Document of dataset 6228

Dataset record

Type
Metadata dataset
title in English
Cyanobacteria in microbial mats from Antarctic lakes
Description in English
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.

Study Extent: Samples were taken from benthic microbial mats (upper 1 cm), collected in 13 lakes on the Antarctic continent, distributed across eight Antarctic regions belonging to four distinct Antarctic Conservation Biogeographical Regions (ACBR).

Quality Control: DNA concentration and quality were determined using a NanoVue spectrophotometer (GE Healthcare Life Sciences, Little Chalfont, UK). A blank DNA extraction consisting of sterile Milli-Q water was carried out in parallel.

Method step description:

  1. DNA was extracted from the mats using the PowerSoil DNA Isolation Kit (MOBIO Labora- tories, Carlsbad, CA, USA) according to the manufacturer’s instructions with some modifications. Tubes were agitated on a vortex for 20 extra min to ensure a good disintegration of the mats and, if not completely disintegrated, a sterile pestle was used to crush the remaining pieces.
  2. The cyanobacteria-specific primer set CYA359F and CYA781R(a)/CYA781R(b) was used to amplify the V3-V4 variable region of the 16S rRNA gene. PCR reactions consisted of 19 PCR buffer with 1.5 mM MgCl2, 1mg mL 1BSA, 200 uM of each dNTP, 0.2 uM of each primer, 1 U SUPER TAQ plus DNA polymerase (HT Biotechnology, Cambridge, UK), and 4 ng uL^-1 template DNA in a final volume of 50 uL. Amplification was performed using an initial denaturation step at 94°C for 2 min, followed by 30 cycles of 94°C for 45 s, 60°C (for primer 781Ra) or 57°C (for primer 781Rb) for 45 s and 68°C for 45 s, and a final elonga- tion at 68°C for 5 min. Negative controls (PCR mixes with either no DNA or the blank DNA extracts) were always included during PCR amplifications. To minimize stochastic PCR bias, amplification was carried out as six independent PCR reactions (three for each reverse primer) that were pooled before purification.
  3. Replicate PCR reactions were pooled and purified using the GeneJet PCR Purification Kit (Thermo Scientific, Wal- tham, MA, USA). Purified amplicons were quantified using the Quant-iT PicoGreen dsDNA Assay Kit, pooled in equimolar concentrations, and concentrated to 25 uL using the Ami- con Ultra-0.5 mL 30K device (EMD Millipore, Billerica, MA, USA). Pooled libraries were sent to Beckman Coulter Geno- mics (Takeley, UK), where primer dimers were removed using the Agencourt AMPure XP Kit (Beckman Coulter, Brea, CA, USA) and sequencing adapters were ligated to the ampli- cons. Sequences were obtained using the 454 GS FLX+ Titanium platform (454 Life Sciences, Branford, CT, USA).
Abstract in English
Amplicon sequencing dataset targeting Cyanobacteria (16S ssu rRNA gene) in microbial benthic mats from 13 lakes across the Antarctic continent.
License
https://spdx.org/licenses/CC-BY-4.0.html
bibliographicCitation
Pessi I, Lara Y, Durieu B, de C. Maarouf P, Verleyen E, Wilmotte A (2019): Cyanobacteria in microbial mats from Antarctic lakes. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=lacustrine_cyanobacteria_antarctica&v=1.2
Version
1.2

Temporal coverage

Temporal
Start date
1997-01-01
End date
2007-01-01

Geographical coverage

Spatial
Antarctica

Thesaurus terms

Keyword
Dna sequencing
Metadata

Taxonomic terms

Taxon keywords
Cyanobacteria

Ownerships

creator
Igor Pessi
creator
Université de Liège
creator
Yannick Lara
creator
Université de Liège
creator
Benoit Durieu
creator
Université de Liège
creator
Pedro De Carvalho Maalouf
creator
Université de Liège
creator
Elie Verleyen
creator
Universiteit Gent
creator
Annick Wilmotte
creator
Université de Liège
contactPoint
Igor Pessi
contactPoint
Université de Liège

Dataset references

record
Antarctic Ocean Biodiversity Information System
related
Register of Antarctic Species(had role: partially included in)

Document metadata

date created
2019-03-29
date modified
2019-04-10