Maritime and Sub-Antarctic microbial soil fungi communities

Dernière version Publié par SCAR - Microbial Antarctic Resource System le mars 19, 2019 SCAR - Microbial Antarctic Resource System
Date de publication:
19 mars 2019
Licence:
CC-BY 4.0

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Description

Amplicon sequencing dataset (454 pyrosequencing) of microbial soil fungi (based on ITS) from islands in maritime Antarctica and Sub-Antarctica.

Versions

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Cox F, Newsham K, Bol R, Dungait J, Robinson C (2019): Maritime and Sub-Antarctic microbial soil fungi communities. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=maritime_antarctic_soil_fungi_communities&v=1.1

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 6c61d02f-a399-4d88-8e3b-a7068b2d3387.  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

Filipa Cox
  • Créateur
  • Personne De Contact
University of Manchester
Manchester
GB
Kevin Newsham
  • Créateur
British Antarctic Survey
Cambridge
GB
Roland Bol
  • Créateur
Institute of Bio‐ and Geosciences
Jülich
DE
Jennifer Dungait
  • Créateur
Rothamsted Research
Okehampton
GB
Clare Robinson
  • Créateur
University of Manchester
Manchester
GB
Maxime Sweetlove
  • Fournisseur Des Métadonnées
Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
1000 Brussels

Couverture géographique

Bird Island (South Georgia), Signy Island (Antarctica) and Leonie Island (Antarctica)

Enveloppe géographique Sud Ouest [-67,598, -68,356], Nord Est [-54,009, -38,066]

Couverture taxonomique

Fungi, profiled by targeting the ITS marker gene with primers ITS1F and ITS4

Phylum Fungi (Fungi)

Couverture temporelle

Date de début / Date de fin 2011-10-27 / 2011-11-30

Données sur le projet

Pas de description disponible

Titre Maritime and Sub-Antarctic microbial soil fungi communities
Financement This work was funded by an Antarctic Funding Initiative grant from the UK Natural Environment Research Council, under grant numbers NE/H014098/1, NE/H014772/1 and NE/H01408X/1.

Les personnes impliquées dans le projet:

Filipa Cox

Méthodes d'échantillonnage

Soil was collected under populations of Colobanthus quitensis (Kunth) Bartl. and Deschampsia antarctica Desv., the only two native vascular plant species that occur in Antarctica. On each island, 50 mL sterile centrifuge tubes (Corning Inc, Corning, NY, USA) were used to collect samples by hammering them directly into the vertical walls of three soil pits at three depths (2, 4 and 8 cm). Soil was stored at −80 °C within 5 h of collection and was later freeze‐dried to preserve fungal nucleotides.

Etendue de l'étude Between October and November 2011, soil samples were collected from Bird Island (54.0089° S, 38.0662° W), Signy Island (60.7107° S, 45.5849° W) and Léonie Island (67.5984° S, 68.3561° W) in the sub‐Antarctic, low maritime and high maritime Antarctic respectively.

Description des étapes de la méthode:

  1. Total DNA was extracted from five individual 50 mg soil samples, using the RNA PowerSoil Total RNA Isolation and DNA Elution Accessory kits (MoBio Laboratories, Carlsbad, CA, USA). The extracted DNA was amplified in triplicate PCR reactions using ITS1F and ITS4 primers. The ITS4 primer was modified with the 454 A adaptor and a 10-bp barcode specific to each sample, allowing the identification of different samples once pooled, and the ITS1F primer was modified with the 454 B adaptor. This primer design allowed reverse sequencing across the ITS2 region. Triplicate PCR reactions were performed using Phusion HF 2X Master Mix (New England Biolabs, Beverly, MA, USA) using the following amounts per 50 μl reaction: 19 μl H20; 25 μl 2X HF mix; 2.5 μl of each primer; 1 μl template, and the following PCR cycle: initial denaturation of 98°C for 45 s, then for 33 cycles: denaturation: 98°C for 10 s, annealing: 53°C for 30 s, extension: 72°C for 30 s, final extension: 72°C for 7 min. The triplicate PCR products were pooled and subsequently purified using AMPure XP bead purification (Beckman Coulter, Inc, Brea, CA, USA) and quantified using Qubit dsDNA HS Assay (Life Technologies, Carlsbad, CA, USA) before normalization to equal concentrations. The purified and normalized PCR products were run on one plate on the 454 Roche Titanium FLX platform at the Liverpool Centre for Genomic Research.

Citations bibliographiques

  1. Cox, F., Newsham, K. K., Bol, R., Dungait, J. A., & Robinson, C. H. (2016). Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic. Ecology letters, 19(5), 528-536. https://doi.org/10.1111/ele.12587

Métadonnées additionnelles

Identifiants alternatifs 6c61d02f-a399-4d88-8e3b-a7068b2d3387
https://ipt.biodiversity.aq/resource?r=maritime_antarctic_soil_fungi_communities