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Microbial (Bacteria, 16S) Diversity in Antarctic marine sediments (Admiralty Bay and Bransfield Strait)

Latest version published by SCAR - Microbial Antarctic Resource System on Dec 13, 2018 SCAR - Microbial Antarctic Resource System

amplicon dataset of Bacteria (16S ssh rRNA marker gene) found Antarctic marine sediments (Admiralty Bay and Bransfield Strait), sampled in December 2008.

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How to cite

Researchers should cite this work as follows:

Franco D, Signori C, Duarte R, Nakayama C, Campos L, Pellizari V (2018): Microbial (Bacteria, 16S) Diversity in Antarctic marine sediments (Admiralty Bay and Bransfield Strait). v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. http://ipt.biodiversity.aq/resource?r=antarctic_marine_sediment_microbes&v=1.0

Rights

Researchers should respect the following rights statement:

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: 2afaca55-5c1e-456e-be07-53fc268035d7.  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:

Diego Franco
Researcher
Universidade de São Paulo São Paulo BR
Camila Signori
Post doctoral fellow
Universidade de São Paulo São Paulo BR
Rubens Duarte
Assistant professor
Universidade Federal de Santa Catarina Florianópolis BR
Cristina Nakayama
Researcher
Universidade Federal de São Paulo Diadema
Lucia Campos
Researcher
Universidade Federal do Rio de Janeiro Rio de Janeiro BR
Vivian Pellizari
Professor
Universidade de São Paulo São Paulo BR

Who can answer questions about the resource:

Diego Franco
Researcher
Universidade de São Paulo São Paulo BR

Who filled in the metadata:

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

Who else was associated with the resource:

User

Geographic Coverage

King George Island, Antarctica

Bounding Coordinates South West [-62.293, -58.476], North East [-62.08, -58.17]

Taxonomic Coverage

Bacteria 16S ssh rRNA

Domain  Bacteria (Bacteria)

Temporal Coverage

Start Date / End Date 2008-12-01 / 2008-12-06

Project Data

No Description available

Title Microbial Diversity in Antarctic marine sediments
Funding This dataset was funded by the Brazilian Antarctic Program (PROANTAR), and the Brazilian National Council for Scientific and Technological Development – CNPq (MABIREH/IPY/CAML Project n. 520293/2006-1).

The personnel involved in the project:

Diego Franco

Sampling Methods

In total, 15 samples of marine sediments were collected using a Mini Box Corer (MBC) at different depths. The top 5 cm of sediments were transferred to sterile Whirl-Pack sample bags (Nasco, WI, USA) and stored frozen onboard (-20°C). Samples were shipped to the University of São Paulo (USP) after 4 months of sampling.

Study Extent Surface sediment samples were collected along a bathymetric gradient in King George Island (stations 1–9, depths ranging from 100 to 502 m) and NBB – Bransfield Strait (stations 10–15, depths 693–1,147 m), located in the Northwestern Antarctic Peninsula. Sampling was conducted by the Brazilian Navy vessel NApOc Ary Rongel during the austral summer, December 2008.

Method step description:

  1. Genomic DNA was extracted from 0.25 g of surface sediment in quadruplicate using a PowerSoil DNA Kit (MoBio, Carlsbad, CA, USA), according to the manufacturer’s instructions. Microbial 16S rRNA gene fragments were amplified using a set of primers designed by adding a 10-nucleotide barcode to the forward primer, 519F, (5′-CAGCMGCCGCGGTAATWC-3′) and reverse primer 1068R (5′-CTGACGRCRGCCATGC-3′). The amplification reaction was carried out using the Accuprime pfx SuperMix (Thermo Scientific, USA) according to the manufacturer. PCR was performed with a thermal cycler (Thermo Scientific, USA) under the following conditions: 95°C for 5 min, 26 cycles of 95°C for 15 s, 59°C for 30 s and 68°C for 1 min. The PCR products were purified by using a DNA clean & concentrator kit (Zymo Research, USA).
  2. The amplicons from each sample were mixed at equimolar concentrations and then sequenced using GSFLX titanium instruments and reagents (Roche 454, Life Sciences, USA) at the Center for Advanced Technologies in Genomics (University of São Paulo, Brazil).

Bibliographic Citations

  1. Franco, D. C., Signori, C. N., Duarte, R. T., Nakayama, C. R., Campos, L. S., & Pellizari, V. H. (2017). High prevalence of gammaproteobacteria in the sediments of admiralty bay and north bransfield Basin, Northwestern Antarctic Peninsula. Frontiers in microbiology, 8, 153.