Document of dataset 6233

Dataset record

Type
Metadata dataset
title in English
Maritime and Sub-Antarctic microbial soil fungi communities
Description in English
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.
Study Extent: 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.
Method step description:
  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.
Abstract in English
Amplicon sequencing dataset (454 pyrosequencing) of microbial soil fungi (based on ITS) from islands in maritime Antarctica and Sub-Antarctica.
License
https://spdx.org/licenses/CC-BY-4.0.html
bibliographicCitation
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
Version
1.1

Temporal coverage

Temporal
Start date
2011-10-27
End date
2011-11-30

Geographical coverage

Spatial
Antarctica
PSW, Antarctica, South Orkney I., Signy I.
PSW, South Georgia, Bird I.

Thesaurus terms

Keyword
Dna sequencing
Metadata
Soils

Taxonomic terms

Taxon keywords
Fungi

Ownerships

creator
Filipa Cox
creator
The University of Manchester
creator
Kevin Newsham
creator
British Antarctic Survey
creator
Roland Bol
creator
Research Centre Jülich
creator
Jennifer Dungait
creator
Rothamsted Research
creator
Clare Robinson
creator
The University of Manchester
contactPoint
Filipa Cox
contactPoint
The University of Manchester

Dataset references

record
Antarctic Ocean Biodiversity Information System
related
Register of Antarctic Species(had role: partially included in)

Document metadata

date created
2019-04-03
date modified
2019-04-10