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Marine bacterial, archaeal and eukaryotic microbial communities on the continental shelf of the western Antarctic Peninsula

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

Amplicon sequencing dataset (454 pyrosequencing) of microbial Bacteria (16S ssu rRNA), Archaea (16S ssu rRNA) and Eukaryotes (18S ssu rRNA) in seawater on the continental shelf of the Antarctic Peninsula.

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How to cite

Researchers should cite this work as follows:

Luria C, Ducklow H, Amaral-Zettler L (2019): Marine bacterial, archaeal and eukaryotic microbial communities on the continental shelf of the western Antarctic Peninsula. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=marine_bacterial_archaeal_eukaryotic_microbial_communities_western_antarctic_peninsula&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: 3a1bad58-879c-4e66-a780-2441ecf2fe3d.  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:

Catherine Luria
Brown University Providence US
Hugh Ducklow
Lamont-Doherty Earth Observatory of Columbia University Palisades US
Linda Amaral-Zettler
Brown University Providence US

Who can answer questions about the resource:

Catherine Luria
Brown University Providence US
Linda Amaral-Zettler
Brown University Providence US

Who filled in the metadata:

Maxime Sweetlove
Research assistant
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels BE

Who else was associated with the resource:

User

Geographic Coverage

Southern Ocean, Continental shelf off the Antarctic peninsula

Bounding Coordinates South West [-63.97, -73.03], North East [41.64, -64.406]

Taxonomic Coverage

Bacteria (16S ssu rRNA gene, v6 region)

Domain  Bacteria (Bacteria)

Archaea (16S ssu rRNA gene, v6 region)

Domain  Archaea (Archaea)

Eukarya (18S ssu rRNA gene, v9 region)

Domain  Eukarya (Eukaryotes)

Temporal Coverage

Start Date / End Date 2008-01-05 / 2008-01-27

Project Data

http://amarallab.mbl.edu

Title Microbial Inventory Research Across Diverse Aquatic Long Term Eco- logical Research Sites
Identifier MIRADA-LTERS
Funding NSF DEB- 0717390 (MIRADA-LTERS) and NSF Awards OPP- 0217282 and 0823101 (Palmer LTER) from the Antarctic Organisms and Ecosystems Program
Study Area Description Palmer Antarctica LTER

The personnel involved in the project:

Catherine Luria

Sampling Methods

Samples were drawn from 10 and 100 m depths from the northern and southern, inshore and offshore corners of the Palmer LTER sampling grid. We collected duplicate samples using a rosette equipped with 10 l Niskin bottles and conductivity, temperature, and depth (CTD) probes. To contrast summer and winter water, we also collected an additional Austral winter sample from 10 m depth at the northern, inshore sampling site in August 2008, using a submersible pump with silicone tubing. Water samples were filtered (1 to 2 l) through 0.2 μm SterivexTM filters (Millipore), preserved genomic DNA by flooding the 2 ml filter cartridge reservoir with sucrose lysis buffer (40 mM EDTA, 50 mM Tris-HCl, 0.75 M sucrose), and stored the filters at −80°C until processing.

Study Extent Sampling was conducted on the annual Palmer LTER (western coast of the Antarctic Peninsula) midsummer research cruise (January−February 2008)

Method step description:

  1. We extracted DNA using a Puregene DNA extraction kit (Qiagen), with modifications as described by Amaral-Zettler et al. (2009), and stored the DNA at −20°C until PCR amplification. Bacterial and archaeal V6 16S rRNA and eukaryotic V9 18S rRNA gene hypervariable regions were amplified as described previously (Huber et al. 2007, Amaral- Zettler et al. 2009), using ‘barcoded’ primers which al- lowed for multiplexed sequencing (see http://vamps. mbl.edu/resources/primers.php for details). For each sample, we pooled triplicate 50 μl PCR reaction products to minimize propagation of PCR errors and purified them using a QIAquick column-based purification kit (Qiagen). We sequenced purified amplicons on a 454 Genome Sequencer FLX (Roche) according to the manufacturer’s protocols using the LR70 kit.

Bibliographic Citations

  1. Luria, C. M., Ducklow, H. W., & Amaral-Zettler, L. A. (2014). Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula. Aquatic Microbial Ecology, 73(2), 107-121.