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

バージョン

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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。:

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

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: 69245174-bc73-48cc-ae36-3bbbd27c237b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

地理的範囲

Lakes in the McMurdo Dry Valleys, Antarctica

生物分類学的範囲

Fungi, 18S ssu rRNA marker gene

プロジェクトデータ

説明がありません

プロジェクトに携わる要員:

収集方法

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.

Method step description:

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.

書誌情報の引用

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.

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