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Palmer LTER 2014 cruise microbial Eukaryote (18s) plankton

Dernière version Publié par SCAR - Microbial Antarctic Resource System le 19 mars 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 of microbial eukaryotes (18S ssh rRNA v4)living in the plankton of the Southern Ocean around the Western Antarctic Peninsula. Samples were collected during the annual Palmer LTER cruise from Jan to early Feb in 2014 aboard the R/V Laurence M. Gould.

Versions

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Lin Y, Cassar N, Marchetti A, Moreno C, Ducklow H, Li Z (2018): Palmer LTER 2014 cruise microbial Eukaryote (18s) plankton. v1.3. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=palmer_lter_eukaryote_18s_plankton&v=1.3

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 : fd933a3c-e0a9-4c18-8e95-d1128a2be2ca.  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:
-

Yajuan Lin
Duke University
Durham
US
Nicolas Cassar
Duke University
Durham
US
Adrian Marchetti
University of North Carolina at Chapel Hill
Chapel Hill
US
Carly Moreno
University of North Carolina at Chapel Hill
Chapel Hill
US
Hugh Ducklow
Columbia University
Palisades
US
Zuchuan Li
Duke University
Durham
US

Personne pouvant répondre aux questions sur la ressource:

Yajuan Lin
Duke University
Durham
US

Personne ayant renseigné les métadonnées:
-

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

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

Southern Ocean around the Western Antarctic Peninsula.

Enveloppe géographique Sud Ouest [-68,287, -74,184], Nord Est [-63,965, -63,403]

Couverture taxonomique

microbial eukaryote plankton (18S ssh rRNA gene v4 region)

Domain Eukaryota (Eukaryotes)

Données sur le projet

Pas de description disponible

Titre LTER_2014
Financement This work was supported by NSF OPP-1043339, NSF PLR-1440435 (Palmer LTER), NSF OPP-1341479, the “Laboratoire d’Excellence” LabexMER (ANR-10-LABX-19) and co-funded by a grant from the French government under the program “Investissements d’Avenir”.

Les personnes impliquées dans le projet:

Yajuan Li
Nicolas Cassar

Méthodes d'échantillonnage

Surface seawater from the vessel seawater supply line was gently vacuum filtered through a 0.2 µm pore size Millipore Supor filters. Each filter was then preserved immediately in 1 ml of RNA-later and stored at −80 °C.

Etendue de l'étude Samples were taken during the annual Palmer LTER cruise from Jan to early Feb in 2014 aboard the R/V Laurence M. Gould.

Description des étapes de la méthode:

  1. From each sampled station one filter was first split in two halves, one for DNA extraction and the other for later RNA studies. 500 µl of the RNAlater from the original tube was loaded onto an Amicon 10 k column and the column was spun for 15 minutes at 14,000 g to get rid of most of the RNAlater and concentrate cells suspended in RNAlater. The resulting solution (~50 µl) was then added back to the one half filter. The cells on filter were lysed by bead-beating using 0.2 g of zirconium beads in 400 µl of buffer AP1 (Qiagen).
  2. DNA was extracted and purified using Qiagen DNeasy Plant Mini kit following the manufacture’s instruction. 18 S (eukaryotic) rDNA gene fragments were amplified by PCR using V4 primer sets: 18 S forward (5′- CCAGCASCYGCGGTAATTCC-3′) and reverse (5′-ACTTTCGTTCTTGAT-3′). Amplicons from each sample were tagged using dual index fusion primers and a “heterogeneity spacer” was used to improve sequencing quality. The “heterogeneity spacer” is a 0–5 bp of spacer added to the index sequence in order to allow different samples be sequenced out of phase and thus improve the amplicon library sequencing quality. Each PCR reaction (25 µl) consisted of 1U of Platinum Taq DNA Polymerase High Fidelity (Invitrogen), 1 × High Fidelity Buffer, 200 µM dNTPs, 2 mM MgSO4, 0.2 µM each primer, and 5–30 ng extracted environmental DNA template. PCR was conducted with an initial activation step at 94 °C for 3 min, followed by 30 three-step cycles consisting of 94 °C for 30 s, 57 °C for 30 s and 72 °C for 1 min, and a final extension step of 72 °C at 10 min. PCR products in triplicates for each sample were then pooled and purified using QIAquick PCR Purification kit, and the concentration of amplicon DNA was quantified using a Qubit dsDNA assay.
  3. Amplicons from different locations were pooled in equimolar amounts (final concentration ~10 ng/µl) and submitted to Duke Institute for Genomic Sciences and Policy (IGSP) for sequencing using Illumina MiSeq. 300PE platform.

Citations bibliographiques

  1. Lin, Y., Cassar, N., Marchetti, A., Moreno, C., Ducklow, H., & Li, Z. (2017). Specific eukaryotic plankton are good predictors of net community production in the Western Antarctic Peninsula. Scientific reports, 7(1), 14845.

Métadonnées additionnelles

Identifiants alternatifs fd933a3c-e0a9-4c18-8e95-d1128a2be2ca
https://ipt.biodiversity.aq/resource?r=palmer_lter_eukaryote_18s_plankton