benthic communities bacterial in Antarctica and the arctic

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019 SCAR - Microbial Antarctic Resource System

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

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How to cite

Researchers should cite this work as follows:

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

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: aa24508e-09c2-45e0-a348-37f073bb1bee.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Metadata

Contacts

Who created the resource:

Julia Kleinteich
University of Tübingen Tübingen DE
Falk Hildebrand
European Molecular Biology Laboratory Heidelberg DE
Mohammad Bahram
Uppsala University Uppsala SE
Anita Voigt
European Molecular Biology Laboratory Heidelberg DE
Susanna Wood
Cawthron Institute Nelson NZ
Anne Jungblut
London Natural History Museum London GB
Frithjof Küpper
Scottish Association for Marine Science Oban GB
Antonio Quesada
Autonomous University of Madrid Madrid ES
Antonio Camacho
University of Valencia Valencia ES
David Pearce
University of Northumbria at Newcastle Newcastle GB
Peter Convey
British Antarctic Survey Cambridge GB
Warwick Vincent
Université Laval Quebec CA
Christiane Zarfl
University of Tübingen Tübingen DE
Peer Bork
European Molecular Biology Laboratory Heidelberg DE
Daniel Dietrich
University of Konstanz Konstanz DE

Who can answer questions about the resource:

Julia Kleinteich
University of Tübingen Tübingen DE

Who filled in the metadata:

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Natural Sciences Rue Vautier 29 1000 Brussels

Who else was associated with the resource:

User

Geographic Coverage

pond, stream and wet soil samples from Sweden, Bulgaria, Antarctica, New Zealand, Canada and Svalbard

Bounding Coordinates South West [-79.847, -79.847], North East [83.107, 173.413]

Taxonomic Coverage

Amplicon sequencing dataset of Bacteria 16S ssu rRNA gene

Domain  Bacteria (Bacteria)

Temporal Coverage

Formation Period 2007-2014

Project Data

No Description available

Title pole-to-pole
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.

The personnel involved in the project:

Julia Kleinteich

Sampling Methods

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.

Study Extent 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.

Method step description:

  1. 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.
  2. 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.
  3. 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.

Bibliographic Citations

  1. 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.

Additional Metadata

Alternative Identifiers aa24508e-09c2-45e0-a348-37f073bb1bee
https://ipt.biodiversity.aq/resource?r=pole_to_pole_bacteria