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Hypolithic and soil bacteria in Miers_Valley, Antarctica

Latest version published by SCAR - Microbial Antarctic Resource System on Feb 1, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (454 pyrosequencing) of Bacteria (16S ssu rRNA gene, v3 region) in hypolithic and soil environments of Miers Valley, Antarctica

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How to cite

Researchers should cite this work as follows:

Makhalanyane T, Valverde A, Birkeland N, Cary S, Tuffin M, Cowan D (2019): Hypolithic and soil bacteria in Miers_Valley, Antarctica. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. http://ipt.biodiversity.aq/resource?r=hypolithic_bacteria_miers_valley_antarctica&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: a126be3e-2889-48df-9d6a-357da4198353.  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:

Thulani Makhalanyane
University of Pretoria Pretoria ZA
Angel Valverde
University of Pretoria Pretoria ZA
Nils-Kare Birkeland
University of Bergen Bergen NO
Stephen Cary
University of Waikato Hamilton NZ
Marla Tuffin
University of Pretoria Pretoria ZA
Don Cowan
University of Pretoria Pretoria ZA

Who can answer questions about the resource:

Thulani Makhalanyane
University of Pretoria Pretoria ZA
Don Cowan
University of Pretoria Pretoria ZA

Who filled in the metadata:

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

Who else was associated with the resource:

User

Geographic Coverage

Miers Valley, Antarctica

Bounding Coordinates South West [-78.1, 164], North East [-78.1, 164]

Taxonomic Coverage

Bacteria (16S ssu rRNA gene, v3 region)

Domain  Bacteria (Bacteria)

Project Data

No Description available

Title Hypolithic and soil bacteria in Miers_Valley, Antarctica
Funding Financial support for this resource was provided by the following organizations: the National Research Foundation (South Africa), the Research Council of Norway (the South Africa Program; grant no. 180352) and the University of the Western Cape.

The personnel involved in the project:

Thulani Makhalanyane

Sampling Methods

A total of 36 samples were collected, 9 from each of the three hypolith types and soil (that is, four habitats), and stored in sterile Whirl-Pak bags (Nasco Inter- national, Fort Atkinson, WI, USA). Equivalent amounts of hypolithic and soil samples were collected aseptically in an area of 1 km2 with similar macro-environmental conditions (that is, slope, aspect, elevation). The spatial arrangement of samples was also similar between habitats, therefore, allowing us to compare the potential influence of micro-environmental factors on beta-diversity across a similar spatial scale.

Study Extent Samples were collected from the coastal Miers Valley region of Eastern Antarctica during the summer season of 2010.

Method step description:

  1. MoBio PowerSoil DNA isolation kit (Mo BIO, Carlsbad, CA, USA). Adsorbed DNA was eluted in 40ml of tris-EDTA buffer and quantified using the Nanodrop 1000 spectrophotometer (NanoDrop Products, Wilmington, DE, USA).
  2. In order to reduce the number of samples for 454 pyrosequencing, equal amounts of DNA from each of the nine samples were pooled according to habitat (n= 4).
  3. Unique four base pair multiplex identifiers were added to the primers for each sample. PCR amplification of the highly variable V3 region of the bacterial 16S rRNA gene was carried out in two steps using HotStar DNA polymerase (QIAGEN GmbH, Hilden, Germany), based on the universal bacterial primers, A8-28F and K517R. In the first PCR step, untagged primers were used in a 20-cycle reaction as described by Azmuda et al. (2012), followed by purification of the amplicons using the GenElute PCR Clean-Up Kit (Sigma-Aldrich, Copenhagen, Denmark). The second reaction was performed with 100ng of the purified PCR amplicons as template and primers containing the 454 FLX adaptors with sample-specific multiple identifiers using 10 PCR reaction cycles (Azmuda et al., 2012). The final products were purified using the Agencourt AMPure purification kit (Agencourt Bioscience Corporation (Beckman Coulter), Beverly, MA, USA) before shipment to GATC Biotech AG (Konstanz, Germany) for pyrosequencing with the GS FLX (Roche 454 Life Sciences, Branford, CT, USA) Titanium chemistry.

Bibliographic Citations

  1. Makhalanyane, T. P., Valverde, A., Birkeland, N. K., Cary, S. C., Tuffin, I. M., & Cowan, D. A. (2013). Evidence for successional development in Antarctic hypolithic bacterial communities. The ISME journal, 7(11), 2080.