ●
• Originador ●
• Usuário ●
• Ponto De Contato

Associate Professor

KTH Royal Institute of Technology

Science for Life Laboratory

Stockholm

SE

anders.andersson@scilifelab.se

http://orcid.org/0000-0002-3627-6899

Bengt Karlson

• ●
• Provedor Dos Metadados ●
• Originador

Researcher

Swedish Meteorological and Hydrological Institute (SMHI)

Göteborg

SE

Bengt.Karlson@smhi.se

Cobertura Geográfica

Water samples from a transect from Kattegatt to the Gulf of Bothnia

Cobertura Temporal

Dados Sobre o Projeto

Nenhuma descrição disponível

O pessoal envolvido no projeto:

Yue Hu

• Autor

Bengt Karlson

• Autor

Sophie Charvet

• Autor

Anders Andersson

• Autor

http://orcid.org/0000-0002-3627-6899

Métodos de Amostragem

Twenty-one water samples were collected in the Kattegat, the Baltic Proper and the Gulf of Bothnia using a FerryBox system installed in the ship TransPaper during 13th–19th of July 2013. The ship followed the route: Gothenburg (Sweden)—Kemi (Finland)—Oulu (Finland)—Lübeck (Germany)—Gothenburg. The FerryBox system consists of a pump with a water inlet at 3 m depth, a circuit of multiple sensors for temperature, conductivity, chlorophyll and phycocyanin fluorescence, turbidity, and oxygen as well as automated water sampling devices. A detailed description of the FerryBox system is found in Karlson et al. (in press). Manual water sampling for DNA analysis was carried out both on the Northward and Southward legs. Approximately, 10 L of seawater were collected in a polycarbonate carboy. Subsamples of 200–500 mL were filtered onto 0.22 μm pore-size mixed cellulose ester membrane filters (Merck Millipore co., Cat. No. GSWP04700) to capture plankton. The filters were frozen in liquid nitrogen on board and kept at −20 to −80°C until DNA extraction. Genomic DNA was extracted using the PowerWater® DNA isolation kit (MO-BIO Laboratories Inc, Carlsbad CA, USA) following the instructions provided by the manufacturer. The V3-V4 regions of bacterial 16S rRNA genes were PCR amplified with primers 341F (CCTACGGGNGGCWGCAG) and 805R (GACTACHVGGGTATCTAATCC) (Herlemann et al., 2011). A two step PCR procedure was applied (Hugerth et al., 2014a), with 35 (25 + 10) PCR cycles. Between the first and second PCR, and prior to pooling libraries, amplicons were purified with 8.8% PEG 6000 (Polyethylene Glycol 6000) (Merck Millipore co., Cat. No. 528877-1KG) precipitation buffer and CA beads (carboxylic acid-coated superparamagnetic beads) (Dynabeads® MyOne™ Carboxylic Acid, Cat. No. 65012; Lundin et al., 2010). Agilent 2100 Bioanalyzer (Agilent, Technologies, DNA 1000 LabChip kit) and Qubit® 2.0 Fluorometer (Invitrogen, Qubit-IT™ dsDNA HS Assay kit) were used for checking the amplicon fragment sizes and quantification. Equimolar amounts of indexed samples were mixed and sequenced with Illumina MiSeq (Illumina Inc, USA) at NGI/Scilifelab Stockholm. The sequencing reads have been submitted to the European Nucleotide Archive (ENA) under accession numbers PRJEB12362. Sequence processing was not conducted as in the journal publication, but by using the https://nf-co.re/ampliseq pipeline in which the denoising (ASV reconstruction) step was conducted with DADA2.

Descrição dos passos do método:

1. See Sampling Description.

Citações bibliográficas

1. Yue O O Hu, Bengt Karlson, Sophie Charvet, Anders F Andersson. Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea. Front Microbiol. 2016 May 12;7:679. https://doi.org/10.3389/fmicb.2016.00679

Metadados Adicionais