Bacteria (16S) in growth laminae of a large conical mats from Lake Untersee, East Antarctic

最新バージョン SCAR - Microbial Antarctic Resource System によって公開 Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (454 pyrosequencing) of Bacterial communities (based on the 16S ssu rRNA gene; using Bacteria and Cyanobacteria-specific primers), of three different strata in a laminated microbial mat sample from Lake Untersee (east Antarctica)

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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。:

Koo H, Mojib N, Hakim J, Hawes I, Tanabe Y, Andersen D, Bej A (2019): Bacteria (16S) in growth laminae of a large conical mats from Lake Untersee, East Antarctic. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacteria_microbial_mats_lake_untersee_antarctica&v=1.1

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: 5ca9edf4-bb76-44d5-a962-bdef14a40c4f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:

Hyunmin Koo
University of Alabama at Birmingham Birmingham US
Nazia Mojib
University of Alabama at Birmingham Birmingham US
Joseph Hakim
University of Alabama at Birmingham Birmingham US
Ian Hawes
University of Canterbury Christchurch NZ
Yukiko Tanabe
National Institute of Polar Research Tachikawa JP
Dale Andersen
University of Alabama at Birmingham Birmingham US
Asim Bej
University of Alabama at Birmingham Birmingham US

リソースに関する質問に答えることができる人:

Hyunmin Koo
University of Alabama at Birmingham Birmingham US

メタデータを記載した人:

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

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

Lake Untersee, East Antarctica

座標(緯度経度) 南 西 [-71.2, 13.45], 北 東 [-71.2, 13.45]

生物分類学的範囲

Bacteria (16S ssu rRNA gene v3-v5)

Domain  Bacteria (Bacteria)

Cyanobacteria (16S ssu rRNA gene, group specific primer)

Domain  Cyanobacteria (Cyanobacteria)

時間的範囲

開始日 2001-01-01

プロジェクトデータ

説明がありません

タイトル Bacteria (16S) in growth laminae of a large conical mats from Lake Untersee, East Antarctic
ファンデイング The creation of this dataset was funded by the Tawani Foundation of Chicago (6803099), the Trottier Family Foundation, NASA’s Exobiology and Astrobiology Programs (NNX08AO19G), and the Arctic and Antarctic Research Institute/Russian Antarctic Expedition.

プロジェクトに携わる要員:

Hyunmin Koo

収集方法

The core was collected by gently inserting a 50 mm diameter sterile polycarbonate core tube through the top of a conical mat structure, then sealing it with rubber stoppers and returning it to the surface. The core was stored in Antarctic Logistics Centre International (ALCI), Cape Town, South Africa facility first at -20°C in a walk-in freezer and then transported to UAB in dry ice and kept in -20°C freezer until used. The top three laminae (herein U1, top lamina; U2, middle lamina; and U3, inner lamina) were separated from the core and selected individually for sequencing. Each lamina was carefully separated using sterile forceps and rinsed with distilled water to avoid carryover of microorganisms between laminae before DNA extraction.

Study Extent The samples were taken from a single core of a conical mat from Lake Untersee, which was collected by scientific divers utilizing SCUBA by accessing the lake ecosystem through a hole made on the ∼3.5 m surface ice.

Method step description:

  1. Five samples from different segments of each lamina of the large conical mat were sliced with a sterile scalpel, transferred into separate microcentrifuge tubes consisting of beads (MO BIO Laboratories Inc., Carlsbad, CA, United States), and homogenized in a high velocity bead beater (BIO101/Savant FastPrep FP120 – Qiagen, Inc., Valencia, CA, United States). DNA was then purified using the PowerBiofilm®DNA isolation Kit (MO BIO Laboratories). The large conical mats used in this study are unique, found only in Lake Untersee. Therefore, to minimize sample collection while obtaining sufficient DNA to investigate the microbial composition of the mat laminae, we used five spatially representative samples from each lamina, and pooled the purified DNA into single samples for amplicon sequencing. The concentration and the quality of the pooled DNA from each mat lamina was determined by using a Lambda II spectrophotometer (Perkin Elmer, Norwalk, Conn.) followed by agarose gel electrophoresis (1% wt/vol agarose in 1X Tris-Acetate-EDTA (TAE) buffer, pH 7.8) to confirm that each sample consists of mostly high molecular weight DNA (>2 kbp). The DNA was then dried in a Savant Speedvac Evaporator SVC 100H and stored at 4°C until used for sequencing.
  2. Bacterial tag-encoded amplicon pyrosequencing was performed using the primers 341F (5′–CCTACGGGAGGCAGCAG–3′) and 907R (5′–CCGTCAATTCMTTTGAGTTT–3′) targeting the V3–V5 region of the 16S rRNA, combined with group-specific primers for cyanobacterial: CYA106F (5′- CGGACGGGTGAGTAACGCGTGA-3′) and CYA781R (5′-GACTACWGGGGTATCTAATCCCWTT-3′). First, a sequencing library was established by using a one-step PCR method with a total of 30 cycles of template DNA amplification with the HotStarTaq Plus Master Mix kit (Qiagen, Inc., Valencia, CA, United States), and amplicons originating and extending from the aforementioned bacteria- and cyanobacteria-specific primers. Then, tag-encoded FLX amplicon pyrosequencing was performed on a Roche 454 FLX instrument with Titanium reagents following the Titanium procedures and RTL protocols at the Research and Testing Laboratory (Lubbock, TX, United States).

書誌情報の引用

  1. Koo, H., Mojib, N., Hakim, J. A., Hawes, I., Tanabe, Y., Andersen, D. T., & Bej, A. K. (2017). Microbial communities and their predicted metabolic functions in growth laminae of a unique large conical mat from Lake Untersee, East Antarctica. Frontiers in microbiology, 8, 1347.

追加のメタデータ

代替識別子 5ca9edf4-bb76-44d5-a962-bdef14a40c4f
https://ipt.biodiversity.aq/resource?r=bacteria_microbial_mats_lake_untersee_antarctica