Integrated Publishing Toolkit(IPT)

free and open access to biodiversity data

Microbial communities (Bacteria and Archaea) in Lake Fryxell (Antarctica) along an oxygen gradient

Latest version published by SCAR - Microbial Antarctic Resource System on Jan 17, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (MiSeq) of Archaea and Bacteria (16S ssu rRNA) in microbial mats at the floor of lake Fryxell (Antarctica).

Downloads

Download the latest version of the metadata-only resource metadata as EML or RTF:

Metadata as an EML file download in English (10 KB)
Metadata as an RTF file download in English (11 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Jungblut A, Hawes I, Mackey T, Krusor M, Doran P, Sumner D, Eiser J, Hillman C, Goroncy A (2019): Microbial communities (Bacteria and Archaea) in Lake Fryxell (Antarctica) along an oxygen gradient. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. http://ipt.biodiversity.aq/resource?r=microbes_antarctic_lake_fryxell_oxygen&v=1.0

Rights

Researchers should respect the following rights statement:

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.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 59b5ae66-7413-448e-889d-681efbc1c00d.  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.

Keywords

Metadata

Contacts

Who created the resource:

Anne Jungblut
The Natural History Museum London GB
Ian Hawes
University of Canterbury Christchurch NZ
Tyler Mackey
University of California Davis US
Megan Krusor
University of California Davis US
Peter Doran
Louisiana State University Baton Rouge US
Dawn Sumner
University of California Davis US
Jonathan Eiser
University of California Davis US
Colin Hillman
University of Canterbury Christchurch NZ
Alexander Goroncy
University of Canterbury Christchurch NZ

Who can answer questions about the resource:

Anne Jungblut
The Natural History Museum London GB

Who filled in the metadata:

Maxime Sweetlove
Assistent researcher
Royal Belgian Institute of Natural Sciences 1000 Brussels BE

Who else was associated with the resource:

User

Geographic Coverage

Lake Fryxell, Antarctica

Bounding Coordinates South West [-77.36, 162.2], North East [-77.36, 162.2]

Taxonomic Coverage

Archaea and Bacteria (16S ssu rRNA gene)

Domain  Bacteria (Bacteria),  Archaea (Archaea)

Project Data

No Description available

Title Microbial communities (Bacteria and Archaea) in Lake Fryxell (Antarctica) along an oxygen gradient
Funding This work was supported in part by NSF grant number 1115245 and NASA grant number NN13AI60G.

The personnel involved in the project:

Peter Doran
Dawn Sumner

Sampling Methods

Samples were collected by a diver by cutting squares of mat from the lake floor and gently lifting them into a plastic box previously cleaned with antibacterial wipes. Box lids were sealed under water and samples returned to the surface and transferred to lakeside laboratory, where they were immediately dissected using flame-sterilized blades and forceps. Pinnacle and ridge-pit mats were dissected according to their distinctively pigmented horizontal upper (pink-purple and brown-purple, respectively), middle (pale purple and green-beige, respectively), and lower (all beige) layers. Prostrate mats were similarly dissected into upper (brown-purple), middle (green- beige), and lower (beige) layers. Dissected subsamples were rinsed in ster- ile deionized water, transferred into sterile plastic tubes, and frozen at 20°C until further analysis.

Study Extent Microbial mat samples representing the main three macroscopic mat morphologies, i.e., cuspate pinnacle, ridge-pit, and prostrate were collected from the floor of Lake Fryxell in November 2012.

Method step description:

  1. DNA extractions of each of the triplicate mat sections were performed using the MoBio PowerDNA biofilm kit according to the manufacturer’s instructions. DNA was quantified using a Qubit fluorometer, and equal amounts of DNA per sample were pooled for 16S rRNA gene amplification. 16S rRNA gene PCR products were amplified in triplicate, pooled, and cleaned using the MoBio UltraClean PCR clean-up kit ac- cording to the manufacturer’s instructions. For the high-throughput se- quencing, we used primers (515f and 806r), described by Caporaso et al., which amplify both archaeal and bacterial 16S rRNA genes, including cyanobacterial 16S rRNA genes.
  2. Sequencing was performed on a MiSeq Illumina sequencer at NZ Genomics Limited, Palmerston North, New Zealand.

Bibliographic Citations

  1. Jungblut, A. D., Hawes, I., Mackey, T. J., Krusor, M., Doran, P. T., Sumner, D. Y., ... & Goroncy, A. K. (2016). Microbial mat communities along an oxygen gradient in a perennially ice-covered Antarctic lake. Appl. Environ. Microbiol., 82(2), 620-630.