メタデータ

Microbial population dynamics along a terrestrial Antarctic moisture gradient

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

メタデータのみリソース のメタデータの最新版をEML または RTF としてダウンロード:

EML ファイルとしてのメタデータ ダウンロード English で (11 KB)
RTF ファイルとしてのメタデータ ダウンロード English で (10 KB)

説明

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.

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。:

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

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

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

リソースに関する質問に答えることができる人:

Kevin Lee
Auckland University of Technology
Auckland
NZ

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

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

McMurdo Dry Valleys, Victoria lands, Antarctica

座標(緯度経度) 南 西 [-77.66, 163.105], 北 東 [-77.658, 163.127]

生物分類学的範囲

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

Domain Bacteria (Bacteria)

時間的範囲

開始日 2015-01-01

プロジェクトデータ

説明がありません

タイトル Microbial population dynamics along a terrestrial Antarctic moisture gradient
ファンデイング The research was funded by a grant from the New Zealand Ministry of Business, Innovation & Employment (UOWX1401) and Yale-NUS College Start-Up Fund.

プロジェクトに携わる要員:

Kevin Lee

収集方法

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.

Study Extent 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.

Method step description:

  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.

書誌情報の引用

  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.

追加のメタデータ