Microbes (16S and 18S rRNA genes) from benthic Antarctic sediments
amplicon sequencing dataset (Illumina MiSeq) of microbial communities (16S and 18S rRNA genes) in 24 samples from benthic Antarctic sediments
The table below shows only published versions of the resource that are publicly accessible.
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
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.
Who created the resource:
Who can answer questions about the resource:
Who filled in the metadata:
Who else was associated with the resource:
Southern Ocean marine sediment samples (Antarctica)
|Bounding Coordinates||South West [-76.55, -102.159], North East [-62.535, 170]|
Bacteria and Archaea (16S ssu rRNA gene, v4 region)
|Domain||Bacteria (Bacteria), Archaea (Archaea)|
Eukaryotes (18S ssu rRNA gene, v4 region)
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:
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:
- 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.
- 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.