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Microbial diversity (Bacteria and Archaea 16S rRNA gene) in geothermal sites of Deception Island volcano, Antarctica
Citatie
Bendia A, Signori C, Franco D, Duarte R, Bohannan B, Pellizari V (2019): Microbial diversity (Bacteria and Archaea 16S rRNA gene) in geothermal sites of Deception Island volcano, Antarctica. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbial_bacterial_and_archaeal_diversity_geothermal_sites_antarctica&v=1.1 https://doi.org/10.15468/fbdsva

Toegang tot data
Gearchiveerde data
Beschikbaarheid: Creative Commons License Deze dataset valt onder een Creative Commons Naamsvermelding 4.0 Internationaal-licentie.

Beschrijving
Amplicon sequencing dataset (Illumina MiSeq) of Bacterial and Archaea microbial diversity (based on the 16S ssu rRNA gene) in surface sediment samples, taken along a temperature gradient (three points, each with three replicates) on two different geothermal active sites (+-10km apart) on Deception Island, Antarctica. meer

In each site, three sediment samples were collected in each of three points with distinct temperatures: Points A and B were defined as samples collected in fumaroles, while point C was glacier samples, collected below the glacier’s edge. Distances between fumaroles and glaciers at each site were approximately 15 m, and the Whalers Bay and Fumarole Bay transects were approximately 10 km apart. All fumaroles were in the intertidal zone, with exception of point B from FB, which was in the subtidal (submerged at 50 cm depth in water column). Samples were stored at -20°C until arrival at the University of São Paulo, Brazil, in April 2014.
Study Extent: Sampling was performed on Deception Island (62°58′ S, 60°39′ W) during the XXXII Brazilian Antarctic Expedition (December 2013–January 2014), with logistical support from the polar vessel Npo. Almirante Maximiano. Surface sediment samples (ca. 5 cm) were collected in fumaroles and glaciers at the geothermally active sites of Fumarole Bay (62°58′02.7′′ S, 60°42′36.4′′ W) and Whalers Bay (62°58′45.1′′ S, 60°33′27.3′′ W).
Method step description:
  1. Total genomic DNA was extracted from 10 g of sediment using a PowerMax Soil DNA Kit (MoBio, United States), according to the manufacturer’s protocol. Extracted DNA was concentrated and purified with PCR OneStep Inhibitor Removal Kit (Zymo Research, United States), and further quantified using Qubit dsDNA HS Assay (Thermo-Fisher Scientific, United States) and Qubit Fluorimeter 1.0 (Thermo-Fisher Scientific, United States). Microbial 16S rRNA gene fragments were amplified using the primers S-D-Bact-0341-b-S-17 and S-D-Bact-0785-a-A-21 for Bacteria, and S-D-Arch-0519-a-S-15 and S-D-Arch-1041-a-A-18 for Archaea (Klindworth et al., 2013), targeting the V3–V4 regions of the gene. The first PCR reaction was carried out with a thermal cycler (Thermo-Fisher Scientific, United States), using 25 μL of KAPA HiFi HotStart Ready Mix (KAPA Biosystems) polymerase, 5 ng of DNA, and 0.2 μM of each primer, under the following conditions: 95°C for 3 min, 30 cycles of 95°C for 30 s, 55 or 67°C for 30 s (for Bacteria and Archaea, respectively), 72°C for 30 s, and a final extension of 72°C for 5 min. After purification (QIAquick Gel Extraction Kit – QIAGEN, United States) and quantification, 50 ng of amplicons was amplified and used for library preparation, under the following conditions: 95°C for 3 min, eight cycles of 95°C for 30 s, 55 and 72°C for 30 s, and 72°C for 5 min. The libraries were purified using an AMPure XP beads kit (Beckman Coulter, United States).
  2. After quality checking (Bioanalyzer 2100, Agilent Technologies, United States), the amplicons from each sample were mixed at equimolar concentrations and then sequenced using the Illumina Miseq platform at the Facilities Center for Research Support (CEFAP, Institute of Biomedical Sciences, University of São Paulo).

Scope
Kernwoorden:
Terrestrisch, Dna sequencing, Metadata, Rrna, PSW, Antarctica, South Shetland I., Deception I., Archaea, Bacteria

Geografische spreiding
PSW, Antarctica, South Shetland I., Deception I. Stations [Marine Regions]
Fumarole Bay and Whalers Bay

Spreiding in de tijd
December 2013 - Januari 2014

Taxonomic coverage
Archaea [WoRMS]
Bacteria [WoRMS]

Parameter
Moleculaire data

Bijdrage door
University of São Paulo (USP), meerdata creator
University of Oregon, meerdata creator

Gerelateerde datasets
Gepubliceerd in:
AntOBIS: Antarctic Ocean Biodiversity Information System, meer
(Gedeeltelijk) opgenomen in:
RAS: Register of Antarctic Species, meer

Dataset status: Afgelopen
Data type: Meta database
Data oorsprong: Onderzoek: veldonderzoek
Metadatarecord aangemaakt: 2019-04-03
Informatie laatst gewijzigd: 2019-04-10
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