Maritime and Sub-Antarctic microbial soil fungi communities

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019 SCAR - Microbial Antarctic Resource System
Publication date:
19 March 2019
License:
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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How to cite

Researchers should cite this work as follows:

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

Rights

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 6c61d02f-a399-4d88-8e3b-a7068b2d3387.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Metadata

Contacts

Filipa Cox
  • Originator
  • Point Of Contact
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 Provider
Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
1000 Brussels

Geographic Coverage

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

Bounding Coordinates South West [-67.598, -68.356], North East [-54.009, -38.066]

Taxonomic Coverage

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

Phylum Fungi (Fungi)

Temporal Coverage

Start Date / End Date 2011-10-27 / 2011-11-30

Project Data

No Description available

Title Maritime and Sub-Antarctic microbial soil fungi communities
Funding 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.

The personnel involved in the project:

Filipa Cox

Sampling Methods

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.

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

Additional Metadata

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