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

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019 SCAR - Microbial Antarctic Resource System

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)

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How to cite

Researchers should cite this work as follows:

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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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.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 81484676-d49f-43f5-8f78-88289267664b.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Metadata

Contacts

Who created the resource:

Maxime Sweetlove
Researcher
Ghent University Krijgslaan 281 9000 Ghent BE
Bjorn Tytgat
Post doctoral assistent
Ghent University Krijgslaan 281 9000 Ghent BE
Elie Verleyen
Professor
Ghent University Krijgslaan 281 9000 Ghent BE
Anne Willems
Professor
Ghent University K.L.Ledeganckstraat 35 9000 Ghent BE
Christian Wurzbacher
Post doctoral researcher
Technical University Munich Munich DE
Henrik Nillson
Professor
University of Gothenburg Gothenburg SE
Annick Wilmotte
Professor
University of Liège Liège BE
Wim Vyverman
Professor
Ghent University Krijgslaan 281 9000 Ghent BE

Who can answer questions about the resource:

Wim Vyverman
Professor
Ghent University Krijgslaan 281 9000 Ghent BE
Elie Verleyen
Professor
Ghent University Krijgslaan 281 9000 Ghent BE

Who filled in the metadata:

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

Who else was associated with the resource:

User
Sweetlov

Geographic Coverage

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

Bounding Coordinates South West [-90, -180], North East [90, -180]

Taxonomic Coverage

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)

Temporal Coverage

Formation Period 1993-2014

Project Data

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.

Title Climate Change and Antarctic Microbial Biodiversity
Identifier CCAMBIO
Funding 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.
Design Description 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.

The personnel involved in the project:

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

Sampling Methods

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.