3a0fa23f-411a-49ec-96ed-3ee8cf7d5696
https://ipt.biodiversity.aq/resource?r=microbes_in_benthic_antarctic_sediments
Microbes (16S and 18S rRNA genes) from benthic Antarctic sediments
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
Maxime
Sweetlove
Royal Belgian Institute for Natural Sciences
Research assistent
Rue Vautier 29
Brussels
1000
BE
msweetlove@naturalsciences.be
user
2019-03-19
eng
amplicon sequencing dataset (Illumina MiSeq) of microbial communities (16S and 18S rRNA genes) in 24 samples from benthic Antarctic sediments
Metadata
GBIF Dataset Type Vocabulary: http://rs.gbif.org/vocabulary/gbif/dataset_type.xml
This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.
Southern Ocean marine sediment samples (Antarctica)
-102.159
170
-62.535
-76.55
2014
2014
Bacteria and Archaea (16S ssu rRNA gene, v4 region)
domain
Bacteria
Bacteria
domain
Archaea
Archaea
Eukaryotes (18S ssu rRNA gene, v4 region)
domain
Eukaryota
Eukaryotes
unkown
Deric
Learman
Central Michigan University
Mt. Pleasant
US
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.
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.
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.
Microbes (16S and 18S rRNA genes) from benthic Antarctic sediments
Deric
Learman
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.
2019-01-09T03:10:00.014+01:00
dataset
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
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.
3a0fa23f-411a-49ec-96ed-3ee8cf7d5696/v1.2.xml