Integrated Publishing Toolkit(IPT)

free and open access to biodiversity data

Microorganisms (eukaryote and bacteria) in Antarctic cryoconite holes.

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

Amplicon sequencing dataset (Illumina MiSeq) of Eukaryotes (18S ssu rRNA) and Bacterial (16S ssu rRNA) microbes in Antarctic cryoconite holes.

Downloads

Download the latest version of the metadata-only resource metadata as EML or RTF:

Metadata as an EML file download in English (10 KB)
Metadata as an RTF file download in English (9 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Sommers P, Darcy J, Gendrom E, Stanish L, Bagshaw E, Porazinska D, Schmidt S (2019): Microorganisms (eukaryote and bacteria) in Antarctic cryoconite holes.. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbes_antarctic_cryoconite&v=1.1

Rights

Researchers should respect the following rights statement:

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: 3adb4fd7-9e77-41e0-aa37-9ca4b72c5eaa.  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:

Pacifica Sommers
University of Colorado at Boulder Boulder US
John Darcy
University of Hawaï at Manoa Manoa US
Eli Gendrom
University of Colorado at Boulder Boulder US
Lee Stanish
National Ecological Observatory Network Boulder US
Elizabeth Bagshaw
Cardiff University Cardiff GB
Dorota Porazinska
University of Colorado at Boulder Boulder US
Steven Schmidt
University of Colorado at Boulder Boulder US

Who can answer questions about the resource:

Pacifica Sommers
University of Colorado at Boulder Boulder US

Who filled in the metadata:

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

Who else was associated with the resource:

User

Geographic Coverage

Cryoconite holes in Taylor Valley, Antarctica

Bounding Coordinates South West [-77.615, 162.967], North East [-77.615, 162.967]

Taxonomic Coverage

Bacteria (16S ssu rRNA gene)

Domain  Bacteria (Bacteria)

Eukaryotes (18S ssu rRNA gene)

Domain  Eukaryota (Eukaryotes)

Temporal Coverage

Start Date 2007-01-01

Project Data

No Description available

Title Antarctic cryoconite 2007
Funding This work was funded by NSF Polar Programs Award 1443578 and by Duke University.

The personnel involved in the project:

Pacifica Sommers

Sampling Methods

A core was collected from the center of each hole using a SIPRE corer. The core was removed and stored in a Ziploc bag that had been triple-rinsed with deionized water. For the samples in which meltwater was present at the time of sampling, the ice lid was removed with the SIPRE corer, and then a water sample was pumped out using a hand powered vacuum pump. A sample of sediment was removed and stored in a triple-rinsed Ziploc bag. On return to the eld laboratory, samples were stored at –20◦C until processing up to 30 days later. Samples were eventually allowed to melt out in the collection bags and water samples were drawn off using syringes, leaving the sediment behind.

Study Extent Nineteen cryoconite holes on glaciers in Taylor Valley (McMurdo Dry Valleys, Antarctica) were sampled between 15 December 2007 and 4 January 2008.

Method step description:

  1. All cryoconite samples were stored frozen at –70◦C to minimize DNA degradation. Between 25 April 2016 and 2 May 2016, the frozen cryoconite sediments were thawed at room temperature and 0.4 g was processed for DNA extraction from each technical replicate separately (47 total from 19 samples) using PowerSoil DNA Isolation Kits (MoBio Inc., Carlsbad, CA, USA), according to the manufacture’s protocol. Extracted genomic DNA was amplified in triplicate using 16S (515f-806r primers) and 18S (1391f-EukBr primers) SSU ribosomal gene markers. Amplified DNA was pooled and normalized to equimolar concentrations using SequalPrep Normalization Plate Kits (Invitrogen), and sequenced using the Illumina MiSeq V2 (2 × 250 bp chemistry) at the BioFrontiers Sequencing Core Facility at the University of Colorado at Boulder.

Bibliographic Citations

  1. Sommers, P., Darcy, J. L., Gendron, E. M., Stanish, L. F., Bagshaw, E. A., Porazinska, D. L., & Schmidt, S. K. (2017). Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes. FEMS microbiology ecology, 94(1), fix167.

Additional Metadata

Alternative Identifiers 3adb4fd7-9e77-41e0-aa37-9ca4b72c5eaa
https://ipt.biodiversity.aq/resource?r=microbes_antarctic_cryoconite