Microbial Fungi in soils on different Sub-Antarctic islands

最新版本 由 SCAR - Microbial Antarctic Resource System 發佈於 Mar 22, 2019 SCAR - Microbial Antarctic Resource System

Aplicon sequencing dataset (454 pyrosequencing) of microbial Fungi (ITS) in soils from Bird Island, Signy Island and Leonie Island (Sub-Antarctica)

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Cox F, Newsham K, Robinson C (2019): Microbial Fungi in soils on different Sub-Antarctic islands. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbial_fungi_from_3_sub_antarctic_islands&v=1.0

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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.

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關鍵字

Metadata

聯絡資訊

資源建立者:

Filipa Cox
University of Manchester Manchester GB
Kevin Newsham
British Antarctic Survey Cambridge GB
Clare Robinson
University of Manchester Manchester GB

可回覆此資源相關問題者:

Filipa Cox
University of Manchester Manchester GB

元數據填寫者:

Maxime Sweetlove
Research assistent
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels BE

與此資源的相關者:

使用者

地理涵蓋範圍

Soils were sampled in Bird Island, Signy Island and Leonie Island (Sub-Antarctica)

界定座標範圍 緯度南界 經度西界 [-67.598, -68.356], 緯度北界 經度東界 [-54.009, -38.066]

分類群涵蓋範圍

Fungi were profiled by sequencing the ITS gene (454 pyrosequencing)

Phylum  Fungi (Fungi)

計畫資料

無相關描述

計畫名稱 Microbial Fungi in soils on different Sub-Antarctic islands
經費來源 Funding was provided by: the Antarctic Funding Initiative grant from the UK Natural Environment Research Council (grant numbers NE/H014098/1, NE/H014772/1 and NE/H01408X/1) and a British Ecological Society Large Research Grant for early career ecologists.

The personnel involved in the project:

Filipa Cox

取樣方法

Soil was collected from under populations of co‐occurring Deschampsia antarctica Desv. and Colobanthus quitensis (Kunth) Bartl., 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 soil samples by hammering them directly into the vertical walls of three pits at three depths (2, 4 and 8 cm). The soil, kept on ice after collection and frozen at −80 °C within 5 h, was freeze dried to preserve fungal nucleotides.

研究範圍 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, between October and November 2011.

方法步驟描述:

  1. Total DNA and RNA were extracted simultaneously from five individual 50 mg samples, taken from each of the tubes of homogenized soil (representing a total of 27 × 5 = 135 samples), using RNA PowerSoil Total RNA Isolation and DNA Elution Accessory kits (MoBio Laboratories, Carlsbad, CA, USA). Extracted DNA was amplified in triplicate PCR reactions using the primers ITS1F and ITS4 as described by Cox et al. (2016), with conditions matching those described below for cDNA. Extracted RNA was treated with a Turbo DNA‐free kit (Life technologies, Carlsbad, CA, USA), checked for the absence of DNA using PCR, and reverse transcribed using AccuScript High‐Fidelity Reverse Transcriptase (Agilent, Santa Clara, CA, USA) and random nonamers. The resulting cDNA was amplified in triplicate PCR reactions using ITS1F (Gardes and Bruns, 1993) and ITS4 (White et al., 1990) primers. The ITS4 primer was modified with the Roche 454 A adapter and a 10 bp barcode specific to each sample, allowing identification of different samples once pooled, and the ITS1F primer was modified with the 454 B adaptor.
  2. The triplicate PCR products were pooled and subsequently purified using AMPure XP bead purification (Beckman Coulter, Inc, Brea, CA, USA) and quantified using a Qubit dsDNA HS Assay (Life Technologies, Carlsbad, CA, USA) before normalization to consistent concentration. The purified and normalized PCR products were run on a single plate, on the 454 Roche Titanium FLX platform at the Liverpool Centre for Genomic Research, at the same time and under identical conditions to the DNA library.

引用文獻

  1. Cox, F., Newsham, K. K., & Robinson, C. H. (2019). Endemic and cosmopolitan fungal taxa exhibit differential abundances in total and active communities of Antarctic soils. Environmental microbiology. https://doi.org/10.1111/1462-2920.14533