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Metagenome assembly of an Amundsen Sea (Antarctica, Southern Ocean) water sample

Citation

Delmont T, Eren M, Veneis J, Post A, Sweetlove M (2019). Metagenome assembly of an Amundsen Sea (Antarctica, Southern Ocean) water sample. Version 1.1. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/9yfu4e accessed via GBIF.org on 2023-02-02.

Description

Seven assembled metagenoms from a metagenomic sequencing (Illumina HiSeq; paired-end) sample taken during a phytoplankton bloom in the Amundsen Sea (Antarctica, Southern Ocean)

Sampling Description

Study Extent

Water samples were taken with a CTD Rosette equipped during a phytoplankton bloom event in the ASP in 2010–2011.

Sampling

A sample was taken from the surface water layer in the center of a bloom (073° 34′243S 112° 40′080W, chlorophyll a > 17 μg/L, temperature of −1.2°C, phosphate: 1.31 μM, nitrite: 0.02 μM, ammonium: 0.05 μM, silicate: 77.8 μM) on 19 December 2010. This sample (6 l, 10 m depth) was passed over a 20 μm mesh, collected onto a 0.2 μm Sterivex membrane filter cartridge by pressure filtration, quickly frozen in the headspace of a LN2 dewar and stored at −80°C.

Method steps

  1. DNA extraction was performed using the Puregene kit (Gentra) after disruption of the cells with lytic enzyme coupled to proteinase K (Sinigalliano et al., 2007). DNA was quantified using a Nanodrop 2000 instrument (Thermo Fisher Scientific, Wilmington, DE).
  2. Metagenomic libraries were generated with the OVATION ultralow kit (NuGen) using 100 ng of DNA and 8 amplification cycles. We constructed overlapping (2X100 nt with ~40 nt of overlap) and gapped (2X108 nt with an insert size of ~600 nt) metagenomic DNA libraries using a Pippin prep electrophoresis platform to precisely select the desired length for DNA fragments to be used for sequencing on a Hiseq platform (Illumina).

Taxonomic Coverages

Geographic Coverages

Amundsen Sea, Southern Ocean

Bibliographic Citations

  1. Delmont, T. O., Eren, A. M., Vineis, J. H., & Post, A. F. (2015). Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica. Frontiers in microbiology, 6, 1090. -

Contacts

Tom Delmont
originator
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US
Murat Eren
originator
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US
Joseph Veneis
originator
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US
Anton Post
originator
University of Rhode Island
Narragansett
US
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
Brussels
1000
BE
email: msweetlove@naturalsciences.be
Tom Delmont
administrative point of contact
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US
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