Bacteria and Archaea biodiversity in Arctic and Subarctic terrestrial ecosystems in Alaska
Citation
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 and Subarctic terrestrial ecosystems in Alaska. Version 1.4. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/hhkhz2 accessed via GBIF.org on 2024-12-12.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.Sampling Description
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.Sampling
Water samples were collected with a Van Dorn bottle. Sediments were sampled thanks to a grab-sampler, peat monoliths (approximately 303030cm) were cut with a bread-knife and soil monoliths with a shovel.Method steps
- 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.
Taxonomic Coverages
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).
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Bacteriacommon name: Bacteria rank: domain
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Archaeacommon name: Archaea rank: domain
Geographic Coverages
Alaska
Bibliographic Citations
Contacts
Maialen Barretoriginator
position: Associate professor
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
Toulouse
FR
email: maialen.barret@ensat.fr
Frederic Thalasso
originator
Cinvestav
Mexico City
MX
Laure Gandois
originator
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
Toulouse
FR
Klara Martinez Cruz
originator
Universidad de Magallanes
Punta Arenas
CL
Armando Sepulveda Jaureguy
originator
Universidad de Magallanes
Punta Arenas
CL
Céline Lavergne
originator
Pontificia Universidad Católica de Valparaíso
Valparaiso
CL
Roman Teisserenc
originator
position: Researcher
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
Toulouse
FR
Polette Aguilar
originator
Pontificia Universidad Católica de Valparaíso
Valparaíso
CL
Oscar Gerardo-Nieto
originator
Cinvestav
Mexico City
MX
Claudia Etchebehere
originator
Instituto de Investigaciones Biológicas Clemente Estable
Montevideo
UY
Bruna Martins
originator
Instituto de Investigaciones Biológicas Clemente Estable
Montevideo
UY
Javier Fochesatto
originator
University of Alaska Fairbanks
Fairbanks
US
Nikita Tananaev
originator
P.I. Melnikov Permafrost Institute
Igarka
RU
Mette Svenning
originator
UiT The Arctic University of Norway
Tromso
NO
Christophe Seppey
originator
UiT The Arctic University of Norway
Tromso
NO
Alexander Tveit
originator
UiT The Arctic University of Norway
Tromso
NO
Rolando Chamy
originator
Pontificia Universidad Católica de Valparaíso
Valparaíso
CL
Maria Soledad Astorga-España
originator
Universidad de Magallanes
Punta Arenas
CL
Andres Mansilla
originator
Universidad de Magallanes
Punta Arenas
CL
Anton Van de Putte
originator
Royal Belgian Institute for Natural Sciences
Brussels
BE
Maxime Sweetlove
originator
Royal Belgian Institute for Natural Sciences
Brussels
BE
Alison Murray
originator
Desert Research Institute
Reno
US
Léa Cabrol
originator
position: Researcher
Institut Méditerranéen d’Océanologie
Marseille
FR
email: lea.cabrol@mio.osupytheas.fr
Maialen Barret
metadata author
position: Associate professor
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
Toulouse
FR
email: maialen.barret@ensat.fr
Maialen Barret
user
email: maialen.barret@ensat.fr
Maialen Barret
administrative point of contact
position: Associate professor
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
Toulouse
FR
email: maialen.barret@ensat.fr
Léa Cabrol
administrative point of contact
position: Researcher
Institut méditerranéen d'Océanologie
Marseille
FR
email: lea.cabrol@mio.osupytheas.fr