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benthic communities bacterial in Antarctica and the arctic

Dernière version Publié par SCAR - Microbial Antarctic Resource System le 19 mars 2019 SCAR - Microbial Antarctic Resource System
Date de publication:
19 mars 2019
Licence:
CC-BY 4.0

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Description

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

Versions

Le tableau ci-dessous n'affiche que les versions publiées de la ressource accessibles publiquement.

Comment citer

Les chercheurs doivent citer cette ressource comme suit:

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

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : aa24508e-09c2-45e0-a348-37f073bb1bee.  SCAR - Microbial Antarctic Resource System publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Scientific Committee on Antarctic Research.

Mots-clé

Metadata

Contacts

Personne ayant créé cette ressource:
-

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

Personne pouvant répondre aux questions sur la ressource:

Julia Kleinteich
University of Tübingen
Tübingen
DE

Personne ayant renseigné les métadonnées:
-

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

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

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

Enveloppe géographique Sud Ouest [-79,847, -79,847], Nord Est [83,107, 173,413]

Couverture taxonomique

Amplicon sequencing dataset of Bacteria 16S ssu rRNA gene

Domain Bacteria (Bacteria)

Couverture temporelle

Epoque de formation 2007-2014

Données sur le projet

Pas de description disponible

Titre pole-to-pole
Financement 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.

Les personnes impliquées dans le projet:

Julia Kleinteich

Méthodes d'échantillonnage

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.

Etendue de l'étude 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.

Description des étapes de la méthode:

  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.

Citations bibliographiques

  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.

Métadonnées additionnelles

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