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Bacteria and Archaea biodiversity in terrestrial ecosystems of Chilean Patagonia

Последняя версия опубликована SCAR - Microbial Antarctic Resource System 15 апреля 2022 г. SCAR - Microbial Antarctic Resource System
Дата публикации:
15 апреля 2022 г.
Лицензия:
CC-BY 4.0

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Описание

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.

Версии

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Как оформить ссылку

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 (2022): Bacteria and Archaea biodiversity in terrestrial ecosystems of Chilean Patagonia. v1.3. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=methanobasepatagonia&v=1.3

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: d98b5000-4d67-4580-a90c-c818452cedcb.  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

methane; greenhouse gas; bacteria; archaea; procaryote; peatland; wetland; soil; lake; sediment; metabarcoding; 16S rRNA; MiSeq; Occurrence; Metadata

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
Karla Martinez Cruz
Universidad de Magallanes
Punta Arenas
CL
Armando Sepulveda Jaureguy
Universidad de Magallanes
Punta Arenas
CL
Céline Lavergne
Pontificia Universidad Católica de Valparaíso
Valparaíso
CL
Roman Teisserenc
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
Pnta 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
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
Léa Cabrol
Researcher
Institut Méditerranéen d'Océanologie
Marseille
FR

Кто еще связан с данным ресурсом:

Maialen Barret
Author
Associate professor
ECOLAB, Université de Toulouse
Toulouse
FR
Léa Cabrol
Researcher
Pontificia Universidad Catolica de Valparaiso
Valparaiso
CL

Географический охват

Chilean Patagonia

Ограничивающие координаты Юг Запад [-54,065, -72,038], Север Восток [-52,073, -68,85]

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 2016-01-13

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 Patagonia [-54.94925011 to -52.0728575, -72.03831167 to -67.33177633] 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
Principal Investigator
Léa Cabrol
Principal Investigator
Frederic Thalasso
Metadata Provider
Karla Martinez Cruz
Metadata Provider
Armando Sepulveda Jaureguy
Metadata Provider
Laure Gandois
Metadata Provider
Roman Teisserenc
Author
Alison Murray
Anton Van de Putte

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 d98b5000-4d67-4580-a90c-c818452cedcb
https://ipt.biodiversity.aq/resource?r=methanobasepatagonia