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. 2017 Apr;28(1):2-7.
doi: 10.7171/jbt.17-2801-009. Epub 2017 Mar 22.

Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer

Sarah S Johnson  1 , Elena Zaikova  2 , David S Goerlitz  3 , Yu Bai  2 , Scott W Tighe  4
Affiliations

Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer

Sarah S Johnson et al. J Biomol Tech. 2017 Apr.

Abstract

The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity. One-direction (1D) genomic libraries were prepared using portable field techniques on DNA isolated from desiccated microbial mats. By adequately insulating the sequencer and laptop, it was possible to run the sequencing protocol for up to 2½ h under arduous conditions.

Keywords: Antarctica; MinION; Nanopore sequencing; extremophiles.

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Figures

FIGURE 1.
FIGURE 1.
Map of Antarctica showing the location of the Dry Valleys (A). DNA sequenced in this study was isolated from paleomat samples collected in Victoria Valley, Wright Valley, and Taylor Valley (B). MinION calibrations were performed in the Albert P. Crary Science and Engineering Center at McMurdo Station, as well as on the peak of Hut Point Peninsula on Ross Island (C). Field sequencing runs were performed in the vicinity of Lake Fryxell in Taylor Valley (D).
FIGURE 2.
FIGURE 2.
Modern microbial mat sample from Lake Vanda in Wright Valley, collected at the sediment-water interface beneath 2 cm of ice (A) and a desiccated paleomat from the vicinity of Lake Vida in Victoria Valley, removed from beneath 20 cm of soil (B).
FIGURE 3.
FIGURE 3.
The ONT MinION MK1B performing a calibration test on Hut Point Peninsula (left), as well as a sequencing run in the field in Taylor Valley (right).
See this image and copyright information in PMC

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