元數據

Microbial (16S) diversity in sediments of the former subglacial Hodgson lake (Antarctica)

最新版本 由 SCAR - Microbial Antarctic Resource System 發佈於 2019年3月19日 SCAR - Microbial Antarctic Resource System
發布日期:
2019年3月19日
授權條款:
CC-BY 4.0

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說明

Amplicon sequencing dataset (454 pyrosequencing) of microorganisms (16S ssu rRNA gene) in sediments of the former subglacial Hodgson lake (Antarctica). Exploratory study (1 sample).

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。:

Pearce D, Hodgson D, Thorne M, Burns G, Cockell C (2019): Microbial (16S) diversity in sediments of the former subglacial Hodgson lake (Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=hodgson_lake_microbes&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: b315baf6-9fed-405d-a3ee-d585aae81a1c。  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:
-

David Pearce
British Antarctic Survey
Cambridge
GB
Dominic Hodgson
British Antarctic Survey
Cambridge
GB
Michael Thorne
British Antarctic Survey
Cambridge
GB
Gavin Burns
British Antarctic Survey
Cambridge
GB
Charles Cockell
University of Edinburgh
Edinburgh
GB

可回覆此資源相關問題者:

David Pearce
British Antarctic Survey
Cambridge
GB

元數據填寫者:
-

Maxime Sweetlove
Research assistent
Royal Belgian Institute of 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

Lake Hodgson, Antarctica

界定座標範圍 緯度南界 經度西界 [-72.009, -68.462], 緯度北界 經度東界 [-72.009, -68.462]

分類群涵蓋範圍

Bacteria and Archaea (16S ssu rRNA gene)

Domain Bacteria (Bacteria), Archaea (Archaea)

時間涵蓋範圍

起始日期 2000-01-01

計畫資料

無相關描述

計畫名稱 Hodgson Lake metagenome
經費來源 Funding was provided by theNatural Environment Research Council funding through the British Antarctic Survey and the Antarctic Funding Initiative.

參與計畫的人員:

David Pearce

取樣方法

A 3.8 m sediment core was extracted at a depth of 93.4 m below the ice surface inside a virkon sterilized and polycarbonate lined core barrel. When taken all core samples remained within the core liners and were immediately frozen until sub-sampling in a clean class II microbiological safety cabinet in Cambridge. Gloves were used at all times and instruments used in laboratory manipulations were autoclaved.

研究範圍 Lake Hodgson, Antarctica

方法步驟描述:

  1. Samples of frozen surface sediment (~0.5 g) were removed from sediment cores for DNA extraction. DNA extractions were carried out using the PowerSoil DNA isolation kit (Mo Bio, Carlsbad, CA, USA) following the manufacturers standard protocol. The resulting DNA was quantified using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Each extraction from 0.5 g sediment produced ~250 ng of DNA in 100 μL nuclease free water. 16S RNA gene amplification was carried out on sediment DNA obtained from the four depth sections A–C (15 ng input DNA) using forward primer 787f ATT AGA TAC CCN GGT AG and reverse primer 1492Rm GNT ACC TTG TTA CGA CTT at an annealing temperature of 50 °C to produce amplicons of 705 bp. PCR reactions were 15 μL and contained 1× PCR buffer, 2.0 mM MgCl2, 0.25 mM dNTPs, 0.25 mM each primer, 0.4 Units BioTaq (Bioline, London, UK) and ca. 15 ng template DNA. For Thermocycling: 1 ×95 °C for 50 s; 30 ×95 °C for 20 s, 50 °C for 30 s, 72 °C for 3 min (ramp 72 °C at 0.3 °C s−1); 1 ×72 °C for 10 min. Multiple PCR amplifications (24 in total) were cleaned and pooled to produce 900 ng of 16S enriched DNA for 454 library preparation.
  2. An amplicon library was generated using the Rapid Library Preparation kit and following the manufacturer’s recommendations in the GS FLX Titanium Series Rapid Library Preparation Method Manual (Roche). Briefly, the PCR amplicons were purified using AMPure beads (Agencourt Bioscience Corporation, Beverly, MA, USA), adaptors were blunt-end ligated to the fragment and the dsDNA amplicon library was quantitated via fluorometry using Quanti-iT Pico Green reagents (Invitrogen, Carlsbad, CA, USA). The library was then subjected to clonal amplification by emulsion PCR followed by pyrosequencing on a 454 GS FLX sequencer according to the manufacturer’s instructions (NEB NextQuick 454 library prep kit E6090).

引用文獻

  1. Pearce, D. A., Hodgson, D. A., Thorne, M. A., Burns, G., & Cockell, C. S. (2013). Preliminary analysis of life within a former subglacial lake sediment in Antarctica. Diversity, 5(3), 680-702.

額外的詮釋資料

替代的識別碼 b315baf6-9fed-405d-a3ee-d585aae81a1c
https://ipt.biodiversity.aq/resource?r=hodgson_lake_microbes