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PeerJ. 2014 Aug 19;2:e520. doi: 10.7717/peerj.520. eCollection 2014.

Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.

Author information

1
Department of Biology, San Diego State University , San Diego, CA , USA.
2
Computational Sciences Research Center, San Diego State University , San Diego, CA , USA.
3
Department of Biology, San Diego State University , San Diego, CA , USA ; Ion Torrent Research & Development Group, Thermo Fisher Scientific , Carlsbad, CA , USA.
4
Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre , Geert Grooteplein, GA, Nijmegen , The Netherlands ; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro , Brazil.
5
Advanced Applications Group, Life Technologies, Inc. , Beverly, MA , USA.
6
Advanced Applications Group, Life Technologies, Inc. , Beverly, MA , USA ; Life Sciences Group, Thermo Fisher Scientific , South San Francisco, CA , USA.
7
Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego , La Jolla, CA , USA.
8
Caribbean Research and Management of Biodiversity (CARMABI) , Willemstad , Curacao ; Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Amsterdam , The Netherlands.
9
Department of Biology, San Diego State University , San Diego, CA , USA ; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro , Brazil ; Division of Mathematics and Computer Science, Argonne National Laboratory , Argonne, IL , USA.

Abstract

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.

KEYWORDS:

Coral reef; Environmental microbiology; Expeditions; Genomics; Metagenomics; Sequencing; Vibrio

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