Bacterial in the Amundsen Sea Polynya (Southern Ocean): community composition in environmental samples and mesocosm experiment

Inga Richert1, Julie Dinasquet2, Ramiro Logares3, Lasse Riemann2, Patricia Yager4, Annelie Wendeberg5, Stefan Bertilsson1, Maxime Sweetlove6

1 Uppsala University, Uppsala, Sweden; 2 University of Copenhagen, Helsingør, Denmark; 3 Institute of Marine Sciences, Barcelona, Spain; 4 University of Georgia, Athens, United States; 5 Microbial Ecosystem Services Group, Leipzig, Germany; 6 Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000, Brussels, Belgium

Corresponding author(s): Inga RichertJulie DinasquetRamiro LogaresLasse RiemannPatricia YagerAnnelie WendebergStefan Bertilsson, Maxime Sweetlove (msweetlove@naturalsciences.be)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Richert I, Dinasquet J, Logares R, Riemann L, Yager P, Wendeberg A, Bertilsson S (2019): Bacterial in the Amundsen Sea Polynya (Southern Ocean): community composition in environmental samples and mesocosm experiment. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacterial_diversity_admunsen_sea_southern_ocean&v=1.1

Abstract

Amplicon sequencing dataset (454 pyrosequencing) of microbial diversity (Bacteria, based on the 16S ssu rRNA gene) in the Amundsen Sea Polynya. This dataset was used in a study where the Amundsen Sea Polynya (Southern Ocean) was used as a model system to investigate important environmental factors that shape the coastal Southern Ocean microbiota. Population dynamics of abundant taxa was studied in both environmental samples and microcosm experiments.

Keywords: Metadata

Project details

Project title: ASPIRE Microbiome
Personnel: Inga Richert
Funding: The creation of this dataset was made possible with funding of the Swedish Research Council and by the US National Science Foundation Office of Polar Programs (ANT-0839069). Sequencing was made possible by an instrument grant from the K&A Wallenberg foundation.

Data published through GBIF: https://ipt.biodiversity.aq/resource?r=bacterial_diversity_admunsen_sea_southern_ocean

Taxonomic coverage

General taxonomic coverage description: Bacteria 16S ssu rRNA gene
Taxonomic ranks
Domain: Bacteria
Common names: Bacteria

Spatial coverage

General spatial coverage: Amundsen Sea Polynya, Southern Ocean, Antarctica
Coordinates: 74°13'12''S and 71°51'36''S Latitude; 118°28'12''W and 112°0'0''W Longitude 

Formation period: 2010-11 to 2011-01

Methods

Method step description: 
- . 	Processing of the samples used in the mesocosm experiments: To assess bacterioplankton responses to light and dark conditions in the absence of larger predators and eukaryotic phytoplankton, 0.2 μm  filtered seawater in 1 L acid washed polycarbonate bottles was inoculated with 5% [v/v] 0.6 μm  filltered seawater from the same depth using a vacuum pump to a total volume of 1 L.  The experimental design by station included two factors (water mass source of inoculum: epipelagic and mesopelagic) with two treatments (dark and light) for each inoculum. Triplicate incubations were conducted under the dark and light conditions using water from each of three stations: 35 (73°27′95′′S, 112°10′41′′W ), 50 (73° 41′60′′S, 115°25′03′′W ) and 57.2 (73°70′73′′S, 113°26′5′′W ). Each experiment included one inoculum from the light-exposed AASW, and one from the mesopelagic zone from either WW or mCDW. Each 0.2-μm  ltered seawater medium came from the same depth and station as its inoculum.  The light source imitated light levels at approximately 20–50 m below the surface (Philips TLD-18W/18 blue, 1.5–1.99 *10−2 μmol photons s−1 m−2) in a PAR range of 400–500 nm (according to manufacturer), excluding the short-wavelength UV. After a 7-day incubation at near in situ temperature (0.5°C), bacteria from the full sample volume were collected by vacuum  filtration onto 0.2-μm, 47-mm Supor  filters (Pall, Lund, Sweden) and stored at −80°C in sucrose lysis buffer (20% sucrose, 50 mM EDTA, 50 mM TrisHCl, pH = 8). Darkness was achieved by covering the bottles with black and lightproof foil.
- . 	The DNA was extracted using a phenol-chloroform extraction approach as previously described (Riemann et al., 2000). Prior to extraction, microorganisms were enzymatically digested for 30 min with lysozyme at 37°C followed by an overnight digestion with Proteinase K (both 20 mg ml−1, Sigma Aldrich) at 55°C (Boström et al., 2004). The 16S rRNA genes were amplified using the bacterial primers Bakt_341F (CCTACGGGNGGCWGCAG) and Bakt_805R (GACTACHVGGGTATCTAATCC) with 454-Lib-L adapters and sample-specific barcodes on the reverse primer (Herlemann et al., 2011). Each set consisted of up to 72 samples with individual barcodes pooled for sequencing.Triplicate PCR reactions for each sample were carried out with 10 to 70 ng extracted environmental DNA as template. Each 20-μl reaction also contained Phusion Hot Start high- delity DNA polymerase ( thermo Scientific). Ampli cation was carried out by initial denaturation at 98°C for 30 seconds followed by 25 cycles of an initial 98°C denaturation for 30 seconds, subsequent annealing at 50°C for 30 seconds and 30-second extension at 72°C.  ese 25 cycles were followed by a  final 7-min extension at 72°C. Triplicate reactions for each sample were pooled and PCR products were purified using the Agencourt AMPure XP kit according to manufacturer instructions (Beckman Coulter) and quantified with a Picogreen quantification essay (Invitrogen). Equimolar amounts of amplicon from each sample were pooled and sequenced by 454 pyrosequencing using Titanium chemistry at the SNP/SEQ SciLifeLab platform hosted by Uppsala University (Sweden).
Study extent description: Sampling was conducted during the austral summer (November 2010 to January 2011) from the icebreaker Nathaniel B. Palmer. Samples from 15 stations were obtained to include samples from the three major water masses of the Amundsen Sea Polynya and its margins (71–75°S, 110–120°W) during the summer season.
Sampling description: Seawater was collected in 12 L Niskin bottles attached to a 24-bottle SBE 32 rosette; coupled to the rosette was a system of sensors reading depth-resolved pro les of temperature [° C], conductivity [S m−1], oxygen [mg L−1], photosynthetically active radiation (PAR) [μmol photons s−1 m−2 ] and  uorescence [mg m−3 chl-a] for each cast (SBE 911, Sea-Bird Electronics, Bellevue, Washington, USA). Water samples for incubation experiments were processed immediately at 2°C in a temperature-controlled room.

Metadata language: English
Date of metadata creation: 2019-01-23
Hierarchy level: Dataset

References
Richert, I., Dinasquet, J., Logares, R., Riemann, L., Yager, P. L., Wendeberg, A., & Bertilsson, S. (2015). The influence of light and water mass on bacterial population dynamics in the Amundsen Sea Polynya.