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Microbial (16S) diversity in sediments of the former subglacial Hodgson lake (Antarctica)

Última versión Publicado por SCAR - Microbial Antarctic Resource System en 19 de marzo de 2019 SCAR - Microbial Antarctic Resource System
Fecha de publicación:
19 de marzo de 2019
Licencia:
CC-BY 4.0

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Descripción

Amplicon sequencing dataset (454 pyrosequencing) of microorganisms (16S ssu rRNA gene) in sediments of the former subglacial Hodgson lake (Antarctica). Exploratory study (1 sample).

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:

Pearce D, Hodgson D, Thorne M, Burns G, Cockell C (2019): Microbial (16S) diversity in sediments of the former subglacial Hodgson lake (Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=hodgson_lake_microbes&v=1.1

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. Este trabajo está autorizado bajo una Licencia Creative Commons Atribución/Reconocimiento 4.0 Internacional (CC-BY) 4.0.

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: b315baf6-9fed-405d-a3ee-d585aae81a1c.  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

¿Quién creó el recurso?:
-

David Pearce
British Antarctic Survey
Cambridge
GB
Dominic Hodgson
British Antarctic Survey
Cambridge
GB
Michael Thorne
British Antarctic Survey
Cambridge
GB
Gavin Burns
British Antarctic Survey
Cambridge
GB
Charles Cockell
University of Edinburgh
Edinburgh
GB

¿Quién puede resolver dudas acerca del recurso?:

David Pearce
British Antarctic Survey
Cambridge
GB

¿Quién documentó los metadatos?:
-

Maxime Sweetlove
Research assistent
Royal Belgian Institute of natural sciences
Rue Vautier 29
1000 Brussels
BE

¿Quién más está asociado con el recurso?:

Usuario

Cobertura geográfica

Lake Hodgson, Antarctica

Coordenadas límite Latitud Mínima Longitud Mínima [-72,009, -68,462], Latitud Máxima Longitud Máxima [-72,009, -68,462]

Cobertura taxonómica

Bacteria and Archaea (16S ssu rRNA gene)

Dominio Bacteria (Bacteria), Archaea (Archaea)

Cobertura temporal

Fecha Inicial 2000-01-01

Datos del proyecto

No hay descripción disponible

Título Hodgson Lake metagenome
Fuentes de Financiación Funding was provided by theNatural Environment Research Council funding through the British Antarctic Survey and the Antarctic Funding Initiative.

Personas asociadas al proyecto:

David Pearce

Métodos de muestreo

A 3.8 m sediment core was extracted at a depth of 93.4 m below the ice surface inside a virkon sterilized and polycarbonate lined core barrel. When taken all core samples remained within the core liners and were immediately frozen until sub-sampling in a clean class II microbiological safety cabinet in Cambridge. Gloves were used at all times and instruments used in laboratory manipulations were autoclaved.

Área de Estudio Lake Hodgson, Antarctica

Descripción de la metodología paso a paso:

  1. Samples of frozen surface sediment (~0.5 g) were removed from sediment cores for DNA extraction. DNA extractions were carried out using the PowerSoil DNA isolation kit (Mo Bio, Carlsbad, CA, USA) following the manufacturers standard protocol. The resulting DNA was quantified using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Each extraction from 0.5 g sediment produced ~250 ng of DNA in 100 μL nuclease free water. 16S RNA gene amplification was carried out on sediment DNA obtained from the four depth sections A–C (15 ng input DNA) using forward primer 787f ATT AGA TAC CCN GGT AG and reverse primer 1492Rm GNT ACC TTG TTA CGA CTT at an annealing temperature of 50 °C to produce amplicons of 705 bp. PCR reactions were 15 μL and contained 1× PCR buffer, 2.0 mM MgCl2, 0.25 mM dNTPs, 0.25 mM each primer, 0.4 Units BioTaq (Bioline, London, UK) and ca. 15 ng template DNA. For Thermocycling: 1 ×95 °C for 50 s; 30 ×95 °C for 20 s, 50 °C for 30 s, 72 °C for 3 min (ramp 72 °C at 0.3 °C s−1); 1 ×72 °C for 10 min. Multiple PCR amplifications (24 in total) were cleaned and pooled to produce 900 ng of 16S enriched DNA for 454 library preparation.
  2. An amplicon library was generated using the Rapid Library Preparation kit and following the manufacturer’s recommendations in the GS FLX Titanium Series Rapid Library Preparation Method Manual (Roche). Briefly, the PCR amplicons were purified using AMPure beads (Agencourt Bioscience Corporation, Beverly, MA, USA), adaptors were blunt-end ligated to the fragment and the dsDNA amplicon library was quantitated via fluorometry using Quanti-iT Pico Green reagents (Invitrogen, Carlsbad, CA, USA). The library was then subjected to clonal amplification by emulsion PCR followed by pyrosequencing on a 454 GS FLX sequencer according to the manufacturer’s instructions (NEB NextQuick 454 library prep kit E6090).

Referencias bibliográficas

  1. Pearce, D. A., Hodgson, D. A., Thorne, M. A., Burns, G., & Cockell, C. S. (2013). Preliminary analysis of life within a former subglacial lake sediment in Antarctica. Diversity, 5(3), 680-702.

Metadatos adicionales

Identificadores alternativos b315baf6-9fed-405d-a3ee-d585aae81a1c
https://ipt.biodiversity.aq/resource?r=hodgson_lake_microbes