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Arctic multi-year sea ice Bacteria

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

Amplicon sequencing dataset (454 pyrosequencing) of Bacteria (16S marker gene) in two multi-year sea-ice cores from the Arctic.

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How to cite

Researchers should cite this work as follows:

Hatam I, Lange B, Beckers J, Haas C, Lanoil B, Charchuk R (2019): Arctic multi-year sea ice Bacteria. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=arctic_multiyear_sea_ice_bacteria&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: 9f8879f7-ae24-4c6c-9209-d62408e5dcbb.  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:

Ido Hatam
University of Alberta Edmonton CA
Benjamin Lange
University of Alberta Edmonton CA
Justin Beckers
University of Alberta Edmonton CA
Christian Haas
University of Alberta Edmonton CA
Brian Lanoil
University of Alberta Edmonton CA
Rhianna Charchuk
University of Alberta Edmonton CA

Who can answer questions about the resource:

Ido Hatam
University of Alberta Edmonton CA
Brian Lanoil
University of Alberta Edmonton CA

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

Landfast ice off the northern shore of northern Ellesmere Island Nunavut, Canada (82.54905°N, −62.37685°W).

Bounding Coordinates South West [82.549, -62.377], North East [82.549, -62.377]

Taxonomic Coverage

Bacteria, targeted with the 16S ssu rRNA marker gene (v1-v3 region)

Domain  Bacteria (Bacteria)

Temporal Coverage

Formation Period 2011-05

Project Data

No Description available

Title Arctic multi-year sea ice Bacteria
Funding Support was provided by the Natural Science and Engineering Research Council of Canada (NSERC) Discovery Grant program and the Polar Continental Shelf Program (PCSP); the Northern Scientific Training Program (NSTP) and Circumpolar-Boreal Arctic Research (C-BAR) programs.

The personnel involved in the project:

Ido Hatam

Sampling Methods

Two parallel cores were sampled using Kovacs Mark II 9 cm corer (Kovacs Enterprise, Roseburg, Oregon) and a 36 V electric hand drill. Prior to drilling, the core barrel was rinsed with sterile deionized water (Milli-Q Integral Water Purification System, EMD Millipore Corporation, Billerica, MA). The two cores were immediately sectioned on site to 30-cm intervals using a hand saw (rinsed in deionized water and wiped with an ethanol wipe) and placed in UV-sterilized polypropylene bags.

Study Extent Two ice cores were taken during May 2011 at one site on landfast ice off the northern shore of northern Ellesmere Island Nunavut, Canada (82.54905°N, −62.37685°W).

Method step description:

  1. Ice samples used were thawed at room temperature in the dark, and were filtered individually through 0.22-μm-pore-size polyethersulfone membrane filters (Pall, Mississauga, ON, Canada). Direct melting was used to avoid nonspecific addition of DNA and dilution of samples. All glassware was sterilized using 10% household bleach solution followed by thorough washing in sterile deionized water between samples to prevent cross-contamination. Each filter was placed in a microfuge tube and submerged in RNAlater® solution (Life Technologies, Burlington, ON, Canada) and stored at −20 °C for later DNA extraction.
  2. DNA was extracted from preserved filters by bead beating using the FastDNA® SPIN Kit for Soil (MP Biomedicals, Solon, OH) as instructed by the manufacturer. Filters from equivalent 30-cm sections of duplicate ice cores were combined prior to DNA extraction to ensure sufficient DNA yield. Seawater duplicate samples were processed individually.
  3. Molecular Research LP (Shallowater, TX) performed pyrosequencing of the V1-V3 regions of the bacterial 16S rRNA gene as described in Dowd et al. (2008). Amplification was performed using HotStarTaq Plus Master Mix Kit (Qiagen, Valencia, CA) under the following conditions: 94 °C for 3 min, followed by 28 cycles of 94 °C for 30 s; 53 °C for 40 s; and 72 °C for 1 min with a final elongation step at 72 °C for 5 min. Gene-specific forward PCR primer sequences were tagged with the sequencing adapters for GS FLX Titanium chemistry, an 8 base barcode, and a linker sequence. All PCRs were performed in triplicate, mixed in equal concentrations, and purified using Agencourt AMPure beads (Agencourt Bioscience Corporation, MA). FLX-Titanium amplicon pyrosequencing was performed using the Genome Sequencer FLX System (Roche, Branford, CT).

Bibliographic Citations

  1. Hatam, I., Charchuk, R., Lange, B., Beckers, J., Haas, C., & Lanoil, B. (2014). Distinct bacterial assemblages reside at different depths in Arctic multiyear sea ice. FEMS microbiology ecology, 90(1), 115-125. https://doi.org/10.1111/1574-6941.12377

Additional Metadata

Alternative Identifiers 9f8879f7-ae24-4c6c-9209-d62408e5dcbb
https://ipt.biodiversity.aq/resource?r=arctic_multiyear_sea_ice_bacteria