Hypolithic and soil bacteria in Miers_Valley, 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 (16S ssu rRNA gene, v3 region) in hypolithic and soil environments of Miers Valley, Antarctica

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Makhalanyane T, Valverde A, Birkeland N, Cary S, Tuffin M, Cowan D (2019): Hypolithic and soil bacteria in Miers_Valley, Antarctica. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=hypolithic_bacteria_miers_valley_antarctica&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: a126be3e-2889-48df-9d6a-357da4198353。  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:

Thulani Makhalanyane
University of Pretoria Pretoria ZA
Angel Valverde
University of Pretoria Pretoria ZA
Nils-Kare Birkeland
University of Bergen Bergen NO
Stephen Cary
University of Waikato Hamilton NZ
Marla Tuffin
University of Pretoria Pretoria ZA
Don Cowan
University of Pretoria Pretoria ZA

可回覆此資源相關問題者:

Thulani Makhalanyane
University of Pretoria Pretoria ZA
Don Cowan
University of Pretoria Pretoria ZA

元數據填寫者:

Maxime Sweetlove
Research assistant
Royal Belgian Institute for 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

Miers Valley, Antarctica

界定座標範圍 緯度南界 經度西界 [-78.1, 164], 緯度北界 經度東界 [-78.1, 164]

分類群涵蓋範圍

Bacteria (16S ssu rRNA gene, v3 region)

Domain  Bacteria (Bacteria)

計畫資料

無相關描述

計畫名稱 Hypolithic and soil bacteria in Miers_Valley, Antarctica
經費來源 Financial support for this resource was provided by the following organizations: the National Research Foundation (South Africa), the Research Council of Norway (the South Africa Program; grant no. 180352) and the University of the Western Cape.

The personnel involved in the project:

Thulani Makhalanyane

取樣方法

A total of 36 samples were collected, 9 from each of the three hypolith types and soil (that is, four habitats), and stored in sterile Whirl-Pak bags (Nasco Inter- national, Fort Atkinson, WI, USA). Equivalent amounts of hypolithic and soil samples were collected aseptically in an area of 1 km2 with similar macro-environmental conditions (that is, slope, aspect, elevation). The spatial arrangement of samples was also similar between habitats, therefore, allowing us to compare the potential influence of micro-environmental factors on beta-diversity across a similar spatial scale.

研究範圍 Samples were collected from the coastal Miers Valley region of Eastern Antarctica during the summer season of 2010.

方法步驟描述:

  1. MoBio PowerSoil DNA isolation kit (Mo BIO, Carlsbad, CA, USA). Adsorbed DNA was eluted in 40ml of tris-EDTA buffer and quantified using the Nanodrop 1000 spectrophotometer (NanoDrop Products, Wilmington, DE, USA).
  2. In order to reduce the number of samples for 454 pyrosequencing, equal amounts of DNA from each of the nine samples were pooled according to habitat (n= 4).
  3. Unique four base pair multiplex identifiers were added to the primers for each sample. PCR amplification of the highly variable V3 region of the bacterial 16S rRNA gene was carried out in two steps using HotStar DNA polymerase (QIAGEN GmbH, Hilden, Germany), based on the universal bacterial primers, A8-28F and K517R. In the first PCR step, untagged primers were used in a 20-cycle reaction as described by Azmuda et al. (2012), followed by purification of the amplicons using the GenElute PCR Clean-Up Kit (Sigma-Aldrich, Copenhagen, Denmark). The second reaction was performed with 100ng of the purified PCR amplicons as template and primers containing the 454 FLX adaptors with sample-specific multiple identifiers using 10 PCR reaction cycles (Azmuda et al., 2012). The final products were purified using the Agencourt AMPure purification kit (Agencourt Bioscience Corporation (Beckman Coulter), Beverly, MA, USA) before shipment to GATC Biotech AG (Konstanz, Germany) for pyrosequencing with the GS FLX (Roche 454 Life Sciences, Branford, CT, USA) Titanium chemistry.

引用文獻

  1. Makhalanyane, T. P., Valverde, A., Birkeland, N. K., Cary, S. C., Tuffin, I. M., & Cowan, D. A. (2013). Evidence for successional development in Antarctic hypolithic bacterial communities. The ISME journal, 7(11), 2080.

額外的元數據

替代的識別碼 a126be3e-2889-48df-9d6a-357da4198353
https://ipt.biodiversity.aq/resource?r=hypolithic_bacteria_miers_valley_antarctica