Bacterioplankon from lakes on Byers Peninsula (2008)

Latest version published by SCAR - Microbial Antarctic Resource System on Jun 16, 2021 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (Illumina MiSeq) targeting Bacteria (16S ssu rRNA) in samples (n=9) taken in 2008 from Byers Peninsula (Antarctica).

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How to cite

Researchers should cite this work as follows:

Picazo A, Rochera C, Villaescusa J A, Javier Miralles-Lorenzo J, Velazquez D, Quesada A, Camacho A (2021): Bacterioplankon from lakes on Byers Peninsula (2008). v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacterioplankon_byers_peninsula_lakes_2008&v=1.0

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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.

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This resource has been registered with GBIF, and assigned the following GBIF UUID: 625b1148-c88d-459b-b3e7-d7504cc6d97d.  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:

Antonio Picazo
University of Valencia Valencia ES
Carlos Rochera
University of Valencia Valencia ES
Juan Antonio Villaescusa
University of Valencia Valencia ES
Javier Javier Miralles-Lorenzo
University of Valencia Valencia ES
David Velazquez
Universidad Autónoma de Madrid Madrid ES
Antonio Quesada
Universidad Autónoma de Madrid Madrid ES
Antonio Camacho
University of Valencia Valencia ES

Who can answer questions about the resource:

Antonio Camacho
University of Valencia Valencia ES

Who filled in the metadata:

Maxime Sweetlove
Royal Belgian Institute of Natural Sciences Brussels BE

Who else was associated with the resource:

User
Antonio Camacho
University of Valencia Valencia ES

Geographic Coverage

Lakes from Beyers Peninsula (Antarctica)

Bounding Coordinates South West [-62.661, -61.112], North East [-62.631, -61.006]

Temporal Coverage

Start Date / End Date 2008-01-28 / 2008-02-08

Project Data

No Description available

Title Bacterioplankon from lakes on Byers Peninsula (2008)
Funding This study was supported by grants CGL2005-06549-C02-02/ANT to AC and CTM2016-79741-R to AQ, both funded by the Spanish Ministry of Education and Science, by European FEDER funds, a way to make Europe.

The personnel involved in the project:

Antonio Camacho

Sampling Methods

Samples in all lakes were obtained from surface depths (0.5–1 m), and approximately in the center of the lake. Samples were then filtered with a vacuum system onto 0.2 μm polycarbonate filters (Nucleopore, Whatman) and stored frozen (−20°C) in Allprotect Tissue Reagent (QIAGEN).

Study Extent Water samples (n=9) were collected during January and February 2008, in lakes Chester Cone, Midge Lake, Escondido, Limnopolar, Turbio, Somero, and Refugio (Beyers Peninsula, Antarctica)
Quality Control The extracted and amplified DNA pool was subjected to an analysis with a Qubit dsDNA HS, Agilent 4200 TapeStation High Sensitivity DNA and Kapa Illumina Library Quantification qPCR assays.

Method step description:

  1. DNA extraction from each filter was performed with the EZNA Soil DNA isolation kit (Omega Bio-Tek, Inc., Norcross, GA, United States) following the instructions given by the supplier. Sequencing of the region V4 of the 16S rRNA gene was done using the Illumina MiSeq system (2×250 bp) at the genomics facilities of the Research Technology Support Facility of the Michigan State University, United States. For each sample, Illumina compatible, dual indexed amplicon libraries of the 16S-V4 rRNA hypervariable region were created with primers 515f/806r. PCR reactions are composed of 5 μL of 4 μM equimolar primer set, 0.15 μL of AccuPrime Taq DNA High Fidelity Polymerase, 2 μL of 10× AccuPrime PCR Buffer II (Thermo Fisher Scientific, catalog no. 12346094), 11.85 μL of PCR-grade water, and 1 μL of DNA template. The PCR conditions used consisted of 2 min at 95°C, followed by 30 cycles of 95°C for 20 s, 55°C for 15 s, and 72°C for 5 min, followed by 72°C for 10 min.
  2. Completed libraries were batch normalized using Invitrogen SequalPrep DNA Normalization Plates. The DNA was sequenced on an 2x250bp Illumina MiSeq v2 flow cell using a MiSeq v2 500 cycle reagent cartridge.

Bibliographic Citations

  1. Picazo, A., Rochera, C., Villaescusa, J. A., Miralles-Lorenzo, J., Velázquez, D., Quesada, A., & Camacho, A. (2019). Bacterioplankton community composition along environmental gradients in lakes from Byers Peninsula (Maritime Antarctica) as determined by Next-Generation Sequencing. Frontiers in microbiology, 10, 908.