Marine bacterial, archaeal and eukaryotic microbial communities on the continental shelf of the western Antarctic Peninsula

Dernière version Publié par SCAR - Microbial Antarctic Resource System le mars 19, 2019 SCAR - Microbial Antarctic Resource System
Date de publication:
19 mars 2019
Licence:
CC-BY 4.0

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Description

Amplicon sequencing dataset (454 pyrosequencing) of microbial Bacteria (16S ssu rRNA), Archaea (16S ssu rRNA) and Eukaryotes (18S ssu rRNA) in seawater on the continental shelf of the Antarctic Peninsula.

Versions

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Luria C, Ducklow H, Amaral-Zettler L (2019): Marine bacterial, archaeal and eukaryotic microbial communities on the continental shelf of the western Antarctic Peninsula. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=marine_bacterial_archaeal_eukaryotic_microbial_communities_western_antarctic_peninsula&v=1.1

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. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 3a1bad58-879c-4e66-a780-2441ecf2fe3d.  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

Catherine Luria
  • Créateur
  • Personne De Contact
Brown University
Providence
US
Hugh Ducklow
  • Créateur
Lamont-Doherty Earth Observatory of Columbia University
Palisades
US
Linda Amaral-Zettler
  • Créateur
  • Personne De Contact
Brown University
Providence
US
Maxime Sweetlove
  • Fournisseur Des Métadonnées
Research assistant
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
1000 Brussels
BE

Couverture géographique

Southern Ocean, Continental shelf off the Antarctic peninsula

Enveloppe géographique Sud Ouest [-63,97, -73,03], Nord Est [41,64, -64,406]

Couverture taxonomique

Bacteria (16S ssu rRNA gene, v6 region)

Domain Bacteria (Bacteria)

Archaea (16S ssu rRNA gene, v6 region)

Domain Archaea (Archaea)

Eukarya (18S ssu rRNA gene, v9 region)

Domain Eukarya (Eukaryotes)

Couverture temporelle

Date de début / Date de fin 2008-01-05 / 2008-01-27

Données sur le projet

http://amarallab.mbl.edu

Titre Microbial Inventory Research Across Diverse Aquatic Long Term Eco- logical Research Sites
Identifiant MIRADA-LTERS
Financement NSF DEB- 0717390 (MIRADA-LTERS) and NSF Awards OPP- 0217282 and 0823101 (Palmer LTER) from the Antarctic Organisms and Ecosystems Program
Description du domaine d'étude / de recherche Palmer Antarctica LTER

Les personnes impliquées dans le projet:

Catherine Luria

Méthodes d'échantillonnage

Samples were drawn from 10 and 100 m depths from the northern and southern, inshore and offshore corners of the Palmer LTER sampling grid. We collected duplicate samples using a rosette equipped with 10 l Niskin bottles and conductivity, temperature, and depth (CTD) probes. To contrast summer and winter water, we also collected an additional Austral winter sample from 10 m depth at the northern, inshore sampling site in August 2008, using a submersible pump with silicone tubing. Water samples were filtered (1 to 2 l) through 0.2 μm SterivexTM filters (Millipore), preserved genomic DNA by flooding the 2 ml filter cartridge reservoir with sucrose lysis buffer (40 mM EDTA, 50 mM Tris-HCl, 0.75 M sucrose), and stored the filters at −80°C until processing.

Etendue de l'étude Sampling was conducted on the annual Palmer LTER (western coast of the Antarctic Peninsula) midsummer research cruise (January−February 2008)

Description des étapes de la méthode:

  1. We extracted DNA using a Puregene DNA extraction kit (Qiagen), with modifications as described by Amaral-Zettler et al. (2009), and stored the DNA at −20°C until PCR amplification. Bacterial and archaeal V6 16S rRNA and eukaryotic V9 18S rRNA gene hypervariable regions were amplified as described previously (Huber et al. 2007, Amaral- Zettler et al. 2009), using ‘barcoded’ primers which al- lowed for multiplexed sequencing (see http://vamps. mbl.edu/resources/primers.php for details). For each sample, we pooled triplicate 50 μl PCR reaction products to minimize propagation of PCR errors and purified them using a QIAquick column-based purification kit (Qiagen). We sequenced purified amplicons on a 454 Genome Sequencer FLX (Roche) according to the manufacturer’s protocols using the LR70 kit.

Citations bibliographiques

  1. Luria, C. M., Ducklow, H. W., & Amaral-Zettler, L. A. (2014). Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula. Aquatic Microbial Ecology, 73(2), 107-121.

Métadonnées additionnelles