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

Version 1.1 published by SCAR - Microbial Antarctic Resource System on Dec 4, 2018 SCAR - Microbial Antarctic Resource System
Publication date:
04 December 2018
License:
CC-BY-NC 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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How to cite

Please be aware, this is an old version of the dataset.  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

Rights

Researchers should respect the following rights statement:

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.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 0ea51b6e-d02f-495e-a29b-73783e4060c0.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

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

Contacts

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

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