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
研究者應依照以下指示引用此資源。:
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
權利
研究者應尊重以下權利聲明。:
此資料的發布者及權利單位為 SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF 註冊
此資源已向GBIF註冊,並指定以下之GBIF UUID: 3d255a2a-c297-4588-b67c-e0c2b4a31709。 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
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- 元數據提供者
- Research assistent
- Rue Vautier 29
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] |
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分類群涵蓋範圍
Bacteria were profiled by targeting the 16S ssu rRNA gene
Domain | Bacteria (Bacteria) |
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Archaea were profiled by targeting the 16S ssu rRNA gene
Domain | Archaea (Archaea) |
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Fungi (and some other Eukaryote groups) were profiled by targeting the ITS marker
Phylum | Fungi (Fungi) |
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計畫資料
無相關描述
計畫名稱 | Microbiome (Bacteria, Archaea and fungi) from University Valley Permafrost cores (Antarctica) |
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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:
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. |
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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:
- 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.
- 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
- 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
替代的識別碼 | 3d255a2a-c297-4588-b67c-e0c2b4a31709 |
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https://ipt.biodiversity.aq/resource?r=microbiome_university_valley_permafrost_antarctica |