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Maritime and Sub-Antarctic microbial soil fungi communities
Citation
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 https://dx.doi.org/10.15468/dj9dju
Contact: Cox, Filipa

Access data
Archived data
Availability: Creative Commons License This dataset is licensed under a Creative Commons Attribution 4.0 International License.

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

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.

Scope
Keywords:
Terrestrial, Dna sequencing, Metadata, Soils, Antarctica, PSW, Antarctica, South Orkney I., Signy I., PSW, South Georgia, Bird I., Fungi

Geographical coverage
Antarctica Stations [Marine Regions]
Leonie Island
PSW, Antarctica, South Orkney I., Signy I. [Marine Regions]
PSW, South Georgia, Bird I. [Marine Regions]

Temporal coverage
27 October 2011 - 30 November 2011

Taxonomic coverage
Fungi [WoRMS]

Parameter
Molecular data

Contributors
Helmholtz Association; Research Centre Jülich (FZJ), moredata creator
Natural Environment Research Council; British Antarctic Survey (BAS), moredata creator
Rothamsted Research, moredata creator
The University of Manchester, moredata creator

Dataset status: Completed
Data type: Metadata
Data origin: Research: field survey
Metadatarecord created: 2019-04-03
Information last updated: 2019-04-10
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