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

Última versión Publicado por SCAR - Microbial Antarctic Resource System en 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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Versiones

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¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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 (2017): Bacteria and Archaea biodiversity in Arctic terrestrial ecosystems affected by climate change in Northern Siberia. v1.4. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=methanobase&v=1.4

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0 License.

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: 3f922dfb-0b72-4130-933a-a2f4beb3eef7.  SCAR - Microbial Antarctic Resource System publica este recurso, y está registrado en GBIF como un publicador de datos avalado por Scientific Committee on Antarctic Research.

Palabras Clave

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

Contactos

¿Quién creó el recurso?:

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

¿Quién puede resolver dudas acerca del recurso?:

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

¿Quién documentó los metadatos?:

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

¿Quién más está asociado con el recurso?:

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

Cobertura Geográfica

North Siberia

Coordenadas límite Latitud Mínima Longitud Mínima [67.44, 86.59], Latitud Máxima Longitud Máxima [67.53, 86.71]

Cobertura Taxonómica

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).

Reino  Bacteria,  Arcaea

Cobertura Temporal

Fecha Inicial 2016-07-22

Datos del Proyecto

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

Título Methanobase
Identificador METHANOBASE ELAC2014-DCC092
Fuentes de Financiación ERANET-LAC joint call 2014
Descripción del Área de Estudio Siberia [67.444346 to 67.53515, 86.707043 to 86.591957] Lakes (water, sediments), peatlands (hollows, edges, hummocks) and mineral soils
Descripción del Diseño 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.

Personas asociadas al proyecto:

Investigador Principal
Maialen Barret
Investigador Principal
Léa Cabrol
Proveedor de los Metadatos
Céline Lavergne
Proveedor de los Metadatos
Frederic Thalasso
Proveedor de los Metadatos
Karla Martinez Cruz
Proveedor de los Metadatos
Armando Sepulveda Jaureguy
Proveedor de los Metadatos
Laure Gandois
Autor
Roman Teisserenc
Nikita Tananaev
Alison Murray
Anton Van de Putte

Métodos de Muestreo

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.

Área de Estudio 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.

Descripción de la metodología paso a paso:

  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.

Metadatos Adicionales

Propósito 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.
Identificadores Alternativos 3f922dfb-0b72-4130-933a-a2f4beb3eef7
https://ipt.biodiversity.aq/resource?r=methanobase