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

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.

Sampling

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.

Method steps

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.

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

1. Bacteria
   common name: Bacteria rank: domain
2. Archaea
   common name: Archaea rank: domain

Eukaryotes (18S ssu rRNA gene, v4 region)

1. Eukaryota
   common name: Eukaryotes rank: domain

Southern Ocean marine sediment samples (Antarctica)