K-Axis eukaryote Operational Taxonomic Units (OTU) table and contextual data

Sampling
Samples were collected on board the RSV Aurora Australis between 22 January and 17 February 2016. The cruise surveyed the region south of the Kerguelen Plateau including the Princess Elizabeth Trough and BANZARE Bank in a series of eight transects covering 8165 km. Plankton communities were collected at 45 conductivity temperature depth (CTD) stations and seven additional underway stations, with biological replicates collected at two stations (52 independent sites). Surface water was sampled from 4 plus or minus 2 m depth using the uncontaminated seawater line. Deep Chlorophyll Maximum (DCM, 10-74 m) water samples were obtained using 10 L Niskin bottles mounted on a Seabird 911+ CTD. Plankton communities were size-fractionated by sequentially filtering 10 L seawater through 25 mm 20 micron (nylon) and 5 micron filters (PVDF), and 0.45 micron Sterivex filters (PVDF). Filters were stored frozen at -80 °C.
DNA extraction and high-throughput sequencing
DNA was extracted from half of each filter using the MoBio PowerSoil DNA Isolation kit at the Australian Genome Research Facility (AGRF, Adelaide, Australia; http://www.agrf.org.au). The V4 region of the 18S rDNA (approximately 380 bp excluding primers) was PCR-amplified using universal eukaryotic primers from all extracts and sequenced on an Illumina MiSeq v2 (2 x 250 bp paired-end) following the Ocean Sampling Day protocol (Piredda et al. 2017). Amplicon library preparation and high-throughput sequencing were carried out at the Ramaciotti Centre for Genomics (Sydney, Australia).
Sequence analysis, OTU picking and assignment followed the Biomes of Australian Soil Environments (BASE) workflow (Bissett et al. 2016). Taxonomy was assigned to OTUs based on the PR2 database using the ‘classify.seqs’ command in mothur version 1.31.2 with default settings and a bootstrap cut-off of 60%. OTUs representing any terrestrial contaminants (e.g. human) and samples with low sequencing coverage (less than 7000 reads) were removed from the dataset.
The date of sea ice melt for each station was estimated from daily SSM/I-derived sea-ice spatial concentration from the National Snow and Ice Data Centre (NSIDC) at 25 x 25 km resolution. Days since melt was considered to be the number of days between the date on which sea ice concentration first fell below 15% and the date of sampling.
Other environmental variables included are in situ chlorophyll a, as an indicator of biological production, and near-surface salinity (mean over the upper 10 m) as an indicator for recent sea ice melt. Both environmental measurements were taken from the associated CTD seawater samples. The surface chlorophyll a in seawater (1-2 L) collected in Niskin bottles was analysed by high performance liquid chromatography (HPLC, provided by Karen Westwood and Imojen Pearce, Australian Antarctic Division, doi:10.4225/15/5a94c701b98a8).
Sampling times are given in UTC.

Tags: 18S RIBOSOMAL RNA, ACE/CRC, ADS > Automated DNA Sequencer, AMD, AMD/AU, CEOS, CONTINENT > ANTARCTICA, CTD > Conductivity, Temperature, Depth, EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > PROTISTS > PLANKTON, EARTH SCIENCE > OCEANS > OCEAN CHEMISTRY > CHLOROPHYLL, EARTH SCIENCE > OCEANS > SALINITY/DENSITY > SALINITY, EUKARYOTE, GEOGRAPHIC REGION > POLAR, ILLUMINA MISEQ, LABORATORY, NISKIN BOTTLES, OCEAN > SOUTHERN OCEAN > BANZARE BANK, OCEAN > SOUTHERN OCEAN > PRINCESS ELIZABETH TROUGH, R/V AA > R/V Aurora Australis
Organization: Australian Ocean Data Network