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

Maialen Barret1, Frederic Thalasso2, Laure Gandois1, Klara Martinez Cruz3, Armando Sepulveda Jaureguy3, Céline Lavergne4, Roman Teisserenc1, Polette Aguilar5, Oscar Gerardo-Nieto2, Claudia Etchebehere6, Bruna Martins6, Javier Fochesatto7, Nikita Tananaev8, Mette Svenning9, Christophe Seppey9, Alexander Tveit9, Rolando Chamy5, Maria Soledad Astorga-España3, Andres Mansilla3, Anton Van de Putte10, Maxime Sweetlove10, Alison Murray11, Léa Cabrol12, Maialen Barret13

1 Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France), Toulouse, France; 2 Cinvestav, Mexico City, Mexico; 3 Universidad de Magallanes, Punta Arenas, Chile; 4 Pontificia Universidad Católica de Valparaíso, Valparaiso, Chile; 5 Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile; 6 Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay; 7 University of Alaska Fairbanks, Fairbanks, United States; 8 P.I. Melnikov Permafrost Institute, Igarka, Russian Federation; 9 UiT The Arctic University of Norway, Tromso, Norway; 10 Royal Belgian Institute for Natural Sciences, Brussels, Belgium; 11 Desert Research Institute, Reno, United States; 12 Institut Méditerranéen d’Océanologie, Marseille, France; 13 

Corresponding author(s): Maialen Barret (maialen.barret@ensat.fr)Frederic ThalassoLaure GandoisKlara Martinez CruzArmando Sepulveda JaureguyCéline LavergneRoman TeisserencPolette AguilarOscar Gerardo-NietoClaudia EtchebehereBruna MartinsJavier FochesattoNikita TananaevMette SvenningChristophe SeppeyAlexander TveitRolando ChamyMaria Soledad Astorga-EspañaAndres MansillaAnton Van de PutteMaxime SweetloveAlison MurrayLéa Cabrol (lea.cabrol@mio.osupytheas.fr)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource 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 (2018): Bacteria and Archaea biodiversity in Arctic and Subarctic terrestrial ecosystems in Alaska. v1.3. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=methanobasealaska&v=1.3

Abstract

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.

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

Project details

Project title: Methanobase
Personnel: Maialen Barret
Funding: ERANET-LAC joint call 2014
Study area descriptions/descriptor: 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.

Data published through GBIF: https://ipt.biodiversity.aq/resource?r=methanobasealaska

Taxonomic coverage

General taxonomic coverage description: 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).
Taxonomic ranks
Domain: Bacteria, Archaea
Common names: Bacteria, Archaea

Spatial coverage

General spatial coverage: Alaska
Coordinates: 63°12'36''N and 68°37'12''N Latitude; 150°48'0''W and 147°39'0''W Longitude 

Temporal coverage: June 27, 2016

Methods

Method step description: 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.
Study extent description: 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 description: 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.

Metadata language: English
Date of metadata creation: 2018-04-11
Hierarchy level: Dataset