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

Latest version published by SCAR - Microbial Antarctic Resource System on Dec 4, 2018 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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How to cite

Researchers should cite this work as follows:

Cabrol L, Barret M, Thalasso F, Gandois L, Lavergne C, Martinez Cruz K, Sepulveda Jaureguy A, Fochesatto G J (2018): Bacteria and Archaea biodiversity in Arctic and Subarctic terrestrial ecosystems in Alaska. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. http://ipt.biodiversity.aq/resource?r=methanobasealaska&v=1.1

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The publisher and rights holder of this work is 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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Keywords

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

Contacts

Who created the resource:

Léa Cabrol
Researcher
Institut méditerranéen d'Océanologie Marseille FR
Maialen Barret
Associate professor
ECOLAB, Université de Toulouse Toulouse FR
Frederic Thalasso
Professor
CINVESTAV Mexico MX
Laure Gandois
Researcher
ECOLAB, Université de Toulouse Toulouse FR
Céline Lavergne
Postdoc
Pontificia Universidad Catholica de Valparaiso Valparaiso CL
Karla Martinez Cruz
Associate professor
Universidad de Magallanes Punta Arenas CL
Armando Sepulveda Jaureguy
Postdoc
Universidad de Magallanes Punta Arenas CL
Gilberto Javier Fochesatto
Associate professor
University of Alaska Fairbanks Fairbanks US

Who can answer questions about the resource:

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

Who filled in the metadata:

Maialen Barret

Who else was associated with the resource:

User
Maialen Barret

Geographic Coverage

Alaska

Bounding Coordinates South West [63.21, -150.8], North East [68.62, -147.65]

Taxonomic Coverage

Bacteria and Archaea

Temporal Coverage

Start Date 2016-06-27

Project Data

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

Title Methanobase
Identifier METHANOBASE ELAC2014-DCC092
Funding ERANET-LAC joint call 2014
Study Area Description Alaska Lakes (water, sediments), peatlands (hollows, edges, hummocks) and mineral soils
Design Description 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.

The personnel involved in the project:

Maialen Barret

Sampling Methods

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.

Study Extent 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.

Method step description:

  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.

Additional Metadata

Alternative Identifiers http://ipt.biodiversity.aq/resource?r=methanobasealaska