Soil microbiome (Bacteria) on Keller Peninsula (Antarctica)

Dernière version Publié par SCAR - Microbial Antarctic Resource System le Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (454 pyrosequencing and Ion Torrent) of Bacteria (16S ssu rRNA gene) in ice-free soils of Keller Peninsula (Antarctica)

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Roesch L, Fulthorpe R, Pereira A, Pereira C, Lemos L, Barbosa A, Suleiman A, Gerber A, Pereira M, Loss A, de Costa E (2019): Soil microbiome (Bacteria) on Keller Peninsula (Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antarctic_soil_microbiome_keller_peninsula&v=1.1

Droits

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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.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 48350841-8927-4c78-bbc1-24c01a4d5586.  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:

Luiz Roesch
Universidade Federal do Pampa Sao Gabriel BR
Roberta Fulthorpe
University of Toronto at Scarborough Scarborough CA
Antonio Pereira
Universidade Federal do Pampa Sao Gabriel BR
Clarissa Pereira
Universidade Federal do Pampa Sao Gabriel BR
Leondro Lemos
Universidade Federal do Pampa Sao Gabriel BR
Anthony Barbosa
Universidade Federal do Pampa Sao Gabriel BR
Afnan Suleiman
Universidade Federal do Pampa Sao Gabriel BR
Alexandra Gerber
Unidade de Genômica Computacional Darcy Fontoura de Almeida Rio de Janeiro BR
Marcos Pereira
Universidade Federal Rural do Rio de Janeiro Rio de Janeiro BR
Arcangelo Loss
Universidade Federal Rural do Rio de Janeiro Rio de Janeiro BR
Elias de Costa
Universidade Federal Rural do Rio de Janeiro Rio de Janeiro BR

Personne pouvant répondre aux questions sur la ressource:

Luiz Roesch
Universidade Federal do Pampa Sao Gabriel BR

Personne ayant renseigné les métadonnées:

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

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

Keller Peninsula, Antarctica

Enveloppe géographique Sud Ouest [-64.294, -58.482], Nord Est [-62.062, -56.691]

Couverture taxonomique

Bacteria, based on the 16S ssu rRNA gene

Domain  Bacteria (Bacteria)

Couverture temporelle

Epoque de formation 2009-2010

Données sur le projet

Pas de description disponible

Titre Soil microbiome (Bacteria) on Keller Peninsula (Antarctica)
Financement This work was supported by the INCT-APA (CNPq process No. 574018/2008-5, FAPERJ E-26/170.023/2008) and Ministry of Science and Technology, and the Secretariat for the Marine Resources Interministerial Committee (SECIRM). Additional funding was provided via a fellowships from the CNPq (process number 503370/2009-6).

Les personnes impliquées dans le projet:

Luiz Roesch

Méthodes d'échantillonnage

A total of 12 soil samples were chosen for sampling and were taken from a variety of plant communities having different soil features. Soil was collected removing the plant cover and taking cores of 5 cm diameter and 5 cm depth. All soil was stored on ice upon collection and transported to the laboratory for extraction.

Etendue de l'étude Soil samples were collected on the Keller Peninsula, King George Island, Antarctica during the austral summer of 2009–2010.

Description des étapes de la méthode:

  1. DNA was isolated from at least 1 g of mixed soil using the PowerSoilTM DNA Isolation Kit (MO BIO) as described by the manufacturer. The genomic DNA concentration and purity were determined by spectrophotometry.
  2. Twelve independent PCR reactions were performed for each soil sample with the primers 338R and 27F for the amplification of the V1–V2 hypervariable regions of the 16S rRNA gene. PCR was performed with the GoTaq PCR core system (Promega, Madi- son, WI, USA). The mixtures contained 5 ul of 10× PCR buffer, 200 mM dNTPs, 100 mM of each primer, 2.5 U of Taq polymerase and approximately 100ng of DNA template in a final volume of 50 ul. The PCR conditions were 94 ◦ C for 2 min, 30 cycles of 94◦C for 45s; 55◦C for 45s; and 72◦C for 1min extension; followed by 72 ◦C for 6 min. The 16S rRNA gene fragments were sequenced using 454 GS FLX Titanium (Lib-L) chemistry for unidirectional sequencing of the amplicon libraries. Barcoded primers were used to multiplex the amplicon pools so they could be sequenced together and computationally separated afterward. To do this, 8-base barcodes were added to the 5′-end of the reverse primers using the self-correcting barcode method of Hamady et al. (2008). The primers were attached to the GS FLX Titanium Primer A (5′ -CCATCTCATCCCTGCGTGTCTCCGACTCAG-3′ ) and Primer B (5′ - CCTATCCCCTGTGTGCCTTGGCAGTC-3′ ) sequences, modified for use with GS FLX Titanium emPCR Kits (Lib-L) and a two-base linker sequence was inserted between the 454 adapter and the 16S rRNA primers to reduce any effect the composite primer might have on PCR efficiency. The PCR products for each of the 12 samples were purified and combined in equimolar ratios with the quantitative DNA binding method (SequalPrep Kit, Invitrogen, Carlsbad, CA, USA) to create a DNA pool that was used for pyrosequencing from the A-Key adaptor.

Citations bibliographiques

  1. Roesch, L. F., Fulthorpe, R. R., Pereira, A. B., Pereira, C. K., Lemos, L. N., Barbosa, A. D., ... & da Costa, E. M. (2012). Soil bacterial community abundance and diversity in ice-free areas of Keller Peninsula, Antarctica. Applied soil ecology, 61, 7-15.|Rampelotto, P. H., Barboza, A. D. M., Pereira, A. B., Triplett, E. W., Schaefer, C. E. G., de Oliveira Camargo, F. A., & Roesch, L. F. W. (2015). Distribution and interaction patterns of bacterial communities in an ornithogenic soil of Seymour Island, Antarctica. Microbial ecology, 69(3), 684-694.

Métadonnées additionnelles

Identifiants alternatifs 48350841-8927-4c78-bbc1-24c01a4d5586
https://ipt.biodiversity.aq/resource?r=antarctic_soil_microbiome_keller_peninsula