Soil microbiome (Bacteria) on Keller Peninsula (Antarctica)

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

Amplicon sequencing dataset (454 pyrosequencing and Ion Torrent) of Bacteria (16S ssu rRNA gene) in ice-free soils of Keller Peninsula (Antarctica)

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Versiones

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¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

Roesch L, Fulthorpe R, Pereira A, Pereira C, Lemos L, Barbosa A, Suleiman A, Gerber A, Pereira M, Loss A, de Costa E (2019): Soil microbiome (Bacteria) on Keller Peninsula (Antarctica). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antarctic_soil_microbiome_keller_peninsula&v=1.1

Derechos

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. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: 48350841-8927-4c78-bbc1-24c01a4d5586.  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

Metadata

Contactos

¿Quién creó el recurso?:

Luiz Roesch
Universidade Federal do Pampa Sao Gabriel BR
Roberta Fulthorpe
University of Toronto at Scarborough Scarborough CA
Antonio Pereira
Universidade Federal do Pampa Sao Gabriel BR
Clarissa Pereira
Universidade Federal do Pampa Sao Gabriel BR
Leondro Lemos
Universidade Federal do Pampa Sao Gabriel BR
Anthony Barbosa
Universidade Federal do Pampa Sao Gabriel BR
Afnan Suleiman
Universidade Federal do Pampa Sao Gabriel BR
Alexandra Gerber
Unidade de Genômica Computacional Darcy Fontoura de Almeida Rio de Janeiro BR
Marcos Pereira
Universidade Federal Rural do Rio de Janeiro Rio de Janeiro BR
Arcangelo Loss
Universidade Federal Rural do Rio de Janeiro Rio de Janeiro BR
Elias de Costa
Universidade Federal Rural do Rio de Janeiro Rio de Janeiro BR

¿Quién puede resolver dudas acerca del recurso?:

Luiz Roesch
Universidade Federal do Pampa Sao Gabriel BR

¿Quién documentó los metadatos?:

Maxime Sweetlove
research assistent
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels BE

¿Quién más está asociado con el recurso?:

Usuario

Cobertura Geográfica

Keller Peninsula, Antarctica

Coordenadas límite Latitud Mínima Longitud Mínima [-64.294, -58.482], Latitud Máxima Longitud Máxima [-62.062, -56.691]

Cobertura Taxonómica

Bacteria, based on the 16S ssu rRNA gene

Dominio  Bacteria (Bacteria)

Cobertura Temporal

Periodo de Formación 2009-2010

Datos del Proyecto

No hay descripción disponible

Título Soil microbiome (Bacteria) on Keller Peninsula (Antarctica)
Fuentes de Financiación This work was supported by the INCT-APA (CNPq process No. 574018/2008-5, FAPERJ E-26/170.023/2008) and Ministry of Science and Technology, and the Secretariat for the Marine Resources Interministerial Committee (SECIRM). Additional funding was provided via a fellowships from the CNPq (process number 503370/2009-6).

Personas asociadas al proyecto:

Luiz Roesch

Métodos de Muestreo

A total of 12 soil samples were chosen for sampling and were taken from a variety of plant communities having different soil features. Soil was collected removing the plant cover and taking cores of 5 cm diameter and 5 cm depth. All soil was stored on ice upon collection and transported to the laboratory for extraction.

Área de Estudio Soil samples were collected on the Keller Peninsula, King George Island, Antarctica during the austral summer of 2009–2010.

Descripción de la metodología paso a paso:

  1. DNA was isolated from at least 1 g of mixed soil using the PowerSoilTM DNA Isolation Kit (MO BIO) as described by the manufacturer. The genomic DNA concentration and purity were determined by spectrophotometry.
  2. Twelve independent PCR reactions were performed for each soil sample with the primers 338R and 27F for the amplification of the V1–V2 hypervariable regions of the 16S rRNA gene. PCR was performed with the GoTaq PCR core system (Promega, Madi- son, WI, USA). The mixtures contained 5 ul of 10× PCR buffer, 200 mM dNTPs, 100 mM of each primer, 2.5 U of Taq polymerase and approximately 100ng of DNA template in a final volume of 50 ul. The PCR conditions were 94 ◦ C for 2 min, 30 cycles of 94◦C for 45s; 55◦C for 45s; and 72◦C for 1min extension; followed by 72 ◦C for 6 min. The 16S rRNA gene fragments were sequenced using 454 GS FLX Titanium (Lib-L) chemistry for unidirectional sequencing of the amplicon libraries. Barcoded primers were used to multiplex the amplicon pools so they could be sequenced together and computationally separated afterward. To do this, 8-base barcodes were added to the 5′-end of the reverse primers using the self-correcting barcode method of Hamady et al. (2008). The primers were attached to the GS FLX Titanium Primer A (5′ -CCATCTCATCCCTGCGTGTCTCCGACTCAG-3′ ) and Primer B (5′ - CCTATCCCCTGTGTGCCTTGGCAGTC-3′ ) sequences, modified for use with GS FLX Titanium emPCR Kits (Lib-L) and a two-base linker sequence was inserted between the 454 adapter and the 16S rRNA primers to reduce any effect the composite primer might have on PCR efficiency. The PCR products for each of the 12 samples were purified and combined in equimolar ratios with the quantitative DNA binding method (SequalPrep Kit, Invitrogen, Carlsbad, CA, USA) to create a DNA pool that was used for pyrosequencing from the A-Key adaptor.

Referencias Bibliográficas

  1. Roesch, L. F., Fulthorpe, R. R., Pereira, A. B., Pereira, C. K., Lemos, L. N., Barbosa, A. D., ... & da Costa, E. M. (2012). Soil bacterial community abundance and diversity in ice-free areas of Keller Peninsula, Antarctica. Applied soil ecology, 61, 7-15.|Rampelotto, P. H., Barboza, A. D. M., Pereira, A. B., Triplett, E. W., Schaefer, C. E. G., de Oliveira Camargo, F. A., & Roesch, L. F. W. (2015). Distribution and interaction patterns of bacterial communities in an ornithogenic soil of Seymour Island, Antarctica. Microbial ecology, 69(3), 684-694.

Metadatos Adicionales

Identificadores Alternativos 48350841-8927-4c78-bbc1-24c01a4d5586
https://ipt.biodiversity.aq/resource?r=antarctic_soil_microbiome_keller_peninsula