Palmer LTER 2014 cruise microbial Eukaryote (18s) plankton

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019 SCAR - Microbial Antarctic Resource System

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.

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How to cite

Researchers should cite this work as follows:

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

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: fd933a3c-e0a9-4c18-8e95-d1128a2be2ca.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Metadata

Contacts

Who created the resource:

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

Who can answer questions about the resource:

Yajuan Lin
Duke University Durham US

Who filled in the metadata:

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

Who else was associated with the resource:

User

Geographic Coverage

Southern Ocean around the Western Antarctic Peninsula.

Bounding Coordinates South West [-68.287, -74.184], North East [-63.965, -63.403]

Taxonomic Coverage

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

Domain  Eukaryota (Eukaryotes)

Project Data

No Description available

Title LTER_2014
Funding 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”.

The personnel involved in the project:

Yajuan Li
Nicolas Cassar

Sampling Methods

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.

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

Method step description:

  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.

Bibliographic Citations

  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.

Additional Metadata

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