Cyanobacteria in microbial mats from Antarctic lakes

Версии

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Как оформить ссылку

Исследователи должны дать ссылку на эту работу следующим образом:

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

Права

Исследователи должны соблюдать следующие права:

Публикующей организацией и владельцем прав на данную работу является SCAR - Microbial Antarctic Resource System. Эта работа находится под лицензией Creative Commons Attribution (CC-BY 4.0).

Регистрация в GBIF

Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: a41ad9bd-cf79-48fa-89a0-102ddf4d4e61.  SCAR - Microbial Antarctic Resource System отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке Scientific Committee on Antarctic Research.

Ключевые слова

Metadata

Контакты

Географический охват

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

Таксономический охват

Cyanobacteria (16S ssu rRNA gene)

Временной охват

Данные проекта

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.

Исполнители проекта:

Методы сбора

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.

Описание этапа методики:

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).

Библиографические ссылки

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.

Дополнительные метаданные