Somente metadatos

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

Versão mais recente publicado por SCAR - Microbial Antarctic Resource System em 19 de Março de 2019 SCAR - Microbial Antarctic Resource System
Publication date:
19 de Março de 2019
License:
CC-BY 4.0

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Descrição

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

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

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

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: b315baf6-9fed-405d-a3ee-d585aae81a1c.  SCAR - Microbial Antarctic Resource System publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por Scientific Committee on Antarctic Research.

Palavras-chave

Metadata

Contatos

Quem criou esse 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

Quem pode responder a perguntas sobre o recurso:

David Pearce
British Antarctic Survey
Cambridge
GB

Quem preencher os metadados:
-

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

Quem mais foi associado com o recurso:

Usuário

Cobertura Geográfica

Lake Hodgson, Antarctica

Coordenadas delimitadoras Sul Oeste [-72,009, -68,462], Norte Leste [-72,009, -68,462]

Cobertura Taxonômica

Bacteria and Archaea (16S ssu rRNA gene)

Domínio Bacteria (Bacteria), Archaea (Archaea)

Cobertura Temporal

Data Inicial 2000-01-01

Dados Sobre o Projeto

Nenhuma descrição disponível

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

O pessoal envolvido no projeto:

David Pearce

Métodos de Amostragem

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 Estudo Lake Hodgson, Antarctica

Descrição dos passos do método:

  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).

Citações 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.

Metadados Adicionais

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