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

資料紀錄

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亦存在 2 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

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如何引用

研究者應依照以下指示引用此資源。:

Andersson A, Karlson B (2024). 16S data from: Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea (Hu et al. 2016). Version 1.11. KTH Royal Institute of Technology. Occurrence dataset. https://www.gbif.se/ipt/resource?r=sbdi-asv-3&v=1.11

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 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 註冊

此資源已向GBIF註冊，並指定以下之GBIF UUID: 9e29a2fe-d780-48a8-a93f-9ce041f9202f。  KTH Royal Institute of Technology 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

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

時間涵蓋範圍

計畫資料

無相關描述

參與計畫的人員:

取樣方法

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.

方法步驟描述:

1. See Sampling Description.

引用文獻

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

額外的詮釋資料