benthic communities bacterial in Antarctica and the arctic

Julia Kleinteich1, Falk Hildebrand2, Mohammad Bahram3, Anita Voigt2, Susanna Wood4, Anne Jungblut5, Frithjof Küpper6, Antonio Quesada7, Antonio Camacho8, David Pearce9, Peter Convey10, Warwick Vincent11, Christiane Zarfl1, Peer Bork2, Daniel Dietrich12, Maxime Sweetlove13

1 University of Tübingen, Tübingen, Germany; 2 European Molecular Biology Laboratory, Heidelberg, Germany; 3 Uppsala University, Uppsala, Sweden; 4 Cawthron Institute, Nelson, New Zealand; 5 London Natural History Museum, London, United Kingdom; 6 Scottish Association for Marine Science, Oban, United Kingdom; 7 Autonomous University of Madrid, Madrid, Spain; 8 University of Valencia, Valencia, Spain; 9 University of Northumbria at Newcastle, Newcastle, United Kingdom; 10 British Antarctic Survey, Cambridge, United Kingdom; 11 Université Laval, Quebec, Canada; 12 University of Konstanz, Konstanz, Germany; 13 Royal Belgian Institute for Natural Sciences, Rue Vautier 29, 1000, Brussels

Corresponding author(s): Julia KleinteichFalk HildebrandMohammad Bahram (Mohammad.Bahram@ebc.uu.se)Anita VoigtSusanna WoodAnne JungblutFrithjof Küpper (fkuepper@abdn.ac.uk)Antonio QuesadaAntonio CamachoDavid PearcePeter ConveyWarwick VincentChristiane ZarflPeer BorkDaniel Dietrich, 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

Kleinteich J, Hildebrand F, Bahram M, Voigt A, Wood S, Jungblut A, Küpper F, Quesada A, Camacho A, Pearce D, Convey P, Vincent W, Zarfl C, Bork P, Dietrich D (2018): benthic communities bacterial in Antarctica and the arctic. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=pole_to_pole_bacteria&v=1.2

Abstract

Amplicon sequencing dataset of benthic Bacteria (16S ssh rRNA gene) occurring in pools, streams and wet soils of (sub-)Arctic and (sub-)Antarctic regions

Keywords: Metadata

Project details

Project title: pole-to-pole
Personnel: Julia Kleinteich
Funding: This study was funded by: the Carl Zeiss foundation for PhD funding, the Marie-Curie COFUND-BEIPD PostDoc fellowship for PostDoc funding, FNRS travel funding and the logistical and financial support by UNIS, the Natural Environment Research Council (NERC) Antarctic Funding Initiative AFI-CGS-70 (collaborative gearing scheme), the Excellence Initiative at the University of Tübingen funded by the German Federal Ministry of Education and Research and the German Research Foundation (DFG),  MetaHIT (HEALTH-F4-2007-201052), Microbios (ERC-AdG-502 669830, the European Molecular Biology Laboratory (EMBL), Helge Ax:son Johnsons Stiftelse and PUT1317, the DFG funded project DI698/18-1 Dietrich and the Marie Curie International Research Staff Exchange Scheme Fellowship (PIRSES-GA-2011-295223). Operations in the Canadian High Arctic were supported by the Natural Sciences and Engineering Research Council of Canada (NSERC), ArcticNet and the Polar Continental Shelf Program (PCSP). The UK NERC (WP 4.3 of Oceans 2025 core funded  the expedition to Baffin Island. Additional funding was provided by the TOTAL Foundation (Paris), the Spanish Ministry of Science and Technology through project LIMNOPOLAR (POL200606635 and CGL2005-06549-C02-01/ANT to AQ as well as CGL2005-06549-C02-02/ANT to AC, the last of these co-financed by European FEDER funds), the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland), funded by the Scottish Funding Council (HR09011) and contributing institutions.

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

Taxonomic coverage

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

Spatial coverage

General spatial coverage: pond, stream and wet soil samples from Sweden, Bulgaria, Antarctica, New Zealand, Canada and Svalbard
Coordinates: 79°50'49.2''S and 83°6'25.2''N Latitude; 79°50'49.2''W and 173°24'46.8''E Longitude 

Formation period: 2007-2014

Methods

Method step description: 
- . 	Microbial DNA was extracted from 0.05 to 0.1 g subsamples using the PowerSoil® DNA Isolation Kit (Qiagen, Germantown, USA) following the manufacturer's recommendations and DNA eluted in sterile DNAse-free water. The DNA quality and quantity was assessed using a NanoDrop (NanoDrop 3300 Fluorospectrometer, ThermoScientific). DNA extracts were stored frozen (−20°C) for no longer than three months before subsequent processing. Samples from Northern Canada were extracted as described in Jungblut et al. (2010), dried and stored frozen.
- . 	DNA obtained from 90 environmental samples was amplified using primers targeting the V3-V4 region of the 16S rRNA gene (F319 5′-ACTCCTACGGGAGGCAGCAG-3′, R806 5′-GGACTACHVGGGTWTCTAAT-3′)., using a dual multiplexing approach and a “heterogeneity spacer” of 0–3 bp length between the Illumina adapter and the forward/reverse primer sequence to increase read quality. PCR was carried out according to the manual of the Q5 high-fidelity polymerase (New England BioLabs, Ipswich, USA) with a final primer concentration of 0.2 μM and an annealing temperature of 65°C for 15 cycles.
- . 	The PCR product (1 μl) was used in the second PCR. This PCR was performed using the forward and barcoded reverse primers from the NEXTflex™ 16S V1-V3 Amplicon-Seq Kit (Bioo Scientific, Austin, Texas, USA) at final concentrations of 0.15 μM and an annealing temperature of 65°C for 25 cycles. The remaining PCR conditions were as indicated in manufacturer's instructions for the Q5 high-fidelity polymerase. PCR products were cleaned up with the Agencourt AMPure XP—PCR Purification system (Beckman Coulter, Brea, USA) according to the manufacturer's instructions, and multiplexed at equal concentration. Sequencing was performed using a 300 bp paired-end sequencing protocol on the Illumina MiSeq platform (Illumina, San Diego, USA) at the Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg.
Study extent description: Samples from microbial communities growing on wet soil, in small streams and ponds were collected during several field campaigns (three in each of the Arctic, the Antarctic and non-polar regions) between 2007 and 2014.
Sampling description: Samples were collected in sterile tubes or bags using a sterile spatula or similar equipment. All samples were stored frozen (−20°C) or freeze-dried and stored frozen until further use.

Metadata language: English
Date of metadata creation: 2018-12-10
Hierarchy level: Dataset

References
Kleinteich, J., Hildebrand, F., Bahram, M., Voigt, A. Y., Wood, S. A., Jungblut, A. D., ... & Convey, P. (2017). Pole-to-pole connections: Similarities between Arctic and Antarctic microbiomes and their vulnerability to environmental change. Frontiers in Ecology and Evolution, 5, 137.