Microbial fungal communities (18S) of Antarctic Dry Valley lakes

Keilor Rojas-Jimenez1, Christian Wurzbacher2, Elizabeth Charlotte Bourne1, Amy Chiuchiolo3, John Priscu3, Hans-Peter Grossart1, Maxime Sweetlove4

1 eibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; 2 Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; 3 Montana State University, Bozeman, United States; 4 Royal Belgian Instutute for Natural Sciences, Rue Vautier 29, 1000, Brussels

Corresponding author(s): Keilor Rojas-JimenezChristian WurzbacherElizabeth Charlotte BourneAmy ChiuchioloJohn PriscuHans-Peter Grossart, Maxime Sweetlove (msweetlove@naturalsciences.be)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Rojas-Jimenez K, Wurzbacher C, Bourne E C, Chiuchiolo A, Priscu J, Grossart H (2018): Microbial fungal communities (18S) of Antarctic Dry Valley lakes. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=fungal_communities_of_antarctic_dry_valley_lakes&v=1.2

Abstract

Amplicon sequencing dataset (Illumina MiSeq) of microbial fungi (18S ssu rRNA gene, v7-v8) in Antarctic Dry Vallei lakes.

Keywords: Metadata

Project details

Project title: Microbial fungal communities (18S) of Antarctic Dry Valley lakes
Personnel: Keilor Rojas-Jimenez
Funding: Funding was provided by the Leibniz “Mycolink” SAW project (Pakt/SAW-2014-IGB-1) given to HPG and ECB. JCP was funded by US National Science Foundation grants PLR1439774, PLR1115245, PLR 1543537 and NASA NRA NNH14ZDA001N-PSTAR.

Data published through GBIF: https://ipt.biodiversity.aq/resource?r=fungal_communities_of_antarctic_dry_valley_lakes

Taxonomic coverage

General taxonomic coverage description: Fungi, 18S ssu rRNA marker gene
Taxonomic ranks
Domain: Fungi
Common names: Fungi

Spatial coverage

General spatial coverage: Lakes in the McMurdo Dry Valleys, Antarctica
Coordinates: 78°5'60''S and 77°37'1.2''S Latitude; 162°22'1.2''E and 166°40'1.2''E Longitude 

Methods

Method step description: 
- . 	DNA from the microorganisms in the filters was extracted using a phenol-chloroform protocol. From 12 samples of the West and East lobes of Lake Bonney, we also extracted RNA using an RNeasy Mini Kit (QIAGEN, Germany). The RNA was converted to cDNA with a One-Step RT-PCR Kit (QIAGEN, Germany) according to the manufacturer’s instructions. We amplified the V7 and V8 regions of the 18S rRNA gene using primers FF390 (5′-CGATAACGAACGAGACCT-3′) and FR1 (5′-AICCATTCAATCGGTAIT-3′).
- . 	For the 25 µl PCR reaction, we used a proof reading enzyme (Herculase II Fusion Polymerase, Agilent Technologies, Santa Clara, USA) and 40 ng DNA (or cDNA) as a template with the following conditions; 95 °C for 3 min initial denaturation followed by 35 cycles at 95 °C for 45 s, 52 °C for 1 min, 72 °C for 1 min, and a final extension at 72 °C for 5 min. The 96 resulting amplicons (~350 bp) went into the library preparation for Illumina MiSeq sequencing according to the protocol presented by the Illumina customer letter for 16 S sequencing with custom primers (Illumina guide to 16 S amplicon sequencing, Part # 15044223 Rev. A) and the Nextera index kit (Illumina, San Diego, USA). The samples were sequenced on a MiSeq sequencer (Illumina, San Diego, USA) with v3 2 × 300 nt chemistry. Sequences were demultiplexed with flexbar resulting in 6.4 M sequences.
Study extent description: Samples were taken during the austral summers of 2011–2012 from five lake basins in the Taylor and Miers Valleys that are the focus of the McMurdo Dry Valleys Long-Term Ecological Research program (MCM LTER).
Sampling description: Water samples (1–2 l) were collected at selected depths through a ~30 cm diameter borehole in the ca. 4 m thick ice covers of each lake using sterile Niskin bottles. To prevent the introduction of contaminants into the lakes, precautions were taken to drill just to the surface of the water. Prior to use, each corer was rinsed properly. For each lake a different sampler was used to avoid cross contamination. In addition, we established a suitable waiting period between the drilling and the water sampling. Then, the samples were filtered through 5.0 µm Puradisc Cellulose Nitrate syringe filters (Gelman Sciences, USA) and subsequently through 0.2 µm Sterivex filters (Millipore, USA) to distinguish between particle-associated and small free-living eukaryotes. Filters were stored with 2.0 ml of Puregene lysis buffer at −80 °C until further processing and nucleic acid extraction.

Metadata language: English
Date of metadata creation: 2018-12-17
Hierarchy level: Dataset

References
Rojas-Jimenez, K., Wurzbacher, C., Bourne, E. C., Chiuchiolo, A., Priscu, J. C., & Grossart, H. P. (2017). Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica. Scientific reports, 7(1), 15348.