Hypolithic and soil bacteria in Miers_Valley, Antarctica

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Publication date:
19 de Março de 2019
CC-BY 4.0

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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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Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

Makhalanyane T, Valverde A, Birkeland N, Cary S, Tuffin M, Cowan D (2019): Hypolithic and soil bacteria in Miers_Valley, Antarctica. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=hypolithic_bacteria_miers_valley_antarctica&v=1.1


Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: a126be3e-2889-48df-9d6a-357da4198353.  SCAR - Microbial Antarctic Resource System publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por Scientific Committee on Antarctic Research.




Thulani Makhalanyane
  • Originador
  • Ponto De Contato
University of Pretoria
Angel Valverde
  • Originador
University of Pretoria
Nils-Kare Birkeland
  • Originador
University of Bergen
Stephen Cary
  • Originador
University of Waikato
Marla Tuffin
  • Originador
University of Pretoria
Don Cowan
  • Originador
  • Ponto De Contato
University of Pretoria
Maxime Sweetlove
  • Provedor Dos Metadados
Research assistant
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
1000 Brussels

Cobertura Geográfica

Miers Valley, Antarctica

Coordenadas delimitadoras Sul Oeste [-78,1, 164], Norte Leste [-78,1, 164]

Cobertura Taxonômica

Bacteria (16S ssu rRNA gene, v3 region)

Domínio Bacteria (Bacteria)

Dados Sobre o Projeto

Nenhuma descrição disponível

Título Hypolithic and soil bacteria in Miers_Valley, Antarctica
Financiamento 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.

O pessoal envolvido no projeto:

Thulani Makhalanyane

Métodos de Amostragem

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.

Área de Estudo Samples were collected from the coastal Miers Valley region of Eastern Antarctica during the summer season of 2010.

Descrição dos passos do método:

  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.

Citações bibliográficas

  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.

Metadados Adicionais

Identificadores alternativos a126be3e-2889-48df-9d6a-357da4198353