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

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019 SCAR - Microbial Antarctic Resource System

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

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How to cite

Researchers should cite this work as follows:

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

Rights

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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.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: b315baf6-9fed-405d-a3ee-d585aae81a1c.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Metadata

Contacts

Who created the resource:

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

Who can answer questions about the resource:

David Pearce
British Antarctic Survey Cambridge GB

Who filled in the metadata:

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

Who else was associated with the resource:

User

Geographic Coverage

Lake Hodgson, Antarctica

Bounding Coordinates South West [-72.009, -68.462], North East [-72.009, -68.462]

Taxonomic Coverage

Bacteria and Archaea (16S ssu rRNA gene)

Domain  Bacteria (Bacteria),  Archaea (Archaea)

Temporal Coverage

Start Date 2000-01-01

Project Data

No Description available

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

The personnel involved in the project:

David Pearce

Sampling Methods

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.

Study Extent Lake Hodgson, Antarctica

Method step description:

  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).

Bibliographic Citations

  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.

Additional Metadata

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