Microorganisms (Bacteria 16S; Eukaryota 18S) from soil crusts in polar (Arctic and Antarctic) ecosystems

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

Amplicon sequencing dataset (Illumina MiSeq) of Bacteria and Eukaryotes in Soil crusts on Svalbard and Antarctica

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Rippin M, Lange S, Sausen N, Becker B (2019): Microorganisms (Bacteria 16S; Eukaryota 18S) from soil crusts in polar (Arctic and Antarctic) ecosystems. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microorganisms_polar_biological_soil_crusts&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: a9a93a1e-4470-49c3-a98c-72f36c382090。  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:

Martin Rippin
University of Cologne Cologne DE
Sebastian Lange
University of Cologne Cologne DE
Nicole Sausen
University of Cologne Cologne DE
Burkhard Becker
University of Cologne Cologne DE

可回覆此資源相關問題者:

Martin Rippin
University of Cologne Cologne DE
Burkhard Becker
University of Cologne Cologne DE

元數據填寫者:

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

與此資源的相關者:

使用者

地理涵蓋範圍

Biological crusts were sampled in Antarctica at the Spanish Juan Carlos I Antarctic Base, and on Svalbard at Breinosa Gruve 7, Endalen, Ny-Alesund and Todalen

界定座標範圍 緯度南界 經度西界 [-62.665, -60.395], 緯度北界 經度東界 [78.923, 15.761]

分類群涵蓋範圍

Bacteria were targeted by sequencing the 16S ssu rRNA gene (v2-v3 region)

Domain  Bacteria (Bacteria)

Eukaryotes were targeted by sequencing the 18S ssu rRNA gene (v4 region)

Domain  Eukaryota (Eukaryotes)

時間涵蓋範圍

起始日期 / 結束日期 2014-08-24 / 2015-02-05

計畫資料

無相關描述

計畫名稱 Polarcrust
經費來源 This study was funded by the Deutsche Forschungsgemeinschaft (DFG) within the project ‘Polarcrust’ (BE1779/18-1) which is part of the Priority Program 1158 ‘Antarctic Research’.

The personnel involved in the project:

Martin Rippin

取樣方法

The nucleic acid content of the samples was preserved using the LifeGuard Soil Preservation Solution (MO BIO Laboratories, Carlsbad, CA, USA) according to the manufacturer's instructions and stored at −80°C.

研究範圍 Biological soil crust samples were collected from the Arctic Svalbard, Norway and Livingston Island, Antarctic Peninsula, in August 2014 and January 2015, respectively.

方法步驟描述:

  1. Total nucleic acids were extracted from the samples (all in triplicates, except NA that was only one sample) using the cetyltrimethylammonium bromide protocol according to Rippin, Komsic-Buchmann and Becker (2016) with several modifications: The LifeGuard Soil Preservation Solution was not removed prior to the extraction and the aqueous phase, retained after the second chloroform washing step, was further processed using the peqGOLD Plant RNA Kit (peqlab/VWR International, Erlangen, Germany) according to the manufacturer's instructions.
  2. To obtain DNA, the extract was treated with RNase A (Thermo Fisher Scientific, Waltham, MA, USA) as suggested in the manual and purified using the illustra MicroSpin S-400 HR Columns (GE Healthcare, Little Chalfont, UK). RNA-based metabarcoding was only performed for the samples NÅ and JC as the sampling sites are most comparable in terms of climate (seaside, similar precipitation patterns etc.). RNA was purified by DNA removal using DNase I (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer's protocol. cDNA synthesis was performed using the Revert Aid H Minus First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, Waltham, MA, USA).
  3. The extraction of DNA from all cultivated algae except K. crenulatum was carried out using the DNeasy Plant Kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. The harvested filaments of K. crenulatum were processed using a modified version of the cetyltrimethylammonium bromide protocol described by Rippin, Komsic-Buchmann and Becker (2016). After the second chloroform washing step, the upper phase was collected. The DNA was precipitated with isopropanol at −20°C for at least 1 h. After a washing step with 75% ethanol, the DNA was eluted in RNase-free water.
  4. Amplicons were generated for all triplicates (for NA three technical replicates were produced) using the Kapa HiFi HotStart DNA Polymerase (Roche, Basel, Switzerland). To analyze the eukaryotic diversity, we targeted the ribosomal small subunit (SSU) V4 region with the universal eukaryotic primers TAReuk454FWD1 (5′-CCAGCASCYGCGGTAATTCC-3′) and TAReukREV3 (5′-ACTTTCGTTCTTGATYRA-3′) designed by Stoeck et al. (Stoeck et al. 2010) (Amplicon size ≈ 380 bp). Similarly, the prokaryotic 16S rRNA gene V2-V3 region was amplified using the universal primers 104F (5′-GGCGVACGGGTGMGTAA-3′) and 515R (5′-TTACCGCGGCKGCTGGCAC-3′) taken from Lange et al. (Lange et al. 2015) (Amplicon size ≈ 400 bp). The eukaryotic amplicons of the BSC samples were amplified employing the following protocol: an initial denaturation step at 95°C for 3 min and 25 3-step cycles at 98°C for 20 s, at 49°C for 15 s and 72°C for 35 s were followed by a final elongation at 72°C for 1 min. The prokaryotic target was amplified in a similar way; however, the 25 cycles included 20 s at 98°C, 10 s at 65°C and 15 s at 72°C. Each template was amplified three times (NA was amplified nine times) with each primer pair and these triplicates were pooled in an equimolar manner to minimize PCR bias. For the MC, the templates, obtained from the cultivated algae, the bryophyte Physcomitrella patens and the liverwort Marchantia polymorpha (both supplied by O. Artz, AG Höcker, Botanical Institute, University of Cologne), were only targeted with eukaryotic primers and the PCR protocol consisted of 30 cycles of 20 s at 98°C, 15 s at 51.8°C and 35 s at 72°C. All PCR products were purified using the Agencourt® AMPure® XP system (Beckman Coulter, Brea, CA, USA) according to the manufacturer's protocol.

引用文獻

  1. Rippin, M., Lange, S., Sausen, N., & Becker, B. (2018). Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding. FEMS microbiology ecology, 94(4), fiy036. https://doi.org/10.1093/femsec/fiy036
  2. Williams, L., Borchhardt, N., Colesie, C., Baum, C., Komsic-Buchmann, K., Rippin, M., ... & Büdel, B. (2017). Biological soil crusts of Arctic Svalbard and of Livingston Island, Antarctica. Polar Biology, 40(2), 399-411.

額外的元數據

替代的識別碼 a9a93a1e-4470-49c3-a98c-72f36c382090
https://ipt.biodiversity.aq/resource?r=microorganisms_polar_biological_soil_crusts