Microbial fungal communities (18S) of Antarctic Dry Valley lakes

最新版本 由 SCAR - Microbial Antarctic Resource System 發佈於 Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (Illumina MiSeq) of microbial fungi (18S ssu rRNA gene, v7-v8) in Antarctic Dry Vallei lakes.

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Rojas-Jimenez K, Wurzbacher C, Bourne E C, Chiuchiolo A, Priscu J, Grossart H (2018): Microbial fungal communities (18S) of Antarctic Dry Valley lakes. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=fungal_communities_of_antarctic_dry_valley_lakes&v=1.2

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

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此資源已向GBIF註冊,並指定以下之GBIF UUID: 69245174-bc73-48cc-ae36-3bbbd27c237b。  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:

Keilor Rojas-Jimenez
eibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin DE
Christian Wurzbacher
Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin DE
Elizabeth Charlotte Bourne
eibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin DE
Amy Chiuchiolo
Research associate
Montana State University Bozeman US
John Priscu
Montana State University Bozeman US
Hans-Peter Grossart
eibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin DE

可回覆此資源相關問題者:

Keilor Rojas-Jimenez
eibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin DE

元數據填寫者:

Maxime Sweetlove
Research assistent
Royal Belgian Instutute for Natural Sciences Rue Vautier 29 1000 Brussels

與此資源的相關者:

使用者

地理涵蓋範圍

Lakes in the McMurdo Dry Valleys, Antarctica

界定座標範圍 緯度南界 經度西界 [-78.1, 162.367], 緯度北界 經度東界 [-77.617, 166.667]

分類群涵蓋範圍

Fungi, 18S ssu rRNA marker gene

Domain  Fungi (Fungi)

計畫資料

無相關描述

計畫名稱 Microbial fungal communities (18S) of Antarctic Dry Valley lakes
經費來源 Funding was provided by the Leibniz “Mycolink” SAW project (Pakt/SAW-2014-IGB-1) given to HPG and ECB. JCP was funded by US National Science Foundation grants PLR1439774, PLR1115245, PLR 1543537 and NASA NRA NNH14ZDA001N-PSTAR.

The personnel involved in the project:

Keilor Rojas-Jimenez

取樣方法

Water samples (1–2 l) were collected at selected depths through a ~30 cm diameter borehole in the ca. 4 m thick ice covers of each lake using sterile Niskin bottles. To prevent the introduction of contaminants into the lakes, precautions were taken to drill just to the surface of the water. Prior to use, each corer was rinsed properly. For each lake a different sampler was used to avoid cross contamination. In addition, we established a suitable waiting period between the drilling and the water sampling. Then, the samples were filtered through 5.0 µm Puradisc Cellulose Nitrate syringe filters (Gelman Sciences, USA) and subsequently through 0.2 µm Sterivex filters (Millipore, USA) to distinguish between particle-associated and small free-living eukaryotes. Filters were stored with 2.0 ml of Puregene lysis buffer at −80 °C until further processing and nucleic acid extraction.

研究範圍 Samples were taken during the austral summers of 2011–2012 from five lake basins in the Taylor and Miers Valleys that are the focus of the McMurdo Dry Valleys Long-Term Ecological Research program (MCM LTER).

方法步驟描述:

  1. DNA from the microorganisms in the filters was extracted using a phenol-chloroform protocol. From 12 samples of the West and East lobes of Lake Bonney, we also extracted RNA using an RNeasy Mini Kit (QIAGEN, Germany). The RNA was converted to cDNA with a One-Step RT-PCR Kit (QIAGEN, Germany) according to the manufacturer’s instructions. We amplified the V7 and V8 regions of the 18S rRNA gene using primers FF390 (5′-CGATAACGAACGAGACCT-3′) and FR1 (5′-AICCATTCAATCGGTAIT-3′).
  2. For the 25 µl PCR reaction, we used a proof reading enzyme (Herculase II Fusion Polymerase, Agilent Technologies, Santa Clara, USA) and 40 ng DNA (or cDNA) as a template with the following conditions; 95 °C for 3 min initial denaturation followed by 35 cycles at 95 °C for 45 s, 52 °C for 1 min, 72 °C for 1 min, and a final extension at 72 °C for 5 min. The 96 resulting amplicons (~350 bp) went into the library preparation for Illumina MiSeq sequencing according to the protocol presented by the Illumina customer letter for 16 S sequencing with custom primers (Illumina guide to 16 S amplicon sequencing, Part # 15044223 Rev. A) and the Nextera index kit (Illumina, San Diego, USA). The samples were sequenced on a MiSeq sequencer (Illumina, San Diego, USA) with v3 2 × 300 nt chemistry. Sequences were demultiplexed with flexbar resulting in 6.4 M sequences.

引用文獻

  1. Rojas-Jimenez, K., Wurzbacher, C., Bourne, E. C., Chiuchiolo, A., Priscu, J. C., & Grossart, H. P. (2017). Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica. Scientific reports, 7(1), 15348.

額外的元數據

替代的識別碼 69245174-bc73-48cc-ae36-3bbbd27c237b
https://ipt.biodiversity.aq/resource?r=fungal_communities_of_antarctic_dry_valley_lakes