Antarctic pack ice Bacterial (16S) communities
Citation
Eronen-Rasimus E, Luhtanen A, Rintala J, Delille B, Dieckmann G, Karkman A, Tison J, Sweetlove M (2019). Antarctic pack ice Bacterial (16S) communities. Version 1.2. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/wzcryt accessed via GBIF.org on 2024-08-27.Description
Amplicon sequencing dataset of Bacterial communities (16S ssu rRNA gene) in pack ice from the Southern Ocean, near Antarctica.Sampling Description
Study Extent
The samples were collected from 10 pack-ice stations along the Weddell and Lazarev Seas during the Antarctic Winter Ecosystem Climate Study (AWECS, leg ANT-XXIX/6)-expedition aboard the R/V Polarstern during the austral winter in June–July 2013.Sampling
The ice cores were drilled with a trace-metal-clean (electropolished steel) ice auger, 14 cm in diameter. Two ice cores were collected and pooled at each station for the microbiological analyses. We emphasised careful sampling and subsequent sample processing to avoid contamination. The ice cores collected were cut with an ethanol-wiped handsaw into two to seven pieces, depending on the ice thickness (each horizon 10–30 cm), crushed and placed in sterile plastic containers at 4 °C over night in darkness after which the rest of the ice was quickly melted in a water bath with constant stirring. The melted samples were immediately filtered after becoming fully melted.Method steps
- For the DNA extractions, approximately 500 ml of the melted sea-ice were filtered onto sterile 0.22-μm membrane filters (Ø 47 mm; Whatman GE Healthcare, Little Chalfont, Kent, UK) and frozen in liquid nitrogen and later transferred to –80 °C.
- The bacterial community DNA was extracted from the filters with a PowerSoil DNA Isolation Kit (Mo Bio Laboratories Inc, Carlsbad, CA, USA), as described by Eronen-Rasimus et al. (2014), 6 months after the cruise. In addition to the samples, negative controls without the sample were extracted.
- The 16S ribosomal RNA gene region from V1 to part of the V3 was amplified with a polymerase chain reaction, using the universal bacterial primers F8 and R492. A two-step polymerase chain reaction and Illumina MiSeq (Illumina Inc, San Diego, CA, USA) paired-end multiplex sequencing were performed at the Institute of Biotechnology, University of Helsinki, Finland.
Taxonomic Coverages
Bacteria 16S ssu rRNA marker gene, v1-v3
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Bacteriacommon name: Bacteria rank: domain
Geographic Coverages
Antarctica: Southern Ocean: Wedell Sea
Bibliographic Citations
- Eronen-Rasimus, E., Luhtanen, A. M., Rintala, J. M., Delille, B., Dieckmann, G., Karkman, A., & Tison, J. L. (2017). An active bacterial community linked to high chl-a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community. The ISME Journal, 11(10), 2345. -
Contacts
Eeva Eronen-Rasimusoriginator
University of Helsink
Helsink
FI
Anne-Mari Luhtanen
originator
University of Helsink
Helsink
FI
Janne-Markus Rintala
originator
University of Helsink
Helsink
FI
Bruno Delille
originator
Université de Liège
Liège
BE
Gerhard Dieckmann
originator
Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research,
Bremerhaven
DE
Antti Karkman
originator
University of Helsink
Helsink
FI
Jean-Louis Tison
originator
Université Libre de Bruxelles
Campus du Solbosch CP160/03, avenue F.D. Roosevelt 50
Brussels
1050
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Istitute for Natural Sciences
Rue Vautier 29
Brussels
1000
email: msweetlove@naturalsciences.be
Eeva Eronen-Rasimus
administrative point of contact
University of Helsink
Helsink
FI