Bacteria and Archaea in different soil types on King George Island (South Shetland Islands, Antarctica)

最新版本 由 SCAR - Microbial Antarctic Resource System 發佈於 Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (454 pyrosequencing) of Bacteria and Archaea (16S ssu rRNA gene) in three sets of environmentally distinct soil samples on King George Island (Antarctica)

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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。:

Pershina E, Ivanova E, Abakumov E, Andronova E (2019): Bacteria and Archaea in different soil types on King George Island (South Shetland Islands, Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacteria_and_archaea_in_different_king_george_island_soils&v=1.1

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

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此資源已向GBIF註冊,並指定以下之GBIF UUID: 84d7d83b-94d2-4d44-a541-2c9e51e0f972。  SCAR - Microbial Antarctic Resource System 發佈此資源,並經由Scientific Committee on Antarctic Research同意向GBIF註冊成為資料發佈者。

關鍵字

Metadata

聯絡資訊

資源建立者:

E. Pershina
All-Russia Research Institute for Agricultural Microbiology St. Petersburg RU
E. Ivanova
All-Russia Research Institute for Agricultural Microbiology St. Petersburg RU
E. Abakumov
St. Petersburg State University St. Petersburg RU
E. Andronova
All-Russia Research Institute for Agricultural Microbiology St. Petersburg RU

可回覆此資源相關問題者:

E. Pershina
All-Russia Research Institute for Agricultural Microbiology St. Petersburg RU

元數據填寫者:

Maxime Sweetlove
Research assistent
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels BE

與此資源的相關者:

使用者

地理涵蓋範圍

King George Island (Southern Shetland Islands:Antarctica)

界定座標範圍 緯度南界 經度西界 [-62.276, -59.032], 緯度北界 經度東界 [-62.113, -58.938]

分類群涵蓋範圍

Bacteria and Archaea (16S ssu rRNA gene, v4 region)

Domain  Bacteria (Bacteria),  Archaea (Archaea)

時間涵蓋範圍

起始日期 / 結束日期 2016-01-22 / 2016-02-02

計畫資料

無相關描述

計畫名稱 Soil biota dynamics in chronoseries of post-technogenic landscapes: analyses of soil ecological effectiveness of ecosystems restoration
經費來源 This work was supported by the Russian Scientific Foundation projects 17-16-01030, ‘Soil biota dynamics in chronoseries of post-technogenic landscapes: analyses of soil ecological effectiveness of ecosystems restoration’ (soil sampling, agrochemical analysis, preparation of the manuscript), and 14-26-00094 P, ‘Analysis of the soil microbiomes’ genetic and evolutionary potential for increasing plant productivity and soil fertility’ (molecular analysis, pyrosequencing, bioinformatics).

The personnel involved in the project:

E. Pershina

取樣方法

Soil samples (50 g) were collected from five points at each site by the ‘envelope method’ (four points in the corners of the square and one in the centre). All samples were homogenized, and five subsamples of 0.2 g each were used for the DNA extractions.

研究範圍 Soils samples were taken from King George Island (Fildes Peninsula) and Nelson Island during the 61st Russian Antarctic expedition in 2016.

方法步驟描述:

  1. Following the manufacturer’s instructions, DNA was extracted from the 0.2 g soil samples using the PowerSoil DNA Isolation Kit (Mobio Laboratories, Solana Beach, CA, USA), which included a bead-beating step. The samples were homogenized twice using a Precellys 24 tissue homogenizer (Bertin Corp, USA) for 30 s at 6.5 m s-1. The purity and quantity of the DNA were tested by electrophoresis in 0.5 × TAE buffer on 1% agarose gels. DNA concentrations were measured at 260nm using a SPECTROStar Nano microplate reader (BMG Labtech, Ortenberg, Germany). The average DNA yield was 2–5 μg at concentrations of 10–50 ng μL-1. The purified DNA templates were amplified with the universal multiplex primers F515 5′-GTGCCAGCMGCCGCGGTAA-3′ and R806 5′-GGACTACVSGGGTATCTAAT-3′ (Bates et al. 2011), which target the variable V4 region of bacterial and archaeal 16S rRNA genes. Each multiplex primer contained the adapter, a 4 bp key (TCAG), a 10 bp barcode, and the primer sequences. The amplified product was expected to be 400 bp long. The purification, pooling and pyrosequencing of the amplicons were performed with specified reagents according to the manufacturer’s instructions (Roche, Branford, USA). Pyrosequencing was performed with a Roche 454 GS Junior system in the Core Centrum ‘Genomic Technologies, Proteomics and Cell Biology’ (All-Russia Research Institute for Agricultural Microbiology).

引用文獻

  1. Pershina, E. V., Ivanova, E. A., Abakumov, E. V., & Andronov, E. E. (2018). The impacts of deglaciation and human activity on the taxonomic structure of prokaryotic communities in Antarctic soils on King George Island. Antarctic Science, 30(5), 278-288.

額外的元數據

替代的識別碼 84d7d83b-94d2-4d44-a541-2c9e51e0f972
https://ipt.biodiversity.aq/resource?r=bacteria_and_archaea_in_different_king_george_island_soils