Metadata dataset Registered June 13, 2019

    Bacteria and Archaea biodiversity in terrestrial ecosystems of Chilean Patagonia

    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.

    Geographic scope

    Description

    Chilean Patagonia

    Latitude
    From -54.065 to -52.073
    Longitude
    From -72.038 to -68.85

    Temporal scope

    range
    January 13, 2016 - January 13, 2016

    Taxonomic scope

    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).

    Coverage
    BacteriaBacteriaArchaeaArchaea

    Methodology

    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.

    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 steps
    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.

    Contacts

    • Maialen Barret

      Originator
      Metadata author
      Administrative point of contact
      Organization
      Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
      Position
      Associate professor
      Roles
      Originator
      Metadata author
      Administrative point of contact
      Email
    • Frederic Thalasso

      Originator
      Organization
      Cinvestav
      Roles
      Originator
    • Laure Gandois

      Originator
      Organization
      Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
      Roles
      Originator
    • Karla Martinez Cruz

      Originator
      Organization
      Universidad de Magallanes
      Roles
      Originator
    • Armando Sepulveda Jaureguy

      Originator
      Organization
      Universidad de Magallanes
      Roles
      Originator
    • Céline Lavergne

      Originator
      Organization
      Pontificia Universidad Católica de Valparaíso
      Roles
      Originator
    • Roman Teisserenc

      Originator
      Organization
      Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
      Roles
      Originator
    • Polette Aguilar

      Originator
      Organization
      Pontificia Universidad Católica de Valparaíso
      Roles
      Originator
    • Oscar Gerardo-Nieto

      Originator
      Organization
      Cinvestav
      Roles
      Originator
    • Claudia Etchebehere

      Originator
      Organization
      Instituto de Investigaciones Biológicas Clemente Estable
      Roles
      Originator
    • Bruna Martins

      Originator
      Organization
      Instituto de Investigaciones Biológicas Clemente Estable
      Roles
      Originator
    • Javier Fochesatto

      Originator
      Organization
      University of Alaska Fairbanks
      Roles
      Originator
    • Nikita Tananaev

      Originator
      Organization
      P.I. Melnikov Permafrost Institute
      Roles
      Originator
    • Mette Svenning

      Originator
      Organization
      UiT The Arctic University of Norway
      Roles
      Originator
    • Christophe Seppey

      Originator
      Organization
      UiT The Arctic University of Norway
      Roles
      Originator
    • Alexander Tveit

      Originator
      Organization
      UiT The Arctic University of Norway
      Roles
      Originator
    • Rolando Chamy

      Originator
      Organization
      Pontificia Universidad Católica de Valparaíso
      Roles
      Originator
    • Maria Soledad Astorga-España

      Originator
      Organization
      Universidad de Magallanes
      Roles
      Originator
    • Andres Mansilla

      Originator
      Organization
      Universidad de Magallanes
      Roles
      Originator
    • Anton Van de Putte

      Originator
      Organization
      Royal Belgian Institute for Natural Sciences
      Roles
      Originator
    • Maxime Sweetlove

      Originator
      Organization
      Royal Belgian Institute for Natural Sciences
      Roles
      Originator
    • Alison Murray

      Originator
      Organization
      Desert Research Institute
      Roles
      Originator
    • Léa Cabrol

      Originator
      Metadata author
      Administrative point of contact
      Organization
      Institut Méditerranéen d’Océanologie
      Roles
      Originator
      Metadata author
      Administrative point of contact
      Email
    • Maialen Barret

      Author
      Organization
      ECOLAB, Université de Toulouse
      Position
      Associate professor
      Roles
      Author
    • Léa Cabrol

      Administrative point of contact
      Organization
      Pontificia Universidad Catolica de Valparaiso
      Position
      Researcher
      Roles
      Administrative point of contact

    GBIF registration

    Registration date
    June 13, 2019
    Metadata last modified
    April 15, 2022
    Publication date
    April 15, 2022
    Hosted by
    Antarctic Biodiversity Information Facility (ANTABIF)
    Installation
    ANTABIF IPT
    Endpoints
    EML
    Preferred identifier
    10.15468/wv6xcg
    Alternative identifiers

    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 terrestrial ecosystems of Chilean Patagonia. Version 1.3. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/wv6xcg accessed via GBIF.org on 2025-08-05.