Hypolithic and soil bacteria in Miers_Valley, Antarctica
Citation
Makhalanyane T, Valverde A, Birkeland N, Cary S, Tuffin M, Cowan D, Sweetlove M (2019). Hypolithic and soil bacteria in Miers_Valley, Antarctica. Version 1.1. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/1ztibo accessed via GBIF.org on 2024-08-31.Description
Amplicon sequencing dataset (454 pyrosequencing) of Bacteria (16S ssu rRNA gene, v3 region) in hypolithic and soil environments of Miers Valley, AntarcticaSampling Description
Study Extent
Samples were collected from the coastal Miers Valley region of Eastern Antarctica during the summer season of 2010.Sampling
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.Method steps
- 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).
- 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).
- 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.
Taxonomic Coverages
Bacteria (16S ssu rRNA gene, v3 region)
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Bacteriacommon name: Bacteria rank: domain
Geographic Coverages
Miers Valley, Antarctica
Bibliographic Citations
- 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. -
Contacts
Thulani Makhalanyaneoriginator
University of Pretoria
Pretoria
ZA
Angel Valverde
originator
University of Pretoria
Pretoria
ZA
Nils-Kare Birkeland
originator
University of Bergen
Bergen
NO
Stephen Cary
originator
University of Waikato
Hamilton
NZ
Marla Tuffin
originator
University of Pretoria
Pretoria
ZA
Don Cowan
originator
University of Pretoria
Pretoria
ZA
Maxime Sweetlove
metadata author
position: Research assistant
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
Brussels
1000
BE
email: msweetlove@naturalsciences.be
Thulani Makhalanyane
administrative point of contact
University of Pretoria
Pretoria
ZA
Don Cowan
administrative point of contact
University of Pretoria
Pretoria
ZA