Microbial fungal communities (18S) of Antarctic Dry Valley lakes
Citation
Rojas-Jimenez K, Wurzbacher C, Bourne E C, Chiuchiolo A, Priscu J, Grossart H, Sweetlove M (2019). Microbial fungal communities (18S) of Antarctic Dry Valley lakes. Version 1.2. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/nfhiio accessed via GBIF.org on 2024-09-01.Description
Amplicon sequencing dataset (Illumina MiSeq) of microbial fungi (18S ssu rRNA gene, v7-v8) in Antarctic Dry Vallei lakes.Sampling Description
Study Extent
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
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.Method steps
- 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.
Taxonomic Coverages
Fungi, 18S ssu rRNA marker gene
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Fungicommon name: Fungi rank: domain
Geographic Coverages
Lakes in the McMurdo Dry Valleys, Antarctica
Bibliographic Citations
- 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. -
Contacts
Keilor Rojas-Jimenezoriginator
eibniz-Institute of Freshwater Ecology and Inland Fisheries
Berlin
DE
Christian Wurzbacher
originator
Leibniz-Institute of Freshwater Ecology and Inland Fisheries
Berlin
DE
Elizabeth Charlotte Bourne
originator
eibniz-Institute of Freshwater Ecology and Inland Fisheries
Berlin
DE
Amy Chiuchiolo
originator
position: Research associate
Montana State University
Bozeman
US
John Priscu
originator
Montana State University
Bozeman
US
Hans-Peter Grossart
originator
eibniz-Institute of Freshwater Ecology and Inland Fisheries
Berlin
DE
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Instutute for Natural Sciences
Rue Vautier 29
Brussels
1000
email: msweetlove@naturalsciences.be
Keilor Rojas-Jimenez
administrative point of contact
eibniz-Institute of Freshwater Ecology and Inland Fisheries
Berlin
DE