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Microbes (16S and 18S rRNA genes) from benthic Antarctic sediments

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019 SCAR - Microbial Antarctic Resource System

amplicon sequencing dataset (Illumina MiSeq) of microbial communities (16S and 18S rRNA genes) in 24 samples from benthic Antarctic sediments

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How to cite

Researchers should cite this work as follows:

Learman D, Henson M, Thrash C, Temperton B, Brannock P, Santos S, Mahon A, Halanych K (2019): Microbes (16S and 18S rRNA genes) from benthic Antarctic sediments. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbes_in_benthic_antarctic_sediments&v=1.2

Rights

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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.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 3a0fa23f-411a-49ec-96ed-3ee8cf7d5696.  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:

Deric Learman
Central Michigan University Mt. Pleasant US
Michael Henson
Louisiana State University Baton Rouge US
Cameron Thrash
Louisiana State University Baton Rouge US
Ben Temperton
University of Exeter Exeter GB
Pamela Brannock
Auburn University Auburn US
Scott Santos
Auburn University Auburn US
Andrew Mahon
Central Michigan University Mt. Pleasant US
Kenneth Halanych
Auburn University Auburn US

Who can answer questions about the resource:

Deric Learman
Central Michigan University Mt. Pleasant US

Who filled in the metadata:

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

Who else was associated with the resource:

User

Geographic Coverage

Southern Ocean marine sediment samples (Antarctica)

Bounding Coordinates South West [-76.55, -102.159], North East [-62.535, 170]

Taxonomic Coverage

Bacteria and Archaea (16S ssu rRNA gene, v4 region)

Domain  Bacteria (Bacteria),  Archaea (Archaea)

Eukaryotes (18S ssu rRNA gene, v4 region)

Domain  Eukaryota (Eukaryotes)

Temporal Coverage

Start Date 2014-01-01

Project Data

No Description available

Title Microbes (16S and 18S rRNA genes) from benthic Antarctic sediments
Funding Funds through NSF Antarctic Program: Award Number 1043670 and 1043745, and from Central Michigan University Faculty Research and Creative Endeavors Committee and College of Science and Technology.

The personnel involved in the project:

Deric Learman

Sampling Methods

Samples were collected on the Antarctic shelf at depths ranging from 223 to 820 m. The top 3 cm of sediments were transferred into sampling tubes and stored frozen (−80°C). Samples were shipped frozen to Central Michigan University within 3 months of collection.

Study Extent Surface sediment samples were collected from the continental shelf of Antarctica during two research cruises. The first cruise (Dec. 2013–Feb. 2014, RVIB Nathaniel B. Palmer) sampled Western Antarctica, which includes the Amundsen Sea, Bellingshausen Sea, and Ross Sea, using a multicorer. The second cruise (Nov.–Dec. 2014, ASRV Laurence M. Gould) sampled the Antarctic Peninsula using a box corer.

Method step description:

  1. DNA was extracted using a PowerSoil DNA extraction kit (MoBio) following the manufacturer's protocol. Approximately 4–8 extractions were completed on each sediment sample and pooled and concentrated with a DNA Clean and Concentrator kit (Zymo) due to low yields from some of the samples. DNA was then quantified using the Qubit2.0 Fluorometer (Life Technologies) and stored at −20°C. Bacterial and archaeal sequences were generated from the V4 region of 16S rRNA gene using the primer set 515f and 806r while eukaryotic sequences were obtained with the V4 region of the 18S rRNA gene using the primer set 1391r and EukBR. Resulting amplicons were sequenced on an Illumina MiSeq as paired-end (PE) reads of 250-bp at Michigan State University's (MSU) Research Technology Support Facility (RTSF) Genomics Core.

Bibliographic Citations

  1. Learman, D. R., Henson, M. W., Thrash, J. C., Temperton, B., Brannock, P. M., Santos, S. R., ... & Halanych, K. M. (2016). Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure. Frontiers in microbiology, 7, 284.

Additional Metadata

Alternative Identifiers 3a0fa23f-411a-49ec-96ed-3ee8cf7d5696
https://ipt.biodiversity.aq/resource?r=microbes_in_benthic_antarctic_sediments