Microbial diversity (Bacteria and Archaea 16S rRNA gene) in geothermal sites of Deception Island volcano, Antarctica

Última versión Publicado por SCAR - Microbial Antarctic Resource System en Mar 19, 2019 SCAR - Microbial Antarctic Resource System

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.

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¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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

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El publicador y propietario de los derechos de este trabajo es SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

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Este recurso ha sido registrado en GBIF con el siguiente UUID: 4d74304b-a18f-4e3c-9a1f-efbaead8931c.  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.

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Metadata

Contactos

¿Quién creó el recurso?:

Amanda Bendia
Universidade de São Paulo São Paulo BR
Camila Signori
Universidade de São Paulo São Paulo BR
Diego Franco
Universidade de São Paulo São Paulo BR
Rubens Duarte
Universidade de São Paulo São Paulo BR
Brendan Bohannan
University of Oregon Eugene US
Vivian Pellizari
Universidade de São Paulo São Paulo BR

¿Quién puede resolver dudas acerca del recurso?:

Amanda Bendia
Universidade de São Paulo São Paulo BR
Vivian Pellizari
Universidade de São Paulo São Paulo BR

¿Quién documentó los metadatos?:

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

¿Quién más está asociado con el recurso?:

Usuario

Cobertura Geográfica

Geothermal anomalies at Fumarole Bay and Whalers Bay, Deception Island, Antarctica

Coordenadas límite Latitud Mínima Longitud Mínima [-63.18, -60.71], Latitud Máxima Longitud Máxima [-62.06, -60.67]

Cobertura Taxonómica

Bacteria (v3-v4 of the 16S ssu rRNA, targeted with the primer pair S-D-Bact-0341-b-S-17 and S-D-Bact-0785-a-A-21) and Archaea (v3-v4 of the 16S ssu rRNA, targeted with the primer pair S-D-Arch-0519-a-S-15 and S-D-Arch-1041-a-A-18)

Dominio  Bacteria (Bacteria),  Archaea (Archaea)

Cobertura Temporal

Periodo de Formación 2013-12 to 2014-01

Datos del Proyecto

No hay descripción disponible

Título Microsfera and INCT-Criosfera
Fuentes de Financiación This study was part of the projects Microsfera (CNPq 407816/2013-5) and INCT-Criosfera (CNPq 028306/2009) and supported by the Brazilian National Counsel of Technological and Scientific Development (CNPq) and the Brazilian Antarctic Program (ProAntar). The São Paulo Research Foundation – FAPESP supported the following fellowships that made the creation of this dataset possible: 2012/23241-0, (2012/11037-0, and 2016/16183-5.

Personas asociadas al proyecto:

Amanda Bendia

Métodos de Muestreo

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.

Área de Estudio 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).

Descripción de la metodología paso a paso:

  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).

Referencias Bibliográficas

  1. Bendia, A. G., Signori, C. N., Franco, D. C., Duarte, R. T., Bohannan, B. J., & Pellizari, V. H. (2018). A Mosaic of Geothermal and Marine Features Shapes Microbial Community Structure on Deception Island Volcano, Antarctica. Frontiers in Microbiology, 9.

Metadatos Adicionales

Identificadores Alternativos 4d74304b-a18f-4e3c-9a1f-efbaead8931c
https://ipt.biodiversity.aq/resource?r=microbial_bacterial_and_archaeal_diversity_geothermal_sites_antarctica