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Maritime and Sub-Antarctic microbial soil fungi communities

Citation

Cox F, Newsham K, Bol R, Dungait J, Robinson C, Sweetlove M (2019). Maritime and Sub-Antarctic microbial soil fungi communities. Version 1.1. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/dj9dju accessed via GBIF.org on 2023-01-31.

Description

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

Sampling Description

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.

Sampling

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.

Method steps

  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.

Taxonomic Coverages

Fungi, profiled by targeting the ITS marker gene with primers ITS1F and ITS4
  1. Fungi
    common name: Fungi rank: phylum

Geographic Coverages

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

Bibliographic Citations

  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

Contacts

Filipa Cox
originator
University of Manchester
Manchester
GB
Kevin Newsham
originator
British Antarctic Survey
Cambridge
GB
Roland Bol
originator
Institute of Bio‐ and Geosciences
Jülich
DE
Jennifer Dungait
originator
Rothamsted Research
Okehampton
GB
Clare Robinson
originator
University of Manchester
Manchester
GB
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
Brussels
1000
email: msweetlove@naturalsciences.be
Filipa Cox
administrative point of contact
University of Manchester
Manchester
GB
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