元數據

Microbial population dynamics along a terrestrial Antarctic moisture gradient

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

下載最新版本資源元數據的EML或RTF文字檔。

元數據EML檔 下載 在 English 中 (11 KB)
元數據RTF文字檔 下載 在 English 中 (10 KB)

說明

Amplicon sequencing dataset (Illumina MiSeq) of Bacteria (16S ssu rRNA gene) in soil samples from the McMurdo Dry Valleys (Antarctica) taken along a moisture gradient.

版本

以下的表格只顯示可公開存取資源的已發布版本。

如何引用

研究者應依照以下指示引用此資源。:

Lee K, Caruso T, Archer S, Gillman L, Lau M, Cary C, lee C, Pointing S (2019): Microbial population dynamics along a terrestrial Antarctic moisture gradient. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbes_terrestrial_antarctic_moisture_gradient&v=1.2

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: f1516a8a-2f31-4215-b6df-7cdb37c98655。  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:
-

Kevin Lee
Auckland University of Technology
Auckland
NZ
Tancredi Caruso
Queen’s University Belfast
Belfast
GB
Stephen Archer
Auckland University of Technology
Auckland
NZ
Len Gillman
Auckland University of Technology
Auckland
NZ
Maggie Lau
Princeton University
Princeton
US
Craig Cary
University of Waikato
Hamilton
NZ
Charles lee
University of Waikato
Hamilton
US
Stephen Pointing
National University of Singapore
Singapore
SG

可回覆此資源相關問題者:

Kevin Lee
Auckland University of Technology
Auckland
NZ

元數據填寫者:
-

Maxime Sweetlove
Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
1000 Brussels

與此資源的相關者:

使用者

地理涵蓋範圍

McMurdo Dry Valleys, Victoria lands, Antarctica

界定座標範圍 緯度南界 經度西界 [-77.66, 163.105], 緯度北界 經度東界 [-77.658, 163.127]

分類群涵蓋範圍

Bacteria, based on amplicon sequencing of the 16S ssu rRNA marker gene (v3-v4region)

Domain Bacteria (Bacteria)

時間涵蓋範圍

起始日期 2015-01-01

計畫資料

無相關描述

計畫名稱 Microbial population dynamics along a terrestrial Antarctic moisture gradient
經費來源 The research was funded by a grant from the New Zealand Ministry of Business, Innovation & Employment (UOWX1401) and Yale-NUS College Start-Up Fund.

參與計畫的人員:

Kevin Lee

取樣方法

We adopted a zonal sampling approach where soils were retrieved that matched visible delineations along linear transects extending across the hyporheic zone from the water’s edge at each sampling station: Zone (1) Saturated soil adjacent to water’s edge; Zone (2) Wet soil as indicated by dark coloration; Zone (3) Ephemerally wet soil, dry but with evidence for previous water indicated by surface evaporites; Zone (4) Dry soil with no indication of recent moisture. Soils from each zone in each transect were recovered using aseptic technique and saturated with Lifeguard solution (Qiagen, Netherlands) (n = 16) with parallel sampling for geochemical and moisture analysis (n = 16). All samples were stored in darkness frozen at -20oC until processed.

研究範圍 Sampling was conducted around the hyporheic zone of Spaulding Pond, Taylor Valley in the McMurdo Dry Valleys of Antarctica, during the austral summer of 2015. Four transects were defined in north-east (S77◦ 39.489′ , E163◦ 07.501′ ), south-east (S77◦ 39.513′ , E◦ 163 07.626′ ), south (S77◦ 39.589′ , E◦ 163 07.006′ ), and north-west (S77◦ 39.470′, E◦163 06.336′) facing hyporheic moisture gradients.

方法步驟描述:

  1. Samples were thawed on ice and three 0.5 g extractions were conducted using the CTAB method optimized for Antarctic oligotrophic environmental samples (Archer et al., 2015). DNA yield was measured in ng/g soil. Illumina MiSeq libraries were prepared as per manufacturer’s protocol (Metagenomic Sequencing Library Preparation Part # 15044223 Rev. B; Illumina, San Diego, CA, United States) as previously described (Lee et al., 2016). PCR targeting the V3–V4 regions of bacterial and archaeal 16S rRNA gene with the primer set: PCR1 forward (5′ TCGTCGGCAGCGTCAGATGT GTATAAGAGA CAGCCTACGG GNGGCWGCAG 3′ ) and PCR1 reverse (5′ GTCTCGTGGG CTCGGAGATG TGTATAAGAG ACAGGACTAC HVGGGTATCT AATCC 3′) was conducted using KAPA HiFi Hotstart Readymix (Kapa Biosystems, Wilmington, MA, United States) and the following thermocycles: (1) 95◦C for 3 min, (2) 25 cycles of 95◦C for 30 s, 55◦C for 30 s, ◦C for 30 s, 72◦C for 5 min, and (3) holding the samples at 4◦C. The amplicons were then indexed using Nextera XT index kit (Illumina). AMPure XP beads (Beckman-Coulter, Brea, CA, United States) was used to purified the amplicon. Sequencing was conducted with an Illumina MiSeq system (Illumina) with the 500 cycle V2chemistry at Auckland University of Technology, New Zealand. A 5% PhiX spike-in was used, as per manufacturer’s recommendation.

引用文獻

  1. Lee, K. C., Archer, S. D. J., Caruso, T., Gillman, L., Lau, M. C., Cary, S. C., ... & Pointing, S. B. (2018). Stochastic and deterministic effects of a moisture gradient on soil microbial communities in the McMurdo Dry Valleys of Antarctica. Frontiers in Microbiology, 9, 2619.

額外的詮釋資料

替代的識別碼 f1516a8a-2f31-4215-b6df-7cdb37c98655
https://ipt.biodiversity.aq/resource?r=microbes_terrestrial_antarctic_moisture_gradient