IMIS | Flanders Marine Institute
 

Flanders Marine Institute

Platform for marine research

IMIS

Publications | Institutes | Persons | Datasets | Projects | Maps
[ report an error in this record ] Print this page

Antarctic pack ice Bacterial (16S) communities
Citation
Eronen-Rasimus E, Luhtanen A, Rintala J, Delille B, Dieckmann G, Karkman A, Tison J (2018): Antarctic pack ice Bacterial (16S) communities. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. Https://ipt.biodiversity.aq/resource?r=antarctic_pack_ice_bacterial_communities&v=1.2 https://dx.doi.org/10.15468/wzcryt

Access data
Archived data
Availability: Creative Commons License This dataset is licensed under a Creative Commons Attribution 4.0 International License.

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

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.

Scope
Keywords:
Marine, Antarctica, Metadata, Pack ice, Rrna, PSW, Weddell Sea, Bacteria

Geographical coverage
PSW, Weddell Sea [Marine Regions]

Temporal coverage
21 June 2013 - 26 July 2013

Taxonomic coverage
Bacteria [WoRMS]

Parameter
Molecular data

Contributors
Alfred Wegener Institute for Polar- and Marine Research (AWI), moredata creator
Université de Liège (ULG), moredata creator
Université Libre de Bruxelles (ULB), moredata creator
University of Helsinki, moredata creator

Related datasets
Other relation:
AntOBIS: Antarctic Ocean Biogeographic Information System, more

Dataset status: Completed
Data type: Metadata
Data origin: Research: field survey
Metadatarecord created: 2019-03-28
Information last updated: 2019-04-10
All data in the Integrated Marine Information System (IMIS) is subject to the VLIZ privacy policy