Palmer LTER 2014 cruise microbial Eukaryote (18s) plankton

Última versión publicado por SCAR - Microbial Antarctic Resource System el mar 19, 2019 SCAR - Microbial Antarctic Resource System
Fecha de publicación:
19 de marzo de 2019
CC-BY 4.0

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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.


La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.

¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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.


Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es SCAR - Microbial Antarctic Resource System. Esta obra está bajo una licencia Creative Commons de Atribución/Reconocimiento (CC-BY 4.0).

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: fd933a3c-e0a9-4c18-8e95-d1128a2be2ca.  SCAR - Microbial Antarctic Resource System publica este recurso y está registrado en GBIF como un publicador de datos avalado por Scientific Committee on Antarctic Research.

Palabras clave



Yajuan Lin
  • Originador
  • Punto De Contacto
Duke University
Nicolas Cassar
  • Originador
Duke University
Adrian Marchetti
  • Originador
University of North Carolina at Chapel Hill
Chapel Hill
Carly Moreno
  • Originador
University of North Carolina at Chapel Hill
Chapel Hill
Hugh Ducklow
  • Originador
Columbia University
Zuchuan Li
  • Originador
Duke University
Maxime Sweetlove
  • Proveedor De Los Metadatos
Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
1000 Brussels

Cobertura geográfica

Southern Ocean around the Western Antarctic Peninsula.

Coordenadas límite Latitud Mínima Longitud Mínima [-68,287, -74,184], Latitud Máxima Longitud Máxima [-63,965, -63,403]

Cobertura taxonómica

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

Dominio Eukaryota (Eukaryotes)

Datos del proyecto

No hay descripción disponible

Título LTER_2014
Fuentes de Financiación 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”.

Personas asociadas al proyecto:

Yajuan Li
Nicolas Cassar

Métodos de muestreo

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.

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

Descripción de la metodología paso a paso:

  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.

Referencias bibliográficas

  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.

Metadatos adicionales

Identificadores alternativos fd933a3c-e0a9-4c18-8e95-d1128a2be2ca