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

Versions

The table below shows only published versions of the resource that are publicly accessible.

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

Rights

Researchers should respect the following rights statement:

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

Geographic Coverage

Amundsen Sea, Southern Ocean

Temporal Coverage

Project Data

No Description available

The personnel involved in the project:

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.

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