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
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
- Organization
- Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
- Position
- Associate professor
- Roles
- Originator
Metadata author
Administrative point of contact
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
- Organization
- Institut Méditerranéen d’Océanologie
- Roles
- Originator
Metadata author
Administrative point of contact
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