Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation

Erin Bertrand1, John McCrow1, Ahmed Moustafa1, Hong Zheng1, Jeffrey McQuaid1, Tom Delmont2, Anton Post3, Rachel Sipler4, Jenna Spackeen4, Kai Xu5, Deborah Bronk4, David Hutchins5, Andrew Allen1, Maxime Sweetlove6

1 J. Craig Venter Institute, La Jolla, United States; 2 josephine Bay Paul Center, Woods Hole, United States; 3 University of Rhode Island, Narragansett, United States; 4 Virginia Institute of Marine Science, Gloucester Point, United States; 5 University of Southern California, Los Angeles, United States; 6 Royal Belgian Institute for Natural Sciences, Rue Vautier 29, Brussels, Belgium

Corresponding author(s): Erin BertrandJohn McCrowAhmed MoustafaHong ZhengJeffrey McQuaidTom DelmontAnton PostRachel SiplerJenna SpackeenKai XuDeborah BronkDavid HutchinsAndrew Allen, Maxime Sweetlove (msweetlove@naturalsciences.be)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

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

Abstract

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.

Keywords: Metadata

Project details

Project title: Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation
Personnel: Erin Bertrand, Andrew Allen, Deborah Bronk, David Hutchins, Anton Post
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.

Data published through GBIF: https://ipt.biodiversity.aq/resource?r=southern_ocean_experimental_metatranscriptome

Taxonomic coverage

General taxonomic coverage description: RNA metatranscriptome
Taxonomic ranks
Domain: Eukaryota, Bacteria, Archaea
Common names: Eukaryotes, Bacteria, Archaea

Spatial coverage

General spatial coverage: Souther Ocean sea water of the ice edge, near McMurdo Sound, Antarctica
Coordinates: 77°37'1.2''S and 77°37'1.2''S Latitude; 164°28'26.4''E and 164°28'26.4''E Longitude 

Temporal coverage: January 16, 2013

Methods

Method step description: 
- . 	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.
- . 	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).
- . 	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.
Study extent description: 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).
Sampling description: 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.

Metadata language: English
Date of metadata creation: 2019-01-07
Hierarchy level: Dataset

References
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.