メタデータ

Microbiome (Bacteria, Archaea and fungi) from University Valley Permafrost cores (Antarctica)

最新バージョン SCAR - Microbial Antarctic Resource System によって公開 2019/03/19 SCAR - Microbial Antarctic Resource System

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説明

Amplicon sequencing dataset (Bacteria and Archaea based on 16S ssu rRNA gene, Fungi and other eukaryotes, based on the ITS marker) of microorganisms in permafrost samples (two cores with three different depths) taken in University Valley, Antarctica.

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。:

Goordial J, Davila A, Lacelle D, Pollard W, Marinova M, Greer C, DiRuggiero J, McKay C, Whyte L (2019): Microbiome (Bacteria, Archaea and fungi) from University Valley Permafrost cores (Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbiome_university_valley_permafrost_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: 3d255a2a-c297-4588-b67c-e0c2b4a31709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:
-

Jacqueline Goordial
McGill University
Ste-Anne-de-Bellevue
CA
Alfonso Davila
NASA Ames Research Center
Moffett Field
US
Denis Lacelle
University of Ottawa
Ottawa
CA
Wayne Pollard
McGill University
Montreal
CA
Margarita Marinova
NASA Ames Research Center
Moffett Field
US
Charles Greer
National Research Council Canada
Montreal
CA
Jocelyn DiRuggiero
The Johns Hopkins University
Baltimore
US
Christopher McKay
NASA Ames Research Center
Moffett Field
US
Lyle Whyte
McGill University
Ste-Anne-de-Bellevue
CA

リソースに関する質問に答えることができる人:

Jacqueline Goordial
McGill University
Ste-Anne-de-Bellevue
CA

メタデータを記載した人:
-

Maxime Sweetlove
Research assistent
Royal Belgian Institute of 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

University Valley, McMurdo Dry Valleys, Antarctica

座標(緯度経度) 南 西 [-77.864, 160.729], 北 東 [-77.864, 160.729]

生物分類学的範囲

Bacteria were profiled by targeting the 16S ssu rRNA gene

Domain Bacteria (Bacteria)

Archaea were profiled by targeting the 16S ssu rRNA gene

Domain Archaea (Archaea)

Fungi (and some other Eukaryote groups) were profiled by targeting the ITS marker

Phylum Fungi (Fungi)

プロジェクトデータ

説明がありません

タイトル Microbiome (Bacteria, Archaea and fungi) from University Valley Permafrost cores (Antarctica)
ファンデイング This work was supported by NASA ASTEP program and with field support via NSF/OPP (project B-302-M). Support was provided by the Natural Sciences and Engineering Research Council (NSERC) Discovery Grant Program, NSERC Northern Supplements Program and NSERC CREATE Canadian Astrobiology Training Program (CATP).

プロジェクトに携わる要員:

Jacqueline Goordial

収集方法

University Valley permafrost core samples were collected with a SIPRE corer (USA Cold Regions Research and Engineering Laboratory, Hanover, NH, USA). The cores were 0.3 km apart from each other. Samples were shipped to McGill University in a thermally insulated box and maintained at −20 °C until processing. All sample handling and processing were carried out according to protocols developed for low biomass permafrost soils to minimize contamination. Initial core processing took place in a walk-in freezer held at −5 °C in a dedicated laminar flow hood where 1 cm of the outside of the core was removed with a sterilized chisel. An additional 1 cm of the outside core was removed in a biological safety cabinet at room temperature immediately before samples being weighed and aliquoted for analysis. Dedicated biological safety cabinets, which had been pretreated to remove DNA/RNA or cells, were used for sample processing, nucleic acid extraction and PCR preparation.

Study Extent Samples were taken in December 2009 from permafrost soils in University Valley (1650–1800 m above sea level (a.s.l.)), located 450 m above Beacon Valley in the Quartermain Range. Samples analysed in this study were located near the head of the valley close to the glacier, a shadowed region where the soil surface experiences few thaw hours, and where the uppermost 50 cm of ice content in the ice-cemented permafrost formed from water vapour diffusion into the cryotic soils rather than from liquid water.
Quality Control Negative controls (H2O in place of soil) underwent identical handling during the extraction procedure and were used as templates for PCR using 16S rRNA gene primers (27 F and 1492 R) to ensure no contamination during extraction.

Method step description:

  1. Community DNA was extracted from 2 g of permafrost soil using the UltraClean Soil DNA Isolation kit (MoBio Laboratories Inc., Carlsbad, CA, USA), as described in the alternative protocol for maximum yield, and a bead beating step was added to aid lysis. For each sample, five extractions were performed and the resulting DNA was pooled and concentrated.
  2. DNA was sent for small subunit rDNA pyrosequencing analyses at the Research and Testing Laboratory (Lubbock, TX, USA) using the Roche 454 GS-FLX platform (Roche 454, Branford, CT, USA). Sample libraries were prepared with the following primers for bacterial 16S rRNA gene (28F-5′-GAGTTTGATCNTGGCTCAG-3′, 519R-5′-GTNTTACNGCGGCKGCTG-3′), archaeal 16S rRNA gene (349F-5′-GYGCASCAGKCGMGAAW-3′, 806R-5′-GGACTACVSGGGTATCTAAT-3′), Eukaryal/fungal internal transcribed region (ITS) (ITS1F-5′-CTTGGTCATTTAGAGGAAGTAA-3′, ITS4R-5′-TCCTCCGCTTATTGATATGC-3′) genes.

書誌情報の引用

  1. Goordial, J., Davila, A., Lacelle, D., Pollard, W., Marinova, M. M., Greer, C. W., ... & Whyte, L. G. (2016). Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica. The ISME journal, 10(7), 1613.

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