Bacterial Diversity Assessment in Antarctic Terrestrial and Aquatic Microbial Mats

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

Bacterial data (16S rRNA) from terrestrial and aquatic Microbial mats in continental Antarctic.

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如何引用

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Tytgat B, Vrleyen E, Obbels D, Peeters K, De Wever A, D'hondt S, De Meyer T, van Criekinge W, Vyverman W, Willems A (2018): Bacterial Diversity Assessment in Antarctic Terrestrial and Aquatic Microbial Mats. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacterial_diversity_antarctica_microbial_mats&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: f3a8b1d6-a1d1-4292-8a7e-19c63a0825bd。  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

lake; soil; bacteria; antarctica; 16S

聯絡資訊

資源建立者:

Bjorn Tytgat
Post doctoral assistent
Ghent University Krijgslaan 281 9000 Gent BE
Elie Vrleyen
Professor
Ghent University Krijgslaan 281 9000 Gent BE
Dagmar Obbels
PhD student
Ghent University Krijgslaan 281 9000 Gent BE
Karolien Peeters
Post doctoral researcher
Ghent University Krijgslaan 281 9000 Gent BE
Aake De Wever
Post doctoral assistent
Royal Belgian Institute for Natural Sciences Krijgslaan 281 1000 Brussels BE
Sofie D'hondt
Lab technician
Ghent University
Tim De Meyer
Professor
Ghent University
Wim van Criekinge
Post doctoral researcher
GhentUniversity
Wim Vyverman
Professor
Ghent University
Anne Willems
Professor
Ghent Univeristy

可回覆此資源相關問題者:

Bjorn Tytgat
Post doctoral assistent
Ghent University Krijgslaan 281 9000 Gent BE

元數據填寫者:

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

與此資源的相關者:

內容提供者
Bjorn Tytgat
Post doctoral assistent
Ghent University Krijgslaan 281 9000 Gent BE
內容提供者
Karolien Peeters
Post doctoral researcher
Ghent University 9000 Gent BE
內容提供者
Anne Willems
Professor
Ghent University 9000 Gent BE

地理涵蓋範圍

soil samples and lake samples from East Antarctica

界定座標範圍 緯度南界 經度西界 [-80.45, -67.45], 緯度北界 經度東界 [-67.7, 39.8]

分類群涵蓋範圍

Bacterial 16S amplicons (V1-V3 region)

Domain  Bacteria (Bacteria)

時間涵蓋範圍

起始日期 / 結束日期 2003-01-01 / 2007-01-01

計畫資料

CCAMBIO (Climate Change and Antarctic Microbial Biodiversity) is an academic project funded by the Belgian Federal Science Policy (BELSPO). Its main objective is to study the diversity, biogeographic zoning and genomic make-up of lacustrine microbial mat communities in the Antarctic Realm. CCAMBIO is composed by researchers from four Belgian Universities and Institutes (University of Liège, Ghent University, National Botanical Garden of Belgium and Royal Belgian Institute of Natural Sciences), as well as collaborators from the British Antarctic Survey.

計畫名稱 CCAMBIO
辨識碼 CCAMBIO
經費來源 Belgian Science Policy Office (BelSPO) project SD/BA/03

The personnel involved in the project:

Bjorn Tytgat
Elie Verleyen
Dagmar Obbels
Anne Willems
Wim Vyverman

取樣方法

Two terrestrial and seven limnetic microbial mat samples were collected aseptically during different field campaigns in December/January 2003 (PQ1, TM2 and TM4) and in January 2007 (BB50, BB115, LA3, SK5, WO10 and SO6). All samples were kept frozen during transport and stored at 220uC.

研究範圍 One sample (PQ1) was collected on Pourquoi-Pas Island off the west coast of Graham Land (Antarctic Peninsula). All other samples were collected from Eastern Antarctic habitats. The two terrestrial microbial mat samples (BB50 and BB115) were taken near the Utsteinen nunatak in the Sør Rondane Mountains (Dronning Maud Land). Three samples were from Lu ̈tzow-Holm Bay (Dronning Maud Land), namely from a small saline lake in Langhovde (LA3), from Naka-Tempyo Lake (SK5) in Skarvsnes, and from a small saline pond (WO10) in West Ongul Island. One sample (SO6) was taken from Lake Melkoye (unofficial name) in Schirmacher Oasis (Dronning Maud Land). The two remaining samples were collected in the Transantarctic Mountains. Sample TM2 was taken from Forlidas Pond (Dufek Massif, Pensacola Mountains), while sample TM4 was taken from Lundstro ̈m Lake (Shackleton Range).

方法步驟描述:

  1. DNA was extracted from frozen samples using 5 g per sample. Extracellular DNA was first removed as described by Corinaldesi et al. and DNA extraction was subsequently performed according to Zwart et al. Sequencing of the 16S rRNA V1–V3 regions was performed using forward primer pA (AGAGTTTGATCCTGGCTCAG 8–27) and reverse primer BKL1 (GTATTACCGCGGCTGCTGGCA 536– 516). Because it proved impossible to concatenate the comple- mentary reads due to insufficient overlap, the forward and reverse sequences were analyzed separately. The forward reads hence cover the complete V1 and V2 regions, whereas the reverse reads cover the V3 and part of the V2 region for the longest sequences.
  2. Multiplexing was done with barcodes proposed by Parames- waran et al. Each PCR mixture contained 1–2 ml of template DNA, 2 ml of fusion primers and barcodes (10 mM), 2.5 ml dNTPs (10 mM), 1.5 ml of 10x buffer, 0.25 ml of 5 U/ml FastStart High Fidelity Polymerase (Roche) and was adjusted to a final volume of 25 ml with sterile HPLC-water. PCR cycling included 3 min at 94uC, followed by 35 cycles of 94uC for 30 s, 55uC for 60 s and 72uC for 90 s and finally 8 min at 72uC. PCR products were purified using a High Pure PCR Product Purification Kit (Roche).
  3. Pyrosequencing was performed on a Roche 454 GS FLX Titanium machine at NXTGNT (Ghent, Belgium) after quality control of the DNA with a Qubit 2.0 Fluorometer (Life Technologies) and a Bioanalyzer (Agilent Technologies).

引用文獻

  1. Tytgat, B., Verleyen, E., Obbels, D., Peeters, K., De Wever, A., D’hondt, S., ... & Willems, A. (2014). Bacterial diversity assessment in Antarctic terrestrial and aquatic microbial mats: a comparison between bidirectional pyrosequencing and cultivation. PloS one, 9(6), e97564.

額外的元數據

替代的識別碼 f3a8b1d6-a1d1-4292-8a7e-19c63a0825bd
https://ipt.biodiversity.aq/resource?r=bacterial_diversity_antarctica_microbial_mats