Bacteria and Archaea biodiversity in Arctic and Subarctic terrestrial ecosystems in Alaska

Последняя версия опубликована SCAR - Microbial Antarctic Resource System Jun 13, 2019 SCAR - Microbial Antarctic Resource System

Methane emissions from aquatic and terrestrial ecosystems play a crucial role in global warming, which is particularly affecting high-latitude ecosystems. As major contributors to methane emissions in natural environments, the microbial communities involved in methane production and oxidation deserve a special attention. Microbial diversity and activity are expected to be strongly affected by the already observed (and further predicted) temperature increase in high-latitude ecosystems, eventually resulting in disrupted feedback methane emissions. The METHANOBASE project has been designed to investigate the intricate relations between microbial diversity and methane emissions in Arctic, Subarctic and Subantarctic ecosystems, under natural (baseline) conditions and in response to simulated temperature increments. We report here a small subunit ribosomal RNA (16S rRNA) analysis of lake, peatland and mineral soil ecosystems.

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Исследователи должны дать ссылку на эту работу следующим образом:

Barret M, Thalasso F, Gandois L, Martinez Cruz K, Sepulveda Jaureguy A, Lavergne C, Teisserenc R, Aguilar P, Gerardo-Nieto O, Etchebehere C, Martins B, Fochesatto J, Tananaev N, Svenning M, Seppey C, Tveit A, Chamy R, Soledad Astorga-España M, Mansilla A, Van de Putte A, Sweetlove M, Murray A, Cabrol L (2018): Bacteria and Archaea biodiversity in Arctic and Subarctic terrestrial ecosystems in Alaska. v1.3. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=methanobasealaska&v=1.3

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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 Non Commercial (CC-BY-NC) 4.0 License.

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Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: 0ea51b6e-d02f-495e-a29b-73783e4060c0.  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; methane; greenhouse gas; bacteria; archaea; procaryote; peatland; wetland; soil; lake; sediment; metabarcoding; 16S rRNA; MiSeq

Контакты

Кто является создателем ресурса:

Maialen Barret
Associate professor
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France) Toulouse FR
Frederic Thalasso
Cinvestav Mexico City MX
Laure Gandois
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France) Toulouse FR
Klara Martinez Cruz
Universidad de Magallanes Punta Arenas CL
Armando Sepulveda Jaureguy
Universidad de Magallanes Punta Arenas CL
Céline Lavergne
Pontificia Universidad Católica de Valparaíso Valparaiso CL
Roman Teisserenc
Researcher
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France) Toulouse FR
Polette Aguilar
Pontificia Universidad Católica de Valparaíso Valparaíso CL
Oscar Gerardo-Nieto
Cinvestav Mexico City MX
Claudia Etchebehere
Instituto de Investigaciones Biológicas Clemente Estable Montevideo UY
Bruna Martins
Instituto de Investigaciones Biológicas Clemente Estable Montevideo UY
Javier Fochesatto
University of Alaska Fairbanks Fairbanks US
Nikita Tananaev
P.I. Melnikov Permafrost Institute Igarka RU
Mette Svenning
UiT The Arctic University of Norway Tromso NO
Christophe Seppey
UiT The Arctic University of Norway Tromso NO
Alexander Tveit
UiT The Arctic University of Norway Tromso NO
Rolando Chamy
Pontificia Universidad Católica de Valparaíso Valparaíso CL
Maria Soledad Astorga-España
Universidad de Magallanes Punta Arenas CL
Andres Mansilla
Universidad de Magallanes Punta Arenas CL
Anton Van de Putte
Royal Belgian Institute for Natural Sciences Brussels BE
Maxime Sweetlove
Royal Belgian Institute for Natural Sciences Brussels BE
Alison Murray
Desert Research Institute Reno US
Léa Cabrol
Researcher
Institut Méditerranéen d’Océanologie Marseille FR

Кто может ответить на вопросы о ресурсе:

Maialen Barret
Associate professor
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France) Toulouse FR
Léa Cabrol
Researcher
Institut méditerranéen d'Océanologie Marseille FR

Кем заполнены метаданные:

Maialen Barret
Associate professor
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France) Toulouse FR

Кто еще связан с данным ресурсом:

User
Maialen Barret

Географический охват

Alaska

Ограничивающие координаты Юг Запад [63.21, -150.8], Север Восток [68.62, -147.65]

Таксономический охват

Bacterial and Archaea diversity was profiled by targeting the V4-V5 region of the 16S SSU rRNA gene for high throughput metabarcode (amplicon) sequencing, using the Illumia MiSeq platform (2x 250bp).

Domain  Bacteria (Bacteria),  Archaea (Archaea)

Временной охват

Дата начала 2016-06-27

Данные проекта

METHANOgenic Biodiversity and activity in Arctic, subarctic and Subantarctic Ecosystems affected by climate change

Название Methanobase
Идентификатор METHANOBASE ELAC2014-DCC092
Финансирование ERANET-LAC joint call 2014
Описание района исследования Alaska Lakes (water, sediments), peatlands (hollows, edges, hummocks) and mineral soils
Описание плана выполнения исследований The METHANOBASE project has been designed to investigate the intricate relations between microbial diversity and methane emissions in Arctic, Subarctic and Subantarctic ecosystems, under natural (baseline) conditions and in response to simulated temperature increments.

Исполнители проекта:

Maialen Barret

Методы сбора

Water samples were collected with a Van Dorn bottle. Sediments were sampled thanks to a grab-sampler, peat monoliths (approximately 30*30*30cm) were cut with a bread-knife and soil monoliths with a shovel.

Охват исследования Samples were collected in summer 2015, without any temporal replication. A total of 19 ecosystems were studied in Alaska, USA. The selected sites are representative of this Subantarctic region: lakes, peatlands, Nothofagus forest, pampa In each site, various samples were collected to take into account the local heterogeneity: different depths in water column and sediments, soil horizons, hollows/edges/hummocks.

Описание этапа методики:

  1. After collection, samples were stored at 4°C prior to further processing. Liquid samples were filtered at 0.45µm until clogging and the filters were stored at -20°C. DNA was extracted from these filters using the PowerWater DNA isolation kit (MOBIO) while DNA was extracted from solid samples using the PowerSoil DNA isolation kit (MOBIO). DNA extracts were kept at -20°C. The V4-V5 region of 16S rRNA gene was amplified in the following conditions: 515F and 928R primers (Wang & Qian, 2009. doi:10.1371/journal.pone.0007401), 2min at 94°C, 30 cycles of 60s at 94°C, 40s at 65°C and 30s at 72°C, and 10 min at 72°C. Amplicon sequencing was carried out with Illumina MiSeq technology (2x250pb, V3). Denoising of the sequences dataset and OTU clustering was carried using the FROGS pipeline (Auer et al., 2017. doi:10.1093/bioinformatics/btx791). BLAST was used for taxonomic affiliation.

Дополнительные метаданные

Альтернативные идентификаторы https://ipt.biodiversity.aq/resource?r=methanobasealaska