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

最新版本 published by SCAR - Microbial Antarctic Resource System on 3月 19, 2019 SCAR - Microbial Antarctic Resource System
發布日期:
2019年3月19日
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CC-BY 4.0

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說明

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.

版本

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如何引用

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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

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關鍵字

Metadata

聯絡資訊

Jacqueline Goordial
  • 出處
  • 連絡人
McGill University
Ste-Anne-de-Bellevue
CA
Alfonso Davila
  • 出處
NASA Ames Research Center
Moffett Field
US
Denis Lacelle
  • 出處
University of Ottawa
Ottawa
CA
Wayne Pollard
  • 出處
McGill University
Montreal
CA
Margarita Marinova
  • 出處
NASA Ames Research Center
Moffett Field
US
Charles Greer
  • 出處
National Research Council Canada
Montreal
CA
Jocelyn DiRuggiero
  • 出處
The Johns Hopkins University
Baltimore
US
Christopher McKay
  • 出處
NASA Ames Research Center
Moffett Field
US
Lyle Whyte
  • 出處
McGill University
Ste-Anne-de-Bellevue
CA
Maxime Sweetlove
  • 元數據提供者
  • Research assistent
Royal Belgian Institute of Natural Sciences
  • Rue Vautier 29
1000 Brussels
BE

地理涵蓋範圍

University Valley, McMurdo Dry Valleys, Antarctica

界定座標範圍 緯度南界 經度西界 [-77.864, 160.729], 緯度北界 經度東界 [-77.864, 160.729]

分類群涵蓋範圍

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)

計畫資料

無相關描述

計畫名稱 Microbiome (Bacteria, Archaea and fungi) from University Valley Permafrost cores (Antarctica)
經費來源 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).

參與計畫的人員:

Jacqueline Goordial

取樣方法

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.

研究範圍 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.
品質控管 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.

方法步驟描述:

  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.

引用文獻

  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.

額外的詮釋資料