Microbial communities (Bacteria, Eukaryotes and Fungi) in Arctic, Antarctic and Sub-Antarctic lacustrine biofilms

元數據
最新版本 published by SCAR - Microbial Antarctic Resource System on 三月 19, 2019 SCAR - Microbial Antarctic Resource System
發布日期:
2019年3月19日
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CC-BY 4.0

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說明

Amplicon sequencing (Illumina MiSeq, 300bp Paired-end) dataset of microbial mats samples collected in the literal zone of Arctic, Antarctic and Sub-Antarctic lakes. Samples were taken during the course of field expeditions between 1993 and 2014. Sequencing targeted Bacteria (16S ssu rRNA marker gene, v1-v3 region), eukaryotes (18S ssu rRNA, v4 region) and microbial fungi (ITS marker gene)

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。:

Sweetlove M, Tytgat B, Verleyen E, Willems A, Wurzbacher C, Nillson H, Wilmotte A, Vyverman W (2019): Microbial communities (Bacteria, Eukaryotes and Fungi) in Arctic, Antarctic and Sub-Antarctic lacustrine biofilms. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbial_bacteria_fungi_and_eukaryotes_in_arctic_antarctic_and_subantarctic_lacustrine_biofilms&v=1.1

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此資料的發布者及權利單位為 SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

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關鍵字

Metadata

聯絡資訊

Maxime Sweetlove
  • 元數據提供者
Researcher
Ghent University
Krijgslaan 281
9000 Ghent
BE
Bjorn Tytgat
  • 出處
Post doctoral assistent
Ghent University
Krijgslaan 281
9000 Ghent
BE
Elie Verleyen
  • 出處 ●
  • 連絡人
Professor
Ghent University
Krijgslaan 281
9000 Ghent
BE
Anne Willems
  • 出處
Professor
Ghent University
K.L.Ledeganckstraat 35
9000 Ghent
BE
Christian Wurzbacher
  • 出處
Post doctoral researcher
Technical University Munich
Munich
DE
Henrik Nillson
  • 出處
Professor
University of Gothenburg
Gothenburg
SE
Annick Wilmotte
  • 出處
Professor
University of Liège
Liège
BE
Wim Vyverman
  • 出處 ●
  • 連絡人
Professor
Ghent University
Krijgslaan 281
9000 Ghent
BE
Maxime Sweetlove
  • 元數據提供者
Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
1000 Brussels
BE
Sweetlov
  • 使用者

地理涵蓋範圍

Sampled regions include: the Arctic (Greenland, Norway, Svalbard), Sub-Antarctic Islands (Macquarie island and Marion Island) and Antarctic (the Antarctic Peninsula, Continental Antarctica)

界定座標範圍 緯度南界 經度西界 [-90, -180], 緯度北界 經度東界 [90, -180]

分類群涵蓋範圍

High throughput (Illumina) amplicon sequencing of Bacteria (16S ssu rRNA), Eukaryotes (18S ssu rRNA) and microbial fungi (ITS)

Domain Eukaryota (Eukaryotes), Bacteria (Bacteria)
Phylum Fungi (Fungi)

時間涵蓋範圍

彙整期間 1993-2014

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 and sub-polar environments.
研究設計描述 Lakes from different regions in Antarctica, Sub-Antarctica and the Arctic were sampled, and sequencing was preformed of the 16S and 18S rRNA and ITS marker genes to 1) provide a base-line inventory of microbial eukaryotes biodiversity, 2) test hypotheses about biogeography and species distributions, and 3) test hypotheses on macro-ecological patterns in microbes.

參與計畫的人員:

Maxime Sweetlove
Bjorn Tytgat
Elie Verlyen
Anne Willems
Wim Vyverman
Annick Wilmotte

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 233 lakes covering 17.35° latitude in the Northern Hemisphere (61.39°N to 78.74°N) and 37.16° in the Southern Hemisphere (46.84°S to 84°S), including the major biogeographical regions in Antarctica, Sub-Antarctica and the Arctic.
品質控管 To assess overall sequence quality and estimate the parameters for bioinformatics processing, each run also included two replicates of positive control sample (mock community) containing bacterial or eukaryote taxa on the respective bacterial and eukaryote runs.

方法步驟描述:

  1. Extracellular proteins and DNA from 1.5-3 g subsamples were removed (Corinaldesi et al., 2005), after which genomic DNA was extracted using a phenol-chloroform based protocol (Zwart et al., 1998). For Bacteria, the V1-V3 region of the 16S SSU rRNA gene was targeted for bacteria with domain-specific universal primer sets (Edwards et al., 1989; Cleenwerck et al., 2007), while for eukaryotes, V4 region of the 18S ssu rRNA gene was targeted with the primers of Stoeck et al. (2010). . The polymerase chain reaction was performed in duplicate to level out stochastic artefacts, and amplicon libraries were barcoded using the NEXTERA XT index kit (Illumina Inc.) according to manufacturer's instructions. Libraries were sequenced on an Illumina MiSeq machine (300 bp, Paired-end), while each run was spiked with 20% PhiX DNA (Illumina Inc.) to reduce cluster density.