Metadata-only

benthic communities bacterial in Antarctica and the arctic

Последняя версия опубликована SCAR - Microbial Antarctic Resource System 19 марта 2019 г. SCAR - Microbial Antarctic Resource System
Дата публикации:
19 марта 2019 г.
Лицензия:
CC-BY 4.0

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Описание

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

Версии

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Как оформить ссылку

Исследователи должны дать ссылку на эту работу следующим образом:

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

Права

Исследователи должны соблюдать следующие права:

Публикующей организацией и владельцем прав на данную работу является SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Регистрация в GBIF

Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: aa24508e-09c2-45e0-a348-37f073bb1bee.  SCAR - Microbial Antarctic Resource System отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке Scientific Committee on Antarctic Research.

Ключевые слова

Metadata

Контакты

Кто является создателем ресурса:
-

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

Кто может ответить на вопросы о ресурсе:

Julia Kleinteich
University of Tübingen
Tübingen
DE

Кем заполнены метаданные:
-

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

Кто еще связан с данным ресурсом:

User

Географический охват

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

Ограничивающие координаты Юг Запад [-79,847, -79,847], Север Восток [83,107, 173,413]

Таксономический охват

Amplicon sequencing dataset of Bacteria 16S ssu rRNA gene

Domain Bacteria (Bacteria)

Временной охват

Период формирования 2007-2014

Данные проекта

Описание отсутсвует

Название pole-to-pole
Финансирование 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.

Исполнители проекта:

Julia Kleinteich

Методы сбора

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.

Охват исследования 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.

Описание этапа методики:

  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.

Библиографические ссылки

  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.

Дополнительные метаданные

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