Arctic multi-year sea ice Bacteria

Dernière version Publié par SCAR - Microbial Antarctic Resource System le 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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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

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

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 9f8879f7-ae24-4c6c-9209-d62408e5dcbb.  SCAR - Microbial Antarctic Resource System publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Scientific Committee on Antarctic Research.

Mots-clé

Metadata

Contacts

Personne ayant créé cette ressource:

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

Personne pouvant répondre aux questions sur la ressource:

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

Personne ayant renseigné les métadonnées:

Maxime Sweetlove
Research assistent
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels BE

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

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

Enveloppe géographique Sud Ouest [82.549, -62.377], Nord Est [82.549, -62.377]

Couverture taxonomique

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

Domain  Bacteria (Bacteria)

Couverture temporelle

Epoque de formation 2011-05

Données sur le projet

Pas de description disponible

Titre Arctic multi-year sea ice Bacteria
Financement 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.

Les personnes impliquées dans le projet:

Ido Hatam

Méthodes d'échantillonnage

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.

Etendue de l'étude 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).

Description des étapes de la méthode:

  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).

Citations bibliographiques

  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

Métadonnées additionnelles

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