Maritime and Sub-Antarctic microbial soil fungi communities

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Cox F, Newsham K, Bol R, Dungait J, Robinson C (2019): Maritime and Sub-Antarctic microbial soil fungi communities. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. http://ipt.biodiversity.aq/resource?r=maritime_antarctic_soil_fungi_communities&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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此資源已向GBIF註冊，並指定以下之GBIF UUID: 6c61d02f-a399-4d88-8e3b-a7068b2d3387。  SCAR - Microbial Antarctic Resource System 發佈此資源，並經由Scientific Committee on Antarctic Research同意向GBIF註冊成為資料發佈者。

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Metadata

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地理涵蓋範圍

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

分類群涵蓋範圍

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

時間涵蓋範圍

計畫資料

無相關描述

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取樣方法

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.

方法步驟描述:

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.

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