Microbial communities (Bacteria, Eukaryotes and Fungi) in Arctic, Antarctic and Sub-Antarctic lacustrine biofilms
Citation
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. Version 1.1. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/c5mt5n accessed via GBIF.org on 2024-08-18.Description
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)Sampling Description
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.Sampling
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.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 steps
- 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.
Taxonomic Coverages
High throughput (Illumina) amplicon sequencing of Bacteria (16S ssu rRNA), Eukaryotes (18S ssu rRNA) and microbial fungi (ITS)
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Eukaryotacommon name: Eukaryotes rank: domain
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Bacteriacommon name: Bacteria rank: domain
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Fungicommon name: Fungi rank: phylum
Geographic Coverages
Sampled regions include: the Arctic (Greenland, Norway, Svalbard), Sub-Antarctic Islands (Macquarie island and Marion Island) and Antarctic (the Antarctic Peninsula, Continental Antarctica)
Bibliographic Citations
Contacts
Maxime Sweetloveoriginator
position: Researcher
Ghent University
Krijgslaan 281
Ghent
9000
BE
Bjorn Tytgat
originator
position: Post doctoral assistent
Ghent University
Krijgslaan 281
Ghent
9000
BE
Elie Verleyen
originator
position: Professor
Ghent University
Krijgslaan 281
Ghent
9000
BE
Anne Willems
originator
position: Professor
Ghent University
K.L.Ledeganckstraat 35
Ghent
9000
BE
Christian Wurzbacher
originator
position: Post doctoral researcher
Technical University Munich
Munich
DE
Henrik Nillson
originator
position: Professor
University of Gothenburg
Gothenburg
SE
Annick Wilmotte
originator
position: Professor
University of Liège
Liège
BE
Wim Vyverman
originator
position: Professor
Ghent University
Krijgslaan 281
Ghent
9000
BE
email: wim.vyverman@ugent.be
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
Brussels
1000
BE
email: msweetlove@naturalsciences.be
Sweetlov
user
Wim Vyverman
administrative point of contact
position: Professor
Ghent University
Krijgslaan 281
Ghent
9000
BE
email: wim.vyverman@ugent.be
Elie Verleyen
administrative point of contact
position: Professor
Ghent University
Krijgslaan 281
Ghent
9000
BE
email: elie.verleyen@ugent.be