Hypolithic and soil bacteria in Miers_Valley, Antarctica

最新バージョン SCAR - Microbial Antarctic Resource System によって公開 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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バージョン

次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。

引用方法

研究者はこの研究内容を以下のように引用する必要があります。:

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

権利

研究者は権利に関する下記ステートメントを尊重する必要があります。:

パブリッシャーとライセンス保持者権利者は SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF登録

このリソースをはGBIF と登録されており GBIF UUID: a126be3e-2889-48df-9d6a-357da4198353が割り当てられています。   Scientific Committee on Antarctic Research によって承認されたデータ パブリッシャーとして GBIF に登録されているSCAR - Microbial Antarctic Resource System が、このリソースをパブリッシュしました。

キーワード

Metadata

連絡先

リソースを作成した人:

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

リソースに関する質問に答えることができる人:

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

メタデータを記載した人:

Maxime Sweetlove
Research assistant
Royal Belgian Institute for Natural Sciences Rue Vautier 29 1000 Brussels BE

他に、リソースに関連付けられていた人:

データ利用者

地理的範囲

Miers Valley, Antarctica

座標(緯度経度) 南 西 [-78.1, 164], 北 東 [-78.1, 164]

生物分類学的範囲

Bacteria (16S ssu rRNA gene, v3 region)

Domain  Bacteria (Bacteria)

プロジェクトデータ

説明がありません

タイトル Hypolithic and soil bacteria in Miers_Valley, Antarctica
ファンデイング 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.

プロジェクトに携わる要員:

Thulani Makhalanyane

収集方法

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.

Study Extent Samples were collected from the coastal Miers Valley region of Eastern Antarctica during the summer season of 2010.

Method step description:

  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.

書誌情報の引用

  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.

追加のメタデータ

代替識別子 a126be3e-2889-48df-9d6a-357da4198353
https://ipt.biodiversity.aq/resource?r=hypolithic_bacteria_miers_valley_antarctica