Soil microbiome (Bacteria) on Keller Peninsula (Antarctica)

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

Amplicon sequencing dataset (454 pyrosequencing and Ion Torrent) of Bacteria (16S ssu rRNA gene) in ice-free soils of Keller Peninsula (Antarctica)

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版本

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如何引用

研究者應依照以下指示引用此資源。:

Roesch L, Fulthorpe R, Pereira A, Pereira C, Lemos L, Barbosa A, Suleiman A, Gerber A, Pereira M, Loss A, de Costa E (2019): Soil microbiome (Bacteria) on Keller Peninsula (Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antarctic_soil_microbiome_keller_peninsula&v=1.1

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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: 48350841-8927-4c78-bbc1-24c01a4d5586。  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:

Luiz Roesch
Universidade Federal do Pampa Sao Gabriel BR
Roberta Fulthorpe
University of Toronto at Scarborough Scarborough CA
Antonio Pereira
Universidade Federal do Pampa Sao Gabriel BR
Clarissa Pereira
Universidade Federal do Pampa Sao Gabriel BR
Leondro Lemos
Universidade Federal do Pampa Sao Gabriel BR
Anthony Barbosa
Universidade Federal do Pampa Sao Gabriel BR
Afnan Suleiman
Universidade Federal do Pampa Sao Gabriel BR
Alexandra Gerber
Unidade de Genômica Computacional Darcy Fontoura de Almeida Rio de Janeiro BR
Marcos Pereira
Universidade Federal Rural do Rio de Janeiro Rio de Janeiro BR
Arcangelo Loss
Universidade Federal Rural do Rio de Janeiro Rio de Janeiro BR
Elias de Costa
Universidade Federal Rural do Rio de Janeiro Rio de Janeiro BR

可回覆此資源相關問題者:

Luiz Roesch
Universidade Federal do Pampa Sao Gabriel BR

元數據填寫者:

Maxime Sweetlove
research assistent
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels BE

與此資源的相關者:

使用者

地理涵蓋範圍

Keller Peninsula, Antarctica

界定座標範圍 緯度南界 經度西界 [-64.294, -58.482], 緯度北界 經度東界 [-62.062, -56.691]

分類群涵蓋範圍

Bacteria, based on the 16S ssu rRNA gene

Domain  Bacteria (Bacteria)

時間涵蓋範圍

彙整期間 2009-2010

計畫資料

無相關描述

計畫名稱 Soil microbiome (Bacteria) on Keller Peninsula (Antarctica)
經費來源 This work was supported by the INCT-APA (CNPq process No. 574018/2008-5, FAPERJ E-26/170.023/2008) and Ministry of Science and Technology, and the Secretariat for the Marine Resources Interministerial Committee (SECIRM). Additional funding was provided via a fellowships from the CNPq (process number 503370/2009-6).

The personnel involved in the project:

Luiz Roesch

取樣方法

A total of 12 soil samples were chosen for sampling and were taken from a variety of plant communities having different soil features. Soil was collected removing the plant cover and taking cores of 5 cm diameter and 5 cm depth. All soil was stored on ice upon collection and transported to the laboratory for extraction.

研究範圍 Soil samples were collected on the Keller Peninsula, King George Island, Antarctica during the austral summer of 2009–2010.

方法步驟描述:

  1. DNA was isolated from at least 1 g of mixed soil using the PowerSoilTM DNA Isolation Kit (MO BIO) as described by the manufacturer. The genomic DNA concentration and purity were determined by spectrophotometry.
  2. Twelve independent PCR reactions were performed for each soil sample with the primers 338R and 27F for the amplification of the V1–V2 hypervariable regions of the 16S rRNA gene. PCR was performed with the GoTaq PCR core system (Promega, Madi- son, WI, USA). The mixtures contained 5 ul of 10× PCR buffer, 200 mM dNTPs, 100 mM of each primer, 2.5 U of Taq polymerase and approximately 100ng of DNA template in a final volume of 50 ul. The PCR conditions were 94 ◦ C for 2 min, 30 cycles of 94◦C for 45s; 55◦C for 45s; and 72◦C for 1min extension; followed by 72 ◦C for 6 min. The 16S rRNA gene fragments were sequenced using 454 GS FLX Titanium (Lib-L) chemistry for unidirectional sequencing of the amplicon libraries. Barcoded primers were used to multiplex the amplicon pools so they could be sequenced together and computationally separated afterward. To do this, 8-base barcodes were added to the 5′-end of the reverse primers using the self-correcting barcode method of Hamady et al. (2008). The primers were attached to the GS FLX Titanium Primer A (5′ -CCATCTCATCCCTGCGTGTCTCCGACTCAG-3′ ) and Primer B (5′ - CCTATCCCCTGTGTGCCTTGGCAGTC-3′ ) sequences, modified for use with GS FLX Titanium emPCR Kits (Lib-L) and a two-base linker sequence was inserted between the 454 adapter and the 16S rRNA primers to reduce any effect the composite primer might have on PCR efficiency. The PCR products for each of the 12 samples were purified and combined in equimolar ratios with the quantitative DNA binding method (SequalPrep Kit, Invitrogen, Carlsbad, CA, USA) to create a DNA pool that was used for pyrosequencing from the A-Key adaptor.

引用文獻

  1. Roesch, L. F., Fulthorpe, R. R., Pereira, A. B., Pereira, C. K., Lemos, L. N., Barbosa, A. D., ... & da Costa, E. M. (2012). Soil bacterial community abundance and diversity in ice-free areas of Keller Peninsula, Antarctica. Applied soil ecology, 61, 7-15.|Rampelotto, P. H., Barboza, A. D. M., Pereira, A. B., Triplett, E. W., Schaefer, C. E. G., de Oliveira Camargo, F. A., & Roesch, L. F. W. (2015). Distribution and interaction patterns of bacterial communities in an ornithogenic soil of Seymour Island, Antarctica. Microbial ecology, 69(3), 684-694.

額外的元數據

替代的識別碼 48350841-8927-4c78-bbc1-24c01a4d5586
https://ipt.biodiversity.aq/resource?r=antarctic_soil_microbiome_keller_peninsula