Cyanobacteria in microbial mats from Antarctic lakes

Última versión Publicado por SCAR - Microbial Antarctic Resource System en Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset targeting Cyanobacteria (16S ssu rRNA gene) in microbial benthic mats from 13 lakes across the Antarctic continent.

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¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: a41ad9bd-cf79-48fa-89a0-102ddf4d4e61.  SCAR - Microbial Antarctic Resource System publica este recurso, y está registrado en GBIF como un publicador de datos avalado por Scientific Committee on Antarctic Research.

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Metadata

Contactos

¿Quién creó el recurso?:

Igor Pessi
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Yannick Lara
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Benoit Durieu
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Pedro de C. Maarouf
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE
Elie Verleyen
Ghent University Krijgslaan 281 9000 Ghent BE
Annick Wilmotte
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE

¿Quién puede resolver dudas acerca del recurso?:

Igor Pessi
University of Liège Alle ́e du Six Aouˆt 13, B6a 4000 Liège BE

¿Quién documentó los metadatos?:

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Natural Sciences Rue Vautier 29 1000 Brussels BE

¿Quién más está asociado con el recurso?:

Usuario

Cobertura Geográfica

Circum-Antarctic sampling of benthic microbial mats in lakes (n=13)

Coordenadas límite Latitud Mínima Longitud Mínima [-82.45, -67.233], Latitud Máxima Longitud Máxima [-66.283, 100.233]

Cobertura Taxonómica

Cyanobacteria (16S ssu rRNA gene)

Filo  Cyanobacteria (Cyanobacteria)

Cobertura Temporal

Periodo de Formación 1997-2007

Datos del Proyecto

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.

Título Climate Change and Antarctic Microbial Biodiversity
Identificador CCAMBIO
Fuentes de Financiación Belgian Science Policy Office (BelSPO) project SD/BA/03
Descripción del Área de Estudio Microbial mats in the benthic and littoral zon of lakes in polar environments.
Descripción del Diseño Lakes from different regions in Antarctica were sampled, and sequencing was preformed of the 16S marker genes to provide a base-line inventory of microbial eukaryotes biodiversity and test hypotheses about biogeography and species distributions

Personas asociadas al proyecto:

Igor Pessi

Métodos de Muestreo

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.

Área de Estudio 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).
Control de Calidad 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.

Descripción de la metodología paso a paso:

  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).

Referencias Bibliográficas

  1. Pessi, I. S., Maalouf, P. D. C., Laughinghouse IV, H. D., Baurain, D., & Wilmotte, A. (2016). On the use of high‐throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats. Journal of phycology, 52(3), 356-368.
  2. Pessi, I. S., Lara, Y., Durieu, B., Maalouf, P. D. C., Verleyen, E., & Wilmotte, A. (2018). Community structure and distribution of benthic cyanobacteria in Antarctic lacustrine microbial mats. FEMS microbiology ecology, 94(5), fiy042.

Metadatos Adicionales

Identificadores Alternativos a41ad9bd-cf79-48fa-89a0-102ddf4d4e61
https://ipt.biodiversity.aq/resource?r=lacustrine_cyanobacteria_antarctica