Author: Maxime Sweetlove
Keywords: Metadata

Antarctic snow algae communities

Matthew Davey^1, Louisa Norman^1, Peter Sterk^1, Maria Huete-Ortega^1, Freddy BunBury^1, Bradford Kin Wai Loh^1, Lloyd Peck^2, Peter Conevy^2, Kevin Newsham^2, Alison Smith^1, Maxime Sweetlove^3

1 University of Cambridge, Cambridge, United Kingdom; 2 British Antarctic Survey, Cambridge, United Kingdom; 3 Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000, Brussels, Belgium

Corresponding author(s): Matthew DaveyLouisa NormanPeter SterkMaria Huete-OrtegaFreddy BunBuryBradford Kin Wai LohLloyd PeckPeter ConevyKevin NewshamAlison Smith, 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

Davey M, Norman L, Sterk P, Huete-Ortega M, BunBury F, Kin Wai Loh B, Peck L, Conevy P, Newsham K, Smith A (2019): Antarctic snow algae communities. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. http://ipt.biodiversity.aq/resource?r=antarctic_snow_algae_communities&v=1.0

Abstract

Amplicon sequencing dataset of Eukaryotes (18S-ITS) and Bacteria (16S) in green and red snow algae blooms on Antarctic snow.

Keywords: Metadata

Project details

Project title: Antarctic snow algae communities
Personnel: Matthew Davey
Funding: The research expedition was funded by a NERC Collaborative Gearing Scheme award (RJCGS14MPD) in 2014/15. Additional support was given by the European Union (project no. 215G) INTERREG IVB ‘Energetic Algae’ (EnAlgae) program and a Leverhulme Trust Research Grant (RPG-2017-077). The metabarcoding analysis was supported by a Collaboration Voucher from the British Antarctic Survey and carried out by the Cambridge Genomic Services (University of Cambridge, Department of Pathology).

Data published through GBIF: http://ipt.biodiversity.aq/resource?r=antarctic_snow_algae_communities

Taxonomic coverage

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

General taxonomic coverage description: Eukaryotes (18S ssu rRNA- ITS marker)
Taxonomic ranks
Domain: Eukarya
Common names: Eukaryotes

Spatial coverage

General spatial coverage: Rothera Point, Anchorage Island, Léonie Island and Lagoon Island: Ryder Bay: Antarctic Peninsula
Coordinates: 67°35'8''S and 67°35'8''S Latitude; 68°7'59''W and 68°7'59''W Longitude 

Formation period: 2015-01/02

Methods

Method step description: 
- . 	Samples were returned within 3 h of sampling to the Bonner Laboratory (Rothera Research Station, Ryder Bay, Antarctica), where they were melted in 4 °C lit incubators (Sanyo). 10 ml of snow melt was pelleted using centrifugation (2000 g for 10 min, 4 °C), after which the supernatant was discarded and the remaining algal pellet was flash frozen in liquid nitrogen and stored at -80 °C.
- . 	Frozen pellets (approximately 1cm3) of field-collected algal communities from 10 ml snow melt were allowed to thaw before being resuspended in 1 ml of RNase-free water. After transferring to a clean 1.5 ml microfuge tube, the samples were ground with sterilised sand before adding another 1 ml of RNase-free water and subsequent transfer to a 15 ml capacity tube to which 3 ml of SDS-EB buffer (2% SDS, 400 mM NaCl, 40 mM EDTA, 100 mM Tris-HCl, pH8.0) were added, followed by mixing by vortexing and shaking for 5 min at 4 °C. Subsequently, 3 ml of chloroform were added, mixed gently by inversion and the whole suspension was centrifuged for 5 min at 2000 g and 4 °C, resulting in a two phase separation. The top aqueous phase was transferred to a new 15 ml capacity tube and two volumes of 100% chilled ethanol were added before incubating overnight at -20 °C. 
- . 	The following day, the mix was spun at 6800 g at 0 °C for 30 min. After carefully discharging the supernatant, the pellet was resuspended with 1 ml of ethanol (70%) and recovered in a clean microfuge tube before determining total RNA concentration and quality. Libraries of the fourth hypervariable (V4) domain of 16S rRNA gene and internal transcribed spacer region (ITS) of rRNA gene were produced using the NEXTflexTM “16S V4” and “18S ITS” Amplicon-Seq Library Prep Kit and primers (BIOO Scientific, Austin, TX), respectively. For consistency we hereafter use the term “ITS” for the NEXTflex 18S-ITS region. The microbial 16S rRNA gene forward primer (V4 Forward) sequence was: 5’-
GACGCTCTTCCGATCTTATGGTAATTGTGTGCCAGCMGCCGCGGTAA-3’ and the reverse primer (V4 Reverse) sequence was: 5’- TGTGCTCTTCCGATCTAGTCAGTCAGCCGGACTACHVGGGTWTCTAAT-3’. The
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eukaryotic ITS forward primer (18S ITS Forward) sequence CTCTTTCCCTACACGACGCTCTTCCGATCTTCCGTAGGTGAACCTGCGG-3’
reverse primer (18S ITS Forward) CTGGAGTTCAGACGTGTGCTCTTCCGATCTTCCTCCGCTTATTGATATGC-3’. Samples were sequenced by Cambridge Genomic Services (Cambridge, UK) using an Illumina MiSeq v3 600-Cycle Sequencer following the manufacturer’s protocol and primers.
Study extent description: Snow algae communities were collected from layers of green and red dominant snow algal blooms at four locations in Ryder Bay, Antarctic Peninsula (Rothera Point, Anchorage Island, Léonie Island and Lagoon Island) in austral summer (Jan–Feb) 2015. 
Sampling description: Snow samples were (1-5cm depth) taken in 6 x 50 ml sterile plastic sample tubes. The algae were collected by filling a sterile 50 ml tube with snow, which was not compacted. 

Metadata language: English
Date of metadata creation: 2019-02-05
Hierarchy level: Dataset

References
Davey, M. P., Norman, L., Sterk, P., Huete‐Ortega, M., Bunbury, F., Loh, B. K. W., ... & Smith, A. G. (2019). Snow algae communities in Antarctica–metabolic and taxonomic composition. New Phytologist.