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

最新バージョン SCAR - Microbial Antarctic Resource System により出版 3 19, 2019 SCAR - Microbial Antarctic Resource System

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説明

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)

バージョン

次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。

引用方法

研究者はこの研究内容を以下のように引用する必要があります。:

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

権利

研究者は権利に関する下記ステートメントを尊重する必要があります。:

パブリッシャーとライセンス保持者権利者は SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF登録

このリソースをはGBIF と登録されており GBIF UUID: 81484676-d49f-43f5-8f78-88289267664bが割り当てられています。   Scientific Committee on Antarctic Research によって承認されたデータ パブリッシャーとして GBIF に登録されているSCAR - Microbial Antarctic Resource System が、このリソースをパブリッシュしました。

キーワード

Metadata

連絡先

Maxime Sweetlove
  • メタデータ提供者
Researcher
Ghent University
Krijgslaan 281
9000 Ghent
BE
Bjorn Tytgat
  • 最初のデータ採集者
Post doctoral assistent
Ghent University
Krijgslaan 281
9000 Ghent
BE
Elie Verleyen
  • 最初のデータ採集者
  • 連絡先
Professor
Ghent University
Krijgslaan 281
9000 Ghent
BE
Anne Willems
  • 最初のデータ採集者
Professor
Ghent University
K.L.Ledeganckstraat 35
9000 Ghent
BE
Christian Wurzbacher
  • 最初のデータ採集者
Post doctoral researcher
Technical University Munich
Munich
DE
Henrik Nillson
  • 最初のデータ採集者
Professor
University of Gothenburg
Gothenburg
SE
Annick Wilmotte
  • 最初のデータ採集者
Professor
University of Liège
Liège
BE
Wim Vyverman
  • 最初のデータ採集者
  • 連絡先
Professor
Ghent University
Krijgslaan 281
9000 Ghent
BE
Maxime Sweetlove
  • メタデータ提供者
Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
1000 Brussels
BE
Sweetlov
  • データ利用者

地理的範囲

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

座標(緯度経度) 南 西 [-90, -180], 北 東 [90, -180]

生物分類学的範囲

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)

時間的範囲

生成(収集)期間 1993-2014

プロジェクトデータ

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.

タイトル Climate Change and Antarctic Microbial Biodiversity
識別子 CCAMBIO
ファンデイング Belgian Science Policy Office (BelSPO) project SD/BA/03
Study Area Description Microbial mats in the benthic and littoral zon of lakes in polar and sub-polar environments.
研究の意図、目的、背景など(デザイン) 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.

プロジェクトに携わる要員:

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

収集方法

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.

Study Extent 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.
Quality Control 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.

Method step description:

  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.