Microbial Fungi in soils on different Sub-Antarctic islands

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Última versión publicado por SCAR - Microbial Antarctic Resource System el mar. 22, 2019 SCAR - Microbial Antarctic Resource System
Fecha de publicación:
22 de marzo de 2019
Licencia:
CC-BY 4.0

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Descripción

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

Versiones

La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.

¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es SCAR - Microbial Antarctic Resource System. Esta obra está bajo una licencia Creative Commons de Atribución/Reconocimiento (CC-BY 4.0).

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: a5b4d692-96bf-4acf-8809-b546e9938a5d.  SCAR - Microbial Antarctic Resource System publica este recurso y está registrado en GBIF como un publicador de datos avalado por Scientific Committee on Antarctic Research.

Palabras clave

Metadata

Contactos

Filipa Cox
  • Originador ●
  • Punto De Contacto
University of Manchester
Manchester
GB
Kevin Newsham
  • Originador
British Antarctic Survey
Cambridge
GB
Clare Robinson
  • Originador
University of Manchester
Manchester
GB
Maxime Sweetlove
  • Proveedor De Los Metadatos
  • Research assistent
Royal Belgian Institute of Natural Sciences
  • Rue Vautier 29
1000 Brussels
BE

Cobertura geográfica

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

Coordenadas límite Latitud Mínima Longitud Mínima [-67,598, -68,356], Latitud Máxima Longitud Máxima [-54,009, -38,066]

Cobertura taxonómica

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

Filo Fungi (Fungi)

Datos del proyecto

No hay descripción disponible

Título Microbial Fungi in soils on different Sub-Antarctic islands
Fuentes de Financiación 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.

Personas asociadas al proyecto:

Filipa Cox

Métodos de muestreo

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.

Área de Estudio 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.

Descripción de la metodología paso a paso:

  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.

Referencias bibliográficas

  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