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

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

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

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How to cite

Researchers should cite this work as follows:

Delmont T, Eren M, Veneis J, Post A (2019): Metagenome assembly of an Amundsen Sea (Antarctica, Southern Ocean) water sample. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=amundsen_sea_metagenome&v=1.1

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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: 4f0d3a6f-c91e-4db9-a2f3-6a6007e620e2.  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:

Tom Delmont
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US
Murat Eren
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US
Joseph Veneis
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US
Anton Post
University of Rhode Island Narragansett US

Who can answer questions about the resource:

Tom Delmont
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US

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

Amundsen Sea, Southern Ocean

Bounding Coordinates South West [-73.342, -112.401], North East [-73.342, -112.401]

Temporal Coverage

Start Date 2010-12-19

Project Data

No Description available

Title ASPIRE Microbiome
Funding This work was performed with financial support from NSF Antarctic Sciences awards ANT-1142095.

The personnel involved in the project:

Anton Post

Sampling Methods

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.

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

Method step description:

  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).

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.

Additional Metadata

Alternative Identifiers 4f0d3a6f-c91e-4db9-a2f3-6a6007e620e2
https://ipt.biodiversity.aq/resource?r=amundsen_sea_metagenome