Bacterial diversity in closed cryoconite holes in Southern Victoria Land (Antarctica)

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Researchers should cite this work as follows:

Webster-Brown J, Hawes I, Jungblut A, Wood S, Christenson H (2019): Bacterial diversity in closed cryoconite holes in Southern Victoria Land (Antarctica). v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacteria_in_closed_cryoconite_holes_antarctica&v=1.2

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

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This resource has been registered with GBIF, and assigned the following GBIF UUID: f03a9318-a568-433a-9c5d-db0b88b7e2a4.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

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Geographic Coverage

Diamind and Koettliz Glaciers (Southern Victoria Land, Antarctica)

Taxonomic Coverage

Bacteria were profiled based on amplicon sequencing of the 16S ssu rRNA gene

Sampling Methods

Access through the ice lid was accomplished using a 50-mm diameter Kovacs ice drill, which was cleaned between each hole with antibacterial wipes. Water samples were collected directly into three 60-mL centrifuge tubes for determination of major ions and isotopes, using a manual vacuum apparatus. A sample (1 L) was collected by vacuum into an acid-washed PVC bottle. A subsample (100 mL) filtered (Whatman GF/F) into an acid-washed polyethylene bottle and frozen for later nutrient analysis.

Method step description:

1. DNA was extracted from sediment using the MoBio Power Soil kit (USA). Biosystems, USA). A region of the 16S rRNA gene covering the V3 and 4 sections was ampli ed by PCR (iCycler; Biorad) using bacterial-speci c primers 515F and 806R (Caporaso et al. 2011). PCR reactions were performed in 50 μL volumes with the reaction mixture containing; 45 μL of Platinu PCR SuperMix High Fidelity (Life Technologies, USA), 10 μM of each primer, and 10–20 ng of template DNA. The reaction mix- ture was held at 94◦C for 2 min followed by 27 cycles of 94◦C for 30 s, 54◦C for 30 s, 68◦C for 45 s, with a nal extension step at 68◦C for 5 min. PCR products were puri ed (Agencour AMPur XP Kit; Beckman Coulter, USA), quanti ed (Qubit 20 Fluorometer, Life Technologies, USA), diluted to 1 ng μL−1 and submitted to New Zealand Genomics Limited (Auckland, New Zealand) for library preparation. Libraries were sequenced on a MiSeq Illumina platform (2 × 250 reads).

Bibliographic Citations

1. Webster-Brown, J. G., Hawes, I., Jungblut, A. D., Wood, S. A., & Christenson, H. K. (2015). The effects of entombment on water chemistry and bacterial assemblages in closed cryoconite holes on Antarctic glaciers. FEMS microbiology ecology, 91(12). https://doi.org/10.1093/femsec/fiv144

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