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 Mar 19, 2019 SCAR - Microbial Antarctic Resource System

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.

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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

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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 : 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

Personne ayant créé cette ressource:

Catherine Luria
Brown University Providence US
Hugh Ducklow
Lamont-Doherty Earth Observatory of Columbia University Palisades US
Linda Amaral-Zettler
Brown University Providence US

Personne pouvant répondre aux questions sur la ressource:

Catherine Luria
Brown University Providence US
Linda Amaral-Zettler
Brown University Providence US

Personne ayant renseigné les métadonnées:

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

Autres personnes associées à la ressource:

Utilisateur

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

Identifiants alternatifs 3a1bad58-879c-4e66-a780-2441ecf2fe3d
https://ipt.biodiversity.aq/resource?r=marine_bacterial_archaeal_eukaryotic_microbial_communities_western_antarctic_peninsula