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Antarctic pack ice Bacterial (16S) communities

Latest version published by SCAR - Microbial Antarctic Resource System on Dec 17, 2018 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset of Bacterial communities (16S ssu rRNA gene) in pack ice from the Southern Ocean, near Antarctica.

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How to cite

Researchers should cite this work as follows:

Eronen-Rasimus E, Luhtanen A, Rintala J, Delille B, Dieckmann G, Karkman A, Tison J (2018): Antarctic pack ice Bacterial (16S) communities. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. http://ipt.biodiversity.aq/resource?r=antarctic_pack_ice_bacterial_communities&v=1.0

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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: bd9de0e6-69c1-4ec6-b49b-fa6f84454163.  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:

Eeva Eronen-Rasimus
Post doctoral researcher
University of Helsink Helsink FI
Anne-Mari Luhtanen
Researcher
University of Helsink Helsink FI
Janne-Markus Rintala
Adjunct professor
University of Helsink Helsink FI
Bruno Delille
Research associate
Université de Liège Liège BE
Gerhard Dieckmann
Senior scientist
Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven DE
Antti Karkman
Post doctoral researcher
University of Helsink Helsink FI
jean-louis Tison
Université Libre de Bruxelles Campus du Solbosch CP160/03, avenue F.D. Roosevelt 50 1050 Brussels

Who can answer questions about the resource:

Eeva Eronen-Rasimus
Post doctoral researcher
University of Helsink Helsink FI

Who filled in the metadata:

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

Who else was associated with the resource:

User

Geographic Coverage

Antarctica: Southern Ocean: Wedell Sea

Bounding Coordinates South West [-67.949, -0.006], North East [-61.526, 0.122]

Taxonomic Coverage

Bacteria 16S ssu rRNA marker gene, v1-v3

Domain  Bacteria (Bacteria)

Temporal Coverage

Start Date / End Date 2013-06-21 / 2013-07-26

Project Data

No Description available

Title Antarctic pack ice Bacterial (16S) communities
Funding The creation of this dataset was supported by the Walter and Andrée de Nottbeck Foundation, Academy of Finland and the Belgian Science Policy (Bigsouth project, SD/CA/05).

The personnel involved in the project:

Eeva Eronen-Rasimus

Sampling Methods

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.

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.

Method step description:

  1. 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.
  2. 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.
  3. 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.

Bibliographic Citations

  1. 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.