Description
Amplicon sequencing (Illumina MiSeq, 300bp Paired-end) dataset of microbial mats samples collected in the literal zone of Arctic, Antarctic and Sub-Antarctic lakes. Samples were taken during the course of field expeditions between 1993 and 2014. Sequencing targeted Bacteria (16S ssu rRNA marker gene, v1-v3 region), eukaryotes (18S ssu rRNA, v4 region) and microbial fungi (ITS marker gene)
Versions
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Comment citer
Les chercheurs doivent citer cette ressource comme suit:
Sweetlove M, Tytgat B, Verleyen E, Willems A, Wurzbacher C, Nillson H, Wilmotte A, Vyverman W (2019): Microbial communities (Bacteria, Eukaryotes and Fungi) in Arctic, Antarctic and Sub-Antarctic lacustrine biofilms. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbial_bacteria_fungi_and_eukaryotes_in_arctic_antarctic_and_subantarctic_lacustrine_biofilms&v=1.1
Droits
Les chercheurs doivent respecter la déclaration de droits suivante:
L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.
Enregistrement GBIF
Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 81484676-d49f-43f5-8f78-88289267664b. SCAR - Microbial Antarctic Resource System publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Scientific Committee on Antarctic Research.
Mots-clé
Metadata
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Couverture géographique
Sampled regions include: the Arctic (Greenland, Norway, Svalbard), Sub-Antarctic Islands (Macquarie island and Marion Island) and Antarctic (the Antarctic Peninsula, Continental Antarctica)
| Enveloppe géographique | Sud Ouest [-90, -180], Nord Est [90, -180] |
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Couverture taxonomique
High throughput (Illumina) amplicon sequencing of Bacteria (16S ssu rRNA), Eukaryotes (18S ssu rRNA) and microbial fungi (ITS)
| Domain | Eukaryota (Eukaryotes), Bacteria (Bacteria) |
|---|---|
| Phylum | Fungi (Fungi) |
Couverture temporelle
| Epoque de formation | 1993-2014 |
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Données sur le projet
CCAMBIO (Climate Change and Antarctic Microbial Biodiversity) is an academic project funded by the Belgian Federal Science Policy (BELSPO). Its main objective is to study the diversity, biogeographic zoning and genomic make-up of lacustrine microbial mat communities in the Antarctic Realm. CCAMBIO is composed by researchers from four Belgian Universities and Institutes (University of Liège, Ghent University, National Botanical Garden of Belgium and Royal Belgian Institute of Natural Sciences), as well as collaborators from the British Antarctic Survey.
| Titre | Climate Change and Antarctic Microbial Biodiversity |
|---|---|
| Identifiant | CCAMBIO |
| Financement | Belgian Science Policy Office (BelSPO) project SD/BA/03 |
| Description du domaine d'étude / de recherche | Microbial mats in the benthic and littoral zon of lakes in polar and sub-polar environments. |
| Description du design | Lakes from different regions in Antarctica, Sub-Antarctica and the Arctic were sampled, and sequencing was preformed of the 16S and 18S rRNA and ITS marker genes to 1) provide a base-line inventory of microbial eukaryotes biodiversity, 2) test hypotheses about biogeography and species distributions, and 3) test hypotheses on macro-ecological patterns in microbes. |
Les personnes impliquées dans le projet:
Méthodes d'échantillonnage
Microbial mat samples were collected in the littoral or deeper parts of the euphotic zone of the lakes using a spatula or gravity corer, respectively. The upper 1 cm of the core was aseptically removed and kept dark and cool until transfer to -20°C.
| Etendue de l'étude | Samples were taken from benthic microbial mats (upper 1 cm), collected in 233 lakes covering 17.35° latitude in the Northern Hemisphere (61.39°N to 78.74°N) and 37.16° in the Southern Hemisphere (46.84°S to 84°S), including the major biogeographical regions in Antarctica, Sub-Antarctica and the Arctic. |
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| Contrôle qualité | To assess overall sequence quality and estimate the parameters for bioinformatics processing, each run also included two replicates of positive control sample (mock community) containing bacterial or eukaryote taxa on the respective bacterial and eukaryote runs. |
Description des étapes de la méthode:
- Extracellular proteins and DNA from 1.5-3 g subsamples were removed (Corinaldesi et al., 2005), after which genomic DNA was extracted using a phenol-chloroform based protocol (Zwart et al., 1998). For Bacteria, the V1-V3 region of the 16S SSU rRNA gene was targeted for bacteria with domain-specific universal primer sets (Edwards et al., 1989; Cleenwerck et al., 2007), while for eukaryotes, V4 region of the 18S ssu rRNA gene was targeted with the primers of Stoeck et al. (2010). . The polymerase chain reaction was performed in duplicate to level out stochastic artefacts, and amplicon libraries were barcoded using the NEXTERA XT index kit (Illumina Inc.) according to manufacturer's instructions. Libraries were sequenced on an Illumina MiSeq machine (300 bp, Paired-end), while each run was spiked with 20% PhiX DNA (Illumina Inc.) to reduce cluster density.
Métadonnées additionnelles
| Identifiants alternatifs | 81484676-d49f-43f5-8f78-88289267664b |
|---|---|
| https://ipt.biodiversity.aq/resource?r=microbial_bacteria_fungi_and_eukaryotes_in_arctic_antarctic_and_subantarctic_lacustrine_biofilms |