Fungi (LSU) in soils from the South Shetland island, Antarctic Peninsula island, and Union Glacier

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

Amplicon sequencing dataset of microbial Fungi (LSU D1-D2) of terrestrial habitats in Antarctica, including eight islands of the South Shetland Archipelago, two islands on the Antarctic Peninsula and Union Glacier.

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Baeza M, Barahona S, Alcaino J, Cifuentes V (2018): Fungi (LSU) in soils from the South Shetland island, Antarctic Peninsula island, and Union Glacier. v1.3. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=fungi_soils_s_shetland_and_antarctica&v=1.3

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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 : 11c8e968-361d-4cea-abae-67450fa03fe8.  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:

Marcelo Baeza
Universidad de Chile Santiago CL
Salvador Barahona
Universidad de Chile Santiago CL
Jennifer Alcaino
Universidad de Chile Santiago CL
Victor Cifuentes
Universidad de Chile Santiago CL

Personne pouvant répondre aux questions sur la ressource:

Marcelo Baeza
Universidad de Chile Santiago CL

Personne ayant renseigné les métadonnées:

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

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

South Shetland Islands, Union Glacier (Antarctica)

Enveloppe géographique Sud Ouest [-79.82, -83.31], Nord Est [-62.1, -58.1]

Couverture taxonomique

LSU marker gene for microbial soil Fungi

Phylum  Fungi (Fungi)

Couverture temporelle

Date de début / Date de fin 2010-01-01 / 2015-01-01

Données sur le projet

Pas de description disponible

Titre FONDECYT grant 1130333
Financement This work was supported by Comisión Nacional de Investigación Científica y Tecnológica (No. FONDECYT grant 1130333).

Les personnes impliquées dans le projet:

Marcelo Baeza
Salvador Barahona
Jennifer Alcaino
Victor Cifuentes

Méthodes d'échantillonnage

Samples were collected in sterile 50 ml plastic tubes, which were sealed and shipped at -20°C to the Genetics Laboratory of the Faculty of Science at the Universidad de Chile. Once samples arrived at the laboratory, they were maintained at -80°C until processing.

Etendue de l'étude Soil samples were gathered during several expeditions to Antarctica, including Union Glacier, Lagotellerie island, King George, Deception, Snow, Dee, Livingstone, Greenwich, Robert, Nelson and Litchfield islands.

Description des étapes de la méthode:

  1. A PowerSoil DNA Isolation Kit (MO BIO Laboratories Inc., Carlsbad, CA, United States) was used for direct DNA extraction from soil samples. The manufacturers’ instructions were followed, with only one modification, the disruption step, was performed using a Mini Beadbeater-16 cell disrupter (BioSpec Bartlesville, United States) instead of vortex agitation, as no PCR-amplicons were obtained in reactions using samples obtained through vortex agitation.
  2. The PCR reactions were performed using 1 μl of DNA sample (direct or 1/10 dilution), 5 units of Taq DNA polymerase, dNTP mix at 0.4 mM each, forward and reverse primers at 1 mM final each, PCR buffer and MgCl2 2 mM. Amplification was performed using a 2720 (Applied Biosystems) thermal cycler using the following protocol: initial denaturation at 94°C for 3 min; 35 cycles of denaturation at 94°C for 30 s, annealing at 50°C for 3 min, and extension at 72°C for 3 min; and a final extension step at 72°C for 10 min. The universal primers F63 (5′-GCA TAT CAA TAA GCG GAG GAA AAG-3′) and LR3 (5′-GGT CCG TGT TTC AAG ACG G-3′) were used; these primers have been described as specific for amplifying the fungal D1/D2 region of the large subunit ribosomal gene (LSU). In all PCR reactions, the same forward primer (F63) was used, but the reverse primer (LR3) was specific for each soil sample as a 454 adapter, a specific barcode and a linker sequence were added.
  3. Sequencing was performed at OMICS Solutions (Santiago, Chile) using the Ion 314TM Chip Kit v2 (Thermo Fisher) and Ion Torrent personal genome machine (PGM), according to the manufacturer’s instructions (Rothberg et al., 2011). Three independent runs were performed: (i) samples from King George Island; (ii) samples from Deception, Snow, Dee, Livingstone, Greenwich, Robert, Nelson and Litchfield islands; and iii) samples from Lagotellerie and Union Glacier.

Citations bibliographiques

  1. Baeza, M., Barahona, S., Alcaíno, J., & Cifuentes, V. (2017). Amplicon-Metagenomic Analysis of Fungi from Antarctic Terrestrial Habitats. Frontiers in microbiology, 8, 2235.
  2. Carrasco, M., Rozas, J. M., Barahona, S., Alcaíno, J., Cifuentes, V., & Baeza, M. (2012). Diversity and extracellular enzymatic activities of yeasts isolated from King George Island, the sub-Antarctic region. BMC microbiology, 12(1), 251.
  3. Troncoso, E., Barahona, S., Carrasco, M., Villarreal, P., Alcaíno, J., Cifuentes, V., & Baeza, M. (2017). Identification and characterization of yeasts isolated from the South Shetland Islands and the Antarctic Peninsula. Polar Biology, 40(3), 649-658.
  4. Barahona, S., Yuivar, Y., Socias, G., Alcaíno, J., Cifuentes, V., & Baeza, M. (2016). Identification and characterization of yeasts isolated from sedimentary rocks of Union Glacier at the Antarctica. Extremophiles, 20(4), 479-491.

Métadonnées additionnelles

Identifiants alternatifs 11c8e968-361d-4cea-abae-67450fa03fe8
https://ipt.biodiversity.aq/resource?r=fungi_soils_s_shetland_and_antarctica