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Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation

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

Metatranscriptome dataset (targeting all mRNA) from Southern Ocean sea water samples (1 control, 3 treatments, 3 replicates per treatment), near the ice edge at McMurdo Sound (Antarctica). All samples were incubated 24h at 0°C, ~45 μmol photons m-2 s-1 of constant light. Treatments existed of: 1) addition of 1 nM FeCl3; 2) addition of 200 pM cyanocobalamin; or 3) addition of 200 pM cyanocobalamin and 1 nM FeCl3.

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How to cite

Researchers should cite this work as follows:

Bertrand E, McCrow J, Moustafa A, Zheng H, McQuaid J, Delmont T, Post A, Sipler R, Spackeen J, Xu K, Bronk D, Hutchins D, Allen A (2019): Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=southern_ocean_experimental_metatranscriptome&v=1.2

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: ddd527ae-1539-4189-ac4a-a731640badcf.  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:

Erin Bertrand
J. Craig Venter Institute La Jolla US
John McCrow
J. Craig Venter Institute La Jolla US
Ahmed Moustafa
J. Craig Venter Institute La Jolla US
Hong Zheng
J. Craig Venter Institute La Jolla US
Jeffrey McQuaid
J. Craig Venter Institute La Jolla US
Tom Delmont
josephine Bay Paul Center Woods Hole US
Anton Post
University of Rhode Island Narragansett US
Rachel Sipler
Virginia Institute of Marine Science Gloucester Point US
Jenna Spackeen
Virginia Institute of Marine Science Gloucester Point US
Kai Xu
University of Southern California Los Angeles US
Deborah Bronk
Virginia Institute of Marine Science Gloucester Point US
David Hutchins
Professor
University of Southern California Los Angeles US
Andrew Allen
J. Craig Venter Institute La Jolla US

Who can answer questions about the resource:

Erin Bertrand
J. Craig Venter Institute La Jolla US

Who filled in the metadata:

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Natural Sciences Rue Vautier 29 Brussels BE

Who else was associated with the resource:

User

Geographic Coverage

Souther Ocean sea water of the ice edge, near McMurdo Sound, Antarctica

Bounding Coordinates South West [-77.617, 164.474], North East [-77.617, 164.474]

Taxonomic Coverage

RNA metatranscriptome

Domain  Eukaryota (Eukaryotes),  Bacteria (Bacteria),  Archaea (Archaea)

Temporal Coverage

Start Date 2013-01-16

Project Data

No Description available

Title Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation
Funding This study was funded by National Science Foundation (NSF) Antarctic Sciences Awards 1103503, 0732822 and 1043671, 1043748, 1043635, and 1142095; Gordon and Betty Moore Foundation Grant GBMF3828; and NSF Ocean Sciences Award 1136477.

The personnel involved in the project:

Erin Bertrand
Andrew Allen
Deborah Bronk
David Hutchins
Anton Post

Sampling Methods

Water was pumped to the surface using a trace metal clean diaphragm pump and acid cleaned teflon tubing and dispensed into trace metal clean (TMC) 50 L carboys. Sampling occurred between 18:00 and 19:00 in open air, with wind coming from over open water, NNE to NE. The carboys were protected from light with dark plastic bags and returned to the Crary Laboratory at McMurdo Station via helicopter within one hour of sampling, where it was stored overnight at 0°C and then split into twelve 2.7 L TMC polycarbonate bottles.

Study Extent On 16 Jan 2013, seawater was collected from 3 m depth at the sea ice edge in McMurdo Sound of the Ross Sea (77° 36.999’ S 165° 28.464’ E).

Method step description:

  1. Three bottles were left as unamended controls, three were amended with 1 nM FeCl3, three were amended with 200 pM cyanocobalamin, and three had 200 pM cyanocobalamin and 1 nM Fe added. Iron concentrations in the cobalamin stock were such that < 6 pM iron was added with 200 pM cobalamin (measured via flow injection). Bottles were placed in an indoor incubator at 0°C, ~45 μmol photons m-2 s-1 of constant light. This level of irradiance is in between levels typical for 3 m depth in open water and under the sea ice, and was selected because the harvested community would have experienced both under ice and open water light regimes in the recent past.
  2. For RNA extraction, 1 billion copies of each of two RNA standards were added to each filter (#1, #8 ArrayControl Spots and Spikes, Life Technologies, with polyA tails). RNA was extracted from Sterivex filters using the Trizol reagent manufacturer’s protocol (Life Technologies); Trizol was added to the filter membrane after it had been extracted from the plastic housing on dry ice using a sterile pipe cutter, razor blade, and forceps. 450- 800 ng RNA was obtained per filter. RNAeasy MinElut Cleanup kit was applied (Qiagen) and ribosomal RNA was removed with Ribo-Zero Magnetic kits, employing a mix of plant, bacterial, and human/mouse/rat formulations in a ratio of 2:1:1 (Epicentre).
  3. The resulting mRNA enrichment was purified using an Agencourt RNAClean XP kit and 2 ng of rRNA depleted RNA was subjected to amplification and cDNA synthesis using the Ovation RNA-Seq System V2 (NuGEN), which applies both polyA and random hexamer primers. 1 μg of the resulting high quality cDNA pool was fragmented to a mean length of 200 bp. Libraries were constructed using a Truseq RNA Sample Prep kit v2 (IlluminaTM), applying the manufacturer’s protocol from the end-repair step. The libraries were then subjected to paired-end sequencing via Illumina Hiseq.

Bibliographic Citations

  1. Bertrand, E. M., McCrow, J. P., Moustafa, A., Zheng, H., McQuaid, J. B., Delmont, T. O., ... & Bronk, D. A. (2015). Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge. Proceedings of the National Academy of Sciences, 112(32), 9938-9943.

Additional Metadata

Alternative Identifiers ddd527ae-1539-4189-ac4a-a731640badcf
https://ipt.biodiversity.aq/resource?r=southern_ocean_experimental_metatranscriptome