Hypolithic and soil bacteria in Miers_Valley, Antarctica

Dernière version Publié par SCAR - Microbial Antarctic Resource System le Mar 19, 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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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

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L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

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Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : a126be3e-2889-48df-9d6a-357da4198353.  SCAR - Microbial Antarctic Resource System publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Scientific Committee on Antarctic Research.

Mots-clé

Metadata

Contacts

Personne ayant créé cette ressource:

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

Personne pouvant répondre aux questions sur la ressource:

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

Personne ayant renseigné les métadonnées:

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

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

Miers Valley, Antarctica

Enveloppe géographique Sud Ouest [-78.1, 164], Nord Est [-78.1, 164]

Couverture taxonomique

Bacteria (16S ssu rRNA gene, v3 region)

Domain  Bacteria (Bacteria)

Données sur le projet

Pas de description disponible

Titre Hypolithic and soil bacteria in Miers_Valley, Antarctica
Financement 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.

Les personnes impliquées dans le projet:

Thulani Makhalanyane

Méthodes d'échantillonnage

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.

Etendue de l'étude Samples were collected from the coastal Miers Valley region of Eastern Antarctica during the summer season of 2010.

Description des étapes de la méthode:

  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.

Citations bibliographiques

  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.

Métadonnées additionnelles

Identifiants alternatifs a126be3e-2889-48df-9d6a-357da4198353
https://ipt.biodiversity.aq/resource?r=hypolithic_bacteria_miers_valley_antarctica