Microbiome (Archaea, Bacteria and Eukaryota) of lake Fryxell and lake Bonney (McMurdo Dry Valleys, Antarctica)

Study Extent

Sampling occurred during the Austral summer and autumn in lake Fryxell and lake Bonney, Antarctica

Sampling

Duplicate samples were collected at depths of 6 m (bacterial and primary production maximum) and 9 m (chemocline; chlorophyll-a maximum) in lake Fryxell (2 November 2007 and 25 March 2008) and 13 m (chemocline; bacterial production, chlorophyll-a, primary production maximum) and 18 m (hypersaline, bottom of trophogenic zone) in lake Bonney (west Lobe; 30 November 2007 and 12 March 2008). Samples for DNA extraction were filtered onto 0.2-μM Sterivex filters (Millipore, Billerica, MA, USA) and stored with 2.0 ml of Puregene lysis buffer at −20 °C until further processing.

Method steps

1. DNA extraction protocols can be found at http://amarallab.mbl.edu.
2. The V6 hypervariable regions of Archaa and bacteria were amplified, while for Eukaryota, amplification of the V9 hypervariable region followed established protocols (Amaral-Zettler et al., 2009). We multiplex-sequenced the resulting amplicons using bar-coded primers (Huber et al., 2007; Amaral-Zettler et al., 2009) on a 454 Genome Sequencer FLX (Roche, Switzerland) using the manufacturer’s recommended protocol.

Archaea were profiled by targeting the v6 region of the 16S ssu rRNA gene

1. Archaea
   common name: Archaea rank: domain

Bacteria were profiled by targeting the v6 region of the 16S ssu rRNA gene

1. Bacteria
   common name: Bacteria rank: domain

Eukaryota were profiled by targeting the v9 region of the 18S ssu rRNA gene

1. Eukaryota
   common name: Eukaryotes rank: domain

Lake Fryxell and lake Bonney, McMurdo Dry Valleys, Antarctica