Microbial diversity (Bacteria and Archaea 16S rRNA gene) in geothermal sites of Deception Island volcano, Antarctica

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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。:

Bendia A, Signori C, Franco D, Duarte R, Bohannan B, Pellizari V (2019): Microbial diversity (Bacteria and Archaea 16S rRNA gene) in geothermal sites of Deception Island volcano, Antarctica. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbial_bacterial_and_archaeal_diversity_geothermal_sites_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: 4d74304b-a18f-4e3c-9a1f-efbaead8931c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

Geothermal anomalies at Fumarole Bay and Whalers Bay, Deception Island, Antarctica

生物分類学的範囲

Bacteria (v3-v4 of the 16S ssu rRNA, targeted with the primer pair S-D-Bact-0341-b-S-17 and S-D-Bact-0785-a-A-21) and Archaea (v3-v4 of the 16S ssu rRNA, targeted with the primer pair S-D-Arch-0519-a-S-15 and S-D-Arch-1041-a-A-18)

時間的範囲

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

In each site, three sediment samples were collected in each of three points with distinct temperatures: Points A and B were defined as samples collected in fumaroles, while point C was glacier samples, collected below the glacier’s edge. Distances between fumaroles and glaciers at each site were approximately 15 m, and the Whalers Bay and Fumarole Bay transects were approximately 10 km apart. All fumaroles were in the intertidal zone, with exception of point B from FB, which was in the subtidal (submerged at 50 cm depth in water column). Samples were stored at -20°C until arrival at the University of São Paulo, Brazil, in April 2014.

Method step description:

1. Total genomic DNA was extracted from 10 g of sediment using a PowerMax Soil DNA Kit (MoBio, United States), according to the manufacturer’s protocol. Extracted DNA was concentrated and purified with PCR OneStep Inhibitor Removal Kit (Zymo Research, United States), and further quantified using Qubit dsDNA HS Assay (Thermo-Fisher Scientific, United States) and Qubit Fluorimeter 1.0 (Thermo-Fisher Scientific, United States). Microbial 16S rRNA gene fragments were amplified using the primers S-D-Bact-0341-b-S-17 and S-D-Bact-0785-a-A-21 for Bacteria, and S-D-Arch-0519-a-S-15 and S-D-Arch-1041-a-A-18 for Archaea (Klindworth et al., 2013), targeting the V3–V4 regions of the gene. The first PCR reaction was carried out with a thermal cycler (Thermo-Fisher Scientific, United States), using 25 μL of KAPA HiFi HotStart Ready Mix (KAPA Biosystems) polymerase, 5 ng of DNA, and 0.2 μM of each primer, under the following conditions: 95°C for 3 min, 30 cycles of 95°C for 30 s, 55 or 67°C for 30 s (for Bacteria and Archaea, respectively), 72°C for 30 s, and a final extension of 72°C for 5 min. After purification (QIAquick Gel Extraction Kit – QIAGEN, United States) and quantification, 50 ng of amplicons was amplified and used for library preparation, under the following conditions: 95°C for 3 min, eight cycles of 95°C for 30 s, 55 and 72°C for 30 s, and 72°C for 5 min. The libraries were purified using an AMPure XP beads kit (Beckman Coulter, United States).
2. After quality checking (Bioanalyzer 2100, Agilent Technologies, United States), the amplicons from each sample were mixed at equimolar concentrations and then sequenced using the Illumina Miseq platform at the Facilities Center for Research Support (CEFAP, Institute of Biomedical Sciences, University of São Paulo).

書誌情報の引用

1. Bendia, A. G., Signori, C. N., Franco, D. C., Duarte, R. T., Bohannan, B. J., & Pellizari, V. H. (2018). A Mosaic of Geothermal and Marine Features Shapes Microbial Community Structure on Deception Island Volcano, Antarctica. Frontiers in Microbiology, 9.

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