Cyanobacteria in microbial mats from Antarctic lakes

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

Amplicon sequencing dataset targeting Cyanobacteria (16S ssu rRNA gene) in microbial benthic mats from 13 lakes across the Antarctic continent.

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研究者應依照以下指示引用此資源。:

Pessi I, Lara Y, Durieu B, de C. Maarouf P, Verleyen E, Wilmotte A (2019): Cyanobacteria in microbial mats from Antarctic lakes. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=lacustrine_cyanobacteria_antarctica&v=1.2

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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: a41ad9bd-cf79-48fa-89a0-102ddf4d4e61。  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:

Igor Pessi
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Yannick Lara
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Benoit Durieu
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Pedro de C. Maarouf
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Elie Verleyen
Ghent University Krijgslaan 281 9000 Ghent BE
Annick Wilmotte
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE

可回覆此資源相關問題者:

Igor Pessi
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE

元數據填寫者:

Maxime Sweetlove
Research assistent
Royal Belgian Institute for 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

Circum-Antarctic sampling of benthic microbial mats in lakes (n=13)

界定座標範圍 緯度南界 經度西界 [-82.45, -67.233], 緯度北界 經度東界 [-66.283, 100.233]

分類群涵蓋範圍

Cyanobacteria (16S ssu rRNA gene)

Phylum  Cyanobacteria (Cyanobacteria)

時間涵蓋範圍

彙整期間 1997-2007

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 Climate Change and Antarctic Microbial Biodiversity
辨識碼 CCAMBIO
經費來源 Belgian Science Policy Office (BelSPO) project SD/BA/03
研究區域描述 Microbial mats in the benthic and littoral zon of lakes in polar environments.
研究設計描述 Lakes from different regions in Antarctica were sampled, and sequencing was preformed of the 16S marker genes to provide a base-line inventory of microbial eukaryotes biodiversity and test hypotheses about biogeography and species distributions

The personnel involved in the project:

Igor Pessi

取樣方法

Microbial mat samples were collected in the littoral or deeper parts of the euphotic zone of the lakes using a spatula or gravity corer, respectively. The upper 1 cm of the core was aseptically removed and kept dark and cool until transfer to -20°C.

研究範圍 Samples were taken from benthic microbial mats (upper 1 cm), collected in 13 lakes on the Antarctic continent, distributed across eight Antarctic regions belonging to four distinct Antarctic Conservation Biogeographical Regions (ACBR).
品質控管 DNA concentration and quality were determined using a NanoVue spectrophotometer (GE Healthcare Life Sciences, Little Chalfont, UK). A blank DNA extraction consisting of sterile Milli-Q water was carried out in parallel.

方法步驟描述:

  1. DNA was extracted from the mats using the PowerSoil DNA Isolation Kit (MOBIO Labora- tories, Carlsbad, CA, USA) according to the manufacturer’s instructions with some modifications. Tubes were agitated on a vortex for 20 extra min to ensure a good disintegration of the mats and, if not completely disintegrated, a sterile pestle was used to crush the remaining pieces.
  2. The cyanobacteria-specific primer set CYA359F and CYA781R(a)/CYA781R(b) was used to amplify the V3-V4 variable region of the 16S rRNA gene. PCR reactions consisted of 19 PCR buffer with 1.5 mM MgCl2, 1mg mL 1BSA, 200 uM of each dNTP, 0.2 uM of each primer, 1 U SUPER TAQ plus DNA polymerase (HT Biotechnology, Cambridge, UK), and 4 ng uL^-1 template DNA in a final volume of 50 uL. Amplification was performed using an initial denaturation step at 94°C for 2 min, followed by 30 cycles of 94°C for 45 s, 60°C (for primer 781Ra) or 57°C (for primer 781Rb) for 45 s and 68°C for 45 s, and a final elonga- tion at 68°C for 5 min. Negative controls (PCR mixes with either no DNA or the blank DNA extracts) were always included during PCR amplifications. To minimize stochastic PCR bias, amplification was carried out as six independent PCR reactions (three for each reverse primer) that were pooled before purification.
  3. Replicate PCR reactions were pooled and purified using the GeneJet PCR Purification Kit (Thermo Scientific, Wal- tham, MA, USA). Purified amplicons were quantified using the Quant-iT PicoGreen dsDNA Assay Kit, pooled in equimolar concentrations, and concentrated to 25 uL using the Ami- con Ultra-0.5 mL 30K device (EMD Millipore, Billerica, MA, USA). Pooled libraries were sent to Beckman Coulter Geno- mics (Takeley, UK), where primer dimers were removed using the Agencourt AMPure XP Kit (Beckman Coulter, Brea, CA, USA) and sequencing adapters were ligated to the ampli- cons. Sequences were obtained using the 454 GS FLX+ Titanium platform (454 Life Sciences, Branford, CT, USA).

引用文獻

  1. Pessi, I. S., Maalouf, P. D. C., Laughinghouse IV, H. D., Baurain, D., & Wilmotte, A. (2016). On the use of high‐throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats. Journal of phycology, 52(3), 356-368.
  2. Pessi, I. S., Lara, Y., Durieu, B., Maalouf, P. D. C., Verleyen, E., & Wilmotte, A. (2018). Community structure and distribution of benthic cyanobacteria in Antarctic lacustrine microbial mats. FEMS microbiology ecology, 94(5), fiy042.

額外的元數據

替代的識別碼 a41ad9bd-cf79-48fa-89a0-102ddf4d4e61
https://ipt.biodiversity.aq/resource?r=lacustrine_cyanobacteria_antarctica