Bacteria and Archaea biodiversity in terrestrial ecosystems of Chilean Patagonia

Latest version published by SCAR - Microbial Antarctic Resource System on Apr 15, 2022 SCAR - Microbial Antarctic Resource System
Publication date:
15 April 2022
License:
CC-BY 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

Researchers should cite this work as follows:

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. v1.3. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=methanobasepatagonia&v=1.3

Rights

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: d98b5000-4d67-4580-a90c-c818452cedcb.  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

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

Contacts

Maialen Barret
  • Metadata Provider
  • Author
  • Originator
  • Point Of Contact
Associate professor
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
Toulouse
FR
Frederic Thalasso
  • Originator
Cinvestav
Mexico City
MX
Laure Gandois
  • Originator
Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245, Université de Toulouse, France)
Toulouse
FR
Karla 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
Valparaíso
CL
Roman Teisserenc
  • Originator
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
Pnta 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
  • Metadata Provider
  • Originator
  • Point Of Contact
Institut Méditerranéen d’Océanologie
Marseille
FR

Geographic Coverage

Chilean Patagonia

Bounding Coordinates South West [-54.065, -72.038], North East [-52.073, -68.85]

Taxonomic Coverage

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).

Domain Bacteria (Bacteria), Archaea (Archaea)

Temporal Coverage

Start Date 2016-01-13

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 Patagonia [-54.94925011 to -52.0728575, -72.03831167 to -67.33177633] 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
  • Principal Investigator
Léa Cabrol
  • Principal Investigator
Frederic Thalasso
  • Metadata Provider
Karla Martinez Cruz
  • Metadata Provider
Armando Sepulveda Jaureguy
  • Metadata Provider
Laure Gandois
  • Metadata Provider
Roman Teisserenc
  • Author
Alison Murray
Anton Van de Putte

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

Alternative Identifiers d98b5000-4d67-4580-a90c-c818452cedcb
https://ipt.biodiversity.aq/resource?r=methanobasepatagonia