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Bacteria and Archaea biodiversity in Arctic terrestrial ecosystems affected by climate change in Northern Siberia

Dernière version Publié par SCAR - Microbial Antarctic Resource System le 15 avril 2022 SCAR - Microbial Antarctic Resource System
Date de publication:
15 avril 2022
Licence:
CC-BY 4.0

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Description

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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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

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 Arctic terrestrial ecosystems affected by climate change in Northern Siberia. v1.5. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=methanobase&v=1.5

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 : 3f922dfb-0b72-4130-933a-a2f4beb3eef7.  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

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

Contacts

Personne ayant créé cette ressource:
-

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
Valparaiso
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
Valparaiso
CL
María Soledad Astorga-España
Universidad de Magallanes
Punta Arenas
CL
Andrés 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

Personne pouvant répondre aux questions sur la ressource:

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

Personne ayant renseigné les métadonnées:
-

Maialen Barret
Associate professor
ECOLAB, Université de Toulouse
Toulouse
FR
Léa Cabrol
Researcher
Institut Méditerranéen d'Océanologie
Marseille
FR

Autres personnes associées à la ressource:

Maialen Barret
Auteur
Associate professor
EcoLab, Université de Toulouse, CNRS
Toulouse
FR
Léa Cabrol
Auteur
Researcher
Pontificia Universidad Catolica de Valparaiso
Valparaiso
CL

Couverture géographique

North Siberia

Enveloppe géographique Sud Ouest [67,44, 86,59], Nord Est [67,53, 86,71]

Couverture taxonomique

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).

Kingdom Bacteria, Arcaea

Couverture temporelle

Date de début 2016-07-22

Données sur le projet

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

Titre Methanobase
Identifiant METHANOBASE ELAC2014-DCC092
Financement ERANET-LAC joint call 2014
Description du domaine d'étude / de recherche Siberia [67.444346 to 67.53515, 86.707043 to 86.591957] Lakes (water, sediments), peatlands (hollows, edges, hummocks) and mineral soils
Description du design 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.

Les personnes impliquées dans le projet:

Maialen Barret
Chercheur Principal
Léa Cabrol
Chercheur Principal
Céline Lavergne
Fournisseur des Métadonnées
Frederic Thalasso
Fournisseur des Métadonnées
Karla Martinez Cruz
Fournisseur des Métadonnées
Armando Sepulveda Jaureguy
Fournisseur des Métadonnées
Laure Gandois
Fournisseur des Métadonnées
Roman Teisserenc
Auteur
Nikita Tananaev
Alison Murray
Anton Van de Putte

Méthodes d'échantillonnage

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.

Etendue de l'étude Samples were collected in summer 2016, without any temporal replication. A total of 18 ecosystems were studied in Siberia, Russia (around Igarka). The selected sites are representative of this Arctic region: lakes (including glaciar, thermokarst), peatlands (including palsa complexes), taiga forest, tundra, discontinuous permafrost. 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.

Description des étapes de la méthode:

  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.

Métadonnées additionnelles

Objet This table reports the GPS coordinates of the ecosystems which were sampled for microbial survey, methane emission rates, potential methanogenic and methanotrophic activities measurement in lab, and physico-chemical characterization.
Identifiants alternatifs 3f922dfb-0b72-4130-933a-a2f4beb3eef7
https://ipt.biodiversity.aq/resource?r=methanobase